title: CIC_HUS_014_60662

source_name: DNA of sample 014 with an hematological malignancy


title: CIC_HUS_020_59447

status: Public on Nov 21 2016

type: genomic

city: Salamanca

first: María

last: Abáigar

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer

hyb_protocol: 20 µg of each labeled test and the corresponding sex-matched reference DNA were mixed and co-hybridized to the NimbleGen aCGH slide overnight at 42°C. After hybridization, slides were washed following the manufacturer's instructions (Roche NimbleGen) (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

scan_protocol: Slides were scanned with a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen), set at 532 nm and 635 nm, with a 2-µm resolution, to produce images in TIFF format according to the manufacturer's instructions (Roche NimbleGen) (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

data_processing: Raw data were extracted from the scanned images and analyzed using the segMNT algorithm from NimbleScan software (version2.6; Roche NimbleGen) (http://www.nimblegen.com/downloads/support/NimbleScan_v2p6_UsersGuide.pdf). SignalMap (version1.9; Roche NimbleGen) was used for visual examination of the resulting data (http://www.nimblegen.com/products/lit/05434564001_NG_SignalMap_UGuide_v1p9p1.pdf).

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA reference sample

label_protocol: Test sample and it's corresponding reference sample are labeled in parallel. 500 ng of each genomic DNA test sample was labeled with Cy3 using a Cy3-random nonamer, whereas 500 ng of each genomic DNA reference sample was labeled with Cy5 using a Cy5-random nonamer, according to the manufacturer's instructions (Roche NimbleGen) (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf <http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf>)

extract_protocol: Genomic DNA (gDNA) was isolated from methanol-acetic-acid stored bone marrow samples after cytogenetic analysis. The pellet cells from cytogenetics were washed twice with PBS 1x, and then isolated using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s standard protocol. gDNA concentration and quality were determined spectrophotometrically (ND-1000; NanoDrop Technologies) by calculating the 260/280 and A260/230 ratios. gDNA integrity was evaluated by electrophoresis on 1% agarose gels.

tag: reference source info

value: Human Genomic DNA (Promega; Madison, WI, USA)

source_name: DNA of sample 020 with an hematological malignancy

tag: tissue

value: bone marow

tag: gender

value: Male

tag: age

tag: who 2008 classification


title: CIC_HUS_019_59019

source_name: DNA of sample 019 with an hematological malignancy


title: CIC_HUS_016_62195

source_name: DNA of sample 016 with an hematological malignancy


title: OE24

type: RNA

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

country: USA

institute: University of Kentucky

description: mRNA abundance data

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

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console sofware using default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: P1 olfactory mucosa, Emx2(fl/fl)

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

growth_protocol: OmpCre:Emx2(fl/+) and Emx2(fl/fl) mice were bred in standard laboratory conditions

extract_protocol: Olfactory mucosa were dissected and total RNA isolated using TriReagent.

treatment_protocol: MIce of the desired genotypes were raised to 1 day postnatal.

value: olfactory mucosa

tag: background strain

value: mixed 129 x C57BL/6J

tag: genotype

tag: phenotype

value: control littermate


title: AraC + F1F2

type: protein

city: Taipei City

first: Pei-Yu

last: Wu

address: 128 Academia Road, Section 2, Nankang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

hyb_protocol: Human Cytokine Antibody Arrays C1 kit (Raybiotech, AAH-CYT-1) was used according to the manufacturer’s instructions. Briefly, the arrays were blocked, incubated with 100 μL of CM overnight, incubated with biotin-conjugated antibodies (1/250) for 2 hours and with HRP-linked secondary antibody (1/1000) overnight. The membranes were incubated with chemiluminescent substrate and exposed to x-ray film for 15 minutes before development.

scan_protocol: Intensity of images was determined by ImageQuant LAS 4000 (GE Healthcare Life Science) and analyzed using Image J software.

data_processing: To obtain relative expression, signal intensity was subtracted for negative controls and normalized to internal positive.

molecule: protein

source_name: conditioned media from U937 F1F2 cells treated with cytarabine.

label_protocol: Samples were labeled according to the manufacturer’s instructions.

growth_protocol: AML line U937 cells were retrovirally transduced with vector (Vec) or TIFA DN fragments (F1F2 and F2F3), selected for stable expression, and grown according to standard protocols.

extract_protocol: The conditioned media were centrifuged at 4 degree Celsius for 20 min and the cell-free supernatant was collected.

treatment_protocol: Equal numbers of cultured U937 cells were treated with 10 μM cytarabine for 72 h.

tag: cell line

tag: cell type

value: AML


title: AraC

source_name: conditioned media from U937 vector cells treated with cytarabine.


title: PBS

source_name: conditioned media from U937 vector cells


title: B9_020212

description: mRNA abundance data

source_name: P3 olfactory mucosa, 123Cre:Lhx2(fl/fl)

growth_protocol: 123Cre:Lhx2(fl/+) and Lhx2(fl/fl) mice were bred in standard laboratory conditions

treatment_protocol: MIce of the desired genotypes were raised to 3 days postnatal.

value: Knockout

tag: developmental stage


title: OL751

description: mRNA abundance data

source_name: P26 olfactory mucosa, OmpCre:Lhx2(fl/+)

growth_protocol: OmpCre:Lhx2(fl/+) and Lhx2(fl/fl) mice were bred in standard laboratory conditions

treatment_protocol: Mice of the desired genotypes were raised to 26 days postnatal.


title: OL909

description: mRNA abundance data


title: CIC_HUS_008_59739

source_name: DNA of sample 008 with an hematological malignancy

value: Female

value: RCUD


title: OL582

description: mRNA abundance data

source_name: P26 olfactory mucosa, Lhx2(fl/+)


title: OE13

description: mRNA abundance data

source_name: P1 olfactory mucosa, OmpCre:Emx2(fl/+)


title: CIC_HUS_005_59443

source_name: DNA of sample 005 with an hematological malignancy

value: RARS


title: OL908

description: mRNA abundance data

source_name: P26 olfactory mucosa, OmpCre:Lhx2(fl/fl)


title: OL589

description: mRNA abundance data


title: OL584

description: mRNA abundance data


title: OL749

description: mRNA abundance data


title: CIC_HUS_004_59764

source_name: DNA of sample 004 with an hematological malignancy

value: RCMD


title: DK2-07, biological replicate 3

status: Public on Nov 20 2016

city: Kgs. Lynbgy

first: Juliane

middle: Charlotte

last: Thøgersen

address: Matematiktorvet build. 301

department: Systems Biology

country: Denmark

institute: Technical University of Denmark

description: late-stage isolate (2007)

hyb_protocol: The labeled cDNA was hybridized on an Affymetrix P. aeruginosa PAO1 gene chip and stained on a GeneChip Fluidics Station 450

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to manufacturer's instruction.

data_processing: The raw data (.cel files) were obtained using the Affymetrix GeneChip Operating System 1.4. The raw cel-files were extracted in R by use of the package affy followed by qspline normalization and calculation of gene expression index values using robust multiarray average expression measure.

label: biotin-ddUTP

organism: Pseudomonas aeruginosa

label_protocol: The cDNA was purified with a Qiagen PCR Purification Kit (Qiagen) and fragmented using DNase I (Promega). Fragmented cDNA was labeled using labeling reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega).

growth_protocol: Cells were grown in morpholinepropanesulfonic acid (MOPS)-buffered minimal medium supplemented with 10 mM glucose to an optical density (600 nm) of 0.4 prior to Affymetrix P. aeruginosa GeneChip microarray analysis

extract_protocol: RNA was extracted with an RNeasy Mini Kit (Qiagen) and transcribed to cDNA using a SuperScript III Reverse Transcriptase (Invitrogen).

treatment_protocol: Cells were treated according to Yang et al, Evolutionary dynamics of bacteria in a human host environment, PNAS 2011: Harvested cells were mixed immediately with RNAprotect Bacteria Reagent (Qiagen) and stored at −80 °C.

tag: isolate

tag: clone

value: DK2 clone


title: CIC_HUS_003_59335

source_name: DNA of sample 003 with an hematological malignancy


title: CIC_HUS_007_61845

source_name: Genomic DNA reference sample

source_name: DNA of sample 007 with an hematological malignancy


title: CIC_HUS_001_59742

source_name: DNA of sample 001 with an hematological malignancy


title: DK2-07, biological replicate 1

description: late-stage isolate (2007)


title: DK2-07, biological replicate 2

description: late-stage isolate (2007)


title: DK2-91, biological replicate 3

description: late-stage isolate (1991)


title: DK2-91, biological replicate 2

description: late-stage isolate (1991)


title: AraC + F2F3

source_name: conditioned media from U937 F2F3 cells treated with cytarabine.


title: CIC_HUS_002_59861

source_name: DNA of sample 002 with an hematological malignancy


title: DK2-91, biological replicate 1

description: late-stage isolate (1991)


title: DK2-WT, biological replicate 3

description: non-adapted


title: OL583

description: mRNA abundance data


title: CIC_HUS_009_59933

source_name: DNA of sample 009 with an hematological malignancy


title: DK2-WT, biological replicate 2

description: non-adapted


title: Wild_type _ZM4_with_ethanol_vs_no_ethanol (Replicate B)

status: Public on Nov 19 2016

city: MEXICO DISTRITO FEDERAL

first: Rosa Maria

middle: Gutierrez

last: Rios

state: DISTRITO FEDERAL

address: AV. UNIVERSIDAD 3000, UNAM, CU

department: Molecular Microbiology

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

description:
Biological replicate 2 of 3.(ZM4 ethanol vs ZM4 no ethanol stress)
http://berry.engin.umich.edu/oligoarraydb/organismPage.php?ORG=Zymomonas%20mobilis%20subsp.%20mobilis%20ZM5

hyb_protocol: Zymomonas mobilis subsp. mobilis ZM4 has 1998 genes. MYcoarray have designed 5102 probes surveying 1894 genes (or 94.8% of all genes) for this organism. The array format was 3x15K, this slide contains 3 arrays of 15000 spots per array. One array consists of a grid of 160 columns by 94 rows. The siza of probe was 45mer. The Zymomonas mobilis chips from Mycroarray were re-hydrated with water vapor at 60° C, and fixed with two cycles of UV light (1200J). Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42° c, and then washed tree times with 1X SCC, 0.05% SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix form Molecular Devices. All images were captured using 10 µ resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing:
Microarray data analysis was performed with free sofware genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates anlaysis and selecting differentially expressed genes. The goal of genArise is to identify wich of the gene show good evidence of being differentially expressed. The sofware identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of strandard deviation a data point is form the mean. zi= (Ri - mean(R)) / sd (R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standar deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviation would be the significantly differntially expressed genes.
With the software genArise, is to identify wich of the gene show good evidence of being differentially expressed. The sofware identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of strandard deviation a data point is form the mean. zi= (Ri - mean(R)) / sd (R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standar deviation of the log-ratio. With this criterion, the elements with a z-score > 1.5 standard deviation would be the significantly differntially expressed genes.

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: ethanol stress

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporanting dUTP-Alexa555 or DUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the aobsorbance at 555 nm for Alexa555 and 650 nm for Alexa647. The sample ZM4_without Ethanol was labeled with Alexa555 and the sample ZM4_with Ethanol was labeled with Alexa647. The sample ER79ap_without Ethanol was labeled with Alexa555 and the sample ER79ap_with Ethanol was labeled with Alexa647

growth_protocol: Zymomonas mobilis ZM4 and derivative ER79ap were grown in the medium reported by Bringer et al. (1985) but in wich the potassium phosphates were substituted by MES (100 mM, pH6). This modified medium was designated as MR-MES. Liquid cultures were performed in 350-ml minifermenters, containing 200 ml of MR-MES, without aeration, at 30° C, 100 rpm, and an initial pH of 6. The inoculum was prepared from a fresh colony obtained from solid MR-MES medium (agar 15 g/L). A single colony was seed in a test tube containing 10 ml of culture medium and incubated overnight (30° C and 250 rpm). Enough culture volume was used to start mini-fermenter cultures at 0.025 DO. Ethanol was added at 70 g/L.

extract_protocol: Total RNA was extracted from mid-log phase cells (with and without 70 g/L of ethanol) with a Quick-RNATM miniPrep (ZymoResearch, CA, USA) as described by the manufacturer

tag: strain

value: wild type

source_name: none ethanol stress


title: Mutant_type _ER79ap_with_ethanol_vs_no_ethanol (Replicate A)

description:
Biological replicate 1 of 3. (Mutant ER79ap ethanol vs ER79ap no ethanol stress)
http://berry.engin.umich.edu/oligoarraydb/organismPage.php?ORG=Zymomonas%20mobilis%20subsp.%20mobilis%20ZM7

value: mutant ER79ap


title: Mutant_type _ER79ap_with_ethanol_vs_no_ethanol (Replicate C)

description:
Biological replicate 3 of 3. (Mutant ER79ap ethanol vs ER79ap no ethanol stress)
http://berry.engin.umich.edu/oligoarraydb/organismPage.php?ORG=Zymomonas%20mobilis%20subsp.%20mobilis%20ZM9


title: Wild_type _ZM4_with_ethanol_vs_no_ethanol (Replicate C)

description:
Biological replicate 3 of 3.(ZM4 ethanol vs ZM4 no ethanol stress)
http://berry.engin.umich.edu/oligoarraydb/organismPage.php?ORG=Zymomonas%20mobilis%20subsp.%20mobilis%20ZM6


title: Mutant_type _ER79ap_with_ethanol_vs_no_ethanol (Replicate B)

description:
Biological replicate 2 of 3. (Mutant ER79ap ethanol vs ER79ap no ethanol stress)
http://berry.engin.umich.edu/oligoarraydb/organismPage.php?ORG=Zymomonas%20mobilis%20subsp.%20mobilis%20ZM8


title: Wild_type _ZM4_with_ethanol_vs_no_ethanol (Replicate A)

description:
Biological replicate 1 of 3. (ZM4 ethanol vs ZM4 no ethanol stress)
http://berry.engin.umich.edu/oligoarraydb/organismPage.php?ORG=Zymomonas%20mobilis%20subsp.%20mobilis%20ZM4


title: glucose replicate 2

city: Xiamen

first: Kai

last: Tang

address: Zhourong quan BLV 3-313, Xiamen University, Xianan, Xiamen

country: China

institute: Xiamen University

description: Treat glucose replicate 2

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Christiangramia flava

source_name: Cells treated gulcose  replicate 2

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: G. flava JLT2011 were cultured on minimal media (2.3% (w/v) sea salts, 0.05% (w/v) yeast extract, 0.05% NH4Cl (w/v) and 50 mM L-1 Tris-HCl, pH 7.8

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: G. flava JLT2011 and G. forsetii KT0803 were cultured on minimal media (2.3% (w/v) sea salts, 0.05% (w/v) yeast extract, 0.05% NH4Cl (w/v) and 50 mM L-1 Tris-HCl, pH 7.8), with a final concentration of 0.2% of one of the following carbon sources: D-glucose， xylan (oat spelts), pectin (apple)

tag: growth phase

value: expotential phase


title: BW25113 wild-type rifampicin pre-treatment 3 h ampicillin persisters

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from persister cells of E. coli BW25113 wild-type (pre-treated with 25 ug/mL rifampicin 30 mins) after 3 hours growth in LB ampicillin 100 ug/mL

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: Channel 1

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: One-day old single colony was inoculated in 2 mL of LB for 16 h at 37C at 250 rpm. Overnight culture was diluted to be OD 0.05 at 600nm in 25 mL in LB and incubated at 37C at 250 rpm until OD 0.8 at 600nm (harvested at this OD). To 22 mL of cells, 25 mg/mL of rifampicin was added, and incubated at 37C at 250 rpm for 30 min. After rifampicin treatment, cells were centrifuged at 13000 rpm for 1 min and resuspended in LB broth and incubated for an additional 30 mins. 22 uL of 100 mg/mL ampicillin (final conc. 100 ug/mL) was then added directly to the 22 mL of culture and incubated for 3 hours. After 3 h, cell pellet was collected by centrifuging at 8500 rpm at 4C for 2 min. Supernatant was discarded and the cell pellet was resuspended with 1 mL RNAlater. Then the sample was centrifuged and the supernatant was discarded, the final cell pellet was immediately frozen in dry ice and stored at -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: E. coli BW25113 wild-type

tag: time

tag: treatment

value: ampicillin 100 ug/mL

tag: medium

value: LB

value: Planktonic cells inoculated at OD 0.05 at 600nm, grown to OD 0.8 at 600nm, exposed to 25 ug/mL rifampicin for 30 mins, then exposed to 100 ug/mL ampicillin for 3 h.

tag: temp


title: CIC_HUS_006_59812

tag: reference source info

value: Human Genomic DNA (Promega; Madison, WI, USA)

source_name: DNA of sample 006 with an hematological malignancy

tag: tissue

value: bone marow

tag: gender


title: d2_cont1

city: SYDNEY

first: Irina

last: VOINEAGU

address: High ST

country: Australia

institute: UNSW

description:
Control, 48h
9878593032_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression data was log2 transformed and quantile normalized using the Lumi Bioconductor package.

label: Biotin

source_name: Human Primary Astrocytes

label_protocol: Standard Illumina labeling protocol

growth_protocol: Human primary astrocytes were isolated from a 16 to 19 week old post mortem fetal brain obtained following informed written consent. All experiments were approved and performed in accordance with guidelines provided by the Human Ethics Committee from the University of New South Wales (UNSW Ethic approval HREC 03187). Cells were cultured in RPMI 1640 medium (Life Technologies) supplemented with 10% fetal bovine serum, 1% streptomycin (10,000 μg/ml), 1% penicillin (10,000 units/ml) and 1% Fungizone (2.5 μg/ml) (v/v %). Cells were seeded in 6-well cell culture plates at a density of 50,000 cells per well and incubated overnight at 37°C, 5 % CO2 before Topotecan treatment.

extract_protocol: Total RNA was extracted using the Qiagen miRNEasy kit according to manufacturer’s protocol. The extraction included an on-column DNase treatment. Total RNA was eluted in 30 μl RNase-free water and stored at -80°C.

treatment_protocol: Human primary astrocytes were treated with 300 nM Topotecan (Sigma Aldrich) or 0.1% dimethylsulphoxide (DMSO) as a vehicle control. Treatment was carried out in technical triplicate wells for 24h or 48h.

value: Control (0.1% DMSO)

tag: culture time

tag: replicate


title: DK2-WT, biological replicate 1

description: non-adapted


title: d2_topo1

description:
Topotecan, 48h
9878593032_H

value: Topotecan 300nM


title: d1_topo3

description:
Topotecan, 24h
9878593032_F


title: d2_topo2

description:
Topotecan, 48h
9878593032_J


title: d1_cont2

description:
Control, 24h
9878593032_C


title: d1_cont3

description:
Control, 24h
9878593032_E


title: HUC1 10M As

city: Baltimore

first: Akira

last: Oki

state: MD

address: 1550 Orleans street

institute: Johns hopkins university

description: SAMPLE 2

data_processing: The non-normalized data were generated by GenomeStudio, and the data were normalized using quantile normalisation using lumi packages in R.

source_name: normal urothelial cell

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit

growth_protocol: HUC1 cells were culture in F-12K medium supplemented with 10% fetal bovine serum (FBS), and BFTC 905 and 909 cells were cultured in DMEM with 10% FBS

extract_protocol: RNA was extracted with the QIAzol Lysis Reagent followed by phnol extraction and ethanol precipitation.

treatment_protocol: Normal urothelial HUC1 cells were chronically exposed to 1μM arsenic trioxide in F-12K medium for 10 months, which induced malignant transformation (10M As cells). To determine the arsenic withdrawal effect, 10M As cells were cultured without arsenic for 2.5 months (10M As/2M UT).

value: normal urothelial cell line

tag: phenotype

value: arsenic exposure for 10 months


title: d1_cont1

description:
Control, 24h
9878593032_A


title: d1_topo2

description:
Topotecan, 24h
9878593032_D


title: d2_cont3

description:
Control, 48h
9878593032_K


title: BFTC 909

description: SAMPLE 5

source_name: bladder cancer cell

tag: cell line

value: BFTC 909

value: bladder cancer cell line

value: cell line that was established from arsenic exposed urothelial carcinma patient


title: d2_cont2

description:
Control, 48h
9878593032_I


title: d1_topo1

description:
Topotecan, 24h
9878593032_B


title: HUC1 10M UT

description: SAMPLE 1

tag: cell type

value: arsenic naïve


title: BFTC 905

description: SAMPLE 4

value: BFTC 905


title: glucose replicate 1

description: Treat glucose replicate 1

source_name: Cells treated glucose replicate 1


title: xylan replicate3

description: Treat xylan replicate3

source_name: Cells treated xylan replicate3


title: d2_topo3

description:
Topotecan, 48h
9878593032_L


title: HUC1 10M As/2M UT

description: SAMPLE 3

value: arsenic exposure for 10 months and withdrawal for 2.5 months


title: pectin replicate2

description: Treat pectin replicate2

source_name: Cells treated with pectin replicate2

value: expotential phase


title: pectin replicate3

description: Treat pectin replicate3

source_name: Cells treated with pectin replicate3


title: pectin replicate1

description: Treat pectin replicate1

source_name: Cells treated with pectin replicate1


title: xylan replicate1

description: Treat xylan replicate1

source_name: Cells treated xylan replicate1


title: xylan replicate2

description: Treat xylan replicate2

source_name: Cells treated xylan replicate2


title: H1975NSCLC_48h_EGF_2

status: Public on Nov 18 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 48h

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The method Single Channel Array Normalization (SCAN) was used for the preprocessing. The mapping of probes to genes were made with the Netaffix.v.34 annotation file which is made available by the array manufacturer.

source_name: H1975 NSCLC

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

growth_protocol: H1975 NSCLC cells were seeded in 6-well-plates with 1,33x10(-5) cells per well. After incubation for 3 days, cells were washed 3 times and supplemented with medium without FCS for overnight starvation

extract_protocol: Total cellular RNA was isolated with the NucleoSpin RNA II kit according to the manufacturers' instructions.

treatment_protocol: Cells were stimulated with 50 ng/ml of EGF diluted in starvation medium. Samples were harvested after 0, 0.5, 1, 2, 4, 6, 8, 12, 24 and 48 hours.

tag: time(h)

value: EGF


title: H1975NSCLC_18h_EGF_2

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 18h


title: H1975NSCLC_48h_EGF_3


title: H1975NSCLC_4h_EGF_1

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 4h


title: H1975NSCLC_12h_EGF_2

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 12h


title: H1975NSCLC_24h_control_3

description: H1975 NSCLC cells for 24h in starvation medium

treatment_protocol: Cells were treated with starvation medium. Samples were harvested after 0, 0.5, 1, 2, 4, 6, 8, 12, 24 and 48 hours.

tag: time [h]

value: starvation medium


title: H1975NSCLC_48h_control_1

description: H1975 NSCLC cells for 48h in starvation medium


title: H1975NSCLC_48h_control_2


title: H1975NSCLC_0.5h_EGF_3

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 0.5h


title: H1975NSCLC_24h_EGF_2

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 24h


title: H1975NSCLC_48h_EGF_1


title: H1975NSCLC_1h_EGF_1

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 1h


title: H1975NSCLC_24h_EGF_1


title: H1975NSCLC_2h_EGF_3

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 2h


title: H1975NSCLC_24h_control_1


title: H1975NSCLC_6h_EGF_1

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 6h


title: H1975NSCLC_0.5h_EGF_1


title: H1975NSCLC_1h_control_1

description: H1975 NSCLC cells for 1h in starvation medium


title: H1975NSCLC_0.5h_control_2

description: H1975 NSCLC cells for 0.5h in starvation medium


title: H1975NSCLC_2h_control_1

description: H1975 NSCLC cells for 2h in starvation medium


title: H1975NSCLC_4h_control_3

description: H1975 NSCLC cells for 4h in starvation medium


title: Primary mammary tumor [Wnt_4679_251502810454_S01_CGH-v4_4]

city: Bethesda

first: Jeffrey

middle: E

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

description: See Zhu M et al. Genome Biol 2011, 12:R77.

hyb_protocol: Labeled DNAs were purified with Amicon Ultra-0.5Kd filters and hybridized to Agilent 44K CGH arrays for 44 hours at 65oC

scan_protocol: The arrays were scanned using Agilent DNA microarray scanner G2539A

data_processing:
The array features were extracted using the Agilent Feature Extraction v10.7. The copy numbers were analyzed using Agilent Genomic Workbench 5.0 program
The ADM-2 algorithm identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score.

source_name: Primary mammary tumor dissected from female mice

label_protocol: 500ng of genomic DNA were lebeled with Cy3 or Cy5 using Enzo CGH labeling kit (Enzo Life Scineces)

extract_protocol: Genomic DNA was purified from tumors or spleen (as reference) using Dneasy Blood and Tissue kit (Qiagen)

tag: primary tumor

value: invasive mammary tumor

tag: gem model

tag: malignancy

value: mammary gland tumor

source_name: pooled mice spleen

value: normal mammary

value: pooled normal

value: normal mammary gland


title: Primary mammary tumor [Wnt_4677_251502810338_S01_susieCGH_4]


title: H1975NSCLC_24h_EGF_3


title: H1975NSCLC_48h_control_3


title: H1975NSCLC_0h_control_3

description: H1975 NSCLC cells for 0h in starvation medium


title: Primary mammary tumor [Wnt_4675_251502810338_S01_susieCGH_2]


title: H1975NSCLC_0h_control_1


title: Primary mammary tumor [Wnt_4676_251502810338_S01_susieCGH_3]


title: H1975NSCLC_6h_control_2

description: H1975 NSCLC cells for 6h in starvation medium


title: Primary mammary tumor [Wnt_4635_251502810340_S01_CGH-v4_10_Apr08_1]


title: Primary mammary tumor [PyMt342_251502810096_S01_CGH-v4_91_1_1]

value: MMTV-PyMT


title: Primary mammary tumor [PyMt317_251502810094_S01_CGH-v4_91_1_1]


title: Primary mammary tumor [PyMt341_251502810095_S01_CGH-v4_91_1_1]


title: Primary mammary tumor [PyMt 4 1_251502810337_S01_CGH-v4_10_Apr08_1]


title: Primary mammary tumor [PyMt 3_251502810337_S01_CGH-v4_10_Apr08_1_2]


title: Primary mammary tumor [PyMT_11570_251502810454_S01_CGH_3]


title: Primary mammary tumor [PyMt435_251502810098_S01_CGH-v4_91_1_1]


title: Primary mammary tumor [P53_5809_251502810099_S01_CGH-v4_91_1_1]

value: p53fl/fl ;MMTV-cre transplant


title: Primary mammary tumor [P53_1573_251502810100_S01_CGH-v4_91_1_2]


title: Primary mammary tumor [P53_5851_251502810099_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [P53_8546_251502810100_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [P53_2979_251502810100_S01_CGH-v4_91_1_1]


title: Primary mammary tumor [Hras_An1_3_251502810115_S01_CGH-v4_91_1_1.t]

value: MMTV-H-Ras


title: Primary mammary tumor [Hras_An3_3_251502810115_S01_CGH-v4_91_1_3.t]


title: Primary mammary tumor [H2NA_251502810094_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [Hras_An2_3_251502810115_S01_CGH-v4_91_1_2.t]


title: Primary mammary tumor [H2N64_251502810193_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [Haras_An5_3RPT_251502810194_S01_CGH-v4_91_1]


title: Primary mammary tumor [H2N61_251502810097_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [H2N53_251502810096_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [C3TAg_8_RPT_251502810195_S01_CGH-v4_91_1_3.]

value: C3(1)/SV40 T/t-antigens


title: Primary mammary tumor [H2N1_251502810095_S01_CGH-v4_91_1_3]


title: Primary mammary tumor [C3TAg_7RPT_251502810195_S01_CGH-v4_91_1_2.t]


title: Primary mammary tumor [PyMT_11567_251502810454_S01_CGH_2]


title: Primary mammary tumor [C3TAg2_251502810094_S01_CGH-v4_91_1_2]


title: Primary mammary tumor [C Myc_4An7_251502810094_S01_CGH-v4_91_1_4.t]

value: MMTV-c-Myc


title: Primary mammary tumor [Hras_An4_3_251502810115_S01_CGH-v4_91_1_4.t]


title: H1975NSCLC_8h_EGF_1

description: H1975 NSCLC cells treated with 50 ng/ml of EGF for 8h


title: Primary mammary tumor [C Myc_04004021_251502810096_S01_CGH-v4_91_1]


title: Primary mammary tumor [C Myc_04005648_251502810098_S01_CGH-v4_91_1]


title: Primary mammary tumor [C3TAg_5RPT_251502810195_S01_CGH-v4_91_1_1.t]


title: Primary mammary tumor [Brca_54_251502810116_S01_CGH-v4_91_1_4]


title: Primary mammary tumor [Brcap53_682__251502810114_S01_CGH-v4_91_1_1]


title: Primary mammary tumor [Brca_14_251502810116_S01_CGH-v4_91_1_2]


title: Primary mammary tumor [C Myc_043508_251502810095_S01_CGH-v4_91_1_4]


title: Primary mammary tumor [PyMt427_251502810097_S01_CGH-v4_91_1_1]


title: Primary mammary tumor [Brcap53_503__251502810113_S01_CGH-v4_91_1_2]


title: Primary mammary tumor [Brca_42_251502810116_S01_CGH-v4_91_1_3]


title: Normal gallbladder NO3

city: Shanghai

first: Huaifeng

last: Li

address: NO.1665, kongjiang road, Shanghai, China

department: general surgery

institute: Xinhua hospital affiliated to Shanghai jiaotong university, school of medicine

description: gene expression of GBC

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: gallbladder cancer,NO3

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: tissues were cut off immediately after cholecystectomy, put into and stored in liquid nitrogen before total RNA extration

tag: disease state

value: normal

value: frozen tissue

value: female

tag: age


title: Cancer gallbladder NO3

description: gene expression of GBC

source_name: paired adjacent normal gallbladder tissue, NO3

value: cancer


title: Cancer gallbladder NO2

description: gene expression of GBC

source_name: paired adjacent normal gallbladder tissue, NO2

value: male


title: Cancer gallbladder NO1

description: gene expression of GBC

source_name: gallbladder cancer,NO1


title: Normal gallbladder NO2

description: gene expression of GBC

source_name: gallbladder cancer,NO2


title: H1975NSCLC_0h_control_2

tag: treatment


title: Cancer gallbladder NO4

description: gene expression of GBC

source_name: paired adjacent normal gallbladder tissue, NO4


title: P 6h3

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: The Affymetrix GeneTitan automatic work flow was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

source_name: Seed_P 6h

label_protocol: The Ambion WT Expression Kit (cat. #4411974) and Affymetrix WT Terminal Labeling and controls kit (cat. #901524) are used for Affymetrix whole transcript expression profiling experiments

growth_protocol: For the transcriptome analyses Col-0 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of 100 plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006). After harvet, the seeds are stored in room termperature until they relase dormancy and reach 100% germination. two layers of Blue blotter paper (Anchorpaper company, www.seedpaper.com) were equilibrated with 48 ml demineralized water in plastic trays (15 x 21 cm). seeds were spread on wetted papers. Piled up trays were wrapped in a closed transparent plastic bag. The experiment was carried out in a 22°C incubator under continuous light (143 μmol m-2s-1)

extract_protocol: The polysome associated RNA is isolated from the polysome region of a linear sucrose gradient and total RNA is isolated from the raw extraction buffer  purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from after-ripened seeds during seed germination with three biological replicates at each germinantion stage.

tag: genetic ecotype

value: Columbia (Col-0)

value: after-ripened dry and imbibed seeds

tag: time point


title: Normal gallbladder NO4

description: gene expression of GBC

source_name: gallbladder cancer,NO4

tag: tissue


title: Primary mammary tumor [C Myc_04004022_251502810097_S01_CGH-v4_91_1]

value: invasive mammary tumor


title: P 26h3

source_name: Seed_P 26h


title: Normal gallbladder NO1

description: gene expression of GBC

source_name: paired adjacent normal gallbladder tissue, NO1

tag: gender


title: P 48h2

source_name: Seed_P 48h


title: P 72h2

source_name: Seed_P 72h


title: P 72h3


title: P 6h2


title: Primary mammary tumor [C3TAg4_251502810095_S01_CGH-v4_91_1_2]

value: mammary gland tumor


title: P dry3

source_name: Seed_P dry


title: P 26h1


title: Primary mammary tumor [P53_5817_251502810099_S01_CGH-v4_91_1_2]

value: normal mammary


title: EpiLCs d2 shTet1/2

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

description: Gene expression of  EpiLCs in Tet1/Tet2 KD

hyb_protocol: Labelled RNA were hybridised to an Affymetrix MG-430 PM array strip (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: Slide scan was performed by GeneAtlas (Affymetrix)

data_processing: The scan images were processed by expression console (Affymetrix)

source_name: mouse ESCs

label_protocol: Total RNA (150 ng) was labelled using a GeneChip 3′ IVT Express Kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: ES cells were cultured in feeder-free conditions in Glasgow Minimum Essential Medium (GMEM) (WAKO) containing 10% FCS (Invitrogen), 1 mM glutamine (WAKO), nonessential amino acid (WAKO) and 0.1 mM mercaptoethanol (WAKO) and supplemented with LIF (WAKO). Induction of EpiLCs was performed as described previously (Hayashi et al., 2011). EpiLCs were induced from ESCs in N2B27 basal medium containing 20 ng/mL activin A (Peprotech), 12 ng/mL bFGF (Invitrogen), and 0.1-1% KSR for 2 days on a dish coated with 16.7 µg/mL human plasma fibronectin (Millipore). Two days after EpiLC induction, cells were collected and replated (0.5-1.0 × 105) with or without doxycycline in GK15 medium on a dish coated with 16.7 µg/mL human plasma fibronectin.

extract_protocol: Total RNA was purified using the PureLinkTM RNA Mini Kit (Ambion).

tag: genotype/variation

value: Tet1/Tet2 KD


title: P 6h1


title: EpiLCs  shTet1/2 +P14

description: Gene expression of  EpiLCs + P14 in Tet1/Tet2 KD

value: Tet1/Tet2 KD + PRDM14


title: P dry2


title: P 26h2


title: P 72h1


title: EpiLCs d2

description: Gene expression of  EpiLCs

value: Scramble


title: T 72h3

source_name: Seed_T 72h


title: EpiLCs+P14

description: Gene expression of  EpiLCs + P14

value: Scramble + PRDM14


title: Control_4

city: Ottawa

first: Nikolai

middle: L

last: Chepelev

state: Ontario

address: 50 Colombine Driveway

department: Environmental Health Science and Research Bureau

country: Canada

institute: Health Canada

hyb_protocol: Samples were hybridised to Agilent G3 Mouse GE 8x60K microarrays.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

label_protocol: 200 ng of each sample was labelled with Cyanine 5-CTP (Cy5); universal reference total mouse RNA (Agilent Technologies) was labelled with Cyanine 3-CTP (Cy3).

extract_protocol: There were 5 animals in both treated and in the vehicle control group and they were harvested 24 h after the last exposure. Mice were anesthetized using isoflurane gas and then euthanized via cervical dislocation followed by chest cavity opening.

treatment_protocol: Adult male Muta™Mouse were administered benzo[a]pyrene (BaP, CAS no. 50-32-8, now also known as benzo[pqr]tetraphene; purity ≥ 98%, Cambridge Isotopes, Tewksbury, MA) dissolved in highly refined olive oil (Sigma-Aldrich, Oakville, ON, Canada) delivered at 0.005 ml/g body weight and 70 mg/kg bw per day by oral gavage for three consecutive days.

tag: sample id

tag: strain

value: Muta Mouse

value: hippocampus

source_name: universal reference total mouse RNA

tag: manufacturer

value: Agilent Technologies


title: P dry1


title: EpiLCs d4

description: Gene expression of  EpiLCs

tag: cell line


title: BaP_4

source_name: hippocampus,vehicle control


title: T 26h3

source_name: Seed_T 26h


title: P 48h1


title: Control_3


title: ESCs

description: Gene expression of  ESCs


title: BaP_3


title: T 48h3

source_name: Seed_T 48h


title: P 48h3


title: liver-PBS-24h-rep3

city: Jena

first: Ilse

middle: Denise

last: Jacobsen

address: Beutenbergstr. 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
donor_18
Sample name: 9993942084_F

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization (DirHyb) Assay, Illumina

scan_protocol: iScan Control Software

data_processing: Raw data was pre-processed using the lumi package for R, including background correction (bgAdjust) and subsequent data normalization using variance stabilization transformation and quantile normalization.

label: Alexa 555 streptavidin (Invitrogen / Life technologies)

source_name: mouse,mock-infection,24h, liver

growth_protocol: Candida albicans stationary phase growth in YPD

extract_protocol: RNA isolation kit, Qiagen GmbH, Hilden, Germany

treatment_protocol: tain vein fungal infection

value: liver

tag: infectious agent

value: mock (PBS)

tag: hours post infection

value: BALB/c


title: BaP_2


title: liver-PBS-24h-rep1

description:
donor_16
Sample name: 9993942080_F

label_protocol: Whole-Genome Gene Expression Direct Hybridization (DirHyb) Assay, Illumina

value: female


title: T 48h2


title: T 6h3

source_name: Seed_T 6h


title: spleen-PBS-24h-rep3

description:
donor_18
Sample name: 9993942008_H

source_name: mouse,mock-infection,24h, spleen

value: spleen


title: T 26h2

value: Columbia (Col-0)


title: Control_2

value: male


title: spleen-PBS-24h-rep1

description:
donor_16
Sample name: 9993942080_B


title: 8b_Xylose_log_T60_F9

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

description:
_42_HT08_Cy3
HT08_F9_T60min_F

hyb_protocol: Hybridizations were conducted using an 12-bay hybridization station (BioMicro Systems, Inc., UT), arrays dried using a Maui wash system (BioMicro Systems, Inc.).

scan_protocol: Arrays were scanned with a Surescan high-resolution DNA microarray scanner (Agilent Technologies, CA)

data_processing: The images were quantified using NimbleScan software (Roche NimbleGen, IN). Statistical analyses were done with JMP Genomics 4.1 software (SAS Institute, NC), essentially as described previously [PMID 20484677]. The data were normalized using the LOWESS normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the False Discovery Rate (FDR) testing method (p < 0.05).

organism: Zymomonas mobilis

label_protocol: ds-cDNA was labeled, hybridized, arrays washed, and scanned following the NimbleGen protocols.

growth_protocol: Z. mobilis 8b was revived from frozen glycerol stocks for ~6-8 hrs in 10 mL RM (10 g/L yeast extract, 2 g/L KH2PO4) + 2% glucose at 33oC prior to inoculating overnight seed cultures in RM + 5% glucose (5% glucose) using shake flasks filled to 80% capacity at 33C at 120 rpm.  When the glucose concentration reached approximately 20-40 g/L, cells were spun down at 3,840 x g for 10 min at room temperature (RT) and resuspended in either RMG (8% glucose) or RMX (8% xylose) at a 10-fold concentration and used as inocula for fermentation studies. Fermentations were performed in BioStat-Q Plus fermentors (Sartorius Stedim Biotech, France) at 300-mL working volumes using Z. mobilis 8b. RMG or RMX media were used for fermentation. The fermentors were inoculated at an OD600nm unit of 0.1 approximately. The fermentation was conducted at 30°C, 150 rpm, pH 6.0 with 2 N KOH for pH control.

extract_protocol: RNA was isolated essentially described previously  [PMID 19154596]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: Cell biomass was frozen immediately after centrifugation.

value: subsp. mobilis 8b

tag: sugar source

value: xylose

tag: supplemented with

value: 3 g/L furfural

tag: growth stage

value: log phase

value: 60min post-furfural shock

value: cell biomass


title: T 72h2

value: after-ripened dry and imbibed seeds


title: liver-PBS-24h-rep2

description:
donor_17
Sample name: 9993942080_H


title: spleen-PBS-24h-rep2

description:
donor_17
Sample name: 9993942079_F


title: BaP_1

value: Muta Mouse


title: T dry2

source_name: Seed_T dry


title: T dry3


title: Control_1

value: hippocampus


title: 8b_Xylose_log_T60_F8

description:
_39_HT08_Cy3
HT08_F8_T60min_F


title: kidney-PBS-24h-rep3

description:
donor_18
Sample name: 9993942086_B

source_name: mouse,mock-infection,24h, kidney

value: kidney


title: T 72h1


title: kidney-PBS-24h-rep2

description:
donor_17
Sample name: 9993942008_A


title: 8b_Xylose_log_T15_F7

description:
_35_HT08_Cy3
HT08_F7_T15min_F

value: 15min post-furfural shock


title: T 26h1


title: T 48h1


title: 8b_Xylose_log_T15_F9

description:
_41_HT08_Cy3
HT08_F9_T15min_F


title: liver-systemic_fungal_infection-72h-rep3

description:
donor_15
Sample name: 9993942080_D

source_name: mouse,C.albicans-infection,72h, liver

value: liver


title: kidney-PBS-24h-rep1

description:
donor_16
Sample name: 9993942079_D

value: mock (PBS)

value: BALB/c


title: 8b_Xylose_log_T15_F8

description:
_38_HT08_Cy3
HT08_F8_T15min_F


title: 8b_Xylose_log_T60_F7

description:
_36_HT08_Cy3
HT08_F7_T60min_F


title: 8b_Gluc_log_T60_F3

description:
_27_HT08_Cy3
HT08_F3_T60min_1_2

value: glucose


title: liver-systemic_fungal_infection-72h-rep1

description:
donor_13
Sample name: 9993942086_F

value: female


title: liver-systemic_fungal_infection-72h-rep2

description:
donor_14
Sample name: 9993942008_C


title: 8b_Gluc_log_T60_F2

description:
_24_HT08_Cy3
HT08_F2_T60min_1_2


title: 8b_Gluc_log_T60_F1

description:
_21_HT08_Cy3
HT08_F1_T60min_1_2


title: spleen-systemic_fungal_infection-72h-rep2

description:
donor_14
Sample name: 9993942080_C

source_name: mouse,C.albicans-infection,72h, spleen

value: spleen


title: spleen-systemic_fungal_infection-72h-rep1

description:
donor_13
Sample name: 9993942086_G


title: T 6h1

value: Columbia (Col-0)


title: 8b_Gluc_log_T15_F3

description:
_26_HT08_Cy3
HT08_F3_T15min_1_2

value: subsp. mobilis 8b


title: 8b_Gluc_log_T15_F1

description:
_20_HT08_Cy3
HT08_F1_T15min_1_2

value: 3 g/L furfural


title: spleen-systemic_fungal_infection-72h-rep3

description:
donor_15
Sample name: 9993942082_G


title: kidney-systemic_fungal_infection-72h-rep2

description:
donor_14
Sample name: 9993942084_C

source_name: mouse,C.albicans-infection,72h, kidney


title: T 6h2


title: kidney-systemic_fungal_infection-72h-rep3

description:
donor_15
Sample name: 9993942080_G


title: kidney-systemic_fungal_infection-72h-rep1

description:
donor_13
Sample name: 9993942080_A


title: T dry1


title: 8b_Gluc_log_T15_F2

description:
_23_HT08_Cy3
HT08_F2_T15min_1_2

value: log phase


title: 8b_Xylose_log_T0_F8

description:
_37_HT08_Cy3
HT08_F8_T0_F

value: xylose

value: 0min (before furfural shock)


title: liver-systemic_fungal_infection-24h-rep6

description:
donor_12
Sample name: 9993942076_A

source_name: mouse,C.albicans-infection,24h, liver


title: 240 minutes after ndt80 block release_timecourse_II

city: Stony Brook

first: Bruce

last: Futcher

state: NY

address: STONY BROOK UNIVERSITY

department: Molecular Genetics & Microbiology

institute: Stony Brook University

hyb_protocol: Agilent gene expression Hybridization kit (5188-5242)

scan_protocol: Agilent G2505B serial # US451R2860 pixel 5

data_processing: Agilent Feature Extraction 9.501

organism: Saccharomyces cerevisiae

source_name: A14201_240 minutes after ndt80 block release

label_protocol: Agilent Quick Amp labeling kit two color (5190-0441)

growth_protocol: yeast cells were grow in YPD plate overnight, in YPD liquid medium to saturation, diluted in YPA medium and cultured overnight, shift to sporulation medium.

extract_protocol: total RNA was extracted by Ribopure yeast kit (Ambion) (Am1926)

treatment_protocol: After 6 hours in sporulation medium, 1μM beta-estradiol is added to the culture to induce NDT80 expression.

tag: timepoint

value: 240 minutes after ndt80 block release

source_name: A14201 in Ndt80 block (6 hours in SPO medium)


title: 220 minutes after ndt80 block release_timecourse_II

source_name: A14201_220 minutes after ndt80 block release

value: 220 minutes after ndt80 block release


title: 200 minutes after ndt80 block release_timecourse_II

source_name: A14201_200 minutes after ndt80 block release

value: 200 minutes after ndt80 block release


title: liver-systemic_fungal_infection-24h-rep4

description:
donor_10
Sample name: 9993942076_H

tag: age


title: 8b_Gluc_log_T0_F3

description:
_25_HT08_Cy3
HT08_F3_T0_1_2

value: cell biomass


title: 8b_Xylose_log_T0_F9

description:
_40_HT08_Cy3
HT08_F9_T0_F


title: 8b_Xylose_log_T0_F7

description:
_34_HT08_Cy3
HT08_F7_T0_F


title: 8b_Gluc_log_T0_F1

description:
_19_HT08_Cy3
HT08_F1_T0_1_2


title: liver-systemic_fungal_infection-24h-rep5

description:
donor_11
Sample name: 9993942084_G


title: spleen-systemic_fungal_infection-24h-rep5

description:
donor_11
Sample name: 9993942076_D

source_name: mouse,C.albicans-infection,24h, spleen


title: 8b_Xylose_Furfural_late_log_F12

description:
_48_HT08_Cy3
HT08_F12_Stationary_2

value: 2 g/L furfural

value: stationary phase


title: 160 minutes after ndt80 block release_timecourse_II

source_name: A14201_160 minutes after ndt80 block release

value: 160 minutes after ndt80 block release


title: 140 minutes after ndt80 block release_timecourse_II

source_name: A14201_140 minutes after ndt80 block release

value: 140 minutes after ndt80 block release


title: FaDU_shTP63_rep3

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: FaDU HNSCC cells treated with shRNA against TP63 (replicate 2)

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix Human Gene 1.0 ST array (transcript (gene) version) at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) in the R (version 2.15.1) Bioconductor package.

source_name: FaDU HNSCC cell line

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: Cells were maintained at 37°C in 5% CO2 in either RPMI or DMEM or DMEM/F12 supplemented with 10% FBS, penicillin, and streptomycin.

extract_protocol: Total RNA was isolated using QIAshredder and RNeasy Plus Mini kit (both Qiagen) following manufacturer’s instructions. qRT-PCR for cell line (1 μg total RNA as template) using iQTM SYBR® Green Supermix (BioRad) was performed following manufacturer’s instructions.

treatment_protocol: RNA collected 72 hours following lentiviral knockdown by shRNA for TP63 or control vector. Lentiviral production and mRNA analysis of cell lines were performed as described (Ramsey et al., 2013, JCI).

value: FaDU

tag: treatment


title: 180 minutes after ndt80 block release_timecourse_II

source_name: A14201_180 minutes after ndt80 block release

value: 180 minutes after ndt80 block release


title: 8b_Gluc_log_T0_F2

description:
_22_HT08_Cy3
HT08_F2_T0_1_2

value: glucose


title: kidney-systemic_fungal_infection-24h-rep6

description:
donor_12
Sample name: 9993942008_E

source_name: mouse,C.albicans-infection,24h, kidney

value: kidney

value: female

value: BALB/c


title: FaDU_shTP63_rep2

description: FaDU HNSCC cells treated with shRNA against TP63 (replicate 1)


title: 120 minutes after ndt80 block release_timecourse_II

source_name: A14201_120 minutes after ndt80 block release

value: 120 minutes after ndt80 block release


title: FaDU_shTP63_rep4

description: FaDU HNSCC cells treated with shRNA against TP63 (replicate 3)


title: 8b_Xylose_Furfural_late_log_F11

description:
_46_HT08_Cy3
HT08_F11_Stationary_2

value: subsp. mobilis 8b

value: xylose


title: 8b_Xylose_Furfural_late_log_F10

description:
_44_HT08_Cy3
HT08_F10_Stationary_1


title: 100 minutes after ndt80 block release_timecourse_II

source_name: A14201_100 minutes after ndt80 block release

value: 100 minutes after ndt80 block release


title: 8b_Xylose_Furfural_log_F12

description:
_47_HT08_Cy3
HT08_F12_Log

value: log phase


title: JHU029_shTP63_rep2

description: JHU-029 HNSCC cells treated with shRNA against TP63 (replicate 2)

source_name: JHU-029 HNSCC cell Line


title: kidney-systemic_fungal_infection-24h-rep5

description:
donor_11
Sample name: 9993942084_D


title: spleen-systemic_fungal_infection-24h-rep6

description:
donor_12
Sample name: 9993942086_D

value: spleen


title: JHU029_shTP63_rep3

description: JHU-029 HNSCC cells treated with shRNA against TP63 (replicate 3)


title: 80 minutes after ndt80 block release_timecourse_II

source_name: A14201_80 minutes after ndt80 block release

value: 80 minutes after ndt80 block release


title: kidney-systemic_fungal_infection-24h-rep4

description:
donor_10
Sample name: 9993942076_G


title: 8b_Xylose_Furfural_log_F11

description:
_45_HT08_Cy3
HT08_F11_Log

value: 2 g/L furfural

value: cell biomass


title: 40 minutes after ndt80 block release_timecourse_II

source_name: A14201_40 minutes after ndt80 block release

value: 40 minutes after ndt80 block release


title: liver-systemic_fungal_infection-24h-rep2

description:
donor_8
Sample name: 9993942079_A

value: liver


title: JHU029_shTP63_rep1

description: JHU-029 HNSCC cells treated with shRNA against TP63 (replicate 1)


title: 60 minutes after ndt80 block release_timecourse_II

source_name: A14201_60 minutes after ndt80 block release

value: 60 minutes after ndt80 block release


title: spleen-systemic_fungal_infection-24h-rep4

description:
donor_10
Sample name: 9993942082_B


title: liver-systemic_fungal_infection-24h-rep3

description:
donor_9
Sample name: 9993942084_E

source_name: mouse,C.albicans-infection,24h, liver


title: 8b_Gluc_Furfural_stationary_F6

description:
_33_HT08_Cy3
HT08_F6_Stationary_3_2

value: stationary phase


title: FaDU_shCtrl_new_rep2

description: FaDU HNSCC cells treated with control shRNA (replicate 1)

value: FaDU

value: shControl


title: JHU029_shCtrl_rep1

description: JHU-029 HNSCC cells treated with control shRNA (replicate 1)


title: FaDU_shCtrl_new_rep3

description: FaDU HNSCC cells treated with control shRNA (replicate 2)


title: 20 minutes after ndt80 block release_timecourse_II

source_name: A14201_20 minutes after ndt80 block release

value: 20 minutes after ndt80 block release


title: 8b_Xylose_Furfural_log_F10

description:
_43_HT08_Cy3
HT08_F10_Log


title: 8b_Gluc_Furfural_log_F6

description:
_32_HT08_Cy3
HT08_F6_Log_1_1

value: glucose


title: 8b_Gluc_Furfural_log_F5

description:
_30_HT08_Cy3
HT08_F5_Log_3_2


title: liver-systemic_fungal_infection-24h-rep1

description:
donor_7
Sample name: 9993942086_E

value: female

value: BALB/c


title: spleen-systemic_fungal_infection-24h-rep2

description:
donor_8
Sample name: 9993942076_B


title: JHU029_shCtrl_rep3

description: JHU-029 HNSCC cells treated with control shRNA (replicate 3)


title: 15 minutes after ndt80 block release_timecourse_II

source_name: A14201_15 minutes after ndt80 block release

value: 15 minutes after ndt80 block release

source_name: A14201 in Ndt80 block (6 hours in SPO medium)


title: 5 minutes after ndt80 block release_timecourse_II

source_name: A14201_5 minutes after ndt80 block release

value: 5 minutes after ndt80 block release


title: 8b_Gluc_Furfural_stationary_F5

description:
_31_HT08_Cy3
HT08_F5_Stationary_3_1

value: subsp. mobilis 8b


title: spleen-systemic_fungal_infection-24h-rep3

description:
donor_9
Sample name: 9993942086_C

source_name: mouse,C.albicans-infection,24h, spleen

value: spleen


title: JHU029_shCtrl_rep2

description: JHU-029 HNSCC cells treated with control shRNA (replicate 2)


title: 8b_Gluc_Furfural_stationary_F4

description:
_29_HT08_Cy3
HT08_F4_Stationary_3_2


title: 10 minutes after ndt80 block release_timecourse_II

source_name: A14201_10 minutes after ndt80 block release

value: 10 minutes after ndt80 block release


title: FaDU_shCtrl_rep4

description: FaDU HNSCC cells treated with control shRNA (replicate 3)


title: 10 minutes before ndt80 block release_timecourse_II

source_name: A14201_10 minutes before ndt80 block release

value: 10 minutes before ndt80 block release


title: 2 minutes after ndt80 block release_timecourse_II

source_name: A14201_2 minutes after ndt80 block release

value: 2 minutes after ndt80 block release


title: spleen-systemic_fungal_infection-24h-rep1

description:
donor_7
Sample name: 9993942086_H


title: HaCaT_shTP63_rep2

description: HaCaT immortalized keratinocyte (HFK) cells treated with shRNA against TP63 (replicate 2)

source_name: HaCaT immortalized keratinocyte (HFK) cell line

value: HaCaT


title: kidney-systemic_fungal_infection-24h-rep2

description:
donor_8
Sample name: 9993942079_C

source_name: mouse,C.albicans-infection,24h, kidney

value: kidney


title: 8b_Gluc_Furfural_log_F4

description:
_28_HT08_Cy3
HT08_F4_Log_2_1

value: 2 g/L furfural

value: log phase

value: cell biomass


title: 5 minutes before ndt80 block release_timecourse_II

source_name: A14201_5 minutes before ndt80 block release

value: 5 minutes before ndt80 block release


title: HaCaT_shTP63_rep3

description: HaCaT immortalized keratinocyte (HFK) cells treated with shRNA against TP63 (replicate 3)


title: ndt80 block release (6 hours in SPO medium)_timecourse_II

source_name: A14201_ndt80 block release (6 hours in SPO medium)


title: HaCaT_shCtrl_rep3

description: HaCaT immortalized keratinocyte (HFK) cells treated with control shRNA (replicate 3)

value: shControl


title: liver-systemic_fungal_infection-12h-rep6

description:
donor_6
Sample name: 9993942008_D

source_name: mouse,C.albicans-infection,12h, liver

value: liver


title: kidney-systemic_fungal_infection-24h-rep1

description:
donor_7
Sample name: 9993942076_E

value: female


title: kidney-systemic_fungal_infection-24h-rep3

description:
donor_9
Sample name: 9993942086_A

value: BALB/c


title: 15 minutes before ndt80 block release_timecourse_II

source_name: A14201_15 minutes before ndt80 block release

value: 15 minutes before ndt80 block release


title: HaCaT_shTP63_rep1

description: HaCaT immortalized keratinocyte (HFK) cells treated with shRNA against TP63 (replicate 1)


title: Tumor OCT Curl Rep30

city: New York

first: Julia

middle: Nanyi

last: Zhao

address: 408 68th Streer

department: Surgery

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Hybridization was performed using the following protocol: GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays.

scan_protocol: The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for image processing.

data_processing: Affymetrix Expression Console software version 1.4.1 was used for primary analysis, and SST-RMA was used as the processing algorithm.

source_name: PDAC tumor_LTS cohort

label_protocol: Labeling was performed using the following protocol: GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays.

growth_protocol: OCT fresh frozen resected human PDAC tumors

extract_protocol: Sections were brought to containers with 70% ethanol for OCT removal. Total RNA from fresh frozen OCT embedded tissues was extracted using TRIzol RNA Isolation Reagents.

treatment_protocol: Not applicable

tag: cohort

value: overall survival of >3 years postsurgery; long term survivors (LTS)

value: human pancreatic ductal adenocarcinoma (PDAC) tumor


title: HaCaT_shCtrl_rep2

description: HaCaT immortalized keratinocyte (HFK) cells treated with control shRNA (replicate 2)


title: 240 minutes after ndt80 block release_timecourse_I

source_name: A14201_240 minutes after ndt80 block release

tag: time point

value: 240 minutes


title: Tumor OCT Curl Rep29

tag: tissue


title: FaDU_shACTL6A_B02_rep3

description: FaDU HNSCC cells treated with shRNA against ACTL6A (construct B02, replicate 3)

source_name: FaDU HNSCC cell line

treatment_protocol: RNA collected 72 hours following lentiviral knockdown by shRNA for ACTL6A or control vector. Lentiviral production and mRNA analysis of cell lines were performed as described (Ramsey et al., 2013, JCI). shRNA sequences for ACTL6A are CGGTACTTCAAGTGTCAGATT and ACCTTACGTTTCATAGCTTTA.

value: FaDU

value: shACTL6A B02


title: liver-systemic_fungal_infection-12h-rep5

description:
donor_5
Sample name: 9993942079_H

tag: gender


title: Tumor OCT Curl Rep28


title: Tumor OCT Curl Rep27


title: 220 minutes after ndt80 block release_timecourse_I

source_name: A14201_220 minutes after ndt80 block release

value: 220 minutes


title: HaCaT_shCtrl_rep1

description: HaCaT immortalized keratinocyte (HFK) cells treated with control shRNA (replicate 1)

value: HaCaT


title: liver-systemic_fungal_infection-12h-rep4

description:
donor_4
Sample name: 9993942082_D


title: 200 minutes after ndt80 block release_timecourse_I

source_name: A14201_200 minutes after ndt80 block release

value: 200 minutes


title: FaDU_shACTL6A_B02_rep2

description: FaDU HNSCC cells treated with shRNA against ACTL6A (construct B02, replicate 2)


title: Tumor OCT Curl Rep26


title: 180 minutes after ndt80 block release_timecourse_I

source_name: A14201_180 minutes after ndt80 block release

value: 180 minutes

source_name: A14201 in Ndt80 block (6 hours in SPO medium)


title: 172 minutes after ndt80 block release_timecourse_I

description: Two replicates were performed for the 172 minute timepoint. The processed data were averaged for the arrays.

source_name: A14201_172 minutes after ndt80 block release

value: 172 minutes


title: FaDU_shACTL6A_A07_rep3

description: FaDU HNSCC cells treated with shRNA against ACTL6A (construct A07, replicate 3)

value: shACTL6A A07


title: spleen-systemic_fungal_infection-12h-rep4

description:
donor_4
Sample name: 9993942084_H

source_name: mouse,C.albicans-infection,12h, spleen

value: spleen


title: 156 minutes after ndt80 block release_timecourse_I

source_name: A14201_156 minutes after ndt80 block release

value: 156 minutes


title: Tumor OCT Curl Rep24


title: Tumor OCT Curl Rep20


title: Tumor OCT Curl Rep25


title: spleen-systemic_fungal_infection-12h-rep5

description:
donor_5
Sample name: 9993942082_E


title: spleen-systemic_fungal_infection-12h-rep6

description:
donor_6
Sample name: 9993942082_H


title: FaDU_shCtrl_rep3

value: shControl


title: Tumor OCT Curl Rep23


title: kidney-systemic_fungal_infection-12h-rep6

description:
donor_6
Sample name: 9993942079_E

source_name: mouse,C.albicans-infection,12h, kidney

value: kidney

value: female


title: kidney-systemic_fungal_infection-12h-rep4

description:
donor_4
Sample name: 9993942084_B

value: BALB/c


title: FaDU_shACTL6A_A07_rep1

description: FaDU HNSCC cells treated with shRNA against ACTL6A (construct A07, replicate 1)


title: FaDU_shCtrl_rep2


title: Tumor OCT Curl Rep19

value: overall survival of >3 years postsurgery; long term survivors (LTS)


title: kidney-systemic_fungal_infection-12h-rep5

description:
donor_5
Sample name: 9993942082_C


title: FaDU_shACTL6A_B02_rep1

description: FaDU HNSCC cells treated with shRNA against ACTL6A (construct B02, replicate 1)


title: Tumor OCT Curl Rep22

value: human pancreatic ductal adenocarcinoma (PDAC) tumor


title: liver-systemic_fungal_infection-12h-rep2

description:
donor_2
Sample name: 9993942079_G

value: liver


title: liver-systemic_fungal_infection-12h-rep3

description:
donor_3
Sample name: 9993942008_F


title: 164 minutes after ndt80 block release_timecourse_I

source_name: A14201_164 minutes after ndt80 block release

value: 164 minutes


title: FaDU_shACTL6A_A07_rep2

description: FaDU HNSCC cells treated with shRNA against ACTL6A (construct A07, replicate 2)

value: FaDU


title: 140 minutes after ndt80 block release_timecourse_I

source_name: A14201_140 minutes after ndt80 block release

value: 140 minutes


title: Tumor OCT Curl Rep21


title: FaDU_shCtrl_rep1

description: FaDU HNSCC cells treated with control shRNA (replicate 1)


title: liver-systemic_fungal_infection-12h-rep1

description:
donor_1
Sample name: 9993942076_C


title: liver-systemic_fungal_infection-8h-rep6

source_name: mouse,C.albicans-infection,8h, liver

value: C. albicans

tag: mouse strain


title: 148 minutes after ndt80 block release_timecourse_I

source_name: A14201_148 minutes after ndt80 block release

value: 148 minutes


title: 132 minutes after ndt80 block release_timecourse_I

description: Two replicates were performed for the 132 minute timepoint. The processed data were averaged for the arrays.

source_name: A14201_132 minutes after ndt80 block release

value: 132 minutes


title: Tumor OCT Curl Rep17


title: Tumor OCT Curl Rep18


title: liver-systemic_fungal_infection-8h-rep5


title: 100 minutes after ndt80 block release_timecourse_I

description: This array failed quality control therefore no processed data are provided for this sample.

source_name: A14201_100 minutes after ndt80 block release

value: 100 minutes


title: 116 minutes after ndt80 block release_timecourse_I

source_name: A14201_116 minutes after ndt80 block release

value: 116 minutes


title: spleen-systemic_fungal_infection-12h-rep2

description:
donor_2
Sample name: 9993942082_F

value: spleen


title: 124 minutes after ndt80 block release_timecourse_I

source_name: A14201_124 minutes after ndt80 block release

value: 124 minutes


title: spleen-systemic_fungal_infection-12h-rep3

description:
donor_3
Sample name: 9993942084_A


title: Tumor OCT Curl Rep15

source_name: PDAC tumor_STS cohort

value: median survival of >3 month and <1 year postsurgery; short term survivors (STS)


title: 108 minutes after ndt80 block release_timecourse_I

source_name: A14201_108 minutes after ndt80 block release

value: 108 minutes


title: spleen-systemic_fungal_infection-8h-rep6

source_name: mouse,C.albicans-infection,8h, spleen

value: female


title: liver-systemic_fungal_infection-8h-rep4

value: BALB/c


title: spleen-systemic_fungal_infection-8h-rep5


title: kidney-systemic_fungal_infection-8h-rep6

source_name: mouse,C.albicans-infection,8h, kidney

value: kidney


title: Tumor OCT Curl Rep14

value: human pancreatic ductal adenocarcinoma (PDAC) tumor


title: kidney-systemic_fungal_infection-12h-rep3

description:
donor_3
Sample name: 9993942079_B


title: spleen-systemic_fungal_infection-12h-rep1

description:
donor_1
Sample name: 9993942080_E


title: kidney-systemic_fungal_infection-12h-rep1

description:
donor_1
Sample name: 9993942076_F


title: Tumor OCT Curl Rep12


title: kidney-systemic_fungal_infection-12h-rep2

description:
donor_2
Sample name: 9993942082_A


title: Tumor OCT Curl Rep16

source_name: PDAC tumor_LTS cohort

value: overall survival of >3 years postsurgery; long term survivors (LTS)


title: 84 minutes after ndt80 block release_timecourse_I

source_name: A14201_84 minutes after ndt80 block release

value: 84 minutes

source_name: A14201 in Ndt80 block (6 hours in SPO medium)


title: 76 minutes after ndt80 block release_timecourse_I

source_name: A14201_76 minutes after ndt80 block release

value: 76 minutes


title: kidney-systemic_fungal_infection-8h-rep5


title: Tumor OCT Curl Rep13


title: 92 minutes after ndt80 block release_timecourse_I

source_name: A14201_92 minutes after ndt80 block release

value: 92 minutes


title: spleen-systemic_fungal_infection-8h-rep4

value: C. albicans


title: Tumor OCT Curl Rep10


title: 68 minutes after ndt80 block release_timecourse_I

source_name: A14201_68 minutes after ndt80 block release

value: 68 minutes


title: Tumor OCT Curl Rep11


title: kidney-systemic_fungal_infection-8h-rep4


title: 60 minutes after ndt80 block release_timecourse_I

source_name: A14201_60 minutes after ndt80 block release

value: 60 minutes


title: 20 minutes after ndt80 block release_timecourse_I

source_name: A14201_20 minutes after ndt80 block release

value: 20 minutes


title: Tumor OCT Curl Rep8


title: 1(Comma-D):1(erbB2+)_REP2

city: Clemson

first: Alex

last: Feltus

state: SC

address: 302C Biosytstems Research Complex

department: Genetics & Biochemistry

institute: Clemson University

description: F_1:1 erbB2+_Cancer_erbB2+_P-erbB2+

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: A total of eighteen samples (6 groups in triplicate) were analyzed with the Mouse Gene 1.0 ST Arrays from Affymetrix (http://www.affymetrix.com).  Samples were RMA normalized and log2 gene expression matrices processed using R v3.1.2 and the following Bioconductor (Gentleman, Carey et al., 2004) v3.1 packages: affy (Gautier, Cope et al., 2004), limma (Ritchie, Phipson et al., 2015), and oligo (Carvalho & Irizarry, 2010) according to standard procedures described in (Smyth, Ritchie et al., 2016).

source_name: Comma-D:MMTC-neu cell mix

label_protocol: As per manufacturer's instructions.

growth_protocol: MMTV-neu cells were maintained in DMEM supplemented with 10% FBS and 1% antibiotic/antimycotic. COMMA-D cells were grown in DMEM/F12 with 2% FBS, 0.1M HEPES, 1% antibiotic/antimycotic, 10 ug/ml insulin, 5 ng/ml EGF and 4 ug/ml gentamicin added. Co-cultures of MMTV-neu and COMMA-D cells were grown in COMMA-D medium. All cultures were grown at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from the sorted samples using an RNAaqueous Micro kit (Ambion, Austin, TX) that utilizes glass fiber filter column purification.  Isolated total RNA was then treated with DNase (Qiagen, Valencia, CA) to remove any DNA contamination.  The concentration of RNA was determined using a NanoDrop and the RNA integrity was analyzed with a RNA nano chip on a Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were detached by trypsin, washed once with PBS and resuspended in 100 ul of diluent containing primary antibody (1:50; anti-erbB2) and incubated for 30 min at 4C.  The cells were then washed 2 x 10 min and resuspended in 100 ul of diluent containing biotinylated secondary antibody (1:100) and incubated for 15 min at 4C. The cells were then washed 2 x 10 min and resuspended in 80:20 mix of diluent and anti-biotin magnetic beads (Miltenyi) and incubated for 15 min at 4C. The cells were then washed 2 x 10 min and resuspended in 500 ul of running buffer and separated through a LS column (Miltenyi).  The positive and depleted fractions were collected. RNA was isolated from the sorted cells.

tag: cell type

value: Comma-D:MMTC-neu cell mix

tag: group

value: Cancer


title: 1(Comma-D):1(erbB2+)_REP3

description: F_1:1 erbB2+_Cancer_erbB2+_P-erbB2+


title: 1(Comma-D):1(erbB2+)_REP1

description: F_1:1 erbB2+_Cancer_erbB2+_P-erbB2+


title: 1(Comma):50(erbB2+)_REP2

description: E_1:50 erbB2+_Redirected_erbB2+_P-erbB2-

value: Redirected


title: Tumor OCT Curl Rep7

value: median survival of >3 month and <1 year postsurgery; short term survivors (STS)


title: 1(Comma):50(erbB2+)_REP1


title: Tumor OCT Curl Rep5


title: 190 minutes after ndt80 block release_timecourse_I

source_name: A14201_190 minutes after ndt80 block release

tag: strain

value: 190 minutes


title: Tumor OCT Curl Rep3


title: Candida albicans-systemic mouse infection-liver-8h_rep3

hyb_protocol: co-hybridized at a ratio of 1:1 with common reference

scan_protocol: 428TM array scanner, Affymetrix

data_processing: Using R 2.15.2 with library limma. Printtiploess for within-array normalisation. Quantile normalisation (Manormbet function) between different arrays.s

organism: Candida albicans

source_name: common reference, log-phase growth in YPD, 37°C

label_protocol: Low RNA Input Fluorescent Linear amplification Kit, Agilent Technologies, Santa Clara, CA, USA

growth_protocol: stationary growth, YPD, 30°C

treatment_protocol: tail vein infection of mice

tag: control type

value: common reference

source_name: liver isolation, 8h p.i.

tag: candida albicans strain

tag: host mouse tissue

value: liver


title: 1(Comma-D):1(erbB2-)_REP3

description: D_1:1 erbB2-_Normal_erbB2-_P-erbB2-

value: Normal


title: Tumor OCT Curl Rep6

value: human pancreatic ductal adenocarcinoma (PDAC) tumor


title: 1(Comma-D):1(erbB2-)_REP1

description: D_1:1 erbB2-_Normal_erbB2-_P-erbB2-


title: 1(Comma-D):50(erbB2-)_REP2

description: C_1:50 erbB2-_Normal_erbB2-_P-erbB2-


title: Tumor OCT Curl Rep2


title: Tumor OCT Curl Rep4


title: Candida albicans-systemic mouse infection-liver-8h_rep1

tag: hours post infection


title: Tumor OCT Curl Rep1


title: 1(Comma):50(erbB2+)_REP3


title: 1(Comma-D):1(erbB2-)_REP2

description: D_1:1 erbB2-_Normal_erbB2-_P-erbB2-


title: 1(Comma-D):50(erbB2-)_REP1

description: C_1:50 erbB2-_Normal_erbB2-_P-erbB2-


title: Neu_REP3

source_name: MMTV-neu cells

value: MMTV-neu cells


title: 1(Comma-D):50(erbB2-)_REP3

description: C_1:50 erbB2-_Normal_erbB2-_P-erbB2-


title: Candida albicans-systemic mouse infection-kidney-24h_rep5

source_name: kidney isolation, 24h p.i.

value: kidney


title: Candida albicans-systemic mouse infection-kidney-24h_rep6


title: Candida albicans-systemic mouse infection-liver-8h_rep2


title: Tumor OCT Curl Rep9

source_name: PDAC tumor_STS cohort


title: Neu_REP2


title: Neu_REP1


title: Comma-D_REP3

source_name: Comma-D cells

value: Comma-D cells


title: Comma-D_REP2


title: 160948

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according the Agilent protocol

scan_protocol: We used a Surescan provided by Agilent and controled by SureScan Software

data_processing: the data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent

source_name: Glioma

label_protocol: DNA was labeled with the sureTag labeling kit accirding the agilent protocol

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

tag: disease state

value: Glioma

source_name: Male DNA control provided in SureTag Labeling Kit

tag: sample type

value: commercial DNA from cell lines


title: Candida albicans-systemic mouse infection-kidney-24h_rep2


title: Comma-D_REP1


title: Candida albicans-systemic mouse infection-kidney-24h_rep3


title: Candida albicans-systemic mouse infection-kidney-24h_rep4


title: Candida albicans-systemic mouse infection-kidney-24h_rep1


title: Candida albicans-systemic mouse infection-kidney-12h_rep7

source_name: kidney isolation, 12h p.i.


title: IAV - induced memory P14, day 100_2

city: Iowa City

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: IAV - induced memory P14, day 100

hyb_protocol: Biotin labeled ss-cDNA was hybridized with Affymetrix GeneChip Mouse Transcriptome Array 1.0. Affymetrix Model 3000 scanner (with 7G upgrade)

data_processing: Data were collected using Affymetrix Commands Console operating software (AGCC) v4.1.2. Microarray data was imported into Affymetrix Expression Console 1.4.1.46 and data normalized using the SST-RMA method.  Normalized data was imported into Affymetrix Transcriptome Analysis Console 4.0.0.466 and an ANOVA comparison was done between late and early samples, and genes that met the criteria of 1.25 fold change and a p-value of <0.05 were examined further.

source_name: P14 CD8 T cells flow sorted from spleen of mice infeceted with IAV

label_protocol: 1ng of total RNA was converted to amplified ss-cDNA using the Affymetrix GeneChip WT Pico Reagent Kit. Following fragmentation (fragment size ~40-70nt), the samples were labeled with biotin.

extract_protocol: Qiagen RNeasy mini kit was used for RNA extraction accoriding to the manufacturer's protocol.

treatment_protocol: Naive female C57Bl/6 mice (thy1.2) were seeded with naive P14 cells (thy1.1) and intranasally infected with recombinant IAV PR8-GP33. 20 (early memory) or >100 (late memory) days later, spleen-derived memory P14 cells were isolated and total RNA extracted.

value: P14 CD8 T cells

value: spleen

tag: days after infection

value: female


title: Candida albicans-systemic mouse infection-kidney-12h_rep6


title: Candida albicans-systemic mouse infection-kidney-12h_rep8


title: Candida albicans-systemic mouse infection-kidney-12h_rep5


title: IAV - induced memory P14, day 100_3

description: IAV - induced memory P14, day 100

scan_protocol: Affymetrix Model 3000 scanner (with 7G upgrade)


title: IAV - induced memory P14, day 100_4

description: IAV - induced memory P14, day 100


title: IAV - induced memory P14, day 100_1

description: IAV - induced memory P14, day 100


title: IAV-induced memory P14, day 20_5

description: IAV-induced memory P14, day 20


title: Candida albicans-systemic mouse infection-kidney-12h_rep3


title: IAV - induced memory P14, day 100_5

description: IAV - induced memory P14, day 100


title: Candida albicans-systemic mouse infection-kidney-12h_rep2


title: IAV-induced memory P14, day 20_3

description: IAV-induced memory P14, day 20


title: IAV-induced memory P14, day 20_4

description: IAV-induced memory P14, day 20


title: 0GyH7/ reference male mouse1

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing:
Agilent Genomic Workbench Software (v 7.0.) was used and performed FuzzyZero correction.  Agilent Feature Extraction Software (version 10.7.1.1) also performed the following Normalization.
The log ratio i is the measure of differential expression between the red and green channels for every probe i:   LogRatioi =Log10 (ProcessedSignalr/（ProcessedSignalg）  where ProcessedSignalrand ProcessedSignalg are signals post dye normalization and post surrogate processing in the red and green channels, respectively.     The dye-normalized signal is calculated by multiplying the background-subtracted signal by the dye normalization factor: DyeNormSignal = (BGSubSignal/MultDetrendSignal) × DNF     DNF:　LinearDyeNormFactor  The linear dye normalization method assumes that dye bias is not intensity-dependent and therefore takes a global approach to dye normalization.  A linear dye normalization factor is computed per channel by setting the geometric mean of signal intensity of the normalization features equal to 1000:

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse1


title: 40 minutes after ndt80 block release_timecourse_I

source_name: A14201_40 minutes after ndt80 block release

value: 40 minutes

source_name: A14201 in Ndt80 block (6 hours in SPO medium)


title: reference male mouse1/ 0GyH7

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: reference male mouse1/ 0GyH8


title: IAV-induced memory P14, day 20_2

first: Thomas

description: IAV-induced memory P14, day 20


title: Candida albicans-systemic mouse infection-kidney-12h_rep1


title: IAV-induced memory P14, day 20_1

description: IAV-induced memory P14, day 20


title: 0GyH6/ reference male mouse1


title: Day7_Oct4-Venus+_1

status: Public on Nov 17 2016

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo

description:
Gene expression data from SFEBq day7 Oct4-Venus+ cells isolated from SFEBq-cultured mouse embryonic stem cells (day7, Oct4-Venus+ fraction)
OLV2-1 cell line, SFEBq day7, Oct4-Venus+ fraction, sorted by FACS

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: The data were analyzed with Expression Console Version 1. 1 using Affymetrix default analysis settings. Clustering analysis was performed using Gene Spring GX12 (Digital Biology).

source_name: mouse_SFEBq_day7_Oct4-Venus+ fraction, sorted by FACS

label_protocol: Fragmentation of aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3’ IVT Express KitUser Manual, 2013, Affymetrix).

growth_protocol: OLV2-1 (Oct4-Venus knock-in mouse embryonic stem cell line)

extract_protocol: Total RNA was purified with the RNeasy Micro Kit according to the manufacturer’s instructions.

treatment_protocol: Oct4-Venus mouse ESCs (OLV2-1) were cultured in SFEBq condition as reported previously (Eiraku M et al., (2008) Cell Stem Cell 3:519-532). To isolate undifferentiated ESCs and epiblast stem cell-like (EpiSC-like) cells, undifferentiated ESCs and SFEBq cell aggregates on day3 were dissociated with 0.25% (v/v) trypsin/imM EDTA, incubated for 1 hour in SFEBq medium to recover surface antigens, washed with 2% FBS (v/v) in PBS, and stained with allophycocyanin-conjugated CD31 antibody (BD pharmingen; 557690) or control Rat IgG2a (BD pharmingen; 557690) for 45 minutes on ice. After staining, cells were washed with 2% FBS (v/v) in PBS and subjected to cell sorting. The Venus+/CD31+ subpopulation of Oct4-Venus mESCs and a Venus+/CD31− population of SFEBq day 3 cell aggregates were defined as mESCs and EpiSC-like cells, respectively. To isolate day7 Oct4-Venus cells, SFEBq day7 cell aggregates were dissociated with PBS containing 1mM EDTA. Venus+ cell fraction was sorted and subjected to cell sorting. PI was used to exclude dead cells. Cell isolation was performed on a FACS AriaII with FACS Diva Software (BD Biosciences).

tag: cell line

tag: culture protocol

value: SFEBq day7

value: SFEBq day7 Oct4-Venus+ cells

tag: fraction

value: Oct4-Venus+ fraction


title: EpiSC-like_1

description:
Gene expression data from epiblast stem cell (EpiSC)-like cells isolated from mouse SFEBq-cultured embryonic stem cells (day3, Oct4-Venus+/Pecam1- fraction)
OLV2-1 cell line, SFEBq day3, Oct4-Venus+/Pecam1- fraction, sorted by FACS

source_name: mouse_epiblast_stem_cell_like_cell, sorted by FACS

value: SFEBq day3

value: epiblast stem cell (EpiSC)-like cells

value: Oct4-Venus+/Pecam1- fraction


title: 0GyH5/ reference male mouse1


title: 0GyH8/ reference male mouse1


title: lung cancer tissue and adjcent normal tissue from patient 7

city: Guangzhou

first: Lei

last: Yang

address: Xinzao, Panyu District,

institute: Guangzhou medical university

description: Stage 2 samples

hyb_protocol: Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit  (Cat#5188‐5380, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven  (Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 65℃, 20rpm for 24 hours.  Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set  (Cat#5188‐5226, Agilent technologies, Santa Clara, CA, US) in staining dishes  (Cat#121, Thermo Shandon, Waltham, MA, US) follow the manufacturer’s  instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent  technologies, Santa Clara, CA, US),scan resolution= 3μm, PMT 100% to generate tiff  image.

data_processing: Raw data was acquired and normalized(algorithm: LOWESS) using Feature  Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: lung cancer tissue 7

label_protocol: Genomic DNA was digested by two Restriction Enzymes AluI (Cat#R6281, Promega, Madison, WI, US) and RsaI (Cat#R6371, Promega, Madison, WI, US), follow  the instructions provided by the manufacture.Experimental sample and control sample were labeled with Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US) and Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) respectively, using  Agilent Genomic DNA Labeling Kit PLUS (Cat#5188‐5309, Agilent technologies, Santa  Clara, CA, US) followed the manufacturer’s instructions. Labeled DNA fragments were  purified using Amicon Ultra‐0.5, Ultracel‐30 Membrane,30 kDa(Cat#UFC5030BK,  Millipore, Billerica, MA, US). Measured the absorbance at A260nm (DNA),A550nm  (Cyanine 3),and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific  Activity.

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN,  GmBH, Germany). Use Nano Drop (Cat#ND‐1000, ThermoFisher, Waltham, MA, US)  and 1% agarose gel electrophoresis to check the quantity and quality of purified  DNA.

value: lung cancer tissue

value: Female

tag: age

tag: tumor stage

value: III

source_name: lung adjcent normal tissue 7

value: lung normal tissue


title: EpiSC-like_2


title: lung cancer tissue and adjcent normal tissue from patient 8

description: Stage 2 samples

source_name: lung cancer tissue 8

tag: tissue

tag: gender

value: I

source_name: lung adjcent normal tissue 8


title: mcf7/tcell95/5

type: SRA

city: Houston

first: Ronak

middle: Y

last: Patel

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
target capture DNA
95% MCF7 – 5% T-cell (CD8+ T-cells)

library_source: genomic

data_processing:
Read mapping and methylation level calling was performed using Bismark (Krueger and Andrews, 2011).
Average level of methylation over each targeted region was computed
Genome_build: hg19
Supplementary_files_format_and_content: Column 1: Chromosome; Column 2: Start position ;  Column 3: End position ; Column 4: Percent methylation;  Column 5: Number of reads methylated in that position; Column 6: Number of reads unmethylated in that position

source_name: see source of individual cell lines

growth_protocol: Normal Human Mammary Epithelial Cells (Clonetics), primary human fibroblasts (Asterand), human CD8+ cytotoxic T-cells (Sanguine), and breast cancer cell lines – MCF7, MDA-MB-231, MDA-MB-361, HCC1954, HCC1569, MCF10A (ATCC)—were cultured according to the respective manufacturer protocol. Logarithmically growing cultures were harvested at ~75-90% confluency. Frozen, primary human breast tumor tissue and adjacent normal tissue were obtained with local Institutional Review Board (IRB# PRO11090404) from the University of Pittsburgh’s Health Science Tissue Bank.

extract_protocol:
Frozen samples were pulverized with mortar and pestle under liquid nitrogen conditions. DNA from cell culture, tumor tissue, normal tissue, and buffy coat was isolated using Qiagen’s DNeasy Blood and Tissue kit and bisulfite converted with the EpiTect Bisulfite Kit (Qiagen).
A set of 1000 target regions of around 300bp in length were preselected for targeted bisulfite sequencing. Primer pairs designed to specifically amplify each selected target region were designed by RainDance Technologies. The ThunderStorm BS-seq assay using that set of primer pairs was performed at RainDance Technologies according to the manufacturer’s specification. That assay uses a microfluidic chip to perform multiplex amplification of bisulfite treated DNA using the set of primers designed to amplify the selected set of genomic regions. This step is followed by sequencing of PCR product. Target regions were sequenced on average to 200X coverage.

value: mcf7/tcell 95/5

value: Cell line mix


title: Day7_Oct4-Venus+_2

tag: cell type


title: mcf7/hmec75/25

description:
target capture DNA
75% MCF7 –25% HMEC (Normal Human Mammary Epithelial Cells)

value: mcf7/hmec 75/25


title: reference male mouse1/ 0GyH2


title: 0GyH2/ reference male mouse1


title: lung cancer tissue and adjcent normal tissue from patient 1

description: Stage 1 samples

source_name: lung cancer tissue 1

value: Male

source_name: lung adjcent normal tissue 1


title: Candida albicans-systemic mouse infection-kidney-12h_rep4

source_name: common reference, log-phase growth in YPD, 37°C

value: common reference

value: kidney


title: lung cancer tissue and adjcent normal tissue from patient 3

description: Stage 1 samples

source_name: lung cancer tissue 3

source_name: lung adjcent normal tissue 3


title: reference male mouse1/ 0GyH6

value: tail


title: lung cancer tissue and adjcent normal tissue from patient 4

description: Stage 1 samples

source_name: lung cancer tissue 4

value: II

source_name: lung adjcent normal tissue 4


title: lung cancer tissue and adjcent normal tissue from patient 5

description: Stage 2 samples

source_name: lung cancer tissue 5

source_name: lung adjcent normal tissue 5


title: mcf7/hmec95/5

description:
target capture DNA
95% MCF7 – 5% HMEC (Normal Human Mammary Epithelial Cells)

value: mcf7/hmec 95/5


title: reference male mouse1/ 0GyH5

source_name: reference male mouse1


title: lung cancer tissue and adjcent normal tissue from patient 2

description: Stage 1 samples

source_name: lung cancer tissue 2

value: IV

source_name: lung adjcent normal tissue 2


title: mcf7/fibro 75/25

description:
target capture DNA
75% MCF7 – 25% cancer associated fibroblast

value: mcf7/fibro 75/25


title: mcf7/fibro95/5

description:
target capture DNA
95% MCF7 – 5% cancer associated fibroblast

value: mcf7/fibro 95/5


title: mcf7/tcell 75/25

description:
target capture DNA
75% MCF7 – 25% T-cell (CD8+ T-cells)

value: mcf7/tcell 75/25


title: t47d

description: target capture DNA

source_name: ATCC

value: Breast

value: Tumor Cell line

tag: subtype

value: Luminal


title: MDA MB231

description: target capture DNA

value: Basal


title: CD8+ T cells

description: target capture DNA

source_name: Sanguine

value: T cells

value: Normal T Cells

value: Normal T


title: reference male mouse1/ 0GyH3

tag: strain


title: lung cancer tissue and adjcent normal tissue from patient 6

description: Stage 2 samples

source_name: lung cancer tissue 6

value: lung cancer tissue

value: Male

source_name: lung adjcent normal tissue 6

value: lung normal tissue


title: 0GyH3/ reference male mouse1

value: tail


title: HCC1569

description: target capture DNA


title: reference male mouse1/ 0GyH1


title: 0GyHF/ reference male mouse1


title: reference male mouse1/ 0GyHF


title: HSTB29

description: target capture DNA

source_name: Tumor Bank

value: Tumor

value: ER+


title: TCGA20

description: target capture DNA

source_name: TCGA

value: ER-


title: TCGA12

description: target capture DNA


title: mcf7

description: target capture DNA


title: MDA MB 361

description: target capture DNA


title: ESC_1

description:
Gene expression data from undifferentiated mouse embryonic stem cells (Oct4-Venus+ fraction)
OLV2-1 cell line, Oct4-Venus+ fraction, sorted by FACS

source_name: mouse_embryonic_stem_cell, sorted by FACS

value: undifferentiated

value: undifferentiated ESCs

value: Oct4-Venus+ fraction


title: HCC1954

description: target capture DNA

value: Breast


title: fibroblasts

description: target capture DNA

source_name: Asterand

value: Cancer Asso. Fibroblasts


title: HSTB30

description: target capture DNA


title: TCGA5

description: target capture DNA

value: Normal

value: adjacent to ER+


title: 0GyH1/ reference male mouse1


title: TCGA15

description: target capture DNA


title: TCGA9

description: target capture DNA


title: TCGA18

description: target capture DNA


title: TCGA16

description: target capture DNA


title: HSTB6

description: target capture DNA


title: TCGA3

description: target capture DNA


title: HSTB7

description: target capture DNA


title: HSTB8

description: target capture DNA


title: reference male mouse1/ 0GyHM


title: HSTB5

description: target capture DNA


title: 0GyHM/ reference male mouse1


title: TCGA6

description: target capture DNA


title: HSTB12

description: target capture DNA


title: HSTB28

description: target capture DNA


title: HSTB26

description: target capture DNA


title: HSTB27

description: target capture DNA


title: HSTB2

description: target capture DNA


title: HSTB18

description: target capture DNA


title: HSTB4

description: target capture DNA


title: HSTB22

description: target capture DNA


title: HSTB19

description: target capture DNA

value: adjacent to ER-


title: HSTB25

description: target capture DNA


title: HSTB20

description: target capture DNA


title: HSTB24

description: target capture DNA


title: HSTB23

description: target capture DNA


title: HSTB21

description: target capture DNA


title: HSTB10

description: target capture DNA


title: HSTB14

description: target capture DNA


title: HSTB16

description: target capture DNA


title: HSTB13

description: target capture DNA


title: HSTB11

description: target capture DNA


title: HSTB9

description: target capture DNA