title: 14010_v_H99, rep.2

city: Murfreesboro

first: Erin

last: McClelland

state: TN

address: 1301 East Main Street, P.O. Box 60

department: Biology

institute: Middle Tennessee State University

description: Strains were started from frozen stock and grown to log-phase in YPD

hyb_protocol: Each sample pair (~24ul) is resuspended in formamide-based  hybridization buffer (vial 7-Genisphere) (26ul),  and Array 50dT blocker (Genisphere) (2ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity in the dark.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 900 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and nuclease-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 4 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.

scan_protocol: The microarray slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer, San Mateo, CA) to detect Cy3 and Cy5 fluorescence.  Laser power was kept constant and photomultiplier tube values were set for optimal intensity with minimal background.  An additional scan (low PMT) was done for each slide with the PMT such that <1% of the elements were saturating in order to characterize spots which were saturated at the higher PMT setting.

data_processing: The gene expression data were averaged across the RNA pools and analyzed (GeneSpring 7.2, Agilent, Redwood City, CA) taking into account the local background intensity and the Cy3/Cy5 dye swap. Twenty percent of the data were used to calculate the Lowess fit at each point and then a Lowess curve was fit to the log-intensity versus log-ratio plot.  After this, the mean signal to Lowess-adjusted controlled ratios was calculated.  The cross-chip averages were derived from the antilog of the mean of the natural log ratios across the two microarrays.  The data were then filtered in the following manner.  First, oligonucleotide elements that received a “present” call by the ScanArray software in half of the high PMT scans in either dye were identified for each condition and all others were excluded from the analysis.  Second, the data were filtered for genes in which the mean of the replicates had > 2-fold change and p<0.05. The Benjamini & Hoechberg false discovery rate for multiple testing corrections was then done for all genes showing changes in gene expression (p<0.01). The normalized log ratios are presented in the file Ratio_test_v_refence.txt on the series level.

organism: Cryptococcus neoformans

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere).  Modified oligo-dT primers are utilized in which a fluorophore/dendrimer specific oligo sequence is attached to the 5’ end of the dT primer.  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 2ug of total RNA and the solution is incubated at 80C for 5 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (0.5ul), 5X first strand buffer (2ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (0.5ul), 0.1M DTT (1ul), and Superscript II RNase H- Reverse Transcriptase (0.5ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 1.0M NaOH/ 100mM EDTA (1.0ul) and incubation at 65C for 10 minutes then neutralized with 2M Tris-HCL, pH 7.5 (1.2ul).  For RNA expression level comparison, samples are paired.

growth_protocol: C. neoformans serotype A strains H99 and the mouse-passaged strains 12602 and 14010 were grown from frozen stocks in Yeast Peptone Dextrose (YPD) media for 36 hours (mid-log phase) at 37 ºC and then washed three times with phosphate buffered saline (PBS).  Approximately 2 x 10e7 - 2 x 10e8 cells were used for RNA extraction.

extract_protocol: RNA was extracted using the Rneasy Midi Kit and genomic DNA removed using the Message Clean Kit from GenHunter.

tag: strain

tag: passage

value: High virulence mouse-passaged strain

value: Pre-passage wild-type strain


title: Probable AD 7

status: Public on Aug 11 2016

type: RNA

city: Shah Alam

first: Ainon

middle: Zahariah

last: Samsudin

state: Selangor

address: Bandar Puncak Alam

country: Malaysia

institute: University Teknologi Mara

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416966_S01_GE1_107_Sep09_1_1

hyb_protocol: 0.825 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Gene Expression blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2534A) 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 using cleaning tissue.

scan_protocol: Slides were scanned immediately after washing on the Agilent microarray scanner G2505B (Agilent Technology) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent Technology) using default parameters (protocol available at http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_Gene Expression_OneColor_6.7.pdf) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low Input Quick Amp Labeling 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.

extract_protocol: RNA was prepared using the Ribopure Blood RNA Purification kit (Ambion Technologies, USA) following the manufacturer's recommendations. Then treated with an on-column DNase digestion agent. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from participant was preserved in RNA later immediately

tag: diagnosis

value: Probable Alzheimer's Disease

tag: tissue

value: whole blood

tag: age

tag: gender

value: male


title: OVCA-CellLine-HCC5006CL_SNP6

type: genomic

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays werewashed and scanned according to manufacturer instructions (Affymetrix)

data_processing:
CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings.  CEL files were imported into Partek Genomics Suite Software with correction for fragment length, GC content, probe sequence. The corrected probe intensities were then quantile normalized. Copy number profiles were generated using Partek's Paired Copy Number Analysis workflow using patient matched constitutional DNA (ie. BloodLine) as a baseline for defining somatic alterations in each OVCA sample (tumour/cell line/xenograft). The Genomic Segmentation algorithm was applied with SNR=0.3, a 30 marker minimum segment size, and p-values < 10-7 for defining copy number alterations (CNAs).
SNP array normalized probe data = UTSWovca_SNP_Feb2015_AllCopyNumber_transpose.txt

label: biotin

molecule: genomic DNA

source_name: OVCA-CellLine

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Tumour cells were enriched from malignant effusions (OVCA tumour ascites) by two or more cycles of low speed centrifugation plus differential substrate attachment. Cell lines were cultured in ACL4 or RPMI growth media supplemented with 5% FBS. Xenografts were generated by injecting purified tumour cells intraperitoneally into athymic nude mice.

extract_protocol: Genomic DNA was extracted from cell pellets using the Qiagen DNeasy Blood and Tissue kit

treatment_protocol: No treatments were applied

tag: sample type

value: cell line

tag: sample source id

value: Female

tag: cell type

value: ovarian carcinoma


title: Probable AD 8

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416966_S01_GE1_107_Sep09_1_2


title: Non-demented control 10

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416965_S01_GE1_107_Sep09_2_4

value: Non-demented control


title: Non-demented control 8

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416965_S01_GE1_107_Sep09_2_2


title: OVCA-CellLine-HCC5079CL_SNP6


title: Non-demented control 9

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416965_S01_GE1_107_Sep09_2_3


title: OVCA-CellLine-HCC5011CL_SNP6


title: 14010_v_ H00,rep.1

country: USA


title: H99_v_12602, rep.2

value: Low virulence mouse-passaged strain


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#1

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: Naïve 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned on an Illumina BeadArray Reader

data_processing: Signal intensities were quantile normalized using the Bioconductor package lumi (v.2.14.1).

organism: Mus musculus

source_name: mouse splenocytes

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: After FACS-sorting , T-cells were washed twice with cold PBS and cell pellets were frozen and stored at -80C until all samples were collected. RNA was isolated using Qiagen RNeasy Plus Mini and Micro Kit per the manufacturer’s instructions and the yield was determined on a Qubit® 2.0 Fluorometer (Life Technologies, Grand Island, NY). Samples were subsequently analyzed for RNA integrity using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA). RNA that was determined to be of high quality (RINe ≥ 6.5) was amplified using the Ovation® PicoSL WTA System V2 (NuGEN Technologies, Inc., San Carlos, CA), biotin labeled using the Encore® BiotinIL Module (NuGEN Technologies, Inc., San Carlos, CA), and subsequently processed on a MouseRef-8 v2.0 Expression BeadChip (Illumina, Inc., San Diego, CA).

treatment_protocol: Naïve (CD44 low) CD8 T cells were isolated from spleens of transgenic TCR SV40-I (Thy1.1) transgenic mice (transgenic mice expressing CD8 T cells specific for epitope I of the SV40 large T antigen) and sorted by flow cytometric analysis for CD8+/CD44low.

value: TCR SV40-I transgenic CD8 T cells

tag: cell subtype


title: 12602_v_H99, rep.2


title: Non-demented control 7

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416965_S01_GE1_107_Sep09_2_1


title: Data Heifer #10995_11v14

city: Quebec

first: Léonie

last: Morin-Doré

state: Quebec

address: 2440, boulevard Hochelaga

department: Animal Sciences

institute: Laval University

description: Rep 4 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

label_protocol: For each sample, aRNA was labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (Cy3/Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). The labeled product was then purified with the Pico-Pure RNA Isolation Kit.

extract_protocol:
Total RNA was extracted from the pools using the AllPrep DNA/RNA micro kit, following the Parallel gDNA and total RNA extraction protocol. Total RNA integrity and concentration were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto
Amp protocol: To generate enough material for hybridization, the samples were linearly amplified. Antisense RNA (aRNA) was produced using the RiboAmp®HSPlus RNA Amplification kit (Thermo fisher Scientific). After two amplification rounds of 6 hr each, the

treatment_protocol:
Ovarian stimulation: Each heifer was first treated with progesterone (CIDR) during the luteal phase. The dominant follicle was aspirated 36 hours prior to administration of hormones. The ovarian stimulation program consisted of 6 injections of 30mg FSH ad
Embryo production: In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)

tag: developmental stage

tag: breed (cattle)

value: holstein

tag: time of embryo collection

value: 168 hpf (hours post-in-vitro fertilization)

tag: heifer age

value: 14 months

tag: tissue or cell type

value: embryo

value: 11 months


title: Data Heifer #10991_11v14

description: Rep 2 of 4


title: Data Heifer #10994_11v14

description: Rep 3 of 4


title: H99_v_14010, rep.2


title: H99_v_14010, rep.1


title: Non-demented control 6

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416965_S01_GE1_107_Sep09_1_4

value: female


title: OVCA-TumourHCC5011T_SNP6

source_name: OVCA-Tumour

value: Tumour


title: 12602_v_H99, rep.1

value: Pre-passage wild-type strain


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#2

description: Naïve 2


title: Probable AD 6

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416965_S01_GE1_107_Sep09_1_3

value: Probable Alzheimer's Disease


title: MCF-7 expt 2 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

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: MCF7 + 25nm ethanol for 4 weeks

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 2 µg total RNA sample, which was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy5 dye staining.

growth_protocol: MCF-7 is an established cell line derived from a human breast cancer. Cells were maintained in culture in T-25 plastic flasks and transferred to 6 well plastic plates for experiments.

extract_protocol: Total RNA was extracted using the Mirvana total RNA extraction kit and the manufacturer's procedure.

treatment_protocol: Ethanol was added in 10 microliter volumes to fresh culture medium each 3 days throughout the treatment. Control wells received no ethanol.

tag: cell line

value: malignant breast cancer


title: Data Heifer #10994

description: Rep 3 of 4

extract_protocol:
Total RNA was extracted from the pools using the AllPrep DNA/RNA micro kit, following the Parallel gDNA and total RNA extraction protocol. Total RNA integrity and concentration were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) with the RNA PicoLab Chip (Agilent Technologies).
Amp protocol: To generate enough material for hybridization, the samples were linearly amplified. Antisense RNA (aRNA) was produced using the RiboAmp®HSPlus RNA Amplification kit (Thermo fisher Scientific). After two amplification rounds of 6 hr each, the aRNA output was quantified using the NanoDrop ND-1000 (Nano-Drop Technologies, Wilmington, DE).

treatment_protocol:
Ovarian stimulation: Each heifer was first treated with progesterone (CIDR) during the luteal phase. The dominant follicle was aspirated 36 hours prior to administration of hormones. The ovarian stimulation program consisted of 6 injections of 30mg FSH administered at 12h intervals. Ovum pick up was performed 43h after the last FSH injection. Using transvaginal ultrasonography, follicular diameters were then measured and cumulus-oocyte complexes were collected by transvaginal puncture, under epidural, with needle aspiration. COCs and granulosa cells were collected in warm HEPES-buffered Tyrode's medium containing Hepalean and transferred to laboratory for IVM.
Embryo production : In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)

value: 8 months


title: Data Heifer #10989

description: Rep 1 of 4


title: Non-demented control 5

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416965_S01_GE1_107_Sep09_1_2

value: whole blood


title: MCF-7 expt 2 control

source_name: MCF-7 control


title: Data Heifer #10995

description: Rep 4 of 4


title: MCF-7 expt 1 ethanol


title: Data Heifer #10991

description: Rep 2 of 4


title: H99_v_12602_rep.1


title: Probable AD 5

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416965_S01_GE1_107_Sep09_1_1

value: male


title: Data Heifer #10989_11v14

description: Rep 1 of 4


title: Non-demented control 4

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416103_S01_GE1_107_Sep09_2_4


title: MCF-7 expt 1 control


title: Probable AD 4

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416103_S01_GE1_107_Sep09_2_3


title: Probable AD 3

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416103_S01_GE1_107_Sep09_2_2


title: P15_v_H99_rep.2

hyb_protocol: 2ug of each aRNA was paired, then fragmented according to manufacturer’s protocol (Fragmentation Reagents; ABI-Ambion).  Each paired, fragmented sample was normalized to 13ul, then suspended in Formamide-based hybridization buffer (vial 7-Genisphere) (26ul) and Kreablock (Kreatech Diagnostics) (13ul).  The hybridization solution was heated to 70C for 5 minutes, then allowed to cool to room temperature.  48ul of hybridization solution was added to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Slides were gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays were treated with Dyesaver (Genisphere).

data_processing: Background subtracted raw intensity values were extracted from the .gpr files from each of the channels. The box plots showed minimum variability of the expression values and therefore no normalization was required. The data has been transformed into two-class unpaired data format as required by Significance Analysis of Microarrays (SAM) software. Using t-statistic as the test statistic, 100 random permutations, k-Nearest neighbor imputer and 10 neighbors, we selected probes with false discovery rate 0 or an insignificant value. The log ratio data for test/reference are presented in the file "Log_ratio_test_v_reference.txt" available on the series record.

label_protocol: RNA transcripts were first amplified by T7 linear amplification using MessageAmpII aRNA amplification kit; (ABI-Ambion, cat#AM 1751).   700ng of RNA (11ul) was primed with an oligo-dT T7 primer (1ul) by heating to 70C for 10 minutes, then cooled on ice for 3 minutes.  For 1st strand cDNA synthesis, each RNA received 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and reverse transcriptase (1ul) (Superscript II; Invitrogen).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a short column cleanup according to manufacturer’s protocol (DNA Clean and Concentrator 5; Zymo Research), invitro-transcription was carried out by adding non-modified bases (ATP, CTP, GTP, and UTP) (4ul of each), 10x T7 reaction buffer (4ul), and T7 RNA polymerase enzyme mix (4ul).    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (60ul), the aRNAs were cleaned with Rneasy columns (Qiagen) according to manufacturer’s protocol. aRNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy/DY-ULS (either cy3 or cy5)(2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled aRNAs were purified with Kreapure gel columns (Kreatech Diagnostics) according to manufacturer’s protocol.  The labeled RNAs were then quantitated on a NanoDrop spectrophotometer.

growth_protocol: C. neoformans serotype A strains H99, 176-1 #8, 176-1 #8-15 and the Galleria-passaged strain P15 were grown from frozen stocks in Yeast Peptone Dextrose (YPD) media for 36 hours (mid-log phase) at 37 ºC and then washed three times with phosphate buffered saline (PBS).  Approximately 2 x 10e7 - 2 x 10e8 cells were used for RNA extraction.

value: Galleria-passaged strain

value: Wild-type strain


title: Non-demented control 3

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416103_S01_GE1_107_Sep09_2_1

value: Non-demented control


title: H99_v_P15_rep.2


title: Probable AD 2

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416103_S01_GE1_107_Sep09_1_3


title: Probable AD 1

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416103_S01_GE1_107_Sep09_1_2


title: P15_v_H99_rep.1

description: Strains were started from frozen stock and grown to log-phase in YPD


title: H99_v_P15_rep.1


title: Non-demented control 1

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416103_S01_GE1_107_Sep09_1_1


title: 8_v_8-15_rep.2

value: 176-1 disrupted strain

value: 176-1 reconstituted strain


title: 8-15_v_8_rep. 2


title: 8_v_H99_rep.2


title: Non-demented control 2

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416103_S01_GE1_107_Sep09_1_4


title: H99_v_8_rep.2


title: 8_v_8-15rep.1


title: 8_v_H99_rep.1


title: H99_v_8_rep.1


title: 8-15_v_8_rep. 1


title: DMPT_rep4

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description:
DMPT treated R. norvegicus sample
X14578_852_RNC_DMPT_Rep_4_.Rat230_2..CEL

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA). Array hybridization, washing, and staining were performed according to the Affymetrix recommended protocol FS450-0004.

scan_protocol: Affymetrix Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm.

organism: Rattus norvegicus

source_name: DMPT treated

label_protocol: Four nanograms (4 ng) of total RNA was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol and labeled with biotin following the Encore Biotin Module. Five micrograms (5 μg) of amplified, biotin-labeled RNAs were fragmented and hybridized to each array for 18 hr at 45 C in a rotating hybridization.

growth_protocol: At the start of the study, the animals were 5–6 weeks of age. The animals were housed 2 per cage. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) were made available ad libitum. The care of animals on this study was according to National Institutes of Health (NIH) procedures as described in the ‘‘The U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals,’’ available from the Office of Laboratory Animal Welfare, NIH, Department of Health and Human Services, RKLI, Bethesda, MD or online at http://grants.nih.gov/grants/olaw/olaw.htm#pol.

extract_protocol: After LCM of the nasal cavity transitional cell epithelium, RNA was extracted from the control and 120 mg/kg groups, according to the NTP protocol for laser capture microdissected samples (http://www.niehs.nih.gov/research/resources/protocols/extraction/picoscale/index.cfm). The RNA was analyzed for quantity and purity by ultraviolet analysis using the Nano-Drop ND-1000 (NanoDropTechnologies, Wilmington, DE). Samples were concentrated using Microcon filters (Millipore, Billerica, MA). All samples were evaluated for RNA integrity by gel electrophoresis using the Flash Gel RNA cassette system (Lonza, Rockland, ME). Experiments to assess the quality of the isolated RNA, cDNA synthesis, pre-amplification, and microarray hybridization were all performed at the University of Pennsylvania Molecular Profiling Facility. The A260/A280 ratio ranged 1.56-2.17 (average 1.95, standard deviation 0.16), and the A260/A230 ratio ranged 0.27-1.77 (average 0.97, standard deviation 0.43). The average±standard deviation totalf RNA in nanograms isolated per pooled sample was 29.1±15.9 (L3) and 19.7±3.5 (L3 lethargus). The quality of RNA was further assessed using Agilent 2100 Bioanalyzer. RNA was accepted for further microarray processing if the RNA Integrity Number was >5.

treatment_protocol: DMPT (lot #C15Y012, >99% pure; Alfa Aesar, Ward Hill, MA) was prepared for oral gavage administration in corn oil (Lot# 12-542; Welch, Holme & Clark Co., Inc. Newark, NJ) to deliver DMPT at doses of 0, 1, 6, 20, 60, or 120 mg/kg/day for 5 consecutive days to male F344/N rats in a volume of 2.5-ml/kg body weight.

tag: animal id

value: animal 9

value: 5-6 weeks

tag: treated with

value: 120 mg/kg DMPT


title: DMPT_rep3

description:
DMPT treated R. norvegicus sample
X14576_852_RNC_DMPT_Rep_3_.Rat230_2..CEL

value: animal 7

tag: strain


title: DMPT_rep2

description:
DMPT treated R. norvegicus sample
X14574_852_RNC_DMPT_Rep_2_.Rat230_2..CEL

value: animal 5


title: DMPT_rep5

description:
DMPT treated R. norvegicus sample
X14579_852_RNC_DMPT_Rep_5_.Rat230_2..CEL

value: animal 10


title: OVCA-Tumour-HCC5050T_METH

description:
ovarian carcinoma
HCC5050T-8942351135_R05C02

hyb_protocol: As per manufacturer's instructions (Illumina)

data_processing: Raw array data were exported from Illumina's GenomeStudio software and processed using a 450K BeadChip pipeline employing the BioConductor packages 'lumi' and 'methylumi' to generate normalized methylation beta-values (Touleimat et al, Epigenomics 4, 325-341, 2012); File = UTSW_OVCA_Normalized_Methylation_forGEO.csv

label: Cy5 and Cy3

growth_protocol: Tumour cells were enriched from malignant effusions (OVCA tumour ascites) by two or more cycles of low speed centrifugation plus differential substrate attachment. Cell lines were cultured in ACL4 or RPMI growth media supplemented with 5% FBS.

value: Tumour

tag: tag

value: Female


title: Veh_rep4

description:
R. norvegicus vehicle control sample
X14575_852_RNC_Veh_Rep_4_.Rat230_2..CEL

source_name: vehicle control

value: animal 6

value: Vehicle


title: OVCA-Tumour-HCC5048T_METH

description:
ovarian carcinoma
HCC5048T-9388306110_R01C02

scan_protocol: As per manufacturer's instructions (Illumina)


title: Veh_rep3

description:
R. norvegicus vehicle control sample
X14573_852_RNC_Veh_Rep_3_.Rat230_2..CEL

value: animal 4


title: OVCA-CellLine-HCC5036CL_METH

description:
ovarian carcinoma
HCC5036CL-9388306110_R06C01

label_protocol: As per manufacturer's instructions (Illumina)

value: cell line


title: Veh_rep5

description:
R. norvegicus vehicle control sample
X14577_852_RNC_Veh_Rep_5_.Rat230_2..CEL

value: animal 8

value: male


title: Veh_rep2

description:
R. norvegicus vehicle control sample
X14572_852_RNC_Veh_Rep_2_.Rat230_2..CEL

value: animal 3


title: OVCA-Tumour-HCC5036T_METH

description:
ovarian carcinoma
HCC5036T-9388306110_R05C01


title: OVCA-CellLine-HCC5048CL_METH

description:
ovarian carcinoma
HCC5048CL-9388306110_R02C02


title: DMPT_rep1

description:
DMPT treated R. norvegicus sample
X14570_852_RNC_DMPT_Rep_1_.Rat230_2..CEL

value: animal 1


title: OVCA-CellLine-HCC5050CL_METH

description:
ovarian carcinoma
HCC5050CL-8942351135_R06C02


title: OVCA-Tumour-HCC5032T_METH

description:
ovarian carcinoma
HCC5032T-8942351135_R03C02


title: MCF-7 2.5 mM acetaldehyde for 1 week

hyb_protocol: Hybridization was carried out by the UCLA DNA Microarray Facility according to the Affymetrix protocol.

scan_protocol: Scans were carried out by the UCLA DNA Microarray Facility using the Affymetrix machinery and software.

data_processing: Data were processed and presented as rma values.

source_name: cell culture, 6 well

label_protocol: Labeling was carried out by the UCLA DNA Microarray Facility according to the Affymetrix protocol.

extract_protocol: Cells were washed once with phosphate buffered saline pH 7.4 and RNA was extracted using the RNeasy Plus Micro kit.

treatment_protocol: Cells were grown in culture in 6 well plates in minimal essentail medium Eagle plus 10 percent fetal bovine serum and 0.01 mg/ml bovine insulin. Ethanol was added to each well in a volume of 10 microliters to achieve concentrations ranging from 0 to 25 mM. The 25 mM and control (0 mM) treatments were carried on for 1 week or 4 weeks, and RNA was extracted for analysis.

value: malignant breast cancer


title: MCF-7 25 mM ethanol for 4 weeks, expt 2


title: OVCA-CellLine-HCC5032CL_METH

description:
ovarian carcinoma
HCC5032CL-8942351135_R04C02


title: fer-1_82h_E. coli OP50 + 6h Neo/Str_rep1

city: Durham

first: Brian

middle: P

last: Head

address: Box 3580 DUMC

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

hyb_protocol: Hybridization was performed in the Agilent Rotisserie Hybridization Oven (Agilent) for 17 hours.

scan_protocol: Agilent B scanner according to standard Agilent protocols (Agilent).

data_processing: Log2 transformation and quantile normalization using Partek Genomics Suite (Partek).

organism: Caenorhabditis elegans

source_name: fer-1, plus antibiotics, 82h

label_protocol: Total RNA was converted to Cy-3-labeled, linearly amplified cRNA using the Low Input Quick Amp (LIQA) One-Color Microarray-Based Gene Expression Analysis Kit (Agilent)

growth_protocol: Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 72 hours. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 72 hours and then exposed to P. aeruginosa PA14 for 4 hours. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 72 hours, exposed to P. aeruginosa PA14 for 4 hours, and then treated with Neomycin and shifted to E. coli OP50 plus Streptomycin plates for 6, 12, or 24 hours to resolve the infection. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 82 hours. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 76 hours and then treated with Neomycin and shifted to E. coli OP50 plus Streptomycin plates for 6 hours. Animals were kept at 25dC.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) and the RNeasy Plus Universal Kit (Qiagen).

treatment_protocol: For recovery, 200ug/ml Neomycin in M9 was used to rinse worms and Streptomycin was included in plates at 50ug/ml.

tag: genotype

tag: hours

tag: diet

value: E. coli OP50

tag: condition

value: plus antibiotics


title: MCF-7 25 mM ethanol for 4 weeks, expt 1


title: OVCA-Tumour-HCC5030T_METH

description:
ovarian carcinoma
HCC5030T-8942351135_R01C02

tag: sample type

tag: sample source id


title: OVCA-Tumour-HCC5022T_METH

description:
ovarian carcinoma
HCC5022T-9388306110_R03C01


title: fer-1_82h_E. coli OP50_rep2

source_name: fer-1, no antibiotics, 82h

value: no antibiotics


title: OVCA-CellLine-HCC5024CL_METH

description:
ovarian carcinoma
HCC5024CL-8942351135_R06C01


title: fer-1_82h_E. coli OP50 + 6h Neo/Str_rep2


title: fer-1_82h_E. coli OP50 + 6h Neo/Str_rep3


title: MCF-7 control for 4 week expt, expt 1

tag: cell type


title: OVCA-CellLine-HCC5030CL_METH

description:
ovarian carcinoma
HCC5030CL-8942351135_R02C02


title: MCF-7 25 mM ethanol for 1 week


title: fer-1_82h_E. coli OP50_rep1


title: OVCA-CellLine-HCC5022CL_METH

description:
ovarian carcinoma
HCC5022CL-9388306110_R04C01


title: OVCA-Tumour-HCC5023T_METH

description:
ovarian carcinoma
HCC5023T-8942351135_R01C01


title: OVCA-CellLine-HCC5019CL_METH

description:
ovarian carcinoma
HCC5019CL-9388306110_R02C01


title: OVCA-Tumour-HCC5024T_METH

description:
ovarian carcinoma
HCC5024T-8942351135_R05C01


title: OVCA-CellLine-HCC5023CL_METH

description:
ovarian carcinoma
HCC5023CL-8942351135_R02C01


title: OVCA-Tumour-HCC5019T_METH

description:
ovarian carcinoma
HCC5019T-9388306110_R01C01


title: OVCA-Tumour-HCC5018T_METH

description:
ovarian carcinoma
HCC5018T-8942351135_R03C01


title: MCF-7 control for 1 week experiment


title: MCF-7 control for MCF12A-MCF7 ratio


title: fer-1_100h_E. coli OP50 + P. aeruginosa PA14 + 24h Neo/Str recovery_rep3

source_name: fer-1, infected then treated for 24h, 100h

value: E. coli OP50 then P. aeruginosa PA14 then E. coli OP50

value: recovered


title: OVCA-CellLine-HCC5018CL_METH

description:
ovarian carcinoma
HCC5018CL-8942351135_R04C01


title: MCF12A control

description: grown as per ATCC instructions

value: non-malignant breast cancer


title: OVCA-CellLine-HCC5012CL_METH

description:
ovarian carcinoma
HCC5012CL-8942351011_R06C02


title: fer-1_82h_E. coli OP50 + P. aeruginosa PA14 + 6h Neo/Str recovery_rep2

source_name: fer-1, infected then treated for 6h, 82h


title: fer-1_100h_E. coli OP50 + P. aeruginosa PA14 + 24h Neo/Str recovery_rep1


title: HUVECs treated with PM2.5, biological rep3

city: Beijing

first: Hejing

last: Hu

state: Beijing

address: No.10 of XiToutiao street ouside YouAnmen, Fengtai district

department: Department of Toxicology and Sanitary Chemistry

country: China

institute: School of Public Health, Capital Medical University

description: HUVECs treated with PM2.5

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

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HUVECs

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

growth_protocol: HUVECs treated with PM2.5, and DMEM, respectively for 24 h

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

treatment_protocol: The stock suspensions of PM2.5 were sonicated for 5 min before HUVECs exposure. Cultured HUVECs were treated with PM2.5 at the concentrations of 50 μg/mL for 24 h. Controls were supplied with an equivalent volume of DMEM without PM2.5.

value: HUVECs


title: OVCA-Tumour-HCC5012T_METH

description:
ovarian carcinoma
HCC5012T-8942351011_R05C02

value: Tumour

value: Female


title: fer-1_82h_E. coli OP50 + P. aeruginosa PA14 + 6h Neo/Str recovery_rep1


title: fer-1_72h_E. coli OP50_rep3

source_name: fer-1, uninfected, 72h

value: uninfected


title: fer-1_88h_E. coli OP50 + P. aeruginosa PA14 + 12h Neo/Str recovery_rep2

source_name: fer-1, infected then treated for 12h, 88h


title: fer-1_88h_E. coli OP50 + P. aeruginosa PA14 + 12h Neo/Str recovery_rep1


title: Mendias_002_Male.2

city: Ann Arbor

first: Christopher

middle: Louis

last: Mendias

state: Michigan

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

institute: University of Michigan

description: basal conditions of wild-type mouse

hyb_protocol: Following Labeling procedure, 3.75 ug of biotinylated cDNA were hybridized at 48C – WT on a Mouse Gene ST 2.1 strip array, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

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

data_processing: Data was analyzed using the oligo Bioconductor packages implemented in the R-statistical environment version 3.1.1. RMA was used to fit log2 transformed expression values

source_name: male adult C57Bl/6 mouse, 3 RNA wells/sample

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 12.5 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: Mice were housed in specific pathogen free conditions and provided food and water ad libidum. Prior to removing hindlimb plantarflexor tendons for analysis, mice were anesthetized with ketamine and xylazine. After tissues were surgically removed, mice were sacrificed by cervical dislocation and induction of a bilateral pneumothorax.

extract_protocol: The Achilles and plantaris tendons from each animal were combined, homogenized in QIAzol and RNA was isolated using a miRNeasy micro kit supplemented with DNase treatment.

treatment_protocol: no treatment administered, study done to evaluate normal expression profiles of male and female tenocytes

tag: gender

tag: age

value: four months

tag: tissue

value: plantarflexor tendons

value: tenocytes


title: fer-1_88h_E. coli OP50 + P. aeruginosa PA14 + 12h Neo/Str recovery_rep3


title: Mendias_003_Female.1

description: basal conditions of wild-type mouse

source_name: female adult C57Bl/6 mouse, 3 RNA wells/sample

value: female


title: fer-1_76h_E. coli OP50 + P. aeruginosa PA14_rep2

source_name: fer-1, infected, 76h

value: E. coli OP50 then P. aeruginosa PA14

value: infected


title: fer-1_76h_E. coli OP50 + P. aeruginosa PA14_rep1


title: fer-1_72h_E. coli OP50_rep2


title: Mendias_001_Male.1

description: basal conditions of wild-type mouse

value: male


title: fer-1_76h_E. coli OP50 + P. aeruginosa PA14_rep3


title: HUVECs treated with PM2.5, biological rep2

description: HUVECs treated with PM2.5


title: Mendias_004_Female.2

description: basal conditions of wild-type mouse


title: HUVECs as control, biological rep1

description: HUVECs treated with DMEM as control


title: fer-1_72h_E. coli OP50_rep1

value: E. coli OP50


title: HUVECs as control, biological rep2

description: HUVECs treated with DMEM as control


title: HUVECs treated with PM2.5, biological rep1

description: HUVECs treated with PM2.5


title: S7E_rep3

status: Public on Aug 10 2016

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: Biological replicate 3 of 3, dye flip

hyb_protocol: Labelled cDNA was hybridized according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

scan_protocol: Arrays were scanned on GenePix 4000B scanner and images were quantified GenePic Pro 6.1 software

data_processing: Background subtraction and lowess normalization was applied according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

organism: Schizosaccharomyces pombe

source_name: WT

label_protocol: Total RNA was reverse transcribed and labelled according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

growth_protocol: Cells were innoculated at an OD~0.1 in 25mL YES media and collected by centrifugation at mid-log-phase growth (OD~0.5). Replicates indicate separately grown biological replicates

extract_protocol: Total RNA was isolated by Acid-phenol extraction followed by ethanol precipitation and resuspension in 50uL TE buffer

tag: genotype/variation

value: WT

value: rpb1-S7E 18 repeats 'rump' + 14x YSPTSPE


title: Veh_rep1

description:
R. norvegicus vehicle control sample
X14571_852_RNC_Veh_Rep_1_.Rat230_2..CEL

value: animal 2

value: 5-6 weeks

value: Vehicle


title: MCF-7 control for 4 week expt, expt 2

value: malignant breast cancer


title: fer-1_82h_E. coli OP50 + P. aeruginosa PA14 + 6h Neo/Str recovery_rep3

value: E. coli OP50 then P. aeruginosa PA14 then E. coli OP50

value: recovered


title: S7E_rep2

description: Biological replicate 2 of 3, dye flip


title: S2A_rep4

description: Biological replicate 4 of 4

value: rpb1-S2A 18 repeats 'rump' + 14x YAPTSPS


title: patient 045 NSCLC core needle biopsy [045_547]

city: Houston

first: Yasminka

middle: Aleksandra

last: Jakubek

state: TX

address: 1155 Pressler St

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

description: Genomic DNA extracted was genotyped using Illumina HumanOmniExpressExome-8 v1.2 Genotyping BeadChips.

hyb_protocol: Genomic DNA samples (200 ng) were processed using the Illumina Infinium HD assay protocol.

scan_protocol: BeadChip images were then captured using an Illumina iScan system.

data_processing:
Raw genotyping data was generated using the Illumina GenomeStudio Genotyping (GT) Module Software.
Genotype calls, gc score, theta, R, B-allele frequency, and log R were obtained from csv output files from GenomeStudio Genotyping (GT) Module Software.

label: C-Bio and A-DNP

source_name: NSCLC core needle biopsy

extract_protocol: Genomic DNA was isolated from all samples (n=435) using the QIAamp DNA kit from Qiagen according to the manufacturer’s instructions.

tag: patient diagnosis

value: Lung adenocarcinoma

tag: smoking status

value: Never


title: S2A/S7A_rep5

description: Biological replicate 5 of 5, dye flip

value: rpb1-S2AS7A 18 repeats 'rump' + 14x YAPTSPA


title: patient 045 NSCLC core needle biopsy [045_546]

label_protocol: Genomic DNA samples (200 ng) were processed using the Illumina Infinium HD assay protocol.


title: patient 045 NSCLC core needle biopsy [045_548]


title: fer-1_100h_E. coli OP50 + P. aeruginosa PA14 + 24h Neo/Str recovery_rep2


title: patient 045 NSCLC core needle biopsy [045_545]


title: patient 045 NSCLC core needle biopsy [045_544]


title: patient 045 NSCLC core needle biopsy [045_542]


title: patient 045 NSCLC core needle biopsy [045_543]


title: patient 045 small adjacent airway [045_346]

source_name: small airway adjacent to the NSCLC


title: S7A_rep4

description: Biological replicate 4 of 4

value: rpb1-S7A 18 repeats 'rump' + 14x YSPTSPA


title: S2A/S7A_rep4

description: Biological replicate 4 of 5, dye flip


title: S7E_rep1

description: Biological replicate 1 of 3


title: patient 045 blood cells [045_347]

source_name: blood cells


title: patient 045 small adjacent airway [045_344]


title: patient 045 small adjacent airway [045_343]


title: S7A_rep1

description: Biological replicate 1 of 4


title: S2A/S7A_rep3

description: Biological replicate 3 of 5


title: S7A_rep3

description: Biological replicate 3 of 4, dye flip


title: patient 045 small adjacent airway [045_342]


title: S2A/S7A_rep1

description: Biological replicate 1 of 5, dye flip


title: S2A_rep1

description: Biological replicate 1 of 4


title: S2A_rep2

description: Biological replicate 2 of 4, dye flip


title: S7A_rep2

description: Biological replicate 2 of 4, dye flip


title: HUVECs as control, biological rep3

description: HUVECs treated with DMEM as control

value: HUVECs


title: S2A/S7A_rep2

description: Biological replicate 2 of 5


title: patient 044 small adjacent airway [044_339]

value: Lung squamous cell carcinoma

value: Former


title: patient 045 normal lung tissue [045_341]

source_name: normal lung tissue


title: patient 045 NSCLC [045_340]

source_name: NSCLC tumor


title: S2A_rep3

description: Biological replicate 3 of 4, dye flip


title: patient 044 small adjacent airway [044_338]


title: patient 044 small adjacent airway [044_337]


title: patient 045 NSCLC core needle biopsy [045_541]


title: patient 044 normal lung tissue [044_334]


title: patient 044 small adjacent airway [044_335]


title: patient 044 NSCLC [044_333]


title: patient 044 small adjacent airway [044_336]


title: patient 045 small adjacent airway [045_345]


title: patient 043 small adjacent airway [043_331]


title: patient 043 small adjacent airway [043_330]


title: patient 043 blood cells [043_332]


title: patient 043 small adjacent airway [043_327]


title: patient 043 small adjacent airway [043_328]


title: patient 042 NSCLC core needle biopsy [042_539]

value: Current


title: patient 043 NSCLC [043_325]


title: patient 042 NSCLC core needle biopsy [042_538]


title: patient 042 NSCLC core needle biopsy [042_537]


title: patient 042 NSCLC core needle biopsy [042_534]


title: patient 043 small adjacent airway [043_329]


title: patient 042 NSCLC core needle biopsy [042_533]


title: patient 042 NSCLC core needle biopsy [042_535]


title: patient 043 normal lung tissue [043_326]


title: patient 042 blood cells [042_355]


title: patient 042 NSCLC core needle biopsy [042_536]


title: patient 042 small adjacent airway [042_354]


title: patient 042 small adjacent airway [042_353]


title: patient 042 small adjacent airway [042_351]


title: patient 042 normal lung tissue [042_349]


title: patient 042 small adjacent airway [042_352]


title: patient 042 small adjacent airway [042_350]


title: patient 041 blood cells [041_324]


title: patient 041 small adjacent airway [041_323]


title: patient 041 small adjacent airway [041_322]


title: patient 041 small adjacent airway [041_320]


title: patient 041 NSCLC [041_318]


title: patient 041 normal lung tissue [041_319]


title: patient 041 small adjacent airway [041_321]


title: patient 040 NSCLC core needle biopsy [040_517]


title: patient 040 small adjacent airway [040_315]


title: patient 040 blood cells [040_317]


title: patient 040 NSCLC core needle biopsy [040_512]


title: patient 040 small adjacent airway [040_316]


title: patient 040 NSCLC core needle biopsy [040_513]


title: patient 040 small adjacent airway [040_314]


title: patient 040 small adjacent airway [040_312]


title: patient 042 NSCLC core needle biopsy [042_540]


title: patient 040 small adjacent airway [040_313]


title: patient 040 normal lung tissue [040_311]


title: patient 040 NSCLC core needle biopsy [040_511]


title: patient 040 NSCLC core needle biopsy [040_515]


title: patient 042 NSCLC [042_348]


title: patient 039 NSCLC core needle biopsy [039_510]


title: patient 040 NSCLC [040_310]


title: patient 039 NSCLC core needle biopsy [039_509]


title: patient 039 NSCLC core needle biopsy [039_508]


title: patient 040 NSCLC core needle biopsy [040_516]


title: patient 039 NSCLC core needle biopsy [039_507]


title: patient 039 NSCLC core needle biopsy [039_506]


title: patient 039 NSCLC core needle biopsy [039_504]


title: patient 040 NSCLC core needle biopsy [040_518]


title: patient 039 small adjacent airway [039_277]


title: patient 039 small adjacent airway [039_276]


title: patient 039 NSCLC core needle biopsy [039_505]


title: patient 040 NSCLC core needle biopsy [040_514]


title: patient 039 small adjacent airway [039_274]


title: patient 039 small adjacent airway [039_273]


title: patient 039 NSCLC core needle biopsy [039_503]


title: patient 039 small adjacent airway [039_275]


title: patient 038 small adjacent airway [038_266]


title: patient 039 NSCLC [039_271]


title: patient 038 small adjacent airway [038_268]


title: patient 038 NSCLC [038_264]


title: patient 039 normal lung tissue [039_272]


title: patient 037 small adjacent airway [037_263]


title: patient 038 small adjacent airway [038_269]


title: patient 038 small adjacent airway [038_270]


title: patient 037 NSCLC core needle biopsy [037_497]


title: patient 037 NSCLC core needle biopsy [037_495]


title: patient 037 NSCLC core needle biopsy [037_496]


title: patient 037 small adjacent airway [037_262]


title: patient 037 NSCLC core needle biopsy [037_499]


title: patient 037 NSCLC core needle biopsy [037_502]


title: patient 038 normal lung tissue [038_265]


title: patient 037 small adjacent airway [037_260]


title: patient 037 small adjacent airway [037_261]


title: patient 038 small adjacent airway [038_267]


title: patient 036 NSCLC core needle biopsy [036_494]


title: patient 037 normal lung tissue [037_258]


title: patient 037 NSCLC [037_257]


title: patient 036 NSCLC core needle biopsy [036_491]


title: patient 036 NSCLC core needle biopsy [036_490]


title: patient 037 NSCLC core needle biopsy [037_501]


title: patient 037 NSCLC core needle biopsy [037_500]


title: patient 037 NSCLC core needle biopsy [037_498]


title: patient 037 blood cells [037_309]


title: patient 036 NSCLC core needle biopsy [036_488]


title: patient 036 NSCLC core needle biopsy [036_489]


title: patient 036 blood cells [036_308]


title: patient 036 small adjacent airway [036_253]


title: patient 035 small adjacent airway [035_239]


title: patient 035 NSCLC [035_236]


title: patient 036 NSCLC core needle biopsy [036_492]


title: patient 036 small adjacent airway [036_250]


title: patient 034 NSCLC core needle biopsy [034_486]


title: patient 036 small adjacent airway [036_254]


title: patient 034 NSCLC core needle biopsy [034_485]


title: patient 036 NSCLC [036_255]


title: patient 037 small adjacent airway [037_259]


title: patient 036 NSCLC core needle biopsy [036_487]


title: patient 035 blood cells [035_306]


title: patient 036 small adjacent airway [036_252]


title: patient 036 small adjacent airway [036_251]


title: patient 035 small adjacent airway [035_238]


title: patient 036 NSCLC core needle biopsy [036_493]


title: patient 034 NSCLC core needle biopsy [034_484]


title: patient 035 small adjacent airway [035_242]


title: patient 035 small adjacent airway [035_241]


title: patient 036 normal lung tissue [036_256]


title: patient 034 NSCLC core needle biopsy [034_483]


title: patient 034 NSCLC core needle biopsy [034_482]


title: patient 035 normal lung tissue [035_237]


title: patient 034 NSCLC core needle biopsy [034_481]


title: patient 034 NSCLC core needle biopsy [034_479]


title: patient 034 NSCLC core needle biopsy [034_480]


title: patient 034 small adjacent airway [034_235]


title: patient 034 small adjacent airway [034_234]


title: patient 034 small adjacent airway [034_233]


title: patient 034 small adjacent airway [034_231]


title: patient 034 small adjacent airway [034_232]


title: patient 034 normal lung tissue [034_230]


title: patient 033 NSCLC core needle biopsy [033_552]


title: patient 033 NSCLC core needle biopsy [033_550]


title: patient 033 NSCLC core needle biopsy [033_551]


title: patient 033 small adjacent airway [033_209]


title: patient 033 normal lung tissue [033_207]


title: patient 034 NSCLC [034_229]


title: patient 032 NSCLC core needle biopsy [032_477]


title: patient 033 small adjacent airway [033_208]


title: patient 032 NSCLC core needle biopsy [032_473]


title: patient 032 NSCLC core needle biopsy [032_475]


title: patient 032 NSCLC core needle biopsy [032_478]


title: patient 032 NSCLC core needle biopsy [032_474]


title: patient 032 blood cells [032_305]


title: patient 032 normal lung tissue [032_203]


title: patient 032 NSCLC core needle biopsy [032_476]


title: patient 032 small adjacent airway [032_205]


title: patient 032 small adjacent airway [032_204]


title: patient 032 NSCLC [032_202]


title: patient 031 NSCLC core needle biopsy [031_472]


title: patient 031 NSCLC core needle biopsy [031_470]


title: patient 031 NSCLC core needle biopsy [031_469]


title: patient 031 NSCLC core needle biopsy [031_468]


title: patient 031 NSCLC core needle biopsy [031_471]


title: patient 031 blood cells [031_304]


title: patient 033 NSCLC core needle biopsy [033_549]


title: patient 031 NSCLC core needle biopsy [031_467]


title: patient 031 small adjacent airway [031_194]


title: patient 031 small adjacent airway [031_193]


title: patient 033 NSCLC [033_206]


title: patient 031 NSCLC [031_191]


title: patient 030 NSCLC core needle biopsy [030_455]


title: patient 030 NSCLC core needle biopsy [030_452]


title: patient 030 NSCLC core needle biopsy [030_453]


title: patient 030 NSCLC core needle biopsy [030_458]


title: patient 030 NSCLC core needle biopsy [030_451]


title: patient 030 NSCLC core needle biopsy [030_454]


title: patient 030 NSCLC [030_183]


title: patient 030 blood cells [030_303]


title: patient 029 normal lung tissue [029_170]


title: patient 029 small adjacent airway [029_171]


title: patient 030 normal lung tissue [030_184]


title: patient 030 small adjacent airway [030_185]


title: patient 029 small adjacent airway [029_172]


title: patient 028 NSCLC core needle biopsy [028_445]


title: patient 028 NSCLC core needle biopsy [028_448]


title: patient 030 small adjacent airway [030_186]


title: patient 028 NSCLC core needle biopsy [028_449]


title: patient 028 NSCLC core needle biopsy [028_446]


title: patient 029 NSCLC [029_169]


title: patient 031 normal lung tissue [031_192]


title: patient 030 NSCLC core needle biopsy [030_457]


title: patient 030 NSCLC core needle biopsy [030_456]


title: patient 028 NSCLC core needle biopsy [028_444]


title: patient 028 blood cells [028_302]


title: patient 028 small adjacent airway [028_167]


title: patient 028 normal lung tissue [028_166]


title: patient 028 NSCLC [028_165]


title: patient 027 NSCLC core needle biopsy [027_532]


title: patient 028 NSCLC core needle biopsy [028_450]


title: patient 027 NSCLC core needle biopsy [027_530]


title: patient 027 NSCLC core needle biopsy [027_529]


title: patient 027 NSCLC core needle biopsy [027_528]


title: patient 027 NSCLC core needle biopsy [027_527]


title: patient 027 NSCLC core needle biopsy [027_531]


title: patient 027 NSCLC core needle biopsy [027_526]


title: patient 027 blood cells [027_301]


title: patient 027 normal lung tissue [027_157]


title: patient 027 small adjacent airway [027_158]


title: patient 027 nasal epithelia [027_160]

source_name: nasal epithelia


title: patient 026 NSCLC core needle biopsy [026_441]


title: patient 027 NSCLC [027_156]


title: patient 026 NSCLC core needle biopsy [026_439]


title: patient 026 NSCLC core needle biopsy [026_440]


title: patient 026 NSCLC core needle biopsy [026_438]


title: patient 026 NSCLC core needle biopsy [026_442]


title: patient 026 NSCLC core needle biopsy [026_437]


title: patient 026 NSCLC core needle biopsy [026_436]


title: patient 026 NSCLC core needle biopsy [026_435]


title: patient 026 nasal epithelia [026_155]


title: patient 028 small adjacent airway [028_168]


title: patient 026 small adjacent airway [026_154]


title: patient 026 NSCLC [026_151]


title: patient 025 blood cells [025_300]


title: patient 026 small adjacent airway [026_153]


title: patient 025 small adjacent airway [025_149]


title: patient 025 nasal epithelia [025_150]


title: patient 027 NSCLC core needle biopsy [027_525]


title: patient 027 small adjacent airway [027_159]


title: patient 025 normal lung tissue [025_145]


title: patient 025 NSCLC [025_144]


title: patient 024 NSCLC core needle biopsy [024_433]


title: patient 024 NSCLC core needle biopsy [024_434]


title: patient 024 NSCLC core needle biopsy [024_430]


title: patient 024 NSCLC core needle biopsy [024_431]


title: patient 024 NSCLC core needle biopsy [024_429]


title: patient 024 NSCLC core needle biopsy [024_432]


title: patient 024 NSCLC core needle biopsy [024_428]


title: patient 024 NSCLC core needle biopsy [024_427]


title: patient 024 nasal epithelia [024_143]


title: patient 024 small adjacent airway [024_142]


title: patient 024 small adjacent airway [024_141]


title: patient 024 NSCLC [024_139]


title: patient 023 blood cells [023_298]


title: patient 023 nasal epithelia [023_137]


title: patient 024 normal lung tissue [024_140]


title: patient 023 large airway [023_138]

source_name: mainstem bronchus


title: patient 023 small adjacent airway [023_135]


title: patient 026 normal lung tissue [026_152]


title: patient 023 NSCLC [023_133]


title: patient 022 large airway [022_132]


title: patient 022 blood cells [022_297]


title: patient 023 normal lung tissue [023_134]


title: patient 022 nasal epithelia [022_131]


title: patient 025 small adjacent airway [025_148]


title: patient 022 small adjacent airway [022_130]


title: patient 022 NSCLC [022_127]


title: patient 021 blood cells [021_296]


title: patient 022 normal lung tissue [022_128]


title: patient 021 large airway [021_126]


title: patient 022 small adjacent airway [022_129]


title: patient 021 nasal epithelia [021_125]


title: patient 024 blood cells [024_299]


title: patient 021 small adjacent airway [021_123]


title: patient 021 normal lung tissue [021_122]


title: patient 021 small adjacent airway [021_124]


title: patient 020 blood cells [020_295]


title: patient 020 large airway [020_120]


title: patient 020 nasal epithelia [020_119]


title: patient 020 small adjacent airway [020_118]


title: patient 020 small adjacent airway [020_117]


title: patient 020 normal lung tissue [020_116]


title: patient 019 large airway [019_114]


title: patient 019 blood cells [019_294]


title: patient 019 small adjacent airway [019_112]


title: patient 020 NSCLC [020_115]


title: patient 019 nasal epithelia [019_113]


title: patient 019 normal lung tissue [019_110]


title: patient 018 blood cells [018_293]


title: patient 018 large airway [018_108]


title: patient 018 small adjacent airway [018_105]


title: patient 018 small adjacent airway [018_106]


title: patient 018 normal lung tissue [018_104]


title: patient 017 NSCLC core needle biopsy [017_425]


title: patient 017 NSCLC core needle biopsy [017_426]


title: patient 018 NSCLC [018_103]


title: patient 017 NSCLC core needle biopsy [017_422]


title: patient 017 NSCLC core needle biopsy [017_424]


title: patient 017 NSCLC core needle biopsy [017_423]


title: patient 021 NSCLC [021_121]


title: patient 017 blood cells [017_292]


title: patient 017 NSCLC core needle biopsy [017_421]


title: patient 017 NSCLC [017_097]


title: patient 016 NSCLC core needle biopsy [016_524]


title: patient 016 NSCLC core needle biopsy [016_523]


title: patient 017 nasal epithelia [017_101]


title: patient 017 small adjacent airway [017_100]


title: patient 016 NSCLC core needle biopsy [016_522]


title: patient 016 NSCLC core needle biopsy [016_520]


title: patient 019 NSCLC [019_109]


title: patient 016 large airway [016_096]


title: patient 016 blood cells [016_291]


title: patient 016 nasal epithelia [016_095]


title: patient 016 small adjacent airway [016_094]


title: patient 016 normal lung tissue [016_092]


title: patient 018 nasal epithelia [018_107]


title: patient 016 small adjacent airway [016_093]


title: patient 016 NSCLC core needle biopsy [016_521]


title: patient 016 NSCLC core needle biopsy [016_519]


title: patient 015 NSCLC core needle biopsy [015_420]


title: patient 015 NSCLC core needle biopsy [015_419]


title: patient 016 NSCLC [016_091]


title: patient 015 NSCLC core needle biopsy [015_418]


title: patient 015 NSCLC core needle biopsy [015_417]


title: patient 015 large airway [015_090]


title: patient 015 small adjacent airway [015_088]


title: patient 017 normal lung tissue [017_098]


title: patient 015 small adjacent airway [015_087]


title: patient 015 nasal epithelia [015_089]


title: patient 015 normal lung tissue [015_086]


title: patient 015 blood cells [015_290]


title: patient 015 NSCLC [015_085]


title: patient 014 large airway [014_084]


title: patient 014 nasal epithelia [014_083]


title: patient 014 small adjacent airway [014_082]


title: patient 014 small adjacent airway [014_081]


title: patient 014 normal lung tissue [014_080]


title: patient 014 NSCLC [014_079]


title: patient 013 blood cells [013_288]


title: patient 013 large airway [013_078]


title: patient 015 NSCLC core needle biopsy [015_415]


title: patient 013 nasal epithelia [013_077]


title: patient 013 small adjacent airway [013_076]


title: patient 015 NSCLC core needle biopsy [015_416]


title: patient 013 small adjacent airway [013_075]


title: patient 013 normal lung tissue [013_074]


title: patient 012 large airway [012_072]


title: patient 012 nasal epithelia [012_071]


title: patient 012 blood cells [012_287]


title: patient 012 small adjacent airway [012_070]


title: patient 012 normal lung tissue [012_068]


title: patient 014 blood cells [014_289]


title: patient 011 small adjacent airway [011_063]


title: patient 012 NSCLC [012_067]


title: patient 012 small adjacent airway [012_069]


title: patient 011 NSCLC [011_061]


title: patient 011 nasal epithelia [011_065]


title: patient 011 normal lung tissue [011_062]


title: patient 010 blood cells [010_285]


title: patient 010 large airway [010_060]


title: patient 010 nasal epithelia [010_059]


title: patient 010 small adjacent airway [010_058]


title: patient 010 normal lung tissue [010_056]


title: patient 010 NSCLC [010_055]


title: patient 013 NSCLC [013_073]


title: patient 011 large airway [011_066]


title: patient 011 blood cells [011_286]


title: patient 009 blood cells [009_284]


title: patient 009 large airway [009_054]


title: patient 009 nasal epithelia [009_053]


title: patient 009 small adjacent airway [009_052]


title: patient 009 small adjacent airway [009_051]


title: patient 009 normal lung tissue [009_050]


title: patient 008 NSCLC core needle biopsy [008_414]


title: patient 009 NSCLC [009_049]


title: patient 008 NSCLC core needle biopsy [008_412]


title: patient 008 NSCLC core needle biopsy [008_411]


title: patient 008 NSCLC core needle biopsy [008_409]


title: patient 008 NSCLC core needle biopsy [008_410]


title: patient 008 NSCLC core needle biopsy [008_413]


title: patient 008 blood cells [008_283]


title: patient 008 nasal epithelia [008_047]


title: patient 008 small adjacent airway [008_046]


title: patient 008 small adjacent airway [008_045]


title: patient 008 normal lung tissue [008_044]


title: patient 008 NSCLC core needle biopsy [008_407]


title: patient 008 large airway [008_048]


title: patient 007 NSCLC core needle biopsy [007_404]


title: patient 007 NSCLC core needle biopsy [007_403]


title: patient 007 NSCLC core needle biopsy [007_401]


title: patient 007 large airway [007_042]


title: patient 007 small adjacent airway [007_039]


title: patient 007 NSCLC core needle biopsy [007_402]


title: patient 007 normal lung tissue [007_038]


title: patient 007 NSCLC [007_037]


title: patient 006 nasal epithelia [006_035]


title: patient 007 blood cells [007_282]


title: patient 006 small adjacent airway [006_034]


title: patient 007 small adjacent airway [007_040]


title: patient 008 NSCLC [008_043]


title: patient 008 NSCLC core needle biopsy [008_408]


title: patient 006 normal lung tissue [006_032]


title: patient 006 large airway [006_036]


title: patient 006 NSCLC [006_031]


title: patient 006 small adjacent airway [006_033]


title: patient 005 nasal epithelia [005_029]


title: patient 005 small adjacent airway [005_028]


title: patient 005 small adjacent airway [005_027]


title: patient 005 normal lung tissue [005_026]


title: patient 005 NSCLC [005_025]


title: patient 005 large airway [005_030]


title: patient 004 nasal epithelia [004_023]


title: patient 004 small adjacent airway [004_022]


title: patient 007 NSCLC core needle biopsy [007_406]


title: patient 004 blood cells [004_281]


title: patient 004 small adjacent airway [004_021]


title: patient 007 nasal epithelia [007_041]


title: patient 004 NSCLC [004_019]


title: patient 003 blood cells [003_280]


title: patient 003 large airway [003_018]


title: patient 003 small adjacent airway [003_016]


title: patient 003 small adjacent airway [003_015]


title: patient 003 NSCLC [003_013]


title: patient 002 large airway [002_012]


title: patient 003 normal lung tissue [003_014]


title: patient 002 small adjacent airway [002_010]


title: patient 002 blood cells [002_279]


title: patient 002 small adjacent airway [002_009]


title: patient 001 blood cells [001_278]


title: patient 001 large airway [001_006]


title: patient 002 normal lung tissue [002_008]


title: patient 001 small adjacent airway [001_003]


title: patient 001 small adjacent airway [001_004]


title: patient 001 nasal epithelia [001_005]


title: patient 004 large airway [004_024]


title: patient 001 NSCLC [001_001]


title: patient 004 normal lung tissue [004_020]


title: Sample_986 CD_1_Sigmoid Colon

city: Boston

first: Ramnik

middle: J

last: Xavier

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description: CD_1_Sigmoid Colon

hyb_protocol: according to the manufacturer’s protocol

data_processing:
Data from each version of probeset (lot) was first independently normalized and samples were analyzed for quality controls using following steps.
Background noise was estimated using mean expression levels of spiked-in negative controls
Estimated noise value was subtracted from raw counts data for each sample. Negative count values were reset to 1
Count values of spike-in positive controls were summed per sample and the average value was used to estimate a scaling factor for each sample. Expression value of each sample was adjusted using the sample specific normalization factor
Samples with higher than acceptable background noise and positive control based scaling factor <0.3 or >3.0 were identified as outliers and removed from analysis
Next, geometric mean of housekeeping genes was computed for each sample and the average value was used to compute the normalization factor. Data was adjusted in a similar fashion as was done previously with spiked-in positive controls
Finally, samples with housekeeping-genes based normalization factor <0.2 or >5.0 were removed as outliers.
Data Lots 2 & 3 were independently calibrated to Lot 1 using following steps.
The average of medians of calibration samples, for a given pair of lots, was computed and used to estimate normalization factor for each sample.
Each lot was scaled with the normalization factor computed in the previous step.
Geometric means of counts per gene between repeated samples was computed within a lot and a calibration factor was estimated per gene.
Calibration per gene was applied for the non-reference lot. All computations were performed in MATLAB. Nine hundred and eighty-nine samples passed data normalization and quality control.

molecule: polyA RNA

source_name: Sigmoid Colon

label_protocol: Extracted RNA (100ng) was used as input for expression profiling on the NanoString platform according to manufacturer's specifications.

extract_protocol: Using a combined Trizol (Life Technologies)-chloroform extraction and the RNeasy Midi Kit (Qiagen) for RNA extraction, total RNA was extracted by manufacturer’s protocol and RNA purity and quantity was measured by NanoDrop spectrophotometer (Promega).

treatment_protocol: At the time of endoscopy, mucosal biopsies were collected in RNA-later (Qiagen) and stored at -80°C ahead of downstream processing. If samples were collected at the time of surgery, mucosal tissue sample obtained from bowel resection specimens with colonoscopic biopsy forceps were processed immediately or stored at 4°C for processing within 12 hours. Intestinal source location and inflammation status was indicated as “uninflamed” or “inflamed” based on the endoscopic or gross appearance of the tissue by the endoscopist or investigator at time of surgical specimen collection.

tag: patient id

tag: disease

value: CD

tag: inflamed (0=no, 1=yes)

tag: nanostring codeset


title: Sample_987 CD_0_Rectum

scan_protocol: according to the manufacturer’s protocol

source_name: Rectum


title: Sample_988 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: patient 002 nasal epithelia [002_011]


title: Sample_989 UC_0_Rectum

value: UC


title: patient 003 nasal epithelia [003_017]


title: patient 002 NSCLC [002_007]


title: Sample_984 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_981 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_983 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_977 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_979 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_976 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_982 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_980 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: patient 001 normal lung tissue [001_002]


title: Sample_975 UC_1_Rectum


title: Sample_978 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_974 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_972 UC_0_Rectum


title: Sample_973 Indeterminate_0_Rectum

value: Indeterminate


title: Sample_970 CD_1_Rectum


title: Sample_967 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_968 CD_1_Rectum


title: Sample_965 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_966 CD_0_Rectum


title: Sample_969 CD_1_Rectum


title: Sample_971 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_985 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_964 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_963 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_960 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_961 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_959 UC_1_Rectum


title: Sample_962 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_958 UC_1_Rectum


title: Sample_957 UC_1_Rectum


title: Sample_954 CD_1_Rectum


title: Sample_956 UC_1_Rectum


title: Sample_953 CD_1_Rectum


title: Sample_955 CD_1_Rectum


title: Sample_952 CD_0_Rectum


title: Sample_950 CD_1_Rectum


title: Sample_949 CD_1_Rectum


title: Sample_945 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_947 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_944 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_946 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_948 CD_1_Rectum


title: Sample_943 UC_1_Rectum


title: Sample_942 UC_1_Rectum


title: Sample_939 UC_1_Rectum


title: Sample_938 UC_1_Rectum


title: Sample_937 UC_1_Rectum


title: Sample_940 UC_1_Rectum


title: Sample_936 UC_1_Rectum


title: Sample_935 UC_1_Rectum


title: Sample_934 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_951 CD_1_Rectum


title: Sample_931 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_933 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_932 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_930 UC_0_Rectum


title: Sample_928 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_929 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_926 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_941 CD_1_Rectum


title: Sample_927 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_925 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_923 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_922 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_921 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_919 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_915 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_917 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_916 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_918 Indeterminate_0_Sigmoid Colon

description: Indeterminate_0_Sigmoid Colon


title: Sample_913 UC_0_Rectum


title: Sample_912 UC_0_Rectum


title: Sample_910 UC_0_Rectum


title: Sample_911 UC_0_Rectum


title: Sample_909 UC_0_Rectum


title: Sample_907 UC_0_Rectum


title: Sample_906 UC_0_Rectum


title: Sample_905 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_902 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_903 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_904 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_901 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_924 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_920 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_899 CD_0_Rectum


title: Sample_914 UC_1_Rectum


title: Sample_896 CD_0_Rectum


title: Sample_897 CD_0_Rectum


title: Sample_908 UC_0_Rectum


title: Sample_898 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_900 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_893 CD_0_Rectum


title: Sample_892 CD_0_Rectum


title: Sample_891 CD_0_Rectum


title: Sample_887 CD_0_Rectum


title: Sample_895 CD_0_Rectum


title: Sample_888 CD_0_Rectum


title: Sample_889 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_890 CD_0_Rectum


title: Sample_885 CD_0_Rectum


title: Sample_886 CD_0_Rectum


title: Sample_883 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_880 CD_0_Ascending Colon

description: CD_0_Ascending Colon

source_name: Ascending Colon


title: Sample_881 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum

source_name: Terminal Ileum


title: Sample_879 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_882 UC_0_Descending Colon

description: UC_0_Descending Colon

source_name: Descending Colon


title: Sample_877 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_874 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_894 CD_0_Rectum


title: Sample_878 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_875 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_873 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_872 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_871 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_870 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_868 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_867 UC_1_Colon

source_name: Colon


title: Sample_869 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_884 CD_0_Rectum


title: Sample_864 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_865 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_863 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_861 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_860 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_858 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_862 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_866 UC_0_Rectum


title: Sample_859 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_876 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_855 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_853 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_854 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_851 UC_1_Terminal Ileum

description: UC_1_Terminal Ileum


title: Sample_852 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_848 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_849 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_847 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_845 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_846 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_843 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_842 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_840 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_844 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_841 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_838 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_839 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_856 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_834 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_837 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_857 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_833 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_835 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_836 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_830 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_850 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_831 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_832 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_828 CD_1_Colon


title: Sample_829 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_827 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_826 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_825 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_823 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_822 CD_1_Colon


title: Sample_821 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_820 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_818 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_819 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_817 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_814 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_816 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_813 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_810 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_812 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_806 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_811 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_803 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_804 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_809 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_808 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_807 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_797 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_824 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_796 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_815 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_798 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_801 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_802 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_800 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_795 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_799 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_794 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_793 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_791 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_790 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_792 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_788 CD_0_Colon


title: Sample_787 CD_1_Colon


title: Sample_786 CD_0_Colon


title: Sample_785 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_789 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_805 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_784 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_781 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_783 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_782 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_780 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_778 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_774 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_775 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_773 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_768 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_769 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_770 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_772 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_776 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_767 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_766 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_765 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_763 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_764 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_761 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_760 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_779 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_755 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_757 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_777 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_756 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_758 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_771 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_753 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_752 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_749 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_754 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_759 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_762 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_748 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_750 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_747 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_742 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_744 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_741 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_745 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_740 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_736 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_746 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_739 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_743 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_738 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_735 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_737 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_733 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_734 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_732 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_730 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_729 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_728 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_751 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_727 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_731 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_724 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_725 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_726 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_723 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_722 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_721 Indeterminate_0_Terminal Ileum

description: Indeterminate_0_Terminal Ileum


title: Sample_719 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_720 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_718 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_712 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_710 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_711 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_708 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_707 CD_0_Transverse Colon

description: CD_0_Transverse Colon

source_name: Transverse Colon


title: Sample_709 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_695 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_694 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_696 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_691 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_693 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_689 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_690 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_705 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_704 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_706 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_692 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_713 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_703 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_714 UC_0_Rectum


title: Sample_701 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_716 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_715 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_698 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_697 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_687 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_683 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_717 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_685 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_686 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_684 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_680 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_681 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_682 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_676 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_678 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_674 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_679 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_671 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_675 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_673 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_666 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_668 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_672 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_665 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_669 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_667 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_663 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_664 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_662 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_670 UC_0_Cecum

source_name: Cecum


title: Sample_688 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_661 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_660 UC_0_Cecum


title: Sample_677 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_656 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_658 CD_0_Cecum


title: Sample_657 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_699 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_652 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_654 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_653 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_655 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_651 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_649 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: K


title: Sample_648 CD_0_Cecum

value: E


title: Sample_650 UC_0_Cecum


title: Sample_647 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: D


title: Sample_646 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: C


title: Sample_642 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_644 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: A


title: Sample_641 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_659 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_640 UC_0_Cecum


title: Sample_639 CD_0_Cecum


title: Sample_637 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_635 CD_0_Cecum


title: Sample_638 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_636 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_634 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_628 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_633 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_627 UC_1_Transverse Colon

description: UC_1_Transverse Colon


title: Sample_622 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_631 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_621 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_623 UC_1_Rectum


title: Sample_645 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_625 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_629 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_702 UC_0_Rectum


title: Sample_626 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_620 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_624 UC_0_Cecum


title: Sample_618 UC_0_Cecum


title: Sample_616 UC_1_Rectum


title: Sample_617 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_615 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_614 UC_1_Rectum


title: Sample_619 UC_1_Rectum


title: Sample_613 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_630 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_612 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_632 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_609 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_608 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_610 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_605 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_606 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_607 CD_1_Rectum


title: Sample_604 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_603 CD_1_Cecum


title: Sample_601 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_602 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_598 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_643 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_599 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_600 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_594 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_596 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_597 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_591 CD_1_Ascending Colon

description: CD_1_Ascending Colon


title: Sample_593 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_611 UC_1_Cecum


title: Sample_700 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_587 CD_1_Rectum


title: Sample_588 CD_0_Descending Colon

description: CD_0_Descending Colon