title: 57C: nephroureterectomy from patient 153

city: Burlington

first: Travis

last: Sullivan

address: 41 Mall Rd.

institute: Lahey Hospital & Medical Center

data_processing:
Non-normalized data are the Cq values computed by the Bio-Rad CFX themal cycler software, no adjustment to baseline backgrounds were made
Each microRNA of interest was normalized to the average Cq of miR-125b-5p and miR-185-5p within each sample.   2^-deltaCq, where deltaCq = (Cq_Target − Cq_miR-125b-5p and miR-185-5p_mean).
Fold change (delta delta Ct) values were not computed for this dataset
Matrix normalized worksheet reports normalized signal (against each samples average for miR-125b-5p and miR-185-5p).

source_name: upper tract urothelial carcinoma

label_protocol: cDNA and RT-PCR were performed using a miRCURY LNA custom PCR panel, currently provided by Qiagen formerly from Exiqon, following the manufacturer's recommendations

extract_protocol: Total RNA was isolated using the Ambion RecoverAll Total Nucleic Acid Isolation Kit for FFPE following the manufacturer's recommendations

tag: tissue preparation

value: FFPE

value: upper tract urothelial carcinoma

tag: grade/ invasive

value: high/ non-invasive


title: Patient_196

status: Public on Jan 01 2019

type: RNA

city: Berlin

first: Henrik

last: Seidel

address: Muellerstr. 178

country: Germany

institute: Bayer AG

data_processing: Normalized continous values were calculated with an in-house developed algorithm for all miRNAs detected in at least 50% of samples, values below detection threshold were imputed. Dichotomized values (1 / 0 for detected / not detected) were calculated for all miRNAs detected in less than 50% of samples.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: plasma

label_protocol: 18 μl of purified total RNA was reverse transcribed in 90-μL-reactions using the Universal cDNA Synthesis Kit II and the UniSP6 spike-in (Exiqon). Conditions for reverse transcription reaction were incubation at 42°C for 60 minutes followed by five minutes at 95°C. The resulting cDNA was subsequently diluted 60 times in the ExiLENT SYBR® Green master mix (Exiqon) and assayed in 10 μL reactions according to the manufacturer's instruction. As inter-plate calibrator we used UniSP3 oligonucleotide. Relative quantitative real-time PCR was performed using the HT7900 (Applied Biosystems). RT-PCR conditions were incubation at 95°C for 10 minutes followed by 45 cycles of 95°C for 10 seconds and 60°C for one minute.

extract_protocol: RNA was isolated from plasma using the mirCury RNA isolation kit (Exiqon)

treatment_protocol: untreated (baseline expression)

tag: arm

value: Placebo

tag: os

tag: ttp

tag: batch

tag: unisp2 outlier

value: FALSE

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status

value: good


title: pTpA_1E8_YPGal_R2

type: SRA

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

country: USA

institute: The Broad Institute

description: 20161024_average_promoter_ELs_per_seq_3p1E7_Gal_ALL.shuffled.txt.gz

library_source: genomic

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints.
Promoters were aligned to themselves using Bowtie2 (72) to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP).  Note that Abf1TATA sorting bin 16 (R4) was accidentally pooled with part of bin 11 (R9) and so was left out of all analyses and the processed data.
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Random promoter library

growth_protocol: Libraries were transformed into yeast (strain Y8205) using the lithium acetate method, starting with 1L of yeast harvested at an OD of 0.3-0.4 , ensuring a complexity of at least 1E8 was achieved (with the exception of the high-quality pTpA library where a dilution series was performed to achieve the desired complexity). The yeast were then grown in SD-Ura for two days, diluting the media by 1:4 three times during this period.  Media was then changed to YPD, growing for at least 5 generations prior to cell sorting. For YPGly and YPGal experiments, the same pTpA transformation was used and the culture was grown for at least 8 generations (due to the change in carbon source). In the final 10 hours of growth prior to cell sorting, the cultures were allowed to grow continuously in log phase, never achieving an OD above 0.6, by diluting in fresh media.  All cultures were grown in a shaker incubator, at 30C and approximately 250 RPM.

extract_protocol:
Plasmids were isolated using Qiagen spin miniprep kits, as adapted for yeast according to the manufacturer's website. Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins, done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura (supplemented with 1% Gal for Gal sort) and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center.

treatment_protocol: Prior to sort, yeast were spun down, washed once in ice-cold PBS, and then suspended in ice-cold PBS and kept on ice until cell sorting.

tag: media

value: YPGal

tag: libraryid


title: 56C: nephroureterectomy from patient 152

tag: tissue


title: pTpA_1E8_YPGal_R19


title: 13: NAC NSC

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Basecalls performed using BaseCall  version 1.1.2
Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read) are discarded and then mapped to mm10 whole genome using HISAT2 v2.0.4 with parameters:  --phred64 --sensitive --no-discordant --no-mixed -I  1 -X 1000, mapped to gene reference using Bowtie2 v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
Screening DEGs using EBSeq,we defined a gene as a DEG (differentially expressed gene) when foldchange ≥2 and PPEE ≤ 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files include FPKM values for each Sample.

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol: N2 media with EGF and bFGF

extract_protocol:
TRIZOL
1) Total RNA treatment  a) RNase H Probe (rRNA depletion): Hybridize the rRNA with DNA probe and digest the DNA/RNA  hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after  purification.  b) Oligo dT Selection (mRNA enrichment): Use oligo dT beads to select mRNA with poly A tail.  2) RNA fragment and reverse transcription  Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer.  3) End repair and adaptor ligation  End repair the dscDNA to blunt end and phosphate at 5’ end, 3’ end forms an “A” cohesive end. And  then ligate to the bubble adapter with protruding T of 3’ end.  4) PCR amplification  5) Single strand separation and cyclization  Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA  ligase.  6)DNA nanoball making7) Sequencing on BGISEQ-500 platform

treatment_protocol: 48 hrs with PQ or NAC

value: Neural progenitor cells


title: Patient_195

value: Regorafenib 160 mg


title: bladder_cancer_RC_sample_133

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)
HuEx-1_0-st-v2.r2.pgf
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

growth_protocol: Not Applicable

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)

treatment_protocol: Not Applicable

tag: pstage

tag: gender

value: Female

tag: cluster

value: bladder cancer RC sample


title: bladder_cancer_RC_sample_132

value: Male


title: 54C: nephroureterectomy from patient 151

tag: tissue preparation

tag: grade/ invasive

value: low/ non-invasive


title: 52C: nephroureterectomy from patient 150


title: pTpA_1E8_YPGal_R18


title: 5: con-H3K4m3

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the mm10 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Genome_build: mm10
Supplementary_files_format_and_content: Bw files were transformed from wig files generated using macs2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
a) End repair, Adaptor ligation: The ends of the IP / Input DNA are complemented and phosphorylated at the 5 'end, the 3' end is protruded a
sticky end of "A" and then a bubbly joint with a "T" protruding at the 3 'end.
b) PCR amplification: The ligation product is subjected to PCR amplification by specific primers.
c) Single chain separation and cyclization: PCR products are heat-denatured into single-stranded, and then single-stranded DNA is cyclized with a bridge
primer to obtain a single-stranded circular DNA library.
d) Sequencing: Sequencing is performed using the resulting amplified product DNA Nano balls (DNB).

value: adult neural progenitor cells


title: pTpA_1E8_YPGal_R17


title: 50C: nephroureterectomy from patient 149


title: pTpA_1E8_YPGal_R16


title: Patient_201

tag: arm

tag: os


title: pTpA_1E8_YPGal_R15


title: primary melanocyte C202_1

type: genomic

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

description: Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-24-v1-1_a Genotyping BeadChips (Illumina)

hyb_protocol: Resuspended samples are denatured, then hybridized to locus-specific 50-mer oligonucleotides which are attached to 1-micron beads on the BeadChip.  These 50-mer probes stop one base before the location of interest.  Enzymatic single-base extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates tagged nucleotides on the BeadChip, which are subsequently fluorophore-labeled during staining. The fluorescent label determines the genotype call for the sample.

scan_protocol: The Illumina iScan scans the BeadChips at two wavelengths to detect the fluorescent label, creating image files that are converted into genotype calls based on the detected fluorescence.

data_processing: Genomic DNA extracted from primary melanocytes was genotyped using Illumina Infinium human OmniExpress array

label: C-Bio and A-DNP

source_name: primary melanocyte

label_protocol: 200ng of genomic DNA, quantitated using Quant-iT™ PicoGreen dsDNA Reagent (ThermoFisher Scientific, Waltham, MA, USA) is denatured and neutralized, then isothermally amplified by whole-genome amplification.  The amplified product is enzymatically fragmented, then precipitated and re-suspended.

growth_protocol: Primary melanocyte cultures were grown in Dermal Cell Basal Medium (ATCC® PCS-200-030™) supplemented with Melanocyte Growth Kit (ATCC® PCS-200-041™) and 1% Amphotericin B/Penicillin/Streptomycin (120-096-711, Quality Biological) at 37°C with 5% CO2, and trypsinized with Trypsin/EDTA Solution (R-001-100, Cascade Biologics) as well as Trypsin Neutralizer Solution (R-002-100, Cascade Biologics). Media was changed every 2-3 days when necessary.

extract_protocol: Genomic DNA was isolated from primary melanocyte cultrue using Gentra Puregene Cell Kit (158745, Qiagen)

tag: disease

value: Melanocyte

value: SKin


title: 49C: nephroureterectomy from patient 148


title: 48C: nephroureterectomy from patient 147


title: 45C: nephroureterectomy from patient 146


title: pTpA_1E8_YPGal_R14


title: pTpA_1E8_YPGal_R13


title: Patient_194

tag: ttp

tag: batch

tag: unisp2 outlier


title: Patient_193

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Patient_192

tag: dct hemo

tag: hemo status


title: primary melanocyte C236_1

tag: tissue


title: Patient_190

value: bad


title: Patient_189


title: Patient_191


title: 41C: nephroureterectomy from patient 145

value: FFPE


title: pTpA_1E8_YPGal_R12

tag: media

tag: libraryid


title: 40C: nephroureterectomy from patient 144

value: upper tract urothelial carcinoma


title: pTpA_1E8_YPGal_R11


title: Patient_187


title: 39C: nephroureterectomy from patient 143


title: bladder_cancer_RC_sample_128

tag: pstage

tag: gender

tag: cluster


title: 38C: nephroureterectomy from patient 142

tag: tissue preparation

tag: grade/ invasive

value: high/ non-invasive


title: bladder_cancer_RC_sample_126


title: pTpA_1E8_YPD_R9

description: 20160609_average_promoter_ELs_per_seq_pTpA_ALL.shuffled.txt.gz

value: YPD


title: 36C: nephroureterectomy from patient 141


title: bladder_cancer_RC_sample_125


title: Patient_186

tag: arm

tag: os

value: FALSE


title: bladder_cancer_RC_sample_127


title: Patient_188

tag: ttp

tag: batch


title: Patient_185

value: Placebo

tag: unisp2 outlier

tag: unisp4 outlier


title: primary melanocyte C104_1

tag: disease


title: bladder_cancer_RC_sample_130


title: Patient_184

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo


title: primary melanocyte C72_1

tag: tissue


title: primary melanocyte C171_1


title: primary melanocyte C10_1


title: pTpA_1E8_YPD_R8

tag: media

tag: libraryid


title: bladder_cancer_RC_sample_123

tag: pstage

tag: gender


title: bladder_cancer_RC_sample_129

tag: cluster


title: bladder_cancer_RC_sample_122


title: bladder_cancer_RC_sample_131


title: 35C: nephroureterectomy from patient 140

tag: tissue preparation

tag: grade/ invasive


title: bladder_cancer_RC_sample_124


title: Patient_183

tag: arm

tag: os

tag: hemo status

value: good


title: pTpA_1E8_YPD_R7


title: 31C: nephroureterectomy from patient 139


title: primary melanocyte C56_1


title: bladder_cancer_RC_sample_121


title: pTpA_1E8_YPD_R6


title: 24C: nephroureterectomy from patient 135


title: pTpA_1E8_YPD_R4


title: 26C: nephroureterectomy from patient 137


title: pTpA_1E8_YPD_R5


title: Patient_182

tag: ttp

tag: batch

tag: unisp2 outlier


title: pTpA_1E8_YPD_R3


title: bladder_cancer_RC_sample_120


title: pTpA_1E8_YPD_R2


title: primary melanocyte C201_1

tag: disease


title: bladder_cancer_RC_sample_119


title: 27C: nephroureterectomy from patient 138


title: Patient_180

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Patient_181

tag: dct hemo


title: 23C: nephroureterectomy from patient 134

tag: tissue


title: 25C: nephroureterectomy from patient 136


title: Patient_179


title: primary melanocyte C136_1


title: Patient_178


title: pTpA_1E8_YPD_R19

tag: media

tag: libraryid


title: 22C: nephroureterectomy from patient 133


title: Patient_177


title: 20C: nephroureterectomy from patient 132


title: 19C: nephroureterectomy from patient 131


title: bladder_cancer_RC_sample_118

tag: pstage

tag: gender

tag: cluster


title: Patient_176

tag: arm


title: bladder_cancer_RC_sample_117


title: pTpA_1E8_YPD_R16


title: pTpA_1E8_YPD_R17


title: Patient_175

tag: os


title: bladder_cancer_RC_sample_115


title: 18C: nephroureterectomy from patient 130

tag: tissue preparation

tag: grade/ invasive


title: bladder_cancer_RC_sample_116


title: Patient_174

tag: ttp

tag: batch

tag: hemo status


title: 14C: nephroureterectomy from patient 129


title: 13C: nephroureterectomy from patient 128


title: Patient_173

tag: unisp2 outlier

tag: unisp4 outlier


title: pTpA_1E8_YPD_R13


title: pTpA_1E8_YPD_R18


title: pTpA_1E8_YPD_R14


title: pTpA_1E8_YPGal_R10

value: YPGal


title: Patient_171

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Patient_172

value: Regorafenib 160 mg

tag: dct hemo


title: 12C: nephroureterectomy from patient 127

tag: tissue


title: pTpA_1E8_YPD_R15

tag: media

tag: libraryid


title: pTpA_1E8_YPD_R12


title: bladder_cancer_RC_sample_111

tag: pstage

tag: gender


title: 10C: nephroureterectomy from patient 125


title: bladder_cancer_RC_sample_112

tag: cluster


title: bladder_cancer_RC_sample_113

value: Female


title: pTpA_1E8_YPD_R11


title: bladder_cancer_RC_sample_114

value: bladder cancer RC sample


title: pTpA_1E8_YPD_R10


title: bladder_cancer_RC_sample_109

value: Male


title: bladder_cancer_RC_sample_108


title: bladder_cancer_RC_sample_110


title: 9C: nephroureterectomy from patient 124


title: Patient_168

tag: arm

tag: os


title: Patient_169


title: 7C: nephroureterectomy from patient 123

tag: tissue preparation

tag: grade/ invasive

value: low/ non-invasive


title: Abf1TATA_1E8_YPD_R9

description: 20160609_average_promoter_ELs_per_seq_Abf1TATA_ALL.shuffled.txt.gz


title: bladder_cancer_RC_sample_106


title: bladder_cancer_RC_sample_107


title: 11C: nephroureterectomy from patient 126


title: Patient_167

tag: ttp

tag: batch


title: Patient_166

tag: unisp2 outlier

tag: hemo status

value: medium


title: Patient_170

tag: unisp4 outlier

tag: unisp6 outlier


title: Patient_165

tag: cel-mir-39-3p outlier

tag: dct hemo


title: Abf1TATA_1E8_YPD_R7

tag: media


title: 5C: nephroureterectomy from patient 121

tag: tissue


title: 4C: nephroureterectomy from patient 120


title: Abf1TATA_1E8_YPD_R6

tag: libraryid


title: Abf1TATA_1E8_YPD_R5


title: bladder_cancer_RC_sample_105

tag: pstage

tag: gender


title: bladder_cancer_RC_sample_103

tag: cluster


title: bladder_cancer_RC_sample_104


title: Patient_164

tag: arm

tag: os


title: bladder_cancer_RC_sample_102


title: Patient_163


title: Abf1TATA_1E8_YPD_R8


title: 2C: nephroureterectomy from patient 118

tag: tissue preparation

tag: grade/ invasive


title: Patient_161

tag: ttp

tag: batch


title: 6C: nephroureterectomy from patient 122


title: 1C: nephroureterectomy from patient 117


title: Abf1TATA_1E8_YPD_R3


title: Abf1TATA_1E8_YPD_R2


title: 133B: nephroureterectomy from patient 116


title: 3C: nephroureterectomy from patient 119


title: 131B: nephroureterectomy from patient 115


title: Patient_159

tag: unisp2 outlier

tag: hemo status


title: 129B: nephroureterectomy from patient 114


title: Abf1TATA_1E8_YPD_R4


title: Abf1TATA_1E8_YPD_R19


title: Patient_158

tag: unisp4 outlier

tag: unisp6 outlier


title: Patient_160

tag: cel-mir-39-3p outlier

tag: dct hemo


title: bladder_cancer_RC_sample_100

tag: tissue


title: Patient_162


title: bladder_cancer_RC_sample_99


title: Abf1TATA_1E8_YPD_R17

tag: media

tag: libraryid


title: Abf1TATA_1E8_YPD_R18


title: 127B: nephroureterectomy from patient 113


title: bladder_cancer_RC_sample_97

tag: pstage

tag: gender


title: bladder_cancer_RC_sample_101

tag: cluster


title: bladder_cancer_RC_sample_96


title: Patient_156

tag: arm

tag: os


title: bladder_cancer_RC_sample_95


title: 123B: nephroureterectomy from patient 112

tag: tissue preparation

tag: grade/ invasive


title: Abf1TATA_1E8_YPD_R16


title: Abf1TATA_1E8_YPD_R15


title: bladder_cancer_RC_sample_98


title: Patient_155

tag: ttp

tag: batch


title: Patient_157

tag: unisp2 outlier

tag: hemo status


title: 121B: nephroureterectomy from patient 111


title: Abf1TATA_1E8_YPD_R14


title: 116B: nephroureterectomy from patient 110


title: Patient_154

tag: unisp4 outlier

tag: unisp6 outlier


title: Abf1TATA_1E8_YPD_R13


title: Abf1TATA_1E8_YPD_R12


title: 102B: nephroureterectomy from patient 108


title: 101B: nephroureterectomy from patient 107


title: Abf1TATA_1E8_YPD_R11


title: Patient_153

tag: cel-mir-39-3p outlier

tag: dct hemo


title: Patient_152


title: Abf1TATA_1E8_YPD_R10

tag: media


title: Patient_150


title: Patient_149


title: 98B: nephroureterectomy from patient 105

tag: tissue


title: Patient_148


title: S32

city: New York

first: Weijia

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10

source_name: flow sorted donor CXCR5+PD1hi CD4 cells from spleens of F1 mice day 7

extract_protocol:
RNAEasy kit
Single-end sequencing at 51bp read length was performed on a HiSeq 4000 (Illumina, San Diego CA)
standard mRNA library

tag: cell type

value: CD4 TFH

tag: group

value: C5aR TFH T cells from F1

tag: genotype/variation


title: S31


title: 105B: nephroureterectomy from patient 109


title: 95B: nephroureterectomy from patient 104


title: S34

value: WT TFH T cells from F1

value: WT


title: bladder_cancer_RC_sample_94

tag: pstage

tag: gender

tag: cluster


title: bladder_cancer_RC_sample_93


title: bladder_cancer_RC_sample_91


title: 92B: nephroureterectomy from patient 103

tag: tissue preparation

value: FFPE

value: upper tract urothelial carcinoma

tag: grade/ invasive


title: bladder_cancer_RC_sample_92


title: bladder_cancer_RC_sample_90


title: Patient_147

tag: arm

tag: os

tag: ttp

tag: batch


title: S33


title: bladder_cancer_RC_sample_89


title: bladder_cancer_RC_sample_87


title: 100B: nephroureterectomy from patient 106


title: bladder_cancer_RC_sample_86


title: Patient_151

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier

tag: hemo status


title: bladder_cancer_RC_sample_84

tag: tissue


title: 91B: nephroureterectomy from patient 102


title: bladder_cancer_RC_sample_88


title: S38

source_name: flow sorted naïve CD62Lhi CD44 lo CD4 T cells

tag: cell type

value: naive CD4 T cells

value: Naive_WT CD4 T cells


title: Patient_145

value: Placebo

value: FALSE

tag: cel-mir-39-3p outlier

tag: dct hemo


title: S37

tag: group

tag: genotype/variation


title: Patient_146

value: good


title: 90B: nephroureterectomy from patient 101


title: Patient_144


title: S36

value: Naive_C5aR CD4 T cells


title: bladder_cancer_RC_sample_85

tag: pstage

tag: gender

tag: cluster


title: 87B: nephroureterectomy from patient 99

tag: tissue preparation

tag: grade/ invasive

value: high/ non-invasive


title: 76B: nephroureterectomy from patient 98


title: S35


title: 71B: nephroureterectomy from patient 97


title: Patient_142

tag: arm

value: Regorafenib 160 mg

tag: os

tag: ttp


title: 70B: nephroureterectomy from patient 96


title: 68B: nephroureterectomy from patient 95


title: bladder_cancer_RC_sample_83

value: Male

value: bladder cancer RC sample


title: Patient_141

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: 88B: nephroureterectomy from patient 100

tag: tissue

value: low/ non-invasive


title: Patient_140

tag: unisp6 outlier

tag: hemo status


title: 66B: nephroureterectomy from patient 94


title: bladder_cancer_RC_sample_82

value: Female


title: Patient_138

tag: cel-mir-39-3p outlier

tag: dct hemo


title: Patient_139

value: medium


title: Patient_143


title: Patient_137


title: 65B: nephroureterectomy from patient 93


title: bladder_cancer_RC_sample_81


title: Patient_136


title: bladder_cancer_RC_sample_79


title: 58B: nephroureterectomy from patient 92


title: bladder_cancer_RC_sample_80


title: 56B: nephroureterectomy from patient 91


title: 55B: nephroureterectomy from patient 90


title: Patient_134


title: Patient_135


title: bladder_cancer_RC_sample_76


title: bladder_cancer_RC_sample_74


title: bladder_cancer_RC_sample_78


title: bladder_cancer_RC_sample_75


title: bladder_cancer_RC_sample_73


title: bladder_cancer_RC_sample_77


title: Patient_133


title: 50B: nephroureterectomy from patient 89


title: 46B: nephroureterectomy from patient 88


title: bladder_cancer_RC_sample_72


title: RNA-seq_Liver_cisplatin_1

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
reads were aligned using STAR
filtering step to remove: (i) reads with mapping quality less than 20, (ii) read pairs with unexpected orientations and greater than 500Kb mapping distance between the read pair, and (iii) reads that are mapped to greater than 10 positions in the genome
Read counts for each gene were obtained using FeatureCounts
DESeq2 was used for differential expression analysis
Batch effect is adjusted using ComBat with batch as a known covariate
genome_build: mm10
Supplementary_files_format_and_content: text file including gene list with read counts

source_name: Liver

growth_protocol: Six or seven-month-old wild-type (C57BL/6J) female mice weighing around 25-28 g were purchased from Jackson Laboratory (Bar Harbor, ME).  Without further indications, mice are kept under a 12-h light/12-h dark regimen.

extract_protocol:
Total RNA was extracted from mouse kidney, liver, lung and spleen using TRIzol RNA extraction (Thermo Fisher Scientific).  After phase separation, RNA was purified using the PureLink RNA Mini Kit (Thermo Fisher Scientific).  Purified total RNA sample was treated with DNase I (TURBO DNA-freeTM kit, Ambion Inc.) to remove traces of DNA.  RNA library was prepared using NEBNext Ultra RNA library prep kit (Illumina) according to manufacturer’s instruction.
Total RNA starting with 1ug was poly-A selected, fragmented by random priming and then converted to cDNA using ProtoScript II reverse transcriptase.  The cDNA was then end-repaired, adenylated and ligated with Illumina sequencing adaptors.  Libraries from all samples were pooled and sequenced using an Illumina HiSeq 4000 with 50-bp pair-end read.

treatment_protocol: All mice were treated with drug at ZT1 (8 am) and sacrificed at ZT5 (12 pm).  Single dose of clinical cisplatin (1mg/ml or 3.3 mM/L, Fresenius Kabi Pharceutical company) was administered by intraperitoneal injection at 10 mg cis-DDP/Kg body weight.  Same volume of saline solution (154 mM) was administered by intraperitoneal injection to control group mouse.

tag: strain

tag: Sex

value: female

value: Liver

tag: cisplatin

value: Yes

tag: time after treatment


title: 45B: nephroureterectomy from patient 87

tag: tissue preparation

value: FFPE

value: upper tract urothelial carcinoma


title: RNA-seq_Liver_control_2

value: No


title: Patient_132

value: Placebo


title: Patient_130

value: FALSE


title: Patient_131

value: good


title: RNA-seq_Liver_cisplatin_2


title: RNA-seq_Liver_control_1


title: 43B: nephroureterectomy from patient 86

tag: grade/ invasive


title: bladder_cancer_RC_sample_71

tag: pstage

tag: gender

tag: cluster


title: bladder_cancer_RC_sample_70


title: RNA-seq_Kidney_cisplatin_2

source_name: Kidney

value: Kidney


title: 42B: nephroureterectomy from patient 85


title: 38B: nephroureterectomy from patient 84


title: Patient_128

tag: arm

tag: os

tag: ttp

tag: batch


title: Patient_129

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier


title: RNA-seq_Kidney_cisplatin_1

tag: tissue


title: RNA-seq_Kidney_control_2

tag: strain


title: bladder_cancer_RC_sample_69


title: 36B: nephroureterectomy from patient 83


title: Patient_127

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status


title: bladder_cancer_RC_sample_66


title: bladder_cancer_RC_sample_65


title: Patient_126


title: RNA-seq_Kidney_control_1

tag: Sex

tag: cisplatin

tag: time after treatment


title: 34B: nephroureterectomy from patient 82

tag: tissue preparation

tag: grade/ invasive

value: high/ non-invasive


title: bladder_cancer_RC_sample_67

tag: pstage

tag: gender

tag: cluster


title: 32B: nephroureterectomy from patient 81


title: 21B: nephroureterectomy from patient 80


title: bladder_cancer_RC_sample_68


title: XR-seq_Spleen_1

data_processing:
Library strategy: XR-seq
cutadapt is used to trim reads with adaptor sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG at the 3’ end and discard untrimmed reads
BWA is used for read alignment
Picard tools (http://broadinstitute.github.io/picard/) is used for filtering, sorting, deduplication, and indexing
Post-alignment filtering steps were adopted using Rsamtools
We keep reads that (i) have mapping quality greater than 20, (ii) are of length 21bp to 31bp, and (iii) have GG dinucleotide sequence 5-8 bp upstream from the 3’ end of the reads
Reads from the TS and NTS strands are separated using known gene annotations for mm10 by Ensembl
genome_build: mm10
Supplementary_files_format_and_content: text file including gene list with read counts

source_name: Spleen

extract_protocol:
 Genomic DNA were extracted using PurLink Genomic DNA kit (Thermo).  Four hours after injecting cisplatin or saline solution (control group), the mice were sacrificed by carbon dioxide exposure, the kidneys, liver, lung and spleen were removed and washed extensively with cold phosphate buffered saline (PBS), and then homogenized them.  The chromatin fraction was then pelleted.  The supernatants (containing low molecular DNA-protein fragments) were harvested and immunoprecipitated (IP) with anti-TFIIH (p89 antibody (G-10), and p62 antibody (H-10), Santa-Cruz Biotechnology).  The eluted DNA were isolated using phenol-chloroform and ethanol precipitation.
The low-molecular excision products were immunoprecipitated with anti-TFIIH (p89 antibody and p62 antibody), and ligated to adaptors on the both ends.  After second round immunoprecipitated with cisplatin-specific anti-body, the Pt-DNA adducts were reversed by incubating in NaCN (200 mM) over-night.  Then the damage free DNAs were amplified by PCR to get XR-seq libraries and sequenced using an Illumina HiSeq 4000 with 50-bp single-end read.

value: Spleen


title: XR-seq_Lung_2

source_name: Lung

value: Lung


title: bladder_cancer_RC_sample_64

value: bladder cancer RC sample


title: Patient_124

tag: arm

value: Regorafenib 160 mg

tag: os

tag: ttp

tag: batch


title: Patient_123

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier


title: Patient_125

tag: cel-mir-39-3p outlier

tag: dct hemo


title: Patient_122

tag: hemo status


title: 14B: nephroureterectomy from patient 78

tag: tissue


title: XR-seq_Lung_1

tag: strain

tag: Sex

tag: cisplatin

tag: time after treatment


title: 13B: nephroureterectomy from patient 77

tag: tissue preparation

tag: grade/ invasive


title: XR-seq_Liver_2


title: 10B: nephroureterectomy from patient 76

value: low/ non-invasive


title: Patient_120

tag: arm


title: XR-seq_Liver_1


title: XR-seq_Kidney_2


title: 9B: nephroureterectomy from patient 75


title: XR-seq_Kidney_1


title: Patient_119

tag: os


title: 19B: nephroureterectomy from patient 79


title: Damage-seq_Spleen_2

data_processing:
Library strategy: DNA-seq
cutadapt was used to remove reads with adaptor sequence GACTGGTTCCAATTGAAAGTGCTCTTCCGATCT at the 5’ end
BWA is used for read alignment
Picard tools (http://broadinstitute.github.io/picard/) is used for filtering, sorting, deduplication, and indexing
Post-alignment filtering steps were adopted using Rsamtools
we only keep reads that (i) have mapping quality greater than 20, (ii) have GG dinucleotide sequencing 1-2 bp upstream from the 5’ end of the reads
Reads from the TS and NTS strands are separated using known gene annotations for mm10 by Ensembl
genome_build: mm10
Supplementary_files_format_and_content: text file including gene list with read counts

extract_protocol:
 Genomic DNA were extracted using PurLink Genomic DNA kit (Thermo).
Purified DNA (~1 µg) were used for End-repair and dA-tailing and adaptor ligation (NEBNext Ultra II DNA Library Prep Kit) following manufacture’s instruction.  The DNA was then processed second adaptor ligation.   After quality check, the DNA samples were purified with HighPrep PCR beads, and ligated DNA were PCR amplified by NEBNext Ultra II PCR Master Mix with NEBNext Multiplex Oligos for Illumina (New England Biolabs).  The PCR libraries were purified with HighPrep PCR beads.  Libraries from all samples were pooled and sequenced using an Illumina HiSeq 4000 with 50-bp single-end read.


title: bladder_cancer_RC_sample_60

tag: pstage

tag: gender

value: Male

tag: cluster


title: 53C: nephroureterectomy from patient 74

value: high/ invasive


title: Damage-seq_Spleen_1

value: female


title: bladder_cancer_RC_sample_61


title: bladder_cancer_RC_sample_62


title: bladder_cancer_RC_sample_56


title: bladder_cancer_RC_sample_59


title: bladder_cancer_RC_sample_63


title: Patient_121

tag: ttp

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: 51C: nephroureterectomy from patient 73


title: bladder_cancer_RC_sample_54


title: Patient_116

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status


title: Patient_117


title: Patient_118


title: bladder_cancer_RC_sample_58

tag: tissue


title: bladder_cancer_RC_sample_57


title: 46C: nephroureterectomy from patient 72


title: 44C: nephroureterectomy from patient 71


title: Damage-seq_Lung_2

tag: strain

tag: Sex

tag: cisplatin

value: Yes

tag: time after treatment


title: Patient_115

tag: arm

tag: os


title: XR-seq_Spleen_2


title: Damage-seq_Lung_1


title: 43C: nephroureterectomy from patient 70

tag: tissue preparation

value: FFPE

tag: grade/ invasive


title: bladder_cancer_RC_sample_53

tag: pstage

tag: gender

tag: cluster


title: Patient_114

tag: ttp

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: Damage-seq_Liver_2

value: Liver


title: Patient_113

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status

value: medium


title: 42C: nephroureterectomy from patient 69

tag: tissue

value: upper tract urothelial carcinoma


title: Damage-seq_Liver_1

tag: strain

tag: Sex

tag: cisplatin

tag: time after treatment


title: Damage-seq_Kidney_1


title: Damage-seq_Kidney_2


title: bladder_cancer_RC_sample_52

value: Female


title: 34C: nephroureterectomy from patient 67

tag: tissue preparation

tag: grade/ invasive


title: 37C: nephroureterectomy from patient 68

value: low/ invasive


title: 33C: nephroureterectomy from patient 66


title: Patient_112

tag: arm

value: Placebo

tag: os

value: FALSE

value: good


title: Patient_110

tag: ttp


title: PD-15

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.0.14 with default parameters
Reads per gene were counted with HT-Seq/0.6.1
Read counts were normalized with R package DESeq2
Supplementary_files_format_and_content: raw counts of sequencing reads for the  genes

source_name: stomach-corpus epithelial cells

growth_protocol: The villin-PPARD and their WT littermates at ages 10,25 and 55 weeks were killed and the the stomachs were opened and the epithenial cells were manually scraped from the mouse gastric corpuses and then stored in Trizol at -80C freezer till further analysis

extract_protocol:
The scraped gastric corpus epithenial cells from the villin-PPARD and their WT lilletermates at ages 10,25, and 55 weeks were harvested and total RNAs were extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 500ng of total RNA for the construction of sequencing libraries.
Illumina-compatible mRNA libraries were constructed using the TruSeq RNA sample prep kit v2 (Illumina, Inc). Five hundred nanograms of total RNA were enriched for Poly-A mRNA using Oligo-dT magnetic beads. The resulting Poly-A mRNA was fragmented to a median size of 150 bp using divalent cations. Randomly primed first- and second-strand synthesis was then performed to create double-stranded cDNA. The ends of the double-stranded cDNA fragments were repaired, 5′-phosphorylated, and 3′-A tailed, and then the Illumina-specific Y-shaped indexed adapters were ligated. The adaptor-ligated fragments were then purified and enriched by 7 cycles of PCR amplification. The amplified library was then quantified by quantitative PCR using a library quantification kit (KAPA Biosystems) and assessed for size distribution using the Bioanalyzer system (Agilent Technologies). Eight libraries were multiplexed and sequenced on an Illumina HiSeq4000 instrument using the 75-bp paired-end format. After sequencing, BCL files were converted into “.fastq.gz” files, and individual sample libraries were de-multiplexed using CASAVA 1.8.2 with no mismatches.

tag: cell type

value: stomach-corpus epithelial cells

tag: genotype

value: villin-PPARD

tag: age

value: 10 weeks


title: 32C: nephroureterectomy from patient 65


title: 30C: nephroureterectomy from patient 64


title: bladder_cancer_RC_sample_55

tag: pstage

tag: gender

tag: cluster

value: bladder cancer RC sample


title: PD-14


title: Patient_108

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status


title: bladder_cancer_RC_sample_51

tag: tissue


title: Patient_109

tag: arm

value: Regorafenib 160 mg


title: Neg-15

value: WT


title: Patient_107

tag: os


title: 29C: nephroureterectomy from patient 63

tag: tissue preparation

tag: grade/ invasive

value: high/ invasive


title: Patient_106

tag: ttp

value: bad


title: Patient_111


title: 28C: nephroureterectomy from patient 62

value: FFPE


title: bladder_cancer_RC_sample_50

value: Male


title: Patient_105


title: bladder_cancer_RC_sample_48


title: 17C: nephroureterectomy from patient 60


title: Patient_104


title: Patient_103


title: PD-54

tag: cell type

tag: genotype

tag: age

value: 55 weeks


title: PD-55


title: bladder_cancer_RC_sample_46

tag: pstage

tag: gender

tag: cluster


title: bladder_cancer_RC_sample_44


title: bladder_cancer_RC_sample_47


title: Neg-14


title: 8C: nephroureterectomy from patient 58

value: upper tract urothelial carcinoma


title: bladder_cancer_RC_sample_45


title: PD-52


title: Patient_102

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: bladder_cancer_RC_sample_43


title: PD-53


title: bladder_cancer_RC_sample_49


title: Patient_101

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

value: medium


title: 21C: nephroureterectomy from patient 61

tag: tissue


title: PD-51


title: bladder_cancer_RC_sample_42


title: bladder_cancer_RC_sample_41


title: Neg-55


title: Patient_100

tag: arm

tag: os

tag: hemo status


title: bladder_cancer_RC_sample_39


title: 120B: nephroureterectomy from patient 56

tag: tissue preparation

tag: grade/ invasive


title: Neg-54

tag: cell type

tag: genotype


title: 115B: nephroureterectomy from patient 55


title: Patient_99

tag: ttp


title: Neg-53

tag: age


title: bladder_cancer_RC_sample_40

tag: pstage

tag: gender

tag: cluster


title: 110B: nephroureterectomy from patient 53


title: Neg-52


title: Patient_98

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: 132B: nephroureterectomy from patient 57


title: Patient_96

value: Not Treated

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo


title: bladder_cancer_RC_sample_36

tag: tissue


title: Patient_97

tag: arm

tag: os

tag: hemo status


title: Patient_95


title: bladder_cancer_RC_sample_38

value: Female


title: Neg-51

tag: cell type


title: PD-23

tag: genotype

value: 25 weeks


title: bladder_cancer_RC_sample_35


title: PD-24


title: 106B: nephroureterectomy from patient 51

tag: tissue preparation

tag: grade/ invasive

value: low/ invasive


title: Patient_94

value: Placebo

tag: ttp

value: FALSE

value: good


title: bladder_cancer_RC_sample_37

tag: pstage

tag: gender

value: bladder cancer RC sample


title: bladder_cancer_RC_sample_34

tag: cluster


title: 104B: nephroureterectomy from patient 50


title: bladder_cancer_RC_sample_31


title: 114B: nephroureterectomy from patient 54


title: PD-22

value: stomach-corpus epithelial cells

value: villin-PPARD

tag: age


title: bladder_cancer_RC_sample_32


title: 99B: nephroureterectomy from patient 48

value: high/ invasive


title: Patient_92

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: PD-21


title: 94B: nephroureterectomy from patient 46


title: Neg-23

value: WT


title: Neg-22


title: bladder_cancer_RC_sample_33


title: Neg-24


title: Neg-21


title: Patient_93

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo


title: 103B: nephroureterectomy from patient 49

value: FFPE

tag: tissue


title: bladder_cancer_RC_sample_29

value: Male


title: 89B: nephroureterectomy from patient 45


title: 16C: nephroureterectomy from patient 59


title: 86B: nephroureterectomy from patient 44


title: Patient_88

tag: arm

value: Regorafenib 160 mg

tag: os

tag: hemo status


title: Patient_89


title: PD-13

tag: cell type

tag: genotype

value: 10 weeks


title: 83B: nephroureterectomy from patient 43

tag: tissue preparation

value: upper tract urothelial carcinoma

tag: grade/ invasive


title: bladder_cancer_RC_sample_27

tag: pstage

tag: gender


title: bladder_cancer_RC_sample_28

tag: cluster


title: bladder_cancer_RC_sample_25


title: 97B: nephroureterectomy from patient 47


title: Patient_87

tag: ttp

tag: batch


title: bladder_cancer_RC_sample_26


title: Patient_86

tag: unisp2 outlier

tag: unisp4 outlier

value: medium


title: Patient_90

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: bladder_cancer_RC_sample_23

tag: tissue


title: PD-11

tag: age


title: 80B: nephroureterectomy from patient 42


title: 69B: nephroureterectomy from patient 40


title: 79B: nephroureterectomy from patient 41


title: Patient_85

tag: arm

tag: os

tag: dct hemo


title: Neg-12

tag: cell type

tag: genotype


title: Neg-13


title: Patient_91

tag: hemo status


title: Patient_84


title: Patient_83


title: 63B: nephroureterectomy from patient 38

tag: tissue preparation

tag: grade/ invasive


title: bladder_cancer_RC_sample_22

tag: pstage

tag: gender

value: Female

tag: cluster


title: PD-12


title: Patient_81

tag: ttp

tag: batch

tag: unisp2 outlier


title: 54B: nephroureterectomy from patient 37


title: SD2

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm9 mouse reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file including gene name, RefSeq id, locus, RPKM value of each gene in each sample

source_name: mouse glioblastoma tumor cells derived from FvB/C57BL6; tumor cells injected into immune-compromised RAG1-/- mice

growth_protocol: iEIP (Nestin-CreERT2; cInk4a/Arf Lox/Lox; cPten Lox/Lox; hGFAP-tTA; tetO-EGFRviii) glioma cells were infected by Control and Slug viruses. 10,000,000 cells were resuspended in 50% Matrigel in PBS, and injected into each flank of RAG1-/- mice.

extract_protocol:
Tumor tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the tumor size was between 200 and 400 mm3, the mice were randomly assigned to control water and doxycycline water groups. 2g/L doxycyclin in drinking water containing 2% sucrose was provided to the mice.

tag: strain

value: subcutaneous mouse GBM

value: Transgene tetOEGFRviii; Ink/Arf-/-; Pten-/-

tag: host genotype

tag: treatment

value: Slug virus, doxycyclin water


title: Patient_82

tag: arm

value: Placebo

value: FALSE

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Patient_80

tag: os

tag: dct hemo

value: good


title: bladder_cancer_RC_sample_24

tag: tissue

value: bladder cancer RC sample


title: SD3

tag: genotype


title: bladder_cancer_RC_sample_21

tag: pstage


title: 37B: nephroureterectomy from patient 36

tag: tissue preparation

tag: grade/ invasive


title: 64B: nephroureterectomy from patient 39


title: SD1


title: bladder_cancer_RC_sample_20

tag: gender

tag: cluster


title: bladder_cancer_RC_sample_30


title: bladder_cancer_RC_sample_17


title: 33B: nephroureterectomy from patient 35


title: Patient_79

tag: ttp

tag: batch

tag: unisp2 outlier

tag: hemo status


title: Neg-11

tag: cell type

value: stomach-corpus epithelial cells

tag: age


title: Patient_78

tag: arm

tag: unisp4 outlier

tag: unisp6 outlier


title: S3

tag: strain

tag: host genotype

tag: treatment

value: Slug virus, control water


title: bladder_cancer_RC_sample_19

tag: pstage

tag: tissue


title: S2

tag: genotype


title: 20B: nephroureterectomy from patient 34

tag: tissue preparation

tag: grade/ invasive

value: high/ invasive


title: 16B: nephroureterectomy from patient 33

value: FFPE


title: S1


title: 11B: nephroureterectomy from patient 32


title: Patient_77

tag: os

tag: ttp

tag: cel-mir-39-3p outlier

tag: dct hemo


title: CD2

value: Control virus, doxycyclin water


title: bladder_cancer_RC_sample_18

tag: gender

value: Male

tag: cluster


title: Patient_76

tag: arm

value: Regorafenib 160 mg

tag: batch

tag: unisp2 outlier

tag: hemo status


title: bladder_cancer_RC_sample_15


title: bladder_cancer_RC_sample_14


title: 7B: nephroureterectomy from patient 31

value: upper tract urothelial carcinoma


title: CD1

tag: strain

tag: host genotype


title: bladder_cancer_RC_sample_16

tag: pstage


title: Patient_74

tag: unisp4 outlier

tag: unisp6 outlier


title: Patient_75


title: bladder_cancer_RC_sample_12

tag: tissue


title: C2

tag: genotype

tag: treatment

value: Control virus, control water


title: bladder_cancer_RC_sample_13


title: bladder_cancer_RC_sample_11

value: Female


title: Patient_72

tag: os

tag: ttp


title: Patient_73

tag: cel-mir-39-3p outlier

tag: dct hemo


title: C1

value: subcutaneous mouse GBM


title: Patient_70

value: medium


title: bladder_cancer_RC_sample_9

tag: gender

tag: cluster


title: C3

value: Transgene tetOEGFRviii; Ink/Arf-/-; Pten-/-


title: Patient_68

tag: arm

value: Placebo

tag: batch


title: Spring_ 10ug Ag_21d_9

city: Leioa

first: Nerea

last: Duroudier

address: Bº Sarriena s/n

country: Spain

institute: University of the Basque Country

description: Gene expression after 21 days of dietary exposure to 10 µg/L of Ag NPs in spring

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 600 ng. Volume: 40 µL. Temperature (ºC): 65. Duration: 17 hours at 10 rpm in the hybridization oven. After hybridization, microarrays were washed following manufacturer´s instructions.

scan_protocol: Hybridized microarrays were scanned on a G2565CA DNA microarray scanner (Agilent Technologies) with ozone barrier slide covers (Agilent Technologies P/N G2505-60550). Scan resolution: 3µm; Dye Channel: green

data_processing: The scanned images were analyzed with Feature Extraction Software v.10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09, Design File: 078472_D_F_20150925) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mytilus galloprovincialis

source_name: Digestive gland_Spring_10ug Ag_1 day_org 9

label_protocol: RNA samples (100 ng) were retro-transcribed and labelled using the Low Input Quick Amp Labelling Kit, One Colour (Agilent Technologies, 5190-2305) following the manufacturer’s instructions.

growth_protocol: Mussels Mytilus galloprovincialis 3.5-4.5 cm in shell length were collected in autumn (November 2013) and spring (March 2014) from San Felipe, Galicia (43° 27.599'N, 8° 17.904'W). Upon arrival to the laboratory, mussels were placed in an acclimation tank (temperature =15.6°C, salinity =28.7, conductivity =36.4 mS/cm, pH =7.7 at light regime 12 h/12 h L/D) for 5 days without feeding. Then mussels were fed with Isochrysis galbana microalgae (20x106 cells/mussel·day) for additional 5 days.

extract_protocol: About 50-100 mg of digestive gland of 10 female mussels per treatment were individually homogenized in TRIzol® Reagent (Invitrogen, Carlsbad, USA) using a Precellys®24 homogenizer (Bertin Technologies, France) at a shaking speed of 6000 rpm for 2 cycles of 25 seconds each. Total RNA was isolated following the manufacturer´s recommendations and treated with the RNase-Free DNase Set (Qiagen, Venlo, The Netherlands) to digest contaminating DNA. Then, total RNA was purified by using the RNeasy Mini Kit (Qiagen). The integrity and quality of purified RNA was checked both spectrophotometrically (A260/280; Epoch Biotek; Winooski, Vermont, USA) and by capillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies). Samples with a A260/280 ratio around 2 and showing a good electropherogram were selected for microarray hybridizations.

treatment_protocol: Mussels in the control tank were fed for 21 days with the microalgae Isochrysis galbana (20x106 cells/mussel·day) and mussels in the treatment tank were fed for 21 days with the same dose of microalgae I. galbana (20x106 cells/mussel·day) previously exposed for 24 hours to 1 μg Ag/L Ag NPs in spring or to 10 μg Ag/L Ag NPs in autumn and in spring. Water was renewed every day before animal feeding. After 1 and 21 days of exposure, digestive gland of mussels was dissected out, immersed in RNA later, snap-frozen in liquid nitrogen and stored at -80°C until processing.

tag: size

value: 3.5-4.5 cm shell length

value: 21 days of dietary exposure to 10 ug/L of Ag NPs in spring


title: Patient_71

tag: unisp2 outlier

value: FALSE

tag: hemo status

value: good


title: bladder_cancer_RC_sample_7

tag: pstage

value: bladder cancer RC sample


title: Patient_69

tag: unisp4 outlier


title: bladder_cancer_RC_sample_8


title: Spring_ 10ug Ag_21d_8

source_name: Digestive gland_Spring_10ug Ag_1 day_org 8


title: Spring_ 10ug Ag_21d_7

source_name: Digestive gland_Spring_10ug Ag_1 day_org 7


title: Patient_66

tag: unisp6 outlier


title: Spring_ 10ug Ag_21d_2

source_name: Digestive gland_Spring_10ug Ag_1 day_org 2


title: Patient_65

source_name: plasma


title: Patient_67


title: bladder_cancer_RC_sample_6

tag: tissue


title: TH1_Donor 8_Adalimumab

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

description: Gene expression profiling of Th1 cells from donor 8 (Adalimumab incubated co-culture)

hyb_protocol: Affymetrix GeneTitan protocol

scan_protocol: Affymetrix cel analysis

data_processing: Bioconductor/R RMA

label_protocol: Affymetrix in vitro transcription

extract_protocol: Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA), but with subsequent RNA clean-up of the water phase using the RNeasy Qiagen MinElute kit (Qiagen, Germantown, MD). The quality of the RNA was confirmed on the Agilent Bioanalyzer using RNA Nano chips (Agilent Technologies, Santa Clara, CA).

tag: donor

value: Donor 8

tag: cell type

value: Adalimumab


title: Spring_ 10ug Ag_21d_4

source_name: Digestive gland_Spring_10ug Ag_1 day_org 4

tag: treatment


title: Spring_ 10ug Ag_21d_3

source_name: Digestive gland_Spring_10ug Ag_1 day_org 3


title: bladder_cancer_RC_sample_2

source_name: FFPE bladder cancer


title: TH1_Donor 8_Control

description: Gene expression profiling of Th1 cells from donor 8 (control co-culture)

value: control


title: Spring_ 1ug Ag_21d_7

description: Gene expression after 21 days of dietary exposure to 1 µg/L of Ag NPs in spring

source_name: Digestive gland_Spring_1ug Ag_21 days_org 7

value: 21 days of dietary exposure to 1 ug/L of Ag NPs in spring


title: bladder_cancer_RC_sample_4


title: Spring_ 1ug Ag_21d_8

source_name: Digestive gland_Spring_1ug Ag_21 days_org 8


title: TH1_Donor 7_Adalimumab

description: Gene expression profiling of Th1 cells from donor 7 (Adalimumab incubated co-culture)

value: Donor 7


title: DICER Morpholino_1-1_II

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

data_processing:
A minimum of 13 -15 million 50bp sequencing reads were collected from each sample.
The data were pre-processed to remove the adapters using cutadapt
pre-processed reads were analysed using miRDeep2 software (https://www.mdc-berlin.de/8551903/en/)
Supplementary_files_format_and_content: counts of small RNA sequences

organism: Nematostella vectensis

source_name: whole animal

extract_protocol:
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual, the small (18-30 nt long) RNA were purified on a denaturing 15% acrylamide gel, from 20 μg total RNA per sample. RNAs were eluted from the acrylamide bands overnight in 0.3 M NaCl, then ethanol/glycogen-precipitated.
Small RNA libraries were constructed as described in Phillip Zamore Lab Illumina TruSeq Small RNA Cloning Protocol April, 2014 (http://www.umassmed.edu/zamore/resources/protocols/). Each library was indexed in order to multiplex 30 samples per sequencing run on the Illumina.

treatment_protocol: The eggs were injected with Morpholino Antisense Oligonucleotide. The RNA periodate is carried out as follow, half of each sample was oxidized (5X borate buffer, ph=8.6; 5 μL freshly prepared 50mM sodium periodate) for 30 minutes at 25 degrees C, then precipitated with sodium acetate, ethanol and glycogen; the other half was not treated.

tag: developmental stage

value: Early planula

tag: treated

value: Morpholino

tag: barcode

value: ACTGAT


title: bladder_cancer_RC_sample_5

tag: gender

value: Male


title: TH1_Donor 6_Adalimumab

description: Gene expression profiling of Th1 cells from donor 6 (Adalimumab incubated co-culture)

value: Donor 6


title: 108B: nephroureterectomy from patient 52

source_name: upper tract urothelial carcinoma

tag: tissue preparation

value: FFPE

value: upper tract urothelial carcinoma

tag: grade/ invasive

value: high/ invasive


title: DICER Morpholino_1-1_I

value: GAGTGG


title: Patient_64

tag: arm

value: Regorafenib 160 mg

tag: os

tag: ttp

tag: batch

value: FALSE

tag: cel-mir-39-3p outlier

tag: dct hemo

value: medium


title: Patient_63

value: Placebo

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier

tag: hemo status

value: good


title: Control Morpholino_1-1_II

value: GGTAGC


title: Spring_ 1ug Ag_21d_4

source_name: Digestive gland_Spring_1ug Ag_21 days_org 4

value: Female

tag: size

value: 3.5-4.5 cm shell length

tag: treatment

value: 21 days of dietary exposure to 1 ug/L of Ag NPs in spring


title: TH1_Donor 7_Control

description: Gene expression profiling of Th1 cells from donor 7 (control co-culture)

tag: donor

value: Donor 7

tag: cell type

value: control


title: TH1_Donor 6_Control

description: Gene expression profiling of Th1 cells from donor 6 (control co-culture)


title: Spring_ 1ug Ag_21d_2

source_name: Digestive gland_Spring_1ug Ag_21 days_org 2

tag: gender


title: Patient_62


title: bladder_cancer_RC_sample_1

tag: pstage

value: Male

tag: cluster

tag: tissue

value: bladder cancer RC sample


title: bladder_cancer_RC_sample_3


title: Spring_ 1ug Ag_21d_5

source_name: Digestive gland_Spring_1ug Ag_21 days_org 5


title: Control Morpholino_1-1_I

tag: developmental stage

value: Early planula

tag: treated

value: Morpholino

tag: barcode

value: CGTACG


title: TH1_Donor 5_Adalimumab

description: Gene expression profiling of Th1 cells from donor 5 (Adalimumab incubated co-culture)

value: Donor 5

value: Adalimumab


title: TH1_Donor 5_Control

description: Gene expression profiling of Th1 cells from donor 5 (control co-culture)


title: Spring_ 1ug Ag_21d_1

source_name: Digestive gland_Spring_1ug Ag_21 days_org 1


title: PIWI2_splice Morpholino_12

value: CTTGTA


title: TH1_Donor 4_Adalimumab

description: Gene expression profiling of Th1 cells from donor 4 (Adalimumab incubated co-culture)

value: Donor 4


title: TH1_Donor 4_Control

description: Gene expression profiling of Th1 cells from donor 4 (control co-culture)


title: Patient_60

tag: arm

value: Regorafenib 160 mg

tag: os

tag: ttp

tag: batch

value: FALSE

tag: cel-mir-39-3p outlier


title: Patient_59

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier

tag: dct hemo

tag: hemo status

value: good


title: Control Morpholino_9

value: GATCAG


title: Patient_58

value: Placebo


title: TH1_Donor 3_Adalimumab

description: Gene expression profiling of Th1 cells from donor 3 (Adalimumab incubated co-culture)

tag: donor

value: Donor 3

tag: cell type

tag: treatment


title: Control Morpholino_8

value: ACTTGA


title: Spring_ Control_21d_10

description: Gene expression after 21 days of dietary exposure to 0 µg/L of Ag NPs in spring

source_name: Digestive gland_Spring_Control_21 days_org 10

tag: gender

value: Female

tag: size

value: 3.5-4.5 cm shell length

value: 21 days of dietary exposure to 0 ug/L of Ag NPs in spring


title: Patient_61

value: medium


title: Spring_ Control_21d_7

source_name: Digestive gland_Spring_Control_21 days_org 5


title: TH1_Donor 2_Adalimumab

description: Gene expression profiling of Th1 cells from donor 2 (Adalimumab incubated co-culture)

value: Donor 2


title: HEN1 splice Morpholino_4 untreated

tag: developmental stage

value: Early planula

tag: treated

value: Morpholino

value: TGACCA


title: Patient_56

tag: arm


title: Patient_57

tag: os


title: TH1_Donor 3_Control

description: Gene expression profiling of Th1 cells from donor 3 (control co-culture)

value: control


title: HEN1 splice Morpholino_3 oxidized

value: Morpholino and RNA periodate

tag: barcode

value: TTAGGC


title: bladder_cancer_RC_sample_10

tag: pstage

value: Male

tag: cluster

tag: tissue

value: bladder cancer RC sample


title: PIWI2_splice Morpholino_11

value: GGCTAC


title: Spring_ Control_21d_4

source_name: Digestive gland_Spring_Control_21 days_org 4


title: Spring_ Control_21d_5


title: Control Morpholino_1 oxidized

value: ATCACG


title: Control Morpholino_2 untreated

value: CGATGT


title: Spring_ Control_21d_2

source_name: Digestive gland_Spring_Control_21 days_org 2


title: Patient_55

value: Regorafenib 160 mg

tag: ttp

tag: batch

tag: unisp2 outlier

value: FALSE

tag: unisp4 outlier

tag: cel-mir-39-3p outlier


title: Patient_54

tag: unisp6 outlier

tag: dct hemo

tag: hemo status


title: Patient_53

value: Placebo


title: Hen1 Translation blocking_9

data_processing:
A minimum of 13 -15 million 50bp sequencing reads were collected from each sample.
The data were pre-processed to remove the adapters using cutadapt
pre-processed reads were analysed using miRDeep2 software (https://www.mdc-berlin.de/8551903/en/)
Genome_build: counts of small RNA sequences

treatment_protocol: The eggs were injected with Morpholino Antisense Oligonucleotide

value: GATCAG


title: TH1_Donor 1_Control

description: Gene expression profiling of Th1 cells from donor 1 (control co-culture)

tag: donor

value: Donor 1

tag: cell type

tag: treatment


title: Patient_52

tag: arm

value: good


title: Patient_51

tag: os

value: medium


title: Spring_ 10ug Ag_1d_8

description: Gene expression after 1 day of dietary exposure to 10 µg/L of Ag NPs in spring

source_name: Digestive gland_Spring_10ug Ag_1 day_org 8

tag: gender

value: Female

tag: size

value: 3.5-4.5 cm shell length

value: 1 day of dietary exposure to 10 ug/L of Ag NPs in spring


title: Hen1 Translation blocking _8

tag: developmental stage

value: Early planula

tag: treated

value: Morpholino

tag: barcode

value: ACTTGA


title: Hen1 splice Morpholino_2


title: Patient_50

source_name: plasma

tag: ttp

tag: batch

value: bad


title: TH1_Donor 2_Control

description: Gene expression profiling of Th1 cells from donor 2 (control co-culture)

value: Donor 2

value: control


title: TH1_Donor 1_Adalimumab

description: Gene expression profiling of Th1 cells from donor 1 (Adalimumab incubated co-culture)

value: Adalimumab


title: Spring_ 10ug Ag_1d_7

source_name: Digestive gland_Spring_10ug Ag_1 day_org 7


title: Spring_ Control_21d_9

source_name: Digestive gland_Spring_Control_21 days_org 9

value: 21 days of dietary exposure to 0 ug/L of Ag NPs in spring


title: Hen1 splice Morpholino_1

value: ATCACG


title: Spring_ 10ug Ag_1d_6

source_name: Digestive gland_Spring_10ug Ag_1 day_org 6


title: Spring_ 10ug Ag_1d_5

source_name: Digestive gland_Spring_10ug Ag_1 day_org 5


title: Control Morpholino_12

value: CTTGTA


title: Patient_49

value: Placebo

tag: unisp2 outlier

value: FALSE

tag: unisp4 outlier


title: Spring_ 10ug Ag_1d_4

source_name: Digestive gland_Spring_10ug Ag_1 day_org 4


title: Control Morpholino_11

source_name: whole animal

value: GGCTAC


title: Control Morpholino_5

value: ACAGTG


title: Control Morpholino_4

value: TGACCA


title: Patient_45

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Patient_46

value: Regorafenib 160 mg

tag: dct hemo

tag: hemo status


title: Patient_47

value: medium


title: Spring_ 1ug Ag_1d_10

description: Gene expression after 1 day of dietary exposure to 1 µg/L of Ag NPs in spring

source_name: Digestive gland_Spring_1ug Ag_1 day_org 10

value: Female

value: 3.5-4.5 cm shell length

value: 1 day of dietary exposure to 1 ug/L of Ag NPs in spring


title: Spring_ 10ug Ag_1d_2

source_name: Digestive gland_Spring_10ug Ag_1 day_org 2

value: 1 day of dietary exposure to 10 ug/L of Ag NPs in spring


title: Spring_ 1ug Ag_1d_7

source_name: Digestive gland_Spring_1ug Ag_1 day_org 7


title: Patient_43


title: Patient_48


title: Spring_ 1ug Ag_1d_6

source_name: Digestive gland_Spring_1ug Ag_1 day_org 6


title: Patient_42


title: Patient_40

value: bad


title: Patient_39


title: Patient_41


title: Spring_ 1ug Ag_1d_2

source_name: Digestive gland_Spring_1ug Ag_1 day_org 2


title: Patient_44


title: Patient_38


title: Spring_ Control_1d_8

description: Gene expression after 1 day of dietary exposure to 0 µg/L of Ag NPs in spring

source_name: Digestive gland_Spring_Control_1 day_org 8

value: 1 day of dietary exposure to 0 ug/L of Ag NPs in spring


title: Patient_37


title: Spring_ 1ug Ag_1d_9

source_name: Digestive gland_Spring_1ug Ag_1 day_org 9


title: Spring_ 1ug Ag_1d_1

source_name: Digestive gland_Spring_1ug Ag_1 day_org 1


title: Patient_36


title: Patient_35


title: Spring_ Control_1d_10

source_name: Digestive gland_Spring_Control_1 day_org 10


title: Spring_ Control_1d_6

source_name: Digestive gland_Spring_Control_1 day_org 6


title: Spring_ Control_1d_1

source_name: Digestive gland_Spring_Control_1 day_org 1


title: Spring_ Control_1d_5

source_name: Digestive gland_Spring_Control_1 day_org 5


title: N044_ROC10110

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: nasal swab

hyb_protocol: Followed Affymetrix standard hybridization protocol for Human Clariom D chips.

scan_protocol: Chips were scanned with Affymetrix 7G scanner at the standard setting.

data_processing: The raw chip data files (.CEL) were processed through Affymetrix standard analysis pipeline for RMA background correction, median-polish summarization and quantile normalization. The .CHP files were generated at gene-level.

label_protocol: RNAs were amplified with the Affymetrix WT Pico whole transcript amplification (WTA) kit to generate cDNA targets labeled with biotin.

extract_protocol: RNA was extracted using the Absolutely RNA Miniprep Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions.

treatment_protocol: The blood samples obtained by venipuncture were drawn into a Tempus tube (Applied Biosystems, Foster City, CA). The nasopharynx was washed with normal saline by a trained study coordinator and a nasal swab was obtained using a mid-turbinate flocked swab (Copan Diagnostics, Inc., Murrieta, CA). The nasal swab was immediately placed in RNAprotect (Qiagen, Valencia, CA). The nasal swab in RNAprotect was stored for 1-5 days at 4°C, after which cells were pelleted, suspended in lysis buffer containing BME, and homogenized by passing the lysate 10-12 times through a 28- gauge needle.

value: F

tag: age (months)

tag: infection

value: respiratory syncytial virus

tag: symptomatic

value: Yes


title: N046_ROC10115

description: nasal swab

value: M


title: N043_ROC10104

description: nasal swab


title: Spring_ Control_1d_2

source_name: Digestive gland_Spring_Control_1 day_org 2

tag: treatment


title: Autumn_ 10ug Ag_21d_6

description: Gene expression after 21 days of dietary exposure to 10 µg/L of Ag NPs in autumn

source_name: Digestive gland_Autumn_10ug Ag_21 days_org 6

tag: gender

value: 21 days of dietary exposure to 10 ug/L of Ag NPs in autumn


title: Autumn_ 10ug Ag_21d_8

source_name: Digestive gland_Autumn_10ug Ag_21 days_org 8

tag: size


title: N030_ROC10069

description: nasal swab


title: N006_ROC10010

description: nasal swab


title: N040_ROC10096

description: nasal swab

value: No


title: N005_ROC10009

description: nasal swab


title: Patient_33

data_processing: Normalized continous values were calculated with an in-house developed algorithm for all miRNAs detected in at least 50% of samples, values below detection threshold were imputed. Dichotomized values (1 / 0 for detected / not detected) were calculated for all miRNAs detected in less than 50% of samples.

source_name: plasma

tag: arm

tag: os

value: FALSE

value: good


title: N041_ROC10099

description: nasal swab


title: Patient_32


title: Patient_31

value: Placebo


title: Patient_34

value: Regorafenib 160 mg


title: N045_ROC10112

description: nasal swab


title: Patient_30


title: Patient_28


title: Patient_29

value: medium


title: Autumn_ 10ug Ag_21d_4

source_name: Digestive gland_Autumn_10ug Ag_21 days_org 4

value: Female


title: Patient_27


title: Autumn_ 10ug Ag_21d_1

source_name: Digestive gland_Autumn_10ug Ag_21 days_org 1

value: 3.5-4.5 cm shell length


title: N018_ROC10036

description: nasal swab


title: Autumn_ Control_21d_9

description: Gene expression after 21 days of dietary exposure to 0 µg/L of Ag NPs in autumn

source_name: Digestive gland_Autumn_Control_21 days_org 9

value: 21 days of dietary exposure to 0 ug/L of Ag NPs in autumn


title: SWI524: Cold Bio#2

city: Newark

first: Karl

last: Franke

state: Delaware

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: University of Delaware

data_processing:
Library strategy: PARE-seq
Adapters were trimmed from reads.
PARE reads were mapped to their appropriate genome using bowtie 0.12.7
PARE libraries were normalized to TP10M
RNAseq reads were mapped to the Brachypodium genome using STAR 2.5.3a with ENCODE standard settings.
RNAseq libraries were normalized using RSEM 1.2.31
Genome_build: Brachypodium distachyon JGI v3.1
Genome_build: Panicum virgatum JGI v4.1
Genome_build: Sorghum bicolor JGI v3.1.1
Supplementary_files_format_and_content: RNAseq proccessed data files are RSEM normalized gene counts. PARE processed data files indicate the prominence of PARE reads mapping to predicted miRNA target sites.

organism: Panicum virgatum

source_name: Above ground tissue

growth_protocol: Seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h-light, 4 h-dark cycle. Leaf, stem, and panicle tissues were harvested from six-week old plants. Leaf tissue was the blade of first and second leaf from the top, not including the leaf sheath. Stem tissue was harvested from just above the first top node to just below the second node, including both nodes as well as the leaf sheath of the second leaf. Panicle tissue was harvested from plants with immature, unfertilized flowers from the tip of the spikelet to just above, but not including, the panicle node at approximately 10 h into the subjective day. To collect root tissue, seeds were husked, surface-sterilized with a 50% bleach solution, rinsed with sterile water, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in sterile plastic boxes. Root tissue was harvested from three-week old plants from the tip of the root to just below, but not including the seed.

extract_protocol:
RNAs were isolated using Trizol reagent (Molecular Research Center).
PARE libraries were constructed as described (German et al., 2008). RNA-seq libraries were constructed using the ScriptSeq RNA-Seq Library Preparation Kit from Illumina (Cat#SSV21124) and sequenced using Illumina HiSeq 2500.

tag: strain

tag: stress

value: Cold

tag: tissue

value: Above ground tissue


title: SWI523: Control for Cold Bio#2


title: Autumn_ 10ug Ag_21d_3

source_name: Digestive gland_Autumn_10ug Ag_21 days_org 3


title: Autumn_ 10ug Ag_21d_2

source_name: Digestive gland_Autumn_10ug Ag_21 days_org 2


title: Patient_25

extract_protocol: RNA was isolated from plasma using the mirCury RNA isolation kit (Exiqon)

tag: ttp

tag: batch

tag: unisp2 outlier


title: N026_ROC10058

description: nasal swab


title: Autumn_ Control_21d_2

source_name: Digestive gland_Autumn_Control_21 days_org 2


title: Autumn_ Control_21d_6

source_name: Digestive gland_Autumn_Control_21 days_org 6


title: Patient_24

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Autumn_ Control_21d_5

source_name: Digestive gland_Autumn_Control_21 days_org 5


title: Autumn_ Control_21d_7

source_name: Digestive gland_Autumn_Control_21 days_org 7


title: N033_ROC10075

description: nasal swab

tag: age (months)

value: picornavirus (rhinovirus)


title: N015_ROC10028

description: nasal swab

tag: infection


title: Autumn_ Control_21d_1

source_name: Digestive gland_Autumn_Control_21 days_org 1


title: N020_ROC10041

description: nasal swab

value: F

tag: symptomatic


title: Autumn_ 10ug Ag_1d_9

description: Gene expression after 1 day of dietary exposure to 10 µg/L of Ag NPs in autumn

source_name: Digestive gland_Autumn_10ug Ag_1 day_org 9

tag: treatment

value: 1 day of dietary exposure to 10 ug/L of Ag NPs in autumn


title: Autumn_ 10ug Ag_1d_7

source_name: Digestive gland_Autumn_10ug Ag_1 day_org 7

tag: gender


title: N023_ROC10050

description: nasal swab


title: N028_ROC10064

description: nasal swab

value: Yes


title: SWI521: Control for Cold Bio#1


title: N024_ROC10053

description: nasal swab

value: M

value: picornavirus (enterovirus D68)


title: N025_ROC10055

description: nasal swab

value: No


title: N017_ROC10033

description: nasal swab


title: SWI500: Stem Bio#2

source_name: Stem

value: Stem


title: Patient_23

value: FALSE

tag: dct hemo

tag: hemo status

value: good


title: SWI499: Panicle Bio#2

source_name: Panicle

value: Panicle


title: Patient_26

tag: arm

value: Regorafenib 160 mg

tag: os


title: Patient_21


title: Patient_20


title: SWI498: Leaf Bio#2

source_name: Leaf

tag: strain

tag: stress

value: Leaf


title: Patient_22

source_name: plasma

tag: ttp


title: Patient_19

tag: batch


title: SWI382: Panicle Bio#1

tag: tissue


title: SWI353: Stem Bio#1


title: Patient_18

tag: unisp2 outlier

tag: unisp4 outlier


title: Autumn_ 10ug Ag_1d_6

source_name: Digestive gland_Autumn_10ug Ag_1 day_org 6

value: Female

tag: size

value: 3.5-4.5 cm shell length


title: Autumn_ 10ug Ag_1d_5

source_name: Digestive gland_Autumn_10ug Ag_1 day_org 5


title: SWI352: Leaf Bio#1


title: N019_ROC10039

description: nasal swab

tag: age (months)


title: Autumn_ 10ug Ag_1d_2

source_name: Digestive gland_Autumn_10ug Ag_1 day_org 2


title: Patient_17

value: Placebo

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: N016_ROC10031

description: nasal swab

tag: infection

tag: symptomatic


title: Autumn_ 10ug Ag_1d_1

source_name: Digestive gland_Autumn_10ug Ag_1 day_org 1

tag: gender

tag: treatment


title: SWI562: Panicle

description: small RNA

data_processing:
Reads were trimmed of adapters and mapped to the genome using bowtie 0.12.7
Reads matching the genome more than 20 times or those which were not between 20-24nt were discarded
A modified version of miREAP was used to predict miRNA precursors based on reads mapped to the genome
Stem loop structure folding was predicted using unafold and scored based on abundance and strand bias
miRNA precursors which passed the above criteria and contained conserved miRNAs were kept as final candidates
Genome_build: Panicum virgatum JGI v4.1
Supplementary_files_format_and_content: A tab delimited table listing predicted miRNA precursor locations within the genome, data recarding the predicted folding of the precursor,  the sequences of the miRNA and miRNA*, and the name of an already annotated miRNA with the same sequence if applicable.

extract_protocol:
RNA was extracted using Trizol
Small RNA libraries were constructed as described in Jeong et al. 2013  10.1186/gb-2013-14-12-r145


title: Autumn_Control_1d_8

description: Gene expression after 1 day of dietary exposure to 0 µg/L of Ag NPs in autumn

source_name: Digestive gland_Autumn_Control_1 day_org 8

value: 1 day of dietary exposure to 0 ug/L of Ag NPs in autumn


title: Autumn_Control_1d_7

source_name: Digestive gland_Autumn_Control_1 day_org 7


title: Patient_16

tag: arm

tag: dct hemo

tag: hemo status


title: N012_ROC10021

description: nasal swab

value: picornavirus (cosxackievirus A2)


title: SWI534: Stem

description: small RNA

tag: strain


title: N011_ROC10019

description: nasal swab

value: picornavirus (rhinovirus)


title: N009_ROC10015

description: nasal swab


title: N008_ROC10013

description: nasal swab


title: Autumn_Control_1d_5

source_name: Digestive gland_Autumn_Control_1 day_org 5


title: N003_ROC10005

description: nasal swab


title: SWI561: Leaf

description: small RNA


title: Patient_14

tag: os

tag: ttp


title: SWI553: Above ground tissue

description: small RNA

source_name: Re-water after Drought

tag: tissue

value: Above ground tissue


title: N046_ROC10116

description: whole blood

value: respiratory syncytial virus

value: Yes


title: Autumn_Control_1d_3

source_name: Digestive gland_Autumn_Control_1 day_org 3


title: Patient_13

tag: batch

tag: unisp2 outlier


title: Patient_15

tag: unisp4 outlier


title: SWI552: Above ground tissue

description: small RNA

source_name: Drought


title: N044_ROC10111

description: whole blood

value: F

tag: age (months)


title: Patient_12

tag: unisp6 outlier


title: SWI551: Above ground tissue

description: small RNA

source_name: Control for Drought


title: SWI559: Above ground tissue

description: small RNA

source_name: Cold


title: Patient_11

tag: cel-mir-39-3p outlier


title: N043_ROC10105

description: whole blood

tag: infection


title: SWI560: Above ground tissue

description: small RNA

source_name: Control for Cold


title: Patient_10


title: Autumn_Control_1d_6

source_name: Digestive gland_Autumn_Control_1 day_org 6

tag: size


title: Patient_9


title: Autumn_Control_1d_1

source_name: Digestive gland_Autumn_Control_1 day_org 1

tag: gender


title: N030_ROC10070

description: whole blood

tag: symptomatic


title: N041_ROC10101

description: whole blood

value: M

value: No


title: N045_ROC10114

description: whole blood


title: N040_ROC10098

description: whole blood


title: HL 3

city: Fredericton

first: Pattarasiri

last: Rangsrikitphoti

state: NB

address: 10 Bailey drive

department: Biology

institute: University of New Brunswick

data_processing:
Read Quality: Fastqc was used to check the read qualities before and after read trimming.
Read Trimming: using the Flexible Barcode and Adapter Remover (FLEXBAR version 2.4) program. A minimum of 7 bases was required to match the adapter sequence, which was removed from 3’ end of the read. The first 13 bases on the 5’ end of the read were removed to discard poor quality bases. The maximum uncalled bases was 300 and minimum read length after trimming was 25 bases
Reference Genome: Bigelowiella natans whole genome and gene annotation was downloaded from JGI
Alignment: The paired-end reads were aligned to the reference genome using Tophat2 with parameters -p 8 -r 50 -- library-type fr-firststrand
DEGs: The aligned reads were then assembled with a reference transcriptome annotation to estimate transcript abundances (FPKM) using Cufflinks version 2.2.1. Differentially expressed genes (DEGs) were determined by two criteria. First, they must have corrected p-value (FDR) < 0.01 and, second, a log2 fold change (LFC) < -1 or > 1. Clustering analysis was then performed to determine the transcriptional networks of DEGs using Cluster 3.0 (De Hoon et al. 2002). The FPKM values of each gene were log2-transformed and centered by median values. Output from Cuffdiff can be directly imported into CummeRbund, a package in R, for visualization (Trapnell et al. 2012).
Genome_build: Bigna1
Supplementary_files_format_and_content: tab-delimited text file showing the FPKM values of each gene in each sample; tab-delimited text file showing expression level in log₂fold change (LFC) values.

organism: Bigelowiella natans

source_name: HL

growth_protocol: Cells grown in f/2 fortified, artificial sea water under a 12:12 hour light-dark cycle under low light (LL) at 24˚c and bubbled with air continuously for 4 days in triplicate.

extract_protocol:
Total RNA samples were extracted from cells treated with VL, LL, and HL for 4 hours using modified protocol from Curtis et al. (2012) with additional extraction by Rneasy Plant mini kit (Qiagen, USA).
cDNA libraries were generated using Illumina Truseq stranded mRNA library preparation kit

treatment_protocol: When cells reached cell density of 3E+06 cells ml⁻¹, the cultures were transferred to  very-low light (VL), high light (HL) , or remained under the LL for 4 hours.

tag: stress

value: high light


title: HL 2


title: LL 3

source_name: LL

value: low light


title: LL 2


title: HL 1


title: Patient_7

source_name: plasma

tag: arm

value: FALSE

tag: dct hemo

value: good


title: Patient_8

value: Regorafenib 160 mg

tag: hemo status


title: Patient_6

tag: os


title: LL 1

tag: strain


title: N015_ROC10030

description: whole blood


title: Patient_5

tag: ttp


title: VL 3

source_name: VL

value: very-low light


title: N026_ROC10060

description: whole blood


title: SWI522: Cold Bio#1

source_name: Above ground tissue

value: Cold

tag: tissue


title: Patient_2

value: Placebo

tag: batch

tag: unisp2 outlier


title: N018_ROC10038

description: whole blood

tag: age (months)


title: VL 2


title: VL 1


title: High-intake subcutaneous adipose rep3

city: Chengdu

first: Jiwen

last: Wang

state: Sichuan

address: 211 Humin Road, Wenjiang District

department: Department of Animal Science

country: China

institute: Sichuan Agricultural University

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T3-SF

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5, performed by Novogene. Clean reads were mapped against goose reference genome that includes the mitochondrial genome (AnsCyg_PRJNA183603_v1.0) using Bowtie(v2.11) and the spliced reads aligner, Tophat(v2.12) with default arguments.
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Cufflinks (v.2.1.1).
Cuffquant (part of Cufflinks) was used to generate abundance files, which were applied to Cuffdiff (part of Cufflinks) to detect differentially expressed genes between the two groups.
Transcripts were assembled by Cufflinks (v2.1.1) using -g argument.
Cufflinks generated assembled transcripts in GTF file format for all individuals and these were later merged by tissue using Cuffmerge.
Transcripts in the 6 merged GTF files (3 tissues x 2 treatments) were compared to the reference annotations using Cuffcompare and those transcripts that were in the reference GTF file or had a large overlap with a known transcript were removed. Removed transcripts were marked as “c” or “=” by the custom Python script. By default, transcripts shorter than 200 bp were not be retained.
Protein-coding score were then calculated for remaining transcripts using CPC. The protein-coding score is derived from comparison of a support vector machine learning classifier against a selected protein database. We calculated coding potential against UniRef 90 and transcripts with scores larger than 1 were filtered because of their high coding potential.
Surviving transcripts were then scanned for potential of coding small peptides or functional protein domains using Infernal cmscan against UniRef90.
Survived transcripts were then compared by blastx to the NCBI NR database and UniRef 90. We filtered any transcripts that only had one exon and retained the rest of them as putative lncRNAs. As we did for protein coding genes, we used Cufflinks to quantify the expression of the lncRNAs, and we performed principle variance components analysis and hierarchical clustering analysis.
To obtain genomic characterizations for all identified lncRNA transcripts, we ran FEELnc_classifier.pl (a Perl script in FEELnc).
Genome_build: AnsCyg_PRJNA183603_v1.0 from NCBI
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.  The goose mRNA coordinates are provided in the .gff3 file. The goose lncRNA coordinates are included within goose_lncRNA_fpkm.txt.

organism: Anser cygnoides

source_name: Subcutaneous adipose tissue

growth_protocol: All geese had free access to water at all times.

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

treatment_protocol: All geese were given the same diet (14.29 MJ/Kg metabolizable energy, 8.09% crude protein and 0.14% methionine). The control group had access to diet freely the whole day, while the high-intake feeding group was fed two times a day for days 1-3, 3 times a day for days 4-6, 4 times a day for days 7-17, and 3 times on day 18. The meals on day 1 were 130 g and were increased by 5 g every day. On day 18, the day before the birds were sacrificed, all geese were deprived of feed overnight and they were sacrificed the following morning at 145 days of age.

tag: breed

value: Tianfu

tag: treatment

value: High-intake feeding

value: Subcutaneous adipose

tag: age

value: 145 days after birth


title: High-intake subcutaneous adipose rep2

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T2-SF


title: Patient_4

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier


title: Patient_3


title: High-intake subcutaneous adipose rep1

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T1-SF


title: Patient_1

value: medium


title: w_IBIN_Mlut24_A

city: TAMPERE

first: Mika

last: Ramet

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: sequencing was done in 1 lane

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to dm6 Drosophila melanogaster genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

organism: Drosophila melanogaster

source_name: whole organism

extract_protocol:
total RNAs were extracted with TRI reagent according to the manufacturers protocol (ThermoFisher Scientific) and the resulting RNAs treated with the RapidOut DNA Removal Kit (ThermoFisher Scientific).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)

tag: genotype

tag: infect

value: Micrococcus luteus

tag: infection time

value: 24 hours


title: Control subcutaneous adipose rep2

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C2-SF

value: Control


title: w_IBIN_Mlut24_B

description: sequencing was done in 1 lane


title: w_IBIN_Ecl6_C

description: sequencing was done in 1 lane

value: Enterobacter cloacae

value: 6 hours


title: N020_ROC10043

description: whole blood

tag: gender

value: F

tag: infection

value: picornavirus (rhinovirus)

tag: symptomatic

value: No


title: N017_ROC10035

description: whole blood


title: N033_ROC10077

description: whole blood

value: M


title: N028_ROC10065

description: whole blood

value: Yes


title: N025_ROC10057

description: whole blood


title: N023_ROC10052

description: whole blood


title: w_IBIN_Mlut24_C

description: sequencing was done in 1 lane


title: Control subcutaneous adipose rep1

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C1-SF


title: w_IBIN_Ecl6_B

description: sequencing was done in 1 lane


title: High-intake abdominal adipose rep3

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T3-AF

source_name: Abdominal adipose tissue

value: Abdominal adipose


title: w_IBIN_0h_C

description: sequencing was done in 1 lane

value: 0 hours


title: w_IBIN_Ecl6_A

description: sequencing was done in 1 lane


title: Control subcutaneous adipose rep3

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C3-SF

value: Tianfu


title: High-intake abdominal adipose rep2

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T2-AF

value: High-intake feeding


title: High-intake abdominal adipose rep1

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T1-AF


title: w_IBIN_0h_B

description: sequencing was done in 1 lane


title: N012_ROC10022

description: whole blood

value: picornavirus (cosxackievirus A2)


title: N016_ROC10032

description: whole blood


title: N024_ROC10054

description: whole blood

value: picornavirus (enterovirus D68)


title: N019_ROC10040

description: whole blood


title: w_IBIN_0h_A

description: sequencing was done in 1 lane


title: N009_ROC10016

description: whole blood


title: Control abdominal adipose rep3

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C3-AF

value: 145 days after birth


title: N011_ROC10020

description: whole blood


title: Control abdominal adipose rep2

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C2-AF


title: C564_IBIN_Mlut24_B

description: sequencing was done in 1 lane

value: Micrococcus luteus


title: N003_ROC10006

description: whole blood


title: Control abdominal adipose rep1

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C1-AF


title: RPMI_pH5_aa_flu rep3

city: Braga

first: Rosana

last: Alves

address: Campus de Gualtar

country: Portugal

institute: Universidade do Minho

data_processing:
Raw fastq files were successively processed in the following order through Fastqc (v. 10.1), Trimgalore (v. 3.1), Samtools (v. 1.19), Bowtie2 (v. 2.1) and Htseq (v.  5.4).
Genome alignment was conducted against the C_glabrata_CBS138_version_s02-m04-r05_chromosomes.fasta file provided by Candida Genome Database
Aligned data were quality-controlled via the Partek Genomics Suite software (v. 6.6), according to the manufacturer’s instructions.
Gene expression analysis was performed using Partek Genomics Suite software using a log2 data transformation as the Partek recommended default.
Genome_build: Genome alignment was conducted against the C_glabrata_CBS138_version_s02-m04-r05_chromosomes.fasta file provided by Candida Genome Database

organism: Nakaseomyces glabratus

source_name: biofilm

growth_protocol: Candida glabrata ATCC 2001 was subcultured on Sabouraud dextrose agar (SDA, Difco, Le Pont de Claix, France) medium at 37 °C for 24 h and then inoculated in Sabouraud dextrose broth (SDB; Difco) medium at 37 °C for 20–24 h while shaking at 120 rpm. Yeast cells were harvested by centrifugation after the incubation period (6500 × g, for 10 min at 4 °C), washed twice in phosphate buffered saline (PBS; pH 7, 0.1 M), and the cellular concentration was adjusted to 1×107 cells/mL in each RPMI 1640 medium conditions to be tested (Sigma, St Louis, USA) using an improved Neubauer chamber. Candida biofilms were developed on 24-well polystyrene plates (Orange Scientific, Braine-l'Alleud, Belgium; 12 wells for each condition) containing 1 mL of C. glabrata cell suspension (1×107 cells/mL in RPMI 1640) per well. The plates were then incubated at 37 °C under agitation at 120 rpm.

extract_protocol:
Following Candida biofilm development, each well was gently washed with 1 mL of PBS to remove non-adherent cells. Then biofilms were scraped from the plates with 500 µL of PBS per well, sonicated for 30 s at 30% amplitude (Ultrasonic Processor, Cole-Parmer, IL, USA) in order to separate cells from matrix (Fonseca et al., 2014) and then harvested by centrifugation at 8000 rpm for 10 min at 4 °C. Cells drops were flash frozen in liquid nitrogen and total RNA was isolated from frozen cell pellets using the RiboPure Yeast kit (Ambion, Life Technologies, USA), according to manufacturer’s instructions.  All samples were treated with Turbo DNAse (Ambion) to remove residual DNA, according to manufacturer's instructions. Total RNA yield was quantified using the Nanodrop 1000 (Thermo Scientific) and RNA quality (RNA Integrity Number (RIN) values ≥ 7.0) assessed on a Bioanalyzer 2100 (Agilent Technologies).
All samples were prepared in biological triplicates and subject to removal of rRNA before cDNA library generation.
From these libraries, 50 base single-end sequence reads were produced with Illumina Hiseq 2000

treatment_protocol: After 24 h, 500 μL of media in each well was removed and an equal volume of fresh media was added according to each condition (RPMI at pH 5.0 supplemented with 0.5 % (v/v) acetic acid; RPMI at pH 5.0 supplemented with 0.5% (v/v) acetic acid and 1250 µg/mL fluconazole; RPMI at pH 7.0; and RPMI at pH 7.0 supplemented with 1250 µg/mL fluconazole).

tag: strain

tag: protocol

value: RPMI pH5 + acetic acid + fluconazole


title: C564_IBIN_Mlut24_C

description: sequencing was done in 1 lane

value: 24 hours


title: RPMI_pH5_aa_flu rep2


title: N008_ROC10014

description: whole blood


title: High-intake liver rep3

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T3-liver

source_name: Liver tissue

tag: tissue

value: Liver


title: Regressive 64

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

institute: University College London

hyb_protocol: Thermofisher/Affymetrix Human Clariom D GeneChip as per manufacturer's instructions [Fluidics Station 450]

scan_protocol: Affymetrix Scanner 3000 7G as per manufacturer's instructions

data_processing: Processing was performed using R and Bioconductor. Raw data in CEL format were read using the read.celfiles method from the oligo package, and normalised using RMA.

source_name: Human preinvasive lung squamous cell carcinoma lesions

label_protocol: Thermofisher/Affymetrix WT Pico Kit Biotin labelling module as per manufacturer's instructions

extract_protocol: Laser-capture micro-dissection (LCM) was used to selectively isolate CIS cells for molecular analysis, reducing the extent of contamination by stromal cells. RNA was extracted using the High Pure FFPE RNA Kit (Roche Applied Science, West Sussex, UK) according to manufacturer’s protocol. Quantification was carried out using the Quant-iT RNA assay kit and the Qubit® 2.0 fluorometer (Life Technologies, Paisley, UK).

value: Preinvasive lung squamous cell carcinoma lesions

tag: lesion outcome

value: regression


title: C564_IBIN_Mlut24_A

description: sequencing was done in 1 lane


title: RPMI_pH5_aa_flu rep1


title: High-intake liver rep1

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T1-liver


title: Regressive 63


title: RPMI_pH5_aa rep3

value: RPMI pH5 + acetic acid


title: C564_IBIN_Ecl6_B

description: sequencing was done in 1 lane

value: Enterobacter cloacae

value: 6 hours


title: Regressive 62


title: RPMI_pH5_aa rep2


title: Control liver rep3

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C3-liver

value: Control


title: C564_IBIN_Ecl6_A

description: sequencing was done in 1 lane


title: High-intake liver rep2

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
T2-liver


title: Control liver rep2

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C2-liver


title: C564_IBIN_Ecl6_C

description: sequencing was done in 1 lane


title: Regressive 58


title: Regressive 57


title: C564_IBIN_0h_C

description: sequencing was done in 1 lane


title: RPMI_pH5_aa rep1


title: Regressive 52


title: Control liver rep1

description:
domestic goose
goose_mRNA_fpkm.txt/goose_lncRNA_fpkm.txt
C1-liver


title: RPMI_pH7_flu rep3

value: RPMI pH7 + Fluconazole


title: Regressive 59


title: RPMI_pH7_flu rep2


title: C564_IBIN_0h_A

description: sequencing was done in 1 lane

value: 0 hours


title: B2: Biofilm rep2

city: Evreux

first: Sophie

last: Rodrigues

state: ---US State---

address: 55 rue saint germain

country: France

institute: Université de Rouen

data_processing:
Illumina's base calling software
Sequenced reads were trimmed using Trimmomatic v0.36.4 tool
Reads were mapped to the the reference genome of V. tapetis CECT4600 strain (GenBank assembly accession number GCA_900233005.1) with the Boowtie2 v 2.3.2.2 software
HTseq-count v0.6.1 using the union model was used to calculate the number of reads mapping to each feature
The statistical analysis of differentially expressed genes was performed with the SARTools R package including DESeq2 package
Genome_build: GCA_900233005.1
Supplementary_files_format_and_content: tab-delimited text files include raw counts, pvalues and padj ...

organism: Vibrio tapetis

source_name: Biofilm culture

growth_protocol: Vibrio tapetis was cultivated in Zobell medium for 48h at 18°C with vigorous shaking (for planktonic culture). V. tapetis biofilms were grown at 18°C under hydrodynamic conditions in a three-channel flow cell for 48h.

extract_protocol:
Total RNA extractions were performed using the MasterPure Complete RNA purification Kit (Epicentre, Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: Biofilm culture


title: B3: Biofilm rep3


title: RPMI_pH7_flu rep1


title: Progressive 46

value: progression


title: B1: Biofilm rep1


title: RPMI_pH7 rep3

value: RPMI pH7


title: RPMI_pH7 rep2


title: Regressive 51


title: Progressive 42


title: C564_IBIN_0h_B

description: sequencing was done in 1 lane


title: L3: Liquid rep3

source_name: Planktonic culture

value: Planktonic culture


title: RPMI_pH7 rep1


title: L2: Liquid rep2


title: L1: Liquid rep1