title: Epi71b_central

city: Québec

first: Sylvain

last: Guérin

state: QC

address: 1050 Chemin Ste-Foy

institute: Université Laval

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (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.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data were analyzed using the ArrayStar V4.1 (DNASTAR, Madison, WI) software. All data generated from the array were also analyzed by RMA (Robust Multiarray Analysis) for background correction of the raw values. They were then transformed in log2 base and quantile normalized before a linear model was fitted to the normalized data in order to obtain an expression measure for each probe set.

source_name: Human tissue-engineered cornea, Epi71b (HCECs), wounded, central section

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Toronto, ON). Dye incorporation and cRNA yield were checked with the Nanophotometer pearl (Montréal Biotech).

growth_protocol: All human tissue-engineered corneas were grown under 8% CO2 at 37 °C. Culture medium (Dulbecco-Vogt modification of Eagle’s medium with Ham’s F12 in a 3 : 1 ratio) with supplements (5% FetalClone II serum, 5 μg/mL insulin, 0.4 μg/mL hydrocortisone, 10 ng/mL epidermal growth factor, 10−10 mol/L cholera toxin, 100 μg/ml Penicilin, and 25 μg/ml Gentamycin) was changed after 2–3 days.

extract_protocol:
Isolation protocol: Human corneal epithelial cells (HCECs) were isolated from the limbal area of normal eyes (obtained from the Banque d’Yeux Nationale of the Centre Universitaire d’Ophtalmologie; CHU de Québec, Hôpital du Saint-Sacrement, Québec, QC, Canada) of 44-, 52- and 71 year-old donors. HCECs were cultured with a feeder layer of irradiated murine Swiss-3T3 fibroblasts (ATCC, Rockville, MD) whereas human corneal fibroblasts were isolated from the stromal portion of a 26 days-old donor cornea left after dispase digestion and removal of both the endothelium and epithelium.
2 sections of the human tissue-engineered corneas were isolated: the external ring and the central section. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: Human tissue-engineered corneas were wounded with a 8-mm biopsy punch and placed over a reconstructed stroma to allow proper reepithelialisation.

value: tissue-engineered cornea

tag: cell population

tag: donor age


title: Glioblastoma Tumor 3

status: Public on Apr 21 2018

type: SRA

city: New York

first: Richard

last: Possemato

state: NY

address: 550 First Avenue

department: Pathology

country: USA

institute: NYU School of Medicine

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.4
Sequenced reads were checked for contaminations using fastqscreen v0.5.2 and were mapped to mm10 referece genome using STAR aligner v2.5.3a d with default parameters.
Raw read counts were obtained using featureCounts from subread package v1.4.6-p3
Normalization and differential gene exrpression analysis was performed using DESeq2 v1.14.0
Genome_build: hg19
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.

molecule: total RNA

organism: Homo sapiens

source_name: Glioblastoma

extract_protocol:
Tumors were removed, flash frozen, and RNA was harvested using MAXWELL RSC SIMPLY RNA TISSUE kit by Promega (AS1340).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: high grade glioblastoma tumor

tag: age

tag: gender

value: F


title: ore3-D1_2

type: RNA

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

hyb_protocol: Hybridization was carried out according to NimbleGen protocols.

scan_protocol: Arrays were scanned using the NimbleGen MS 200 Microarray Scanner.

data_processing: Log2 intensities of the probes were first normalized using quantile normalization.

organism: Arabidopsis thaliana

source_name: ore3 leaves, DAT 1

label_protocol: Cy3-based labeling was carried out according to NimbleGen protocols.

growth_protocol: Arabidopsis were grown in the soil for 21 days on an 16:8 light-dark (LD) cycle.

extract_protocol: Total RNA extracted using WelprepTM Total RNA Isolation Reagent following manufacturer's instructions.

treatment_protocol: Leaves were detached and transferred into 24 well plates containing 3 mM MES solution.

tag: developmental stage

value: 12 d after emergence (DAE)

tag: genotype

tag: treatment

value: dark-induced leaf senescence

tag: time

value: 1 d after treatment (DAT)

value: 3rd or 4th leaves


title: Epi71b_external

country: Canada

source_name: Human tissue-engineered cornea, Epi71b (HCECs), wounded, external section


title: Col-D3_2

source_name: Col-0 leaves, DAT 3

value: wt

value: 3 d after treatment (DAT)


title: Col-D2_2

source_name: Col-0 leaves, DAT 2

value: 2 d after treatment (DAT)


title: Epi71b_unwounded

source_name: Human tissue-engineered cornea, Epi71b (HCECs), unwounded


title: Epi44_unwounded

source_name: Human tissue-engineered cornea, Epi44 (HCECs), unwounded


title: Epi44_external

source_name: Human tissue-engineered cornea, Epi44 (HCECs), wounded, external section


title: Col-D1_2

source_name: Col-0 leaves, DAT 1


title: Col-D0_2

source_name: Col-0 leaves, DAT 0

value: control

value: 0 d after treatment (DAT)


title: B cell_+LPS+4u8c_18hr_rep3

city: Pittsburgh

first: Christine

last: Milcarek

state: PA

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

hyb_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.

data_processing: CHP files were generated from CEL files using Expression Console from Affymetrix, using SST-RMA analysis algorithm.

label: biotin

organism: Mus musculus

source_name: wild type B cells

growth_protocol: Primary splenic B cells were isolated from each mouse using MACS columns.

extract_protocol: RNA was isolated from B cells at noted timepoints via Macherey Nagel Nucleospin RNA kits.

treatment_protocol: Unstimulated cells were processed immediately. Stimulated cells were stimulated with LPS at zero hours, plus or minus 4u8c. 4u8c was reconstituted in DMSO, thus -4u8c samples had an equivalent volume of DMSO added as their +4u8c counterparts.

tag: strain/background

tag: genotype/variation

value: Wild type

tag: cell type

value: B cell

value: LPS+4u8c 18hr


title: ore12-D2_1

source_name: ore12 leaves, DAT 2


title: Epi52_external

source_name: Human tissue-engineered cornea, Epi52 (HCECs), wounded, external section


title: Epi52_central

source_name: Human tissue-engineered cornea, Epi52 (HCECs), wounded, central section


title: B cell_+LPS+4u8c_18hr_rep2

scan_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.


title: B cell_+LPS_18hr_rep3

label_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.

value: LPS 18hr


title: B cell_+LPS+4u8c_18hr_rep1


title: non-cancerous lung tissues

type: genomic

city: Kunming

first: Juan

last: Wang

state: Yunnna

address: No. 295 Xichang Road, Kunming, Yunnan Province, China.

department: Department of Clinical Laboratory

country: China

institute: Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China

hyb_protocol: The labeled DNA was purified by isopropanol/ethanol precipitation and hybridized to NimbleGen Human Meth 3x720K CpG RfSq Prom according to the manufacturer’s instructions.

scan_protocol: Signal intensity data were extracted from the scanned images of each array by NimbleScan MS 200 Microarray Scanner and the MS 200 Data Collection Software. Median-centering, quantile normalization, and linear smoothing were performed by the Bioconductor software packages Ringo, limma, and MEDME, respectively.

data_processing: Normalized log2-ratio data were created for each sample, and a sliding-window peak-finding algorithm provided by NimbleScan v2.5 was applied to determine the enriched peaks with specified parameters (sliding window width: 750 bp; miniprobes per peak: 2; p-value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500 bp). A one-sided Kolmogorov–Smirnov test was applied to determine whether the probes were drawn from a significantly more positive distribution of intensity log2-ratios than those in the rest of the array. Each probe received a −log10 p-value score from the windowed Kolmogorov–Smirnov test around that probe. If several adjacent probes rose significantly above a p-value minimum cutoff (−log10) of 2, the region was considered to be an enrichment peak. When comparing two groups' differentially enriched regions, we averaged the log2-ratio values for each group (Experiment and Control) and calculated M′ value for each probe, where M′=Average (log2 MeDIPE/InputE) – Average (log2 MeDIPC/InputC). Then the NimbleScan sliding-window peak-finding algorithm was rerun on these data to find the differential enrichment peaks.

molecule: genomic DNA

source_name: ChIP DNA from non-cancerous lung tissues

label_protocol: A total of 6 µg of the pooled gDNA from each tissue type was digested by MseI, purified by using QIAquick PCR purification kit (Qiagen), and analyzed by agarose gel electrophoresis. MseI-digested gDNA (1.25 µg) was subjected to immunoprecipitation with a mouse monoclonal anti-5-methylcytosine antibody (Diagenode, Liège, Belgium) and then was purified through Qiagen MinElute columns and amplified by using a GenomePlex Complete Whole Genome Amplification (WGA2) kit from Sigma-Aldrich (St Louis, MO, USA). The amplified DNA samples were purified with a QIAquick PCR purification kit. The NimbleGen Dual-Color DNA Labeling kit (Roche NimbleGen Systems, Inc., Madison, WI, USA) was used for labeling according to the manufacturer’s guidelines. Briefly, 1 µg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (immunoprecipitation sample) or Cy3-9mer primer (input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100 U of the Klenow fragment (New England Biolabs, Ipswich, MA, USA) were added, and the mix was incubated at 37°C for 3 h.

extract_protocol: Genomic DNA were extracted and purified from lung cancer and paired non-cancerous tissues using the QIAamp DNA Mini kit(Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

tag: chip antibody

source_name: Input DNA from non-cancerous lung  tissues

tag: sample type

value: input DNA


title: NW3: T4 wt

city: Bethesda

first: Jennifer

middle: Patterson

last: West

state: Md

address: 8 Center Drive

department: Laboratory of Cell and Molecular Biology

institute: NIDDK

data_processing:
Quality trimming (max ambiguity =2) and trimming of 15 nucleotides from the 5’ terminal of all sequences was performed with CLC Genomics Workbench.
Trimmed data was aligned to the E. coli reference genome (NC_012971.2) and an unmapped reads file was generated.
The unmapped reads file, presumably containing sequence derived from the T4 genome, was subsequently aligned to the bacteriophage T4 reference genome (NC_000866.4).
Differential expression experiments consisted of 3 replicates of NapIV NS infected with either wild-type T4D+ or T4motBam.
Count data was normalized to total reads in CLC Genomics Workbench
Statistical analysis was performed in CLC Genomics Workbench using the Baggerley’s Test with False Discovery Rate (FDR) corrected p values.
Genome_build: NC_000866.4
Supplementary_files_format_and_content: Comma seperated value text files include: 1) counts for each gene in all replicates prior to normailzation; 2) normalized values for each gene in all replicates; 4) the fold change of each gene in the two samples as determined  in CLC Genomics Workbench using the Baggerley’s Test; 3) False Discovery Rate (FDR) corrected p values.

organism: Tequatrovirus T4

source_name: Bacteriophage

growth_protocol: NapIV Nonsuppressing E. coli were grown at 37C to early/mid log phase (OD600 ~ 0.4) then infected with moi of 10 of either T4 wt or T4motBam for 5 minutes

extract_protocol:
RNA was isolated  using method II of (Hinton 1989)
rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions.  cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications.  Illumina adaptors sequences based on TruSeq HT Sample Prep Kits were purchase from Integrated DNA Technologies and used in the ligation step.  TruSeq-1 and TruSeq-2 primer were used for PCR enrichment of adaptor ligated DNA.  Library size was verified with a Bioanalyzer using an Agilent High Sensitivity DNA kit.  The concentration of each library was determined using the KAPA Library Quantification Kit for Illumina platforms.  Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the MiSeq 2 x 250 bp Sequencing Kit (Illumina).

value: T4 wt

tag: host

value: NapIV Nonsuppressing E. coli


title: B cell_+LPS_18hr_rep1


title: B cell_-LPS_0hr_rep4

description: 596 B Cell

value: Unstimulated


title: NW2: T4 wt


title: NW1: T4 wt


title: B cell_-LPS_0hr_rep3

description: 600 B Cell


title: B cell_+LPS_18hr_rep2


title: B cell_-LPS_0hr_rep1


title: NM1: T4motBam


title: Epi44_central

source_name: Human tissue-engineered cornea, Epi44 (HCECs), wounded, central section

value: tissue-engineered cornea


title: NM3: T4motBam


title: ore12-D1_1

source_name: ore12 leaves, DAT 1

value: 12 d after emergence (DAE)

value: dark-induced leaf senescence


title: NM2: T4motBam


title: B cell_-LPS_0hr_rep2

description: 807 B Cell


title: ore12-D3_1

source_name: ore12 leaves, DAT 3

value: 3rd or 4th leaves


title: ore12-D0_1

source_name: ore12 leaves, DAT 0


title: lung cancer tissues

source_name: ChIP DNA from lung cancer tissues

value: mouse monoclonal anti-5-methylcytosine antibody

source_name: Input DNA from lung cancer tissues


title: Col-D1_1

value: wt

value: 1 d after treatment (DAT)


title: Col-D3_1

source_name: Col-0 leaves, DAT 3

value: 3 d after treatment (DAT)


title: Col-D2_1

source_name: Col-0 leaves, DAT 2

value: 2 d after treatment (DAT)


title: ore3-D0_1

source_name: ore3 leaves, DAT 0

value: control

value: 0 d after treatment (DAT)


title: ore3-D2_1

source_name: ore3 leaves, DAT 2


title: ore3-D1_1

source_name: ore3 leaves, DAT 1


title: Col-D0_1

source_name: Col-0 leaves, DAT 0


title: ore3-D3_1

source_name: ore3 leaves, DAT 3


title: Microglia_GCM_LN18_6h_rep3

status: Public on Apr 20 2018

city: Warsaw

first: Kacper

middle: Adam

last: Walentynowicz

address: Pastuera 3

department: Neurobiology Centre

country: Poland

institute: Nencki Institute of Experimental Biology PAS

hyb_protocol: Following fragmentation, 7.5 μg of aRNA was hybridized for 16h at 45oC onto 3'IVT GeneChip and Fluidics and Imagining was performed as described in the protocol (P/N 08-0246)

scan_protocol: Array Strips were scanned using GeneAtlas Imaging Station.

data_processing: Data was analysed using R andBioconductor package, perfect match probes were selected, QC was performed, data was normalized using `Robust Multi-Chip' rma command, and limma analysis was done exclusing low expressed genes. Data was corrected for batch effect and statistical analysis was performed.

source_name: Neonatal microglia in vitro treated with GCM for 6h

label_protocol: Following RT and second-starnd synthesis, cDNA was labelled with biotin for 16h at 40oC as recomened in the GeneAtlas 3'IVT Express Kit User Manual (P/N 702833)

growth_protocol: Microglia cells were seeded onto 60 mm plastic dishes (for non-adherent cultures) and incubated for 48 before start of the treatment in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco, MD, USA).

extract_protocol: RNA was extracted using Qiagen, RNeasy Mini Kit with RLT buffer containing β-mercaptoethanol; DNase on-column digestion was performed.

treatment_protocol: Following incubation for 48h post seedeing, fresh GCM was collected and microlia medeium was changed to GCM. Cells were incubated with GCM for 6h and lysed using Qiagen, RNeasy Mini Kit.

tag: strain

value: cortices

value: microglia

tag: stimulated with

value: Glioma Conditioned Medium (GCM) for 6h


title: Microglia_GCM_LN18_6h_rep2


title: Microglia_control_6h_rep3

source_name: Neonatal microglia in vitro control

value: none (control)


title: Microglia_GCM_U87_6h_rep3


title: Microglia_control_6h_rep2


title: Microglia_GCM_LN18_6h_rep1


title: Microglia_GCM_U87_6h_rep1


title: Microglia_GCM_U87_6h_rep2


title: Microglia_control_6h_rep1


title: HIEG clamp Muscle GSK subject #1 after TZD treatment

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70324.gif
Compound Based Treatment: yes

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 5320; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 6413; Parameter Laser Power = 3.53; Parameter Scan Time = 11:07:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.78; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 510; Parameter Scan Power = 100; Parameter Laser on time = 6413; Parameter Laser Power = 3.53; Parameter Scan Time = 11:07:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.78; Performer: Karine,,Clement

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-04-25; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #1 after TZD treatment after HIEG clamp; Parameter Date prepared = 2005-03-01; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-03-24; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 48 years; Parameter Species = human; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Developmental Stage = Type 2 Diabetic after TZD treatment; Parameter Sex/Mating type = female; Performer

value: Karine,,Clement

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-04-25; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Date prepared = 2005-03-01; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #1 after TZD treatment before HIEG clamp; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-03-24; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 48 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: HIEG clamp Muscle GSK subject #6 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70032.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 5480; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-16; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #6 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-12; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 49 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-16; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #6 before TZD treatment before HIEG clamp; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-12; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 49 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: HIEG clamp Muscle GSK subject #9 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70029.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1600, 5240; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-12; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #9 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-18; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 47 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-12; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #9 before TZD treatment before HIEG clamp; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-18; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 47 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: HIEG clamp Muscle GSK subject #1 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70028.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 5320; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-06; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-06; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-03; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #1 before TZD treatment after HIEG clamp; Parameter Date prepared = 2005-03-01; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-04-27; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 48 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = female; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-03; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Date prepared = 2005-03-01; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #1 before TZD treatment before HIEG clamp; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-04-27; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 48 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: HIEG clamp Muscle GSK subject #5 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70037.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5280; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-25; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #5 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-05-22; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 60 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = female; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-25; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #5 before TZD treatment before HIEG clamp; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-05-22; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 60 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: HIEG clamp Muscle GSK subject #7 after TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70328.gif
Compound Based Treatment: yes

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5400; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 6568; Parameter Laser Power = 3.52; Parameter Scan Time = 11:06:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.36; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 6591; Parameter Laser Power = 3.50; Parameter Scan Time = 11:06:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.36; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-19; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #7 after TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-13; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 52 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-19; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #7 after TZD treatment before HIEG clamp; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-13; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 52 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: HIEG clamp Muscle GSK subject #9 after TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70327.gif
Compound Based Treatment: yes

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1840, 5640; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 6633; Parameter Laser Power = 3.51; Parameter Scan Time = 12:22:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.28; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 6633; Parameter Laser Power = 3.51; Parameter Scan Time = 12:22:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.28; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #9 after TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-02-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-18; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 47 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #9 after TZD treatment before HIEG clamp; Parameter Date performed = 2006-02-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-18; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 47 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: EN9774

city: Houston

middle: F

last: Vera

state: Texas

address: 1102 Bates Ave

department: Center for Cell and Gene therapy

institute: Baylor College of Medicine

description:
20170801_mtb-EN-114400-NSXHPIm_EN9774_11.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter PanCancer Immune Profiling Panel containing 770 unique pairs of 35-50bp reporter probes and biotin-labeled capture probes, including internal reference controls. Overnight hybridization occurred for 20 hours at 65°C, then reactions were held at 4°C until they were placed on the nCounter Prep Station.  Wash protocol:  Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and flurophore degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 field of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v3.0.22.

data_processing: RCC files containing raw counts for 770 genes provided from nanostring were loaded into nSolver Analysis Software 3.0 and normalized for housekeeping genes and positive controls.

label: No label in Nanostring

source_name: SmarT-cells (CAR, TBBR and 4/7 ICR modified T cells)

label_protocol: No label is used in Nanostring

extract_protocol: RNA isolation was performed using the RNeasy mini plus kit (QIAGEN)

tag: subject

value: Donor 2

tag: cell type

value: Healthy human donor T cells


title: HIEG clamp Muscle GSK subject #8 after TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs//70322.gif
Compound Based Treatment: yes

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5600; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 6580; Parameter Laser Power = 3.51; Parameter Scan Time = 11:21:32; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 6454; Parameter Laser Power = 3.52; Parameter Scan Time = 11:54:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.77; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-31; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #8 after TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-14; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 64 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = female; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-31; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #8 after TZD treatment before HIEG clamp; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-14; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 64 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: HIEG clamp Muscle GSK subject #2 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70030.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 5320; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-04-20; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #2 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-03-29; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 53 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-04-20; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #2 before TZD treatment before HIEG clamp; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-03-29; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 53 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: HIEG clamp Muscle GSK subject #6 after TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70326.gif
Compound Based Treatment: yes

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 5480; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 6548; Parameter Laser Power = 3.52; Parameter Scan Time = 10:39:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.41; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 6548; Parameter Laser Power = 3.52; Parameter Scan Time = 10:39:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.41; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #6 after TZD treatment after HIEG clamp; Parameter Date prepared = 2006-01-10; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-12; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 49 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Date prepared = 2006-01-10; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #6 after TZD treatment before HIEG clamp; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-12; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 49 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: HIEG clamp Muscle GSK subject #4 after TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70325.gif
Compound Based Treatment: yes

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5280; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 6476; Parameter Laser Power = 3.52; Parameter Scan Time = 12:21:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.81; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 6476; Parameter Laser Power = 3.52; Parameter Scan Time = 12:21:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.81; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-04-24; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #4 after TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-04-11; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 40 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = female; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-04-24; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #4 after TZD treatment before HIEG clamp; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-04-11; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 40 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: EN9775

description:
20170801_mtb-EN-114400-NSXHPIm_EN9775_12.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

value: Donor 3


title: HIEG clamp Muscle GSK subject #7 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70033.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1760, 5920; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-18; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #7 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-13; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 52 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-18; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #7 before TZD treatment before HIEG clamp; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-13; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 52 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: HIEG clamp Muscle GSK subject #3 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70036.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5160; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #3 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-05-22; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 42 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #3 before TZD treatment before HIEG clamp; Parameter Date performed = 2005-03-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-05-22; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 42 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: EN9768

description:
20170801_mtb-EN-114400-NSXHPIm_EN9768_05.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: 1G CAR -modified T-cells


title: 7512578030_R06C02

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, R

label: not applicable

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions

tag: disease status

value: Healthy control

tag: gender

value: female

tag: age

tag: smoking status

value: never smoker

tag: tissue

value: peripheral blood


title: EN9775 (SmarT vs delta constructs)

tag: subject

tag: cell type


title: 7512578030_R06C01

value: MS case


title: EN9767

description:
20170801_mtb-EN-114400-NSXHPIm_EN9767_04.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

value: Donor 1


title: EN9773

description:
20170801_mtb-EN-114400-NSXHPIm_EN9773_10.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512578030_R05C02

value: ever smoker


title: EN9769

description:
20170801_mtb-EN-114400-NSXHPIm_EN9769_06.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: HIEG clamp Muscle GSK subject #8 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70034.gif
Compound Based Treatment: no

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5400; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #8 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-14; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 64 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = female; Performer

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #8 before TZD treatment before HIEG clamp; Parameter Date performed = 2006-01-10; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = two round amplification-Ambion; Parameter Date performed = 2006-04-14; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 64 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: 7512560163_R04C02


title: HIEG clamp Muscle GSK subject #2 after TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70323.gif
Compound Based Treatment: yes

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5300; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 6454; Parameter Laser Power = 3.52; Parameter Scan Time = 11:54:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.77; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 6454; Parameter Laser Power = 3.52; Parameter Scan Time = 11:54:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [114647]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.77; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #2 after TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-03-29; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 53 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #2 after TZD treatment before HIEG clamp; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-03-29; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 53 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic after TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: EN9773 (SmarT vs delta constructs)

extract_protocol: RNA isolation was performed using the RNeasy mini plus kit (QIAGEN)


title: 7512578030_R04C01


title: HIEG clamp Muscle GSK subject #4 before TZD treatment

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70031.gif
Compound Based Treatment: no

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #4 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-04-11; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 40 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = female; Performer

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #4 before TZD treatment before HIEG clamp; Parameter Date performed = 2005-05-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-04-11; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 40 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = female; Performer


title: 7512578030_R02C01


title: EN8932 (SmarT vs delta constructs)

description:
20170623_mtb-EN-113485-NSXPHIm_EN8932_09.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: delta-IL4R -modified T-cells


title: 7512560163_R06C02


title: 7512578030_R01C01


title: EN9774 (SmarT vs delta constructs)


title: 7512578030_R05C01


title: 7512560163_R05C02

value: male


title: 7512578030_R03C01


title: 7512560163_R01C02


title: EN8930 (SmarT vs delta constructs)

description:
20170623_mtb-EN-113485-NSXPHIm_EN8930_07.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: EN8931 (SmarT vs delta constructs)

description:
20170623_mtb-EN-113485-NSXPHIm_EN8931_08.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560163_R03C01


title: EN8949 (SmarT vs delta constructs)

description:
20170623_mtb-EN-113507-NSXHPIm_EN8949_08.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: delta-TGFbRII-modified T-cells


title: EN8948 (SmarT vs delta constructs)

description:
20170623_mtb-EN-113507-NSXHPIm_EN8948_07.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: EN8938 (SmarT vs delta constructs)

description:
20170627_mtb-EN-113508-NSXHPIm_EN8938_03.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: delta-CAR -modified T-cells


title: 7512560163_R01C01


title: 7512560133_R04C02


title: 7512578030_R04C02


title: 7512560133_R03C02


title: 7512560133_R06C02


title: 7512560163_R06C01


title: 7512560163_R02C01


title: 7512560163_R05C01


title: EN8937 (SmarT vs delta constructs)

description:
20170627_mtb-EN-113508-NSXHPIm_EN8937_02.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560163_R02C02


title: 7512560163_R03C02


title: EN8936 (SmarT vs delta constructs)

description:
20170627_mtb-EN-113508-NSXHPIm_EN8936_01.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560133_R01C02


title: EN8935

description:
20170623_mtb-EN-113485-NSXPHIm_EN8935_12.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: 4/7 ICR-modified T-cells


title: 7512560133_R05C02


title: EN8950 (SmarT vs delta constructs)

description:
20170623_mtb-EN-113507-NSXHPIm_EN8950_09.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560133_R06C01


title: EN8933

description:
20170623_mtb-EN-113485-NSXPHIm_EN8933_10.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560133_R05C01


title: 7512560133_R01C01


title: 7512560093_R06C02


title: 7512560133_R04C01


title: EN8932


title: 7512560133_R02C02


title: 7512560133_R02C01


title: 7512560093_R05C02


title: 7512560133_R03C01


title: 7512560093_R02C02


title: EN8930


title: EN8953

description:
20170623_mtb-EN-113507-NSXHPIm_EN8953_12.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: TBBR-modified T-cells


title: EN8931


title: EN8952

description:
20170623_mtb-EN-113507-NSXHPIm_EN8952_11.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560093_R01C01


title: 7512560093_R01C02


title: EN8934

description:
20170623_mtb-EN-113485-NSXPHIm_EN8934_11.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: EN8951

description:
20170623_mtb-EN-113507-NSXHPIm_EN8951_10.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560093_R03C01


title: 7512560093_R05C01


title: EN8950

source_name: delta-TGFbRII -modified T-cells


title: 7512560039_R06C02


title: 7512560039_R03C02


title: 7512560039_R02C02


title: 7512560093_R02C01


title: EN8948


title: 7512560039_R05C02


title: EN8941

description:
20170627_mtb-EN-113508-NSXHPIm_EN8941_06.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation

source_name: CAR-modified T-cells


title: 7512560039_R06C01


title: EN8940

description:
20170627_mtb-EN-113508-NSXHPIm_EN8940_05.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560093_R04C01


title: 7512560163_R04C01


title: 7512560093_R04C02


title: EN8949


title: EN8939

description:
20170627_mtb-EN-113508-NSXHPIm_EN8939_04.RCC
Nanostring data analysis on RNA isolated from transgenically modified human T cells sorted prior to stimulation


title: 7512560039_R04C02


title: 7512560093_R03C02


title: 7512560039_R01C02


title: 7512551044_R04C02


title: 7512560039_R05C01


title: 7512560039_R04C01


title: EN8938

source_name: delta-CAR-modified T-cells


title: 7512560039_R02C01


title: 7512560039_R01C01


title: 7512560093_R06C01


title: EN8937


title: EN8936


title: 7512551044_R01C02


title: 7512551044_R04C01


title: 7512551044_R06C02


title: 7512551044_R01C01


title: cl.413-transduced T cells treated with SGC0946, rep 3

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: A2/MART1 low-affinity TCR (cl.413)-transduced CD8+ T cells were cultured in the presence of SGC0946 and stimulated by the cognate antigen, rep 3

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 2.0 ST array for 16-18 hr at 45°C.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner #4)

data_processing: Raw intensity files were processed using Affymetrix Expression Console (version 1.4.1). Processed using RMA algorithm.

source_name: cl.413 TCR-transduced human CD8+ T cells treated with SGC0946, biological replicate #3

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate.

growth_protocol: Human CD8+ T cells were cultured in vitro (RPMI supplemented with 10% human AB serum, 100 IU/ml IL-2 and 10 ng/ml IL-15).

extract_protocol: RNA was collected from the stimulated T cells 24 hours later using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: CD8+ T cells were individually transduced with A2-MART127-35-specific high-affinity (DMF5) or low-affinity (cl.413) T cell receptor (TCR). TCR-transduced T cells were treated with SGC0946 or DMSO and further cultured for 7 days. After resting overnight in cytokine-free media, they were stimulated by artificial antigen presenting cells that express HLA-A2, CD80 and CD83 loaded with MART127-35 peptide.

value: CD8+ T cells

tag: tcr gene

tag: chemical probe

tag: donor


title: 7512551044_R05C02


title: 7512551044_R03C02


title: 7512551044_R06C01


title: cl.413-transduced T cells treated with DMSO, rep 3

description: A2/MART1 low-affinity TCR (cl.413)-transduced CD8+ T cells were cultured in the presence of control DMSO and stimulated by the cognate antigen, rep 3

source_name: cl.413 TCR-transduced human CD8+ T cells treated with DMSO, biological replicate #3

value: DMSO


title: 7512551044_R03C01


title: 7512551044_R02C02


title: 7512551044_R02C01


title: 7512551038_R06C02


title: cl.413-transduced T cells treated with DMSO, rep 2

description: A2/MART1 low-affinity TCR (cl.413)-transduced CD8+ T cells were cultured in the presence of control DMSO and stimulated by the cognate antigen, rep 2

source_name: cl.413 TCR-transduced human CD8+ T cells treated with DMSO, biological replicate #2


title: 7512551038_R03C02


title: 7512551038_R05C02


title: cl.413-transduced T cells treated with DMSO, rep 1

description: A2/MART1 low-affinity TCR (cl.413)-transduced CD8+ T cells were cultured in the presence of control DMSO and stimulated by the cognate antigen, rep 1

source_name: cl.413 TCR-transduced human CD8+ T cells treated with DMSO, biological replicate #1


title: cl.413-transduced T cells treated with SGC0946, rep 2

description: A2/MART1 low-affinity TCR (cl.413)-transduced CD8+ T cells were cultured in the presence of SGC0946 and stimulated by the cognate antigen, rep 2

source_name: cl.413 TCR-transduced human CD8+ T cells treated with SGC0946, biological replicate #2


title: 7512551038_R04C02


title: 7512551038_R02C02


title: 7512551038_R05C01


title: DMF5-transduced T cells treated with SGC0946, rep 3

description: A2/MART1 high-affinity TCR (DMF5)-transduced CD8+ T cells were cultured in the presence of SGC0946 and stimulated by the cognate antigen, rep 3

source_name: DMF5 TCR-transduced human CD8+ T cells treated with SGC0946, biological replicate #3


title: 7512551038_R06C01


title: 7512560039_R03C01


title: 7512551038_R01C02


title: 7512551038_R02C01


title: 7512551038_R03C01