title: Primary tumour from patient 55

source_name: bone marrow

value: Poor


title: Xenograft from patient 56

status: Public on May 14 2014

type: RNA

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: Hybridisation was performed as outlined in standard Illumina protocols

scan_protocol: Scanning was performed as outlined in standard Illumina protocols

data_processing: Data was exported from Illumina BeadStudio V3.0.14 with no normalisation and no background correction performed (non-normalised). Data was pre-processed using quantile normalisation (normalised) within the LIMMA package in R. Differential gene expression analysis was then performed using LIMMA in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD45+ MNC from spleen

label_protocol: Total RNA was amplified using TotalPrep RNA amplification kit (Ambion) and labelled according to standard Illumina protocols with included chemistry for this array. Arrays were analysed in house at Children's Cancer Institute of Australia, Sydney.

extract_protocol: TriZol Reagent extraction for total RNA.

tag: prednisolone response

value: Good

tag: Sex

value: M


title: Xenograft from patient 54


title: Xenograft from patient 55


title: Primary tumour from patient 56


title: Xenograft from patient 57

value: F


title: Xenograft from patient 26


title: Primary tumour from patient 50


title: Primary tumour from patient 57


title: Primary tumour from patient 51


title: Primary tumour from patient 26


title: Primary tumour from patient 53


title: Xenograft from patient 50


title: Xenograft from patient 51


title: T0901317_v_250

city: Zeist

first: Thomas

last: Kelder

address: Utrechtseweg 48

department: Microbiology & Systems Bioloby

country: Netherlands

institute: TNO

hyb_protocol: Per sample, 750ng of cRNA was used to hybridise to the MouseRef-8 v2 Expression BeadChip (Illumina, Inc., San Diego, CA, U.S.A.). Hybridisation and washing were performed according to the Illumina standard assay procedure.

scan_protocol: Scanning was performed on the Illumina BeadStation 500 (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: Image analysis and extraction of raw and background subtracted expression data were performed with Illumina Genomestudio Gene Expression software using default settings. The probe-level, background subtracted expression values were used as input for lumi package (Du et al. 2008) of the R/Bioconductor project (http://www.bioconductor.org; http://www.r-project.org). Probes were reannotated from the lumi generated nuID identifiers to illumina probeset identifiers using the lumiMouseAll.db bioconductor annotation package (bioconductor version 2.09). The lumi package was used to perform quality control of raw and normalised data and a quantile normalisation.  After the normalisation, unexpressed probes were removed from the further analyses. To be considered expressed, signal detection p-value of the probe was required to be lower than 0.01 in at least one of experiments.

organism: Mus musculus

source_name: T0901317_visceral adipose

label_protocol: The quality control of RNA samples, RNA labelling and hybridisation were performed at ServiceXS (Leiden, The Netherlands). RNA concentration and purity were assessed using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, U.S.A). The RNA quality and integrity was determined using Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.).  Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturers specifications starting with 500 ng total RNA.

growth_protocol: Male LDLr-/- mice, age 10-14 weeks at the start of the experiment, originated from JAX (The Jackson Laboratory, Bar Harbor, Maine 04609, USA) and (3 mice per cage) with a 12 h light-dark cycle (7 a.m.-7 p.m. lights on). The mice had free access to food and water and remained on maintenance chow (Sniff R/M diet V1530, Uden, The Netherlands) until the start of the study.  The mice had free access to food and water and remained on maintenance chow (Sniff R/M diet V1530, Uden, The Netherlands) until the start of the study.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II kit from Macherey-Nagel. RNA samples (eluted in water) were stored at -80 degrees C.

treatment_protocol: During a run-in period of nine weeks, mice were fed Western type, lard based high fat diet (HFD; Research Diets, New Brunswick, NJ; Diet D12541) to establish experimental conditions of obesity-associated hyperglycemia, hyperinsulinemia, hypertriglyceridemia and hypercholesterolemia. One group (n=9) remained on maintenance chow throughout the entire study period (16 weeks) and served as healthy, age-matched control. After the nine week run-in period, the HFD fed mice were matched into thirteen groups based on body weight. The first group (n=9) was sacrificed immediately after matching. The second group (n=15) was continued on HFD until the end of the experiment at t=16 weeks. The fourth group (n=9) was switched to regular chow (dietary lifestyle intervention). The other groups (each n=9) continued on HFD supplemented with drugs typically used in clinical practice. More specifically, following drugs were mixed into HFD ; rosiglitazone (0.010% w/w), pioglitazone (0.010% w/w), T0901317 (0.010% w/w) and salicylate (0.40% w/w).

tag: strain background

tag: genotype/variation

value: LDLR-/-

tag: gender

value: male

tag: age

value: 10-14 wks at the start of the experiment

tag: treatment group

value: HFD 9wks + HFD w/ T0901317 7 wks

tag: tissue

value: Visceral adipose tissue

tag: total duration

value: 16 weeks


title: Xenograft from patient 52


title: Primary tumour from patient 52


title: Primary tumour from patient 54


title: T0901317_v_248


title: T0901317_v_251


title: T0901317_v_243


title: T0901317_v_247


title: T0901317_v_246


title: T0901317_v_244


title: T0901317_s_251

source_name: T0901317_subcutaneous adipose

value: Subcutaneous adipose tissue


title: T0901317_s_245


title: Salicylate_v_303

source_name: Salicylate_visceral adipose

value: HFD 9wks + HFD w/ Salicylate 7 wks


title: T0901317_g_247

source_name: T0901317_gonadal adipose

value: Gonadal adipose tissue


title: T0901317_g_245


title: T0901317_g_244


title: T0901317_s_247


title: T0901317_s_246


title: T0901317_g_246


title: T0901317_s_243


title: Salicylate_v_301


title: Salicylate_v_300


title: Salicylate_v_302


title: Salicylate_v_304


title: Salicylate_v_297


title: Wnt3a_G1_rep4

status: Public on May 15 2014

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: replicate 4

hyb_protocol: Microarrays were hybridized following Illumina's standard hybridization protocol on HumanHT-12 v4 expression BeadChips.

scan_protocol: Processed arrays were scanned on Illumina iScan System array reader according to the manufacturer's instructions.

data_processing: Raw microarray data were imported and preprocessed in GenomeStudio V2011.1 software (Illumina) using background subtraction and quantile normalization. Differential expression analysis of the grouped replicate samples was performed within GenomeStudio on the probe level utilizing the Illumina custom error model with FDR multiple-testing correction.

source_name: G1 phase HeLa cells_Wnt3a CM

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep kit for Illumina arrays.

growth_protocol: HeLa cells were cultured at 37°C with 5% CO2 in RPMI medium supplemented with 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) with on-column DNase digestion following the manufacturer's protocol, quantified with a Thermo NanoDrop and the RNA quality was tested on agarose gel and on Agilent Bioanalyzer.

treatment_protocol: Cells in 15-cm dish plates at 80% confluency were treated for 3 h with either Control, Wnt3a or Dkk1 conditioned media (1:5 dilutions), live-stained with 10 μM Hoechst 33342 in the last 1 h of the treatment, resuspended in ice-cold sorting buffer (DMEM supplemented with 1 μM Hoechst, 5% serum and 1 mM EDTA) and FACS-sorted directly into RLT lysis buffer (Qiagen) on a FacsAria I (BD).

tag: cell line

value: HeLa

tag: cell type

value: cervical carcinoma cells

tag: cell cycle phase

tag: treated with

value: Wnt3a conditioned medium (CM) for 3hr


title: T0901317_s_250


title: T0901317_g_250


title: T0901317_g_251


title: T0901317_s_248


title: Salicylate_s_303

source_name: Salicylate_subcutaneous adipose


title: T0901317_g_243


title: Salicylate_v_298


title: Salicylate_v_305


title: Salicylate_s_305


title: Salicylate_s_298


title: Salicylate_s_301


title: Salicylate_g_302

source_name: Salicylate_gonadal adipose


title: Salicylate_s_304


title: Salicylate_g_303


title: Rosiglitazone_v_277

source_name: Rosiglitazone_visceral adipose

value: HFD 9wks + HFD w/ Rosiglitazone 7 wks


title: Rosiglitazone_v_275


title: Salicylate_g_305


title: Rosiglitazone_v_271


title: Rosiglitazone_v_270


title: Salicylate_s_302


title: Salicylate_g_304


title: Rosiglitazone_v_278


title: Rosiglitazone_s_273

source_name: Rosiglitazone_subcutaneous adipose


title: Rosiglitazone_s_278


title: Rosiglitazone_s_272


title: Salicylate_g_297


title: Skambucha_DSBs_01

type: genomic

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

country: USA

institute: University of California San Francisco

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.7.3.1).

data_processing: In addition to dark spot and control probes, custom probes for repetitive S. pombe DNA were also removed.  Due to the sequence divergence of the S. kambucha genome, some probes may not have efficiently hybridized to the immunoprecipitates.  To identify potentially incompatible probes, the whole-cell input channel was compared with that of a previously published S. pombe DSB array (Fowler et al., 2013).  When log-transformed and plotted, the dye-intensities of >99% of probes were generally linear, indicating efficient hybridization; a small subpopulation exhibited significantly reduced dye signal.  Probes whose dye-intensity was < 1.5 (on a log scale) in either input channel were removed.

molecule: genomic DNA

organism: Schizosaccharomyces kambucha (nom. inval.)

source_name: IP Rec12-FLAG

label_protocol: Immunoprecipitated material and whole-cell extracts were PCR amplified to increase signal and Cy3/Cy5-labeled dUTPs were incorporated.

growth_protocol: Using S. kambucha diploids homozygous for rad50S and rec12-FLAG, 10 mL YEL cultures were started from single colonies and grown overnight at 30 degrees.  These cultures were diluted the next day (1:100 or 1:50) into 100 mL PM medium and grown overnight (~16 hours) at 30 degrees to an OD600 ~1.  Cells from 50 mL were then pelleted and resuspended in 500 mL PM minus nitrogen medium to induce sporulation.  The cells sporulated at 30 degrees.

extract_protocol: Cells were collected after 8.5 hours and lysed without exogenous crosslinking agents.  Cells were first treated with protease inhibitors and then broken with a bead beater, chromatin was sonicated to ~500-1000 bp, and Rec12-FLAG immunoprecipitated.

value: diploid homozygous for rad50S and rec12-FLAG

tag: time

value: 8.5 hours

source_name: Whole-cell input from meiotic cells


title: Rosiglitazone_s_271


title: Rosiglitazone_s_277


title: Rosiglitazone_s_270


title: Rosiglitazone_v_272


title: Rosiglitazone_s_274


title: Salicylate_g_301


title: Rosiglitazone_s_275


title: Salicylate_g_298


title: Rosiglitazone_v_273


title: Rosiglitazone_g_278

source_name: Rosiglitazone_gonadal adipose


title: Rosiglitazone_v_274


title: Salicylate_s_297


title: Salicylate_g_300


title: Rosiglitazone_g_274


title: Rosiglitazone_g_272


title: Rosiglitazone_g_277


title: Pioglitazone_v_282

source_name: Pioglitazone_visceral adipose

value: HFD 9wks + HFD w/ Pioglitazone 7 wks


title: Pioglitazone_v_281


title: Rosiglitazone_g_275


title: Rosiglitazone_g_270


title: Salicylate_s_300


title: Rosiglitazone_g_273


title: Pioglitazone_v_284


title: Pioglitazone_v_287


title: wt_media_wt-1-a

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA

data_processing:
Imagene feature extraction (genes, no bg corr, dye corr)
The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: robot amplification and labeling v1.0

growth_protocol: deletion strain-conditioned media: Wild type and deletion strains were grown for two cell doublings in synthetic complete (SC) media containing 2% glucose. Cells were then harvested by centrifugation at 3952 x g for 3 minutes. The supernatant was decanted and filtered through a 2 µm filter. This pre-conditioned media was then added to wild type cells which were also allowed to grow for two cells doublings before harvesting.

extract_protocol: yeast HTP RNA isolation for robot v2.0

tag: strain

value: wild type

tag: growth medium

value: reference


title: Pioglitazone_v_280

value: LDLR-/-

value: male


title: wt_media_cho2-1-a


title: wt_media_wt-1-b


title: Pioglitazone_v_286

value: 10-14 wks at the start of the experiment


title: Pioglitazone_s_280

source_name: Pioglitazone_subcutaneous adipose


title: Pioglitazone_s_286


title: Pioglitazone_s_285


title: Pioglitazone_s_284


title: wt_media_cho2-1-b


title: wt_media_bur2-1-b


title: Pioglitazone_s_281


title: DL009-wt_in_wt-medium-1b

value: wt-medium


title: DL009-wt_in_npl3-medium


title: wt_media_bur2-1-a


title: DL009-wt_in_cbf1-medium-1a


title: DL009-wt_in_wt-medium-1a


title: Pioglitazone_s_279

value: 16 weeks


title: Pioglitazone_g_282

source_name: Pioglitazone_gonadal adipose


title: DL009-wt_in_npl3-medium-1b


title: wt-37C-t60-1-b

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

growth_protocol: Cells were grown in SC media containing 2% glucose at 30 C for two cell doublings, harvested by centrifugation (3952 x g for 3 minutes) and then re-suspended in 37 C media. Cells were then harvested at the indicated time points by centrifugation.

tag: treatment

value: heat shock

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0


title: DL009-wt_in_cbf1-medium-1b


title: Pioglitazone_s_287

value: Subcutaneous adipose tissue


title: Pioglitazone_g_286

value: Gonadal adipose tissue


title: Pioglitazone_s_282


title: wt-37C-t45-1-a


title: 9wkHFD_v_78

source_name: 9wkHFD_visceral adipose

value: HFD 9wks_sacrificed

value: Visceral adipose tissue

value: 9 weeks


title: wt-37C-t45-1-b


title: Pioglitazone_g_281


title: Pioglitazone_g_284


title: 9wkHFD_v_50


title: Rosiglitazone_g_271

value: HFD 9wks + HFD w/ Rosiglitazone 7 wks


title: Pioglitazone_g_285


title: wt-37C-t5-1-a


title: wt-37C-t5-1-b


title: 9wkHFD_v_41


title: wt-37C-t30-1-a


title: wt-37C-t15-1-b


title: wt-37C-t60-1-a


title: wt-37C-t15-1-a


title: Pioglitazone_g_279


title: 9wkHFD_v_103


title: wt-37C-t30-1-b


title: 9wkHFD_s_78

source_name: 9wkHFD_subcutaneous adipose


title: wt-30C-t45-1-b

growth_protocol: Cells were grown in SC media containing 2% glucose at 37 C for two cell doublings, harvested by centrifugation (3952 x g for 3 minutes) and then re-suspended in 30 C media. Cells were then harvested at the indicated time points by centrifugation.

value: cold shock


title: Pioglitazone_g_280


title: 9wkHFD_s_81


title: wt-30C-t5-1-b


title: 9wkHFD_v_22


title: 9wkHFD_v_120


title: wt-30C-t5-1-a


title: wt-30C-t60-1-b


title: wt-30C-t60-1-a


title: 9wkHFD_s_77


title: 9wkHFD_s_50


title: wt-30C-t45-1-a


title: wt-30C-t30-1-a


title: 9wkHFD_s_22


title: wt-30C-t30-1-b


title: wt-30C-t15-1-a


title: wt-plasm-YCpLac111-V-10000uM_Pi-2-b

growth_protocol: 10 mM phosphate

source_name: refpool


title: wt-30C-t0-1-a


title: wt-30C-t0-1-b


title: wt-30C-t15-1-b


title: 9wkHFD_g_22

source_name: 9wkHFD_gonadal adipose


title: wt-plasm-YCpLac111-V-75uM_Pi-1-b

growth_protocol: 75 µM phosphate

tag: teatment


title: 9wkHFD_s_41


title: 9wkHFD_g_50


title: 9wkHFD_s_103


title: 9wkHFD_s_120


title: Lifestyle_v_310

source_name: Lifestyle_visceral adipose

value: HFD 9 wks_regular chow 7 wks (dietary lifestyle intervention)


title: 9wkHFD_g_77


title: wt-plasm-YCpLac111-V-75uM_Pi-1-a


title: Lifestyle_v_314


title: 9wkHFD_g_103


title: Lifestyle_v_312


title: Lifestyle_s_314

source_name: Lifestyle_subcutaneous adipose


title: Lifestyle_s_313


title: Lifestyle_v_306


title: Lifestyle_v_307


title: 9wkHFD_g_41


title: Lifestyle_v_313


title: Lifestyle_v_309


title: 9wkHFD_g_81


title: 9wkHFD_g_78


title: Lifestyle_s_306


title: Lifestyle_s_307


title: Lifestyle_s_312


title: Lifestyle_g_312

source_name: Lifestyle_gonadal adipose


title: Lifestyle_s_310


title: Lifestyle_g_310


title: Lifestyle_g_314


title: Lifestyle_s_311


title: Lifestyle_g_313


title: Lifestyle_g_306


title: 9wkHFD_g_120


title: Lifestyle_s_309


title: Lifestyle_g_311


title: Lifestyle_g_309


title: chow_v_323

source_name: chow_visceral adipose

value: Chow 16wks (control)


title: chow_v_318


title: Pioglitazone_g_287

value: HFD 9wks + HFD w/ Pioglitazone 7 wks


title: chow_v_315


title: chow_v_319


title: chow_v_316


title: Lifestyle_g_307


title: chow_v_320


title: chow_v_321


title: chow_s_323

source_name: chow_subcutaneous adipose


title: chow_v_317


title: chow_s_320


title: chow_g_321

source_name: chow_gonadal adipose


title: chow_s_319


title: chow_s_317


title: chow_s_318


title: chow_s_316


title: chow_g_317


title: chow_g_319


title: 16wkHFD_v_214

source_name: 16wkHFD_visceral adipose

value: HFD for 16wks


title: chow_g_318

value: LDLR-/-


title: chow_g_320

value: male


title: 16wkHFD_v_213

value: 10-14 wks at the start of the experiment


title: 16wkHFD_v_211


title: wt-plasm-YCpLac111-V-10000uM_Pi-2-a

value: wild type


title: 16wkHFD_v_209

value: 16 weeks


title: 16wkHFD_s_209

source_name: 16wkHFD_subcutaneous adipose


title: 16wkHFD_s_213


title: 16wkHFD_g_211

source_name: 16wkHFD_gonadal adipose


title: chow_s_321


title: 16wkHFD_g_214


title: 16wkHFD_s_214


title: chow_g_323


title: Patient 52 Br02

city: Milan

first: Elisabetta

last: Crippa

address: Via Adamello 16

country: Italy

institute: IFOM-FIRC Institute of Molecular Oncology

description: No additional information

hyb_protocol: Labeled targets from five micrograms of total RNA were hybridized on miRNA microarrays The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris-HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate.

scan_protocol: Processed slides were scanned by using a GenePix 4000B Scanner with the laser set to 635 nm, at power 100 and PMT 800 settings, and a scan resolution of 10 μm. Scanner images were quantified by the GenePix Pro 6.0.0.74 software (Molecular Devices).

data_processing: Poor signal quality of background-corrected intensities were flagged and removed from the analysis, all intensities below 200 were thresholded to the value of 200; the expression values were log2 transformed and a lowess normalization was applied to each slide, using the internal replicates for the normalization. Thenormalized log2-tranformed expression ratios (sample/reference) of each miRNA were averaged and the arrays were median centered. Only the human miRNAs (hsa-miR) were used for further analyses. The miRNA datasets were filtered by removing miRNAs having more than 50% missing (invalid) values for analysis.

source_name: primary breast cancer

label_protocol: Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris-HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.

extract_protocol: RNA isolation was performed using TRIZOL Reagent (Invitrogen) according to manufacturer's instructions. Briefly, colon tissue was homogenized in TRIZOL reagent and chloroform was added and liquid phases were separated with centrifugation. The supernatant was collected and RNA was precipitated with isopropanol washed with 75% ethanol. RNA was resuspended in DEPC treated water and 5 micrograms were used for each microarray experiment.

tag: mutation type

tag: histologic subtype

value: Infiltrating ductal carcinoma

tag: tumour grade

tag: estrogen receptor status

value: negative

tag: progesterone status

value: positive

tag: human epidermal growth factor 2 receptor status


title: 16wkHFD_s_202

tag: strain background

tag: genotype/variation

tag: gender

tag: age

tag: treatment group

tag: tissue

value: Subcutaneous adipose tissue


title: 16wkHFD_v_208

value: Visceral adipose tissue

tag: total duration


title: 16wkHFD_g_209

value: Gonadal adipose tissue


title: 16wkHFD_s_208


title: 16wkHFD_s_211


title: Patient 50 Br31

description: No additional information


title: 16wkHFD_g_213


title: chow_g_316


title: 16wkHFD_v_207


title: 16wkHFD_s_207


title: Patient 49 Br78

description: No additional information

value: BRCAx


title: Hif-1αLSL/LSL

city: Ann Arbor

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

description:
Gene expression data from colons.
Shah_020

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene 1.1 ST Array Strips using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment. RMA was used to fit log2 transformed expression values.

source_name: Colon

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3).

growth_protocol: All mice were C57BL/6 background and maintained in standard cages in a light and temperature-controlled room and were allowed standard chow and water ad libitum.

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

treatment_protocol: Colon mucosal scrapings were got from 6 to 8 weeks old mice

tag: strain

value: 6 to 8 weeks old

value: Colon mucosal scrapings


title: Patient 46 Br24

description: No additional information


title: Patient 47 Br70

description: No additional information


title: Patient 45 Br12

description: No additional information


title: 16wkHFD_g_202


title: Patient 44 Br10

description: No additional information


title: 16wkHFD_g_208


title: Hif-1α+/+

description:
Gene expression data from colons.
Shah_019


title: Cortex_19

city: Boston

first: Meeta

last: Mistry

state: MA

address: 655 Huntington Ave

institute: Harvard School of Public Health

description: Tie2-GFP reporter mouse to purify endothelial cells from E13.5 mouse lung

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip  Scanner 3000).

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) from the Bioconductor affy package using default analysis settings. The corrected PM probes were normalized using quantile normalization and expression measure calculated using median polish. The arrayQualityMetrics package in Bioconductor was used for QC analysis and no outliers were identified.

source_name: Endothelial cells from E13.5 mouse brain

label_protocol: Biotinylated cDNA were prepared according to the NuGEN Ovation RAN Amplification system V2 and FL-Ovation cDNA   Biotin Module V2  kits from 15-30ng  total RNA.

growth_protocol: Homozygous Tie2-GFP transgenic mice (Jackson laboratory, strain 003658) were used for BBB transcriptional profiling. Pregnant mice were obtained following overnight mating (day of vaginal plug was defined as embryonic day 0.5).

extract_protocol: RNA was purified with Arcturus PicoPure RNA isolation kit (Applied biosystemsTM), followed by NuGEN Ovation V2 standard linear amplification and hybridization to Affymetrix Mouse Genome 430 2.0 Array.

treatment_protocol: E13.5 Tie2-GFP embryos were micro-dissected for cortex and lungs. Cortex tissue was carefully cleared of the meninges and choroid plexus.Each tissue was diced with a scalpel, and enzymatically dissociated with a standard collagenase based assay before FACS sorting.

value: Cortex

tag: sample number

tag: cell type

value: GFP positive cells


title: Lung_19

description: Tie2-GFP reporter mouse to purify endothelial cells from E13.5 mouse brain

source_name: Endothelial cells from E13.5 mouse lung

value: Lung

value: Homozygous Tie2-GFP transgenic mice (Jackson laboratory, strain 003658)


title: Patient 43 Br52

description: No additional information

value: Sporadic


title: Patient 42 Br46

description: No additional information

value: Infiltrating ductal carcinoma + gelatinous


title: Cortex_18


title: Patient 51 Br06

description: No additional information

value: Infiltrating ductal carcinoma+infiltrating lobular carinoma


title: Lung_18


title: 16wkHFD_g_207

value: LDLR-/-

value: male

value: 10-14 wks at the start of the experiment

value: HFD for 16wks

value: 16 weeks


title: 16wkHFD_g_205


title: Patient 41 Br33

description: No additional information

value: Infiltrating ductal carcinoma

value: positive

value: negative


title: Patient 40 Br26

description: No additional information


title: Lung_22


title: Cortex_22


title: Patient 48 Br74

description: No additional information

value: BRCAx


title: Lung_72


title: Patient 39 Br94

description: No additional information

value: Infiltrating lobular carinoma


title: Patient 38 Br93

description: No additional information


title: Patient 36 Br85

description: No additional information

value: Gelatinous


title: Patient 37 Br87

description: No additional information


title: Patient 35 Br84

description: No additional information


title: Cortex_72

value: Cortex

value: GFP positive cells


title: 1004-140003_wk12_LS

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 6.

source_name: skin biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: For each patient, one 4-mm skin punch biopsy was collected from lesion located on the trunk or extremities with approximately 0.5 mm or more of induration and approximately 5 mm from the edge of the plaque, and another from macroscopically normal non-lesion on a similar body area to the biopsy plaque (i.e. arm, arm or leg, leg).  Biopsies were kept frozen –80oC until RNA preparation.

tag: subject

tag: visit

value: week 12

tag: skin

value: LS


title: 1005-150005_wk12_LS


title: 1004-140005_wk12_LS


title: Patient 32 Br76

description: No additional information

tag: mutation type

tag: histologic subtype

tag: tumour grade


title: Patient 33 Br80

description: No additional information

tag: estrogen receptor status

tag: progesterone status

tag: human epidermal growth factor 2 receptor status


title: 1004-140002_wk12_LS


title: 1003-130005_wk1_LS

value: week 1


title: 1004-140004_wk12_LS


title: 1004-140003_wk1_LS


title: monocyte-recovery-basal-8

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted at the probe level with background correction using Illumina's BeadStudio software. These raw data were then quantile normalized in R v2.15.2

source_name: patient recovering from sepsis

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Monocytes cultured in complete DMEM media supplemented with antibiotics (100 IU/ml penicillin and 100 µg/ml streptomycin) , in a humidified incubator at 37 °C and 5% CO2.

extract_protocol: RNA was extracted from monocytes using an RNAasy Mini Kit (Qiagen) as per manufacterers specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in microarray assay.

treatment_protocol: Monocytes cultured were untreated or treated ex vivo with LPS(100ng/ml)  for 3h.

tag: treatment

tag: cell

value: monocyte


title: monocyte-sepsis-basal-8

scan_protocol: According to beadchip array manufacturer's protocol

source_name: patient with sepsis


title: 1004-140007_wk12_LS


title: 1005-150002_wk12_LS


title: 1005-150005_wk1_LS


title: 1004-140002_wk1_LS


title: Patient 34 Br81

description: No additional information


title: 1004-140006_wk12_LS


title: Patient 30 Br72

description: No additional information


title: monocyte-sepsis-lps-8

value: LPS


title: 1005-150006_wk1_LS


title: monocyte-recovery-lps-8


title: Patient 31 Br75

description: No additional information


title: Patient 29 Br71

description: No additional information


title: Patient 28 Br69

description: No additional information


title: monocyte-sepsis-lps-7


title: monocyte-sepsis-basal-7


title: Patient 27 Br67

description: No additional information


title: Patient 26 Br62

description: No additional information


title: 1004-140006_wk1_LS


title: Patient 24 Br58

description: No additional information


title: Patient 25 Br61

description: No additional information

value: Sporadic

value: Infiltrating ductal carcinoma + gelatinous


title: 1005-150002_wk1_LS


title: Patient 23 Br57

description: No additional information


title: 1004-140004_wk1_LS


title: Patient 22 Br53

description: No additional information


title: monocyte-recovery-basal-7


title: 1007-170005_Baseline_NL

value: Baseline

value: NL


title: Patient 20 Br50

description: No additional information


title: Patient 21 Br51

description: No additional information

value: Infiltrating ductal carcinoma+infiltrating lobular carinoma


title: monocyte-sepsis-lps-6


title: monocyte-sepsis-lps-5


title: Patient 19 Br49

description: No additional information

value: Infiltrating ductal carcinoma


title: 1004-140001_Baseline_NL


title: 1003-130004_Baseline_NL


title: monocyte-recovery-lps-7


title: 1005-150003_Baseline_NL


title: 1004-140007_wk1_LS


title: monocyte-recovery-lps-5


title: 1005-150001_Baseline_NL


title: monocyte-sepsis-basal-5


title: monocyte-sepsis-basal-6


title: Patient 18 Br45

description: No additional information

value: positive

value: negative


title: 1007-170006_Baseline_NL


title: monocyte-recovery-lps-6


title: 1007-170007_Baseline_NL


title: monocyte-recovery-basal-6


title: Patient 17 Br44

description: No additional information

value: Unknown


title: monocyte-recovery-basal-5


title: 1003-130001_Baseline_NL


title: Patient 16 Br43

description: No additional information


title: monocyte-sepsis-basal-4


title: monocyte-recovery-lps-4


title: Patient 15 Br42

description: No additional information


title: 1010-010001_Baseline_NL


title: 1010-010006_Baseline_NL


title: Patient 14 Br41

description: No additional information


title: 1007-170002_Baseline_NL


title: Patient 13 Br40

description: No additional information


title: 1004-140002_Baseline_NL


title: Preeclampsia-S_A, rep13

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description:
3031_4
Whole blood transcriptome (PAXgene derived).

hyb_protocol: The hybridization was carried out for 17 hours at 65°C using the QIamp labeling kit.

scan_protocol: The microarray slides were scanned with the DNA Microarray scanner G2505C at resolution of 5 µm. The scanned images were analyzed with Feature Extraction Software 10.5.1.

data_processing: The analysis of microarray data was performed and the figures were created using the R (v.2.13) and the Bioconductor software suite. The raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were carried out using hierarchical clustering, principal component analysis (made4 library) and the Linear Models for Microarray Analysis (limma library). We considered genes as differentially expressed when corrected p-value was below 0.05 and the absolute fold change (FC) was higher than 1.5. Two microarrays were discarded from the analysis for technical reasons. Thus, only 36 microarrays are presented.

source_name: preeclampsia, severe, A

label_protocol: In brief, 400 ng of RNA were labeled with cyanine-3 CTP using a Low RNA Input Fluorescent Amplification kit.

extract_protocol: Venous blood samples (2.5 ml) were collected at the time of inclusion in PAXgene tubes (PreAnalytic, Hombrechtikon, Switzerland) at room temperature for 2 hours before freezing. RNA was extracted using PAXgene Blood RNA Kit (Qiagen) with a DNase I step to eliminate DNA contaminants, according to the manufacturer recommendations. The quantity and the quality of RNA were assessed using Nanodrop (Thermo Science, Orsay, France) and a 2100 Bioanalyseur (Agilent Technologies, Massy, France), respectively.

value: blood

tag: disease status

value: preeclampsia

tag: matching

value: A

tag: age

tag: severity

value: S

tag: gestational age (weeks)


title: Patient 12 Br36

description: No additional information


title: monocyte-recovery-basal-4


title: monocyte-healthy-lps-6

source_name: healthy donor


title: 1004-140003_Baseline_NL


title: monocyte-healthy-basal-6


title: monocyte-healthy-lps-5


title: Healthy-NA_B, rep17

description:
3031_2
Whole blood transcriptome (PAXgene derived).

source_name: healthy, B

tag: tissue

value: healthy

value: B


title: Healthy-NA_B, rep18

description:
3031_3
Whole blood transcriptome (PAXgene derived).


title: Patient 11 Br29

description: No additional information


title: monocyte-healthy-basal-5

value: monocyte


title: NGAL overexpression replicate2

city: shantou

first: Enmin

state: guangdong

address: 22 Xinling Road

country: China

institute: Shantou university, medical college

description: Biological replicate 2 of 2. NGAL overexpression compared to empty plasmid.

hyb_protocol: Samples were hybridized with Agilent whole genome oligo microarray in Agilent’s SureHyb Hybridization Chambers according to manufacturer’s instructions.

scan_protocol: After hybridization and washing, the processed slides were scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies.

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 9.5.3) were imported into the Agilent GeneSpring GX software (version 7.3) for further analysis.  The microarray data sets were normalized in GeneSpring GX using the Agilent FE Two-color scenario (LOWESS normalization), and then genes marked present or marginal (“All Targets Value”) were chosen for further analysis. For the 2-color default normalization, (Per Spot and Per Chip: Intensity dependent (Lowess) normalization), each raw intensity value corresponding to the control channel was adjusted using a locally-weighted regression method called Lowess. Signal values for treatment and control were averaged across the two replicates using the raw values for the treatment samples and the Lowess-normalized values for the control samples. All normalized signal values for each channel of each replicate, average signal values for treatment and control and fold changes can be found in the file Gene_Expression_Profiling_Data_Analysis_Report.xls located on the series level. The log 2 ratio of treatment (test)/control (reference) was calculated by dividing the raw treatment signal value by the lowess-normalized control signal value for each sample.

label_protocol: After having passed RNA measurement on the Nanodrop ND-1000 and denaturing gel electrophoresis, the samples were amplified and labeled using the Agilent Quick Amp labeling kit according to manufacturer’s instructions. A repeat was performed by dye-swap.

growth_protocol: Cells were maintained in 199 medium (Invitrogen) containing 10% fetal calf serum (FCS) in an atmosphere of 5% CO2 at 37 ℃. Stable transfected cell clones were selected by G418.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

treatment_protocol: pcDNA3.0-NGAL and pcDNA3.0 were transfected into ESCC cell line EC109, respectively. Stable transfected cell clones were selected by G418, the overexpression of NGAL protein were confirmed by western blot. Total RNAs from NGAL overexpressed cells and control cells were extracted for Agilent whole genome oligo microarray.

tag: cell line

tag: cell type

value: esophageal squamous cell carcinoma

tag: transfection plasmid

value: NGAL


title: Patient 10 Br28

description: No additional information

tag: mutation type


title: Preeclampsia-S_A, rep11

description:
3030_4
Whole blood transcriptome (PAXgene derived).


title: Preeclampsia-S_A, rep12

description:
3031_1
Whole blood transcriptome (PAXgene derived).


title: Patient 9 Br27

description: No additional information

tag: histologic subtype

value: Infiltrating lobular carcinoma


title: Preeclampsia-NS_C, rep5

description:
3030_2
Whole blood transcriptome (PAXgene derived).

source_name: preeclampsia, non-severe, C

value: C

value: NS


title: 1003-130005_Baseline_NL

tag: subject

tag: visit

value: Baseline

tag: skin

value: NL


title: 1005-150005_Baseline_NL


title: 1004-140005_Baseline_NL


title: Patient 8 Br22

description: No additional information

value: Infiltrating ductal carcinoma+infiltrating lobular carinoma

tag: tumour grade

tag: estrogen receptor status

value: positive

tag: progesterone status

tag: human epidermal growth factor 2 receptor status


title: monocyte-healthy-basal-4

tag: treatment

tag: cell


title: monocyte-healthy-lps-4

value: LPS


title: Patient 7 Br20

description: No additional information

value: Infiltrating lobular carinoma

value: negative


title: 1005-150006_Baseline_NL


title: 1005-150002_Baseline_NL


title: Healthy-NA_B, rep16

description:
3030_1
Whole blood transcriptome (PAXgene derived).

value: blood

tag: disease status

tag: matching

tag: age

tag: severity


title: Patient 6 Br18

description: No additional information

value: Infiltrating ductal carcinoma


title: Healthy-NA_B, rep15

description:
3029_2
Whole blood transcriptome (PAXgene derived).

tag: tissue

value: healthy

tag: gestational age (weeks)


title: 1004-140007_Baseline_NL


title: Patient 5 Br15

description: No additional information

tag: mutation type

value: Adenocarcinoma


title: Preeclampsia-S_A, rep10

description:
3029_1
Whole blood transcriptome (PAXgene derived).

value: preeclampsia

value: A

value: S


title: Healthy-NA_B, rep13

description:
3028_3
Whole blood transcriptome (PAXgene derived).

value: B


title: 1007-170007_Baseline_LS

value: LS


title: monocyte-sepsis-lps-3

value: monocyte


title: Patient 4 Br08

description: No additional information

tag: histologic subtype


title: 1004-140006_Baseline_NL

tag: subject

value: Baseline


title: 1007-170005_Baseline_LS

tag: visit


title: Healthy-NA_B, rep14

description:
3028_4
Whole blood transcriptome (PAXgene derived).


title: Patient 3 Br03

description: No additional information


title: monocyte-recovery-lps-3


title: Healthy-NA_B, rep12

description:
3028_2
Whole blood transcriptome (PAXgene derived).


title: monocyte-healthy-lps-3


title: 1004-140001_Baseline_LS

tag: skin


title: monocyte-recovery-basal-3


title: monocyte-healthy-basal-3


title: Healthy-NA_B, rep11

description:
3028_1
Whole blood transcriptome (PAXgene derived).


title: 1003-130004_Baseline_LS


title: monocyte-sepsis-lps-2


title: Patient 1 Br55

description: No additional information

value: Sporadic

tag: tumour grade


title: Patient 2 Br01

description: No additional information

tag: estrogen receptor status


title: 1005-150001_Baseline_LS


title: Preeclampsia-NS_C, rep4

description:
3027_3
Whole blood transcriptome (PAXgene derived).

value: C

value: NS


title: Preeclampsia-S_A, rep9

description:
3027_2
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep9

description:
3027_1
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep10

description:
3027_4
Whole blood transcriptome (PAXgene derived).


title: monocyte-healthy-lps-2

value: LPS


title: Healthy-NA_B, rep8

description:
9337_3
Whole blood transcriptome (PAXgene derived).


title: monocyte-sepsis-lps-1


title: monocyte-recovery-basal-2


title: monocyte-sepsis-basal-2


title: 1005-150003_Baseline_LS


title: 1007-170004_Baseline_LS


title: 1003-130003_Baseline_LS


title: Preeclampsia-S_A, rep8

description:
9337_4
Whole blood transcriptome (PAXgene derived).


title: 1010-010001_Baseline_LS


title: 1007-170006_Baseline_LS


title: Preeclampsia-NS_C, rep3

description:
9337_1
Whole blood transcriptome (PAXgene derived).


title: 1003-130001_Baseline_LS


title: monocyte-recovery-lps-2


title: monocyte-sepsis-basal-1


title: monocyte-healthy-basal-2


title: 1010-010006_Baseline_LS


title: Preeclampsia-S_A, rep7

description:
9337_2
Whole blood transcriptome (PAXgene derived).


title: monocyte-healthy-lps-1


title: monocyte-sepsis-lps-4


title: Preeclampsia-S_A, rep6

description:
9304_4
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep7

description:
9304_3
Whole blood transcriptome (PAXgene derived).


title: 1004-140002_Baseline_LS


title: 1007-170002_Baseline_LS


title: monocyte-healthy-basal-1


title: Preeclampsia-NS_C, rep2

description:
9304_2
Whole blood transcriptome (PAXgene derived).


title: 1004-140003_Baseline_LS


title: NGAL overexpression replicate1

description: Biological replicate 1 of 2. NGAL overexpression compared to empty plasmid.

tag: cell line

tag: cell type

value: esophageal squamous cell carcinoma

tag: transfection plasmid

value: NGAL


title: monocyte-recovery-basal-1

tag: treatment

tag: cell


title: 1003-130005_Baseline_LS


title: 1005-150005_Baseline_LS


title: Preeclampsia-S_A, rep5

description:
9304_1
Whole blood transcriptome (PAXgene derived).

value: blood

tag: disease status

tag: matching


title: Xenograft from patient 57

hyb_protocol: Standard Illumina Protocol, performed by ServiceXS.

data_processing: Data was exported from Illumina GenomeStudio v1.0 into text files and parsed into R for processing using lumi and LIMMA analysis packages.

label: Cy3 and Cy5

source_name: CD45+ MNC from spleen

extract_protocol: Standard phenol chloroform extraction of genomic DNA. Bisulfite conversion was performed using Human Genetic Signatures MethylEasy Xceed Bisulfite Modification Kit

tag: prednisolone response

value: Poor

tag: Sex

value: F


title: monocyte-recovery-lps-1


title: Primary tumour from patient 55

scan_protocol: Standard Illumina Protocol, performed by ServiceXS.

source_name: bone marrow

value: M


title: Preeclampsia-S_A, rep4

description:
9294_2
Whole blood transcriptome (PAXgene derived).

tag: tissue

value: preeclampsia

tag: age

tag: severity

tag: gestational age (weeks)


title: Preeclampsia-S_A, rep2

description:
9031_4
Whole blood transcriptome (PAXgene derived).

value: A


title: 1004-140006_Baseline_LS

tag: subject

tag: visit


title: Xenograft from patient 55

label_protocol: Standard Illumina Protocol, performed by ServiceXS.


title: 1004-140005_Baseline_LS

tag: skin


title: 1004-140004_Baseline_LS


title: Primary tumour from patient 57


title: 1004-140007_Baseline_LS


title: Primary tumour from patient 56

value: Good


title: Xenograft from patient 56


title: 1005-150006_Baseline_LS


title: Healthy-NA_B, rep4

description:
9293_3
Whole blood transcriptome (PAXgene derived).

value: healthy

value: B


title: Preeclampsia-NS_C, rep1

description:
9294_3
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep6

description:
9294_1
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep5

description:
9293_4
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep2

description:
9031_3
Whole blood transcriptome (PAXgene derived).


title: Primary tumour from patient 54


title: Primary tumour from patient 53


title: Preeclampsia-S_A, rep3

description:
9293_2
Whole blood transcriptome (PAXgene derived).

value: S


title: monocyte-sepsis-basal-3

value: monocyte


title: Healthy-NA_B, rep1

description:
9031_2
Whole blood transcriptome (PAXgene derived).


title: Healthy-NA_B, rep3

description:
9293_1
Whole blood transcriptome (PAXgene derived).


title: Xenograft from patient 54


title: Xenograft from patient 53


title: Preeclampsia-S_A, rep1

description:
9031_1
Whole blood transcriptome (PAXgene derived).


title: Hep3B Cells 1.5% Oxygen, biological rep2

city: Aurora

first: Cheng-Jun

last: Hu

state: CO

address: E. 17th Ave

department: Craniofacial Biology

institute: University of Colorado Denver

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
To assess alternative splicing events, raw CEL files were imported into Altanalyze (version 2.0.7) using RMA normalization through Affymetrix Power Tools and Alternative Splicing was summarized at the exon level for Alternative Exons, filtering for probes with DABG P<0.05 or expression below 1.  FIRMA  and Splicing Index was calculated by comparing the hypoxia samples (H) to the normoxia (N) controls.
HuEx-1_0-st-v2.r2.pgf

source_name: Hep3B cells

label_protocol: Standard Affymetrix protocol

growth_protocol: Hep3B cells were cultured at 30-50% confluency in MEM/EBSS (Hyclone) containing 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 100,000 units/L Penicillin/Streptomycin, 1.5 g/L sodium bicarbonate, and 1X non-essential amino acids (NEAA). Prior to hypoxia treatment, 25 mM HEPES was added to growth media and cells were incubated under normoxia (21% O2) or hypoxia (1.5% O2) for 12-16 hrs.

extract_protocol: RNA was prepared using a Qiagen RNeasy Plus RNA extraction kit.

value: Hep3B Hepatoma Cell Line

tag: oxygen concentration


title: Hep3B Cells 1.5% Oxygen, biological rep1

treatment_protocol: Prior to hypoxia treatment, 25 mM HEPES was added to growth media and cells were incubated under normoxia (21% O2) or hypoxia (1.5% O2) for 12-16 hrs.

tag: cell line


title: Primary tumour from patient 28


title: Hep3B Cells 1.5% Oxygen, biological rep3


title: Primary tumour from patient 52


title: Xenograft from patient 50


title: IP HeLa2 11.06_(HuGene-1_0-st-v1) reanalysis

city: Montpellier

first: Edouard

last: BERTRAND

address: 1919 Route de Mendes

institute: CNRS

description: total RNA

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner according to manufacturer's instruction : GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays rev.1

data_processing: The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1) using parameters: one side upper, 90 bp bandwidth and perfect match only.Output as txt files parameter have been chosen.

source_name: IP HeLa2 11.06

label_protocol: Samples were prepared and hybridized according to Affymetrix specifications : WTGene termlabel manuelrev1

growth_protocol: HeLa H9 cells were grown to sub-confluency in DMEM, 10% FCS, at 37°C.

extract_protocol: RNAs from beads or cell extracts were homogenized in Trizol and purified with RNeasy mini kit (Qiagen).

treatment_protocol: Cells were extracted in lysis buffer (50mM Tris-HCl pH=7.5, 150mM NaCl, 1mM EDTA, 1% Triton, and protease inhibitors) for 30 min at 4°C. Cellular debris were removed by centrifugation (10 min at 9000 g). Extracts were put on antibody-coated beads for 2h at 4°C (M2 -Sigma). Beads were washed twice in lysis buffer and three times in PBS, and pelleted materials were Trizol.

tag: construct

value: control

value: HeLa H9

tag: antibody

value: M2 antiFlag


title: Primary tumour from patient 51


title: Xenograft from patient 52


title: Primary tumour from patient 26


title: C7_20101105_(HuGene-1_0-st-v1)

description: total RNA

hyb_protocol: Samples were prepared and hybridized according to Affymetrix specifications : WTGene

value: TGS1-LF (long form)


title: Xenograft from patient 26


title: C7b_20101105_(HuGene-1_0-st-v1)

description: total RNA


title: C2_20101105_(HuGene-1_0-st-v1)

description: total RNA

value: TGS1-SF (short form)


title: IP HeLa1 11.06_(HuGene-1_0-st-v1) reanalysis

description: total RNA

source_name: IP HeLa1 11.06


title: IP Flag HeLa 9_(HuGene-1_0-st-v1) reanalysis

description: total RNA

source_name: IP Flag HeLa 9


title: Primary tumour from patient 50


title: Hep3B Cells 21% Oxygen, biological rep3


title: C2b_20101105_(HuGene-1_0-st-v1)

description: total RNA


title: Hep3B Cells 21% Oxygen, biological rep2


title: EtOH 50 nicotine 1_rep2

city: Los Angeles

first: Yong

last: Kim

state: CA

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

description: EtOH 50 mM + nicotine 1 uM

hyb_protocol: not provided

scan_protocol: not provided

label: Biotin

source_name: normal oral tissue

label_protocol: Biotin

growth_protocol: Primary normal human oral keratinocytes were isolated from human oral tissue and cultured in vitro.

extract_protocol: Total RNA was extracted by using Qiagen Rneasy kit

treatment_protocol: Different concentrations of EtOH (0, 20 and 50mM) and nicotine (0, 0.5 and 1 uM) were mixed with culture medium and the cells were exposed for 24 hours.

tag: cell type

value: Normal oral keratinocytes


title: EtOH 50 nicotine 1_rep1

description: EtOH 50 mM + nicotine 1 uM


title: Hep3B Cells 21% Oxygen, biological rep1


title: EtOH 50 nicotine 0.5_rep2

description: EtOH 50 mM + nicotine 0.5 uM


title: EtOH 50 nicotine 0_rep2

description: EtOH 50 mM + nicotine 0 uM


title: EtOH 20 nicotine 1_rep2

description: EtOH 20 mM + nicotine 1 uM


title: EtOH 50 nicotine 0_rep1

description: EtOH 50 mM + nicotine 0 uM


title: EtOH 50 nicotine 0.5_rep1

description: EtOH 50 mM + nicotine 0.5 uM


title: EtOH 20 nicotine 0.5_rep1

description: EtOH 20 mM + nicotine 0.5 uM


title: EtOH 20 nicotine 0_rep2

description: EtOH 20 mM + nicotine 0 uM


title: EtOH 20 nicotine 1_rep1

description: EtOH 20 mM + nicotin 1 uM


title: Liver_Control_rep3

city: Bar Harbor

first: Peter

middle: Thomas

last: Vedell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: Hybridization cocktails containing 3–4 μg of fragmented, end-labeled cDNA were prepared and applied to GeneChip Rat Exon 1.0 ST arrays. The arrays were hybridized for 16 h. A wash and stain script (precommercial FS450_0001 script) was applied using the MES_EukGE-WS2v5_450-DEV fluidics station.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.3 to produce Affymetrix CEL-formatted files which contain quantitative measures for probe hybridization.

data_processing:
The probe-level data are contained in Affymetrix GeneChip Rat Exon 1.0 ST Array probe set CEL files. They were read into the R statistical software using the R/xps package [Stratowa, 2012 (http://www.bioconductor.org/packages/2.11/bioc/html/xps.html)].
RaEx-1_0-st-v1.r2.pgf
RaEx-1_0-st-v1.na31.rn4.transcript.csv

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Liver tissue of rat with Teklad mash (4%) diet.

label_protocol: One microgram of each RNA sample was processed as prescribed by the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay. The GeneChip WT cDNA Synthesis Kit, cDNA Amplification Kit, and Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for target preparation.

growth_protocol: Rat livers dissected at 5 weeks of age.

extract_protocol: Total RNA were isolated by Trizol (Invitrogen, Carlsbad, CA) and purified using the RNeasy Mini Kit and RNase-free DNase Set (Qiagen, Valencia, CA) according to the manufacturers’ protocols.

treatment_protocol: Not applicable

tag: gender

value: female

tag: strain

value: Sprague-Dawley

value: liver

tag: diet

value: Teklad mash (4%) diet

value: 5 weeks


title: Xenograft from patient 51

tag: prednisolone response

value: Good

value: M


title: EtOH 20 nicotine 0_rep1

description: EtOH 20 mM + nicotine 0 uM


title: EtOH 0 nicotine 1_rep2

description: EtOH 0 mM + nicotine 1 uM


title: EtOH 20 nicotine 0.5_rep2

description: EtOH 20 mM + nicotine 0.5 uM


title: EtOH 0 nicotine 0.5_rep2

description: EtOH 0 mM + nicotine 0.5 uM


title: Liver_Control_rep4


title: EtOH 0 nicotine 1_rep1

description: EtOH 0 mM + nicotine 1 uM


title: EtOH 0 nicotine 0.5_rep1

description: EtOH 0 mM + nicotine 0.5 uM


title: Liver_Control_rep2


title: Granulocytes biological rep1

city: Camperdown

first: Justin

state: NSW

address: Building 93 Royal Prince Alfred Hospital

institute: Centenary Institute

description: SAMPLE 10

hyb_protocol: Following fragmentation, cRNAs were hybridized for 17 hrs at 45C on Affymetrix GeneChip Gene 1.0 ST mouse arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The arrays were normalized using the justRMA suite of algorithms from Bioconductor (http://www.bioconductor.org/)

source_name: Granulocytes from mouse bone marrow

label_protocol: Biotinylated cRNAs were genearated according to the standard Affymetrix protocol using 300ng of total RNA.

growth_protocol: Cells were isolated directly from mouse bone marrow without further expansion.

extract_protocol: RNA extraction was performed using Trizol according to the manufacturers' instructions.

treatment_protocol: Cells were not subjected to any treatment.

value: bone marrow

value: Granulocytes


title: Myelocytes biological rep3

description: SAMPLE 9

source_name: Myelocytes from mouse bone marrow

value: Myelocytes


title: EtOH 0 nicotine 0_rep1

description: EtOH 0 mM + nicotine 0 uM


title: EtOH 0 nicotine 0_rep2

description: EtOH 0 mM + nicotine 0 uM


title: Myelocytes biological rep2

description: SAMPLE 8


title: Liver_Control_rep1


title: dkfz_13-006

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: Gene expression data from a glioblastoma tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: Primary brain tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

value: male

tag: h3f3a status

value: WT

tag: location

value: frontal lobe


title: dkfz_13-005

tag: age

value: temporal lobe


title: Liver_MeUAB30_rep3

source_name: Liver tissue of rat with MeUAB30-supplemented diet for 7 days.

tag: tissue

value: MeUAB30-supplemented (200 ppm) Teklad mash (4%) diet for 7 days


title: Xenograft from patient 28

city: Clayton

first: Nicholas

address: Wellington Road

institute: Monash University

value: Poor

tag: Sex


title: dkfz_11-035

value: parieto-occipital


title: dkfz_13-004

value: female

value: the fourth ventricle & brain stem


title: Promyelocytes biological rep3

description: SAMPLE 6

source_name: Promyelocytes from mouse bone marrow

value: Promyelocytes


title: Liver_Targretin_rep1

source_name: Liver tissue of rat with Targretin-supplemented diet for 7 days.

value: Sprague-Dawley

value: liver

value: Targretin-supplemented (150 ppm) Teklad mash (4%) diet for 7 days.


title: dkfz_13-003

value: thalamus


title: Promyelocytes biological rep2

description: SAMPLE 5

value: bone marrow


title: Promyelocytes biological rep1

description: SAMPLE 4


title: Liver_UAB30_rep3

source_name: Liver tissue of rat with UAB30-supplemented diet for 7 days.

value: UAB30-supplemented (200 ppm) Teklad mash (4%) diet for 7 days

value: 5 weeks


title: Liver_MeUAB30_rep4


title: LSKs biological rep2

description: SAMPLE 2

source_name: Hemopoietic stem cells from mouse bone marrow

value: Hemopoietic stem cells


title: Liver_Targretin_rep2


title: Granulocytes biological rep2

description: SAMPLE 11

value: Granulocytes


title: LSKs biological rep1

description: SAMPLE 1


title: Liver_MeUAB30_rep2


title: Patient_12

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Gene expression profile of surgically resected material

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: Liver tissue

label_protocol: aRNA was prepared using 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Gene expression profiles of liver tissues from 12 patients with chronic hepatitis C were used.

value: Liver biopsy sample

value: F

tag: outcome

value: SVR


title: Myelocytes biological rep1

last: Wong

description: SAMPLE 7

value: Myelocytes


title: Patient_11

value: VR


title: LSKs biological rep3

description: SAMPLE 3


title: Liver_Targretin_rep4

value: female


title: Liver_UAB30_rep4


title: Liver_UAB30_rep1


title: Patient_10

value: NVR


title: Patient_09

value: M


title: Liver_MeUAB30_rep1

value: Sprague-Dawley

value: MeUAB30-supplemented (200 ppm) Teklad mash (4%) diet for 7 days


title: Liver_Targretin_rep3

value: liver

value: Targretin-supplemented (150 ppm) Teklad mash (4%) diet for 7 days.


title: Patient_08


title: Liver_UAB30_rep2


title: W2_Mouse myelocytes

data_processing: Comparative threshold (Ct) values were calculated using SDS software v2.3 and RQ manage software (Applied Biosystems). Data were not normalized against a reference RNA because there is no reference that is expressed at equal levels in the nucleus and cytoplasm. Cell equivalent fractions were used for normalization purposes.

label: TaqMan Assay

source_name: myelocytes_Whole cell RNA

label_protocol: 100 ng RNA was reverse transcribed using TaqMan MicroRNA Reverse Transcription Kit and Megaplex RT Primers rodent pool A and B. Complementary DNA was amplified using a TaqMan rodent microRNA A and B Array v2.0  with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System

extract_protocol: Nuclear and cytoplasmic fractions were separated using the PARIS kit (Ambion). RNA was extracted from either the nucleus, cytoplasm and whole cells using Trizol according to the manufacturers' instructions.

value: bone marrow

value: myelocytes

tag: molecule subtype

value: Whole cell RNA


title: Patient_03


title: Granulocytes biological rep3

description: SAMPLE 12


title: Patient_06


title: Patient_05


title: N3_Mouse granulocytes

source_name: granulocytes_Nuclear RNA

value: granulocytes

value: Nuclear RNA


title: Pig 6, pyloric mucosa

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

institute: UNIVERSITY OF BOLOGNA

description: Gene expression data from porcine pyloric mucosa

hyb_protocol: Total mRNA was hybridized on  Affymetrix©Porcine Gene 1.1 ST array strips.  Affymetrix hybridization, wash, and stain Kit for WT Array Strips were used.

scan_protocol: Quantification of transcript expression on a GeneAtlas imaging station (Affymetrix).

data_processing: Performance quality tests of the arrays including the labelling, hybridization, scanning and background signals by a Robust Multichip Analysis were performed on the CEL files using Affymetrix Expression ConsoleTM.

organism: Sus scrofa

source_name: Pig 6, pyloric mucosa

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

growth_protocol: Seven unrelated crossbred (Large White x Landrace) male weaned  pigs (five-six weeks of age,  averagely 11.1 kg BW) were individually housed in cages and fed for five days a standard post-weaning feed. Then, after the morning meal, pigs were slaughtered by an intracardiac injection (Tanax, 0.5 mL/kg body weight; Intervet Italia, Peschiera Borromeo, Italy), after being anaesthetized with sodium thiopental (10 mg/kg body weight).

extract_protocol: Total mRNA was isolated from oxyntic and pyloric mucosa  collected from each subject, according to Qiagen RNeasy® Midi Kit protocol (Qiagen, Hilden, Germany). Purity and integrity evaluation was assessed just before analysis by Agilent Bioanalyzer 2100.

treatment_protocol: For each subject, the stomach was removed, opened along the greater curvature and washed in ice-cold PBS. Tissue samples  from  the oxyntic gland area close to the greater curvature and from pyloric mucosa close to the sphincter were collected and immediately frozen in liquid nitrogen and stored at -80°C until use.

value: pyloric mucosa

tag: genotype

value: Large White X Landrace

value: male

value: 5-6 weeks (weaned)

tag: weight

value: average 11.1 kg live weight


title: Pig 7, oxyntic mucosa

description: Gene expression data from porcine oxyntic mucosa

source_name: Pig 7, oxyntic mucosa

value: oxyntic mucosa


title: Patient_04

value: Liver biopsy sample

value: F

value: SVR


title: W3_Mouse granulocytes

source_name: granulocytes_Whole cell RNA


title: W0_Mouse hemopoietic stem cells (LSKs)

source_name: LSKs_Whole cell RNA

value: hemopoietic stem cells (LSKs)


title: Pig 7, pyloric mucosa

source_name: Pig 7, pyloric mucosa


title: N2_Mouse myelocytes

source_name: myelocytes_Nuclear RNA


title: Patient_01

value: M

value: NVR


title: W1_Mouse promyelocytes

source_name: promyelocytes_Whole cell RNA

value: bone marrow

value: promyelocytes


title: Patient_02


title: N1_Mouse promyelocytes

source_name: promyelocytes_Nuclear RNA


title: Patient_07


title: patient9 periimplantitis tissue

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

institute: University Göttingen

hyb_protocol: Genechip hybridisation, wash and stain kit.

scan_protocol: Array washing and staining as described in chp 6 of above manual using the GeneChip Fluidics station 450 (fluidics script FS450-007). Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning.

data_processing: Microarray data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix). The advanced analysis was done with R (version 2.9) with package limma.

source_name: peri implant bone (main part) and soft tissue

label_protocol: GeneChip Whole Transcript (WT) sense target labeling assay manual, version 4 - starting with 300ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays (omitting RiboMinus procedure).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions with the help of the RNAeasy Kit (Quiagen).

treatment_protocol: After explantation the implants with the adherent tissue were instantly frozen in liquid nitrogen and after that in an -80 °C freezer.

tag: disease state

value: periimplantitis tissue


title: C3_Mouse granulocytes

source_name: granulocytes_Cytoplasmic RNA

value: granulocytes

value: Cytoplasmic RNA


title: Pig 5, oxyntic mucosa

source_name: Pig 5, oxyntic mucosa


title: Pig 4, pyloric mucosa

source_name: Pig 4, pyloric mucosa

value: pyloric mucosa


title: patient11 periimplantitis tissue

value: peri implant bone (main part) and soft tissue


title: Pig 4, oxyntic mucosa

source_name: Pig 4, oxyntic mucosa

value: Large White X Landrace

value: male


title: Pig 3, pyloric mucosa

source_name: Pig 3, pyloric mucosa

value: 5-6 weeks (weaned)

value: average 11.1 kg live weight


title: patient20 periimplantitis tissue


title: C2_Mouse myelocytes

source_name: myelocytes_Cytoplasmic RNA

value: myelocytes


title: C1_Mouse promyelocytes

source_name: promyelocytes_Cytoplasmic RNA


title: patient21 periimplantitis tissue


title: Pig 6, oxyntic mucosa

source_name: Pig 6, oxyntic mucosa

value: oxyntic mucosa


title: patient19 periimplantitis tissue


title: Pig 2, pyloric mucosa

source_name: Pig 2, pyloric mucosa


title: N0_Mouse hemopoietic stem cells (LSKs)

source_name: LSKs_Nuclear RNA

value: Nuclear RNA


title: Pig 5, pyloric mucosa

source_name: Pig 5, pyloric mucosa


title: C0_Mouse hemopoietic stem cells (LSKs)

source_name: LSKs_Cytoplasmic RNA

value: hemopoietic stem cells (LSKs)


title: Pig 2, oxyntic mucosa

source_name: Pig 2, oxyntic mucosa


title: patient15 healthy periimplant tissue

value: healthy periimplant tissue


title: Pig 3, oxyntic mucosa

source_name: Pig 3, oxyntic mucosa


title: patient18 periimplantitis tissue


title: patient7 healthy periimplant tissue


title: Pig 1, pyloric mucosa

source_name: Pig 1, pyloric mucosa


title: Pig 1, oxyntic mucosa

source_name: Pig 1, oxyntic mucosa


title: Rabbit_ID_VV_24hr_1

status: Public on May 13 2014

city: Gainesville

first: Richard

middle: W

last: Moyer

state: FL

address: 1600 SW Archer Rd

institute: University of Florida

description: 363 24hr ID

hyb_protocol: Arrays were hybridized at 60C for 17hrs in a rotating oven and washed per manufacturer protocols.

scan_protocol: G2505 B Scanner (Aglient Technologies) was used to detect signals. Transformation was perfomred with Feature (Cap E) Extraction software version 8.1 (Agilent Technologies).

data_processing: BRB Array Tools 4.2.0 Beta_1_p1 was use for analysis. Median probe intensity was used for array normalization, probe sets were excluded if more than 20% of values were absent. F test with random variance with a significance level of 0.01 for identification of significant probe sets.

organism: Oryctolagus cuniculus

source_name: Intradermal, 24hrs

label_protocol: 2ug of total RNA was used for generation of cDNA via Perkin Elmer kit for Cy3 and Cy5. Cy3 was used as the label for normal skin and Cy5 for experimental samples. The samples were cleaned using Qiagen Rneasy Mini columns.

growth_protocol: Rabbits aged 9 weeks

extract_protocol: Tissue was flash frozen, manually homogenized in lysis buffer with 24 grit silicon carbide sand, RNA isolated via the Qiagen RNeasy kit

treatment_protocol: The hind flank of the animal was infected via intradermal (1000pfu) or scarification (10^9pfu/ml) with vaccinia virus.

tag: infection

value: Vaccinia virus

tag: route of infection

value: Intradermal

tag: time

value: skin

source_name: Normal skin

value: Uninfected


title: Rabbit_ID_VV_24hr_2

description: 359 24hr ID


title: Rabbit_ID_VV_4hr_2

description: 381 4hr ID

source_name: Intradermal, 4hrs


title: Rabbit_ID_VV_4hr_3

description: 501 4hr ID


title: Rabbit_ID_VV_24hr_3

description: 361 24hr ID


title: Rabbit_ID_VV_48hr_1

description: 152 48hr ID

source_name: Intradermal, 48hrs


title: Rabbit_ID_VV_48hr_3

description: 148 48hr ID


title: Rabbit_Scar_VV_4hr_1

description: 376 4hr Scar

source_name: Scarification, 4hrs

value: Scarification


title: Rabbit_ID_VV_48hr_2

description: 147 48hr ID


title: Rabbit_Scar_VV_4hr_2

description: 378 4hr Scar


title: Rabbit_ID_VV_4hr_1

description: 379 4hr ID


title: Rabbit_Scar_VV_48hr_2

description: 386_2 48hr Scar

source_name: Scarification, 48hrs


title: Rabbit_Scar_VV_4hr_3

description: 380 4hr Scar


title: Rabbit_Scar_VV_24hr_1

description: 360 24hr Scar

source_name: Scarification, 24hrs


title: Rabbit_Scar_VV_24hr_2

description: 151_2 24hr Scar


title: Rabbit_Scar_VV_48hr_1

description: 384 48hr Scar


title: Rabbit_Scar_VV_24hr_3

description: 358 24hr Scar


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn29

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
LoLRn29
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

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

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

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of longitudinal, healthy high HLA type T1D sibling (HR), healthy low HLA type T1D sibling (LR), or recent onset (RO) T1D plasma cultured with IL1RA.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder pbmc cells

value: UPN727 PBMC cells

tag: stimulated with


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn25

description:
LoLRn25
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn26

description:
LoLRn26
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn31

description:
LoLRn31
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn24

description:
LoLRn24
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn27

description:
LoLRn27
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn28

description:
LoLRn28
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn30

description:
LoLRn30
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn19

description:
LoLRn19
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn22

description:
LoLRn22
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn23

description:
LoLRn23
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn20

description:
LoLRn20
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn16

description:
LoLRn16
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn17

description:
LoLRn17
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn21

description:
LoLRn21
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn18

description:
LoLRn18
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn14

description:
LoLRn14
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn15

description:
LoLRn15
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn9

description:
LoLRn9
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn13

description:
LoLRn13
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn12

description:
LoLRn12
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn5

description:
LoLRn5
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn60

description:
LoHRn60
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn10

description:
LoLRn10
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn57

description:
LoHRn57
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn4

description:
LoLRn4
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn6

description:
LoLRn6
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn7

description:
LoLRn7
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn2

description:
LoLRn2
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn3

description:
LoLRn3
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn59

description:
LoHRn59
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn55

description:
LoHRn55
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn53

description:
LoHRn53
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn50

description:
LoHRn50
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn52

description:
LoHRn52
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn54

description:
LoHRn54
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn48

description:
LoHRn48
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn45

description:
LoHRn45
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn56

description:
LoHRn56
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn58

description:
LoHRn58
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn51

description:
LoHRn51
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn49

description:
LoHRn49
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn47

description:
LoHRn47
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn44

description:
LoHRn44
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn41

description:
LoHRn41
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn43

description:
LoHRn43
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn42

description:
LoHRn42
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn32

description:
LoHRn32
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn36

description:
LoHRn36
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn33

description:
LoHRn33
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn38

description:
LoHRn38
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn34

description:
LoHRn34
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn37

description:
LoHRn37
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn31

description:
LoHRn31
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn22

description:
LoHRn22
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn29

description:
LoHRn29
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn35

description:
LoHRn35
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn23

description:
LoHRn23
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn28

description:
LoHRn28
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn25

description:
LoHRn25
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn30

description:
LoHRn30
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn24

description:
LoHRn24
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn27

description:
LoHRn27
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn26

description:
LoHRn26
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn21

description:
LoHRn21
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn18

description:
LoHRn18
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn15

description:
LoHRn15
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn20

description:
LoHRn20
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn17

description:
LoHRn17
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn16

description:
LoHRn16
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn19

description:
LoHRn19
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn14

description:
LoHRn14
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn12

description:
LoHRn12
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn13

description:
LoHRn13
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn11

description:
LoHRn11
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn11

description:
LoLRn11
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn8

description:
LoLRn8
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn9

description:
LoHRn9
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn46

description:
LoHRn46
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series  plasma LoLRn1

description:
LoLRn1
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn40

description:
LoHRn40
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn10

description:
LoHRn10
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn7

description:
LoHRn7
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn39

description:
LoHRn39
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn4

description:
LoHRn4
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn1

description:
LoHRn1
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma