title: Liver_48 hrs post partial hepatectomy_rep3

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

institute: Shanghai University

description: Mouse liver, 48 hrs post partial hepatectomy

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Affemetrix miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing:
Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 75 percent of samples in any 1 condition out of 2 conditions have flags in P were chosen for further data analysis.
Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: Liver tissues were collected and frozen immediately in liquid nitrogen.

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

value: Liver

value: male

value: 8 weeks old


title: Liver_48 hrs post partial hepatectomy_rep4

status: Public on Feb 10 2017

type: RNA

department: School of Life Science

country: China

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse liver, 48 hrs post partial hepatectomy

tag: tissue

tag: strain

tag: gender

tag: age


title: Liver_48 hrs post partial hepatectomy_rep1


title: Liver_0 hr post partial hepatectomy_rep4

description: Mouse liver, 0 hr post partial hepatectomy


title: Skn-1 deficient mouse, biological rep5

status: Public on Feb 11 2017

city: Bunkyo-ku

first: Shota

last: Ushiama

state: Tokyo

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

hyb_protocol: aRNA and microarray tip were hybridized at 45C for 16 h

scan_protocol: Fluorescence signals were scanned using the Affymetrix GeneChip System. Affymetrix GeneChip Command Console software was used to reduce the array images to the intensity of each probe (CEL files)

data_processing: The CEL files were quantified with the FARMS using statistical language R and Bioconductor.

label: biotin

source_name: Skn-1 KO mice after 18h fasting_gastrocnemius

label_protocol: Biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3′ IVT Express Kit. In addition, the aRNA was purified and fragmented according to the manufacturer's instructions

growth_protocol: Skn-1/Pou2f3-deficient mice with a mixed 129 x C57BL/6J background were generated and then backcrossed to C57BL/6J for more than 10 generations.All mice were fed a chow.

extract_protocol: RNA was extracted using Trizol reagent(Invitrogen) according to the manufacturer's instructions and purifed by using RNeasy Mini Kit.

treatment_protocol: All mice were fasted for 18 hours before dissection.

tag: strain background

value: mixed 129 x C57BL/6J

tag: Sex

value: 12-16 weeks old

tag: genotype/variation

value: gastrocnemius

tag: time point

value: after 18h fasting


title: Liver_0 hr post partial hepatectomy_rep1

source_name: Mouse liver, 0 hr post partial hepatectomy


title: Liver_0 hr post partial hepatectomy_rep2


title: 012-ST3

city: Bogota

first: Diana

last: Ramirez

state: Bogota

address: Calle 53 Cra 37 Ed. 426

department: Medicine Faculty

country: Colombia

institute: Universidad Nacional de Colombia

description:
male (SAOM)-8 years
Third sample, culture 012 biological replica 3 without treatment (ST)

hyb_protocol: Approximately 5.5μg of target DNA marked was hybridized to the GeneChip at 45° C for 16 hours.

scan_protocol: The hybridized arrays were washed and stained in the fluidics station for GeneChip450 and scanned with the Scanner GCS3000 (Affymetrix). Signal values were computed using the GeneChip™ Comand Console® software.

data_processing:
Raw data were extracted automatically using the data extraction protocol included in the software Affymetrix® Expression Console™.  The statistical significance of the expression data was determined using fold change.  For each SDR set, hierarchical cluster analysis was performed using complete linkage and Euclidean distance as similarity measures.  Enrichment analysis of genes and functional annotation was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp). Each term was assigned a score (EASA), which consists of the p-value modified by the Fisher Exact Test. If the value was less than 0.05 it was classified as enrichment.  All data analysis and visualization of differentially expressed genes were performed using R 3.1.2 (www.r-project.org). The genes obtained in functional annotations were grouped into clusters and those that had a fold change of2and significant p value were selected. Corrections of p value for the statistical significance of the findings were performed by using Bonferroni, Benjamini, and FDR tests.
After importing the CEL files, the data were summarized and normalized using the RMA method implemented in the Affymetrix® Expression Console™.  The results were exported using the RMA analysis and then the gene level protocol was performed for determining differentially expressed genes (DEG).

organism: Homo sapiens

source_name: calvarial fibroblast

label_protocol: The cDNA sense was fragmented and biotinylated using TdT (terminal deoxynucleotidyl transferase) and using the GeneChip WT Terminal labeling kit.

growth_protocol: subperiosteal primary fibroblasts culture of 3 individuals with AS was made. The explant obtained from each patient was broken up into segments of approximately 2 to 3mm, placed in the middle of DMEM® culture medium supplemented with fetal bovine serum at 10% plus antibiotic Penicillin/Streptomycin at 1% at 37 ºC and 5%CO2, fibroblast growth was monitored by observation of the cell culture with an inverted microscope. Once confluence of 70-80% was obtained, subcultures (maximum 5) were performed in order to obtain the concentration of cells necessary for experiments. At the moment there is no availability of more cell cultures.

extract_protocol: Total RNA for each treatment culture was extracted using the extraction kit RNeasy® Mini Kit (74104: Quiagen®) according to manufacturer's conditions. Subsequently, it was quantified with Quibit® RNA Assay Kit (Q32852: Invitrogen®) and stored at -80° C to begin the process of reverse transcription. The purity and integrity of RNA used were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: In order to mimic the activation state of the mutated FGFR2, in 6- wellboxes,80,000 cells per well were sown in 1.600 µL of DMEM medium supplemented with FGF2 (0,069ng / µL) for 24 hours. After this the culture medium was removed from the wells that would go to treatment Idursulfase®, and these received supplemented DMEM plus Idursulfase® added at a concentration of 0.025mg/ml as reported in the literature (24), since there was no difference with the different concentrations used in the previous assay. The wells that served as control were left only with supplemented DMEM. Cells were incubated for 48 hours to proceed to the extraction of total RNA.

tag: diagnosis

value: Apert syndrome tissue

value: calvarial fibroblast


title: Liver_48 hrs post partial hepatectomy_rep2


title: Liver_0 hr post partial hepatectomy_rep3


title: CT5

city: Baltimore

first: Deepak

last: Edward

state: MD

address: SOM Oph Ophthalmology Chairmans Office

department: School of Medicine

country: USA

institute: The Johns Hopkins University

hyb_protocol: Total Affymetrix  Hyb Cocktail plus labeled sample volume of 103.2ul incubated 17hr at 48°C at 60RPM.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Human probesets, from Affy annotation, were extracted, RMA quantile normalized and log2 transformed with Partek Genomis Suite 6.6 .

source_name: Ciliary body

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling kit following manufacturer's standard protocol.

growth_protocol: Specimen preparation. The tumor tissues (n = 7) were dissected from the formalin-fixed, paraffin-embedded (FFPE) tissue block using a dissecting microscope with a sterile No. 11 blade.  For control tissue (n = 8), the ciliary body and epithelium of enucleated eyes with retinoblastoma, where the tumor was confined to the posterior segment, were  dissected.

extract_protocol: QIAGEN RNeasy FFPE Kit following manufacturer's standard protocol.

treatment_protocol: Samples were fixed with formalin and embedded in paraffin.

tag: tissue class

value: Control

tag: tumor class

value: Non-tumor

tag: malignancy class


title: ME1

source_name: Ocular tumor

value: Tumor

value: Malignant

value: Teratoid


title: CT4


title: CT3


title: ME5


title: ME8

value: Non-teratoid


title: CT6


title: CT8


title: CT7


title: ME3


title: ME7


title: ME4

value: Benign


title: ME6


title: CT1


title: CT2


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2990

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description:
Gene expression data from liver
loin eye area (LEA) [cm2]: area of M. longissimus dorsi (Mld) at 13th/14th rib
fat area (FA) [cm2]: fat area on Mld at 13th/14th rib
meat to fat ratio (MFR): ratio of meat and fat area
MV = missing value

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: Liver

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: Adult German Landrace

tag: loin eye area (lea) [cm2]

tag: fat area (fa) [cm2]

tag: meat to fat ratio (mfr)


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2988


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2997


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2986


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2989


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2985


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2993


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2994


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2992


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2995


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2983


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2984


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2979


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2987


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2996


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2991


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2976


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2969


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2980


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2972


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2968


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2971


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2965


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2977


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2966


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2982


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2967


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2970


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2981


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2978


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2964


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2957


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2954


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2958


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2951


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2949


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2953


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2945


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2959


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2961


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2950


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2946


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2963


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2947


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2942


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2952


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2962


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2960


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2956


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2948


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2943


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2955


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2944


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2937


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2941


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2938


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2940


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2936


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2939


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2934


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2935


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2933


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2931


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2928


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2927


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2926


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2925


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2932


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2923


title: MCF12A 4 weeks ethanol

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

description: etoh

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Samples were analyzed using the Affymetrix protocols and data are presented as rma values.
RMA is an arbitrary value for relative gene expression calculated using normalization and control values.

source_name: MCF12A monolayer

label_protocol: Samples were transferred to the UCLA DNA Microarray core facility (1 week exposures) or to the UCLA Pathology Lab (4 week exposures) and analyzed by Affymetrix human Gene 1.0 ST (1 week exposures) or Affymetrix human Gene 1.1 ST (4 week exposures) according to Affymetrix guidelines.

growth_protocol: MCF12A Cells obtained from the American Type Culture Collection (ATCC) were grown in 6 well plastic culture plates in DMEM/F12 plus antibiotic/antimycotic in the presence of 2.5% horse serum supplemented with epidermal growth factor, hydrocortisone, bovine insulin, and cholera toxin. Cells were passaged when they reached 80% confluence.

extract_protocol: For DNA microarray analysis, cells were washed with phosphate buffered saline, pH 7.4, and RNA was extracted using the RNeasy Plus Micro kit. For microRNA analysis, cells were washed with phosphate buffered saline pH 7.4 and RNA was extracted using the miRVana kit.

treatment_protocol: Cells were exposed to 25 mM ethanol or 2.5 mM acetaldehyde for 1 week, following which RNA was extracted. In other experiments, cells were cultured for 4 weeks either in the presence of 2.5% ethanol or 1% acetaldehyde. In one experiment, cells were selected for their ability to grow in soft agar, following which a cellular clone was grown on 6 well plates for further experimental exposure to ethanol and RNA extraction.

tag: cell line

tag: cell type

value: human breast cultures

tag: exposed to

value: 2.5% ethanol  for 4 wks


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2919


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2921


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2929


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2920


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2924


title: MCF12A 4 weeks acetaldehyde

description: Acet

value: 1% acetaldehyde for 4 wks


title: MCF12A control for etoh and acetaldehyde

value: none (control)


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2917


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2922


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2916


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2918


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2915


title: Pa5T3

type: genomic

first: Yu

last: Liu

address: 1678 Dongfang Road, Pudong District

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center

hyb_protocol: A total of 1500ng gDNA samples and 50μg human Cot-1 DNA were dissolved in the hybridization mixture supplied within the Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies).  After denaturation at 95℃ for 3 minutes and incubation at 37℃ for 30 minutes, the mixtures were slowly dispensed onto the gasket.  A microarray slide was then placed onto the gasket slide.  The samples were hybridized in a hybridization oven at 65℃ and 20 rpm for 40 hours.

scan_protocol: Slides were scanned with the Agilent Scanner System, and the Feature Extraction 12.0 (Agilent Technologies) was used for data extraction.

data_processing: The extracted data were subjected to locally weighted scatterplot smoothing to remove potential intensity and/or GC content bias before calculating the log2 copy number ratios in reference to the matching normal.

molecule: genomic DNA

source_name: Lung Cancer

label_protocol: Tumor and reference gDNA (Promega Inc., WI) were labeled with Cy5 and Cy3, respectively, using the Agilent Genomic DNA USL Labeling Kit (Agilent Technologies).

extract_protocol: Genomic DNA (gDNA) was extracted using a DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany).

treatment_protocol: After resection, ten 10-μm fresh frozen sections for each tumor sample or ten 10-μm formalin-fixed paraffin-embedded sections for the regional lymph node metastasis were collected.

tag: source

value: Patient 5

tag: tumor size

source_name: Human genomic DNA (Promega)

tag: sample type

value: reference


title: Pa6T3

value: Patient 6


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2913


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2911


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2910


title: Pa6T1


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2912


title: Pa6WBC

source_name: Peripheral Blood Leukocytes


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2914


title: Pa4T2

value: Patient 4


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2909


title: Pa5WBC


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2906


title: Pa5T1


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2907


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2908


title: Pa5T2


title: Pa4T1


title: Pa3T1

value: Patient 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2905


title: Pa4WBC


title: Pa3WBC


title: Pa2T2

value: Patient 2


title: Pa3T2


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2903


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2902


title: Pa2WBC


title: Pa1LN

source_name: Lymph Node Metastasis

value: Patient 1


title: Pa1T2


title: Pa1T3


title: Pa2T1


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2891


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2898


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2899


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2895


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2901


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2892


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2890


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2894


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2896


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2893


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2889


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2887


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2888


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2897


title: Pa1T1


title: Pa1WBC


title: MGC-803_Control_shRNA-replicate 2

city: Xiamen

first: Wangyu

last: Cai

address: 201-209 South Hubin Rd

department: Department of Gastrointestinal Surgery

institute: Zhongshan Hospital of Xiamen University

description: MGC-803 cells stable expressed Control shRNA

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4×44K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Control MGC-803 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MGC-803 cells were maintained in RPMI-1640 medium contained 10% fetal bovine serum (Gibco, Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA), and cells were maintained at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: MGC-803 cells at 60 to 70% confluence were infected with viral supernatants (PMP22 shRNA2 or Control shRNA) containing 10 mg/ml Polybrene for 24 h. Then, fresh medium with puromycin was used to select a pool of stably expressed cells for one week.

value: MGC-803 gastric cancer cell line

value: control


title: MGC-803_PMP22_shRNA2-replicate 3

description: MGC-803 cells stable expressed PMP22 shRNA2

source_name: PMP22 KD MGC-803 cells

value: PMP22 knockdown


title: MGC-803_PMP22_shRNA2-replicate 1


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2886


title: MGC-803_Control_shRNA-replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2884


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2876


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2882


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2879


title: MGC-803_PMP22_shRNA2-replicate 2


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2874


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2862


title: MGC-803_Control_shRNA-replicate 1


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2878


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2900


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2875


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2883


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2881


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2861


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2864


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2863


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2873


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2877


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2904


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2885


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2872


title: Pa6T2


title: Pa1N

source_name: Adjacent Normal Lung


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2855


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2847


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2840


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2859


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2846


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2842


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2836


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2835


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2721


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2728


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2856


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2724


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2723


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2837


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2731


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2844


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2730


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2843


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2838


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2841


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2719


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2718


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2733


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2717


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2714


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2713


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2726


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2722


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2729


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2711


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2712


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2708


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2637


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2639


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2705


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2710


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2600


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2591


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2620


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2606


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2610


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2624


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2608


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2590


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2596


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2594


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2593


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2635


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2587


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2848


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2589


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2592


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2568


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2581


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2562


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2503


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2579


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2583


title: Liver tissue from adult pig taken at slaughter LPA  DL Le 2577


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2566


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2499


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2501


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2504


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2498


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2497


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2487


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2500


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2494


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2490


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2495


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2496


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2598


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2502


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2469


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2486


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2467


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2464


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2458


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2454


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2455


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2459


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2462


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2434


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2429


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2488


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2442


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2394


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2389


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2391


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2493


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2432


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2446


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2452


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2444


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2385


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2450


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2384


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2386


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2383


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2366


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2448


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2368


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2371


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2352


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2363


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2351


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2354


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2349


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2355


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2343


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2325


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2381


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2328


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2304


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2316


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2346


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2299


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2302


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2321


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2323


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2308


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2292


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2317


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2313


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2296


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2255


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2333


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2330


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2254


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2240


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2239


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2214

value: MV


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2217


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2294


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2211


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2231


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2208


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2295


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2228


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2237


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2256


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2238


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2195


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2180


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2196


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2183


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2176


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2171


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2174


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2226


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2168


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2164


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2150


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2161


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2147


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2138


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2137


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2136


title: T8ML1_treated for 24hr, replicate 3

city: Ann Arbor

first: Ryan

middle: A

last: Wilcox

state: MI

address: 4310 Cancer Center, 1500 E Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 2.5 ug of cDNA were hybridized at 48C on Human Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment. RMA was used to fit log2 transformed expression values

source_name: T8ML1_anti-CD3/CD28 for 24hr

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 50 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 2.5 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

growth_protocol: TCL cells were cultured in RPMI1640 with 10% FCS, at 37 0C, 5% CO2. For T8ML1, 100 IU/ml of IL2 was supplemented.

extract_protocol: Total RNA was extracted by Rneasy

treatment_protocol: TCL cells were treated with/without anti-CD3/CD28 (1:1 ratio of beads to TCL)  at vaious time points.

value: T-cell lymphoma cell line

tag: treated with

value: anti-CD3/CD28 for 24hr


title: TCL3_untreated [RW005.1]

hyb_protocol: Following Labeling procedure, 3.75 ug of cDNA were hybridized at 48C on Human Gene ST 2.1 strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 40 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

growth_protocol: TCL3 cells were cultured in RPMI1640 with 10% FCS, at 37 0C, 5% CO2. For T8ML1, 100 IU/ml of IL2 was supplemented.

treatment_protocol: TCL3 cells were treated with/without anti-CD3/CD28 (1:1 ratio of beads to TCL)  at vaious time points.

tag: subject status

value: a PTCL, NOS patient (TCL3)

value: primary T-cell lymphoma cells

value: none (untreated)


title: TCL2_anti-CD3/CD28 for 12 hr [RW004.5]

source_name: TCL2_anti-CD3/CD28 for 12 hr

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 50 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

growth_protocol: TCL2 cells were cultured in RPMI1640 with 10% FCS, at 37 0C, 5% CO2. For T8ML1, 100 IU/ml of IL2 was supplemented.

treatment_protocol: TCL2 cells were treated with/without anti-CD3/CD28 (1:1 ratio of beads to TCL)  at vaious time points.

value: sezary patient TCL2

value: anti-CD3/CD28 for 12 hr


title: T8ML1_treated for 24hr, replicate 2


title: TCL3_anti-CD3/CD28 for 12 hr [RW005.3]

source_name: TCL3_anti-CD3/CD28 for 12 hr


title: TCL3_untreated [RW005.2]


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2139

value: Adult German Landrace


title: TCL2_untreated [RW004.2]


title: iKCL011-2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
SAMPLE 3.2
undifferentiated hiPSC line iKCL011 replicate 2

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: The data was normalized by GenoSplice for adjustment of type-2 bias using the BMIQ method (Teschendor et al., 2013) from ChAMP R package.

source_name: undifferentiated hiPSC line iKCL011

label_protocol: Standard Illumina Protocol

growth_protocol: iKCL004, iKCL011 and KCL034 cells were grown on Marigel-coated dishes in mTeSR medium; BJ cells were grown on plastic in 10% FBS/DMEM

extract_protocol: genomic DNA was extracted using Qiagen columns; each sample of 500 ng DNA was bisulfite treated (EZ Zymo DNA Kit) according to manufacturer’s recommendations optimized for 450k array.

tag: developmental stage

value: pluripotent, undifferentiated cells


title: T8ML1_treated for 24hr, replicate 1


title: TCL3_anti-CD3/CD28 for 12 hr [RW005.4]


title: TCL2_untreated [RW004.1]


title: TCL2_anti-CD3/CD28 for 12 hr [RW004.4]


title: KCL034-1

description:
SAMPLE 4.1
undifferentiated hESC line KCL034 replicate 1

source_name: undifferentiated hESC line KCL034


title: T8ML1_treated for 8hr, replicate 1

source_name: T8ML1_anti-CD3/CD28 for 8hr

value: anti-CD3/CD28 for 8hr


title: iKCL004-3

description:
SAMPLE 2.3
undifferentiated hiPSC line iKCL004 replicate 3

source_name: undifferentiated hiPSC line iKCL004


title: T8ML1_treated for 8hr, replicate 2


title: T8ML1_treated for 8hr, replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2128


title: iKCL011-1

description:
SAMPLE 3.1
undifferentiated hiPSC line iKCL011 replicate 1


title: KCL034-2

description:
SAMPLE 4.2
undifferentiated hESC line KCL034 replicate 2


title: T8ML1_treated for 4hr, replicate 3

source_name: T8ML1_anti-CD3/CD28 for 4hr

value: anti-CD3/CD28 for 4hr


title: BJ-1

description:
SAMPLE 1.1
Somatic donor line replicate 1

source_name: human neonatal foreskin fibroblasts BJ (ATCC, CRL-2522)

value: BJ

value: human neonatal foreskin fibroblasts


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2127

source_name: Liver


title: T8ML1_treated for 4hr, replicate 1


title: T8ML1_treated for 4hr, replicate 2


title: KCL034-3

description:
SAMPLE 4.3
undifferentiated hESC line KCL034 replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2125


title: T8ML1_untreated, replicate 3


title: iKCL011-3

description:
SAMPLE 3.3
undifferentiated hiPSC line iKCL011 replicate 3


title: TCL1_treated for 12hr, replicate 2

source_name: TCL1_anti-CD3/CD28 for 12h

value: sezary patient TCL1

value: anti-CD3/CD28 for 12h


title: TCL1_treated for 12hr, replicate 3


title: TCL1_treated for 28hr, replicate 2

source_name: TCL1_anti-CD3/CD28 for 28h

value: anti-CD3/CD28 for 28h


title: TCL1_treated for 28hr, replicate 1


title: TCL1_treated for 28hr, replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2126


title: T8ML1_untreated, replicate 1


title: iKCL004-1

description:
SAMPLE 2.1
undifferentiated hiPSC line iKCL004 replicate 1


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2121


title: iKCL004-2

description:
SAMPLE 2.2
undifferentiated hiPSC line iKCL004 replicate 2


title: TCL1_treated for 12hr, replicate 1


title: TCL1_treated for 8hr, replicate 2

source_name: TCL1_anti-CD3/CD28 for 8h

value: anti-CD3/CD28 for 8h


title: T8ML1_untreated, replicate 2

value: T-cell lymphoma cell line


title: TCL1_treated for 8hr, replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2119


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2120


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2122


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2117


title: TCL1_treated for 8hr, replicate 1


title: BJ-2

description:
SAMPLE 1.2
Somatic donor line replicate 2


title: BJ-3

description:
SAMPLE 1.3
Somatic donor line replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2109


title: TCL1_untreated, replicate 3


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2113


title: TCL1_untreated, replicate 2


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2111


title: ECH_Wt_24hpi_rep2

first: Jacques

last: Pédron

address: 4 place Jussieu

department: Biology

institute: Université Pierre et Marie Curie

description: Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation replicat 2

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

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

data_processing: The raw data (.pair file) were analyzed with the ANAIS web interface (http://anais.versailles.inra.fr/; Simon, A., and Biot, E. (2010). ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 26: 2468-2469).

organism: Dickeya dadantii 3937

source_name: Dickeya dadantii 3937 wild type

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

growth_protocol: Bacteria were isolated from Arabidopsis leaf surfaces (6 hpi) or from whole leaf (24 hpi) using the protocol described in Chapelle, E., Alunni, B., Malfatti, P., Solier, L., Pédron, J, Kraepiel, Y., and Van Gijsegem, F. (2015) . A straightforward and reliable method for bacterial in planta transcriptomics: application to the Dickeya dadantii/Arabidopsis thaliana pathosystem. Plant J 82: 352-362.

extract_protocol: Total RNA was extracted by the hot phenol method and DNA was removed by AMBION Dnase treatment

treatment_protocol: Arabidopsis 6 weeks old plants were infected by rapid immersion in a bacterial suspension (5. 107 cfu/mL)

tag: genotype/variation

value: wild type parent

tag: phenotype

value: normal


title: ECH_Wt_6hpi_rep1

description: Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation replicat 1


title: ECH_PecS_6hpi_rep2

description: pecS mutant bacteria isolated from arabidopdis leaves 6 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation replicat 2

source_name: Dickeya dadantii 3937 pecS mutant

tag: strain

value: uidA-Kn interposon in the pecS regulatory gene

value: hypervirulent on plants


title: ECH_Wt_6hpi_rep4

description: Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation for the comparison with pecS mutant bacteria isolated from arabidopdis leaves 6 hours post inoculation replicat 1


title: ECH_PecS_24hpi_rep1

description: pecS mutant bacteria isolated from arabidopdis leaves 24 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation replicat 1


title: ECH_Wt_24hpi_rep1

description: Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation replicat 1


title: ECH_Wt_24hpi_rep3

description: Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation for the comparison with pecS mutant bacteria isolated from arabidopdis leaves 24 hours post inoculation replicat 1


title: ECH_Wt_6hpi_rep3

description: Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation replicat 3


title: ECH_PecS_6hpi_rep1

description: pecS mutant bacteria isolated from arabidopdis leaves 6 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation replicat 1


title: ECH_Wt_6hpi_rep5

description: Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation for the comparison with pecS mutant bacteria isolated from arabidopdis leaves 6 hours post inoculation replicat 2


title: ECH_Wt_6hpi_rep2

description: Wild type bacteria isolated from arabidopsis leaves 6 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation replicat 2


title: ECH_PecS_24hpi_rep2

description: pecS mutant bacteria isolated from arabidopdis leaves 24 hours post inoculation for the comparison with Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation replicat 2


title: TCL1_untreated, replicate 1

value: primary T-cell lymphoma cells

value: none (untreated)


title: Liver tissue from adult pig taken at slaughter LPA DL Le 2110

description:
Gene expression data from liver
loin eye area (LEA) [cm2]: area of M. longissimus dorsi (Mld) at 13th/14th rib
fat area (FA) [cm2]: fat area on Mld at 13th/14th rib
meat to fat ratio (MFR): ratio of meat and fat area
MV = missing value

value: Adult German Landrace


title: ECH_Wt_24hpi_rep4

description: Wild type bacteria isolated from arabidopsis leaves 24 hours post inoculation for the comparison with pecS mutant bacteria isolated from arabidopdis leaves 24 hours post inoculation replicat 2


title: Adult mTEC Rep1

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

description: Gene expression data from Adult Thymus mTEC

hyb_protocol: Hybridisation to Affymetrix Mouse Gene 2.0 ST arrays was performed for 16 hours at 45C with constant rotation. Samples were hybridised according to the Affymetrix specifications: hybridisation cocktails were heated at 99C for 5 minutes and then at 45C for another 5 minutes. Samples were centrifuged at max speed for 1 minute and 200ul was transferred to each array. Hybridisation was carried out for 16 hours at 45C and 60 rpm. Fluidics washing was FS450_0001.

scan_protocol: Arrays were scanned with an Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalised using rma function from the oligo package in R

source_name: 1-2 weeks Adult Thymus mTEC

label_protocol: Up to 5.5g of total RNA was fragmented and labelled using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay as outlined in the manufacturer's instructions.

extract_protocol: RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher, Cat. KIT0202) performed according to the manufacturer's instructions.

treatment_protocol: 10-15 fetal thymi were dissected from E14.5 wildtype embryos and cultured for 7 days in AIM-V. For isolation of embryonic TEC, thymic lobes were dissected and washed once in PBS followed by an incubation of 15 min in PBS containing 0.25% trypsin and 0.02% EDTA and gentle mechanical dissociation to obtain cell suspensions. For isolation of adult TEC, thymic lobes were dissected and cut into small pieces (~10 mm × 10 mm), excess thymocytes removed by sequential washes in HBSS containing FCS 10% (v/v) and incubated for 30 min at 37 °C in HBSS containing FCS, 3.3 mg/ml Liberase and 0.5 mg/ml DNaseI (Roche Diagnostics UK). After incubation, cells suspensions were prepared by gentle mechanical dissociation.

tag: tissue

value: 1-2 weeks Adult Thymus

tag: genotype

value: Wildtype

tag: age

value: 1-2 weeks


title: Adult mTEC Rep2


title: Embryonic mTEC Rep2

description: Gene expression data from E14.5 Fetal Thymus mTEC 7 days in culture

source_name: Embryonic day 14.5 Fetal Thymus mTEC + 7days in Culture

value: E14.5 Fetal Thymus+ 7days in Culture

value: Embryonic day 14.5 + 7days in Culture


title: Adult cTEC Rep1

description: Gene expression data from Adult Thymus cTEC

source_name: 1-2 weeks Adult Thymus cTEC


title: Adult cTEC Rep2


title: muscle_young_WT_rep3

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: RNA samples were hybridized to Mouse Gene 2.0 ST Arrays (Affymetrix) following the manufacturer's protocol

scan_protocol: Arrays were scanned by Affymetrix GeneChip Scanner 3000

data_processing: Arrays were normalized using the robust multi-array average (RMA) algorithm

source_name: whole skeletal muscle

label_protocol: RNA samples were reverse-transcribed, amplified and biotin-labeled using GeneChip WT PLUS Reagent Kit from Affymetrix

extract_protocol: Total RNA was extracted from muscle tissue using Trizol (Invitrogen)

value: 2–3 month

value: Wild-type


title: Embryonic cTEC Rep1

description: Gene expression data from E14.5 Fetal Thymus cTEC 7 days in culture

source_name: Embryonic day 14.5 Fetal Thymus cTEC + 7days in Culture


title: Embryonic mTEC Rep1


title: muscle_young_WT_rep1


title: Embryonic cTEC Rep2


title: LNCaP_CHD1_KO_Rep3

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

hyb_protocol: Standard hyb protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

scan_protocol: Standard scan protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: LNCaP cells

label_protocol: Standard label protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

growth_protocol: LNCaP cells were cultured in Gibco RPMI 1640 Medium with 10% FBS, and PC3 cells were cultured in Ham's F-10 Nutrient Mixture medium with 10% FBS

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

value: LNCaP

value: CHD1 knockout


title: muscle_old_MISR_rep2

value: 24 months

value: MISR


title: muscle_old_MISR_rep1


title: LNCaP_Control_Rep3

value: control


title: muscle_young_WT_rep2


title: muscle_old_WT_rep2


title: LNCaP_CHD1_KO_Rep1


title: muscle_old_WT_rep3


title: Retina_OIR_rep2

first: Chi-Hsiu

address: 300 Longwood Avenue

department: Ophthalmology

institute: Boston Children's Hospital

description:
sncRNA expression data from P17 mouse retina in OIR
9_(miRNA-2_0).CEL

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized to GeneChip® miRNA 2.0 Array (Affymetrix) according to the manufacturer’s instructions.

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

data_processing: The data were analyzed with the Affymetrix miRNA QCTool software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Retina from P17 OIR mouse pup

label_protocol: Biotinylated cRNAs were prepared from using FlashTag™ Biotin HSR RNA Labeling Kit according to the standard Affymetrix protocol.

growth_protocol: C57BL/6J mice (Mus musculus) were born and reared period to experiments under standard conditions of housing, illumination, litter size, and adequate supplies of food and water.

extract_protocol: miRNeasy Micro Kit (Qiagen) was used to isolate total retinal RNA according to the manufacturer's instructions.

treatment_protocol: The OIR model was used in this study. Mouse pups and the nursing mother were exposed to 75% oxygen from postnatal day (P) 7 to P12, and returned to room air. Age-matched normoxic control pups were kept in room air throughout the experiments. Mouse pups were sacrificed at P17, followed by retinal dissection and total RNA extaction.

tag: strain background

value: wild type

value: 75% oxygen from postnatal day P7 to P12

value: retina

tag: tissue type

value: oxygen-induced retinopathy (OIR) retinas


title: PC3_shControl-Rep2

source_name: PC3 cells

tag: cell line

tag: sirna

value: shControl


title: Retina_OIR_rep3

description:
sncRNA expression data from P17 mouse retina in OIR
11_(miRNA-2_0).CEL

tag: exposed to


title: PC3_shCHD1-#1-Rep1


title: PC3_shCHD1-#1-Rep2


title: PC3_shCHD1-#2-Rep3


title: LNCaP_Control_Rep1


title: PC3_shCHD1-#1-Rep3


title: LNCaP_Control_Rep2


title: Retina_OIR_rep1

description:
sncRNA expression data from P17 mouse retina in OIR
8_(miRNA-2_0).CEL


title: PC3_shControl-Rep3


title: PC3_shControl-Rep1


title: PC3_shCHD1-#2-Rep1


title: PC3_shCHD1-#2-Rep2


title: LNCaP_CHD1_KO_Rep2


title: Retina_Ctrl_rep1

description:
sncRNA expression data from P17 mouse retina in normoxia
1_(miRNA-2_0).CEL

source_name: Retina from P17 normoxic mouse pup

value: normoxic condition

value: normoxic retinas


title: Retina_Ctrl_rep2

description:
sncRNA expression data from P17 mouse retina in normoxia
3_(miRNA-2_0).CEL


title: AML sample 64

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description:
SAMPLE 111
Gene expression data from acute leukemic cell samples.

hyb_protocol: RNA were hybridized according to the manufacturer's protocols. The arrays were washed and stained using Fluidics Station 450.

scan_protocol: The images were scanned with GeneChip Scanner 3000 (Affymetrix).

data_processing:
Data were analysed with GeneChip Operating Software (GCOS; Affymetrix).
A genomics signature for the PDC samples has been established with the probes shown in the supplementary file 'genomics_signature.txt'.

source_name: AML sample

label_protocol: RNA were labelled according to the manufacturer's protocols.

extract_protocol: According to manufacturer's recommendations.

value: Bone marrow/blood >65% infiltration

tag: disease state

value: acute myeloid leukemia (AML)

tag: type


title: AML sample 62

description:
SAMPLE 109
Gene expression data from acute leukemic cell samples.


title: AML sample 61

description:
SAMPLE 108
Gene expression data from acute leukemic cell samples.


title: AML sample 65

description:
SAMPLE 112
Gene expression data from acute leukemic cell samples.


title: AML sample 63

description:
SAMPLE 110
Gene expression data from acute leukemic cell samples.


title: Retina_Ctrl_rep3

description:
sncRNA expression data from P17 mouse retina in normoxia
6_(miRNA-2_0).CEL


title: AML sample 60

description:
SAMPLE 107
Gene expression data from acute leukemic cell samples.


title: AML sample 57

description:
SAMPLE 104
Gene expression data from acute leukemic cell samples.


title: AML sample 59

description:
SAMPLE 106
Gene expression data from acute leukemic cell samples.


title: AML sample 58

description:
SAMPLE 105
Gene expression data from acute leukemic cell samples.


title: AML sample 53

description:
SAMPLE 100
Gene expression data from acute leukemic cell samples.


title: PCB

city: Daejeon

first: Gou Young

last: Koh

address: 291 Daehark-ro, Yuseong-gu

country: South Korea

institute: KAIST

description: Gene expression at day 5.5 with CsAYTE

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Mouse Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: CsAYTE induced PCB

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: For induction and differentiation of Flk1+ MPC, sfPCB, PCB, and M+CM, mouse PSC were cultured in differentiation medium without leukemia inhibitory factor.

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

treatment_protocol: CsAYTE was treated whenever medium was changed. DMSO was treated as a control vehicle.

tag: cell type

value: embryonic stem cells

tag: time point

value: day 5.5


title: AML sample 56

description:
SAMPLE 103
Gene expression data from acute leukemic cell samples.


title: M+CM

description: Gene expression at day 10.5

source_name: αMHC+ mature cardiomyocytes


title: AML sample 54

description:
SAMPLE 101
Gene expression data from acute leukemic cell samples.


title: sfPCB

description: Gene expression at day 5.5 without CsAYTE

source_name: Spontaneously formed PCB without CsAYTE


title: Flk1+MPC

description: Gene expression at day 4.5

source_name: Flk1+ MPC as cardiovascular progenitors

value: day 4.5


title: AML sample 49

description:
SAMPLE 96
Gene expression data from acute leukemic cell samples.


title: AML sample 52

description:
SAMPLE 99
Gene expression data from acute leukemic cell samples.


title: AML sample 55

description:
SAMPLE 102
Gene expression data from acute leukemic cell samples.


title: AML sample 50

description:
SAMPLE 97
Gene expression data from acute leukemic cell samples.


title: AML sample 51

description:
SAMPLE 98
Gene expression data from acute leukemic cell samples.


title: Sj_S3_49d_rep3

city: shanghai

first: yang

middle: jian

last: mei

address: minhang district ziyue road No.518

institute: shanghai veterinary research institute

description:
Gene expression of schistosoma japonicum from buffalo infected with scistosoma japonicum for 49d,replicate 3
Agilent Feature Extraction file: S3@252610410005_S01_GE1_105_Dec08_1_3

hyb_protocol: The hybridization used Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).Images were quantified using Agilent Feature Extraction Software (v10.5.1.1).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v 10.5.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Schistosoma japonicum

source_name: Buffalo infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 3

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

growth_protocol: cattle,buffalo,and goat,1-2 year old,healthy,were kept in non-infected areas.And cercariae were provided by Jiangsu Institute of Schistosomiasis Control.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: cattle and buffalo were infected with cercariae by back patch,goats were infected with cercariae by inguinal patch.And after 49d,7w,we collected worms by hepatic portal vein perfusion. Worms were stored in liquid nitrogen as quickly as possible.

tag: isolate

value: Anhui

tag: geographical location

value: China

value: adult worm

tag: gender

value: male and female encircle

tag: host

value: Buffalo


title: Sj_G1_49d_rep1

description:
Gene expression of schistosoma japonicum from goat infected with scistosoma japonicum for 49d,replicate 1
Agilent Feature Extraction file: G1@252610410007_S01_GE1_105_Dec08_2_2

source_name: Goat infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 1

tag: developmental stage

value: Goat


title: Sj_G4_49d_rep2

description:
Gene expression of schistosoma japonicum from goat infected with scistosoma japonicum for 49d,replicate 2
Agilent Feature Extraction file: G4@252610410007_S01_GE1_105_Dec08_2_3

source_name: Goat infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 2


title: Sj_H3_49d_rep3

description:
Gene expression of schistosoma japonicum from cattle infected with scistosoma japonicum for 49d,replicate 3
Agilent Feature Extraction file: H3@252610410005_S01_GE1_105_Dec08_2_2

source_name: Cattle infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 3

value: Cattle


title: Sj_G5_49d_rep3

description:
Gene expression of schistosoma japonicum from goat infected with scistosoma japonicum for 49d,replicate 3
Agilent Feature Extraction file: G5@252610410007_S01_GE1_105_Dec08_2_4

source_name: Goat infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 3


title: AML sample 46

description:
SAMPLE 93
Gene expression data from acute leukemic cell samples.

tag: tissue


title: AML sample 48

description:
SAMPLE 95
Gene expression data from acute leukemic cell samples.


title: Sj_S2_49d_rep2

description:
Gene expression of schistosoma japonicum from buffalo infected with scistosoma japonicum for 49d,replicate 2
Agilent Feature Extraction file: S2@252610410005_S01_GE1_105_Dec08_1_2

source_name: Buffalo infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 2


title: AML sample 47

description:
SAMPLE 94
Gene expression data from acute leukemic cell samples.


title: Sj_H2_49d_rep2

description:
Gene expression of schistosoma japonicum from cattle infected with scistosoma japonicum for 49d,replicate 2
Agilent Feature Extraction file: H2@252610410005_S01_GE1_105_Dec08_2_1

source_name: Cattle infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 2


title: Sj_H1_49d_rep1

description:
Gene expression of schistosoma japonicum from cattle infected with scistosoma japonicum for 49d,replicate 1
Agilent Feature Extraction file: H1@252610410005_S01_GE1_105_Dec08_1_4

source_name: Cattle infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 1


title: Sj_S1_49d_rep1

description:
Gene expression of schistosoma japonicum from buffalo infected with scistosoma japonicum for 49d,replicate 1
Agilent Feature Extraction file: S1@252610410005_S01_GE1_105_Dec08_1_1

source_name: Buffalo infected with schistosoma japonicum,49d,hepatic portal vein perfusion,replicate 1


title: AML sample 45

description:
SAMPLE 92
Gene expression data from acute leukemic cell samples.


title: AML sample 44

description:
SAMPLE 91
Gene expression data from acute leukemic cell samples.


title: FDCPmix bulk (1)

first: Dapeng

address: Gower Street

department: Stem Cell Laboratory

institute: UCL Cancer Institute

description: Gene expression in maintenance culture conditions

hyb_protocol: Each Cy3-labeled cRNA sample (1.6ug as per NanoDrop reading) was hybridised to an individual 44K subarray of 4x44K high-density microarray slide (Whole Mouse Gene Expression Microarrays, Agilent), washed, scanned and feature-extracted as per Agilent protocols.

scan_protocol: Scanning and feature extraction was performed as per Agilent protocols

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent v10.1.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: FDCPmix unfractionated, replicate

label_protocol: Total RNA (150ng) and Agilent One-Color RNA Spike-In were reverse-transcribed and linearly amplified in the presence of Cy3-labeled CTP using Low RNA Input One-Color Kit (Agilent) following Agilent protocols, to generate Cy3-labeled cRNA for hybridisation to high-density microarrays. Quality and yield/specific activity of cRNA were determined using RNA 6000 Nano kit and spectrophotometer (NanoDrop ND- 1000). All samples generated comparable quality cRNA profiles, with specific activities in the range of 10.3 to 12.2 pmol Cy3/mg cRNA.

growth_protocol: Culture conditions are Fisher's medium with low Tyr content + 20% horse serum (batch-tested) + 2% WEHI IL-3 conditioned medium + L-Glutamine 4mM + Penicillin/Streptomycin

extract_protocol: Trizol extraction

treatment_protocol: Cells grown under FDCPmix maintenance culture conditions; cells stained with respective antibodies in medium, and sorted on Dako MoFlo cell sorted.

value: FDCPmix

value: bone marrow

tag: cell population

value: unfractionated


title: AML sample 40

description:
SAMPLE 87
Gene expression data from acute leukemic cell samples.


title: FDCPmix MCP (3)

source_name: FDCPmix Gr1+, replicate


title: FDCPmix bulk (2)


title: AML sample 42

description:
SAMPLE 89
Gene expression data from acute leukemic cell samples.


title: FDCPmix MCP (1)


title: FDCPmix ECP (3)

source_name: FDCPmix Kit-Gr1-, replicate


title: AML sample 43

description:
SAMPLE 90
Gene expression data from acute leukemic cell samples.

source_name: AML sample


title: FDCPmix ECP (2)


title: AML sample 37

description:
SAMPLE 84
Gene expression data from acute leukemic cell samples.


title: FDCPmix ECP (1)


title: E9.5 Sox10 rep2

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Venus-sorted cells

hyb_protocol: Slides were hybridized to Agilent-015087 arrays according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1, August 2006).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 28 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
(4) Remove outliers. Each cell/treatment type (CTT) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.
First we estimate the average square difference (ASD) between replication pairs:
ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is log intensities for i-th CTT and replication j, N = number of CTT. Then we estimate z-value for each CTT: z = (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4, then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: E9.5, Sox10-positive cells

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit, according to the manufacturer's instructions.

growth_protocol: Isolated by dissection of uterus of a pregnant mouse.

extract_protocol: The collected cells were dissolved in TRIZOL-LS reagent. The solution was precipitated according to manufacturer's protocol. Briefly, add equal 300 ul of chloroform to 1ml TRIZOL solution, centrifuge them for 5 minutes, take the supernatant, mix with equal volume of isopropanol, centrifuge them, wash the precipitates with 70% ethanol, and dissolve in nuclease-free water.

treatment_protocol: Trunk area of embryos was dissected and trypsinized, then resuspended in phosphate-buffered saline to be sorted with FACS.

tag: strain/background

value: C57BL6/129Sv hybrid

tag: genotype/variation

value: body trunk

value: 9.5 dpc

value: mixed

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting UMR RNA was mixed with 129ES cell RNA (Life+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube.

tag: sample type

value: reference


title: AML sample 38

description:
SAMPLE 85
Gene expression data from acute leukemic cell samples.

value: Bone marrow/blood >65% infiltration

value: acute myeloid leukemia (AML)


title: AML sample 41

description:
SAMPLE 88
Gene expression data from acute leukemic cell samples.


title: FDCPmix MCP (2)

tag: cell line


title: FDCPmix SR Sca-1lo (3)

source_name: FDCPmix Kit+Gr1-Sca1lo, replicate


title: E9.5 Sox10 rep1

description: Venus-sorted cells


title: AML sample 39

description:
SAMPLE 86
Gene expression data from acute leukemic cell samples.


title: FDCPmix SR Sca-1lo (2)


title: E9.5 Sox1 rep1

description: YFP-sorted cells

source_name: E9.5, Sox1-positive cells

value: C57BL6/CBA hybrid


title: AML sample 36

description:
SAMPLE 83
Gene expression data from acute leukemic cell samples.


title: FDCPmix SR Sca-1lo (1)


title: E9.5 whole rep2

description: Whole embryo

source_name: E9.5, whole embryo

treatment_protocol: Whole embryos were minced with scalpel.

value: whole embryo


title: FDCPmix SR Sca-1hi (3)

source_name: FDCPmix Kit+Gr1-Sca1hi, replicate


title: AML sample 34

description:
SAMPLE 81
Gene expression data from acute leukemic cell samples.


title: AML sample 33

description:
SAMPLE 80
Gene expression data from acute leukemic cell samples.


title: E9.5 Sox1 rep2

description: YFP-sorted cells


title: E9.5 whole rep1

description: Whole embryo


title: AML sample 32

description:
SAMPLE 79
Gene expression data from acute leukemic cell samples.


title: FDCPmix SR Sca-1hi (2)


title: AML sample 35

description:
SAMPLE 82
Gene expression data from acute leukemic cell samples.


title: AML sample 31

description:
SAMPLE 78
Gene expression data from acute leukemic cell samples.


title: AML sample 29

description:
SAMPLE 76
Gene expression data from acute leukemic cell samples.


title: FDCPmix SR Sca-1hi (1)


title: AML sample 28

description:
SAMPLE 75
Gene expression data from acute leukemic cell samples.


title: AML sample 30

description:
SAMPLE 77
Gene expression data from acute leukemic cell samples.


title: Hepa1-6

first: Lei

last: Zhang

address: Yueyang Road

institute: SIBS

description: Gene expression of Hepa1-6 cells

hyb_protocol: 875ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mouse hepatoma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20 ug RNA with the aaUTP according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: E14 and EHe were cultured in Glasgow minimum essential medium (Invitrogen) containing 10% knock-out serum replacement (Invitrogen), 1% fetal bovine serum (HyClone, Logan, UT), 1% penicillin/streptomycin/glutamine, 1% non-essential amino acids (Invitrogen), 0.1 mM 2 mercaptoethanol, 1 mM sodium pyruvate, and 1000 units/ml leukemia inhibitory factor (ESGRO, Chemicon, Temecula, CA). The mouse hepatoma cell line Hepa1–6 was cultured in high glucose Dulbecco’s modified Eagle’s medium (Invitrogen) containing 10% fetal calf serum (Invitrogen) and 1% penicillin/ streptomycin/glutamine.

extract_protocol: RNA was extracted with RNeasy microcolumns (RNeasy lysis buffer, Qiagen), according to the manufacturer’s instructions.

treatment_protocol: For induction of EHe hybrid cells to differentiate by monolayer culture, hybrid cells were dispersed into a single cell suspension with 0.25% trypsin, and plated the cells on the 0.2% gelatin-coated cell culture dish. The cells were differentiated in high glucose Dulbecco’s modified Eagle’s medium (Invitrogen) containing 15% fetal calf serum (Invitrogen) and 1% penicillin/streptomycin/glutamine and changed the medium every 1 or 2 days.

value: Mouse hepatoma cells


title: EheD14

description: Gene expression of EheD14 cells

source_name: Hybrid cells

value: EHe

value: Differentiation of Ehe for 14 days in vitro


title: AML sample 27

description:
SAMPLE 74
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-1191 T vs N

city: Rotterdam

first: Askar

last: Obulkasim

state: Zuid Holland

address: Wytemaweg 80

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia Children's Hospital

hyb_protocol: High-resolution array CGH was performed using custom design 180K Agilent microarrays (4x180k array, Agilent Technologies, Palo Alto, CA, USA, GEO platform GPL8687 containing 180,880 in situ synthesized oligonucleotides representing 169,793 unique chromosomal locations evenly distributed over the genome (spacing ~17 kb) and 4548 additional unique oligonucleotides, located at 238 of the Cancer Census genes  (http://www.sanger.ac.uk/genetics/CGP/Census/)).

scan_protocol: Agilent’s Feature Extraction software (v10.5.1.1) with default settings was applied on the microarray images to quantify the fluorescence intensities

data_processing:
After image quantification, control spots (n = 6539) were removed from the data yielding 174,340 features. Both channels were background corrected by subtracting background median signals from foreground median intensities to obtain an unbiased hybridization signal. Normalization was performed with the R-package CGHcall
The LogX ratios are thus Cy3/Cy5. Normalization was performed with using median of the intensities for the two channels, followed by a post-segmentation mode normalization as previously described. Bioinformatics. 2007 Apr 1;23(7):892-4. Epub 2007 Jan 31. CGHcall: calling aberrations for array CGH tumor profiles. van de Wiel MA1, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B.

source_name: FFPE blocks

label_protocol: Protocol following procedures and components of the ‘DNA labelling kit’ by ENZO Life Science Farmingdale, USA

extract_protocol: DNA was isolated as previously described: High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues. van Essen HF, Ylstra B. Methods Mol Biol. 2012;838:329-41.

treatment_protocol: Genomic DNA extracted using Trizol following manufacturer's instructions

value: esophageal adenocarcinoma tumor

tag: treatment

value: surgery alone

source_name: patient matched normal DNA

value: normal esophageal tissue


title: ES

description: Gene expression of E14 cells

source_name: E14 cell line

value: Embryonic stem cells


title: Treated with surgery alone UGI-1211 T vs N


title: EheD7

description: Gene expression of EheD7 cells

value: Differentiation of Ehe for 7 days in vitro


title: AML sample 25

description:
SAMPLE 72
Gene expression data from acute leukemic cell samples.


title: AML sample 26

description:
SAMPLE 73
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-1210 T vs N


title: Treated with surgery alone UGI-1199 T vs N


title: Ehe

description: Gene expression of EHe cells

value: Hybrids derived from fusion between E14 and Hepa1-6 cells


title: Treated with surgery alone UGI-1120 T vs N


title: Treated with surgery alone UGI-1131 T vs N


title: AML sample 24

description:
SAMPLE 71
Gene expression data from acute leukemic cell samples.


title: AML sample 23

description:
SAMPLE 70
Gene expression data from acute leukemic cell samples.


title: HcT116_shCBX4#3

city: Guang Zhou

first: Xin

state: State...

address: Dongfengdong road 651

institute: Sun Yat-sen University Cancer Center

description: Gene expression of HCT116 transfected with CBX4 shRNA#3

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: HCT116 cell-shCBX4#3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).. RNA was quantified using a NanoDrop ND-100 UV-VIS spectrophotometer

treatment_protocol: HCT116 cell was transfected with control or CBX4 shRNA, then these sample were used for the global transcriptomes analysis.

value: colorectal cancer

tag: morphology

value: epithelial cell


title: HcT116_shCBX4#2

description: Gene expression of HCT116 transfected with CBX4 shRNA#2

source_name: HCT116 cell-shCBX4#2


title: EBOV PBMC, Mky 051783 Day 8

first: Ignacio S.

last: Caballero

address: 620 Albany St., NEIDL 401V

department: NEIDL/Microbiology

institute: Boston University School of Medicine

description: commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons

hyb_protocol: Labeled reference RNA was added to each experimental sample, then samples were hybridized to arrays in Agilent SureHyb-enabled hybridization chambers.  After a 17-hour hybridization, arrays were washed with the Agilent gene expression wash buffers and then placed in Agilent scanner slide holders with ozone-barrier covers.

scan_protocol: Arrays were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent's Feature Extraction software

data_processing: Data were first background-corrected to remove noise from background intensity levels, and then normalized within the arrays using the Limma package in R (R development core team 2010). Following normalization, the reference and experimental samples were compared to generate log fold-change values that represent a change in mRNA expression (either positive or negative).  Data were further processed by zero-transformation, where the normalized values of the pre-infection samples were subtracted from the subsequent timepoints of each monkey, in order to remove animal-intrinsic variables and focus on gene expression changes due to infection only.

organism: Macaca fascicularis

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day8

label_protocol: RNA samples were amplified and labeled with Cy dyes using the Agilent Low-Input Quick Amp Labeling kits

extract_protocol: Total RNA was extracted using TRIzol reagent following the manufacturer's instructions

tag: animal id

value: PBMC

source_name: Universal Human Reference RNA (Stratagene), commercially available

tag: vendor

value: Agilent Technologies

tag: catalog number

tag: rna source

value: 10 different human cell lines


title: Treated with surgery alone UGI-1207 T vs N


title: Treated with surgery alone UGI-1079 T vs N


title: Treated with surgery alone UGI-1103 T vs N


title: AML sample 21

description:
SAMPLE 68
Gene expression data from acute leukemic cell samples.

value: Bone marrow/blood >65% infiltration

tag: disease state

value: acute myeloid leukemia (AML)

tag: type


title: Treated with surgery alone UGI-1086 T vs N


title: HcT116_shcon

description: Gene expression of HCT116 transfected with control shRNA

source_name: HCT116 cell-shcon


title: AML sample 22

description:
SAMPLE 69
Gene expression data from acute leukemic cell samples.

source_name: AML sample


title: Treated with surgery alone UGI-1058 T vs N


title: Treated with surgery alone UGI-1051 T vs N


title: EBOV PBMC, Mky 062063 Day 7

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day7

tag: cell type

tag: time point


title: EBOV PBMC, Mky 061993 Day 6

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day6


title: AML sample 16

description:
SAMPLE 63
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-1024 T vs N


title: EBOV PBMC, Mky 061944 Day 6


title: Treated with surgery alone UGI-1007 T vs N


title: AML sample 19

description:
SAMPLE 66
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-1012 T vs N


title: Treated with surgery alone UGI-1023 T vs N


title: AML sample 15

description:
SAMPLE 62
Gene expression data from acute leukemic cell samples.


title: AML sample 18

description:
SAMPLE 65
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky R060052 Day 5_2

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day5


title: EBOV PBMC, Mky 051822x Day 8


title: EBOV PBMC, Mky 062009x Day 5_1


title: EBOV PBMC, Mky R060052 Day 5_1


title: Treated with surgery alone UGI-1005 T vs N


title: AML sample 13

description:
SAMPLE 60
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-0609 T vs N


title: Treated with surgery alone UGI-0581 T vs N


title: AML sample 20

description:
SAMPLE 67
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky R050148 Day 7


title: AML sample 14

description:
SAMPLE 61
Gene expression data from acute leukemic cell samples.


title: AML sample 17

description:
SAMPLE 64
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky 062009x Day 5_2


title: AML sample 12

description:
SAMPLE 59
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky 062059 Day 4_2

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day4


title: Treated with surgery alone UGI-0566 T vs N


title: EBOV PBMC, Mky 062098 Day 4_2


title: Treated with surgery alone UGI-0560 T vs N


title: EBOV PBMC, Mky 062098 Day 4_1


title: AML sample 11

description:
SAMPLE 58
Gene expression data from acute leukemic cell samples.


title: AML sample 8

description:
SAMPLE 55
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky 051892 Day 3

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day3


title: AML sample 10

description:
SAMPLE 57
Gene expression data from acute leukemic cell samples.


title: AML sample 9

description:
SAMPLE 56
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky 062059 Day 4_1

description: commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons


title: Treated with surgery alone UGI-0357 T vs N


title: Treated with surgery alone UGI-0473 T vs N


title: AML sample 6

description:
SAMPLE 53
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-0342 T vs N


title: Treated with surgery alone UGI-0348 T vs N


title: AML sample 5

description:
SAMPLE 52
Gene expression data from acute leukemic cell samples.


title: AML sample 4

description:
SAMPLE 51
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky 062009x Day 0_2

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day0


title: EBOV PBMC, Mky R050096 Day 1

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient_day1


title: AML sample 7

description:
SAMPLE 54
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky 061973x Day 1


title: EBOV PBMC, Mky 062063 Day 0_2


title: Treated with surgery alone UGI-0269 T vs N


title: EBOV PBMC, Mky 061913 Day 3


title: EBOV PBMC, Mky 051783 Day 0


title: EBOV PBMC, Mky 062098 Day 0_2


title: AML sample 3

description:
SAMPLE 50
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-0116 T vs N


title: Treated with surgery alone UGI-0213 T vs N


title: EBOV PBMC, Mky 062059 Day 0_2


title: AML sample 2

description:
SAMPLE 49
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-0267 T vs N


title: AML sample 1

description:
SAMPLE 48
Gene expression data from acute leukemic cell samples.


title: Treated with surgery alone UGI-0089 T vs N


title: T-ALL sample 33

description:
SAMPLE 45
Gene expression data from acute leukemic cell samples.

source_name: T-ALL sample

value: T-acute lymphoblastic leukemia (T-ALL)

value: IMG


title: EBOV PBMC, Mky R060052 Day 0_2


title: EBOV PBMC, Mky 062063 Day 0_1


title: Treated with surgery alone UGI-0293 T vs N

source_name: FFPE blocks


title: Treated with surgery alone UGI-0073 T vs N

source_name: patient matched normal DNA


title: Treated with surgery alone UGI-0085 T vs N


title: Treated with surgery alone UGI-0084 T vs N


title: T-ALL sample 35

description:
SAMPLE 47
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 32

description:
SAMPLE 44
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky R050148 Day 0


title: T-ALL sample 34

description:
SAMPLE 46
Gene expression data from acute leukemic cell samples.

value: TCRgd


title: EBOV PBMC, Mky 061944 Day 0


title: EBOV PBMC, Mky 062009x Day 0_1


title: T-ALL sample 30

description:
SAMPLE 42
Gene expression data from acute leukemic cell samples.

value: IMd


title: T-ALL sample 31

description:
SAMPLE 43
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0637 T vs N

value: esophageal adenocarcinoma tumor

value: pre-operative chemo


title: EBOV PBMC, Mky R060052 Day 0_1


title: Treated with surgery alone UGI-0068 T vs N

value: surgery alone

value: normal esophageal tissue


title: Treated with pre-operative chemo UGI-0635 T vs N


title: Treated with pre-operative chemo UGI-0634 T vs N


title: EBOV PBMC, Mky 062059 Day 0_1


title: EBOV PBMC, Mky 062098 Day 0_1


title: T-ALL sample 27

description:
SAMPLE 39
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0633 T vs N


title: Treated with pre-operative chemo UGI-0626 T vs N


title: EBOV PBMC, Mky 061913 Day 0


title: EBOV PBMC, Mky 051892 Day 0


title: T-ALL sample 25

description:
SAMPLE 37
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 28

description:
SAMPLE 40
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 21

description:
SAMPLE 33
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 22

description:
SAMPLE 34
Gene expression data from acute leukemic cell samples.

value: IMB


title: T-ALL sample 19

description:
SAMPLE 31
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0561 T vs N


title: T-ALL sample 26

description:
SAMPLE 38
Gene expression data from acute leukemic cell samples.


title: EBOV PBMC, Mky R050096 Day 0

description: commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons


title: T-ALL sample 16

description:
SAMPLE 28
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0558 T vs N


title: EBOV PBMC, Mky 051822x Day 0


title: T-ALL sample 24

description:
SAMPLE 36
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 23

description:
SAMPLE 35
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0563 T vs N


title: Treated with pre-operative chemo UGI-0384 T vs N


title: Treated with pre-operative chemo UGI-0405 T vs N


title: Treated with pre-operative chemo UGI-0427 T vs N


title: T-ALL sample 20

description:
SAMPLE 32
Gene expression data from acute leukemic cell samples.

value: AML+T


title: T-ALL sample 17

description:
SAMPLE 29
Gene expression data from acute leukemic cell samples.

value: Pre-ab


title: Treated with pre-operative chemo UGI-0554 T vs N


title: Treated with pre-operative chemo UGI-0476 T vs N


title: Treated with pre-operative chemo UGI-0589 T vs N


title: T-ALL sample 29

description:
SAMPLE 41
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0460 T vs N


title: Treated with pre-operative chemo UGI-0447 T vs N


title: EBOV PBMC, Mky 061973x Day 0


title: T-ALL sample 15

description:
SAMPLE 27
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 18

description:
SAMPLE 30
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0352 T vs N


title: Treated with pre-operative chemo UGI-0344 T vs N


title: T-ALL sample 14

description:
SAMPLE 26
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 13

description:
SAMPLE 25
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 12

description:
SAMPLE 24
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 11

description:
SAMPLE 23
Gene expression data from acute leukemic cell samples.