title: 435 - 48hrs

source_name: DENV1/435-infected, 48hr

value: DENV1/435 (mutated strain)


title: 435 - 24hrs

status: Public on Aug 29 2017

type: RNA

city: Curitiba

first: Guilherme

middle: Ferreira

last: Silveira

address: Prof Algacyr Munhoz Máder

country: Brazil

institute: Instituto Carlos Chagas

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix) and scanned at the LNLS- Campinas Brazil facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software; core-gene analysis
The generated files were analyzed for quality by the software Expression Console (Affymetrix, Santa Clara, CA). The same software was used to normalize the data by the RMA method. Log-ratio between DENV1/60, DENV1 435, or DENV1 480 infected-mdDCs and mock-infected-mdDCs intensity signal values were generated and a list of differential expressed genes was obtained by using a 2 our higher fold-change. Data clustering was performed by the Cluster 3.0 software with a Euclidian’s distance. Tool for Analysis of GO Enrichments (TANGO), in Expander software was used to obtain a GO with statistical enhancer values of 0.05, and, NCBIEntrez Gene database (www.ncbi.nih.gov) and the Gene Ontology database (www.geneontology.org), to define the most relevant cell signaling and metabolic pathways during mdDC infection with DENV1 60, DENV1 435, or DENV1 480.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DENV1/435-infected, 24hr

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Monocyte-derived dendritic cells (mdDCs) were generated using peripheral blood from healthy volunteers after informed consent and approval of the FIOCRUZ Research Ethics Committee (number 514/09). Mononuclear cells were separated by density gradient using Lymphocyte Separation Medium (Lonza, Walkersville, USA) and CD14+ cells were purified by magnetic immunosorting (Miltenyi Biotec, Auburn, CA), according to the manufacturer’s recommendations. CD14+ cells were cultured for 6-7 days in RPMI 1640 medium containing 100 ng/mL interleukin-4 (IL-4) and 50 ng/mL granulocyte-monocyte colony stimulating factor (GM-CSF; PeproTech, Rocky Hill, NJ), 10% fetal bovine serum (FBS) and 100 IU/µg/mL of penicillin/streptomycin and 2 mM of L-Glutamine (Gibco-BRL, Grand Island, NY). The cultures were assessed by flow cytometry and only cultures with more than 80% of CD1a+ and less than 5% of CD14+ purity were used. C6/36 cells were grown in Leibovitz-15 medium supplemented with 5% FBS and 0.26% of tryptose and 25 µg/mL of gentamicin (all reagents from Gibco-BRL, Grand Island, NY).

extract_protocol: Cells were collected at 8, 24 and 48 hours post infection (hpi) and used to extract total RNA using RNaesy Mini Kit according to the manufacturer’s recommendations (QIAGEN, Valencia, CA). The RNA of all ten mdDC cultures was pooled (75 µg of each) for microarray experiments and compared to mock infected cells using Human Gene 1.0 st v. 1 array GeneChip slides from Affymetrix (Santa Clara, CA). The RNA pool was processed as according to the manufacturer’s recommendations (Affymetrix, Santa Clara, CA) for the amplification and in vitro transcription, purification, tagging, hybridization and scanning of the slides (GeneChip® Scanner 3000).

treatment_protocol: Ten mdDCs cultures were mock-infected or infected with DENV1/60, DENV1/435 or DENV1/480 at an MOI of 5 for two hours in the absence of FBS. The viral inoculum was removed and cells were washed and cultured in RPMI 1640 plus 10% of FBS and 100 IU/µg/mL of penicillin/streptomycin (Gibco-BRL, Grand Island, NY).

tag: cell type

value: Dendrític Cells

tag: infection

tag: time


title: DMx_M36_D_12

city: Houston

first: Mario

last: Sirito

state: TX

address: 1515 Holcombe blvd

department: Cancer Genetics

country: USA

institute: M. D. Anderson Cancer Center

data_processing: from CEL files we genereated DCP files uing dChip 2006 (DNA-Chip Analyzer), Build date: Feb 16 2006 (MBEI analysis model)

source_name: Skeletal Muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5, using 5 ug total RNA

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

tag: biopsy site

value: Deltoid

tag: DMX patient

tag: age 36

tag: Gender

value: M


title: Mock - 24hrs

source_name: Mock-infected, 24hr

value: control


title: Mock - 48hrs

source_name: Mock-infected, 48hr


title: DMx_M53_D_11

hyb_protocol: standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5

tag: age 53


title: 480 - 8hrs

source_name: DENV1/480-infected, 8hr

value: DENV1/480 (mutated strain)


title: DMx_M?_BB_10

scan_protocol: standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5

value: Biceps brachii

tag: age unknown


title: 480 - 24hrs

source_name: DENV1/480-infected, 24hr


title: 435 - 8hrs

source_name: DENV1/435-infected, 8hr


title: 60 - 48hrs

source_name: DENV1/60-infected, 48hr

value: DENV1/60 (parental virus, vBACDV1)


title: DMx_F?_BB_09

value: F


title: 60 - 24hrs

source_name: DENV1/60-infected, 24hr


title: 60 - 8hrs

source_name: DENV1/60-infected, 8hr


title: DMx_M73_BB_05

tag: age 73


title: DMx_F?_TA_02

value: Tibialis anterior


title: DM2_F58_?_18_b

value: unknown

tag: DM2 patient

tag: age 58


title: DMx_F75_BB_04

tag: age 75


title: DM2_F55_?_20_b

tag: age 55


title: DMx_F?_BB_07


title: DMx_M?_BB_03


title: DMx_M28_D_16

tag: age 28


title: DMx_F55_BB_06


title: DMx_F?_BB_08


title: DM2_F51_?_17_b

tag: age 51


title: DM2_F50_?_16_b

tag: age 50


title: Conventional CD4 T cells

city: Seoul

first: Yeon Duk

last: Woo

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University, College of Medicine

description: SAMPLE 1

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina MouseRef-8 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

label: Biotin

organism: Mus musculus

source_name: Mice lymph node

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Mice used for this experiment were raised under specific pathogen free

extract_protocol: mRNA was extracted using QIAGEN Rneasy kit in accordance with the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: lymph node

tag: cell type

value: Conventional CD4 T cells

tag: gender

value: Female


title: Type 1 invariant NKT cells

description: SAMPLE 2

value: Type 1 invariant NKT cells


title: DM2_M51_?_19_b

tag: biopsy site


title: DM2_F65_?_14_b

tag: age 65


title: DMx_F49_BB_01

tag: DMX patient

tag: age 49


title: DM2_F42_?_15_b

tag: age 42

tag: Gender


title: DM2_F43_?_13_b

tag: age 43


title: DM2_M47_VL_11_b

value: Vastus lateralis

tag: DM2 patient

tag: age 47


title: DM2_F37_VL_10_b

tag: age 37


title: DM2_M68_D_05_b

tag: age 68


title: DM2_M69_Q_03_b

value: Quadriceps

tag: age 69


title: DM2_M32_D_06_b

tag: age 32


title: DM2_M54_VL_12_b

tag: age 54


title: DM2_F43_VL_09_b


title: DM2_F47_D_07_b


title: DM2_F57_VL_08_b

tag: age 57


title: DM2_M?_BB_04_b

tag: age unknown


title: DM1_??_?_09_b

tag: DM1 patient


title: DM2_F71_BB_01_b

tag: biopsy site

tag: age 71


title: DM1_M21_?_10_b

tag: age 21


title: DM1_F54_?_06_b


title: DM2_M39_BB_02_b

tag: age 39


title: DM1_F55_D_04_b

tag: age 55


title: DM1_F?_D_03_b

tag: Gender


title: DM1_M25_?_07_b

tag: age 25


title: DM1_F29_BB_08_b

tag: age 29


title: DM1_??_?_05_b


title: MCF7.Id1.2

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: replicate 2

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and only genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

source_name: MCF7 cell line, Id1 overexpressed

label_protocol: Biotin Labeling of RNA at 400ng with Ambion Illumina® TotalPrep RNA Amplification Kit

growth_protocol: MCF7 cells expressing vector control, Id1 or Id2 were grown in DMEM media with 10% FBS

extract_protocol: extraction using trizol

treatment_protocol: To generate MCF7 cells stably overexpressing ID1, ID2 or vector control, respective full length human cDNAs were cloned into lentiviral vector.  Lentivirus was produced by co-transfecting subconfluent human embryonic kidney (HEK) 293T cells with cDNA expression plasmid and packaging plasmids pMDLg/pRRE and RSV-Rev using Lipifectamine 2000. Infectious lentiviruses were collected 48 h after transfection, centrifuged to remove cell debris and filtered through 0.45 um filters (Millipore). MCF7 cells were transduced with the lentiviruses

tag: overexpression

tag: cell line


title: MCF7.Id1.1

description: replicate 1


title: MCF7.Id2.2

description: replicate 2

source_name: MCF7 cell line, Id2 overexpressed


title: MCF7.con.1

description: replicate 1

source_name: MCF7 cell line, control


title: DM1_F?_BB_02_b


title: DM1_F?_BB_01_b


title: MCF7.con.2

description: replicate 2


title: Wg++ embryo, biological rep1

status: Public on Aug 28 2017

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

description: Naïve embryos overexpressing Wg

hyb_protocol: Hybridised using Affymetrix recommended protocol

scan_protocol: Scanned using Affymetrix recommended protocol

data_processing: The data were analyzed with R/Bioconductor and normalised using GC-RMA.

organism: Drosophila melanogaster

source_name: Naïve embryos overexpressing Wg

label_protocol: Labelled using Affymetrix recommended protocol

extract_protocol: Extracted using Affymetrix recommended protocol

tag: tissue

value: embryo

tag: genotype

value: Wg++


title: DisArmed embryo, biological rep2

description: Naïve embryos expressing DisArmed

source_name: Naïve embryos expressing DisArmed

value: DisArmed


title: Wnt4++/Otk++ embryo, biological rep1

description: Naïve embryos overexpressing Wnt4 and Otk


title: Wnt4++ embryo, biological rep2

description: Naïve embryos overexpressing Wnt4

source_name: Naïve embryos overexpressing Wnt4


title: Wild-type embryo, biological rep2

description: Wild type naïve embryos

source_name: Wild type naïve embryos

value: WT


title: arm∆N embryo, biological rep2

description: Naïve embryos expressing arm∆N

source_name: Naïve embryos expressing arm∆N

value: arm∆N


title: arm∆N embryo, biological rep1

description: Naïve embryos expressing arm∆N


title: tcf∆N-short embryo, biological rep1

description: Naïve embryos expressing tcf∆N-short

source_name: Naïve embryos expressing tcf∆N-short

value: tcf∆N-short


title: arm∆N-tcf∆N-short embryo, biological rep2

description: Naïve embryos expressing arm∆N-tcf∆N-short

value: arm∆N-tcf∆N-short


title: DisArmed embryo, biological rep1

description: Naïve embryos expressing DisArmed


title: arm∆N-tcf∆N-short embryo, biological rep1

source_name: Naïve embryos expressing arm∆N-tcf∆N-short


title: Otk++ embryo, biological rep2

description: Naïve embryos overexpressing Otk

source_name: Naïve embryos overexpressing Otk

value: Otk++


title: tcf∆N-long embryo, biological rep2

description: Naïve embryos expressing tcf∆N-long

source_name: Naïve embryos expressing tcf∆N-long

value: tcf∆N-long


title: Wnt4++/Otk++ embryo, biological rep2

source_name: Naïve embryos overexpressing Wnt4 and Otk


title: Otk++ embryo, biological rep1

description: Naïve embryos overexpressing Otk


title: Wnt4++ embryo, biological rep1

description: Naïve embryos overexpressing Wnt4


title: tcf∆N-short embryo, biological rep2

description: Naïve embryos expressing tcf∆N-short


title: MCF7.Id2.1

description: replicate 1


title: Wild-type embryo, biological rep1

description: Wild type naïve embryos


title: tcf∆N-long embryo, biological rep1

description: Naïve embryos expressing tcf∆N-long


title: Wg++ embryo, biological rep2

description: Naïve embryos overexpressing Wg


title: 2mMCP_12rep1_(2m-2mMCP-12)

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple 'Gala' fruit flesh, 1-MCP treated, 2 months cold storage

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Gala apples were harvested from a commercial orchard in 2009 and 2012

extract_protocol: Derived from the apple tissues RNA extraction method (Gasic et al., 2004) and pine tree RNA isolation method (Chang et al., 1993)

treatment_protocol:
Harvested apples were treated with 1-MCP (AgroFreshTM, Dow Chemical Company) at 1ppm (1µL .L-1) for 24 hours, applied to 140 L chambers containing 50 kg of fruits at 20°C. Subsequently, the fruits were transferred to cold storage.
Cold storage at 0 to 0.5°C and 90 to 95% of relative humidity for 60 days, after harvest.

tag: organ

value: Fruit

value: Parenchyma

tag: genetic background

value: Gala

value: Wild-type

tag: year harvested

tag: tissus developmental stage

value: Harvested at optimum maturity

tag: treatment 1

value: 1-MCP application

tag: treatment 2

value: Cold storage for 60 days after harvest


title: 2mMCP_12rep2_(2m-2mMCP-12)


title: 2mC_12rep1_(2m-2mMCP-12)

source_name: Apple 'Gala' fruit flesh, 2 months cold storage


title: Recolte_12rep2_(0-2m-12)

source_name: Apple 'Gala' fruit flesh, at harvest


title: Recolte_12rep2_(0-2mMCP-12)


title: 2mMCP_12rep2_(0-2mMCP-12)


title: 2mC_12rep2_(2m-2mMCP-12)


title: Recolte_12rep1_(0-2mMCP-12)


title: 2mC_12rep2_(0-2m-12)


title: 2mMCP_12rep1_(0-2mMCP-12)


title: Colon_male_young_repl6

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.38.0).

source_name: proximal colon, C57B1/6OlaHsd mouse, male, age 3m

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Male and female C57B1/6OlaHsd (B6) mice were purchased from Harlan (Harlan, Horst, The Netherlands) at an age of eight weeks. Mice were co-housed (5 mice per cage, according to sex) in isolated ventilated cages to limit environmental influences. The mice had ad libitum access to food (D12450B diet; Research Diets Services, Wijk bij Duurstede, the Netherlands) and water. The mice were sacrificed at an age of 3 and 19 months by cervical dislocation under anesthesia (isoflurane and oxygen).  For microarray analysis, approximately 1 cm of proximal colon was frozen in liquid nitrogen and stored at -80°C prior to RNA isolation and transcriptomics. In addition, we included a group of female mice that were ovariectomized (ovx) at 15 months of age to determine the effect of a loss of female sex hormones (human menopause). These mice were also sacrificed at the age of 19 months. During the ovariectomy procedure, the mice were anesthetized with isoflurane and oxygen and two small incisions were made on both ventral sides. Both ovaries were localized, ligated and removed. After surgery the mice received analgesic (Temgesic; 10 µl/g body weight). All mice experiments were performed after receiving approval of the Animal Care Committee of the Groningen University.

extract_protocol: Total RNA was purified using TRIzol (Life Technologies, Calsbad, CA, USA) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice did not receive any specific treatment.

tag: strain/background

tag: genotype/variation

value: wildtype

tag: Sex

value: male

tag: ovariectomized

tag: age group

value: young

tag: age (months)

value: proximal colon

tag: diet group

value: normal diet (Research Diets D12450B)

tag: mouse id


title: Colon_female_young_repl4

source_name: proximal colon, C57B1/6OlaHsd mouse, female, age 3m

value: female

value: no


title: Recolte_12rep1_(0-2m-12)


title: 2MC_09rep1_(2M-2MMCP_09)


title: Colon_female_young_repl3


title: Colon_female_young_repl5


title: Colon_female_young_repl1


title: Colon_female_young_repl2


title: 2mC_12rep1_(0-2m-12)


title: 2MC_09rep2_(2M-2MMCP_09)


title: 2MMCP_09rep2_(4hs-2MMCP_09)


title: Recolte_09rep2_(4hs-2M_09)


title: 2MMCP_09rep2_(2M-2MMCP_09)


title: 2MC_09rep1_(4hs-2M_09)


title: Recolte_09rep2_(4hs-2MMCP_09)


title: 2MMCP_09rep1_(2M-2MMCP_09)


title: Recolte_09rep1_(4hs-2M_09)


title: Colon_male_young_repl2


title: Recolte_09rep1_(4hs-2MMCP_09)


title: Colon_male_young_repl4


title: Colon_male_young_repl1


title: 2MC_09rep2_(4hs-2M_09)


title: Colon_male_young_repl3


title: Colon_male_young_repl5


title: 2MMCP_09rep1_(4hs-2MMCP_09)


title: Colon_female_old_ovx_repl4

source_name: proximal colon, C57B1/6OlaHsd mouse, female, ovariectomized, age 19m

value: yes

value: old


title: Colon_male_old_repl4

source_name: proximal colon, C57B1/6OlaHsd mouse, male, age 19m


title: Colon_male_old_repl3


title: Colon_female_old_repl5

source_name: proximal colon, C57B1/6OlaHsd mouse, female, age 19m


title: Colon_female_old_ovx_repl2


title: Colon_female_old_repl2


title: Colon_female_old_repl1


title: Colon_female_old_repl3


title: Colon_female_old_ovx_repl5


title: Colon_female_old_ovx_repl1


title: UIC #4

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

description: This sample is of wild-type Danio rerio. It is the fourth of four wild-type biological replicates used in this experiment.

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

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

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

organism: Danio rerio

source_name: Danio rerio wild-type

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

growth_protocol: Rx3:GFP embryos were incubated in egg water at 25°C until developmental stage 18 somites (Kimmel et al., 1995)

extract_protocol: Total RNA was extracted using trizol (Qiagen Inc., Valencia, CA, USA) followed by isopropanol precipitation. RNA quality and concentration was determined by bioanalyzer.

treatment_protocol: Rx3:GFP embryos were injected at the one-cell stage with antisense morpholino to either Semaphorin6A or PlexinA2 (Ebert et al., 2014).

tag: condition

value: Wildtype

tag: strain

tag: developmental stage

value: 18 hour postfertilization


title: Sema #4

description: This sample is of a sema6A morphant of Danio rerio. It is the fourth of four sema6A morphant biological replicates used in this experiment.

source_name: Danio rerio sema6A morphant

value: sema6A morphant


title: Plexin #4

description: This sample is of a plexinA2 morphant of Danio rerio. It is the fourth of four plexinA2 morphant biological replicates used in this experiment.

source_name: Danio rerio plexinA2 morphant

value: plexinA2 morphant


title: Colon_male_old_repl5

tag: tissue


title: Sema #3

description: This sample is of a sema6A morphant of Danio rerio. It is the third of four sema6A morphant biological replicates used in this experiment.


title: Plexin #3

description: This sample is of a plexinA2 morphant of Danio rerio. It is the third of four plexinA2 morphant biological replicates used in this experiment.


title: Sema #2

description: This sample is of a sema6A morphant of Danio rerio. It is the second of four sema6A morphant biological replicates used in this experiment.


title: Colon_male_old_repl1


title: UIC #2

description: This sample is of wild-type Danio rerio. It is the second of four wild-type biological replicates used in this experiment.


title: Colon_male_old_repl2


title: Plexin #1

description: This sample is of a plexinA2 morphant of Danio rerio. It is the first of four plexinA2 morphant biological replicates used in this experiment.


title: Sema #1

description: This sample is of a sema6A morphant of Danio rerio. It is the first of four sema6A morphant biological replicates used in this experiment.


title: Plexin #2

description: This sample is of a plexinA2 morphant of Danio rerio. It is the second of four plexinA2 morphant biological replicates used in this experiment.


title: UIC #1

description: This sample is of wild-type Danio rerio. It is the first of four wild-type biological replicates used in this experiment.


title: subtelomere-deletion (SD5)

status: Public on Aug 27 2017

city: Suita

first: Junko

last: Kanoh

state: Osaka

address: 3-1 Yamadaoka

department: Institute for Protein Research

country: Japan

institute: Osaka University

description: Gene expression data of exponentially growing cells

hyb_protocol: After the fragmentation of the biotynylated cRNA, 7.5 microg of the cRNA were hybridized for 16 hours at 45C on GeneChip® Yeast Genome 2.0 Array (Affymetrix). The GeneChips were washed and stained using Mini_euk2v3 protocol in the Affymetrix Fluidics Station 400 (Affymetrix).

scan_protocol: The GeneChips were scanned with a GeneChip® Scanner 3000 G7 (Affymetrix).

data_processing: Data analyses were performed with GeneChip® Operating Software (GCOS 1.4) using default settings and scaling as mormalization method with s_pombe.msk file (Affymetrix) to mask S. cerevisiae probe sets.

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: S. pombe exponentially growing cells

label_protocol: cDNA synthesis and biotinylated cRNA preparation were performed with GeneChip® ３’IVT Express kit (Affymetrix) using 5 ng of polyA RNA with the protocol for 250 ng of total RNA. The IVT reactions were performed for 4 hours at 40˚C.

growth_protocol: Cells were grown in YES liquid medium at 32˚C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And then mRNA was purified by oligo dT column.

treatment_protocol: 4×10^8 cells were used for RNA extraction. Cells were collected by centrifugation, washed by H2O once, and then freezed by liquid nitrogen.

tag: growth stage

value: Exponentially growing cells

tag: genotype

value: Subtelomere-deleted, SD5 (h-)


title: UIC #3

description: This sample is of wild-type Danio rerio. It is the third of four wild-type biological replicates used in this experiment.


title: Colon_female_old_ovx_repl3


title: KO_untreated_rep3

city: Singapore

first: Shirish

last: Shenolikar

state: Singapore

address: 8 College Road

department: Neuroscience and Behavioral Disorders

country: Singapore

institute: Duke-NUS Graduate Medical School

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45°C.

scan_protocol: GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Background adjusted, quantile normalized, and log transformed probe intensities were generated from the Affymetrix mouse 430 2.0 array  via the Robust Multichip Average (RMA) method (PMID 12925520). Probes with an average log signal less than 5.6 in all groups were removed from analysis. After filtering, 26382 of a total of 45101 probe sets were retained for analysis. Unpaired, regularized T-tests were performed in Cyber-T (http://cybert.ics.uci.edu/) with a sliding window of 101 and Bayesian confidence value of 7 (PMID 11395427). Multiple testing was adjusted by control of the false discovery rate (FDR), as per Benjamini and Hochberg (DOI: 10.1111/j.1467-9868.2010.00746.x) . Genes with an absolute fold-change > 1.2 fold and a nominal p value of < 0.01 were considered to be marginally significant.

source_name: KO cells, untreated

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® 3’ IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Mouse embryonic fibroblasts were immortalized with SV40 large T antigen and grown in Dulbecco's modified Eagle's medium (DMEM) 11995 (Life Technologies) supplemented with 10% (v/v) fetal bovine serum (Hyclone), 1X L-Glutamine, 1X MEM NEA and 50 µM beta-mercaptoethanol

extract_protocol: Total RNA was extracted using an Rneasy mini kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells subject to arsenite treatment were treated with 0.1 mM sodium arsenite (dissolved in water) for 2 h prior to cell lysis.

value: homozygous KO

tag: cell type

value: mouse embryonic fibroblast (MEF)

tag: agent

value: untreated


title: wild_type

value: wild-type (h-)


title: KO_arsenite_rep3

source_name: KO cells, arsenite-treated, 2 h

value: arsenite


title: WT_arsenite_rep3

source_name: WT cells, arsenite-treated, 2 h

value: WT


title: WT_untreated_rep2

source_name: WT cells, untreated


title: WT_untreated_rep3


title: KO_arsenite_rep2


title: KO_arsenite_rep1


title: KO_untreated_rep1


title: WT_untreated_rep1


title: WT_arsenite_rep2


title: WT_arsenite_rep1


title: KO_untreated_rep2


title: Colon_female_old_repl4

value: wildtype

value: proximal colon

value: normal diet (Research Diets D12450B)


title: Contralateral-6hrs-rep5

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: Gene expression after 6 hours post-occlusion

hyb_protocol: An equal amount (3.75 µg) of Cy3 cRNA probes were hybridized on SurePrint G3 Mouse Gene Expression 2x400K microarrays (Agilent Technologies). Hybridization was performed for 17 hours, rotating at 10 rpm at 65°C. Samples were washed and dried according to the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using AgilentHD_GX_1color setting for 2x400k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028727_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Contralateral hemisphere, 6 hours post-occlusion, replicate 5

label_protocol: RNA (50 ng) from 5 cerebral hemispheres isolated at 6 hours post-occlusion was labelled using the Low Input Quick Amp WT Labeling kit (Agilent Technologies). RNA spike-in controls were used to adjust possible dye effects. RNA was converted to cDNA using reverse transcriptase and WT primers (T7 promoter primer and random primer with a T7 promoter). T7 RNA polymerase was used for the synthesis and labelling of cRNA with Cy3. The fluorescent labelled cRNA probes were purified using the RNeasy mini kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Mice were sacrified and NaCl transcardial perfusion was performed. Brains were removed and the left (contralateral) and right (ipsilateral) hemispheres were dissected. Cerebral hemispheres were quickly immersed in liquid nitrogen and stored at -80°C. RNA was isolated from cerebral hemispheres using the RNeasy Microarray Tissue kit following the manufacturer’s instructions (Qiagen). RNA integrity was assessed with the Agilent 2100 BioAnalyzer (Agilent Technologies) by measuring the RIN. Measured RIN was always superior to 9.

value: Swiss

tag: gender

value: Male

tag: weight

value: Cerebral cortex


title: MDA-MB-157 0h rep2

status: Public on Aug 26 2017

city: Groningen

first: Anne Margriet

last: Heijink

state: Groningen

address: Hanzeplein 1

institute: University Medical Center Groningen

description:
replicate 2
6898341055_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using percentile shift normalisation with GeneSpring (Agilent)

source_name: Cell line

label_protocol: Total RNA was converted to cDNA, followed by an in vitro transcription step to generate biotin labeled cRNA using the Ambion MessageAmp kit for Illumina arrays

growth_protocol: All four cell lines were grown under ATCC specified growth conditions

extract_protocol: RNA was extracted from cells using the RNAeasy Kit (QIAGEN)

treatment_protocol: Cells were treated with 2 µM cisplatin for 0, 24 or 72 hours

tag: cell line


title: MDA-MB-157 72h rep1

description:
replicate 1
6898341055_C


title: BT549 0h rep1

description:
replicate 1
6898341055_G


title: MDA-MB-231 72h rep2

description:
replicate 2
6898341055_A


title: HCC38 0h rep1

description:
replicate 1
6898341055_I


title: MDA-MB-231 24h rep1

description:
replicate 1
6898341055_F


title: HCC38 24h rep2

description:
replicate 2
6898341055_J


title: BT549 24h rep2

description:
replicate 2
6898341055_B


title: BT549 0h rep2

description:
replicate 2
6898341040_L


title: HCC38 24h rep1

description:
replicate 1
6898341040_K


title: MDA-MB-157 24h rep1

description:
replicate 1
6898341040_G


title: HCC38 72h rep1

description:
replicate 1
6898341040_J


title: Contralateral-6hrs-rep2

source_name: Contralateral hemisphere, 6 hours post-occlusion, replicate 2


title: Ipsilateral-6hrs-rep2

source_name: Ipsilateral hemisphere (ischemia), 6 hours post-occlusion, replicate 2


title: BT549 72h rep2

description:
replicate 2
6898341055_K


title: MDA-MB-157 24h rep2

description:
replicate 2
6898341055_L


title: Ipsilateral-6hrs-rep3

source_name: Ipsilateral hemisphere (ischemia), 6 hours post-occlusion, replicate 3


title: Ipsilateral-6hrs-rep5

source_name: Ipsilateral hemisphere (ischemia), 6 hours post-occlusion, replicate 5


title: BT549 24h rep1

description:
replicate 1
6898341040_H


title: Ipsilateral-6hrs-rep4

source_name: Ipsilateral hemisphere (ischemia), 6 hours post-occlusion, replicate 4


title: MDA-MB-231 24h rep2

description:
replicate 2
6898341040_I


title: MDA-MB-157 72h rep2

description:
replicate 2
6898341040_F


title: HCC38 72h rep2

description:
replicate 2
6898341055_D


title: MDA-MB-231 0h rep1

description:
replicate 1
6898341040_E


title: Contralateral-6hrs-rep3

source_name: Contralateral hemisphere, 6 hours post-occlusion, replicate 3


title: MDA-MB-231 0h rep2

description:
replicate 2
6898341055_H


title: Contralateral-6hrs-rep4

source_name: Contralateral hemisphere, 6 hours post-occlusion, replicate 4


title: Contralateral-6hrs-rep1

source_name: Contralateral hemisphere, 6 hours post-occlusion, replicate 1


title: Ipsilateral-6hrs-rep1

source_name: Ipsilateral hemisphere (ischemia), 6 hours post-occlusion, replicate 1


title: BT549 72h rep1

description:
replicate 1
6898341040_D


title: T84, P. jejuni (isolates CD3:27) rep2 (CTR 22 28 27)

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

description:
SAMPLE 11
6898376032_B.

data_processing: Background was first subtracted from the data and then normalized using Beadstudios cubic spline algorithm.

source_name: T84, P. jejuni (isolates CD3:27)

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

extract_protocol: Total RNA was extracted from T84 polarized tight monolayers by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

value: colon carcinoma cell line T84

tag: treatment

value: P. jejuni (isolates CD3:27)


title: MDA-MB-231 72h rep1

description:
replicate 1
6898341040_B


title: T84, P. jejuni (isolates CD3:28) rep3 (CTR 22 28 27)

description:
SAMPLE 9
6898376032_F.

source_name: T84, P. jejuni (isolates CD3:28)

value: P. jejuni (isolates CD3:28)


title: T84, L. umeaense rep1 (CTR 22 28 27)

description:
SAMPLE 4
6898376032_G.

source_name: T84, L. umeaense

value: L. umeaense


title: T84, P. jejuni (isolates CD3:27) rep1 (CTR 22 28 27)

description:
SAMPLE 10
6898376032_A.


title: T84, L. umeaense rep2 (CTR 22 28 27)

description:
SAMPLE 5
6898376032_H.


title: HCC38 0h rep2

description:
replicate 2
6898341040_A


title: MDA-MB-157 0h rep1

description:
replicate 1
6898341040_C


title: T84, P. jejuni (isolates CD3:27) rep3 (CTR 22 28 27)

description:
SAMPLE 12
6898376032_C.


title: T84, L. umeaense rep3 (CTR 22 28 27)

description:
SAMPLE 6
6898376032_I.


title: T84, CTR rep2 (CTR 22 28 27)

description:
SAMPLE 2
6898376032_K.

source_name: T84, CTR

value: CTR


title: T84, P. jejuni (isolates CD3:28) rep2 (CTR 22 28 27)

description:
SAMPLE 8
6898376032_E.


title: T84, CTR rep1 (CTR 22 28 27)

description:
SAMPLE 1
6898376032_J.


title: T84, P. jejuni (isolates CD3:28) rep1 (CTR 22 28 27)

description:
SAMPLE 7
6898376032_D.


title: T84, CTR rep3 (CTR 22 28 27)

description:
SAMPLE 3
6898376032_L.


title: T84, bacteria mix rep3 (A grav, Bmix Bmix glut)

description:
SAMPLE 9
7677153001_D.

source_name: T84, bacteria mix

extract_protocol: Total RNA was extracted from T84 polarized tight monolayers  by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

value: bacteria mix


title: T84, A. graevenitzii rep3 (A grav, Bmix Bmix glut)

description:
SAMPLE 6
7677153001_G.

source_name: T84, A. graevenitzii

value: A. graevenitzii


title: T84, bacteria mix with gluten rep2 (A grav, Bmix Bmix glut)

description:
SAMPLE 11
7677153001_B.

source_name: T84, bacteria mix with gluten

value: bacteria mix with gluten


title: T84, A. graevenitzii rep2 (A grav, Bmix Bmix glut)

description:
SAMPLE 5
7677153001_H.


title: T84, CTR rep3 (A grav, Bmix Bmix glut)

description:
SAMPLE 3
7677153001_J.


title: T84, bacteria mix rep1 (A grav, Bmix Bmix glut)

description:
SAMPLE 7
7677153001_F.


title: T84, bacteria mix rep2 (A grav, Bmix Bmix glut)

description:
SAMPLE 8
7677153001_E.


title: T84, CTR rep1 (A grav, Bmix Bmix glut)

description:
SAMPLE 1
7677153001_L.


title: T84, A. graevenitzii rep1 (A grav, Bmix Bmix glut)

description:
SAMPLE 4
7677153001_I.


title: RA KD2- biological replicate 2

city: Jerusalem

first: Raghu

last: Edupuganti

address: 2-543, Silberman Building

department: Dept. of Genetics

country: Israel

institute: The Hebrew University

description: Gene expression data from 4 day RA differentiated SET knockdown ESCs

hyb_protocol: According to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000 7G with Autoloader according to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

data_processing: Data processing was performed in GeneExpressionConsole using Robust Multichip Analysis (RMA) probe summarization algorithm. Data was further processed and statistics were generated using R program. Non-expressing genes were filtered out on a pre-determined set point. Differential expression analysis was performed by carrying out a t-test for differences between the average signal values for each gene.

source_name: 4 day differentiated R1 ESCs with SET knockdown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (based on Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were grown in regular ESC medium with 15% FBS.

extract_protocol: R1 ESCs were grown on gelatinized dishes in regular DMEM medium containing 15% ES-grade fetal bovine serum (FBS), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1x Penicillin/ Streptomycin antibiotics, and 1000 U/ml leukemia inhibitory factor (LIF). Differentiation was induced by growing cells in ESC medium with 10% FBS, without LIF and in the presence of RA (1 µM).

treatment_protocol: SET knockdown and control clones were grown in regular ESC medium. For differentiaiton 1 µM retenoic acid was used.

value: 4 day differentiated ESC

tag: background mouse strain

tag: genotype/variation

value: SET knockdown


title: T84, CTR rep2 (A grav, Bmix Bmix glut)

description:
SAMPLE 2
7677153001_K.


title: RA KD1- biological replicate 2


title: T84, bacteria mix with gluten rep3 (A grav, Bmix Bmix glut)

description:
SAMPLE 12
7677153001_C.


title: T84, bacteria mix with gluten rep1 (A grav, Bmix Bmix glut)

description:
SAMPLE 10
7677153001_A.


title: RA KD1- biological replicate 1


title: RA KD2- biological replicate 1


title: ESC KD2- biological replicate 2

description: Gene expression data from R1 ESCs after SET knockdown.

source_name: R1 ESCs with SET knockdown

value: ESC


title: RA Scrambled biological replicate 1

description: Gene expression data from 4 day RA differentiated Scrambled-control ESCs

source_name: 4 day differentiated R1 ESCs (with Scrambled control infection)

value: scrambled control


title: RA Scrambled biological replicate 2


title: ESC KD2- biological replicate 1


title: ESC Scrambled biological replicate 2

description: Gene expression data from scrambled-control ESCs

source_name: R1 ESCs (with Scrambled control infection)


title: ESC KD1- biological replicate 1


title: ESC KD1- biological replicate 2


title: ESC Scrambled biological replicate 1


title: Human Fetal Brain_3999979099_R03C01

status: Public on Aug 25 2017

type: genomic

city: Oxford

first: Helen

last: Spiers

address: Keble Road

institute: University of Oxford

hyb_protocol: Standard Illumina 450K  Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Genome Studio followed by WateRmelon
Data were processed in R, data were normalized using the dasen method of the wateRmelon package.
the raw.csv contain unmethylated and methylated signal intensities

label: cy3, cy5

molecule: genomic DNA

label_protocol: Standard Illumina 450K Protocol

extract_protocol: Genomic DNA was extracted and purified from brain samples using a standard phenol/chloroform extraction

value: Human Fetal Brain

tag: pretreatment

value: BS


title: Human Fetal Brain_3999979089_R06C01


title: Human Fetal Brain_3999979089_R04C01


title: Human Fetal Brain_3999979099_R01C01


title: Human Fetal Brain_3999979099_R06C01


title: Human Fetal Brain_3999979089_R05C01


title: Human Fetal Brain_3999979099_R05C01


title: Human Fetal Brain_3999979086_R06C01


title: Human Fetal Brain_3999979089_R03C01


title: Human Fetal Brain_3999979086_R05C01


title: Human Fetal Brain_3999979086_R03C01


title: Human Fetal Brain_3999979089_R01C01


title: Human Fetal Brain_3999979085_R04C01


title: Human Fetal Brain_3999979086_R01C01


title: Human Fetal Brain_3999979085_R02C01


title: Human Fetal Brain_3999979086_R04C01


title: Human Fetal Brain_3999979080_R02C01


title: Human Fetal Brain_3999979080_R06C01


title: Human Fetal Brain_3999979089_R02C01


title: Human Fetal Brain_3999979080_R05C01


title: Human Fetal Brain_3999979070_R06C01


title: Human Fetal Brain_3999979085_R01C01


title: Human Fetal Brain_3999979085_R06C01


title: Human Fetal Brain_3999979086_R02C01


title: Human Fetal Brain_3999979080_R04C01


title: Human Fetal Brain_3999979099_R04C01


title: Human Fetal Brain_3999979080_R03C01


title: Human Fetal Brain_3999979085_R03C01


title: Human Fetal Brain_3999979080_R01C01


title: Human Fetal Brain_3999979085_R05C01


title: Human Fetal Brain_3999979070_R05C01


title: Human Fetal Brain_3999979070_R03C01


title: Human Fetal Brain_3999979070_R04C01


title: Human Fetal Brain_3999979067_R04C01


title: Human Fetal Brain_3999979067_R03C01


title: Human Fetal Brain_3999979070_R01C01


title: Human Fetal Brain_3999979067_R05C01


title: Human Fetal Brain_3999979070_R02C01


title: Human Fetal Brain_3999979067_R02C01


title: Human Fetal Brain_3999941161_R02C01


title: Human Fetal Brain_3999979013_R04C01


title: Human Fetal Brain_3999979013_R06C01


title: Human Fetal Brain_3999941161_R01C01


title: Human Fetal Brain_3999979013_R01C01


title: Human Fetal Brain_3999979013_R05C01


title: Human Fetal Brain_3999979067_R01C01


title: Human Fetal Brain_3999941152_R04C01


title: Human Fetal Brain_3999932062_R06C01


title: Human Fetal Brain_3999979013_R02C01


title: Human Fetal Brain_3999941152_R06C01


title: Human Fetal Brain_3999941152_R02C01


title: Human Fetal Brain_3999941161_R04C01


title: Human Fetal Brain_3999941152_R05C01


title: Human Fetal Brain_3999979013_R03C01


title: Human Fetal Brain_3999941152_R03C01


title: Human Fetal Brain_3999932062_R05C01


title: Human Fetal Brain_3999941152_R01C01


title: Human Fetal Brain_3999932062_R03C01


title: Human Fetal Brain_3999941161_R05C01


title: Human Fetal Brain_3999941161_R03C01


title: Human Fetal Brain_3999932062_R01C01


title: Human Fetal Brain_3999941161_R06C01


title: Human Fetal Brain_3999979067_R06C01


title: Human Fetal Brain_3999932061_R06C01


title: Human Fetal Brain_3999932061_R04C01


title: Human Fetal Brain_3999932062_R02C01


title: Human Fetal Brain_3999979099_R06C02

value: oxBS


title: Human Fetal Brain_3999932061_R03C01


title: Human Fetal Brain_3999932061_R02C01


title: Human Fetal Brain_3999932062_R04C01


title: Human Fetal Brain_3999932061_R05C01


title: Human Fetal Brain_3999979099_R01C02


title: Human Fetal Brain_3999979099_R05C02


title: Human Fetal Brain_3999979086_R04C02


title: Human Fetal Brain_3999979099_R04C02


title: Human Fetal Brain_3999932061_R01C01


title: Human Fetal Brain_3999979089_R04C02


title: Human Fetal Brain_3999979085_R06C02


title: Human Fetal Brain_3999979089_R06C02


title: Human Fetal Brain_3999979086_R06C02


title: Human Fetal Brain_3999979099_R03C02


title: Human Fetal Brain_3999979089_R03C02


title: Human Fetal Brain_3999979086_R05C02


title: Human Fetal Brain_3999979089_R05C02


title: Human Fetal Brain_3999979086_R02C02


title: Human Fetal Brain_3999979089_R01C02


title: Human Fetal Brain_3999979086_R01C02


title: Human Fetal Brain_3999979080_R06C02


title: Human Fetal Brain_3999979085_R05C02


title: Human Fetal Brain_3999979085_R02C02


title: Human Fetal Brain_3999979085_R01C02


title: Human Fetal Brain_3999979086_R03C02


title: Human Fetal Brain_3999979089_R02C02


title: Human Fetal Brain_3999979080_R05C02


title: Human Fetal Brain_3999979080_R03C02


title: Human Fetal Brain_3999979070_R03C02


title: Human Fetal Brain_3999979070_R04C02


title: Human Fetal Brain_3999979070_R05C02


title: Human Fetal Brain_3999979085_R04C02


title: Human Fetal Brain_3999979070_R06C02


title: Human Fetal Brain_3999979067_R02C02


title: Human Fetal Brain_3999979070_R02C02


title: Human Fetal Brain_3999979080_R04C02


title: Human Fetal Brain_3999979067_R04C02


title: Human Fetal Brain_3999979080_R02C02


title: Human Fetal Brain_3999979067_R03C02


title: Human Fetal Brain_3999979067_R05C02


title: Human Fetal Brain_3999979080_R01C02


title: Human Fetal Brain_3999979070_R01C02


title: Human Fetal Brain_3999979013_R03C02


title: Human Fetal Brain_3999979067_R06C02


title: Human Fetal Brain_3999979013_R02C02


title: Human Fetal Brain_3999979085_R03C02


title: Human Fetal Brain_3999979013_R04C02


title: Human Fetal Brain_3999979067_R01C02


title: Human Fetal Brain_3999979013_R06C02


title: Human Fetal Brain_3999941152_R06C02


title: Human Fetal Brain_3999941161_R05C02


title: Human Fetal Brain_3999941161_R03C02


title: Human Fetal Brain_3999941161_R04C02


title: Human Fetal Brain_3999941152_R04C02


title: Human Fetal Brain_3999941152_R01C02


title: Human Fetal Brain_3999979013_R05C02


title: Human Fetal Brain_3999941152_R02C02


title: Human Fetal Brain_3999941161_R02C02


title: Human Fetal Brain_3999941161_R06C02


title: Human Fetal Brain_3999979013_R01C02


title: Human Fetal Brain_3999941161_R01C02


title: Human Fetal Brain_3999941152_R05C02


title: Human Fetal Brain_3999932062_R05C02


title: Human Fetal Brain_3999932061_R06C02


title: Human Fetal Brain_3999932062_R06C02


title: Human Fetal Brain_3999932062_R03C02


title: Human Fetal Brain_3999932061_R04C02


title: Human Fetal Brain_3999932062_R04C02


title: Human Fetal Brain_3999932062_R01C02


title: Human Fetal Brain_3999932061_R05C02


title: Human Fetal Brain_3999932061_R03C02


title: Human Fetal Brain_3999932061_R01C02


title: Human Fetal Brain_3999932061_R02C02


title: Human Fetal Brain_3999941152_R03C02


title: Chronic lymphocytic leukemia 102 post treatment

city: London

first: Jennifer

last: Edelmann

address: Charterhouse Square

department: Centre for Haemato-/Oncology

institute: Barts Cancer Institute

description: Hybridized to GenomeWide SNP 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix® fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

source_name: peripherel blood

label_protocol: As per manufacturer (Affymetrix®)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for a subset of samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 98 mononuclear cell fractions, 118 CD19-positive fractions, and 52 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: mononuclear cells

tag: ighv mutational status

value: IgHV unmutated

tag: tp53 diruption

value: no TP53 disruption detected

tag: atm disruption

value: del(11q) and ATMmut

value: not annotated

tag: best clinical response


title: Human Fetal Brain_3999932062_R02C02


title: Chronic lymphocytic leukemia 103 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated

value: no ATM disruption detected


title: Chronic lymphocytic leukemia 103 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: FC

value: partial remission


title: Chronic lymphocytic leukemia 101 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 100 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: complete remission


title: Chronic lymphocytic leukemia 102 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR


title: Chronic lymphocytic leukemia 97 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 97 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 99 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 101 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 100 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(17p) and TP53mut


title: Chronic lymphocytic leukemia 98 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 94 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unknown


title: Chronic lymphocytic leukemia 99 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 93 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 93 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 96 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: ATMmut


title: Chronic lymphocytic leukemia 95 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 93 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 98 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 94 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 92 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 95 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 96 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 95 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 94 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 92 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 92 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 97 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 91 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 91 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 90 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 96 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 87 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 89 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 90 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 86 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 89 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 87 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 86 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 84 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 85 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 83 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 81 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 84 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 82 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: non-response


title: Chronic lymphocytic leukemia 80 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 81 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 80 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: Chronic lymphocytic leukemia 81 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: Chronic lymphocytic leukemia 88 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected


title: Chronic lymphocytic leukemia 82 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 79 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 88 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 79 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 85 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 78 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 79 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 77 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 76 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 74 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 76 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 77 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 76 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 83 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 72 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 78 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 73 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 74 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 75 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(11q) and ATMmut


title: Chronic lymphocytic leukemia 78 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: not annotated


title: Chronic lymphocytic leukemia 75 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 72 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 71 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: pltTGFβ_iTreg, replicate 2

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 45101 transcripts

hyb_protocol: The Affymetrix GeneChip Mouse Genome 430 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Foxp3EGFP mice in C57BL/6 (B6) background were used for in vitro iTreg conversion. CD4+ T cells were isolated from splenocytes and CD4+EGFP– cells (naïve CD4+ T cells) were further purified by cell sorting. Platelets were isolated from wild type (WT) C57BL/6 mice and platelet lysates prepared by freeze/thaw were used as a source of pltTGFβ. The level of TGFβ1 in platelet lysates was quantified by ELISA. Purified CD4+EGFP– cells were cultured on 6-well plates coated with anti-CD3 mAb (2.5 µg/ml) in RPMI-1640 media containing 10% fetal bovine serum, 5x10-5 M β-Mercaptoethanol (β-ME), 1 µg/ml anti-CD28 mAb, 100 U/ml IL2, and 5 ng/ml purified TGFβ1 (purTGFβ1, a positive control) (R&D system), or pltTGFβ for 72 hours.

treatment_protocol: Tconv cells were cultured with TGFβ1 at a final concentration of 5 ng/ml for 72 hours.

tag: background strain


title: Chronic lymphocytic leukemia 72 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 73 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: purTGFβ_iTreg, replicate 3


title: pltTGFβ_iTreg, replicate 3


title: Chronic lymphocytic leukemia 77 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated


title: pltTGFβ_iTreg, replicate 1


title: purTGFβ_iTreg, replicate 2


title: Chronic lymphocytic leukemia 73 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected


title: Tconv, replicate 3

source_name: Tconv


title: Chronic lymphocytic leukemia 68 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 71 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+


title: Chronic lymphocytic leukemia 69 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: purTGFβ_iTreg, replicate 1


title: Chronic lymphocytic leukemia 68 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Tconv, replicate 2


title: Chronic lymphocytic leukemia 69 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 67 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 71 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC


title: Chronic lymphocytic leukemia 70 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 87 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Tconv, replicate 1


title: Human papillary fibroblasts_donnor3

city: SAINT-VIANCE

first: VINCENT

last: BARRUCHE

state: If applicable (USA / Canada)

address: ZI de la Nau

department: R&D

institute: SILAB

description:
Gene expression of papillary fibroblast
11_pap_3

hyb_protocol: Following fragmentation, 15 µg of cRNA was hybridized to the GeneChip Human 133 plus 2.0 Arrays (Affymetrix, Inc, California).

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

data_processing: All array data were preprocessed in the statistical language R using the Bioconductor package Linear Models for Microarray Data (“LIMMA”). Background correction was performed using the “normexp” function and in order to make arrays comparable, a quantile normalization was applied to the variance stabilized signal.

source_name: Human papillary fibroblasts

label_protocol: 100 ng of each sample was 3’-labeled with GeneChip 3’ IVT Express Kit (Affymetrix)  according to the manufacturer's instructions.

growth_protocol: Dermatomed papillary or reticular samples were cut into small pieces and explants were cultivated for 2 weeks to allow fibroblast to exit explants.  with Modified Eagle medium (MEM life technologies) supplemented with 10% fetal bovine serum, with penicillin (100 units/ml), streptomycin (100 µg/ml), and fungizone (0.025 µg/ml). They were kept at 37°C at 5%CO2. The primary cultures were re-fed weekly until confluent. Cells were used at passage 1

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen). Quantification and quality assessment of the isolated RNA samples were performed and verified using a NanoDrop 2000c spectrophotometer (ThermoFisher) and an Agilent Bioanalyzer2100 (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: Fibroblasts were cultured in monolayer at 37°C under 5% CO2 in Minimal Essential Medium (MEM; Gibco; Inchinnan Business Park, UK) supplemented with 10% fetal bovine serum (FBS; Sigma), 1% penicillin/streptomycin (Gibco; Inchinnan Business Park, UK), 0.1% fungizone (Gibco; Inchinnan Business Park, UK)

tag: donor id

tag: tissue source

value: breast skin

value: human dermal fibroblasts

tag: cell subpopulation

value: papillary fibroblasts (Fp)

tag: passage

value: passage 1


title: Human papillary fibroblasts_donnor2

description:
Gene expression of papillary fibroblast
09_pap_2

tag: cell type


title: Chronic lymphocytic leukemia 66 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 67 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR

value: partial remission


title: Chronic lymphocytic leukemia 65 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Human papillary fibroblasts_donnor1

description:
Gene expression of papillary fibroblast
03_pap_1


title: Human reticular fibroblasts_donnor3

description:
Gene expression of reticular fibroblast
12_ret_3

source_name: Human reticular fibroblasts

value: reticular fibroblasts (Fr)


title: Human reticular fibroblasts_donnor2

description:
Gene expression of reticular fibroblast
10_ret_2


title: Human reticular fibroblasts_donnor1

description:
Gene expression of reticular fibroblast
04_ret_1


title: Globule-free hepatocyte areas from PIZ mouse liver (pooled 2 mice)

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

description:
Gene expression data for globule free hepatocyte areas
GF Control

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse MTA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000.

data_processing: Transcriptome Analysis Console software(TAC) Affymetrix

source_name: Globule-free Liver

label_protocol: Biotinylated cRNA were prepared using NuGen Ovation WTA System V2 with 50ng input RNA

growth_protocol: Mice were housed in standard conditions with standard chow and harvested at 3 months of age.

extract_protocol: Laser captured tissue was collected in extraction buffer and processed using the Applied Biosystems Pico Pure RNA isolation kit.

treatment_protocol: PIZ mice, transgenic for the human ATZ (mutant alpha-1-antitrypsin gene and promoter), were untreated (housed in standard conditions with standard chow)

tag: strain

tag: disease state

value: PiZ model of ATD

tag: tissue

value: Globule-free hepatocyte areas


title: Chronic lymphocytic leukemia 64 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated

value: ATMmut

tag: treatment


title: Chronic lymphocytic leukemia 65 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected

value: not annotated


title: Chronic lymphocytic leukemia 66 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected


title: Chronic lymphocytic leukemia 62 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: IgHV mutated


title: Chronic lymphocytic leukemia 63 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 62 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 63 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: complete remission


title: Chronic lymphocytic leukemia 65 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC


title: Chronic lymphocytic leukemia 63 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells

value: del(17p) and TP53mut


title: Chronic lymphocytic leukemia 64 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 61 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR


title: Chronic lymphocytic leukemia 62 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 70 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: partial remission


title: CD8+ T Lymphocytes_IV Healthy donor 3 HLA-matched Time 0_replicate 3

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

description:
CD8+_IV_T0_3
Healthy donor 3, male, HLA-matched, 50 years old.

hyb_protocol: Total RNA was hybridized on to the GeneChip Human Genome U133A Array (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions.

scan_protocol: We used the default settings of GCOS software to scan the chips.

data_processing: We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values. R 2.0.1 statistical software was used to perform the normalization of the data according to R. A. Irizarry et al., Biostatistics, 2003. Differentially expressed genes were identified using GeneSpring GX software (Agilent, Palo Alto, CA), by applying a moderated t-test with Storey with bootstrapping multiple testing correction. We selected the differentially expressed genes using a q-value cut-off of 0.05.

source_name: CD8+ T lymphocytes, healthy, day 0

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA, we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

growth_protocol: CD8+ T cells were isolated from the PBMCs of autologous and allogeneic normal, healthy donors by negative selection using specific MACS magnetic beads (Miltenyi Biotec, Bergisch Gladbach, Germany) on MiniMACS columns, following the manufacturer's protocol and subsequently assessed for their functional and phenotypic profiles.

extract_protocol: Total RNA was isolated from freshly-isolated and day 35 cultured CD8+ T cells using TRIzol© reagent (Life Technologies), according to the manufacturer’s instructions. Total RNA integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: For MLTC experiments, PBMCs from RCC patients or HLA-matched healthy donors were co-cultured in 24-well plates (Costar, Corning, USA) at 10^6 cells/well with irradiated RCC stimulator cells (10^5 cells/well) in AIM-V medium (Life Technologies, Invitrogen, Italy) supplemented with 10% heat-inactivated pooled human serum (Sigma (medium Mb)). Recombinant human IL-2 was added on day 3 (250 IU/mL; Proleukin, Chiron, and Emeryville, CA). Responder lymphocytes were restimulated weekly with 10^5 irradiated tumor cells in IL-2-containing medium for 2 weeks prior to responder CD8+ T cells isolation. Isolated CD8+ T cells were cultured for an additional 2 weeks. On day 0 and day 35 of culture, CD8+ T cells were analyzed for gene expression profiles.

tag: disease status

value: healthy

tag: gender

value: male

tag: age

value: 50 years

value: CD8+ T lymphocytes

tag: time point

value: day 0 of culture


title: Globule-containing hepatocyte areas from PIZ mouse liver (pooled 2 mice)

description:
Gene expression data for globule containing hepatocyte areas
GC Control

source_name: Globule-containing Liver

value: PiZ model of ATD

value: Globule-containing hepatocyte areas


title: CD8+ T Lymphocytes_IV Healthy donor 3 HLA-matched Time 35_replicate 1

description:
CD8+_IV_T35_1
Healthy donor 3, male, HLA-matched, 50 years old.

source_name: CD8+ T lymphocytes, healthy, day 35

value: day 35 of culture


title: CD8+ T Lymphocytes_IV Healthy donor 3 HLA-matched Time 0_replicate 2

description:
CD8+_IV_T0_2
Healthy donor 3, male, HLA-matched, 50 years old.


title: Chronic lymphocytic leukemia 60 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

tag: ighv mutational status

value: IgHV unmutated

tag: tp53 diruption

value: no TP53 disruption detected

value: no ATM disruption detected

value: non-response


title: Chronic lymphocytic leukemia 58 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

tag: atm disruption

value: del(11q) and ATMmut

value: not annotated

tag: best clinical response


title: Chronic lymphocytic leukemia 61 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: CD8+ T Lymphocytes_IV Healthy donor 3 HLA-matched Time 35_replicate 2

description:
CD8+_IV_T35_2
Healthy donor 3, male, HLA-matched, 50 years old.

tag: donor id


title: CD8+ T Lymphocytes_IV Healthy donor 3 HLA-matched Time 35_replicate 3

description:
CD8+_IV_T35_3
Healthy donor 3, male, HLA-matched, 50 years old.


title: Chronic lymphocytic leukemia 59 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: FC


title: Chronic lymphocytic leukemia 58 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR

value: complete remission


title: CD8+ T Lymphocytes_IV Healthy donor 3 HLA-matched Time 0_replicate 1

description:
CD8+_IV_T0_1
Healthy donor 3, male, HLA-matched, 50 years old.

value: healthy

value: male

value: 50 years


title: Chronic lymphocytic leukemia 56 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 57 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 59 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: CD8+ T Lymphocytes_TO Healthy donor 2 HLA-matched Time 35_replicate 3

description:
CD8+_TO_T35_3
Healthy donor 2 HLA-matched, 51 years old.

value: 51 years

value: CD8+ T lymphocytes


title: CD8+ T Lymphocytes_TO Healthy donor 2 HLA-matched Time 35_replicate 2

description:
CD8+_TO_T35_2
Healthy donor 2 HLA-matched, 51 years old.

value: day 35 of culture


title: CD8+ T Lymphocytes_TO Healthy donor 2 HLA-matched Time 35_replicate 1

description:
CD8+_TO_T35_1
Healthy donor 2 HLA-matched, 51 years old.


title: Chronic lymphocytic leukemia 55 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: CD8+ T Lymphocytes_TO Healthy donor 2 HLA-matched Time 0_replicate 3

description:
CD8+_TO_T0_3
Healthy donor 2 HLA-matched, 51 years old.

value: day 0 of culture


title: Chronic lymphocytic leukemia 55 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected


title: CD8+ T Lymphocytes_TO Healthy donor 2 HLA-matched Time 0_replicate 2

description:
CD8+_TO_T0_2
Healthy donor 2 HLA-matched, 51 years old.


title: CD8+ T Lymphocytes_TC RCC patient Time 35_replicate 3

description:
CD8+_TC_T35_3
Male patient, 62 years old, affected by renal cell carcinoma, G1, T3aN0M0.

source_name: CD8+ T lymphocytes, RCC, day 35

value: renal cell carcinoma (RCC)

value: 62 years


title: CD8+ T Lymphocytes_TO Healthy donor 2 HLA-matched Time 0_replicate 1

description:
CD8+_TO_T0_1
Healthy donor 2 HLA-matched, 51 years old.


title: Chronic lymphocytic leukemia 60 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: ATMmut

value: not annotated


title: CD8+ T Lymphocytes_TC RCC patient Time 0_replicate 3

description:
CD8+_TC_T0_3
Male patient, 62 years old, affected by renal cell carcinoma, G1, T3aN0M0.

source_name: CD8+ T lymphocytes, RCC, day 0


title: CD8+ T Lymphocytes_TC RCC patient Time 35_replicate 1

description:
CD8+_TC_T35_1
Male patient, 62 years old, affected by renal cell carcinoma, G1, T3aN0M0.


title: Chronic lymphocytic leukemia 56 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: non-response


title: CD8+ T Lymphocytes_TC RCC patient Time 0_replicate 2

description:
CD8+_TC_T0_2
Male patient, 62 years old, affected by renal cell carcinoma, G1, T3aN0M0.


title: Chronic lymphocytic leukemia 54 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(17p) and TP53mut


title: CD8+ T Lymphocytes_TC RCC patient Time 0_replicate 1

description:
CD8+_TC_T0_1
Male patient, 62 years old, affected by renal cell carcinoma, G1, T3aN0M0.


title: CD8+ T Lymphocytes_TC RCC patient Time 35_replicate 2

description:
CD8+_TC_T35_2
Male patient, 62 years old, affected by renal cell carcinoma, G1, T3aN0M0.


title: Chronic lymphocytic leukemia 57 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC

value: partial remission


title: Chronic lymphocytic leukemia 53 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: no ATM disruption detected


title: Chronic lymphocytic leukemia 54 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(11q) and ATMmut


title: Chronic lymphocytic leukemia 52 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated

value: complete remission


title: Chronic lymphocytic leukemia 53 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: Chronic lymphocytic leukemia 53 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: Chronic lymphocytic leukemia 52 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected


title: Chronic lymphocytic leukemia 49 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 50 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 48 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 51 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 49 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 48 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 49 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR


title: Chronic lymphocytic leukemia 47 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 51 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 46 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 50 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 47 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 48 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB1 (6203221042_A_GFPNeg_B1)

first: Tim Xiaoming

last: HU

address: Le Gros Clark Building, South Parks Road

department: Department of Physiology, Anatomy and Genetics

description:
FACS sorted cells
6203221042_A_GFPNeg_B1

hyb_protocol: An Illumina MouseWG-6 Expression BeadChip was used for microarray gene expression profiling, performed according to the manufacturer’s protocol, except that hybridization was performed at 48˚C according to the recommendations by the NuGEN OvationTM RNA Amplification V2 kit.

scan_protocol: Illumina® BeadStudio software was used to extract the raw image data from the scanned beadchips.

data_processing: Genespring GX12.5; The raw intensity data was quantile normalized; all entities were filtered by flags using default criteria in GeneSpring GX 12.5: “present” – detection p- value > 0.8; “absent” – detection p< 0.6; and “marginal” – values in between “present” and “absent”. A gene-level analysis was performed and the entities were filtered by expression (including only those that were between 20-100th percentile in at least one out of the total number of samples).

source_name: Embryonic Intervertebral Disc

label_protocol: Purified RNA samples with a RNA integrity number (RIN) value of at least 7.0 were chosen for subsequent cDNA conversion and linear single-round amplification using the NuGEN OvationTM RNA Amplification V2 kit as per manufacturer’s protocol. Biotin labeling was performed with NuGEN EncoreTM BiotinIL Module kit.

growth_protocol: mouse embryos harvested at required developmental stage

extract_protocol: RNA from FACS sorted cells was extracted using Trizol followed by column purification with the QIAGEN RNeasy Micro kit, including on-column DNase treatment, RNA samples were quantified and checked for their integrity using Agilent RNA Pico 6000 Chip and Agilent 2100 Bioanalyzer software according to the manufacturer’s protocol.

treatment_protocol: GFP(+) cells from respective genotype were FACS sorted

value: Embryonic Intervertebral Disc

tag: developmental stage

tag: geneotype

value: GFP(-)


title: IntervertebralDisc_Embryonic_ReplicateB3 (6203212066_A_GFPNeg_B3)

description:
FACS sorted cells
6203212066_A_GFPNeg_B3


title: Chronic lymphocytic leukemia 45 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: not annotated


title: IntervertebralDisc_Embryonic_ReplicateB2 (6203212024_A_GFPNeg_B2)

description:
FACS sorted cells
6203212024_A_GFPNeg_B2


title: Chronic lymphocytic leukemia 47 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 46 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 50 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+


title: IntervertebralDisc_Embryonic_ReplicateB1 (6203221042_C_HET_B1)

description:
FACS sorted cells
6203221042_C_HET_B1


title: Chronic lymphocytic leukemia 44 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 45 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 46 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB5 (6203212066_F_KO_B5)

description:
FACS sorted cells
6203212066_F_KO_B5


title: IntervertebralDisc_Embryonic_ReplicateB1 (6203221042_D_KO_B1)

description:
FACS sorted cells
6203221042_D_KO_B1


title: IntervertebralDisc_Embryonic_ReplicateB2 (6203221042_E_WT_B2)

description:
FACS sorted cells
6203221042_E_WT_B2

value: WT


title: IntervertebralDisc_Embryonic_ReplicateB5 (6203212066_E_HET_B5)

description:
FACS sorted cells
6203212066_E_HET_B5


title: Chronic lymphocytic leukemia 43 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB4 (6203212066_C_KO_B4)

description:
FACS sorted cells
6203212066_C_KO_B4


title: Chronic lymphocytic leukemia 44 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB5 (6203212066_D_WT_B5)

description:
FACS sorted cells
6203212066_D_WT_B5


title: IntervertebralDisc_Embryonic_ReplicateB2 (6203221042_F_HET_B2)

description:
FACS sorted cells
6203221042_F_HET_B2


title: IntervertebralDisc_Embryonic_ReplicateB3 (6203212024_E_KO_B3)

description:
FACS sorted cells
6203212024_E_KO_B3


title: IntervertebralDisc_Embryonic_ReplicateB4 (6203212066_B_HET_B4)

description:
FACS sorted cells
6203212066_B_HET_B4


title: IntervertebralDisc_Embryonic_ReplicateB3 (6203212024_D_HET_B3)

description:
FACS sorted cells
6203212024_D_HET_B3


title: IntervertebralDisc_Embryonic_ReplicateB4 (6203212024_F_WT_B4)

description:
FACS sorted cells
6203212024_F_WT_B4


title: IntervertebralDisc_Embryonic_ReplicateB3 (6203212024_C_WT_B3)

description:
FACS sorted cells
6203212024_C_WT_B3


title: Chronic lymphocytic leukemia 43 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 44 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 42 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 41 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB2 (6203212024_B_KO_B2)

description:
FACS sorted cells
6203212024_B_KO_B2


title: IntervertebralDisc_Embryonic_ReplicateB7 (7810815013_F_WT_B7)

description:
FACS sorted cells
7810815013_F_WT_B7


title: Chronic lymphocytic leukemia 42 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB3 (7810815013_E_KO_B3)

description:
FACS sorted cells
7810815013_E_KO_B3


title: IntervertebralDisc_Embryonic_ReplicateB5 (7810815013_D_WT_B5)

description:
FACS sorted cells
7810815013_D_WT_B5


title: Chronic lymphocytic leukemia 43 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB4 (7810815013_A_KO_B4)

description:
FACS sorted cells
7810815013_A_KO_B4


title: Chronic lymphocytic leukemia 45 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 42 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB2 (7810815013_C_KO_B2)

description:
FACS sorted cells
7810815013_C_KO_B2


title: IntervertebralDisc_Embryonic_ReplicateB3 (7810815024_F_DN_B3)

description:
FACS sorted cells
7810815024_F_DN_B3


title: Chronic lymphocytic leukemia 39 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 41 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 39 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB2 (7810815024_E_DN_B2)

description:
FACS sorted cells
7810815024_E_DN_B2


title: IntervertebralDisc_Embryonic_ReplicateB1 (7810815024_D_DN_B1)

description:
FACS sorted cells
7810815024_D_DN_B1


title: Chronic lymphocytic leukemia 39 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 38 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: missing response


title: Chronic lymphocytic leukemia 38 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 38 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 37 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB3 (7810815024_C_TAS_B3)

description:
FACS sorted cells
7810815024_C_TAS_B3


title: IntervertebralDisc_Embryonic_ReplicateB2 (7810815024_B_TAS_B2)

description:
FACS sorted cells
7810815024_B_TAS_B2


title: Chronic lymphocytic leukemia 37 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 41 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 36 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 36 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 36 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC


title: Chronic lymphocytic leukemia 40 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: IntervertebralDisc_Embryonic_ReplicateB1 (7810815024_A_TAS_B1)

description:
FACS sorted cells
7810815024_A_TAS_B1


title: Chronic lymphocytic leukemia 40 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Cirrhosis of liver CR562477

city: Philadelphia

first: Moses

middle: Morakortoi

last: Darpolor

address: 423 Guardian Drive

department: Radiology

institute: University of Pennsylvania

description: Based on pathologist report of grouping stage IIIA.

hyb_protocol: Target hybridization was performed on Affymetrix Human GeneChip® Gene 1.0 ST Arrays (Affymetrix, Inc., Santa Clara, CA, USA) according to the manufacturer’s procedures in the GeneChip® Hybridization Oven 645, followed by washing and staining in the GeneChip® Fluidics Station 450.

scan_protocol: Data acquired with GeneChip®  Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA, USA)

data_processing:
The mean absolute deviation of residuals, mean absolute relative log expression, and the positive versus negative Receiver Operator Curve (ROC) Area under Curve (ROC) of the array data were metrics used to assess the overall data quality. The probe-level data (cel files) from all arrays were imported into Partek Genomics Suite software (Partek Incorporated, St. Louis, MO, USA) where RMA normalization was applied yielding log2-transformed expression intensities.
One-way ANOVA was performed on the genes across the 3 groups to provide p-values, and false positive rates were computed using the Benjamini-Hochberg step-up algorithm as implemented in Partek. Pairwise comparisons were made between tissues types providing p-values, log2 ratios, and fold-change values. Within-patient (i.e. tissues from the same human subject) log2 ratios and fold-changes were also calculated for the 3 patient sample pairs.

label: biotin allonamide triphosphate

source_name: Cirrhosis of Liver

label_protocol: Biotin Allonamide Triphosphate was used according to the standard Affymetrix protocol provided in 2012. The Ambion® WT Expression kit was used as suggested by the manufacturer to generate sense strand cDNA from 250 ng total RNA followed by fragmentation and labeling of 5.5 ug of sense strand cDNA with the GeneChip® Wt Terminal labeling kit.

extract_protocol: Homogenized lysate of human tissues (i.e. hepatocellular carcinoma, cirrhotic, and liver) were processed to obtain about 5 mg of high-quality total RNA using a RNeasy Midi Kit (QIAGEN, Valencia, CA, USA). The samples were obtained via tissue biorepository (OriGene Technologies, Inc., Rockville, MD, USA).  The RNA integrity and quality control of 2 mL sample was assessed with NanoDrop® ND-1000 UV spectrophotometer and Agilent® 2100 Bioanalyzer at the Molecular Profiling Facility at the University of Pennsylvania. Degraded samples were eliminated from the study based on the OD A260/A280 ratios, electrophoresis results, 28S/18S rRNA ratios, and RNA Integrity Number (RIN).

treatment_protocol: No treatment was involved with any of the patients.

tag: project id

tag: facility id

tag: sample id

value: liver

value: male

tag: paired

value: J

tag: rin

value: Cirrhosis of liver


title: hepatocellular carcinoma CR562996

source_name: hepatocellular carcinoma

tag: tissue

value: D

tag: disease state

value: hepatocellular carcinoma


title: Cirrhosis of liver CR562008

tag: gender

value: H


title: Cirrhosis of liver CR562293

tag: age

value: I


title: Chronic lymphocytic leukemia 35 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

tag: cell type

value: mononuclear cells CD19-

value: no TP53 disruption detected

value: no ATM disruption detected

tag: treatment


title: Chronic lymphocytic leukemia 40 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

tag: ighv mutational status

value: IgHV unmutated

tag: tp53 diruption

value: non-response


title: Chronic lymphocytic leukemia 34 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: not annotated

tag: atm disruption

tag: best clinical response


title: Fatty changes of liver CR563039

source_name: Fatty changes of Liver

value: F

value: Fatty changes of liver


title: Chronic lymphocytic leukemia 35 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: del(17p) and TP53mut

value: FCR

value: partial remission


title: Chronic lymphocytic leukemia 34 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 33 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 37 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC


title: hepatocellular carcinoma CR561021

value: liver

value: male

value: A


title: Fatty changes of liver CR561701

value: E


title: Cirrhosis of liver CR561042

source_name: Cirrhosis of liver

value: Cirrhosis of liver


title: hepatocellular carcinoma CR562998

value: hepatocellular carcinoma


title: Chronic lymphocytic leukemia 35 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells

value: no ATM disruption detected


title: [6] Photo-Ox IMX-101, 30.2, Rep 4

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for IMX-101 exposures were completely randomized (using a random number generator) with factorial treatment arrangements contrasting parent versus UV-treated chemicals across each concentration series.  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The IMX-101 experiment included UV-treated and parent IMX-101 at the measured exposure concentrations:  3.8, 30.2 and 58.2 mg/L (measured concentrations) each including 4 exposure replicates, in addition to 4 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct ANOVA-based differential transcript expression analyses.  Two-way ANOVA was utilized to test the interactive potential between the UV-treatment and IMX-101 exposures on transcript expression. In the two-way ANOVA tests a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts for the IMX-101 exposure, the UV treatment and the IMX-101 x UV treatment interaction.  In order to identify the specific differences in transcript expression between the parent IMX-101 and the UV-treated IMX-101, post hoc pairwise tests were conducted for all significant targets identified in the UV treatment and the IMX-101 x UV treatment interaction.  The post hoc analysis tested the effects of the UV-treated IMX-101 relative to the parent IMX-101 at each dose-level using a moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

source_name: whole animal

label_protocol: The Agilent Low-Input Quick Amp, One Color Microarray Hybridization protocol (Agilent Technologies) was utilized following manufacturer’s recommendations where 600 ng of total RNA served as the starting material for each biological replicate.

growth_protocol: Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed in the parent and UV-treated IMX-101 exposures where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.

extract_protocol: Total RNA was extracted from 4 whole fish/replicate for all transcript expression experiments.  All samples were flash frozen upon collection and stored at -80 °C until RNA extraction.  Samples were homogenized in lysis buffer with a FAST Prep-24 instrument (MP Biomedicals, Santa Ana, CA) before RNA isolation with RNeasy kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number >7.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading >2.0.

treatment_protocol: Zebrafish larvae were exposed to IMX-101 at  0, 3.8, 30.2 and 58.2 mg/L (measured concentrations) as the parent or UV-irradiated IMX-101.   Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed in the parent or UV-treated IMX-101 where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.

value: larvae

tag: concentration

value: Photo-Ox IMX-101


title: [6] Photo-Ox IMX-101, 58.2, Rep 3


title: Chronic lymphocytic leukemia 33 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated

value: no TP53 disruption detected

value: not annotated


title: Chronic lymphocytic leukemia 34 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: hepatocellular carcinoma CR562705

value: B


title: [6] Photo-Ox IMX-101, 58.2, Rep 1


title: [6] Photo-Ox IMX-101, 58.2, Rep 4


title: hepatocellular carcinoma CR559270


title: non-tumor liver CR561944

source_name: non-tumor liver

value: G

value: non-tumor liver


title: non-tumor liver CR562969

value: D


title: [6] Photo-Ox IMX-101, 30.2, Rep 1


title: Chronic lymphocytic leukemia 33 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

source_name: peripherel blood

value: mononuclear cells CD19+

value: FC

value: partial remission


title: [6] Photo-Ox IMX-101, 3.8, Rep 4