title: Malignant glioma clone U3117MG-C333

source_name: Malignant glioma clone U3117MG-C333


title: Malignant glioma clone U3117MG-C596

status: Public on Dec 13 2016

type: RNA

city: Uppsala

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

country: Sweden

institute: Uppsala University

hyb_protocol: GeneChip® Human Transcriptome Array 2.0 were hybridized for 16 hours in a 45°C incubator. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450

scan_protocol: scanned using the GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings with the Robust Multiarray Averaging (RMA) algorithm.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Malignant glioma clone U3117MG-C596

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: adherent cultures on laminin-coated dishes using neural stem cell media

extract_protocol: RNeasy Plus Mini Kit, QIAGEN

tag: cell type

value: Malignant glioma clone

tag: cell line


title: Malignant glioma clone U3117MG-C563

source_name: Malignant glioma clone U3117MG-C563


title: patient 3.012|Post 1 vaccination IgM

type: protein

city: Frederick

first: Jeff

last: Gildersleeve

state: MD

address: 376 Boyles St.

country: USA

institute: National Cancer Institute

description:
3.012_V2
IgM

hyb_protocol: Arrays were blocked with 3% BSA in PBS buffer for overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000B fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG.  Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

data_processing: First, median pixel intensity of each feature was background subtracted.  Second, signals for features that were saturated at the high photomultipler tube (PMT) setting were calculated by proportionally scaling the value from the low PMT setting according to a correction factor, which was calculated based on mid-intensity signals measured at the high and low PMT settings.  To account for slide-to-slide variations in array processing, microarray data were normalized by median centering based on a reference serum sample analyzed on each slide.  Additionally, a minimum signal of 150 was set as the floor.  Since array features were printed in duplicate and all samples were analyzed on two slides, pre-processing averaged normalized data from 4 technical replicates.  Final data are reported on a log 2 scale.

label: DyLight 649

molecule: protein

source_name: Serum

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti-human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM  (Jackson Immuno, 109-495-043).

extract_protocol: Serum was obtained from peripheral blood samples

treatment_protocol: Diluted 1:50

tag: time point

value: Post 1 vaccination

tag: survival months

tag: event at time of survival analysis

value: Alive


title: patient 3.010|Post 1 vaccination IgM

description:
3.010_V2
IgM


title: Malignant glioma clone U3117MG-C534

source_name: Malignant glioma clone U3117MG-C534


title: Malignant glioma clone U3117MG-C22-repl1

source_name: Malignant glioma clone U3117MG-C22


title: Malignant glioma clone U3117MG-C492

source_name: Malignant glioma clone U3117MG-C492


title: Malignant glioma clone U3117MG-C585

source_name: Malignant glioma clone U3117MG-C585


title: Malignant glioma clone U3117MG-C351

source_name: Malignant glioma clone U3117MG-C351


title: Malignant glioma clone U3117MG-C534-repl1


title: Malignant glioma clone U3117MG-C612-repl1

source_name: Malignant glioma clone U3117MG-C612


title: patient 3.009|Post 1 vaccination IgM

description:
3.009_V2
IgM


title: Malignant glioma clone U3117MG-C585-repl1


title: Malignant glioma clone U3117MG-C333-repl1


title: Malignant glioma clone U3117MG-C75-repl1

source_name: Malignant glioma clone U3117MG-C75


title: patient 3.005|Post 1 vaccination IgM

description:
3.005_V2
IgM

value: Deceased


title: Malignant glioma clone U3117MG-C274

source_name: Malignant glioma clone U3117MG-C274


title: Malignant glioma clone U3117MG-C264

source_name: Malignant glioma clone U3117MG-C264


title: Malignant glioma clone U3117MG-C283

source_name: Malignant glioma clone U3117MG-C283


title: patient 3.004|Post 1 vaccination IgM

description:
3.004_V2
IgM


title: Malignant glioma clone U3117MG-C232

source_name: Malignant glioma clone U3117MG-C232


title: patient 3.060|Pre-vaccination IgM

description:
3.060_V1
IgM

value: Pre-vaccination


title: patient 3.059|Pre-vaccination IgM

description:
3.059_V1
IgM


title: patient 3.054|Pre-vaccination IgM

description:
3.054_V1
IgM


title: patient 3.053|Pre-vaccination IgM

description:
3.053_V1
IgM


title: patient 3.052|Pre-vaccination IgM

description:
3.052_V1
IgM


title: Malignant glioma clone U3117MG-C174

source_name: Malignant glioma clone U3117MG-C174


title: Malignant glioma clone U3117MG-C173

source_name: Malignant glioma clone U3117MG-C173


title: patient 3.051|Pre-vaccination IgM

description:
3.051_V1
IgM


title: Malignant glioma clone U3117MG-C86

source_name: Malignant glioma clone U3117MG-C86


title: Malignant glioma clone U3121MG-C133

source_name: Malignant glioma clone U3121MG-C133


title: Malignant glioma clone U3117MG-C40

source_name: Malignant glioma clone U3117MG-C40


title: Malignant glioma clone U3121MG-C203

source_name: Malignant glioma clone U3121MG-C203


title: Malignant glioma clone U3121MG-C207

source_name: Malignant glioma clone U3121MG-C207


title: Malignant glioma clone U3121MG-C227

source_name: Malignant glioma clone U3121MG-C227


title: patient 3.047|Pre-vaccination IgM

description:
3.047_V1
IgM

source_name: Serum


title: Malignant glioma clone U3117MG-C48

source_name: Malignant glioma clone U3117MG-C48


title: Malignant glioma clone U3118MG-C849-repl1

source_name: Malignant glioma clone U3118MG-C849


title: Malignant glioma clone U3117MG-C22

source_name: Malignant glioma clone U3117MG-C22


title: Malignant glioma clone U3121MG-C109

source_name: Malignant glioma clone U3121MG-C109


title: Malignant glioma cell line U3121MG

source_name: Malignant glioma cell line U3121MG

value: Malignant glioma cell line


title: Malignant glioma clone U3121MG-C187

source_name: Malignant glioma clone U3121MG-C187


title: patient 3.044|Pre-vaccination IgM

description:
3.044_V1
IgM


title: Malignant glioma clone U3118MG-C81-repl1

source_name: Malignant glioma clone U3118MG-C81


title: patient 3.043|Pre-vaccination IgM

description:
3.043_V1
IgM


title: Malignant glioma clone U3118MG-C92-repl1

source_name: Malignant glioma clone U3118MG-C92


title: patient 3.041|Pre-vaccination IgM

description:
3.041_V1
IgM


title: Malignant glioma clone U3118MG-C200-repl1

source_name: Malignant glioma clone U3118MG-C200


title: Malignant glioma clone U3118MG-C220-repl1

source_name: Malignant glioma clone U3118MG-C220


title: Malignant glioma clone U3118MG-C410-repl1

source_name: Malignant glioma clone U3118MG-C410


title: Malignant glioma clone U3118MG-C508-repl1

source_name: Malignant glioma clone U3118MG-C508


title: Malignant glioma clone U3118MG-C38-repl1

source_name: Malignant glioma clone U3118MG-C38


title: Malignant glioma clone U3118MG-C688-repl1

source_name: Malignant glioma clone U3118MG-C688


title: Malignant glioma clone U3118MG-C736-repl1

source_name: Malignant glioma clone U3118MG-C736


title: patient 3.039|Pre-vaccination IgM

description:
3.039_V1
IgM


title: Malignant glioma cell line U3118MG-repl1

source_name: Malignant glioma cell line U3118MG


title: patient 3.037|Pre-vaccination IgM

description:
3.037_V1
IgM

source_name: Serum


title: patient 3.033|Pre-vaccination IgM

description:
3.033_V1
IgM


title: patient 3.032|Pre-vaccination IgM

description:
3.032_V1
IgM


title: Malignant glioma clone U3117MG-C262

source_name: Malignant glioma clone U3117MG-C262


title: Malignant glioma cell line U3118MG-repl2


title: patient 3.031|Pre-vaccination IgM

description:
3.031_V1
IgM


title: Malignant glioma clone U3118MG-C92


title: Malignant glioma clone U3118MG-C906

source_name: Malignant glioma clone U3118MG-C906


title: patient 3.029|Pre-vaccination IgM

description:
3.029_V1
IgM


title: Malignant glioma cell line U3118MG


title: Malignant glioma clone U3118MG-C89

source_name: Malignant glioma clone U3118MG-C89


title: patient 3.028|Pre-vaccination IgM

description:
3.028_V1
IgM


title: Malignant glioma clone U3118MG-C861

source_name: Malignant glioma clone U3118MG-C861


title: patient 3.027|Pre-vaccination IgM

description:
3.027_V1
IgM


title: Malignant glioma clone U3118MG-C849

source_name: Malignant glioma clone U3118MG-C849


title: patient 3.025|Pre-vaccination IgM

description:
3.025_V1
IgM


title: Malignant glioma clone U3118MG-C81


title: Malignant glioma clone U3118MG-C736


title: patient 3.023|Pre-vaccination IgM

description:
3.023_V1
IgM


title: Malignant glioma clone U3118MG-C895

source_name: Malignant glioma clone U3118MG-C895


title: p-Cont

city: Zunyi

first: Lin

last: Xu

state: Guizhou

address: 201 Dalian Road

department: Immunology

country: China

institute: Zunyi Medical College

description: Gene expression in lung cancer tissue in p-Cont injection group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: tumor tissue, after 3 days of last injection of p-Cont

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Tumor mass were collected from human lung cancer xenograft model in nude mice

extract_protocol: Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.then,Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.last,At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: Human lung cancer cell line 95D cells were injected subcutaneously into right flank of Balb/c nude mice (n=8). 7 days later, the plasmid of p-T-miR-7 (100mg) or p-Cont (100mg) was remote given by subcutaneous injection into the left flank of nude mice five times every three days.

tag: host strain

value: Balb/c nude mice

value: Human lung cancer cell line 95D cells

tag: received

value: p-Cont (100mg) plasmid

tag: tissue

value: tumor


title: Control untreated fibroblasts [UT3]

city: Houston

first: Marco

last: Sardiello

state: Texas

address: 1250 Moursund St.

department: Molecular and Human Genetics

institute: Baylor College of Medicine at Neurological Research Institute Texas Children Hospital

hyb_protocol: An aliquot of 750 nanograms of amplified products were loaded onto Illumina Sentrix Beadchip Array human HT12_v4 arrays, hybridized at 58ºC in an Illumina Hybridization Oven (Illumina, Cat# 198361) for 17 hours, washed and incubated with straptavidin-Cy3 to detect biotin-labeled cRNA on the arrays.

scan_protocol: After hybridization arrays were dried and scanned with BeadArray Reader (Illumina, CA)

data_processing: Data were analyzed using GenomeStudio software (Illumina, CA). Clustering and pathway analysis were performed with GenomeStudio and Ingenuity Pathway Analysis (Ingenuity Systems, Inc.) softwares respectively.

source_name: Human fibroblasts

label_protocol: Biotinylated cRNA was synthesized by 14-hour amplification with dNTP mix containing biotin-dUTP and T7 RNA polymerase.

growth_protocol: Control and JNCL fibroblasts were growth in DMEM with10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin.

extract_protocol: Three hundred nanograms of total RNA were amplified and purified using Illumina TotalPrep RNA Amplification Kit (Ambion, cat# IL1791) following kit instructions.

treatment_protocol: Control and JNCL fibroblasts were treated with 100 mM of trehalose for 4 days.

tag: treatment

value: Untreated


title: Malignant glioma clone U3167MG-C778

type: genomic

hyb_protocol: standard protocols for Affymetrix Cytoscan™ HD arrays (Affymetrix® Cytoscan User Guide (P/N 703038 Rev4.) Hybridized probes were captured by streptavidin-phycoerythrin conjugates using the GeneChip® Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G

data_processing:
Affymetrix® Chromosome Analysis Suite (ChAS) 2.0. Affymetrix-algorithm-name = CYTO2. Affymetrix-algorithm-version = 1.16.0. program-name = apt-copynumber-cyto.exe
Affymetrix CytoScan HD array of 30 clonal malignant glioma cultures and 6 bulk cultures representing the parental material used to derive clones.

molecule: genomic DNA

source_name: Malignant glioma clone U3167MG-C778

label_protocol: 250 ng total genomic DNA was digested with the restriction enzyme Nsp I, then ligated to an Nsp I adaptor and further subjected to PCR amplification using a single primer. After fragmentation, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase (TdT)

extract_protocol: Dneasy blood and tissue kit (Qiagen)


title: patient 3.016|Pre-vaccination IgM

description:
3.016_V1
IgM


title: p-T-miR-7

description: Gene expression in lung cancer tissue in p-T-miR-7 injection group

source_name: tumor tissue, after 3 days of last injection of p-T-miR-7

value: p-T-miR-7 (100mg) plasmid


title: Malignant glioma clone U3167MG-C670

source_name: Malignant glioma clone U3167MG-C670


title: Malignant glioma clone U3117MG-C232

source_name: Malignant glioma clone U3117MG-C232


title: Malignant glioma clone U3167MG-C390

source_name: Malignant glioma clone U3167MG-C390


title: Malignant glioma clone U3118MG-C694

source_name: Malignant glioma clone U3118MG-C694


title: Malignant glioma clone U3118MG-C696

source_name: Malignant glioma clone U3118MG-C696


title: Malignant glioma clone U3117MG-C75

source_name: Malignant glioma clone U3117MG-C75


title: Malignant glioma clone U3167MG-C500

source_name: Malignant glioma clone U3167MG-C500


title: Control untreated fibroblasts [UT1]


title: Control untreated fibroblasts [UT2]


title: Malignant glioma clone U3117MG-C75


title: patient 3.012|Pre-vaccination IgM

description:
3.012_V1
IgM

source_name: Serum


title: Control treated fibroblasts [TR3]

value: 100 mM of trehalose


title: patient 3.013|Pre-vaccination IgM

description:
3.013_V1
IgM


title: Malignant glioma clone U3167MG-C723

source_name: Malignant glioma clone U3167MG-C723


title: patient 3.015|Pre-vaccination IgM

description:
3.015_V1
IgM


title: Malignant glioma clone U3065MG-C475

source_name: Malignant glioma clone U3065MG-C475


title: patient 3.010|Pre-vaccination IgM

description:
3.010_V1
IgM


title: Malignant glioma clone U3167MG-C173

source_name: Malignant glioma clone U3167MG-C173


title: Malignant glioma clone U3065MG-C466

source_name: Malignant glioma clone U3065MG-C466


title: patient 3.009|Pre-vaccination IgM

description:
3.009_V1
IgM


title: Malignant glioma clone U3118MG-C440

source_name: Malignant glioma clone U3118MG-C440


title: Malignant glioma clone U3118MG-C508

source_name: Malignant glioma clone U3118MG-C508


title: Malignant glioma clone U3118MG-C553

source_name: Malignant glioma clone U3118MG-C553


title: Malignant glioma clone U3065MG-C78

source_name: Malignant glioma clone U3065MG-C78


title: patient 3.004|Pre-vaccination IgM

description:
3.004_V1
IgM


title: Malignant glioma clone U3118MG-C424

source_name: Malignant glioma clone U3118MG-C424


title: Malignant glioma clone U3065MG-C94

source_name: Malignant glioma clone U3065MG-C94


title: JNCL treated fibroblasts [BT3]

source_name: Human fibroblasts


title: JNCL treated fibroblasts [BT2]


title: Control treated fibroblasts [TR1]


title: Malignant glioma clone U3118MG-C688

source_name: Malignant glioma clone U3118MG-C688


title: Malignant glioma clone U3065MG-C113

source_name: Malignant glioma clone U3065MG-C113


title: Malignant glioma clone U3065MG-C28

source_name: Malignant glioma clone U3065MG-C28


title: Malignant glioma clone U3065MG-C271

source_name: Malignant glioma clone U3065MG-C271


title: Malignant glioma clone U3065MG-C482

source_name: Malignant glioma clone U3065MG-C482


title: Malignant glioma clone U3118MG-C410

source_name: Malignant glioma clone U3118MG-C410


title: Malignant glioma clone U3118MG-C38

source_name: Malignant glioma clone U3118MG-C38


title: patient 3.060|Post 3 vaccinations IgG

description:
3.060_V4
IgG

source_name: Serum

value: Week 48


title: patient 3.059|Post 3 vaccinations IgG

description:
3.059_V4
IgG


title: patient 3.054|Post 3 vaccinations IgG

description:
3.054_V4
IgG


title: JNCL treated fibroblasts [BT1]


title: Malignant glioma clone U3065MG-C34

source_name: Malignant glioma clone U3065MG-C34


title: patient 3.053|Post 3 vaccinations IgG

description:
3.053_V4
IgG


title: Malignant glioma clone U3118MG-C348

source_name: Malignant glioma clone U3118MG-C348


title: JNCL untreated fibroblasts [B3]


title: Malignant glioma clone U3118MG-C694

source_name: Malignant glioma clone U3118MG-C694


title: JNCL untreated fibroblasts [B2]


title: Malignant glioma clone U3118MG-C335

source_name: Malignant glioma clone U3118MG-C335


title: JNCL untreated fibroblasts [B1]


title: Malignant glioma clone U3065MG-C95

source_name: Malignant glioma clone U3065MG-C95


title: patient 3.005|Pre-vaccination IgM

description:
3.005_V1
IgM


title: Malignant glioma clone U3118MG-C358

source_name: Malignant glioma clone U3118MG-C358


title: Malignant glioma clone U3065MG-C46

source_name: Malignant glioma clone U3065MG-C46


title: Control treated fibroblasts [TR2]


title: Malignant glioma clone U3118MG-C29

source_name: Malignant glioma clone U3118MG-C29


title: patient 3.047|Post 3 vaccinations IgG

description:
3.047_V4
IgG


title: patient 3.051|Post 3 vaccinations IgG

description:
3.051_V4
IgG


title: patient 3.044|Post 3 vaccinations IgG

description:
3.044_V4
IgG


title: Malignant glioma clone U3118MG-C219

source_name: Malignant glioma clone U3118MG-C219


title: patient 3.043|Post 3 vaccinations IgG

description:
3.043_V4
IgG


title: hiPSC_definitive _orthochromatic_erythroblast_rep3

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix Human Gene ST array plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were extracted and normalized using Affymetrix Power Tools (APT) rma-sketch and analysed using LIMMA.

label: Biotin

source_name: Orthochromatic erythroblasts isolated after further expansion of CD235a+ definitive progenitors on fibronectin, identified as CD117- CD36- CD235a+ CD45-

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: Pluripotent stem cells were differentiated in StemPro34 using a 3 stage protocol as previously published. Haematopoietic progenitor cells from hiPSCs were defined as CD45+ CD235- on day 12 and were then isloated by FACS for further expansion on OP9 stroma in alpha-MEM, 10%FCS and erythropoietic factors, EPO, SCF, Flt3L.

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

treatment_protocol: Erythroblasts were isolated by fluorescent activated cell sorting based on particular phenotypes: Primitive erythroblasts were defined as CD31+ CD235+ on day 12 of differentiation; pro-erythroblasts from both hiPSC and cord CD34 haematopoietic progenitor cells were defined as CD117+ CD45+ CD36+ CD235+; erythroblast from both sources were defined as CD36+ CD235+ alone, and ortho-erythroblasts collected after extended culture.

value: An hiPSC derived ortho-chromatic erythroblast that represents a late maturation state of adult erythroblasts


title: patient 3.041|Post 3 vaccinations IgG

description:
3.041_V4
IgG


title: Malignant glioma clone U3118MG-C266

source_name: Malignant glioma clone U3118MG-C266


title: Malignant glioma clone U3118MG-C228

source_name: Malignant glioma clone U3118MG-C228


title: Malignant glioma clone U3118MG-C223

source_name: Malignant glioma clone U3118MG-C223


title: hiPSC_definitive _orthochromatic_erythroblast_rep2


title: Malignant glioma clone U3118MG-C220

source_name: Malignant glioma clone U3118MG-C220


title: hiPSC_definitive _orthochromatic_erythroblast_rep1


title: Malignant glioma clone U3118MG-C219


title: UCB_definitive _orthochromatic_erythroblast_rep2

value: An UCB CD34+ derived ortho-chromatic erythroblast that represents a late maturation state of adult erythroblasts


title: Malignant glioma clone U3118MG-C849

source_name: Malignant glioma clone U3118MG-C849


title: patient 3.039|Post 3 vaccinations IgG

description:
3.039_V4
IgG


title: Malignant glioma clone U3118MG-C192

source_name: Malignant glioma clone U3118MG-C192


title: Malignant glioma clone U3118MG-C150

source_name: Malignant glioma clone U3118MG-C150


title: Malignant glioma clone U3118MG-C200

source_name: Malignant glioma clone U3118MG-C200


title: UCB_definitive _orthochromatic_erythroblast_rep1


title: patient 3.033|Post 3 vaccinations IgG

description:
3.033_V4
IgG

source_name: Serum


title: patient 3.037|Post 3 vaccinations IgG

description:
3.037_V4
IgG


title: patient 3.052|Post 3 vaccinations IgG

description:
3.052_V4
IgG


title: patient 3.032|Post 3 vaccinations IgG

description:
3.032_V4
IgG


title: Malignant glioma clone U3118MG-C180

source_name: Malignant glioma clone U3118MG-C180


title: Malignant glioma clone U3118MG-C150


title: hiPSC_primitive_erythroblast_rep5

source_name: Isolated on day 12 of hiPSC differentiation as CD235a+ CD45- erythroblasts

value: Primitive erythroblasts from hiPSCs represents embryonic erythropoiesis observed before E90 in the mouse embryo


title: hiPSC_primitive_erythroblast_rep4


title: UCB_definitive _erythroblast_rep4

source_name: Isolated on day 14 after continued differentiation of CD34+ progenitors on OP9 stroma

value: Umbillical cord derived CD34+ progenitors contribute definitve erythropoiesis that is observed after E95 in the mouse embryo


title: Malignant glioma clone U3118MG-C688

source_name: Malignant glioma clone U3118MG-C688

value: Malignant glioma clone


title: patient 3.029|Post 3 vaccinations IgG

description:
3.029_V4
IgG

value: Alive


title: patient 3.028|Post 3 vaccinations IgG

description:
3.028_V4
IgG

value: Deceased


title: Malignant glioma clone U3118MG-C200


title: patient 3.027|Post 3 vaccinations IgG

description:
3.027_V4
IgG


title: UCB_definitive _erythroblast_rep3


title: Malignant glioma clone U3118MG-C906

source_name: Malignant glioma clone U3118MG-C906


title: Malignant glioma cell line U3065MG-repl1

source_name: Malignant glioma cell line U3065MG


title: hiPSC_definitive _pro-erythroblast_rep5

source_name: Isolated after further expansion of CD235a+ definitive progenitors on fibronectin, identified as CD117+ CD36+ CD235a+ CD45+

value: An hiPSC derived pro-erythroblast that represents an early maturation state of adult erythroblasts


title: patient 3.025|Post 3 vaccinations IgG

description:
3.025_V4
IgG


title: Malignant glioma clone U3118MG-C182

source_name: Malignant glioma clone U3118MG-C182


title: patient 3.023|Post 3 vaccinations IgG

description:
3.023_V4
IgG


title: Malignant glioma clone U3065MG-C475-repl1

source_name: Malignant glioma clone U3065MG-C475


title: hiPSC_definitive _pro-erythroblast_rep2


title: Malignant glioma clone U3118MG-C508

source_name: Malignant glioma clone U3118MG-C508


title: Malignant glioma clone U3065MG-C46-repl1

source_name: Malignant glioma clone U3065MG-C46


title: hiPSC_definitive _pro-erythroblast_rep3


title: patient 3.016|Post 3 vaccinations IgG

description:
3.016_V4
IgG


title: patient 3.015|Post 3 vaccinations IgG

description:
3.015_V4
IgG


title: Malignant glioma cell line U3065MG

value: Malignant glioma cell line


title: patient 3.013|Post 3 vaccinations IgG

description:
3.013_V4
IgG


title: Malignant glioma clone U3118MG-C92

source_name: Malignant glioma clone U3118MG-C92


title: Malignant glioma clone U3065MG-C95

source_name: Malignant glioma clone U3065MG-C95


title: hiPSC_definitive _pro-erythroblast_rep1


title: Malignant glioma clone U3065MG-C94

source_name: Malignant glioma clone U3065MG-C94


title: UCB_definitive _pro-erythroblast_rep3

value: An umbillical cord derived pro-erythroblast that represents an early maturation state of adult erythroblasts


title: patient 3.012|Post 3 vaccinations IgG

description:
3.012_V4
IgG


title: UCB_definitive _pro-erythroblast_rep4


title: Malignant glioma clone U3065MG-C80

source_name: Malignant glioma clone U3065MG-C80


title: Malignant glioma clone U3118MG-C736

source_name: Malignant glioma clone U3118MG-C736


title: hiPSC_definitive _pro-erythroblast_rep4


title: UCB_definitive _pro-erythroblast_rep2


title: patient 3.031|Post 3 vaccinations IgG

description:
3.031_V4
IgG

source_name: Serum


title: Malignant glioma clone U3065MG-C90

source_name: Malignant glioma clone U3065MG-C90


title: patient 3.010|Post 3 vaccinations IgG

description:
3.010_V4
IgG


title: UCB_definitive _pro-erythroblast_rep1


title: patient 3.005|Post 3 vaccinations IgG

description:
3.005_V4
IgG


title: Malignant glioma clone U3065MG-C60

source_name: Malignant glioma clone U3065MG-C60


title: Malignant glioma cell line U3121MG

source_name: Malignant glioma cell line U3121MG


title: patient 3.004|Post 3 vaccinations IgG

description:
3.004_V4
IgG


title: patient 3.009|Post 3 vaccinations IgG

description:
3.009_V4
IgG


title: Malignant glioma clone U3118MG-C38

source_name: Malignant glioma clone U3118MG-C38


title: patient 3.060|Post 1 vaccination IgG

description:
3.060_V2
IgG

value: Week 40


title: hiPSC_definitive _erythroblast_rep3

source_name: Isolated on day 14 after continued differentiation of CD235a- CD45+ progenitors on OP9 stroma

value: hiPSC derived CD45+ progenitors contribute definitve erythropoiesis that is observed after E95 in the mouse embryo


title: hiPSC_definitive _erythroblast_rep4


title: patient 3.054|Post 1 vaccination IgG

description:
3.054_V2
IgG


title: patient 3.059|Post 1 vaccination IgG

description:
3.059_V2
IgG


title: patient 3.053|Post 1 vaccination IgG

description:
3.053_V2
IgG


title: Malignant glioma clone U3065MG-C482

source_name: Malignant glioma clone U3065MG-C482


title: Malignant glioma clone U3065MG-C78

source_name: Malignant glioma clone U3065MG-C78


title: Malignant glioma clone U3065MG-C494

source_name: Malignant glioma clone U3065MG-C494


title: hiPSC_definitive _erythroblast_rep2


title: hiPSC_definitive _erythroblast_rep1


title: patient 3.052|Post 1 vaccination IgG

description:
3.052_V2
IgG


title: Malignant glioma clone U3065MG-C46


title: patient 3.051|Post 1 vaccination IgG

description:
3.051_V2
IgG


title: Malignant glioma cell line U3017MG

source_name: Malignant glioma cell line U3017MG


title: Malignant glioma cell line U3167MG

source_name: Malignant glioma cell line U3167MG


title: UCB_definitive _erythroblast_rep2

source_name: Isolated on day 14 after continued differentiation of CD34+ progenitors on OP9 stroma


title: Malignant glioma clone U3065MG-C466

source_name: Malignant glioma clone U3065MG-C466


title: patient 3.047|Post 1 vaccination IgG

description:
3.047_V2
IgG


title: Malignant glioma clone U3065MG-C34

source_name: Malignant glioma clone U3065MG-C34


title: UCB_definitive _erythroblast_rep1


title: Malignant glioma cell line U3065MG

source_name: Malignant glioma cell line U3065MG


title: Malignant glioma clone U3065MG-C475

source_name: Malignant glioma clone U3065MG-C475


title: Malignant glioma clone U3065MG-C349

source_name: Malignant glioma clone U3065MG-C349


title: patient 3.044|Post 1 vaccination IgG

description:
3.044_V2
IgG

source_name: Serum


title: Malignant glioma cell line U3118MG

source_name: Malignant glioma cell line U3118MG


title: hiPSC_primitive_erythroblast_rep2

source_name: Isolated on day 12 of hiPSC differentiation as CD235a+ CD45- erythroblasts


title: Malignant glioma cell line U3117MG

source_name: Malignant glioma cell line U3117MG


title: patient 3.043|Post 1 vaccination IgG

description:
3.043_V2
IgG


title: patient 3.041|Post 1 vaccination IgG

description:
3.041_V2
IgG


title: Malignant glioma clone U3065MG-C28

source_name: Malignant glioma clone U3065MG-C28


title: patient 3.039|Post 1 vaccination IgG

description:
3.039_V2
IgG


title: hiPSC_primitive_erythroblast_rep1


title: tyd36D2T1

city: Pretoria

first: LynMarie

last: Birkholtz

state: Gauteng

address: c/o Lunnon Road and Heroldt Street, Hatifeld

department: Biochemistry

country: South Africa

institute: University of Pretoria

description: 3D7 Mixed Stage asexual with and without DFMO treatment and putrescine reversal

hyb_protocol: Van Brummelen AC, Olszewski KL, Wilinski D, Llinás M, Louw AI, Birkholtz L, Co-inhibition of Plasmodium falciparum S -Adenosylmethionine Decarboxylase / Ornithine Decarboxylase Reveals Perturbation-specific Compensatory Mechanisms by Transcriptome, Proteome, and Metabolome Analyses. J Biol Chem. 2009;284:4635–46.

scan_protocol: Axon GenePix 4000B Scanner. Images were quantified using GenePix Pro 5.1 (Acuity) software.

data_processing: GenePix Pro 5.1 (Acuity) was used for background subtraction and the Bioconductor, limma, and marray packages in R 3.2.3 were used for within and between-slide normalisation

organism: Plasmodium falciparum

source_name: PF3D7 DFMO 36h RNA

growth_protocol: P. falciparum (3D7 parasites (MRA-102 from MR4, www.mr4.org) were maintained with shaking at 37°C in human erythrocytes, suspended at 5% hematocrit in complete culture medium [RPMI 1640 medium (Sigma-Aldrich) supplemented with 25 mM HEPES (Sigma-Aldrich), 20 mM D-glucose (Sigma-Aldrich), 200 μM hypoxanthine (Sigma-Aldrich), 0.2% (w/v) sodium bicarbonate, 24 μg/ml Gentamycin (Sigma-Aldrich) and 0.5% (w/v) AlbuMAX II] under hypoxic conditions (90% N2, 5% O2, and 5% CO2). Parasite development was monitored with light microscopy through Giemsa staining and parasites were synchronized by repetitive rounds of iso-osmotic sorbitol exposure to obtain >95% synchronization.

treatment_protocol: For the arrested parasites, synchronised ring-stage (approximately 2 hours post merozoite invasion) parasitised erythrocytes (5% haematocrit, 10% parasitaemia) were incubated with IC90 DFMO at 37˚C. Untreated parasite culture was maintained in parallel. Aliquots (15 ml) of parasite culture were removed at 21 and 29 hours post-treatment, washed once with 1x PBS. Pelleted parasitised erythrocytes were subsequently stored at -70°C. For the rescued parasites, synchronised ring-stage parasitised erythrocytes (1% haematocrit, 16% parasitaemia) were incubated with IC90 DFMO at 37˚C for 24 h prior to the addition of putrescine dihydrochloride (2 mM) to induce the onset of the cell cycle. Aliquots (50 ml) of the parasite culture were removed at 27, 30 and 36 hours post treatment, washed twice with 1x PBS and snap frozen in liquid nitrogen, before storing the samples at -70˚C until use.

tag: strain

tag: time after treatment (and reversal) in hours

value: 2mM DFMO for 36 hr

tag: Stage

value: trophozoite

source_name: 3D7 Mixed Stage asexual treated with DFMO, DFMO and Putrescine and untreated parasite Reference Pool


title: 1-ANG

city: Hangzhou

first: Chunhua

last: Weng

address: 866 Yuhang-Tang Road

department: School of Medicine

institute: Zhejiang University

description: Test

data_processing:
Ct values were calculated by SDS 1.2 software (Applied Biosystems) and normalized to MammU6 (miRNA) housekeeping Ct values and expressed as 2-(Ct[microRNA]—Ct[U6])
Fold Change worksheet reports test/control (i.e., ANG/Control) ratios.

label: FAM

source_name: Human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs), passages 3 to 8. HUVECs were cultured in modified endothelial cell growth medium containing 52% M199 medium (Life Technologies), 36% Human Endothelial-SFM (Life Technologies), 10% fetal bovine serum (Life Technologies) and 15 μg/ml endothelial cell growth supplement (Millipore).

extract_protocol: Collect cells with trypsin and washed with PBS, then resuspend in PBS at a density of 2×10E7/ml. Take 10 ul cell suspension and lyse in 90 ul lysis buffer (Tris 15 mM, NaCl 10 mM, MgCl2 3 mM, NP-40 0.3%) for 10 min on ice, and then heat at 99°C for 10 min. Sit the lysate on ice after heating. Take 6 ul lysate as the reverse transcription template. Reverse transcription was performed using Human MegaPlex RT Primer pools. cDNA was amplified using human MegaPlex PreAmp Primer Pools and PreAmp Master mix.The amplified samples were loaded into Taqman microRNA arrays Pool A (377 miRNAs) and pool B (373 miRNAs). Analysed using the 7900 Real Time PCR System (Applied Biosystems)

treatment_protocol: HUVECs were cultured at a density of 5,000 cells/cm2 at 37 °C and starved overnight. Subsequently, they were incubated with  ANG protein (final concentration 1 μg/ml ) or PBS for 6 hr.

value: Human umbilical vein endothelial cells

tag: agent

value: ANG

tag: time


title: 2-Control

description: Control

value: PBS


title: 2-ANG

description: Test


title: tyd36D2T2

label_protocol: Van Brummelen AC, Olszewski KL, Wilinski D, Llinás M, Louw AI, Birkholtz L, Co-inhibition of Plasmodium falciparum S -Adenosylmethionine Decarboxylase / Ornithine Decarboxylase Reveals Perturbation-specific Compensatory Mechanisms by Transcriptome, Proteome, and Metabolome Analyses. J Biol Chem. 2009;284:4635–46.


title: patient 3.037|Post 1 vaccination IgG

description:
3.037_V2
IgG


title: Malignant glioma clone U3065MG-C271

source_name: Malignant glioma clone U3065MG-C271


title: 1-Control

description: Control


title: tyd36D1T2

extract_protocol: Van Brummelen AC, Olszewski KL, Wilinski D, Llinás M, Louw AI, Birkholtz L, Co-inhibition of Plasmodium falciparum S -Adenosylmethionine Decarboxylase / Ornithine Decarboxylase Reveals Perturbation-specific Compensatory Mechanisms by Transcriptome, Proteome, and Metabolome Analyses. J Biol Chem. 2009;284:4635–46.


title: tyd36DP2T2

source_name: PF3D7 DFMO 24h+Putrescine 12h RNA

value: 2mM DFMO for 24 hr and 12 hr subsequent 2mM putrescine addition


title: tyd36D1T1


title: patient 3.032|Post 1 vaccination IgG

description:
3.032_V2
IgG


title: Malignant glioma clone U3118MG-C130

source_name: Malignant glioma clone U3118MG-C130


title: Malignant glioma clone U3065MG-C106

source_name: Malignant glioma clone U3065MG-C106


title: patient 3.031|Post 1 vaccination IgG

description:
3.031_V2
IgG


title: Malignant glioma clone U3065MG-C113

source_name: Malignant glioma clone U3065MG-C113


title: Malignant glioma clone U3065MG-C179

source_name: Malignant glioma clone U3065MG-C179


title: patient 3.029|Post 1 vaccination IgG

description:
3.029_V2
IgG


title: patient 3.033|Post 1 vaccination IgG

description:
3.033_V2
IgG


title: patient 3.028|Post 1 vaccination IgG

description:
3.028_V2
IgG


title: tyd36DP2T1


title: Malignant glioma clone U3065MG-C161

source_name: Malignant glioma clone U3065MG-C161


title: Malignant glioma cell line U3017MG

source_name: Malignant glioma cell line U3017MG


title: Malignant glioma clone U3065MG-C239

source_name: Malignant glioma clone U3065MG-C239


title: patient 3.027|Post 1 vaccination IgG

description:
3.027_V2
IgG

source_name: Serum


title: tyd36DP1T1


title: patient 3.025|Post 1 vaccination IgG

description:
3.025_V2
IgG


title: tyd36DP1T2


title: tyd30D2T1

source_name: PF3D7 DFMO 30h RNA

value: 2mM DFMO for 30 hr post


title: tyd30D1T2


title: tyd30D1T1


title: tyd30D2T2


title: patient 3.023|Post 1 vaccination IgG

description:
3.023_V2
IgG


title: tyd30DP2T1

source_name: PF3D7 DFMO 24h+Putrescine 6h RNA

value: 2mM DFMO for 24hr and 6h subsequent 2mM putrescine addition


title: tyd30DP2T2


title: patient 3.016|Post 1 vaccination IgG

description:
3.016_V2
IgG


title: patient 3.015|Post 1 vaccination IgG

description:
3.015_V2
IgG


title: Malignant glioma clone U3017MG-C48

source_name: Malignant glioma clone U3017MG-C48


title: Malignant glioma clone U3017MG-C5

source_name: Malignant glioma clone U3017MG-C5


title: Malignant glioma clone U3017MG-C53

source_name: Malignant glioma clone U3017MG-C53


title: Malignant glioma clone U3017MG-C3

source_name: Malignant glioma clone U3017MG-C3


title: Malignant glioma clone U3017MG-C33

source_name: Malignant glioma clone U3017MG-C33


title: Malignant glioma clone U3017MG-C43

source_name: Malignant glioma clone U3017MG-C43


title: patient 3.013|Post 1 vaccination IgG

description:
3.013_V2
IgG


title: tyd30DP1T2

source_name: 3D7 Mixed Stage asexual treated with DFMO, DFMO and Putrescine and untreated parasite Reference Pool


title: tyd30DP1T1


title: patient 3.012|Post 1 vaccination IgG

description:
3.012_V2
IgG


title: Malignant glioma clone U3017MG-C28

source_name: Malignant glioma clone U3017MG-C28


title: tyd27D2T2

source_name: PF3D7 DFMO 27h RNA

value: 2mM DFMO for 27 hr


title: Malignant glioma clone U3017MG-C29

source_name: Malignant glioma clone U3017MG-C29

value: Malignant glioma clone


title: tyd27D2T1


title: patient 3.010|Post 1 vaccination IgG

description:
3.010_V2
IgG

value: Alive


title: Malignant glioma clone U3017MG-C20

source_name: Malignant glioma clone U3017MG-C20


title: RS4

city: Boston

middle: R.

last: Farmer

state: MA

address: 72 E. Concord

institute: Boston University

description: UCP1+ beige adipocytes from inguinal adipose tissue of mice treated with roscovitine

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene Array 2.0ST for 16–18 h in a GeneChip® Hybridization oven 640 at 45 °C with rotation (60 r.p.m.). The hybridized samples were washed and stained using Affymetrix fluidics station 450 as per manufacturer’s instruction (Hybridization, Washing and Staining kit, Affymetrix).

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix  GeneChip Mouse Gene 2.0ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package (version 1.36.1) included within in the Bioconductor software suite (version 2.12) and an Entrez Gene-specific probe set mapping (version 17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan. Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM Bioconductor package (version 1.34.0) and using the Area Under the [Receiver Operating Characteristic] Curve (AUC) in Affymetrix Expression Console. Human homologs of mouse genes were identified using HomoloGene (version 68). All microarray analyses were performed using the R environment for statistical computing (version 2.15.1) by the Clinical and Translational Science Institute (CTSI).

organism: Mus musculus

label_protocol: The total RNA (2 ng) was reverse transcribed using GeneChip® WT Pico Reagent Kit (Affymetrix). The resulting cDNA was used as a template for in vitro transcription using GeneChip® WT Pico Kit (Affymetrix). The obtained antisense cRNA was purified using Nucleic Acid Binding Beads (GeneChip® WT Pico Reagent Kit, Affymetrix) and used as a template for reverse transcription to produce single-stranded DNA in the sense orientation. During this step, dUTP was incorporated. The DNA was then fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) and labeled with DNA labeling reagent covalently linked to biotin using terminal deoxynucleotidyl transferase (TdT, GeneChip® WT Pico Reagent Kit, Affymetrix). IVT and cDNA fragmentation quality controls were carried out by running an RNA Pico assay on the Agilent 2100 Bioanalyzer.

growth_protocol: The animals were maintained in a pathogen-free animal facility at 21°C under a 12-h light/12-h dark cycle with access to a standard rodent chow.

extract_protocol: the total RNA was isolated using an RNeasy Plus Micro Kit (Qiagen), and the sample integrity was verified using RNA 6000 Pico Assay RNA chips run on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: FACS-sorted adipocytes obtained from inguinal adipose tissue of UCP1/Tomato mice treated with drugs

value: RS (roscovitine)

value: Inguinal white adipose

value: Brite adipocyte

tag: age

value: 8-10 weeks

tag: facs sorting marker

value: UCP1(GFP) positive


title: RG2

description: UCP1+ beige adipocytes from inguinal adipose tissue of mice treated with rosiglitazone

value: RG (rosiglitazone)

value: Beige adipocyte


title: RG3

source_name: UCP1+ beige adipocytes from inguinal adipose tissue of mice treated with rosiglitazone


title: RS3

source_name: UCP1+ beige adipocytes from inguinal adipose tissue of mice treated with roscovitine


title: tyd27D1T2

value: trophozoite


title: hiPSC_primitive_erythroblast_rep3

source_name: Isolated on day 12 of hiPSC differentiation as CD235a+ CD45- erythroblasts

value: Primitive erythroblasts from hiPSCs represents embryonic erythropoiesis observed before E90 in the mouse embryo


title: RG4


title: Malignant glioma clone U3017MG-C1

source_name: Malignant glioma clone U3017MG-C1


title: Malignant glioma clone U3017MG-C97

source_name: Malignant glioma clone U3017MG-C97


title: tyd27DP2T2

source_name: PF3D7 DFMO 24h+Putrescine 3h RNA

value: 2mM DFMO for 24 hr and 3h subsequent 2mM putrescine addition


title: RS1


title: tyd27D1T1


title: CL4

description: UCP1+ beige adipocytes from inguinal adipose tissue of mice treated with the potent browning agent CL316,243L


title: patient 3.004|Post 1 vaccination IgG

description:
3.004_V2
IgG

source_name: Serum

value: Week 40

value: Deceased


title: Malignant glioma clone U3017MG-C99

source_name: Malignant glioma clone U3017MG-C99


title: patient 3.009|Post 1 vaccination IgG

description:
3.009_V2
IgG


title: patient 3.060|Pre-vaccination IgG

description:
3.060_V1
IgG

value: Week 8


title: Malignant glioma clone U3017MG-C88

source_name: Malignant glioma clone U3017MG-C88


title: patient 3.005|Post 1 vaccination IgG

description:
3.005_V2
IgG


title: tyd27DP1T2


title: CL3

source_name: UCP1+ beige adipocytes from inguinal adipose tissue of mice treated with the potent browning agent CL316,243L


title: patient 3.059|Pre-vaccination IgG

description:
3.059_V1
IgG


title: patient 3.054|Pre-vaccination IgG

description:
3.054_V1
IgG


title: patient 3.053|Pre-vaccination IgG

description:
3.053_V1
IgG


title: patient 3.052|Pre-vaccination IgG

description:
3.052_V1
IgG


title: tyd27DP1T1


title: tyd24D2T2

source_name: PF3D7 DFMO 24h RNA

value: 10mM DFMO


title: BAT4

description: UCP1+ brown adipocytes from brown adipose tissue of untreated mice

value: Control

value: Brown adipose

value: Brown adipocyte


title: BAT3

source_name: UCP1+ brown adipocytes from brown adipose tissue of untreated mice


title: tyd27DP2T1

source_name: 3D7 Mixed Stage asexual treated with DFMO, DFMO and Putrescine and untreated parasite Reference Pool


title: WAT4

description: UCP1- white adipocytes from inguinal adipose tissue of untreated mice

value: White adipocyte

value: UCP1(GFP) negative


title: tyd24D1T2


title: BAT1


title: patient 3.051|Pre-vaccination IgG

description:
3.051_V1
IgG


title: Malignant glioma clone U3017MG-C92

source_name: Malignant glioma clone U3017MG-C92

value: Malignant glioma clone


title: Malignant glioma clone U3017MG-C70

source_name: Malignant glioma clone U3017MG-C70


title: Malignant glioma clone U3017MG-C80

source_name: Malignant glioma clone U3017MG-C80


title: Malignant glioma clone U3017MG-C64

source_name: Malignant glioma clone U3017MG-C64


title: Malignant glioma clone U3017MG-C89

source_name: Malignant glioma clone U3017MG-C89


title: patient 3.047|Pre-vaccination IgG

description:
3.047_V1
IgG

value: Alive


title: tyd24C2T2

source_name: PF3D7 24h Untreated RNA

value: 24 (No treatment)

value: untreated


title: CL1

value: Inguinal white adipose

value: Beige adipocyte

value: 8-10 weeks

value: UCP1(GFP) positive


title: WAT2

source_name: UCP1- white adipocytes from inguinal adipose tissue of untreated mice


title: patient 3.043|Pre-vaccination IgG

description:
3.043_V1
IgG


title: tyd24D2T1

value: trophozoite


title: tyd24D1T1


title: WAT1


title: patient 3.041|Pre-vaccination IgG

description:
3.041_V1
IgG

value: Deceased


title: WAT3


title: patient 3.044|Pre-vaccination IgG

description:
3.044_V1
IgG

value: Week 8


title: patient 3.037|Pre-vaccination IgG

description:
3.037_V1
IgG


title: patient 3.039|Pre-vaccination IgG

description:
3.039_V1
IgG


title: patient 3.033|Pre-vaccination IgG

description:
3.033_V1
IgG


title: Malignant glioma clone U3017MG-C56

source_name: Malignant glioma clone U3017MG-C56


title: patient 3.032|Pre-vaccination IgG

description:
3.032_V1
IgG


title: tyd24C2T1


title: patient 3.031|Pre-vaccination IgG

description:
3.031_V1
IgG


title: patient 3.029|Pre-vaccination IgG

description:
3.029_V1
IgG


title: patient 3.028|Pre-vaccination IgG

description:
3.028_V1
IgG


title: tyd24C1T1


title: female-small intestine-sexmixed-rep 1

city: Tianjin

first: Ming

last: Cui

address: 238 Baidi Road

department: Institute of Radiation Medicine,

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression after 6.5 Gy irradiation with treatment of sex-mixed FMT

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.

source_name: female, small intestine, sex-mixed FMT, 6.5 Gy， rep 1

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: Mice were kept under standard conditions (ambient temperature 22±2℃, air humidity 40–70% and a 12/12-h light/dark cycle) and continuous access to a standard diet and water.

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

treatment_protocol: Conventional, untreated, age-matched male and female were used as donors to collect gut microbiota. The donor’s fecal droppings were collected under SPF conditions. Donor stool was freshly prepared on the day of transplant and that in all cases was prepared and transplanted within 4 h. Donor stool was weighed and diluted with 1 mL of saline per 0.1 g of stool.

value: small intestine

tag: gender

value: female


title: patient 3.027|Pre-vaccination IgG

description:
3.027_V1
IgG


title: female-small intestine-sexmixed-rep 2

source_name: female, small intestine, sex-mixed FMT, 6.5 Gy， rep 2


title: patient 3.025|Pre-vaccination IgG

description:
3.025_V1
IgG

source_name: Serum


title: female-small intestine-sex-mismatched-rep 2

description: Gene expression after 6.5 Gy irradiation with treatment of sex-mismatched FMT

source_name: female, small intestine, sex-mismatched FMT, 6.5 Gy， rep 2


title: patient 3.023|Pre-vaccination IgG

description:
3.023_V1
IgG


title: female-small intestine-saline-rep 3

description: Gene expression after 6.5 Gy irradiation with treatment of saline

source_name: female, small intestine, saline, 6.5 Gy， rep 3


title: female-small intestine-sex-matched-rep 1

description: Gene expression after 6.5 Gy irradiation with treatment of sex-matched FMT

source_name: female, small intestine, sex-matched FMT, 6.5 Gy， rep 1


title: female-small intestine-saline-rep 2

source_name: female, small intestine, saline, 6.5 Gy， rep 2


title: female-small intestine-sex-mismatched-rep 1

source_name: female, small intestine, sex-mismatched FMT, 6.5 Gy， rep 1


title: female-small intestine-sex-matched-rep 3

source_name: female, small intestine, sex-matched FMT, 6.5 Gy， rep 3


title: female-small intestine-sex-matched-rep 2

source_name: female, small intestine, sex-matched FMT, 6.5 Gy， rep 2


title: patient 3.016|Pre-vaccination IgG

description:
3.016_V1
IgG


title: patient 3.015|Pre-vaccination IgG

description:
3.015_V1
IgG


title: patient 3.013|Pre-vaccination IgG

description:
3.013_V1
IgG


title: patient 3.012|Pre-vaccination IgG

description:
3.012_V1
IgG


title: miDicE17.5 WT Replicate 2

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Total RNA was hybridized using the Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner C by using AgilentG3_miRNA protocol, with a scan resolution of 3microns.

data_processing:
Data are extracted with Agilent Feature Extraction Software.
The arrays are normalized using quantile method
The data were further processed with NIA ExAtlas utilities. See http://lgsun.grc.nia.nih.gov/exatlas for details.

source_name: Dicer WTFP (miRNA)

label_protocol: Total RNA was labeled using the Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

extract_protocol: E16.5 and E17.5 mouse embryos from timed-mating were euthanized and footpad skin was dissected out under a dissection microscope, and was frozen on dry ice immediately. Samples were kept in -80C reezer until use. The frozen footpads were pooled (3-5 embryos for one replicate), and miRNA-enriched total RNAs were isolated with mirVana miRNA isolation kit (Ambion, AM1560) according to manufacturer’s standard protocol. Isolated RNAs were kept in -80C freezer until use.

tag: strain background

tag: developmental stage

tag: cell type

value: wild type

value: footpad skin

tag: individual identifier


title: miDicE17.5 KO Replicate 2

source_name: Dicer cKO FP (miRNA)

value: Dicer cKO


title: patient 3.009|Pre-vaccination IgG

description:
3.009_V1
IgG

tag: time point

tag: survival months

tag: event at time of survival analysis


title: miDicE17.5 KO Replicate 1

tag: tissue


title: miDicE17.5 WT Replicate 1


title: male-small intestine-sex-matched-rep 3

source_name: male, small intestine, sex-matched FMT, 6.5 Gy， rep 3

value: male


title: patient 3.005|Pre-vaccination IgG

description:
3.005_V1
IgG


title: male-small intestine-sex-matched-rep 1

source_name: male, small intestine, sex-matched FMT, 6.5 Gy， rep 1


title: male-small intestine-sexmixed-rep 1

source_name: male, small intestine, sex-mixed FMT, 6.5 Gy， rep 1


title: male-small intestine-sexmixed-rep 2

source_name: male, small intestine, sex-mixed FMT, 6.5 Gy， rep 2


title: male-small intestine-sex-mismatched-rep 2

source_name: male, small intestine, sex-mismatched FMT, 6.5 Gy， rep 2


title: miDicE16.5 WT Replicate 2


title: male-small intestine-sex-mismatched-rep 1

source_name: male, small intestine, sex-mismatched FMT, 6.5 Gy， rep 1


title: patient 3.010|Pre-vaccination IgG

description:
3.010_V1
IgG


title: male-small intestine-sex-matched-rep 2

source_name: male, small intestine, sex-matched FMT, 6.5 Gy， rep 2


title: patient 3.004|Pre-vaccination IgG

description:
3.004_V1
IgG

source_name: Serum


title: miDicE16.5 WT Replicate 1


title: Malignant glioma clone U3017MG-C4

source_name: Malignant glioma clone U3017MG-C4

value: Malignant glioma clone

tag: cell line


title: female-small intestine-saline-rep 1

source_name: female, small intestine, saline, 6.5 Gy， rep 1


title: male-small intestine-saline-rep 3

source_name: male, small intestine, saline, 6.5 Gy， rep 3


title: male-small intestine-saline-rep 1

source_name: male, small intestine, saline, 6.5 Gy， rep 1


title: male-small intestine-saline-rep 2

source_name: male, small intestine, saline, 6.5 Gy， rep 2


title: Subcutaneous fat_exercised_slaughter_rep18

status: Public on Dec 12 2016

city: Zaragoza

first: Laura

last: González

address: Av. Montañana 930

country: Spain

institute: Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol using GCOS

data_processing: Expression data were generated with GeneChip Operating Software (GCOS, Affymetrix) and normalization was carried out with Robust Multi-Array Average (RMA) algorithm with quantile normalization.

organism: Ovis aries

source_name: Subcutaneous fat, exercised, slaughter

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

growth_protocol: 14 single reared male lambs were weaned at 48.28 ± 0.85 days of age. 7 lambs were fed a basal concentrate from weaning to slaughter. The other 7 lambs were fed with the same concentrate supplemented with 500 mg dl-α-tocopheryl acetate/kg concentrate during 33.28±1.07 days before slaughter, and the rest of the days the lambs were fed with basal concentrate. Another group of 7 lambs continuously grazed on alfalfa pasture with their dams. Lambs suckled their mothers, grazed, and received the same basal concentrate.

extract_protocol: RNeasy Tissue isolation kit (QIAGEN, Madrid, Spain)

treatment_protocol: Muscle and subcutaneous fat tissue samples obtained at slaughter were mantained at -80ºC until processing for RNA extraction

tag: breed

value: Rasa Aragonesa

tag: treatment

value: Concentrate enriched with vitamin E


title: Subcutaneous fat_exercised_slaughter_rep17


title: Subcutaneous fat_exercised_slaughter_rep21


title: Subcutaneous fat_exercised_slaughter_rep15


title: Subcutaneous fat_exercised_slaughter_rep14

value: Basal concentrate


title: Subcutaneous fat_exercised_slaughter_rep10


title: Subcutaneous fat_exercised_slaughter_rep16


title: miDicE16.5 KO Replicate 2


title: Subcutaneous fat_exercised_slaughter_rep19


title: Subcutaneous fat_exercised_slaughter_rep7

value: Alfalfa grazing


title: Subcutaneous fat_exercised_slaughter_rep9


title: Subcutaneous fat_exercised_slaughter_rep13


title: Subcutaneous fat_exercised_slaughter_rep11


title: Subcutaneous fat_exercised_slaughter_rep8


title: miDicE16.5 KO Replicate 1


title: Subcutaneous fat_exercised_slaughter_rep12


title: Subcutaneous fat_exercised_slaughter_rep6


title: Subcutaneous fat_exercised_slaughter_rep4


title: Subcutaneous fat_exercised_slaughter_rep3


title: Muscle_exercised_slaughter_rep21

source_name: Longissimus thoracis muscle, exercised, slaughter


title: Subcutaneous fat_exercised_slaughter_rep1


title: Subcutaneous fat_exercised_slaughter_rep2


title: Subcutaneous fat_exercised_slaughter_rep5


title: Muscle_exercised_slaughter_rep20


title: Muscle_exercised_slaughter_rep18


title: Muscle_exercised_slaughter_rep17


title: Muscle_exercised_slaughter_rep16


title: tyd24C1T2

source_name: PF3D7 24h Untreated RNA

tag: strain

tag: time after treatment (and reversal) in hours

value: 24 (No treatment)

value: untreated

tag: Stage

source_name: 3D7 Mixed Stage asexual treated with DFMO, DFMO and Putrescine and untreated parasite Reference Pool


title: Muscle_exercised_slaughter_rep19


title: Muscle_exercised_slaughter_rep15


title: Subcutaneous fat_exercised_slaughter_rep20


title: Muscle_exercised_slaughter_rep13


title: Muscle_exercised_slaughter_rep6


title: Muscle_exercised_slaughter_rep9


title: Muscle_exercised_slaughter_rep4


title: Muscle_exercised_slaughter_rep8


title: Muscle_exercised_slaughter_rep2


title: Muscle_exercised_slaughter_rep14


title: Muscle_exercised_slaughter_rep3


title: Muscle_exercised_slaughter_rep11


title: Muscle_exercised_slaughter_rep5


title: Muscle_exercised_slaughter_rep12


title: Muscle_exercised_slaughter_rep1


title: Muscle_exercised_slaughter_rep7


title: Muscle_exercised_slaughter_rep10


title: cTEC2

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

country: Israel

institute: Weizmann Institute

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mo1ST. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Raw data were processed with the RMA algorithm for probe-level normalization and analyzed using GenePattern software

source_name: Cortical TECs from WT mice

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

growth_protocol: Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2

tag: genotype/variation

tag: age

value: 6 weeks

value: Thymic EpCAM+Ly51+

value: cortical thymic epithelial cells (TECs)


title: SpleenB

source_name: Splenic B cells obtained from Adig mice

value: Adig mouse

value: Splenic CD19+

value: CD19+ Splenic B cells


title: mTEC Lo 2

source_name: Immature mTECs from WT mice

value: wild type

value: Thymic EpCAM+Ly51-MHCIIlo

value: immature medullary thymic epithelial cells (mTECs)


title: ThyB-GFP+_1

source_name: Aire.GFP+ Thymic B cells obtained from Adig mice

value: Thymic CD19+GFP+

value: CD19+Aire.GFP+ thymic B cells


title: cTEC3


title: ThyB-GFP+_2


title: cTEC1


title: mTEC Hi 4

source_name: Mature mTECs from WT mice

value: Thymic EpCAM+Ly51-MHCIIhi

value: mature medullary thymic epithelial cells (mTECs)


title: mTEC Hi 2


title: mTEC Hi 3


title: mTEC Lo 4


title: mTEC Lo 3


title: mTEC Hi 1


title: pos_P11_#36

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: mRNA expression profiles from primary tissue

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: Patient #11 / pos RYGB surgery / Sample #36

extract_protocol: RNA extracted using miRVana (Ambion) according to the manufacturers guidelines

treatment_protocol: samples origin from primary human tissue (patients) undergoing RYGB surgery

value: primary tissue


title: mTEC Lo 1


title: int_P14_#26

source_name: Patient #14 / int RYGB surgery / Sample #26

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: pre_P11_#34

source_name: Patient #11 / pre RYGB surgery / Sample #34


title: pre_P15_#28

source_name: Patient #15 / pre RYGB surgery / Sample #28


title: pos_P18_#21

source_name: Patient #18 / pos RYGB surgery / Sample #21


title: pos_P12_#33

source_name: Patient #12 / pos RYGB surgery / Sample #33


title: pre_P17_#22

source_name: Patient #17 / pre RYGB surgery / Sample #22


title: pre_P12_#31

source_name: Patient #12 / pre RYGB surgery / Sample #31


title: int_P18_#20

source_name: Patient #18 / int RYGB surgery / Sample #20


title: int_P15_#29

source_name: Patient #15 / int RYGB surgery / Sample #29


title: pos_P14_#27

source_name: Patient #14 / pos RYGB surgery / Sample #27


title: pos_P17_#24

source_name: Patient #17 / pos RYGB surgery / Sample #24


title: int_P17_#23

source_name: Patient #17 / int RYGB surgery / Sample #23


title: int_P11_#35

source_name: Patient #11 / int RYGB surgery / Sample #35


title: pos_P19_#18

source_name: Patient #19 / pos RYGB surgery / Sample #18


title: pos_P15_#30

source_name: Patient #15 / pos RYGB surgery / Sample #30


title: int_P19_#17

source_name: Patient #19 / int RYGB surgery / Sample #17


title: pre_P18_#19

source_name: Patient #18 / pre RYGB surgery / Sample #19


title: pos_P03_#12

source_name: Patient #3 / pos RYGB surgery / Sample #12


title: pre_P02_#13

source_name: Patient #2 / pre RYGB surgery / Sample #13


title: int_P12_#32

source_name: Patient #12 / int RYGB surgery / Sample #32


title: pre_P19_#16

source_name: Patient #19 / pre RYGB surgery / Sample #16


title: int_P03_#11

source_name: Patient #3 / int RYGB surgery / Sample #11


title: int_P04_#08

source_name: Patient #4 / int RYGB surgery / Sample #08


title: pre_P14_#25

source_name: Patient #14 / pre RYGB surgery / Sample #25


title: int_P02_#14

source_name: Patient #2 / int RYGB surgery / Sample #14


title: pos_P04_#09

source_name: Patient #4 / pos RYGB surgery / Sample #09


title: pre_P03_#10

source_name: Patient #3 / pre RYGB surgery / Sample #10


title: pos_P02_#15

source_name: Patient #2 / pos RYGB surgery / Sample #15


title: pos_P06_#06

source_name: Patient #6 / pos RYGB surgery / Sample #06


title: pre_P04_#07A

source_name: Patient #4 / pre RYGB surgery / Sample #07A


title: pre_P09_#01

source_name: Patient #9 / pre RYGB surgery / Sample #01


title: int_P06_#05

source_name: Patient #6 / int RYGB surgery / Sample #05


title: int_P09_#02

source_name: Patient #9 / int RYGB surgery / Sample #02


title: Oubain 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabain rep-2-2]

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

description: Technical replicate 2 of 3 of biological replicate 2 of 3. Oubain  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.

hyb_protocol: Whole Human Genome 44K arrays (Agilent Technologies, product G4112A) were used for all experiments. RNA samples (825 ng/each) were subjected to fragmentation, followed by 16 h hybridization, washing.

scan_protocol: Agilent Technologies, model G2505B according to the manufacturer’s protocol (manual ID #G4140-90030)

data_processing: Agilent dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantiﬁed using Agilent’s Feature Extraction software (v.7.11) with the default parameters.

source_name: Cystic fibrosis bronchial epithelial cells (CFBE41o−)

label_protocol: Total RNA (1 µg) was subjected to two rounds of ampliﬁcation using the Amino Allyl MessageAMP II aRNA ampliﬁcation kit (Ambion, Applied Biosystems, USA). The integrity and quantity of the aRNA was revaluated by Nanodrop and Agilent Bioanalyzer, and coupled to Cy3 and Cy5 (Amersham Biosciences, UK).

growth_protocol:
CFBE41o− cell lines transduced with TranzVector lentivectors containing ΔF508 CFTR (CFBE41o-ΔF508CFTR) or wildtype CFTR (CFBE41o−CFTR) cells were kindly provided by J.P. Clancy. Cells were maintained in Eagle’s minimum essential medium (EMEM, Wisent, St-Bruno, QC, Canada) plus 10% fetal bovine serum (FBS) in a 5% CO2, 95% air incubator at 37 °C.
polarized_protocol: Cells were seeded at a density of 3 × 105 cells/cm2 on cell culture inserts (Transwell-clear, diameter 12 mm, 0.4 μm pores; Corning, Acton, MA, USA) in multi-well plates and kept submerged (i.e. under liquid–liquid conditions) until they were conﬂuent, after which the apical medium was removed from the upper compartment to allow polarisation at the air–liquid interface.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

value: polarized CFBE41o-cell line

tag: transduction

value: TranzVector lentivectors containing deltaF508 CFTR (CFBE41o-deltaF508CFTR)

source_name: untreated HeLa cells

value: HeLa cells


title: Oubagenin  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabagenin rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2.Oubagenin   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs


title: PJ34  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [PJ34 rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. PJ34   0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: pos_P09_#03

source_name: Patient #9 / pos RYGB surgery / Sample #03


title: pre_P06_#04

source_name: Patient #6 / pre RYGB surgery / Sample #04


title: Minocycline H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Minocycline-H rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. minocycline-H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: 4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [4-AN rep-3-2]

description: Technical replicate 2 of 3 of biological replicate 3 of 3.  4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubain 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabain rep-1-1]

description: Technical replicate 1 of 3 of biological replicate 1 of 3. Oubain  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Minocycline H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Minocycline-H rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. minocycline-H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: PJ34  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [PJ34 rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. PJ34   0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: 4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [4-AN rep-3-1]

description: Technical replicate 1 of 3 of biological replicate 3 of 3. 4-AN   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Minocycline H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Minocycline-H rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. minocycline-H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubain 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabain rep-3-2]

description: Technical replicate 2 of 2 of biological replicate 3 of 3. Oubain  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: 4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [4-AN rep-2-2]

description: Technical replicate 2 of 3 of biological replicate 2 of 3. 4-AN   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: 4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [4-AN rep-2-1]

description: Technical replicate 1 of 3 of biological replicate 2 of 3. 4-AN   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubain 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabain rep-2-1]

description: Technical replicate 1 of 3 of biological replicate 2 of 3. Oubain  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubagenin  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabagenin rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2.Oubagenin   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs


title: PJ34  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [PJ34 rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. PJ34   0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubagenin  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabagenin rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2.Oubagenin   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs


title: 4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [4-AN rep-1-2]

description: Technical replicate 2 of 3 of biological replicate 1 of 3. 4-AN   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubain 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabain rep-1-2]

description: Technical replicate 2 of 3 of biological replicate 1 of 3. Oubain  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: 4-AN  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [4-AN rep-1-1]

description: Technical replicate 1 of 3 of biological replicate 1 of 3. 4-AN   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubagenin  1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabagenin rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2.Oubagenin   1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs


title: PJ34  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [PJ34 rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. PJ34   0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Minocycline H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Minocycline-H rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. minocycline-H 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Oubain 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ouabain rep-3-1]

description: Technical replicate 1 of 2 of biological replicate 3 of 3. Oubain  0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs [Low temperature rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs


title: CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs [Low temperature rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs


title: CFBE41o-ΔF508CFTR untreated cells [NO DMSO rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. CFBE41o-ΔF508CFTR untreated cells


title: CFBE41o-ΔF508CFTR untreated cells [NO DMSO rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. CFBE41o-ΔF508CFTR untreated cells


title: latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [latonduine A rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [latonduine A rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [latonduine A rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11057 rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11060 rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11057 rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ibuprofen rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs [Low temperature rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs


title: CFBE41o-ΔF508CFTR untreated cells [NO DMSO rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. CFBE41o-ΔF508CFTR untreated cells


title: KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11060 rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11060 rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ibuprofen rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [JFD03094 rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [JFD03094 rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [McG339 rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [JFD03094 rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [McG339 rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [latonduine A rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. latonduine A 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ibuprofen rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs [Low temperature rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. CFBE41o-ΔF508CFTR of treated cells at 29°C for 24 hrs


title: KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11057 rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11060 rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. KM11060 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o-ΔF508CFTR untreated cells [NO DMSO rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. CFBE41o-ΔF508CFTR untreated cells


title: KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [KM11057 rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. KM11057 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Ibuprofen rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. Ibuprofen 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Glafenine rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [McG339 rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [JFD03094 rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. JFD03094 0.1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Glafenine rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [ABT888 rep-3-2]

description: Technical replicate 2 of 3 of biological replicate 3 of 3  ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [ABT888 rep-1-2]

description: Technical replicate 2 of 3 of biological replicate 1 of 3. ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [ABT888 rep-3-1]

description: Technical replicate 1 of 3 of biological replicate 3 of 3. ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VX-809 rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VX-809 rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Glafenine rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o−CFTR untreated cells [WT rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. CFBE41o−CFTR untreated cells

value: TranzVector lentivectors containing wildtype CFTR (CFBE41o-CFTR)


title: MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [McG339 rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. MCG339 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o−CFTR untreated cells [WT rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. CFBE41o−CFTR untreated cells


title: ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [ABT888 rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 3. ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR3 rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR1 rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VX-809 rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [Glafenine rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. glafenine 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o−CFTR untreated cells [WT rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. CFBE41o−CFTR untreated cells


title: ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [ABT888 rep-2-2]

description: Technical replicate 2 of 3 of biological replicate 2 of 3. ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR3 rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VX-809 rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. VX-809 1 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR3 rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR1 rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR3 rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. RDR3 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR1 rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [CFTRinh172 rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [RDR1 rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. RDR1 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFBE41o−CFTR untreated cells [WT rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. CFBE41o−CFTR untreated cells


title: ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [ABT888 rep-2-1]

description: Technical replicate 1 of 3 of biological replicate 2 of 3. ABT888 0.01 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [CFTRinh172 rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [capsaicin rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [genistein rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [genistein rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-325 rep 3-2]

description: Technical replicate 2 of 3 of biological replicate 3 of 3.VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [genistein rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [capsaicin rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-325 rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 3.VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [capsaicin rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-325 rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 3.VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [capsaicin rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. capsaicin 100 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [genistein rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. genistein 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-325 rep 3-1]

description: Technical replicate 1 of 3 of biological replicate 3 of 3.VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-8-2]

description: Technical replicate 2 of 2 of biological replicate 8 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-9-1]

description: Technical replicate 1 of 2 of biological replicate 9 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-532 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-532 rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 2. VRT-532 10µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-325 rep 2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 3.VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-532 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-532 rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 2. VRT-532 10µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-9-2]

description: Technical replicate 2 of 2 of biological replicate 9 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-5-2]

description: Technical replicate 2 of 2 of biological replicate 5 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-7-2]

description: Technical replicate 2 of 2 of biological replicate 7 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-532 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-532 rep 1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 2. VRT-532 10µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-8-1]

description: Technical replicate 1 of 2 of biological replicate 8 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-6-1]

description: Technical replicate 1 of 2 of biological replicate 6 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: VRT-532 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-532 rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. VRT-532 10µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-6-2]

description: Technical replicate 2 of 2 of biological replicate 6 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-5-1]

description: Technical replicate 1 of 2 of biological replicate 5 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-7-1]

description: Technical replicate 1 of 2 of biological replicate 7 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-4-2]

description: Technical replicate 2 of 2 of biological replicate 4 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-4-1]

description: Technical replicate 1 of 2 of biological replicate 4 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-3-1]

description: Technical replicate 1 of 2 of biological replicate 3 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-3-2]

description: Technical replicate 2 of 2 of biological replicate 3 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-2-1]

description: Technical replicate 1 of 2 of biological replicate 2 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs [DMSO rep-1-1]

description: Technical replicate 1 of 2 of biological replicate 1 of 9.DMSO (vehicle control) CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: SS_P3 cells_SAHA+MitA_rep.2

city: MARSEILLE

first: CHELBI

last: RABIE

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

description:
P3_2_S.M
US83700202_252800415382_S01_GE1_107_Sep09_2_4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: SS cells_SAHA+MitA_24 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PBMC were collected from 4 Sézary Syndrome (SS) patients and were put in culture without prior further purification because of the high percentage of T lymphocytes and the great majority of CD4+ among them. Cells were expanded for seven days in RPMI medium in the presence of IL-7 (10 ng/ml) and anti-CD28 (mAb ascites 1/400).

extract_protocol: Cells were recovered after drug treatment and RNA was extracted with Qiagen RNeasy® mini Kit. On column DNA digestion was done with Qiagen Rnase-free Dnase set.

treatment_protocol: Expanded cells were treated, or not, with SAHA (2.6 µM) and MitA (223 nM) for 24 h.

tag: subject status

value: Sézary Syndrome (SS) patient

tag: gender

value: female

tag: age (yrs)

value: peripheral blood tumor cells

tag: tumor stage

value: III

tag: % cd3+ in pbmc

tag: cd4+/cd8+ ratio


title: SS_P2 cells_SAHA+MitA_rep.3

description:
P2_3_S.M
US83700202_252800415383_S01_GE1_107_Sep09_1_4

tag: cell type


title: SS_P3 cells_SAHA+MitA_rep.1

description:
P3_1_S.M
US83700202_252800415374_S01_GE1_105_Dec08_2_1


title: SS_P2 cells_SAHA+MitA_rep.1

description:
P2_1_S.M
US83700202_252800415433_S01_GE1_107_Sep09_1_3


title: SS_P4 cells_SAHA+MitA_rep.3

description:
P4_3_S.M
US83700202_252800415397_S01_GE1_107_Sep09_1_1

value: male


title: SS_P4 cells_SAHA+MitA_rep.1

description:
P4_1_S.M
US83700202_252800415433_S01_GE1_107_Sep09_1_4


title: SS_P4 cells_SAHA+MitA_rep.2

description:
P4_2_S.M
US83700202_252800415383_S01_GE1_107_Sep09_2_2


title: SS_P2 cells_SAHA+MitA_rep.2

description:
P2_2_S.M
US83700202_252800415373_S01_GE1_107_Sep09_1_1


title: SS_P1 cells_SAHA+MitA_rep.1

description:
P1_1_S.M
US83700202_252800415375_S01_GE1_107_Sep09_2_1

value: eECPx1/ Roferon CHOPx6


title: SS_P1 cells_SAHA+MitA_rep.3

description:
P1_3_S.M
US83700202_252800415383_S01_GE1_107_Sep09_1_2


title: SS_P4 cells_MitA_rep.3

description:
P4_3_M
US83700202_252800415397_S01_GE1_107_Sep09_1_2

source_name: SS cells_MitA_24 h


title: SS_P2 cells_MitA_rep.3

description:
P2_3_M
US83700202_252800415393_S01_GE1_107_Sep09_1_4


title: SS_P4 cells_MitA_rep.1

description:
P4_1_M
US83700202_252800415433_S01_GE1_107_Sep09_1_1


title: SS_P3 cells_SAHA+MitA_rep.3

description:
P3_3_S.M
US83700202_252800415383_S01_GE1_107_Sep09_2_4


title: SS_P4 cells_MitA_rep.2

description:
P4_2_M
US83700202_252800415374_S01_GE1_105_Dec08_1_2


title: SS_P3 cells_MitA_rep.3

description:
P3_3_M
US83700202_252800415393_S01_GE1_107_Sep09_2_1


title: SS_P1 cells_SAHA+MitA_rep.2

description:
P1_2_S.M
US83700202_252800415433_S01_GE1_107_Sep09_1_2


title: SS_P1 cells_MitA_rep.2

description:
P1_2_M
US83700202_252800415383_S01_GE1_107_Sep09_1_1


title: SS_P2 cells_MitA_rep.1

description:
P2_1_M
US83700202_252800415391_S01_GE1_107_Sep09_2_4


title: SS_P1 cells_MitA_rep.1

description:
P1_1_M
US83700202_252800415375_S01_GE1_107_Sep09_2_2


title: SS_P3 cells_MitA_rep.2

description:
P3_2_M
US83700202_252800415382_S01_GE1_107_Sep09_2_2


title: SS_P3 cells_MitA_rep.1

description:
P3_1_M
US83700202_252800415374_S01_GE1_105_Dec08_2_2


title: SS_P1 cells_MitA_rep.3

description:
P1_3_M
US83700202_252800415393_S01_GE1_107_Sep09_1_3


title: SS_P3 cells_SAHA_rep.3

description:
P3_3_S
US83700202_252800415393_S01_GE1_107_Sep09_1_2

source_name: SS cells_SAHA_24 h


title: CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [CFTRinh172 rep 1-2]

description: Technical replicate 2 of 2 of biological replicate 1 of 2. CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.


title: SS_P2 cells_SAHA_rep.2

description:
P2_2_S
US83700202_252800415373_S01_GE1_107_Sep09_1_3


title: SS_P1 cells_SAHA_rep.1

description:
P1_1_S
US83700202_252800415375_S01_GE1_107_Sep09_2_3


title: SS_P3 cells_SAHA_rep.2

description:
P3_2_S
US83700202_252800415382_S01_GE1_107_Sep09_1_4


title: SS_P1 cells_SAHA_rep.2

description:
P1_2_S
US83700202_252800415391_S01_GE1_107_Sep09_1_4


title: SS_P4 cells_SAHA_rep.1

description:
P4_1_S
US83700202_252800415391_S01_GE1_107_Sep09_2_2


title: SS_P4 cells_SAHA_rep.3

description:
P4_3_S
US83700202_252800415397_S01_GE1_107_Sep09_1_3


title: SS_P3 cells_SAHA_rep.1

description:
P3_1_S
US83700202_252800415374_S01_GE1_105_Dec08_2_3


title: SS_P4 cells_Ctrl_rep.3

description:
P4_3_C
US83700202_252800415397_S01_GE1_107_Sep09_1_4

source_name: SS cells_no drug


title: SS_P2 cells_SAHA_rep.3

description:
P2_3_S
US83700202_252800415383_S01_GE1_107_Sep09_1_3


title: SS_P4 cells_Ctrl_rep.1

description:
P4_1_C
US83700202_252800415397_S01_GE1_107_Sep09_2_4


title: SS_P4 cells_SAHA_rep.2

description:
P4_2_S
US83700202_252800415374_S01_GE1_105_Dec08_1_3