title: L2V18DRBC04 Ex vivo IL-33 stimulated ILC2s in presence of iBET151

growth_protocol:
Cells were cultured with  with IL-2, IL-7, and with  IL-33 (all at 10 ng/ml) for 24 hr.
Lymphocytes were enriched from 150 ml human peripheral blood using lymphoprep (Axis-Shield) according to the manufacturer’s instructions. The collected PBMC fraction was washed with PBS/2% FCS followed by red blood cell lysis with ACK solution for 5 min at room temperature. To pre-enrich ILCs, cells were stained with biotinylated anti-CD3, CD14 and B220 in the presence of TruStain FcX (anti-CD16/CD32) followed by depletion with M280 streptavidin beads (Invitrogen). Subsequently, the enriched fraction was stained with CD45-AF488, CD127-PE-Cy7, CD117-PE, CRTH2-BV421, a lineage cocktail (APC-streptavidin, CD8a, CD11b, CD11c, FceRIa, CD123, CD20, CD56, CD71) and Draq7-viability dye, followed by sorting of ILCs as indicated on an Influx FACS. ILC2s designated as Draq7–(live cells)CD45+Lin–(streptavidin-APC, CD8a, CD11b, CD11c, FceRIa, CD123, CD20, CD56, CD71)CD127+CRTH2+ cells, were purified by flow cytometry from the peripheral blood of 3 individual donors and cultured separately s with IL-2, IL-7, and with  IL-33 (all at 10 ng/ml).

value: 250 nM iBET

value: Ex vivo


title: L2V18DRBC08 Ex vivo IL-33 stimulated ILC2s in presence of iBET151

status: Public on Mar 23 2019

type: SRA

city: Cambridge

first: Mayuri

last: Gogoi

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: Laboratory of Molecular Biology

library_source: transcriptomic

data_processing:
gene expression of iBET151 treated and untreated cells were compared
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Cells from stimulation experiments were harvested by centrifugation, transferred to Trizol (Life Technologies) and stored at -80°C until further processing. RNA was extracted from the aqueous trizol/chloroform phase using the RNeasy Mini kit (Qiagen) followed by off-column DNA digestion using Turbo DNase (Ambion). DNA-free RNA was cleaned and concentrated using a RNeasy Micro Kit (Qiagen) and assessed using a Bioanalyser (Agilent). RNA was processed for RNA sequencing using Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220 and barcoded using Ovation Ultralow Library Systems (Nugen). Barcoded libraries were quantified using Qubit dsDNA BR assay (Invitrogen) and qPCR. Samples were sequenced using an Illumina Hiseq4000 (CRUK Cambridge Institute)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were either treated with or without  250 nM iBET151

tag: ibet treatment

tag: culture conditions


title: preoptic area neuron_B2

city: San Francisco

first: Lily

middle: Y

last: Jan

state: CA

address: 1550 4th Street, Room RH-484A

department: Physiology

country: USA

institute: UCSF

description:
raw_counts_for_stats.txt
normalized_counts.txt

data_processing:
quality control for sequencing was assessed using FastQC
raw reads were trimmed with R-package scythe for adapter contamination, and with sickle for low quality reads
reads were aligned to the mouse reference genome sequence mm10 with STAR, using UCSC annotation from iGenomes
raw read counts were generated by STAR; gene expression values were normalized based on library size as counts per million reads (CPM)
differential expression (DE) analysis was conducted using the Bioconductor package edgeR
principal component analysis (PCA) was conducted using a MATLAB toolbox SCell
Genome_build: mm10
Supplementary_files_format_and_content: text files of raw counts or CPM values for each sample

organism: Mus musculus

source_name: preoptic area neuron

extract_protocol:
glass pippette pick
Smart-seq2, Nextera XT

treatment_protocol: whole-cell patch-clamp recording prior to sample harvest

tag: strain

tag: age

value: 2-3 months

tag: tissue

value: brain, hypothalamus

tag: cell type

value: preoptic area neuron

tag: temperature sensitivity

value: warm-sensitive


title: L2V18DRBC03 Ex vivo IL-33 stimulated ILC2s in absence of iBET151


title: L2V18DRBC07 Ex vivo IL-33 stimulated ILC2s in absence of iBET151


title: L2V18DRBC11 Ex vivo IL-33 stimulated ILC2s in absence of iBET151


title: E4C3

city: Boston

first: Robert

middle: Patrick

last: Sheehan

state: Massachusetts

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

data_processing:
bcl2fastq1.8.3 was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to hg19 genome using STAR in bcbio nextgen package with parameters: analysis: RNAseq,  aligner: star, trim_reads: read_through, adapters: [truseq, polya], quality_format: standard, strandedness: firststrand.
Based on the feature count table generated from STAR alignment, we did differential expression analysis using edgeR. A filtering criterion of mean Count Per Million (CPM) > 1 of each time point in the vehicle-only controls was used, resulting in 13,227 transcripts, in the ProcessedData.csv.
The count table was generated from edgeR analysis after TMM normalization
Genome_build: hg19
Supplementary_files_format_and_content: [ProcessedData.csv] TMM-normalized feature counts from STAR alignment

source_name: human cardiomyocytes

growth_protocol: Cryo-preserved hiPSC-CMs (4 million/vial) were thawed into 75 cm2 flasks in the Cor.4U complete media (Ncardia) for 3 days before reseeding into multi-well plates for treatment. Cells were cultured in an incubation environment of 5% CO2 and 37 °C at a Biosafety level 2 facility. Media was refreshed within 24 hours of thawing and then every other day.

extract_protocol:
Cells treated in 6-well plates were washed with PBS, harvested in RLT buffer from the RNeasy Mini Kit (Qiagen), and frozen at -80 °C until further processing. At the time of RNA purification, samples were thawed at room temperature and processed with QIAshredder (Qiagen) to ensure complete lysis. Total RNA purification was performed following the manufacturer’s protocol for the RNeasy Mini Kit (Qiagen), including a 30 minute on-column DNase digestion step.
RNA Sequencing library preparation was performed with the High Throughput TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero gold (Illumina) following the manufacturer’s protocol. 500 ng of RNA was input for each sample with the addition of 1 µl of 1:100 diluted ERCC spike in mix A (Ambion) to each sample. Libraries were amplified for 15 cycles at the final step of library preparation. Libraries were quantified using Qubit dsDNA HS assay (Thermo Fisher Scientific) and library size and quality was checked on a subset of samples by Bioanalyzer (Agilent). The resulting libraries were composed of cDNA fragments of 330 base pairs on average.

treatment_protocol: One and a half days prior to drug treatment, media were switched to the BMCC media (Ncardia) with 1% fetal bovine serum (FBS, Thermo Fisher Scientific). Then, hiPSC-CMs were continuously cultured in BMCC media with 1% FBS during drug treatment to minimize the interference of serum on the drug-induced effect. During treatment, media was changed every other day.

value: human induced pluripotent stem cell-derived cardiomyocytes

tag: Sex

value: female

tag: drug

value: Erlotinib

tag: dose

tag: time

tag: replicate


title: S4C3

value: Sorafenib


title: L4C3

value: Lapatinib


title: E3C3


title: L3C3

description: Removed from the final analysis due to QC concerns.


title: D4A3

value: DMSO


title: L2D3


title: U4C3

value: Sunitinib


title: L2B3


title: L2V18DRBC12 Ex vivo IL-33 stimulated ILC2s in presence of iBET151


title: E2B3


title: L2V18DRBC15 Ex vivo IL-33 stimulated ILC2s in absence of iBET151


title: E2C3


title: L2V18DRBC16 Ex vivo IL-33 stimulated ILC2s in presence of iBET151


title: U3C3


title: S2D3


title: S2B3


title: L2C3


title: L1C3


title: U2C3


title: U1C3


title: D3A3


title: U2D3


title: S2C3


title: D1A3


title: S4C2


title: E4C2


title: S1C3


title: D2A3


title: E3C2


title: U3C2


title: S3C3


title: E1C3


title: U4C2


title: E2D3


title: D4A2


title: L3C2


title: D3A2


title: L4C2


title: U2D2


title: U2B3


title: E2D2


title: S3C2


title: S2C2


title: L2B2


title: L2C2


title: U1C2


title: U2B2


title: E2B2


title: S2B2


title: E2C2


title: S1C2


title: S2D2


title: L1C2


title: U2C2


title: L4C1


title: U4C1


title: D2A2


title: E1C2


title: L3C1


title: E4C1


title: D1A2


title: S3C1


title: L2D2


title: U3C1


title: D3A1


title: L2C1


title: D4A1


title: E2B1


title: L2D1


title: L2B1


title: U2C1


title: U2B1


title: S2C1


title: E2D1


title: E2C1


title: D1A1


title: E3C1


title: S2D1


title: U2D1


title: L1C1


title: S1C1


title: U1C1


title: E1C1


title: D2A1


title: S4C1


title: S2B1


title: C8

city: Redwood City

first: Kavita

last: Sarin

address: 450 Broadway

department: Dermatology

institute: Stanford Medical School

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq

data_processing:
Base-calling was performed using CASAVA
Reads were aligned to the human genome (hg19) using Tophat (v2.1.1) with an average of 89.6% of the reads mapping.
Featurecounts (v1.5.2) was used to generate count data
DESeq2 (v1.6.3) was used to identify differentially expressed genes between the LM and normal blood samples.
Genome_build: hg19

source_name: Whole blood

extract_protocol:
Whole blood was collected in Tempus RNA tubes and stored at -80°C until RNA extraction, which was performed for all samples simultaneously by the Stanford Functional Genomics Facility. RNA quantification and quality assurance were performed on an Agilent 2100 Bioanalyzer, and library construction was completed using the Illumina preparation kit according to the manufacturer’s instructions.
Libraries were PolyA-enriched and followed by depletion of globin transcripts and ribosomal RNA. Paired-end sequencing of 76 base pair fragments was performed on the Illumina Nextseq, with an average coverage of 53 million reads per sample.

tag: disease state

value: control


title: LM4

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq

value: Lymphatic malformation


title: LM3

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C7

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM9

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM1

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM7

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C9

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C6

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM10

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM6

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM8

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM2

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C4

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: LM5

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C2

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C1

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: C3

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: RHP3861

city: Singapore

first: Huipeng

last: Li

address: 60 Biopolis St, #02-01

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description:
sample 1111
mRNA
QC: PASSED

data_processing:
scRNAseq FASTQ files were aligned to hg19 human genome assembly using STAR 2.5.2a and GENCODEv19 gene models. The STAR parameters were set as follows: --outFilterMultimapNmax=1, --outFilterMismatchNmax=999, --outFilterMismatchNoverLmax=0.04, --outFilterIntronMotifs=RemoveNoncanonical, --alignSJoverhangMin=8, --alignSJDBoverhangMin=1, --alignIntronMax=1000000, --alignMatesGapMax=1000000. Gene FPKM was calculated using RSEM 1.2.31 with the default parameters. Targeted DNA FASTQ files were aligned to the human_g1k_v37_decoy.fasta from GATK bundle 2.8 using BWA 0.7.12. SNPs and INDELS were called using the “gatk_haplotype_caller” with default parameters.
scRNAseq QC: (BAMMR) were calculated as the number of uniquely mapped reads in the aligned BAM file. The rate of exonic reads (ROER) represents the ratio between exonic reads and all mapped reads in the BAM file. The number of detected genes (NODG) was calculated as the total number of genes with FPKM >0. scRNAseq data with NODG ≥3,000 and ROER ≥5% were selected for downstream analysis.
Targeted DNA QC: Variations (SNPs and INDELs) from all sequenced cells were combined into one table using VCFtools. 8 variations were selected for downstream analysis based on the criteria that they were detected in at least 5% of all sequenced cells. Since GATK does not report allelic depth information for the 8 variations in all cells, SAMtools (version 1.3) mpileup was used to extract the allelic depth and total depth for each cell. Targeted DNA data with total depth >=500 for all the 8 selected mutations were chosen for further analysis. The allelic frequency (AF) was calculated as the ratio between the dominant alternative allelic depth and the total depths (DP). A variation was labelled as positive for a cell if its AF>=0.005 and DP>=500 in that cell.
Out of 546 cells sequenced, 507 (20 cells in DMSO condition were also excluded from the downstream analysis) cells with both the scRNAseq data and targeted DNA data passing the QC were selected for downstream analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Comma-separated files include raw FPKM values of all cells that passed QC.
Supplementary_files_format_and_content: cell_gene_FPKM.csv
Supplementary_files_format_and_content: cell_mutation_AF.csv
Supplementary_files_format_and_content: cell_mutation_DP.csv

source_name: PC9 lung cancer cell line

growth_protocol: Human PC9 cell line was maintained in RPMI supplemented with 10% FBS, 200 nM L-glutamine and 1% penicillin – streptomycin (Gibco).

extract_protocol:
The isolation of single cells followed by cDNA synthesis were carried out using the Fluidigm C1 Auto-prep system following the manufacturer's recommended protocol.
The library preparation was carried out following the manufacturer’s recommendation using the Nextera XT Sample Preparation kit (Illumina) with minor modifications and one quarter of the recommended volume.
The cDNA libraries were sequenced on the NextSeq (Illumina) platform for 76 bp single read sequencing run, while the gDNA libraries were sequenced on the MiSeq (Illumina) platform for 250 bp paired-end sequencing run.

treatment_protocol: The parental TKI responsive PC9 cell line was treated with DMSO or 0.1 µM Gefitinib for 48 hours prior to harvesting for single cell analysis. In order to generate TKI-resistant cell lines, Gefitinib was added to the media in a progressively increasing dose from 0.1 µM to 6.4 µM for a period of 3 months.

tag: cell line

value: lung cancer cell line

tag: cell id

tag: cell line group

tag: batch


title: RHP3860

description:
sample 1110
mRNA
QC: PASSED


title: preoptic area neuron_A10


title: C5

description:
Kim_LM_FPKM
Kim_LM_Count-and-DESeq


title: RHP3859

description:
sample 1109
mRNA
QC: PASSED


title: WT d11

city: New York

first: James

middle: J

last: Bieker

state: NY

address: One Gustave Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Mount Sinai School of Medicine

data_processing:
Next generation sequencing was performed on an Illumina NextSeq 500.
Sequencing yielded 75 nt single end reads, >30 million per sample.
Sequenced reads were mapped to the human genome (hg38) using Tophat2
Accepted hits were tested for differential expression analysis using Cuffdiff2 with the blind dispersion method.
Heatmap plots for gene clusters were created in R package pHeatmap.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited csv file that includes samples 1-3 (CDA d11, d15, difft d5) and samples 4-6 (WT d11, d15, and difft d5)

source_name: erythroid cells

growth_protocol: Peripheral blood mononuclear cells underwent a two-step culture based on the Migliaccio protocol to generate erythroid cells: one for proliferation, with harvests at d11 and d15; the second for differentiation that was harvested after the d11 culture was differentiated for an additional 5 days.

extract_protocol:
Total RNA from all samples was isolated with Triazol.
RNA samples were used for polyA+ library preparation using the Bioo Scientific (NEXTflex) Rapid Directional kit (NOVA-5138-07).

tag: klf1 status

value: WT

tag: time point

value: proliferation d11

tag: disease

value: healthy


title: CDA d11

value: CDA E325K

value: Congenital dyserythropoietic anemia


title: WT difft5

value: differentiation d5


title: CDA d15

value: proliferation d15


title: RHP3862

description:
sample 1112
mRNA
QC: PASSED


title: WT d15


title: CDA difft5


title: RHP3856

description:
sample 1106
mRNA
QC: PASSED


title: RHP3854

description:
sample 1104
mRNA
QC: FAILED


title: RHP3857

description:
sample 1107
mRNA
QC: PASSED


title: RHP3850

description:
sample 1100
mRNA
QC: PASSED


title: RHP3855

description:
sample 1105
mRNA
QC: PASSED


title: RHP3840

description:
sample 1090
mRNA
QC: PASSED


title: RHP3852

description:
sample 1102
mRNA
QC: PASSED


title: RHP3858

description:
sample 1108
mRNA
QC: PASSED


title: RHP3853

description:
sample 1103
mRNA
QC: PASSED


title: RHP3851

description:
sample 1101
mRNA
QC: PASSED


title: RHP3839

description:
sample 1089
mRNA
QC: PASSED


title: RHP3844

description:
sample 1094
mRNA
QC: FAILED


title: RHP3848

description:
sample 1098
mRNA
QC: PASSED


title: RHP3845

description:
sample 1095
mRNA
QC: PASSED


title: RHP3843

description:
sample 1093
mRNA
QC: FAILED


title: RHP3842

description:
sample 1092
mRNA
QC: PASSED


title: RHP3847

description:
sample 1097
mRNA
QC: FAILED


title: RHP3841

description:
sample 1091
mRNA
QC: PASSED


title: RHP3835

description:
sample 1085
mRNA
QC: PASSED


title: RHP3834

description:
sample 1084
mRNA
QC: PASSED


title: RHP3836

description:
sample 1086
mRNA
QC: PASSED


title: RHP3846

description:
sample 1096
mRNA
QC: PASSED


title: RHP3833

description:
sample 1083
mRNA
QC: PASSED


title: RHP3832

description:
sample 1082
mRNA
QC: PASSED


title: RHP3829

description:
sample 1079
mRNA
QC: PASSED


title: RHP3825

description:
sample 1075
mRNA
QC: FAILED


title: RHP3826

description:
sample 1076
mRNA
QC: PASSED


title: RHP3831

description:
sample 1081
mRNA
QC: PASSED


title: RHP3830

description:
sample 1080
mRNA
QC: PASSED


title: RHP3824

description:
sample 1074
mRNA
QC: PASSED


title: RHP3849

description:
sample 1099
mRNA
QC: PASSED


title: RHP3819

description:
sample 1069
mRNA
QC: PASSED


title: RHP3838

description:
sample 1088
mRNA
QC: PASSED


title: RHP3823

description:
sample 1073
mRNA
QC: PASSED


title: RHP3827

description:
sample 1077
mRNA
QC: PASSED


title: RHP3828

description:
sample 1078
mRNA
QC: PASSED


title: RHP3817

description:
sample 1067
mRNA
QC: PASSED


title: RHP3818

description:
sample 1068
mRNA
QC: PASSED


title: RHP3821

description:
sample 1071
mRNA
QC: FAILED


title: RHP3820

description:
sample 1070
mRNA
QC: PASSED


title: RHP3815

description:
sample 1065
mRNA
QC: PASSED


title: RHP3816

description:
sample 1066
mRNA
QC: PASSED


title: RHP3837

description:
sample 1087
mRNA
QC: PASSED


title: RHP3814

description:
sample 1064
mRNA
QC: PASSED


title: RHP3811

description:
sample 1061
mRNA
QC: PASSED


title: RHP3812

description:
sample 1062
mRNA
QC: PASSED


title: RHP3808

description:
sample 1058
mRNA
QC: FAILED


title: RHP3813

description:
sample 1063
mRNA
QC: PASSED


title: RHP3807

description:
sample 1057
mRNA
QC: PASSED


title: RHP3801

description:
sample 1051
mRNA
QC: PASSED


title: RHP3803

description:
sample 1053
mRNA
QC: PASSED


title: RHP3809

description:
sample 1059
mRNA
QC: FAILED


title: RHP3802

description:
sample 1052
mRNA
QC: PASSED


title: RHP3822

description:
sample 1072
mRNA
QC: PASSED


title: RHP3804

description:
sample 1054
mRNA
QC: PASSED


title: RHP3810

description:
sample 1060
mRNA
QC: PASSED


title: RHP3806

description:
sample 1056
mRNA
QC: PASSED


title: RHP3789

description:
sample 1039
mRNA
QC: PASSED


title: RHP3788

description:
sample 1038
mRNA
QC: PASSED


title: RHP3790

description:
sample 1040
mRNA
QC: PASSED


title: RHP3800

description:
sample 1050
mRNA
QC: PASSED


title: RHP3784

description:
sample 1034
mRNA
QC: PASSED


title: cohort2.P2LBN9.fastq.gz

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

library_source: genomic

data_processing:
Adaptor and low quality reads were trimmed and filtered using Trim Galore! 0.4.3 (Krueger F) with parameter ‘--fastqc --stringency 5 --rrbs --length 30 --non_directional’. Reads were aligned to the rat genome (RGSC 6.0/rn6) by using Bismark 0.16.3 (Krueger and Andrews 2011) with ‘--non_directional’ mode. CpG sites were called by “bismark_methylation_extractor” function from Bismark.
Genome_build: rn6
Supplementary_files_format_and_content: Methylation level (percentage) of 3,417 reported differential methyaltion regions in two cohorts. They are in .txt format

molecule: genomic DNA

organism: Rattus norvegicus

source_name: buccal swab sample

growth_protocol: Subjects were born to primiparous time-pregnant Sprague-Dawley rat dams (around P75) that were maintained in the quiet animal facility room on a 12 h light/dark cycle with ad libitum access to lab chow and water. Parturition was checked daily, and the day of birth was considered postnatal day 0 (P0). Litter size was adjusted 12 per dam on P1, if needed. On P2, pups from several litters were gathered, and 12 pups (6 males and 6 females) were assigned at random to each dam, to obviate the potential confounding effects of genetic variables and of litter size. Each pup was identified by a rapid (<2 minute) foot pad tattooing using animal tattoo ink (Ketchum).

extract_protocol:
The first buccal swab was collected from both cheeks of each pup prior to randomization on P2, using Hydraflock swab (Puritan diagnostics, LLC). After an hour’s rest with their mother, a  second buccal swab was collected, enabling sufficient DNA from each pup. Pups were then randomized to controls or LBN cages. During P3-P9,  behaviors of dams in both control and adversity/LBN cages was observed daily, to ascertain the generation of fragmented unpredictable caring patterns by the adverse environment (Molet et al. 2016; Davis et al. 2017). On P10, buccal swabs were collected as described for P2, then all litters were transferred to normal bedded cages.
The Buccal swab was placed into the DNA shields™ (Zymo research) immediately after swabbing. DNA was prepared from the DNA shields solution using the Quick-gDNA™ MiniPrep kit (Zymo Research) following  the manufacturer’s protocol. The quantity of double stranded DNA was analyzed using Qubit, and RRBS Libraries were prepared from 40 ng of genomic DNA digested with Msp I and then extracted with DNA Clean & Concentrator™-5 kit (Zymo Research). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Zymo Research). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator for sequencing. Amplified RRBS libraries were quantified and qualified by Qubit, Bioanalyzer (Agilent), and Kapa library quant (Kapa systems), and then sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: The experimental paradigm involved rearing pups and dams in “impoverished” cages for a week (P2-P9) as described elsewhere (Molet et al. 2014; Ivy et al. 2008; Walker et al. 2017). Briefly, routine rat cages were fitted with a plastic-coated aluminum mesh platform sitting ~2.5 cm above the cage floor (allowing collection of droppings). Bedding was reduced to only cover cage floor sparsely, and one-half of a single paper towel was provided for nesting material, creating a limited bedding and nesting (LBN) cage. Control dams and their litters resided in standard bedded cages, containing 0.33 cubic feet of cob bedding, which was also used for nest building. Control and experimental cages were undisturbed during P2–P9, housed in a quiet room with constant temperature and a strong laminar airflow, preventing ammonia accumulation.

value: buccal swab sample

tag: treatment

value: limited bedding and nesting cage

tag: age

tag: strain

value: Sprague Dawley


title: RHP3787

description:
sample 1037
mRNA
QC: PASSED

tag: cell type


title: RHP3798

description:
sample 1048
mRNA
QC: PASSED


title: RHP3797

description:
sample 1047
mRNA
QC: PASSED


title: RHP3799

description:
sample 1049
mRNA
QC: PASSED


title: RHP3805

description:
sample 1055
mRNA
QC: PASSED


title: cohort2.P2C8.fastq.gz

tag: tissue

value: Control


title: RHP3785

description:
sample 1035
mRNA
QC: PASSED


title: cohort2.P2LBN2.fastq.gz


title: RHP3783

description:
sample 1033
mRNA
QC: PASSED


title: cohort2.P2LBN4.fastq.gz


title: RHP3781

description:
sample 1031
mRNA
QC: PASSED


title: cohort2.P2C5.fastq.gz


title: RHP3782

description:
sample 1032
mRNA
QC: PASSED


title: cohort2.P2C11.fastq.gz


title: cohort2.P2C1.fastq.gz


title: cohort2.P10C8.fastq.gz


title: RHP3791

description:
sample 1041
mRNA
QC: PASSED


title: cohort2.P10C5.fastq.gz


title: cohort2.P10LBN4.fastq.gz


title: cohort2.P10LBN9.fastq.gz


title: cohort2.P10C11.fastq.gz


title: cohort2.P10LBN2.fastq.gz


title: cohort1.P10LBN3.fastq.gz


title: cohort2.P10LBN11.fastq.gz


title: cohort2.P2LBN11.fastq.gz


title: cohort1.P10C9.fastq.gz


title: cohort1.P10C12.fastq.gz


title: cohort1.P10LBN12.fastq.gz


title: RHP3780

description:
sample 1030
mRNA
QC: PASSED


title: RHP3774

description:
sample 1024
mRNA
QC: PASSED


title: RHP3775

description:
sample 1025
mRNA
QC: PASSED


title: cohort1.P10LBN9.fastq.gz


title: RHP3778

description:
sample 1028
mRNA
QC: PASSED


title: cohort1.P10LBN4.fastq.gz


title: RHP3779

description:
sample 1029
mRNA
QC: PASSED


title: RHP3777

description:
sample 1027
mRNA
QC: PASSED


title: cohort2.P10C1.fastq.gz


title: cohort1.P10C4.fastq.gz


title: cohort1.P10C3.fastq.gz


title: RHP3772

description:
sample 1022
mRNA
QC: PASSED


title: RHP3776

description:
sample 1026
mRNA
QC: PASSED


title: cohort1.P10C7.fastq.gz


title: cohort1.P10LBN2.fastq.gz


title: cohort1.P2LBN4.fastq.gz


title: RHP3770

description:
sample 1020
mRNA
QC: FAILED


title: RHP3773

description:
sample 1023
mRNA
QC: PASSED


title: cohort1.P10C6.fastq.gz


title: cohort1.P2C9.fastq.gz


title: cohort1.P2LBN12.fastq.gz


title: cohort1.P2LBN3.fastq.gz


title: cohort1.P2LBN9.fastq.gz


title: RHP3771

description:
sample 1021
mRNA
QC: PASSED


title: cohort1.P2C4.fastq.gz


title: F53-3

city: Villenave-d'Ornon

first: Isma

last: Belouah

address: 71 Avenue Edouard Bourlaux

department: Gironde

country: France

institute: Institut National de la Recherche Agronomique (INRA)

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
27_TTAGGC_L001
27_TTAGGC_L005

data_processing:
Gene were mapped to the Solanum lycopersicum var. Heinz assembly v2.40, concatenated with the chloroplast (gi|544163592|ref|NC_007898.3|) and mitochondrial genomes (gi|209887431|gb|FJ374974.1|), and an "artificial chromosome" containing the 8 spike sequences.
Quality and adapter trimming was performed with Trimmomatic v0.32 (ILLUMINACLIP: TruSeq2-SE/PE.fa:2:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MILEN:25). Trimmed reads were mapped to their respective genomes with Star v2.4.2a (--outSAMstrandField intronMotif --outSAMattributes All). The unique counts per locus were quantified with HTSeq v0.6.1 (htseq-count –stranded=no). Normalized FPKM was calculated with cufflinks v2.2.1 (-G). FPKM were then converted to TPM quantification.
For each sample, a standard curve performed with the spikes was used to estimate the concentration (fmol per gFW) from the TPM values.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: Excel files for counts, reads , transcripts per million (tpm) and concentrations (fmol per gram of fresh weight).

organism: Solanum lycopersicum

source_name: tomato fruit

growth_protocol: Tomato fruit were grown under conditions of usual production in a glasshouse.

extract_protocol:
Total RNA was extracted using Pant RNA reagent (PureLink kit, InvitrogenTM) followed by DNase treatment (DNA-free kit, InvitrogenTM) and purified over RNeasy Mini spin columns. Eight internal standards were spiked-in at the beginning of the total RNA extraction.
RNA-seq libraries were prepared according to Illumina's protocols TruSea Stranded mRNA sample prep kit. RNA-seq experiments were performed on a Illumina HiSeq2000 or HiSeq2500 (2x100bp).

treatment_protocol: Tomato fruit were harvested on trusses 5, 6 and 7 and at nine developmental stages. Samples were prepared by first removing seeds, jelly and placenta, and then cutting the pericarp into small pieces, which were immediately frozen in liquid nitrogen. Samples were ground and stored at -80◦C

tag: variety

value: Moneymaker

value: pericarp

tag: day post anthesis


title: cohort1.P2C3.fastq.gz


title: F53-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
25_ATCACG_L001
25_ATCACG_L005


title: cohort1.P2C12.fastq.gz


title: RHP3769

description:
sample 1019
mRNA
QC: PASSED


title: cohort1.P2LBN2.fastq.gz


title: RHP3767

description:
sample 1017
mRNA
QC: PASSED


title: RHP3765

description:
sample 1015
mRNA
QC: PASSED


title: cohort1.P2C6.fastq.gz


title: RHP3764

description:
sample 1014
mRNA
QC: PASSED


title: RHP3763

description:
sample 1013
mRNA
QC: PASSED


title: F50-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
24_ATTCCT_L001
24_ATTCCT_L005


title: RHP3766

description:
sample 1016
mRNA
QC: PASSED


title: cohort1.P2C7.fastq.gz


title: RHP3768

description:
sample 1018
mRNA
QC: PASSED


title: F41-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
17_GTCCGC_L001
17_GTCCGC_L005


title: F41-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
16_CCGTCC_L003
16_CCGTCC_L004


title: F49-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
21_CGTACG_L001
21_CGTACG_L005


title: F50-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
22_GAGTGG_L001
22_GAGTGG_L005


title: F53-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
26_CGATGT_L001
26_CGATGT_L005


title: RHP3760

description:
sample 1010
mRNA
QC: PASSED


title: F34-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
15_ATGTCA_L003
15_ATGTCA_L004


title: RHP3761

description:
sample 1011
mRNA
QC: PASSED


title: F41-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
18_GTGAAA_L001
18_GTGAAA_L005


title: F34-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
13_AGTCAA_L003
13_AGTCAA_L004


title: RHP3762

description:
sample 1012
mRNA
QC: PASSED


title: F28-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
10_TAGCTT_L003
10_TAGCTT_L004


title: F21-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
8_ACTTGA_L003
8_ACTTGA_L004


title: F21-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
9_GATCAG_L003
9_GATCAG_L004


title: F49-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
20_GTTTCG_L001
20_GTTTCG_L005


title: RHP3786

description:
sample 1036
mRNA
QC: PASSED


title: F15-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
6_GCCAAT_L003
6_GCCAAT_L004


title: RHP3756

description:
sample 1006
mRNA
QC: PASSED


title: F34-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
14_AGTTCC_L003
14_AGTTCC_L004


title: RHP3759

description:
sample 1009
mRNA
QC: PASSED


title: F28-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
11_GGCTAC_L003
11_GGCTAC_L004


title: F28-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
12_CTTGTA_L003
12_CTTGTA_L004


title: F15-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
4_TGACCA_L003
4_TGACCA_L004


title: F50-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
23_ACTGAT_L001
23_ACTGAT_L005


title: F8-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
1_ATCACG_L003
1_ATCACG_L004


title: RHP3758

description:
sample 1008
mRNA
QC: PASSED


title: RHP3757

description:
sample 1007
mRNA
QC: FAILED


title: F8-3

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
3_TTAGGC_L003
3_TTAGGC_L004


title: RHP3755

description:
sample 1005
mRNA
QC: PASSED


title: F15-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
5_ACAGTG_L003
5_ACAGTG_L004


title: RHP3752

description:
sample 1002
mRNA
QC: PASSED


title: DHC542

description:
sample 556
Targeted DNA
QC: PASSED


title: RHP3751

description:
sample 1001
mRNA
QC: PASSED


title: RHP3754

description:
sample 1004
mRNA
QC: PASSED


title: DHC540

description:
sample 554
Targeted DNA
QC: PASSED


title: F8-2

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
2_CGATGT_L003
2_CGATGT_L004


title: DHC541

description:
sample 555
Targeted DNA
QC: PASSED


title: RHP3753

description:
sample 1003
mRNA
QC: PASSED


title: DHC539

description:
sample 553
Targeted DNA
QC: PASSED


title: DHC532

description:
sample 546
Targeted DNA
QC: PASSED


title: F21-1

description:
devTom_reads
devTom_tpm
devTom_fmoles.gFW
7_CAGATC_L003
7_CAGATC_L004


title: DHC536

description:
sample 550
Targeted DNA
QC: PASSED


title: DHC534

description:
sample 548
Targeted DNA
QC: PASSED


title: RHP3750

description:
sample 1000
mRNA
QC: PASSED


title: RHP3746

description:
sample 996
mRNA
QC: PASSED


title: DHC533

description:
sample 547
Targeted DNA
QC: PASSED


title: DHC535

description:
sample 549
Targeted DNA
QC: PASSED


title: DHC528

description:
sample 542
Targeted DNA
QC: PASSED


title: DHC537

description:
sample 551
Targeted DNA
QC: PASSED


title: RHP3749

description:
sample 999
mRNA
QC: PASSED


title: RHP3745

description:
sample 995
mRNA
QC: PASSED


title: RHP3747

description:
sample 997
mRNA
QC: PASSED


title: DHC526

description:
sample 540
Targeted DNA
QC: PASSED


title: RHP3748

description:
sample 998
mRNA
QC: FAILED


title: RHP3744

description:
sample 994
mRNA
QC: PASSED


title: DHC531

description:
sample 545
Targeted DNA
QC: PASSED


title: DHC530

description:
sample 544
Targeted DNA
QC: PASSED


title: DHC529

description:
sample 543
Targeted DNA
QC: PASSED


title: DHC524

description:
sample 538
Targeted DNA
QC: PASSED


title: DHC522

description:
sample 536
Targeted DNA
QC: PASSED


title: RHP3743

description:
sample 993
mRNA
QC: PASSED


title: RHP3742

description:
sample 992
mRNA
QC: PASSED


title: DHC520

description:
sample 534
Targeted DNA
QC: PASSED


title: DHC525

description:
sample 539
Targeted DNA
QC: PASSED


title: DHC538

description:
sample 552
Targeted DNA
QC: PASSED


title: DHC519

description:
sample 533
Targeted DNA
QC: PASSED


title: DHC523

description:
sample 537
Targeted DNA
QC: PASSED


title: DHC521

description:
sample 535
Targeted DNA
QC: PASSED


title: RHP3739

description:
sample 989
mRNA
QC: PASSED


title: DHC518

description:
sample 532
Targeted DNA
QC: PASSED


title: DHC514

description:
sample 528
Targeted DNA
QC: PASSED


title: DHC527

description:
sample 541
Targeted DNA
QC: PASSED


title: RHP3741

description:
sample 991
mRNA
QC: PASSED


title: DHC516

description:
sample 530
Targeted DNA
QC: PASSED


title: RHP3736

description:
sample 986
mRNA
QC: PASSED


title: DHC509

description:
sample 523
Targeted DNA
QC: PASSED


title: RHP3740

description:
sample 990
mRNA
QC: PASSED


title: DHC517

description:
sample 531
Targeted DNA
QC: FAILED


title: DHC513

description:
sample 527
Targeted DNA
QC: PASSED


title: DHC515

description:
sample 529
Targeted DNA
QC: PASSED


title: DHC512

description:
sample 526
Targeted DNA
QC: PASSED


title: RHP3735

description:
sample 985
mRNA
QC: PASSED


title: DHC504

description:
sample 518
Targeted DNA
QC: PASSED


title: RHC8157

description:
sample 984
mRNA
QC: PASSED


title: RHC8156

description:
sample 983
mRNA
QC: PASSED


title: RHP3737

description:
sample 987
mRNA
QC: PASSED


title: RHP3738

description:
sample 988
mRNA
QC: PASSED


title: DHC502

description:
sample 516
Targeted DNA
QC: PASSED


title: DHC506

description:
sample 520
Targeted DNA
QC: PASSED


title: DHC501

description:
sample 515
Targeted DNA
QC: PASSED


title: DHC510

description:
sample 524
Targeted DNA
QC: PASSED


title: DHC498

description:
sample 512
Targeted DNA
QC: PASSED


title: RHC8155

description:
sample 982
mRNA
QC: PASSED


title: DHC507

description:
sample 521
Targeted DNA
QC: PASSED


title: DHC500

description:
sample 514
Targeted DNA
QC: PASSED


title: DHC497

description:
sample 511
Targeted DNA
QC: PASSED


title: RHC8154

description:
sample 981
mRNA
QC: PASSED


title: DHC511

description:
sample 525
Targeted DNA
QC: PASSED


title: DHC508

description:
sample 522
Targeted DNA
QC: PASSED


title: DHC491

description:
sample 505
Targeted DNA
QC: PASSED


title: RHC8152

description:
sample 979
mRNA
QC: PASSED


title: DHC505

description:
sample 519
Targeted DNA
QC: PASSED


title: RHC8153

description:
sample 980
mRNA
QC: PASSED


title: DHC489

description:
sample 503
Targeted DNA
QC: PASSED


title: DHC495

description:
sample 509
Targeted DNA
QC: PASSED


title: DHC490

description:
sample 504
Targeted DNA
QC: PASSED


title: DHC494

description:
sample 508
Targeted DNA
QC: PASSED


title: DHC496

description:
sample 510
Targeted DNA
QC: PASSED


title: DHC492

description:
sample 506
Targeted DNA
QC: PASSED


title: RHC8151

description:
sample 978
mRNA
QC: PASSED


title: DHC499

description:
sample 513
Targeted DNA
QC: PASSED


title: DHC488

description:
sample 502
Targeted DNA
QC: PASSED


title: DHC487

description:
sample 501
Targeted DNA
QC: PASSED


title: RHC8148

description:
sample 975
mRNA
QC: PASSED


title: DHC484

description:
sample 498
Targeted DNA
QC: PASSED


title: DHC503

description:
sample 517
Targeted DNA
QC: PASSED


title: RHC8150

description:
sample 977
mRNA
QC: PASSED


title: DHC486

description:
sample 500
Targeted DNA
QC: PASSED


title: DHC485

description:
sample 499
Targeted DNA
QC: PASSED


title: RHC8147

description:
sample 974
mRNA
QC: PASSED


title: DHC483

description:
sample 497
Targeted DNA
QC: PASSED


title: DHC482

description:
sample 496
Targeted DNA
QC: PASSED


title: RHC8145

description:
sample 972
mRNA
QC: PASSED


title: DHC493

description:
sample 507
Targeted DNA
QC: PASSED


title: RHC8146

description:
sample 973
mRNA
QC: PASSED


title: DHC481

description:
sample 495
Targeted DNA
QC: PASSED


title: RHC8149

description:
sample 976
mRNA
QC: PASSED


title: DHC477

description:
sample 491
Targeted DNA
QC: PASSED


title: DHC478

description:
sample 492
Targeted DNA
QC: PASSED


title: RHC8143

description:
sample 970
mRNA
QC: PASSED


title: DHC474

description:
sample 488
Targeted DNA
QC: PASSED


title: DHC480

description:
sample 494
Targeted DNA
QC: PASSED


title: RHC8144

description:
sample 971
mRNA
QC: PASSED


title: DHC479

description:
sample 493
Targeted DNA
QC: PASSED


title: DHC472

description:
sample 486
Targeted DNA
QC: PASSED


title: DHC469

description:
sample 483
Targeted DNA
QC: PASSED


title: RHC8139

description:
sample 966
mRNA
QC: PASSED


title: DHC476

description:
sample 490
Targeted DNA
QC: PASSED


title: DHC471

description:
sample 485
Targeted DNA
QC: PASSED


title: DHC473

description:
sample 487
Targeted DNA
QC: PASSED


title: RHC8141

description:
sample 968
mRNA
QC: PASSED


title: RHC8138

description:
sample 965
mRNA
QC: PASSED


title: DHC468

description:
sample 482
Targeted DNA
QC: PASSED


title: DHC466

description:
sample 480
Targeted DNA
QC: PASSED


title: RHC8142

description:
sample 969
mRNA
QC: PASSED


title: DHC463

description:
sample 477
Targeted DNA
QC: PASSED


title: DHC470

description:
sample 484
Targeted DNA
QC: PASSED


title: DHC467

description:
sample 481
Targeted DNA
QC: PASSED


title: RHC8137

description:
sample 964
mRNA
QC: PASSED


title: DHC458

description:
sample 472
Targeted DNA
QC: PASSED


title: DHC461

description:
sample 475
Targeted DNA
QC: PASSED


title: RHC8133

description:
sample 960
mRNA
QC: PASSED


title: RHC8136

description:
sample 963
mRNA
QC: PASSED


title: DHC460

description:
sample 474
Targeted DNA
QC: PASSED


title: DHC462

description:
sample 476
Targeted DNA
QC: PASSED


title: RHC8132

description:
sample 959
mRNA
QC: FAILED


title: DHC465

description:
sample 479
Targeted DNA
QC: PASSED


title: RHC8140

description:
sample 967
mRNA
QC: PASSED


title: RHC8135

description:
sample 962
mRNA
QC: PASSED


title: DHC459

description:
sample 473
Targeted DNA
QC: PASSED


title: DHC453

description:
sample 467
Targeted DNA
QC: PASSED


title: DHC475

description:
sample 489
Targeted DNA
QC: PASSED


title: DHC451

description:
sample 465
Targeted DNA
QC: PASSED


title: RHC8131

description:
sample 958
mRNA
QC: PASSED


title: DHC454

description:
sample 468
Targeted DNA
QC: PASSED


title: DHC456

description:
sample 470
Targeted DNA
QC: PASSED


title: RHC8134

description:
sample 961
mRNA
QC: PASSED


title: DHC457

description:
sample 471
Targeted DNA
QC: PASSED


title: DHC464

description:
sample 478
Targeted DNA
QC: PASSED


title: DHC447

description:
sample 461
Targeted DNA
QC: PASSED


title: DHC452

description:
sample 466
Targeted DNA
QC: PASSED


title: DHC446

description:
sample 460
Targeted DNA
QC: PASSED


title: RHC8130

description:
sample 957
mRNA
QC: PASSED


title: DHC450

description:
sample 464
Targeted DNA
QC: PASSED


title: DHC444

description:
sample 458
Targeted DNA
QC: PASSED


title: DHC445

description:
sample 459
Targeted DNA
QC: PASSED


title: DHC448

description:
sample 462
Targeted DNA
QC: PASSED


title: RHC8129

description:
sample 956
mRNA
QC: PASSED


title: DHC442

description:
sample 456
Targeted DNA
QC: PASSED


title: DHC455

description:
sample 469
Targeted DNA
QC: PASSED


title: RHC8128

description:
sample 955
mRNA
QC: PASSED


title: RHC8125

description:
sample 952
mRNA
QC: PASSED


title: DHC449

description:
sample 463
Targeted DNA
QC: FAILED


title: DHC440

description:
sample 454
Targeted DNA
QC: PASSED


title: RHC8124

description:
sample 951
mRNA
QC: PASSED


title: RHC8127

description:
sample 954
mRNA
QC: PASSED


title: DHC435

description:
sample 449
Targeted DNA
QC: PASSED


title: DHC436

description:
sample 450
Targeted DNA
QC: PASSED


title: DHC441

description:
sample 455
Targeted DNA
QC: PASSED


title: RHC8126

description:
sample 953
mRNA
QC: PASSED


title: DHC437

description:
sample 451
Targeted DNA
QC: PASSED


title: DHC433

description:
sample 447
Targeted DNA
QC: PASSED


title: RHC8121

description:
sample 948
mRNA
QC: PASSED


title: DHC439

description:
sample 453
Targeted DNA
QC: PASSED


title: DHC431

description:
sample 445
Targeted DNA
QC: PASSED


title: RHC8120

description:
sample 947
mRNA
QC: PASSED


title: DHC434

description:
sample 448
Targeted DNA
QC: PASSED


title: RHC8123

description:
sample 950
mRNA
QC: PASSED


title: DHC428

description:
sample 442
Targeted DNA
QC: PASSED


title: DHC438

description:
sample 452
Targeted DNA
QC: PASSED


title: RHC8122

description:
sample 949
mRNA
QC: PASSED


title: DHC432

description:
sample 446
Targeted DNA
QC: PASSED


title: DHC443

description:
sample 457
Targeted DNA
QC: PASSED


title: DHC423

description:
sample 437
Targeted DNA
QC: PASSED


title: DHC429

description:
sample 443
Targeted DNA
QC: PASSED


title: DHC424

description:
sample 438
Targeted DNA
QC: PASSED


title: DHC422

description:
sample 436
Targeted DNA
QC: PASSED


title: RHC8119

description:
sample 946
mRNA
QC: PASSED


title: DHC425

description:
sample 439
Targeted DNA
QC: PASSED


title: DHC427

description:
sample 441
Targeted DNA
QC: PASSED


title: DHC426

description:
sample 440
Targeted DNA
QC: PASSED


title: RHC8115

description:
sample 942
mRNA
QC: PASSED


title: RHC8118

description:
sample 945
mRNA
QC: PASSED


title: DHC419

description:
sample 433
Targeted DNA
QC: PASSED


title: DHC416

description:
sample 430
Targeted DNA
QC: PASSED


title: DHC417

description:
sample 431
Targeted DNA
QC: PASSED


title: DHC420

description:
sample 434
Targeted DNA
QC: PASSED


title: DHC414

description:
sample 428
Targeted DNA
QC: PASSED


title: RHC8117

description:
sample 944
mRNA
QC: PASSED


title: DHC421

description:
sample 435
Targeted DNA
QC: PASSED


title: DHC413

description:
sample 427
Targeted DNA
QC: PASSED


title: DHC412

description:
sample 426
Targeted DNA
QC: PASSED


title: RHC8114

description:
sample 941
mRNA
QC: PASSED


title: DHC415

description:
sample 429
Targeted DNA
QC: PASSED


title: DHC418

description:
sample 432
Targeted DNA
QC: PASSED


title: DHC430

description:
sample 444
Targeted DNA
QC: PASSED


title: DHC407

description:
sample 421
Targeted DNA
QC: PASSED


title: RHC8111

description:
sample 938
mRNA
QC: PASSED


title: RHC8113

description:
sample 940
mRNA
QC: PASSED


title: DHC410

description:
sample 424
Targeted DNA
QC: PASSED


title: RHC8112

description:
sample 939
mRNA
QC: PASSED


title: RHC8116

description:
sample 943
mRNA
QC: PASSED


title: DHC403

description:
sample 417
Targeted DNA
QC: PASSED


title: DHC399

description:
sample 413
Targeted DNA
QC: PASSED


title: DHC401

description:
sample 415
Targeted DNA
QC: PASSED


title: DHC398

description:
sample 412
Targeted DNA
QC: PASSED


title: DHC411

description:
sample 425
Targeted DNA
QC: PASSED


title: DHC397

description:
sample 411
Targeted DNA
QC: PASSED


title: RHC8109

description:
sample 936
mRNA
QC: PASSED


title: DHC409

description:
sample 423
Targeted DNA
QC: PASSED


title: DHC396

description:
sample 410
Targeted DNA
QC: PASSED


title: DHC395

description:
sample 409
Targeted DNA
QC: PASSED


title: DHC402

description:
sample 416
Targeted DNA
QC: PASSED


title: RHC8108

description:
sample 935
mRNA
QC: PASSED


title: DHC406

description:
sample 420
Targeted DNA
QC: PASSED


title: RHC8110

description:
sample 937
mRNA
QC: PASSED


title: RHC8104

description:
sample 931
mRNA
QC: PASSED


title: RHC8105

description:
sample 932
mRNA
QC: PASSED


title: RHC8106

description:
sample 933
mRNA
QC: PASSED


title: RHC8107

description:
sample 934
mRNA
QC: PASSED


title: DHC405

description:
sample 419
Targeted DNA
QC: PASSED


title: DHC404

description:
sample 418
Targeted DNA
QC: PASSED


title: RHC8103

description:
sample 930
mRNA
QC: PASSED


title: DHC394

description:
sample 408
Targeted DNA
QC: PASSED


title: DHC400

description:
sample 414
Targeted DNA
QC: PASSED


title: RHC8101

description:
sample 928
mRNA
QC: PASSED


title: DHC408

description:
sample 422
Targeted DNA
QC: PASSED


title: DHC390

description:
sample 404
Targeted DNA
QC: PASSED


title: DHC389

description:
sample 403
Targeted DNA
QC: PASSED


title: DHC392

description:
sample 406
Targeted DNA
QC: PASSED


title: RHC8102

description:
sample 929
mRNA
QC: PASSED


title: DHC387

description:
sample 401
Targeted DNA
QC: PASSED


title: RHC8099

description:
sample 926
mRNA
QC: PASSED


title: DHC384

description:
sample 398
Targeted DNA
QC: PASSED


title: DHC385

description:
sample 399
Targeted DNA
QC: PASSED


title: RHC8100

description:
sample 927
mRNA
QC: PASSED


title: DHC381

description:
sample 395
Targeted DNA
QC: PASSED


title: DHC386

description:
sample 400
Targeted DNA
QC: PASSED


title: RHC8094

description:
sample 921
mRNA
QC: PASSED


title: DHC391

description:
sample 405
Targeted DNA
QC: PASSED


title: RHC8093

description:
sample 920
mRNA
QC: PASSED


title: RHC8092

description:
sample 919
mRNA
QC: PASSED


title: DHC382

description:
sample 396
Targeted DNA
QC: PASSED


title: RHC8096

description:
sample 923
mRNA
QC: PASSED


title: DHC383

description:
sample 397
Targeted DNA
QC: PASSED


title: DHC380

description:
sample 394
Targeted DNA
QC: PASSED


title: RHC8097

description:
sample 924
mRNA
QC: PASSED


title: RHC8095

description:
sample 922
mRNA
QC: PASSED


title: RHC8098

description:
sample 925
mRNA
QC: PASSED


title: RHC8091

description:
sample 918
mRNA
QC: PASSED


title: DHC376

description:
sample 390
Targeted DNA
QC: PASSED


title: DHC393

description:
sample 407
Targeted DNA
QC: PASSED


title: DHC379

description:
sample 393
Targeted DNA
QC: PASSED


title: RHC8090

description:
sample 917
mRNA
QC: PASSED


title: DHC378

description:
sample 392
Targeted DNA
QC: PASSED


title: DHC388

description:
sample 402
Targeted DNA
QC: PASSED


title: DHC377

description:
sample 391
Targeted DNA
QC: PASSED


title: RHC8089

description:
sample 916
mRNA
QC: PASSED


title: DHC375

description:
sample 389
Targeted DNA
QC: PASSED


title: DHC373

description:
sample 387
Targeted DNA
QC: PASSED


title: DHC374

description:
sample 388
Targeted DNA
QC: PASSED


title: RHC8088

description:
sample 915
mRNA
QC: PASSED


title: RHC8087

description:
sample 914
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_253 [GNDX-VJM-VAL253]

type: RNA

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded tumor blocks by 1mm punch under RNAse-free conditions. Total RNA was extracted and purified using RNeasy FFPE kit (Qiagen, Valencia, CA)

tag: Sex

value: Male

tag: pstage


title: bladder_cancer_resection_sample_254 [GNDX-VJM-VAL254]


title: DHC372

description:
sample 386
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_256 [GNDX-VJM-VAL256]


title: bladder_cancer_resection_sample_252 [GNDX-VJM-VAL252]


title: bladder_cancer_resection_sample_255 [GNDX-VJM-VAL255]


title: bladder_cancer_resection_sample_251 [GNDX-VJM-VAL251]


title: DHC371

description:
sample 385
Targeted DNA
QC: PASSED


title: DHC370

description:
sample 384
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_250 [GNDX-VJM-VAL250]

value: Female


title: bladder_cancer_resection_sample_249 [GNDX-VJM-VAL249]


title: DHC369

description:
sample 383
Targeted DNA
QC: PASSED


title: RHC8086

description:
sample 913
mRNA
QC: PASSED


title: RHC8083

description:
sample 910
mRNA
QC: PASSED


title: RHC8085

description:
sample 912
mRNA
QC: PASSED


title: RHC8082

description:
sample 909
mRNA
QC: PASSED


title: DHC367

description:
sample 381
Targeted DNA
QC: PASSED


title: RHC8081

description:
sample 908
mRNA
QC: PASSED


title: DHC368

description:
sample 382
Targeted DNA
QC: PASSED


title: RHC8084

description:
sample 911
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_246 [GNDX-VJM-VAL246]


title: DHC366

description:
sample 380
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_244 [GNDX-VJM-VAL244]


title: bladder_cancer_resection_sample_245 [GNDX-VJM-VAL245]


title: bladder_cancer_resection_sample_248 [GNDX-VJM-VAL248]


title: bladder_cancer_resection_sample_247 [GNDX-VJM-VAL247]


title: bladder_cancer_resection_sample_243 [GNDX-VJM-VAL243]


title: RHC8079

description:
sample 906
mRNA
QC: PASSED


title: DHC365

description:
sample 379
Targeted DNA
QC: PASSED


title: RHC8080

description:
sample 907
mRNA
QC: PASSED


title: RHC8077

description:
sample 904
mRNA
QC: PASSED


title: RHC8078

description:
sample 905
mRNA
QC: PASSED


title: DHC363

description:
sample 377
Targeted DNA
QC: PASSED


title: DHC364

description:
sample 378
Targeted DNA
QC: PASSED


title: DHC362

description:
sample 376
Targeted DNA
QC: PASSED


title: RHC8075

description:
sample 902
mRNA
QC: PASSED


title: RHC8076

description:
sample 903
mRNA
QC: PASSED


title: DHC361

description:
sample 375
Targeted DNA
QC: PASSED


title: DHC360

description:
sample 374
Targeted DNA
QC: PASSED


title: RHC8074

description:
sample 901
mRNA
QC: PASSED


title: RHC8073

description:
sample 900
mRNA
QC: PASSED


title: DHC358

description:
sample 372
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_241 [GNDX-VJM-VAL241]


title: bladder_cancer_resection_sample_240 [GNDX-VJM-VAL240]


title: RHC8072

description:
sample 899
mRNA
QC: PASSED


title: DHC357

description:
sample 371
Targeted DNA
QC: PASSED


title: DHC356

description:
sample 370
Targeted DNA
QC: PASSED


title: RHC8071

description:
sample 898
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_237 [GNDX-VJM-VAL237]


title: bladder_cancer_resection_sample_238 [GNDX-VJM-VAL238]


title: RHC8070

description:
sample 897
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_236 [GNDX-VJM-VAL236]


title: bladder_cancer_resection_sample_239 [GNDX-VJM-VAL239]


title: bladder_cancer_resection_sample_235 [GNDX-VJM-VAL235]


title: bladder_cancer_resection_sample_233 [GNDX-VJM-VAL233]


title: bladder_cancer_resection_sample_234 [GNDX-VJM-VAL234]


title: RHC8069

description:
sample 896
mRNA
QC: PASSED


title: DHC354

description:
sample 368
Targeted DNA
QC: PASSED


title: DHC355

description:
sample 369
Targeted DNA
QC: PASSED


title: DHC359

description:
sample 373
Targeted DNA
QC: PASSED


title: RHC8068

description:
sample 895
mRNA
QC: PASSED


title: DHC353

description:
sample 367
Targeted DNA
QC: FAILED


title: bladder_cancer_resection_sample_232 [GNDX-VJM-VAL232]


title: bladder_cancer_resection_sample_231 [GNDX-VJM-VAL231]


title: DHC352

description:
sample 366
Targeted DNA
QC: PASSED


title: RHC8067

description:
sample 894
mRNA
QC: PASSED


title: RHC8066

description:
sample 893
mRNA
QC: PASSED


title: DHC351

description:
sample 365
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_228 [GNDX-VJM-VAL228]


title: DHC350

description:
sample 364
Targeted DNA
QC: FAILED

value: parental


title: bladder_cancer_resection_sample_229 [GNDX-VJM-VAL229]


title: RHC8065

description:
sample 892
mRNA
QC: PASSED

value: lung cancer cell line


title: bladder_cancer_resection_sample_230 [GNDX-VJM-VAL230]


title: RHC8063

description:
sample 890
mRNA
QC: PASSED


title: DHC348

description:
sample 362
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_242 [GNDX-VJM-VAL242]


title: RHC8064

description:
sample 891
mRNA
QC: FAILED


title: RHC8061

description:
sample 888
mRNA
QC: PASSED


title: RHC8062

description:
sample 889
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_227 [GNDX-VJM-VAL227]


title: RHC8060

description:
sample 887
mRNA
QC: PASSED


title: DHC347

description:
sample 361
Targeted DNA
QC: PASSED


title: RHC8059

description:
sample 886
mRNA
QC: PASSED


title: RHC8058

description:
sample 885
mRNA
QC: PASSED


title: DHC343

description:
sample 357
Targeted DNA
QC: PASSED


title: DHC344

description:
sample 358
Targeted DNA
QC: PASSED


title: DHC349

description:
sample 363
Targeted DNA
QC: FAILED


title: RHC8057

description:
sample 884
mRNA
QC: PASSED


title: DHC346

description:
sample 360
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_222 [GNDX-VJM-VAL222]


title: bladder_cancer_resection_sample_223 [GNDX-VJM-VAL223]


title: bladder_cancer_resection_sample_225 [GNDX-VJM-VAL225]


title: bladder_cancer_resection_sample_221 [GNDX-VJM-VAL221]


title: bladder_cancer_resection_sample_226 [GNDX-VJM-VAL226]


title: bladder_cancer_resection_sample_220 [GNDX-VJM-VAL220]


title: RHC8056

description:
sample 883
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_219 [GNDX-VJM-VAL219]


title: DHC341

description:
sample 355
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_224 [GNDX-VJM-VAL224]


title: RHC8054

description:
sample 881
mRNA
QC: PASSED


title: DHC342

description:
sample 356
Targeted DNA
QC: PASSED


title: DHC339

description:
sample 353
Targeted DNA
QC: FAILED


title: DHC340

description:
sample 354
Targeted DNA
QC: PASSED


title: RHC8053

description:
sample 880
mRNA
QC: PASSED


title: DHC338

description:
sample 352
Targeted DNA
QC: FAILED


title: DHC345

description:
sample 359
Targeted DNA
QC: FAILED


title: RHC8051

description:
sample 878
mRNA
QC: PASSED


title: RHC8052

description:
sample 879
mRNA
QC: PASSED


title: DHC337

description:
sample 351
Targeted DNA
QC: PASSED


title: RHC8055

description:
sample 882
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_217 [GNDX-VJM-VAL217]


title: bladder_cancer_resection_sample_216 [GNDX-VJM-VAL216]


title: bladder_cancer_resection_sample_214 [GNDX-VJM-VAL214]


title: bladder_cancer_resection_sample_215 [GNDX-VJM-VAL215]


title: bladder_cancer_resection_sample_213 [GNDX-VJM-VAL213]


title: DHC335

description:
sample 349
Targeted DNA
QC: PASSED


title: DHC334

description:
sample 348
Targeted DNA
QC: PASSED


title: RHC8050

description:
sample 877
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_218 [GNDX-VJM-VAL218]


title: DHC333

description:
sample 347
Targeted DNA
QC: PASSED


title: DHC331

description:
sample 345
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_211 [GNDX-VJM-VAL211]


title: bladder_cancer_resection_sample_212 [GNDX-VJM-VAL212]


title: RHC8047

description:
sample 874
mRNA
QC: PASSED


title: DHC330

description:
sample 344
Targeted DNA
QC: FAILED


title: DHC332

description:
sample 346
Targeted DNA
QC: PASSED


title: RHC8044

description:
sample 871
mRNA
QC: PASSED


title: DHC336

description:
sample 350
Targeted DNA
QC: FAILED


title: bladder_cancer_resection_sample_210 [GNDX-VJM-VAL210]


title: DHC329

description:
sample 343
Targeted DNA
QC: FAILED


title: RHC8043

description:
sample 870
mRNA
QC: PASSED


title: RHC8049

description:
sample 876
mRNA
QC: PASSED


title: DHC328

description:
sample 342
Targeted DNA
QC: FAILED


title: bladder_cancer_resection_sample_209 [GNDX-VJM-VAL209]


title: RHC8048

description:
sample 875
mRNA
QC: PASSED


title: DHC327

description:
sample 341
Targeted DNA
QC: FAILED


title: RHC8042

description:
sample 869
mRNA
QC: PASSED


title: RHC8046

description:
sample 873
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_205 [GNDX-VJM-VAL205]


title: RHC8045

description:
sample 872
mRNA
QC: PASSED


title: DHC326

description:
sample 340
Targeted DNA
QC: FAILED


title: RHC8041

description:
sample 868
mRNA
QC: PASSED


title: RHC8040

description:
sample 867
mRNA
QC: PASSED


title: DHC324

description:
sample 338
Targeted DNA
QC: FAILED


title: DHC325

description:
sample 339
Targeted DNA
QC: FAILED


title: RHC8039

description:
sample 866
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_206 [GNDX-VJM-VAL206]


title: bladder_cancer_resection_sample_204 [GNDX-VJM-VAL204]


title: DHC323

description:
sample 337
Targeted DNA
QC: FAILED


title: RHC8037

description:
sample 864
mRNA
QC: PASSED


title: RHC8038

description:
sample 865
mRNA
QC: PASSED


title: DHC322

description:
sample 336
Targeted DNA
QC: FAILED


title: DHC321

description:
sample 335
Targeted DNA
QC: FAILED


title: bladder_cancer_resection_sample_202 [GNDX-VJM-VAL202]


title: RHC8035

description:
sample 862
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_201 [GNDX-VJM-VAL201]


title: DHC320

description:
sample 334
Targeted DNA
QC: FAILED


title: RHC8036

description:
sample 863
mRNA
QC: PASSED


title: RHC8034

description:
sample 861
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_203 [GNDX-VJM-VAL203]


title: bladder_cancer_resection_sample_200 [GNDX-VJM-VAL200]


title: DHC318

description:
sample 332
Targeted DNA
QC: PASSED


title: DHC319

description:
sample 333
Targeted DNA
QC: FAILED


title: RHC8032

description:
sample 859
mRNA
QC: PASSED


title: DHC317

description:
sample 331
Targeted DNA
QC: FAILED


title: RHC8031

description:
sample 858
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_199 [GNDX-VJM-VAL199]


title: bladder_cancer_resection_sample_197 [GNDX-VJM-VAL197]


title: bladder_cancer_resection_sample_198 [GNDX-VJM-VAL198]


title: DHC316

description:
sample 330
Targeted DNA
QC: FAILED


title: bladder_cancer_resection_sample_196 [GNDX-VJM-VAL196]


title: bladder_cancer_resection_sample_194 [GNDX-VJM-VAL194]


title: bladder_cancer_resection_sample_195 [GNDX-VJM-VAL195]


title: RHC8030

description:
sample 857
mRNA
QC: PASSED


title: DHC315

description:
sample 329
Targeted DNA
QC: PASSED


title: RHC8029

description:
sample 856
mRNA
QC: PASSED


title: DHC314

description:
sample 328
Targeted DNA
QC: FAILED


title: DHC313

description:
sample 327
Targeted DNA
QC: PASSED


title: RHC8028

description:
sample 855
mRNA
QC: PASSED


title: RHC8033

description:
sample 860
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_192 [GNDX-VJM-VAL192]


title: RHC8027

description:
sample 854
mRNA
QC: PASSED


title: RHC8026

description:
sample 853
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_191 [GNDX-VJM-VAL191]


title: bladder_cancer_resection_sample_193 [GNDX-VJM-VAL193]


title: DHC311

description:
sample 325
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_189 [GNDX-VJM-VAL189]


title: DHC310

description:
sample 324
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_190 [GNDX-VJM-VAL190]


title: bladder_cancer_resection_sample_188 [GNDX-VJM-VAL188]


title: DHC309

description:
sample 323
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_187 [GNDX-VJM-VAL187]


title: RHC8023

description:
sample 850
mRNA
QC: PASSED


title: DHC308

description:
sample 322
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_186 [GNDX-VJM-VAL186]


title: DHC307

description:
sample 321
Targeted DNA
QC: PASSED


title: RHC8024

description:
sample 851
mRNA
QC: PASSED


title: DHC306

description:
sample 320
Targeted DNA
QC: PASSED


title: DHC312

description:
sample 326
Targeted DNA
QC: PASSED


title: RHC8025

description:
sample 852
mRNA
QC: PASSED


title: RHC8019

description:
sample 846
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_184 [GNDX-VJM-VAL184]


title: RHC8020

description:
sample 847
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_183 [GNDX-VJM-VAL183]


title: RHC8018

description:
sample 845
mRNA
QC: PASSED


title: RHC8022

description:
sample 849
mRNA
QC: PASSED


title: DHC302

description:
sample 316
Targeted DNA
QC: PASSED


title: RHC8016

description:
sample 843
mRNA
QC: PASSED


title: DHC303

description:
sample 317
Targeted DNA
QC: PASSED


title: DHC301

description:
sample 315
Targeted DNA
QC: PASSED


title: RHC8021

description:
sample 848
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_181 [GNDX-VJM-VAL181]


title: bladder_cancer_resection_sample_182 [GNDX-VJM-VAL182]


title: RHC8015

description:
sample 842
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_179 [GNDX-VJM-VAL179]


title: bladder_cancer_resection_sample_180 [GNDX-VJM-VAL180]


title: DHC305

description:
sample 319
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_185 [GNDX-VJM-VAL185]


title: bladder_cancer_resection_sample_178 [GNDX-VJM-VAL178]


title: DHC304

description:
sample 318
Targeted DNA
QC: PASSED


title: DHC299

description:
sample 313
Targeted DNA
QC: PASSED


title: RHC8013

description:
sample 840
mRNA
QC: PASSED


title: RHC8014

description:
sample 841
mRNA
QC: PASSED


title: RHC8012

description:
sample 839
mRNA
QC: PASSED


title: DHC298

description:
sample 312
Targeted DNA
QC: PASSED


title: DHC297

description:
sample 311
Targeted DNA
QC: FAILED


title: RHC8017

description:
sample 844
mRNA
QC: PASSED


title: RHC8011

description:
sample 838
mRNA
QC: PASSED


title: RHC8010

description:
sample 837
mRNA
QC: PASSED


title: DHC300

description:
sample 314
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_177 [GNDX-VJM-VAL177]


title: bladder_cancer_resection_sample_176 [GNDX-VJM-VAL176]


title: bladder_cancer_resection_sample_174 [GNDX-VJM-VAL174]


title: DHC295

description:
sample 309
Targeted DNA
QC: PASSED


title: DHC294

description:
sample 308
Targeted DNA
QC: PASSED


title: RHC8008

description:
sample 835
mRNA
QC: PASSED


title: RHC8007

description:
sample 834
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_175 [GNDX-VJM-VAL175]


title: DHC292

description:
sample 306
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_171 [GNDX-VJM-VAL171]


title: DHC293

description:
sample 307
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_170 [GNDX-VJM-VAL170]


title: bladder_cancer_resection_sample_172 [GNDX-VJM-VAL172]


title: RHC8006

description:
sample 833
mRNA
QC: PASSED


title: DHC291

description:
sample 305
Targeted DNA
QC: PASSED


title: RHC8005

description:
sample 832
mRNA
QC: PASSED


title: DHC290

description:
sample 304
Targeted DNA
QC: PASSED


title: DHC296

description:
sample 310
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_169 [GNDX-VJM-VAL169]


title: bladder_cancer_resection_sample_167 [GNDX-VJM-VAL167]


title: bladder_cancer_resection_sample_168 [GNDX-VJM-VAL168]


title: bladder_cancer_resection_sample_173 [GNDX-VJM-VAL173]


title: RHC8004

description:
sample 831
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_166 [GNDX-VJM-VAL166]


title: RHC8009

description:
sample 836
mRNA
QC: PASSED


title: DHC289

description:
sample 303
Targeted DNA
QC: PASSED


title: DHC288

description:
sample 302
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_165 [GNDX-VJM-VAL165]


title: RHC8003

description:
sample 830
mRNA
QC: PASSED


title: DHC287

description:
sample 301
Targeted DNA
QC: PASSED


title: RHC8002

description:
sample 829
mRNA
QC: PASSED


title: RHC8000

description:
sample 827
mRNA
QC: PASSED


title: DHC285

description:
sample 299
Targeted DNA
QC: PASSED


title: RHC7998

description:
sample 825
mRNA
QC: PASSED


title: DHC284

description:
sample 298
Targeted DNA
QC: PASSED


title: DHC286

description:
sample 300
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_164 [GNDX-VJM-VAL164]


title: RHC8001

description:
sample 828
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_163 [GNDX-VJM-VAL163]


title: bladder_cancer_resection_sample_207 [GNDX-VJM-VAL207]


title: DHC283

description:
sample 297
Targeted DNA
QC: PASSED


title: RHC7999

description:
sample 826
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_162 [GNDX-VJM-VAL162]


title: bladder_cancer_resection_sample_208 [GNDX-VJM-VAL208]


title: DHC281

description:
sample 295
Targeted DNA
QC: PASSED


title: DHC282

description:
sample 296
Targeted DNA
QC: PASSED


title: DHC279

description:
sample 293
Targeted DNA
QC: PASSED


title: RHC7993

description:
sample 820
mRNA
QC: PASSED


title: RHC7992

description:
sample 819
mRNA
QC: PASSED


title: DHC277

description:
sample 291
Targeted DNA
QC: PASSED


title: RHC7994

description:
sample 821
mRNA
QC: PASSED


title: RHC7996

description:
sample 823
mRNA
QC: PASSED


title: RHC7995

description:
sample 822
mRNA
QC: PASSED


title: RHC7997

description:
sample 824
mRNA
QC: PASSED


title: DHC278

description:
sample 292
Targeted DNA
QC: PASSED


title: DHC280

description:
sample 294
Targeted DNA
QC: PASSED


title: DHC274

description:
sample 288
Targeted DNA
QC: PASSED


title: RHC7991

description:
sample 818
mRNA
QC: PASSED


title: DHC276

description:
sample 290
Targeted DNA
QC: PASSED


title: RHC7990

description:
sample 817
mRNA
QC: PASSED


title: RHC7989

description:
sample 816
mRNA
QC: PASSED


title: RHC7988

description:
sample 815
mRNA
QC: PASSED


title: DHC273

description:
sample 287
Targeted DNA
QC: PASSED


title: DHC275

description:
sample 289
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_158 [GNDX-VJM-VAL158]


title: bladder_cancer_resection_sample_156 [GNDX-VJM-VAL156]


title: bladder_cancer_resection_sample_157 [GNDX-VJM-VAL157]


title: RHC7987

description:
sample 814
mRNA
QC: PASSED


title: RHC7986

description:
sample 813
mRNA
QC: PASSED


title: DHC271

description:
sample 285
Targeted DNA
QC: FAILED


title: DHC272

description:
sample 286
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_154 [GNDX-VJM-VAL154]


title: bladder_cancer_resection_sample_160 [GNDX-VJM-VAL160]


title: RHC7985

description:
sample 812
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_159 [GNDX-VJM-VAL159]


title: bladder_cancer_resection_sample_152 [GNDX-VJM-VAL152]


title: DHC270

description:
sample 284
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_153 [GNDX-VJM-VAL153]


title: bladder_cancer_resection_sample_151 [GNDX-VJM-VAL151]


title: DHC269

description:
sample 283
Targeted DNA
QC: PASSED


title: DHC268

description:
sample 282
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_149 [GNDX-VJM-VAL149]


title: DHC267

description:
sample 281
Targeted DNA
QC: PASSED


title: RHC7983

description:
sample 810
mRNA
QC: PASSED


title: RHC7982

description:
sample 809
mRNA
QC: PASSED


title: RHC7981

description:
sample 808
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_161 [GNDX-VJM-VAL161]


title: RHC7984

description:
sample 811
mRNA
QC: PASSED


title: RHC7980

description:
sample 807
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_155 [GNDX-VJM-VAL155]


title: DHC266

description:
sample 280
Targeted DNA
QC: PASSED


title: DHC264

description:
sample 278
Targeted DNA
QC: PASSED


title: RHC7978

description:
sample 805
mRNA
QC: PASSED


title: RHC7977

description:
sample 804
mRNA
QC: PASSED


title: DHC263

description:
sample 277
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_147 [GNDX-VJM-VAL147]


title: DHC261

description:
sample 275
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_144 [GNDX-VJM-VAL144]

value: pTa


title: RHC7976

description:
sample 803
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_146 [GNDX-VJM-VAL146]


title: bladder_cancer_resection_sample_150 [GNDX-VJM-VAL150]


title: bladder_cancer_resection_sample_148 [GNDX-VJM-VAL148]


title: DHC265

description:
sample 279
Targeted DNA
QC: PASSED


title: RHC7979

description:
sample 806
mRNA
QC: PASSED


title: DHC260

description:
sample 274
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_145 [GNDX-VJM-VAL145]


title: RHC7973

description:
sample 800
mRNA
QC: PASSED


title: RHC7974

description:
sample 801
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_141 [GNDX-VJM-VAL141]


title: DHC259

description:
sample 273
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_140 [GNDX-VJM-VAL140]


title: DHC262

description:
sample 276
Targeted DNA
QC: PASSED


title: DHC258

description:
sample 272
Targeted DNA
QC: PASSED


title: RHC7975

description:
sample 802
mRNA
QC: PASSED


title: DHC257

description:
sample 271
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_142 [GNDX-VJM-VAL142]


title: RHC7972

description:
sample 799
mRNA
QC: PASSED


title: RHC7971

description:
sample 798
mRNA
QC: PASSED


title: DHC255

description:
sample 269
Targeted DNA
QC: PASSED


title: DHC256

description:
sample 270
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_143 [GNDX-VJM-VAL143]


title: RHC7969

description:
sample 796
mRNA
QC: PASSED


title: RHC7970

description:
sample 797
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_137 [GNDX-VJM-VAL137]


title: bladder_cancer_resection_sample_138 [GNDX-VJM-VAL138]


title: RHC7968

description:
sample 795
mRNA
QC: FAILED


title: RHC7967

description:
sample 794
mRNA
QC: PASSED


title: DHC254

description:
sample 268
Targeted DNA
QC: PASSED


title: DHC252

description:
sample 266
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_139 [GNDX-VJM-VAL139]


title: bladder_cancer_resection_sample_132 [GNDX-VJM-VAL132]


title: RHC7966

description:
sample 793
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_131 [GNDX-VJM-VAL131]


title: bladder_cancer_resection_sample_135 [GNDX-VJM-VAL135]


title: bladder_cancer_resection_sample_134 [GNDX-VJM-VAL134]


title: bladder_cancer_resection_sample_136 [GNDX-VJM-VAL136]


title: bladder_cancer_resection_sample_130 [GNDX-VJM-VAL130]


title: DHC251

description:
sample 265
Targeted DNA
QC: PASSED


title: RHC7410

description:
sample 792
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_129 [GNDX-VJM-VAL129]


title: RHC7409

description:
sample 791
mRNA
QC: PASSED


title: DHC249

description:
sample 263
Targeted DNA
QC: PASSED


title: RHC7408

description:
sample 790
mRNA
QC: PASSED


title: DHC248

description:
sample 262
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_128 [GNDX-VJM-VAL128]


title: bladder_cancer_resection_sample_127 [GNDX-VJM-VAL127]


title: bladder_cancer_resection_sample_126 [GNDX-VJM-VAL126]


title: DHC253

description:
sample 267
Targeted DNA
QC: PASSED


title: RHC7407

description:
sample 789
mRNA
QC: PASSED


title: DHC250

description:
sample 264
Targeted DNA
QC: PASSED


title: RHC7406

description:
sample 788
mRNA
QC: PASSED


title: DHC246

description:
sample 260
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_133 [GNDX-VJM-VAL133]


title: DHC247

description:
sample 261
Targeted DNA
QC: PASSED


title: RHC7405

description:
sample 787
mRNA
QC: PASSED


title: RHC7404

description:
sample 786
mRNA
QC: PASSED


title: RHC7403

description:
sample 785
mRNA
QC: PASSED


title: DHC243

description:
sample 257
Targeted DNA
QC: PASSED


title: RHC7402

description:
sample 784
mRNA
QC: PASSED


title: DHC244

description:
sample 258
Targeted DNA
QC: PASSED


title: DHC245

description:
sample 259
Targeted DNA
QC: PASSED


title: DHC242

description:
sample 256
Targeted DNA
QC: PASSED


title: RHC7401

description:
sample 783
mRNA
QC: PASSED


title: DHC241

description:
sample 255
Targeted DNA
QC: PASSED


title: RHC7400

description:
sample 782
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_123 [GNDX-VJM-VAL123]


title: bladder_cancer_resection_sample_124 [GNDX-VJM-VAL124]


title: bladder_cancer_resection_sample_122 [GNDX-VJM-VAL122]


title: bladder_cancer_resection_sample_120 [GNDX-VJM-VAL120]


title: bladder_cancer_resection_sample_125 [GNDX-VJM-VAL125]


title: RHC7399

description:
sample 781
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_121 [GNDX-VJM-VAL121]


title: bladder_cancer_resection_sample_119 [GNDX-VJM-VAL119]


title: DHC239

description:
sample 253
Targeted DNA
QC: PASSED


title: DHC238

description:
sample 252
Targeted DNA
QC: PASSED


title: RHC7398

description:
sample 780
mRNA
QC: PASSED


title: RHC7397

description:
sample 779
mRNA
QC: PASSED


title: DHC237

description:
sample 251
Targeted DNA
QC: PASSED


title: RHC7395

description:
sample 777
mRNA
QC: PASSED


title: DHC235

description:
sample 249
Targeted DNA
QC: PASSED


title: RHC7396

description:
sample 778
mRNA
QC: PASSED


title: DHC236

description:
sample 250
Targeted DNA
QC: PASSED


title: RHC7394

description:
sample 776
mRNA
QC: PASSED


title: DHC240

description:
sample 254
Targeted DNA
QC: PASSED


title: DHC234

description:
sample 248
Targeted DNA
QC: PASSED


title: RHC7392

description:
sample 774
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_115 [GNDX-VJM-VAL115]


title: RHC7393

description:
sample 775
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_114 [GNDX-VJM-VAL114]


title: bladder_cancer_resection_sample_118 [GNDX-VJM-VAL118]


title: DHC233

description:
sample 247
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_110 [GNDX-VJM-VAL110]


title: bladder_cancer_resection_sample_113 [GNDX-VJM-VAL113]


title: RHC7391

description:
sample 773
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_116 [GNDX-VJM-VAL116]


title: bladder_cancer_resection_sample_111 [GNDX-VJM-VAL111]


title: DHC232

description:
sample 246
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_117 [GNDX-VJM-VAL117]


title: bladder_cancer_resection_sample_109 [GNDX-VJM-VAL109]


title: bladder_cancer_resection_sample_108 [GNDX-VJM-VAL108]


title: DHC231

description:
sample 245
Targeted DNA
QC: PASSED


title: DHC230

description:
sample 244
Targeted DNA
QC: PASSED


title: RHC7390

description:
sample 772
mRNA
QC: FAILED


title: DHC229

description:
sample 243
Targeted DNA
QC: PASSED


title: RHC7389

description:
sample 771
mRNA
QC: PASSED


title: DHC228

description:
sample 242
Targeted DNA
QC: PASSED


title: RHC7387

description:
sample 769
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_112 [GNDX-VJM-VAL112]


title: RHC7386

description:
sample 768
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_107 [GNDX-VJM-VAL107]


title: DHC226

description:
sample 240
Targeted DNA
QC: PASSED


title: RHC7388

description:
sample 770
mRNA
QC: PASSED


title: DHC225

description:
sample 239
Targeted DNA
QC: PASSED


title: RHC7384

description:
sample 766
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_103 [GNDX-VJM-VAL103]


title: RHC7385

description:
sample 767
mRNA
QC: PASSED


title: RHC7383

description:
sample 765
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_106 [GNDX-VJM-VAL106]


title: DHC223

description:
sample 237
Targeted DNA
QC: PASSED


title: DHC224

description:
sample 238
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_105 [GNDX-VJM-VAL105]


title: bladder_cancer_resection_sample_104 [GNDX-VJM-VAL104]


title: DHC222

description:
sample 236
Targeted DNA
QC: PASSED


title: RHC7382

description:
sample 764
mRNA
QC: PASSED


title: DHC221

description:
sample 235
Targeted DNA
QC: PASSED


title: DHC227

description:
sample 241
Targeted DNA
QC: PASSED


title: DHC220

description:
sample 234
Targeted DNA
QC: PASSED


title: RHC7380

description:
sample 762
mRNA
QC: PASSED


title: RHC7381

description:
sample 763
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_101 [GNDX-VJM-VAL101]


title: bladder_cancer_resection_sample_99 [GNDX-VJM-VAL99]


title: bladder_cancer_resection_sample_98 [GNDX-VJM-VAL98]


title: bladder_cancer_resection_sample_97 [GNDX-VJM-VAL97]


title: bladder_cancer_resection_sample_100 [GNDX-VJM-VAL100]


title: bladder_cancer_resection_sample_95 [GNDX-VJM-VAL95]


title: bladder_cancer_resection_sample_96 [GNDX-VJM-VAL96]


title: RHC7379

description:
sample 761
mRNA
QC: PASSED


title: RHC7378

description:
sample 760
mRNA
QC: PASSED


title: DHC217

description:
sample 231
Targeted DNA
QC: PASSED


title: DHC216

description:
sample 230
Targeted DNA
QC: PASSED


title: DHC218

description:
sample 232
Targeted DNA
QC: PASSED


title: RHC7377

description:
sample 759
mRNA
QC: PASSED


title: DHC214

description:
sample 228
Targeted DNA
QC: PASSED


title: DHC219

description:
sample 233
Targeted DNA
QC: PASSED


title: RHC7375

description:
sample 757
mRNA
QC: PASSED


title: RHC7373

description:
sample 755
mRNA
QC: PASSED


title: DHC215

description:
sample 229
Targeted DNA
QC: PASSED


title: RHC7376

description:
sample 758
mRNA
QC: PASSED


title: DHC212

description:
sample 226
Targeted DNA
QC: PASSED


title: RHC7371

description:
sample 753
mRNA
QC: PASSED


title: DHC211

description:
sample 225
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_93 [GNDX-VJM-VAL93]


title: bladder_cancer_resection_sample_91 [GNDX-VJM-VAL91]


title: RHC7374

description:
sample 756
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_89 [GNDX-VJM-VAL89]


title: bladder_cancer_resection_sample_88 [GNDX-VJM-VAL88]


title: RHC7370

description:
sample 752
mRNA
QC: PASSED


title: DHC210

description:
sample 224
Targeted DNA
QC: PASSED


title: DHC209

description:
sample 223
Targeted DNA
QC: PASSED


title: DHC207

description:
sample 221
Targeted DNA
QC: PASSED


title: RHC7372

description:
sample 754
mRNA
QC: PASSED


title: DHC206

description:
sample 220
Targeted DNA
QC: PASSED


title: RHC7365

description:
sample 747
mRNA
QC: PASSED


title: RHC7364

description:
sample 746
mRNA
QC: PASSED


title: DHC208

description:
sample 222
Targeted DNA
QC: PASSED


title: RHC7366

description:
sample 748
mRNA
QC: PASSED


title: RHC7368

description:
sample 750
mRNA
QC: PASSED


title: RHC7363

description:
sample 745
mRNA
QC: PASSED


title: RHC7362

description:
sample 744
mRNA
QC: PASSED


title: DHC204

description:
sample 218
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_87 [GNDX-VJM-VAL87]


title: bladder_cancer_resection_sample_86 [GNDX-VJM-VAL86]


title: bladder_cancer_resection_sample_85 [GNDX-VJM-VAL85]


title: RHC7361

description:
sample 743
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_82 [GNDX-VJM-VAL82]


title: bladder_cancer_resection_sample_81 [GNDX-VJM-VAL81]


title: DHC203

description:
sample 217
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_83 [GNDX-VJM-VAL83]


title: DHC201

description:
sample 215
Targeted DNA
QC: PASSED


title: RHC7359

description:
sample 741
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_84 [GNDX-VJM-VAL84]


title: DHC200

description:
sample 214
Targeted DNA
QC: PASSED


title: RHC7358

description:
sample 740
mRNA
QC: PASSED


title: RHC7357

description:
sample 739
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_79 [GNDX-VJM-VAL79]


title: DHC205

description:
sample 219
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_80 [GNDX-VJM-VAL80]


title: RHC7360

description:
sample 742
mRNA
QC: PASSED


title: DHC198

description:
sample 212
Targeted DNA
QC: PASSED


title: DHC202

description:
sample 216
Targeted DNA
QC: PASSED


title: RHC7356

description:
sample 738
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_78 [GNDX-VJM-VAL78]


title: DHC197

description:
sample 211
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_77 [GNDX-VJM-VAL77]


title: RHC7355

description:
sample 737
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_76 [GNDX-VJM-VAL76]


title: RHC7354

description:
sample 736
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_75 [GNDX-VJM-VAL75]


title: RHC7352

description:
sample 734
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_74 [GNDX-VJM-VAL74]


title: DHC193

description:
sample 207
Targeted DNA
QC: PASSED


title: DHC192

description:
sample 206
Targeted DNA
QC: PASSED


title: DHC199

description:
sample 213
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_102 [GNDX-VJM-VAL102]


title: bladder_cancer_resection_sample_73 [GNDX-VJM-VAL73]


title: RHC7351

description:
sample 733
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_72 [GNDX-VJM-VAL72]


title: RHC7350

description:
sample 732
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_71 [GNDX-VJM-VAL71]


title: DHC190

description:
sample 204
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_69 [GNDX-VJM-VAL69]


title: RHC7349

description:
sample 731
mRNA
QC: PASSED


title: DHC195

description:
sample 209
Targeted DNA
QC: PASSED


title: DHC194

description:
sample 208
Targeted DNA
QC: PASSED


title: RHC7353

description:
sample 735
mRNA
QC: PASSED


title: RHC7348

description:
sample 730
mRNA
QC: PASSED


title: RHC7346

description:
sample 728
mRNA
QC: PASSED


title: RHC7345

description:
sample 727
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_68 [GNDX-VJM-VAL68]


title: bladder_cancer_resection_sample_67 [GNDX-VJM-VAL67]


title: DHC186

description:
sample 200
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_66 [GNDX-VJM-VAL66]


title: DHC185

description:
sample 199
Targeted DNA
QC: PASSED


title: RHC7344

description:
sample 726
mRNA
QC: PASSED


title: RHC7342

description:
sample 724
mRNA
QC: PASSED


title: DHC184

description:
sample 198
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_65 [GNDX-VJM-VAL65]


title: DHC189

description:
sample 203
Targeted DNA
QC: PASSED


title: DHC183

description:
sample 197
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_64 [GNDX-VJM-VAL64]


title: bladder_cancer_resection_sample_63 [GNDX-VJM-VAL63]


title: RHC7340

description:
sample 722
mRNA
QC: PASSED


title: RHC7341

description:
sample 723
mRNA
QC: PASSED


title: DHC188

description:
sample 202
Targeted DNA
QC: PASSED


title: RHC7338

description:
sample 720
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_62 [GNDX-VJM-VAL62]


title: bladder_cancer_resection_sample_70 [GNDX-VJM-VAL70]


title: DHC182

description:
sample 196
Targeted DNA
QC: PASSED


title: DHC181

description:
sample 195
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_61 [GNDX-VJM-VAL61]


title: RHC7337

description:
sample 719
mRNA
QC: PASSED


title: RHC7336

description:
sample 718
mRNA
QC: PASSED


title: DHC180

description:
sample 194
Targeted DNA
QC: PASSED


title: DHC178

description:
sample 192
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_59 [GNDX-VJM-VAL59]


title: RHC7334

description:
sample 716
mRNA
QC: PASSED


title: DHC177

description:
sample 191
Targeted DNA
QC: PASSED


title: DHC176

description:
sample 190
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_58 [GNDX-VJM-VAL58]


title: DHC175

description:
sample 189
Targeted DNA
QC: PASSED


title: DHC213

description:
sample 227
Targeted DNA
QC: PASSED


title: RHC7333

description:
sample 715
mRNA
QC: PASSED


title: RHC7332

description:
sample 714
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_56 [GNDX-VJM-VAL56]


title: RHC7331

description:
sample 713
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_60 [GNDX-VJM-VAL60]


title: DHC174

description:
sample 188
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_55 [GNDX-VJM-VAL55]


title: RHC7330

description:
sample 712
mRNA
QC: PASSED


title: DHC173

description:
sample 187
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_57 [GNDX-VJM-VAL57]


title: DHC171

description:
sample 185
Targeted DNA
QC: PASSED


title: DHC172

description:
sample 186
Targeted DNA
QC: PASSED


title: RHC7329

description:
sample 711
mRNA
QC: PASSED


title: RHC7328

description:
sample 710
mRNA
QC: PASSED


title: DHC170

description:
sample 184
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_54 [GNDX-VJM-VAL54]


title: bladder_cancer_resection_sample_53 [GNDX-VJM-VAL53]


title: DHC191

description:
sample 205
Targeted DNA
QC: PASSED


title: RHC7327

description:
sample 709
mRNA
QC: PASSED


title: RHC7326

description:
sample 708
mRNA
QC: PASSED


title: DHC169

description:
sample 183
Targeted DNA
QC: PASSED


title: RHC7325

description:
sample 707
mRNA
QC: PASSED


title: DHC168

description:
sample 182
Targeted DNA
QC: PASSED


title: DHC167

description:
sample 181
Targeted DNA
QC: PASSED


title: RHC7324

description:
sample 706
mRNA
QC: PASSED


title: DHC166

description:
sample 180
Targeted DNA
QC: PASSED


title: RHC7323

description:
sample 705
mRNA
QC: PASSED


title: RHC7322

description:
sample 704
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_90 [GNDX-VJM-VAL90]


title: RHC7321

description:
sample 703
mRNA
QC: PASSED


title: DHC165

description:
sample 179
Targeted DNA
QC: PASSED


title: DHC164

description:
sample 178
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_92 [GNDX-VJM-VAL92]


title: bladder_cancer_resection_sample_49 [GNDX-VJM-VAL49]


title: DHC162

description:
sample 176
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_52 [GNDX-VJM-VAL52]


title: bladder_cancer_resection_sample_51 [GNDX-VJM-VAL51]


title: RHC7319

description:
sample 701
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_94 [GNDX-VJM-VAL94]


title: bladder_cancer_resection_sample_50 [GNDX-VJM-VAL50]


title: RHC7318

description:
sample 700
mRNA
QC: PASSED


title: DHC161

description:
sample 175
Targeted DNA
QC: PASSED


title: RHC7317

description:
sample 699
mRNA
QC: PASSED


title: DHC160

description:
sample 174
Targeted DNA
QC: PASSED


title: RHC7316

description:
sample 698
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_46 [GNDX-VJM-VAL46]


title: bladder_cancer_resection_sample_44 [GNDX-VJM-VAL44]


title: bladder_cancer_resection_sample_48 [GNDX-VJM-VAL48]


title: RHC7315

description:
sample 697
mRNA
QC: PASSED


title: DHC159

description:
sample 173
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_42 [GNDX-VJM-VAL42]


title: bladder_cancer_resection_sample_40 [GNDX-VJM-VAL40]


title: bladder_cancer_resection_sample_45 [GNDX-VJM-VAL45]


title: bladder_cancer_resection_sample_41 [GNDX-VJM-VAL41]


title: DHC157

description:
sample 171
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_43 [GNDX-VJM-VAL43]


title: bladder_cancer_resection_sample_47 [GNDX-VJM-VAL47]


title: RHC7314

description:
sample 696
mRNA
QC: PASSED


title: RHC7313

description:
sample 695
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_39 [GNDX-VJM-VAL39]


title: DHC155

description:
sample 169
Targeted DNA
QC: PASSED


title: RHC7312

description:
sample 694
mRNA
QC: PASSED


title: DHC154

description:
sample 168
Targeted DNA
QC: PASSED


title: RHC7311

description:
sample 693
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_38 [GNDX-VJM-VAL38]


title: RHC7310

description:
sample 692
mRNA
QC: PASSED


title: DHC152

description:
sample 166
Targeted DNA
QC: PASSED


title: RHC7309

description:
sample 691
mRNA
QC: PASSED


title: DHC151

description:
sample 165
Targeted DNA
QC: PASSED


title: DHC158

description:
sample 172
Targeted DNA
QC: PASSED


title: DHC149

description:
sample 163
Targeted DNA
QC: PASSED


title: RHC7308

description:
sample 690
mRNA
QC: PASSED


title: DHC156

description:
sample 170
Targeted DNA
QC: PASSED


title: RHC7306

description:
sample 688
mRNA
QC: PASSED


title: DHC148

description:
sample 162
Targeted DNA
QC: PASSED


title: DHC150

description:
sample 164
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_34 [GNDX-VJM-VAL34]


title: DHC146

description:
sample 160
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_32 [GNDX-VJM-VAL32]


title: RHC7305

description:
sample 687
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_36 [GNDX-VJM-VAL36]


title: RHC7304

description:
sample 686
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_31 [GNDX-VJM-VAL31]


title: bladder_cancer_resection_sample_37 [GNDX-VJM-VAL37]


title: DHC145

description:
sample 159
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_35 [GNDX-VJM-VAL35]


title: RHC7303

description:
sample 685
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_29 [GNDX-VJM-VAL29]


title: DHC144

description:
sample 158
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_30 [GNDX-VJM-VAL30]


title: RHC7307

description:
sample 689
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_28 [GNDX-VJM-VAL28]


title: bladder_cancer_resection_sample_33 [GNDX-VJM-VAL33]


title: bladder_cancer_resection_sample_27 [GNDX-VJM-VAL27]


title: RHC7302

description:
sample 684
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_26 [GNDX-VJM-VAL26]


title: DHC143

description:
sample 157
Targeted DNA
QC: PASSED


title: RHC7301

description:
sample 683
mRNA
QC: PASSED


title: RHC7300

description:
sample 682
mRNA
QC: PASSED


title: DHC141

description:
sample 155
Targeted DNA
QC: PASSED


title: DHC140

description:
sample 154
Targeted DNA
QC: PASSED


title: DHC137

description:
sample 151
Targeted DNA
QC: PASSED


title: RHC7298

description:
sample 680
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_23 [GNDX-VJM-VAL23]


title: DHC136

description:
sample 150
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_22 [GNDX-VJM-VAL22]


title: bladder_cancer_resection_sample_25 [GNDX-VJM-VAL25]


title: bladder_cancer_resection_sample_24 [GNDX-VJM-VAL24]


title: DHC134

description:
sample 148
Targeted DNA
QC: PASSED


title: DHC133

description:
sample 147
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_21 [GNDX-VJM-VAL21]


title: bladder_cancer_resection_sample_20 [GNDX-VJM-VAL20]


title: RHC7296

description:
sample 678
mRNA
QC: PASSED


title: RHC7294

description:
sample 676
mRNA
QC: PASSED


title: RHC7295

description:
sample 677
mRNA
QC: PASSED


title: RHC7293

description:
sample 675
mRNA
QC: PASSED


title: RHC7299

description:
sample 681
mRNA
QC: PASSED


title: DHC142

description:
sample 156
Targeted DNA
QC: PASSED


title: DHC132

description:
sample 146
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_18 [GNDX-VJM-VAL18]


title: bladder_cancer_resection_sample_19 [GNDX-VJM-VAL19]


title: DHC129

description:
sample 143
Targeted DNA
QC: PASSED


title: RHC7292

description:
sample 674
mRNA
QC: PASSED


title: RHC7291

description:
sample 673
mRNA
QC: PASSED


title: DHC135

description:
sample 149
Targeted DNA
QC: PASSED


title: DHC128

description:
sample 142
Targeted DNA
QC: PASSED


title: DHC127

description:
sample 141
Targeted DNA
QC: PASSED


title: RHC7297

description:
sample 679
mRNA
QC: PASSED


title: DHC126

description:
sample 140
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_15 [GNDX-VJM-VAL15]


title: RHC7288

description:
sample 670
mRNA
QC: PASSED


title: DHC125

description:
sample 139
Targeted DNA
QC: PASSED


title: RHC7287

description:
sample 669
mRNA
QC: PASSED


title: RHC7289

description:
sample 671
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_16 [GNDX-VJM-VAL16]


title: bladder_cancer_resection_sample_17 [GNDX-VJM-VAL17]


title: DHC124

description:
sample 138
Targeted DNA
QC: PASSED


title: DHC122

description:
sample 136
Targeted DNA
QC: PASSED


title: RHC7286

description:
sample 668
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_13 [GNDX-VJM-VAL13]


title: bladder_cancer_resection_sample_14 [GNDX-VJM-VAL14]


title: RHC7290

description:
sample 672
mRNA
QC: PASSED


title: RHC7285

description:
sample 667
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_12 [GNDX-VJM-VAL12]


title: bladder_cancer_resection_sample_10 [GNDX-VJM-VAL10]


title: DHC121

description:
sample 135
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_11 [GNDX-VJM-VAL11]


title: RHC7284

description:
sample 666
mRNA
QC: PASSED


title: DHC120

description:
sample 134
Targeted DNA
QC: PASSED


title: DHC119

description:
sample 133
Targeted DNA
QC: PASSED


title: DHC118

description:
sample 132
Targeted DNA
QC: PASSED


title: RHC7280

description:
sample 662
mRNA
QC: PASSED


title: RHC7281

description:
sample 663
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_8 [GNDX-VJM-VAL8]


title: bladder_cancer_resection_sample_9 [GNDX-VJM-VAL9]


title: DHC117

description:
sample 131
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_7 [GNDX-VJM-VAL7]


title: bladder_cancer_resection_sample_6 [GNDX-VJM-VAL6]


title: DHC116

description:
sample 130
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_5 [GNDX-VJM-VAL5]


title: RHC7278

description:
sample 660
mRNA
QC: PASSED


title: DHC115

description:
sample 129
Targeted DNA
QC: PASSED


title: DHC114

description:
sample 128
Targeted DNA
QC: FAILED


title: RHC7283

description:
sample 665
mRNA
QC: PASSED


title: RHC7320

description:
sample 702
mRNA
QC: PASSED


title: RHC7279

description:
sample 661
mRNA
QC: PASSED


title: DHC163

description:
sample 177
Targeted DNA
QC: PASSED


title: RHC7277

description:
sample 659
mRNA
QC: PASSED


title: RHC7282

description:
sample 664
mRNA
QC: PASSED


title: DHC111

description:
sample 125
Targeted DNA
QC: PASSED


title: RHC7276

description:
sample 658
mRNA
QC: PASSED


title: DHC112

description:
sample 126
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_3 [GNDX-VJM-VAL3]


title: bladder_cancer_resection_sample_2 [GNDX-VJM-VAL2]


title: RHC7275

description:
sample 657
mRNA
QC: PASSED


title: RHC7273

description:
sample 655
mRNA
QC: PASSED


title: AHP137

description:
sample 123
Targeted DNA
QC: PASSED


title: RHC7274

description:
sample 656
mRNA
QC: PASSED


title: AHP136

description:
sample 122
Targeted DNA
QC: PASSED


title: RHC7272

description:
sample 654
mRNA
QC: PASSED


title: bladder_cancer_resection_sample_4 [GNDX-VJM-VAL4]


title: AHP135

description:
sample 121
Targeted DNA
QC: PASSED


title: RHC7271

description:
sample 653
mRNA
QC: PASSED


title: RHC7270

description:
sample 652
mRNA
QC: PASSED


title: AHP134

description:
sample 120
Targeted DNA
QC: PASSED


title: bladder_cancer_resection_sample_1 [GNDX-VJM-VAL1]


title: AHP133

description:
sample 119
Targeted DNA
QC: PASSED


title: RHC7269

description:
sample 651
mRNA
QC: PASSED


title: AHP132

description:
sample 118
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_136 [GNDX-MGH-QCFCG136]

tag: cstage


title: bladder_cancer_turbt_sample_134 [GNDX-MGH-QCFCG134]


title: bladder_cancer_turbt_sample_133 [GNDX-MGH-QCFCG133]


title: bladder_cancer_turbt_sample_135 [GNDX-MGH-QCFCG135]


title: RHC7268

description:
sample 650
mRNA
QC: PASSED

tag: cell line


title: AHP131

description:
sample 117
Targeted DNA
QC: PASSED

tag: cell id


title: DHC110

description:
sample 124
Targeted DNA
QC: PASSED

tag: cell line group


title: bladder_cancer_turbt_sample_132 [GNDX-MGH-QCFCG132]


title: RHC7267

description:
sample 649
mRNA
QC: PASSED

tag: batch


title: RHC7266

description:
sample 648
mRNA
QC: PASSED


title: AHP129

description:
sample 115
Targeted DNA
QC: FAILED


title: AHP130

description:
sample 116
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_129 [GNDX-MGH-QCFCG129]


title: bladder_cancer_turbt_sample_128 [GNDX-MGH-QCFCG128]


title: bladder_cancer_turbt_sample_130 [GNDX-MGH-QCFCG130]


title: bladder_cancer_turbt_sample_131 [GNDX-MGH-QCFCG131]


title: bladder_cancer_turbt_sample_126 [GNDX-MGH-QCFCG126]


title: RHC7265

description:
sample 647
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_127 [GNDX-MGH-QCFCG127]


title: bladder_cancer_turbt_sample_125 [GNDX-MGH-QCFCG125]


title: bladder_cancer_turbt_sample_124 [GNDX-MGH-QCFCG124]


title: AHP128

description:
sample 114
Targeted DNA
QC: PASSED


title: AHP126

description:
sample 112
Targeted DNA
QC: PASSED


title: RHC7264

description:
sample 646
mRNA
QC: PASSED


title: AHP127

description:
sample 113
Targeted DNA
QC: PASSED


title: RHC7263

description:
sample 645
mRNA
QC: PASSED