title: T5

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
All experiments were conducted at QIAGEN Genomic Services
Filtering and subsequent mapping was done using theÂ QIAGEN GeneGlobe portal
The poly-A trimmed R1 reads from the above step are aligned to the reference genome using the splice aware aligner STAR. The reference genome used is human GRCh38, to which ERCC spike-in sequences are added. Gencode Release 23 for Human , Gencode Release M15 for mouse and Ensembl Release 91 for Rat was used to annotate splice junctions when building the genome index with STAR. The same transcript models are used for annotating reads during UMI counting.
The aligned reads from the above step are annotated to gene regions. UMIs are then counted for each gene across different cell indices, presented in R2. Before counting UMIs, we drop the following reads:
For targeted enrichment, any read with <= 25 bp aligned after the primer region (i.e.endogenous).
For targeted enrichment, any read which does not begin with a primer sequence.
For targeted enrichment, any read for which the primer is not aligned to the design locus.
For poly-A transcriptome, any read which is mapped to multiple genome loci.
Normalization of UMI counts and subsequent pairwise differential regulation analysis was done using DESeq2
Functional analysis to infer biological insights from the significantly differentially regulated genes were done with Ingenuity Pathway Analysis (IPA).
Genome_build: hg38
Supplementary_files_format_and_content: normalized expression in each sample; all differential regulated genes;  results of differential expression analysis

source_name: Differentiated hiPSCs_3D

extract_protocol:
Cells were harvested and lysed using Qiagen RLT buffer. RNA were extracted using Rneasey micro kit from Qiagen.
The library preparation was done using the QIAseq UPX 3’ Transcriptome Kit (QIAGEN). A total of 10ng purified RNA was converted into cDNA NGS libraries. During reverse transcription, each cell is tagged with a unique ID (up to 384 different IDs) and each RNA molecule is tagged with a unique molecular index (UMI). Then RNA was converted to cDNA. The cDNA was amplified using PCR and during the PCR indices were added. After PCR the samples were purified. Library preparation QC was performed using TapeStation 4200 (Agilent) or Agilent Bioanalyzer. Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using qPCR. The library pool were then sequenced on a NextSeq500 sequencing instrument according to the manufacturer instructions. Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.). FASTQ data were checked using the FastQC tool. Data analysis was performed using the QIAGEN GeneGlobe bioinformatics tool.

tag: source cell type

value: human induced pluriopotent stem cells (hiPSCs)

tag: culture condition

value: Encapsulated in alginate

value: Reprogrammed fibroblast


title: AML-2, primitive

status: Public on Jan 24 2020

type: SRA

city: Aurora

first: Shanshan

last: Pei

state: CO

country: USA

institute: University of Colorado

library_source: transcriptomic

data_processing:
Raw reads generated from the Illumina HiSeq2500 sequencer were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using Trimmomatic-0.36 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35".
Processed/cleaned reads were then mapped to the Homo sapiens reference sequence (GRCh38, hg38) with STAR-2.6.0c given the following parameters: "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
The subread-1.6.1 package (featureCounts) was used to derive gene counts given the following parameters: “-s 2 -t exon -g gene_name”.
Differential expression analysis and data normalization was performed using DESeq2-1.16.1 with an adjusted p-value threshold of 0.05 within an R-3.4.1 environment. A batch factor was given to the differential expression model in order to control for batch differences.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: raw counts produced by deSeq2 analysis provided in txt file

molecule: total RNA

organism: Homo sapiens

source_name: AML Patient G

growth_protocol: Freshly thawed and sorted, no growth involved

extract_protocol:
QIAGEN RNeasy Plus Kit
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.
Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample on the Illumina HiSeq2500 platform.

treatment_protocol: Freshly thawed and sorted, no treatment involved

tag: cell type

value: Primary human AML patient specimen

tag: group

value: primitive

tag: sub-fraction

value: ROSlow enriched LSCs


title: T3


title: T4


title: AML-1, monocytic

source_name: AML Patient A

value: monocytic


title: C6

source_name: Differentiated hiPSCs_CTRL

value: Growth on Matrigel


title: AML-2, monocytic

source_name: AML Patient B


title: T12


title: Decidua-062-cNK

city: Madison

first: Aleksandar

middle: K.

last: Stanic

state: WI

address: 202 S. Park St., Meriter Atrium B

department: Obstetrics and Gynecology

institute: University of Wisconsin - Madison

data_processing:
Base calling: CASAVA 1.8.2
Trimming: We used Skewer to trim Illumina adapters and low-quality 3’ ends with score < 20, and kept resulting reads of at least 30bp.
Alignment and quantification: We used the STAR pipeline within RSEM (v1.3.1) software. Within RSEM, reads were first aligned to the annotated human reference genome GRCh38 (release 94) with STAR (v2.6.1a) using parameter settings outFilterMultimapNmax=20,  outFilterMismatchNoverLmax=0.04, alignIntronMin=20. Gene expression levels were quantified as expected counts (ECs).
Quality control: DESeq2 (v.1.22.2) was used to perform Principal Components Analysis on variance-stabilized counts. PCA identified an outlier sample (Decidua-062-Cluster-10), which we excluded from further analysis, although it is provided here.
Insert size mean and standard deviation were computed by applying ‘samtools stats’ to transcriptome-aligned reads.
Genome_build: GRCh38 (release 94)
Supplementary_files_format_and_content: RSEM expected counts

source_name: Normal term decidua

growth_protocol: De-identified term human (>37 wks GA) placental samples were collected from normal elective cesarean sections under the UW Obstetrical Tissue Bank IRB protocol (#2014-1223). Briefly, decidua basalis was separated from placenta and decidua parietalis was scraped from the embryonic membrane and washed with cold PBS, as previously described (15). Tissue was minced and dissociated in RPMI containing 1 mg/ml of Collagenase type V (Worthington Biochem. Corp.), 2 μg/ml DNAse I (Worthington Biochem. Corp.), using the gentleMACS™ Dissociator system (Miltenyi Biotec Inc. San Diego, CA). Homogenates were then filtered through a 70 μm filter, red blood cells were lysed with ACK lysis buffer (Life Technologies) and mononuclear cells (MCs) were recovered and frozen until processing.

extract_protocol:
Sorted mononuclear cell lysates were processed using the NucleoSpin® RNA XS (Takara Bio USA Inc) according to manufacturer’s instructions. A small aliquot of RNA from each sample was set aside for RNA quality control and quantification. RNA quality was assessed using the Agilent© RNA 6000 Pico Kit and analyzed on the Agilent© 2100 Bioanalyzer. RNA quantity was measured using the NanoDrop™ Spectrophotometer (Thermo Scientific™).
Libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA Inc) and sequenced on the Illumina© HiSeq 2500 system.

treatment_protocol: Prior to FACS sorting, ILCs were enriched using Dynabeads™ Untouched™ Human NK Cells Kit (Invitrogen), allowing for the depletion of T, B, DCs, and macrophages. Enriched ILCs were labeled with Zombie NIR to discriminate dead cells and flourochrome-conjugated monoclonal antibodies (CD3, 14, 16, 19, 34, 45, 49a, 56, 94, 117, 127)  and sorted using the BD FACS Aria II (BD Biosciences) directly into lysing buffer (NucleoSpin® RNA XS, Takara Bio USA Inc, Mountain View, CA) for RNA isolation.

tag: individual

value: Decidual cNK

tag: lineage

value: Lineage Negative CD56DimCD16+


title: L28

data_processing:
All analysis were carried out using CLC Genomics Workbench (version 12.0.2) and CLC Genomics Server (version 11.0.2).
Adapter and quality trimming was done by “Trim Reads” tool from CLC Genomics Workbench
The QC reports were generated by “QC for Sequencing Reads” tool from CLC Genomics Workbench
Read mapping and gene quantification were done by “RNA-seq Analysis” tool from CLC Genomics Workbench
Genome_build: hg38
Supplementary_files_format_and_content: A csv file with normalized expression in each sample

source_name: Differentiated hiPSCs

extract_protocol:
Cells were harvested and lysed using Qiagen RLT buffer. RNA were extracted using Rneasey micro kit from Qiagen.
Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: diff stage

value: beta-like cells

tag: tissue


title: T9


title: MiniCoopR-GFP melanoma, rep6

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were aligned using STAR (v2.6.1d), Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 2013, 29:15-21.
Read counting was performed using htseq-count v0.6.0
Differential gene expression was performed using Deseq2, Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 2014, 15:550.
Genome_build: Zv9
Supplementary_files_format_and_content: Differential gene expression was performed using Deseq2 and outputted in a .csv file with ensembl gene identifiers.

molecule: polyA RNA

organism: Danio rerio

source_name: MiniCoopR-GFP melanoma

growth_protocol: Routine zebrafish husbandry

extract_protocol:
Total RNA was isolated using Rneasy plus mini kit (Qiagen) according to the manufacturer's protocol
Library construction was performed using Illumina reagents according to the manufacturer's protocol

tag: genotype

value: MiniCoopR-GFP

value: zebrafish melanoma


title: MiniCoopR-MyrRSK melanoma, rep5

source_name: MiniCoopR-MyrRSK melanoma

value: MiniCoopR-MyrRSK


title: MiniCoopR-MyrRSK melanoma, rep3


title: MiniCoopR-MyrRSK melanoma, rep6


title: L27


title: MiniCoopR-MyrRSK melanoma, rep1


title: Decidua-062-Cluster-2

value: Decidual ILC population C2


title: MiniCoopR-GFP melanoma, rep5


title: C7


title: T7


title: MiniCoopR-GFP melanoma, rep4


title: AML-3, monocytic

source_name: AML Patient C


title: MiniCoopR-MyrRSK melanoma, rep4


title: MiniCoopR-MyrRSK melanoma, rep2


title: MiniCoopR-GFP melanoma, rep3


title: L26


title: L20

value: Pancreatic progenitor


title: MiniCoopR-GFP melanoma, rep1


title: Decidua-062-Cluster-10

value: Decidual ILC population C10


title: L19


title: MiniCoopR-GFP melanoma, rep2


title: IL4 injected GFP(+) 24 hpi rep2

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

data_processing:
The FastQ files from sequencing were aligned to zebrafish genome (GRCz10/danRer10) using gsnap () with default options. The read counts for each gene were calculated using featureCounts and GTF file from ensemble genome browser (Danio_rerio.GRCz10.81.gtf).
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: The processed data files contain read counts calculated by featureCounts. The first 6 columns is information about the gene (ensembl gene id, chromosome, start, end, strand, length), and the remaining columns contain read counts of each gene in the corresponding sample.

source_name: IL4 injected GFP(+) 24 hpi rep2

growth_protocol: Fish were cultured at 28 °C at a 14:10 h light:dark cycle in a recirculating tank system.

extract_protocol:
Zebrafish brains from Tg(her4.1:EGFP) were dissected after PBS or IL4 injections at 24 hpi. Cells were dissociated with Miltenyi Neural Tissue Dissociation Kit as described (Kyritsis et al., 2012). Cells were sorted with BD Aria II FACS machine, RNA was isolated using Norgen Total RNA Purification Kit.
Complete cDNA was synthesized from the obtained mRNA with SmartScribe reverse transcriptase using a universally tailed poly-dT primer and template switching oligo. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase. After ultrasonic shearing of the amplified cDNA (Covaris S2) samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75bp single-end sequencing on the Illumina HiSeq2000 platform providing on average 31 million reads per sample.

treatment_protocol: Fish brains were injected with PBS or IL4 peptides.

value: brain

tag: age

value: 6 mpf


title: Decidua-056-Cluster-2


title: IL4 injected GFP(-) 24 hpi rep2

source_name: IL4 injected GFP(-) 24 hpi rep2


title: IL4 injected GFP(-) 24 hpi rep1

source_name: IL4 injected GFP(-) 24 hpi rep1


title: L18

value: Reprogrammed fibroblast


title: IL4 injected GFP(+) 24 hpi rep1

source_name: IL4 injected GFP(+) 24 hpi rep1


title: Decidua-056-Cluster-10


title: L15


title: PBS injected GFP(+) 24 hpi rep1

source_name: PBS injected GFP(+) 24 hpi rep1


title: L11


title: PBS injected GFP(+) 24 hpi rep2

source_name: PBS injected GFP(+) 24 hpi rep2


title: PBS injected GFP(-) 24 hpi rep1

source_name: PBS injected GFP(-) 24 hpi rep1


title: PBS injected GFP(-) 24 hpi rep2

source_name: PBS injected GFP(-) 24 hpi rep2


title: L6


title: Decidua-056-cNK

description: PCA identified an outlier sample (Decidua-062-Cluster-10), which we excluded from further analysis.


title: Decidua-053-Cluster-2


title: Decidua-053-Cluster-10


title: L5


title: 48.D235.LPS

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

data_processing:
50bp-length single-end sequences were aligned to the human genome (hg38) using STAR version 2.4.2a.
Samtools 0.1.19 was used to filter alignments to a MAPQ score threshold of 30
Counts per gene were called using featureCounts version 1.4.6 and gencode v24 genome annotation.
Samtools 0.1.19 was used to filter alignments to a MAPQ score threshold of 30
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression analysis was performed separately for each RNA-seq experiment using DESeq2 version 1.10.1 and R version 3.2.3, using time and treatment together as the design parameter

source_name: PBMCs

growth_protocol: To generate monocyte-derived dendritic cells, CD14+ monocytes from PBMC buffy coats were isolated with anti-human CD14 magnetic beads (Miltenyi) and cultured in RPMI containing 10% heat-inactivated fetal bovine serum (FBS), 50 U/ml penicillin, 50 ug/ml streptomycin (P/S), 10 mM HEPES, beta mercaptoethanol, and 2 mM glutamine, in the presence of recombinant human GM-CSF at 10 ng/ml and IL-4 at 50 ng/ml.  Fresh media and cytokines were added to cells (40% by volume) on day 1. On day 4, cells were collected, resuspended in fresh media with cytokines used for infection. To overcome restriction to HIV-1 reverse transcription, virus-like particles packaging Vpx were added to cells prior to infection.

extract_protocol:
Cells were lysed in TRIzol reagent (Thermo Fisher), RNA was isolated according the manufacturer’s instructions, and then samples were submitted to HudsonAlpha Institute for Biotechnology (https://hudsonalpha.org/) for library preparation and RNA-sequencing .
Libraries were prepare by HudsonAlpha Institute for Biotechnology (https://hudsonalpha.org/)

treatment_protocol: DCs from seven unique donors were stimulated by HIV in the presence or not of Vpx or innate immune stimuli (LPS, PolyIC, cGAMP, R848, rIFN)  for 2, 8, 24 or 48 h . Cells were stained for Live/Dead Aqua and CD86 to assess activation status and then all live cells were sorted on a FACSAria (BD Biosciences) based on GFP expression for HIV replication (when applicable) and CD86 for DC maturation.

tag: time

value: lps


title: L4


title: 48.D235.pLKO1.SIV_VPX.GFP_POS

value: GFP+ (G)plko.1GFP + VPX


title: Decidua-053-cNK


title: 48.D235.NL4_3.SIV_VPX.GFP_POS.CD86_LOW

value: GFP+ 86- (G)HIVGFP + VPX


title: isl2

source_name: Pancreatic islets

value: Pancreas


title: isl1


title: 48.D235.pIC

value: poly iC


title: H3K4me2_MP1_S7

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
Sequences were mapped to the human genome (hg19) using bwa with default parameters
BAM files were filtered for quality and proper mapping using samtools view with flags -q10 -F1796
Bigwig coverage files generated using deepTools bamCoverage with parameters: -bs 50 -e 500 --normalizeUsing RPGC --effectiveGenomeSize 2451960000
Peak calling with MACS2, with parameters --slocal=2000 --llocal=50000 --nomodel --extsize=1500 -q .0005 -g hs
Peaks of replicates from of the same kind were merged (union)
Genome_build: hg19

molecule: genomic DNA

source_name: Human skin melanoma

growth_protocol: Cells were growth in MEM completed with 10 % FCS, antibiotics, puruvate, glutamine and vitamines.

extract_protocol:
AMPure XP beads
ChIP libraries were prepared according to illumina Genomic DNA protocol. Briefly, DNA fragments after ChIP were end repaired using two enzyme ( T4 DNA polymerase, T4 PNK), the blunted fragments were then A-tailed using Klenow fragment ( 3'-5- exo-) enzyme, Illumina adaptor ligation to the DNA fragments was carried on using  T4 DNA Ligase from NEB (M0202), Libraries were then amplified for 8 cycles and size selected for an average  of 350 bp, Libraries were then sequenced on NextSeq 500 following the manufacturer instruction.

value: A375 positive

tag: passage

tag: aggressiveness sorting

value: 5 time


title: 48.D235.NS

value: NS


title: isl3


title: H3K4me2_MP1_S6


title: 48.D234.pLKO1.SIV_VPX.GFP_NEG

value: GFP- (G)plko.1GFP + VPX


title: H3K4me2_MWN1_S3

value: A375 negative


title: A375_negative_rep3

description:
Benny_processed_A375.xlsx
sample name:
Benny22

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 83, using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: Human Skin melanoma

extract_protocol: Inhouse poly A based RNA seq

treatment_protocol: Generation of two sub-cell populations originated from a single cell line, differing by their capacity to uptake 2.4 µm beads, was done by the FACS sorter. Each FACS sorting procedure separated cells that did not uptake any particles (“negative”, FL2Low) from the rest of the cells (“positive”, uptake of at least one bead, FLhigh). Therefore, after the first sorting, in each cycle we obtained four different sub-sets of cells: positive-positive; positive-negative, negative-positive, negative-negative. Only the positive-positive and negative-negative were kept for further sorting. In each cycle the sorting enrichment, Δ, was defined as  ∆≡J_+^+-J_+^- where J_+^+ was the percent of positive cells obtained in a sorting procedure on the positive-positive population of the previous cycle, and J_+^- was the percent of positive cells obtained in a sorting procedure on the negative-negative population of the previous cycle. An exception to this definition is the first cycle where both of the percent values of positive cells were calculated relative to the same origin population of cells, yielding J_+^+-J_+^-=0. Each sorting included the flowing steps. Cells were cultured for five generations and incubated with 2.4 µm beads for 24 h. Cells were then washed thoroughly with PBS and detached with trypsin, centrifuged, counted and diluted to 1.0x10^7 cells/ml in PBS. Using a BD-FACSAria-III cell sorter, cells were analyzed and sorted based on the fluorescence intensity distribution (FL-2). The levels of fluorescence intensity indicated accurately on the number of internalized particles, allowing for a highly sensitive uptake-based sorting.

tag: parental cell line

tag: cell population

value: Human Skin melanoma

value: 5 times


title: H3K4me2_MWN1_S2


title: Leiomyoma_PLIN2_siRNA4

city: Chicago

first: Ping

last: Yin

state: IL

address: 303 East Superior Street, Lurie 10-107

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Primary uterine leiomyoma cells

growth_protocol: All cell-based assays were performed on primary cells isolated from fresh leomyoma tissue and passaged once. Primary cells were cultured in DMEM/F12 1:1 (GIBCO/BRL, 11320-082) containing 10% (vol/vol) FBS in a humidified atmosphere in 5% (vol/vol) CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (#74104; Qiagen). All samples were pre-treated with RNase-Free DNase (Qiagen). RNA quality was assessed using the Agilent Bioanalyzer 2100.
Construction of the RNA-seq library was completed per the manufacturer’s instructions using the KAPA Stranded RNA-seq Kit with RiboErase (#KK8483; KAPA Biosystems, Wilmington, MA). The RNA library concentrations were measured by Qubit (Thermo Fisher Scientific) and library quality determined using the Agilent Bioanalyzer 2100.

treatment_protocol: Leiomyoma cells were transfected with PLIN2 small interfering RNA (siRNA; 100 nM, #4392422; Ambion, Foster City, CA) or non-targeting siRNA (100 nM, #4390844; Ambion). siRNAs were resuspended in Opti-MEM reduced-serum media (Thermo Fisher Scientific) and then complexed with Opti-MEM reduced-serum media containing Lipofectamine RNAiMAX (Thermo Fisher Scientific) for 15 minutes before being added to their respective plate of leiomyoma cells. After a 5-hour incubation period, cells were supplemented with equal volumes of phenol-red free DMEM/F12 containing 20% CS-FBS. Cells were then starved 24 hours after transfection with starvation medium. After 72 hours, cells were lysed using buffer RLT containing 1:100 β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, #M3148) in preparation for RNA extraction for RNA-sequencing (RNA-seq).

tag: subject id

value: patient 4

value: Primary uterine leiomyoma cells

tag: passages

value: Primary P1

tag: treatment

value: PLIN2 siRNA 72 h


title: RNA-seq in 0.5uM EPZ6438 treated CD34+ duplicate #2

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

data_processing:
RNA-seq reads is aligned to genome by STAR and bigwig file is generated by RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: hematopietic progenitor and stem cells

growth_protocol: Cord Blood derived CD34+ HSPCs are cutlrued in SFEM II medium supplemented with 100ng/mL human TOP, SCF and FLT3L for 7 days, CD34+ CD38- cells are isolated with Miltenyl CD38 CD34 isolation kit

extract_protocol:
RNA was extracted by Qiagen Allprep DNA/RNA micro kit.
RNA-seq libraries is build by NEB NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: DMSO is added to medium to 1:1000 dilution, EPZ6438 is added to medium to 0.5μM HSPCs are cultured for 7 days

value: EZH2 inhibitor EPZ6438


title: 48.D234.pLKO1.SIV_VPX.GFP_POS


title: 48.D234.NL4_3.SIV_VPX.GFP_POS.CD86_LOW


title: 48.D234.NL4_3.SIV_VPX.GFP_POS.CD86_HIGH

value: GFP+ 86+ (G)HIVGFP + VPX


title: 48.D235.NL4_3.SIV_VPX.GFP_POS.CD86_HIGH


title: Leiomyoma_PLIN2_siRNA3

value: patient 3

tag: cell type


title: Leiomyoma_PLIN2_siRNA2

source_name: Primary uterine myometrial cells

value: patient 2

value: Primary uterine myometrial cells


title: 48.D234.pIC

value: poly iC


title: 48.D234.LPS

value: lps


title: I10R026f03_ES51/10 ; Nervous system

type: RNA

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

hyb_protocol: Labeled cRNA were hybridized onto Human Genome U219 Gene Chip® arrays (Affymetrix).

scan_protocol: Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions. Scanned images were subjected to visual inspection to control for hybridization artifacts and proper grid alignment and analyzed with AGCC 3.0 (Affymetrix) to generate CEL files.

data_processing: All steps were performed in the language R (version 3.1.1) mainly with the packages “affy” (version 1.42.3) and “limma” (version 3.20.9). Initially, the expression data from all 74 chips were quantile normalized with RMA (Robust Multichip Average). Then a non-specific filtering step was included in the analysis to remove low variable genes using the rowSds() function from genefilter package (version 1.46.1 ). All subsequent steps were done with standard Limma functions including an empirical Bayes step and a correction step for multiple testing to determine significance for DE analysis based on a multiple adjusted p value < 0.05 (5% false discovery rate (FDR)).

label: biotin

source_name: controls of vestibular nerve tissue that were obtained post mortem and used as controls

label_protocol: 100 ng of total RNA was biotinylated using the GeneChip ® HT 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Vestibular schwannoma tumor samples were prospectively collected from 67 patients (39 males, 28 females) during their first-time surgical resection. Seven controls of vestibular nerve tissue were obtained post mortem and used as controls. Among the tumor samples 36 were sporadic, 13 NF2-associated, 9 cystic and 9 pre-irradiated regrowing VS comprising five sporadic, one cystic and three NF2-associated tumors. Tumor recurrence time after irradiation was over 3 years and pseudoprogression was excluded by regular imaging. Tumor samples were microdissected by the retrosigmoid approach and were immediately frozen and stored at -80°C. Conventional neuropathological examination with paraffin-embedded tissue sections histologically confirmed the diagnosis (as schwannoma WHO grade I). For all NF2-associated tumors, mutation analysis was performed as previously described. Total RNA was extracted from non-irradiated and irradiated tumors using an RNeasy ® Microarray Tissue Mini Kit System (Qiagen, Valena, CA, USA) according to the manufacturer´s instructions and stored at -80°C. Quantitative and qualitative RNA was verified by a Lab-on-a-Chip-System using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA). Samples with a RIN higher or equal to 5 were selected for analysis.

tag: diagnosis

value: Control

value: Vestibular nerve tissue

tag: radiation

value: non-radiated


title: I10R026f02_ES45/10 ; Nervous system


title: Leiomyoma_Control_siRNA4

value: scrambled control siRNA 72 h


title: I10R026d02_ES43/10 ; Nervous system


title: Multiple Myeloma Replicate44 (miRNA)

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

description:
miRNA expression in plasma of MM patient
SM170

hyb_protocol: Samples were hybridized onto Human miRNA 8X 60 K format microarrays (Agilent Technologies) based on miRBase Release 19.0 at 55 °C for 20 h.

scan_protocol: After hybridization microarrays were washed with Gene Expression Wash Buffer Kit and scanned using SureScan microarray scanner D (Agilent Technologies).

data_processing: Quantitative data values were obtained from the images using Feature Extraction software ver 11.5.1.1 (Agilent) using default parameters.

source_name: Bone marrow

label_protocol: Briefly, 100 ng of total RNA was labeled with cyanine3-pCp using miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Cy3-labeled samples were dried for up to 3 h in the vacuum concentrator and then resuspended in nuclease-free water.

extract_protocol: Plasma cells were obtained from the bone marrow aspirates by magnetic bead separation using the human CD138 RosetteSep kit (Stem Cell Technologies, Vancouver, British Columbia, Canada.The cells were stored in TRIZOL at  −80°C until analysis. Total RNA was isolated from CD138+ sorted cells of myeloma patients using the miRVana RNA isolation kit according to manufactures’ instructions (Ambion, USA).

tag: disease state

value: Multiple Myeloma

value: Plasma Cells

tag: gender

value: M


title: Leiomyoma_PLIN2_siRNA1

value: patient 1


title: Multiple Myeloma Replicate43 (miRNA)

description:
miRNA expression in plasma of MM patient
SM321


title: 48.D225.pLKO1.SIV_VPX.GFP_NEG

value: GFP- (G)plko.1GFP + VPX


title: I10R026b04_ES32/10 ; Nervous system


title: Leiomyoma_Control_siRNA3

value: Primary uterine leiomyoma cells

value: Primary P1


title: Leiomyoma_Control_siRNA2


title: 48.D234.NS

value: NS


title: Inflammatory breast cancer sample 25

type: genomic

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description: Hybridized to Affymetrix CytoScan HD Array

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Arrays were scanned using the GeneChip™ Scanner 3000 7G System

data_processing: The data was processing primarily using the ChAS soiftware

label: Biotin

source_name: breast tissue 25

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted using the QIAsymphony Kit (Qiagen, Valencia, Ca, USA).

value: breast cancer


title: I10R026b03_ES31/10 ; Nervous system


title: 48.D225.NL4_3.SIV_VPX.GFP_POS.CD86_HIGH

value: GFP+ 86+ (G)HIVGFP + VPX


title: Multiple Myeloma Replicate41 (miRNA)

description:
miRNA expression in plasma of MM patient
SM5

value: F


title: I10R026b02_ES21/10 ; Nervous system


title: Leiomyoma_Control_siRNA1

value: Primary uterine myometrial cells


title: Inflammatory breast cancer sample 26

source_name: breast tissue 26


title: Multiple Myeloma Replicate42 (miRNA)

description:
miRNA expression in plasma of MM patient
SM119


title: Inflammatory breast cancer sample 13

source_name: breast tissue 13


title: Inflammatory breast cancer sample 24

source_name: breast tissue 24


title: 48.D225.NL4_3.SIV_VPX.GFP_POS.CD86_LOW

value: GFP+ 86- (G)HIVGFP + VPX


title: Multiple Myeloma Replicate40 (miRNA)

description:
miRNA expression in plasma of MM patient
SM126


title: 48.D225.pIC

value: poly iC


title: I10R026b06_ES34/10 ; Nervous system

value: Control

value: Vestibular nerve tissue


title: I10R026f05_148/07 ; Nervous system

source_name: irradiated NFII associated tumors from the nervous system

value: Vestibular schwannoma WHO grade I

value: Vestibular schwannoma tumor

tag: vs type

value: irradiated


title: Inflammatory breast cancer sample 14

source_name: breast tissue 14


title: Inflammatory breast cancer sample 20

source_name: breast tissue 20


title: Multiple Myeloma Replicate39 (miRNA)

description:
miRNA expression in plasma of MM patient
SM267

value: Multiple Myeloma

value: Plasma Cells

value: M


title: Inflammatory breast cancer sample 6

source_name: breast tissue 6


title: 48h_mock_D184

data_processing:
Unique sequence read pairs were aligned to the human genome (hg38) using bowtie2 (2.2.3), filtered based on mapping score (MAPQ > 30, Samtools (0.1.19)), and duplicates removed (Picard version 1.120).
For establishing the network prior, a merged ATAC-seq Sam file was generated by combining all ATAC-seq conditions. Peak calling was performed with Peakdeck version 1.1 (parameters -bin 160, -STEP 25, -back 5000, -npBack 10000) using the start and end locations of the pairs to define fragment lengths, with a p-value of 1e-4 as the cutoff, outputting 87,681 unique, non-overlapping, high-confidence peaks.
Alternatively, basecalls were performed using CASAVA. Reads were aligned to a combined genome including human chromosomes (hg19), HIV (laboratory construct highly similar to NY5/BRU recombinant clone pNL4-3, GenBank ID = M19921.2) and SIV (isolate Mm251, GenBank ID = M19499.1) sequences using gsnap [Wu, Bioinformatics, 2010] (2015-09-10) and stripping off adapter sequences in a pairwise manner.
Only pairs that aligned uniquely and concordantly to non-mitochondrial human chromosomes were retained. Duplicate pairs of reads were removed based on their start and end chromosomal locations.  Start and end positions of the sequences were adjusted to extend 4 and 5 base pairs respectively to account for transposase adapter insertion (see [Buenrostro, Nature, 2013]).
Peak calling was performed with MACS2 (2.1.0) [Zhang, Genome Biol., 2008] using the start and end locations of the pairs to define fragment lengths. ‘Blacklisted’ regions of known artificially high signal as defined by the Human ENCODE project (www.encodeproject.org/annotations/ENCSR636HFF) were filtered out of peak regions.
Genome_build: hg19; hg38
Supplementary_files_format_and_content: Bigwig files for each biological group were generated by running MACS2 peak calling and outputting a normalized bedgraph file followed by file conversion to bigWig using the bedGraphToBigWig program from genome.ucsc.edu. A table containing rlog peak counts that were calculated across all samples for the 87681 identified peaks is also provided.

source_name: PBMCs

growth_protocol: To generate monocyte-derived dendritic cells, CD14+ monocytes from PBMC buffy coats were isolated with anti-human CD14 magnetic beads (Miltenyi) and cultured in RPMI containing 10% heat-inactivated fetal bovine serum (FBS), 50 U/ml penicillin, 50 ug/ml streptomycin (P/S), 10 mM HEPES, beta mercaptoethanol, and 2 mM glutamine, in the presence of recombinant human GM-CSF at 10 ng/ml and IL-4 at 50 ng/ml.  Fresh media and cytokines were added to cells (40% by volume) on day 1. On day 4, cells were collected, resuspended in fresh media with cytokines, and then mock treated (Vpx alone) or infected with a single-cycle HIV-1 reporter virus (Vpx and HIV-1-GFP).  To overcome restriction to HIV-1 reverse transcription, virus-like particles packaging Vpx were added to cells prior to infection.

extract_protocol:
Nuclei from 50,000 sorted DCs were subjected to a transposase reaction as described in Buenrostro, 2013.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: DCs from three unique donors were treated with Vpx (mock condition) or infected with HIV-1-GFP in the presence of Vpx for 2, 8, 24, or 48 h.  Cells were stained for Live/Dead 405 and CD86 to assess activation status and then live cells were sorted on a FACSAria (BD Biosciences) as indicated (GFP+/- or CD86 high/low).

value: mock


title: 48.D225.LPS

value: lps


title: Inflammatory breast cancer sample 16

source_name: breast tissue 16


title: Inflammatory breast cancer sample 10

source_name: breast tissue 10


title: Inflammatory breast cancer sample 7

source_name: breast tissue 7


title: Inflammatory breast cancer sample 11

source_name: breast tissue 11


title: Inflammatory breast cancer sample 19

source_name: breast tissue 19


title: Inflammatory breast cancer sample 9

source_name: breast tissue 9


title: Multiple Myeloma Replicate38 (miRNA)

description:
miRNA expression in plasma of MM patient
SM188


title: I10R026f04_147/07 ; Nervous system

tag: tissue


title: 48h_mock_D185


title: 48.D225.NS

value: NS


title: 48h_mock_D183


title: 48h_HIV-GFP-CD86low_D185


title: I10R026a12_290/08 ; Nervous system


title: 48.D225.pLKO1.SIV_VPX.GFP_POS

value: GFP+ (G)plko.1GFP + VPX


title: Inflammatory breast cancer sample 22

source_name: breast tissue 22

value: breast cancer


title: Inflammatory breast cancer sample 1

source_name: breast tissue 1


title: Inflammatory breast cancer sample 2

source_name: breast tissue 2


title: Multiple Myeloma Replicate37 (miRNA)

description:
miRNA expression in plasma of MM patient
SM224

source_name: Bone marrow

value: F


title: Inflammatory breast cancer sample 15

source_name: breast tissue 15


title: Inflammatory breast cancer sample 4

source_name: breast tissue 4


title: 48h_HIV-GFP-CD86low_D184


title: Inflammatory breast cancer sample 5

source_name: breast tissue 5


title: I10R026e08_360/09 ; Nervous system

source_name: irradiated cystic associated tumors from the nervous system


title: Control Replicate4 (miRNA)

description:
miRNA expression in plasma of healthy controls
HD Pooled4

value: Mononuclear cells


title: 48h_HIV-GFP-CD86low_D183


title: 48.D223.LPS


title: Multiple Myeloma Replicate35 (miRNA)

description:
miRNA expression in plasma of MM patient
SM201


title: 48.D223.NL4_3.SIV_VPX.GFP_POS.CD86_LOW

value: GFP+ 86- (G)HIVGFP + VPX


title: 48.D223.pIC

value: poly iC


title: Inflammatory breast cancer sample 18

source_name: breast tissue 18


title: 48.D223.NS


title: 24h_mock_D185


title: 48.D180.NS.SIV_VPX_NEG_BIS

description: exp1_infection_with_or_without_Vpx_expression_matrix.txt

value: Vpx(-)


title: 24h_mock_D184


title: 48h_HIV-GFP-CD86hi_D185


title: 48h_HIV-GFP-CD86hi_D183


title: 48.D180.NS.SIV_VPX_BIS

value: Vpx


title: Inflammatory breast cancer sample 3

source_name: breast tissue 3


title: Multiple Myeloma Replicate33 (miRNA)

description:
miRNA expression in plasma of MM patient
SM197


title: 24h_mock_D183

source_name: PBMCs


title: I10R026a29_312/09 ; Nervous system

source_name: irradiated sporadic associated tumors from the nervous system

value: Vestibular schwannoma WHO grade I


title: 48.D180.pLKO1


title: I10R026c20_416/10 ; Nervous system

source_name: non-radiated NFII associated tumors from the nervous system

value: Vestibular schwannoma tumor

value: NFII

value: non-radiated


title: Multiple Myeloma Replicate32 (miRNA)

description:
miRNA expression in plasma of MM patient
SM343

value: Multiple Myeloma

value: Plasma Cells


title: I10R026a27_331/09 ; Nervous system


title: Multiple Myeloma Replicate31 (miRNA)

description:
miRNA expression in plasma of MM patient
SM351

value: M


title: I10R026e01_341/09 ; Nervous system

value: irradiated


title: Inflammatory breast cancer sample 23

source_name: breast tissue 23


title: 48.D180.pLKO1.SIV_VPX_NEG_BIS


title: Multiple Myeloma Replicate36 (miRNA)

description:
miRNA expression in plasma of MM patient
SM325


title: I10R026a16_206/08 ; Nervous system


title: 24h_HIV-GFPpos_D184

value: HIV-GFPpos


title: I10R026a28_372/09 ; Nervous system


title: 48.D180.pLKO1.SIV_VPX_BIS


title: 24h_HIV-GFPpos_D185


title: Multiple Myeloma Replicate30 (miRNA)

description:
miRNA expression in plasma of MM patient
SM237


title: 48.D180.NL4_3.SIV_VPX_NEG_BIS

value: (G)HIVGFP+ Vpx(-)


title: Inflammatory breast cancer sample 8

source_name: breast tissue 8

value: breast cancer


title: Multiple Myeloma Replicate29 (miRNA)

description:
miRNA expression in plasma of MM patient
SM133


title: 48.D180.NS

value: NS


title: 24h_HIV-GFPpos_D183


title: I10R026a26_307/09 ; Nervous system


title: 24h_HIV-GFPneg_D185

value: HIV-GFPneg


title: 24h_HIV-GFPneg_D184


title: 48.D180.NL4_3.SIV_VPX_BIS

value: (G)HIVGFP+ Vpx


title: Multiple Myeloma Replicate27 (miRNA)

description:
miRNA expression in plasma of MM patient
SM48


title: 48.D180.NS.SIV_VPX_NEG


title: Inflammatory breast cancer sample 12

description: Hybridized to Affymetrix CytoScan HD Array

source_name: breast tissue 12


title: 48.D180.NS.SIV_VPX


title: I10R026a14_304/08 ; Nervous system


title: I10R026a13_301/08 ; Nervous system


title: Multiple Myeloma Replicate28 (miRNA)

description:
miRNA expression in plasma of MM patient
SM208


title: 24h_HIV-GFPneg_D183


title: 8h_mock_D185

value: mock


title: Multiple Myeloma Replicate26 (miRNA)

description:
miRNA expression in plasma of MM patient
SM167

value: F


title: I10R026e03_433/10 ; Nervous system


title: I10R026a11_289/08 ; Nervous system


title: I10R026a36_409/10 ; Nervous system


title: 8h_mock_D184


title: 48.D180.pLKO1.SIV_VPX_NEG


title: Multiple Myeloma Replicate23 (miRNA)

description:
miRNA expression in plasma of MM patient
SM330


title: 48.D180.pLKO1.SIV_VPX


title: I10R026a08_259/08 ; Nervous system


title: 8h_mock_D183


title: 8h_HIV-GFP_D185

value: HIV-GFP


title: 48.D180.NL4_3.SIV_VPX_NEG


title: Multiple Myeloma Replicate22 (miRNA)

description:
miRNA expression in plasma of MM patient
SM339


title: I10R026a07_223/08 ; Nervous system

value: Vestibular schwannoma WHO grade I


title: Multiple Myeloma Replicate25 (miRNA)

description:
miRNA expression in plasma of MM patient
SM67


title: I10R026a10_288/08 ; Nervous system

value: Vestibular schwannoma tumor


title: 48.D223.NL4_3.SIV_VPX.GFP_POS.CD86_HIGH

value: GFP+ 86+ (G)HIVGFP + VPX


title: Control Replicate3 (miRNA)

description:
miRNA expression in plasma of healthy controls
HD pooled3

value: Control

value: Mononuclear cells


title: 48.D180.NL4_3.SIV_VPX


title: 48.D179.NS.SIV_VPX_NEG_BIS

value: Vpx(-)


title: 8h_HIV-GFP_D183


title: I10R026a02_168/07 ; Nervous system

value: NFII

value: non-radiated


title: 8h_HIV-GFP_D184


title: 2h_mock_D185


title: 48.D179.NS.SIV_VPX_BIS

value: Vpx


title: 48h_HIV-GFP-CD86hi_D184


title: 2h_mock_D184


title: I10R026a01_159/07 ; Nervous system


title: I10R026a22_237/08 ; Nervous system

source_name: non-radiated cystic associated tumors from the nervous system

value: cystic


title: Multiple Myeloma Replicate21 (miRNA)

description:
miRNA expression in plasma of MM patient
SM24

value: Multiple Myeloma

value: Plasma Cells

value: M


title: 2h_mock_D183


title: I10R026e10_422/10 ; Nervous system


title: 48.D179.pLKO1.SIV_VPX_NEG_BIS


title: Multiple Myeloma Replicate20 (miRNA)

description:
miRNA expression in plasma of MM patient
SM21


title: Multiple Myeloma Replicate17 (miRNA)

description:
miRNA expression in plasma of MM patient
SM69


title: 48.D179.NL4_3.SIV_VPX_NEG_BIS

description: exp1_infection_with_or_without_Vpx_expression_matrix.txt

value: (G)HIVGFP+ Vpx(-)


title: Multiple Myeloma Replicate18 (miRNA)

description:
miRNA expression in plasma of MM patient
SM10


title: 48.D179.pLKO1.SIV_VPX_BIS


title: I10R026e07_357/09 ; Nervous system


title: I10R026e09_399/10 ; Nervous system


title: 2h_HIV-GFP_D185


title: I10R026a09_275/08 ; Nervous system


title: 48.D179.NL4_3.SIV_VPX_BIS

value: (G)HIVGFP+ Vpx


title: 2h_HIV-GFP_D184


title: 48.D179.NS.SIV_VPX_NEG


title: 2h_HIV-GFP_D183


title: Multiple Myeloma Replicate15 (miRNA)

description:
miRNA expression in plasma of MM patient
SM72


title: 48.D179.NS.SIV_VPX


title: Multiple Myeloma Replicate16 (miRNA)

description:
miRNA expression in plasma of MM patient
SM62


title: Multiple Myeloma Replicate24 (miRNA)

description:
miRNA expression in plasma of MM patient
SM87

value: F


title: I10R026e05_293/08 ; Nervous system


title: I10R026e06_337/09 ; Nervous system


title: Multiple Myeloma Replicate14 (miRNA)

description:
miRNA expression in plasma of MM patient
SM96


title: Control Replicate2 (miRNA)

description:
miRNA expression in plasma of healthy controls
HD Pooled2


title: 48.D179.pLKO1.SIV_VPX_NEG


title: I10R026a20_226/08 ; Nervous system


title: 48.D179.pLKO1


title: Multiple Myeloma Replicate13 (miRNA)

description:
miRNA expression in plasma of MM patient
SM100


title: Multiple Myeloma Replicate19 (miRNA)

description:
miRNA expression in plasma of MM patient
SM15


title: 48.D179.pLKO1.SIV_VPX


title: 48.D179.NL4_3.SIV_VPX_NEG


title: 48.D179.NL4_3

value: (G)HIVGFP


title: SR-103 chronic hepatitis C

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: exosome

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Exosome in serum from chronic hepatitis C patients was concentrated by Exoquick.

extract_protocol: Total RNA from liver biopsy was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Sample was obtained after treatment of direct anti-viral drug.

value: chronic hepatitis C


title: SR-80 chronic hepatitis C


title: SR-14 chronic hepatitis C


title: SL-151 chronic hepatitis C


title: I10R026e04_291/08 ; Nervous system

value: Vestibular schwannoma WHO grade I

value: Vestibular schwannoma tumor


title: 48.D179.NL4_3.SIV_VPX


title: Multiple Myeloma Replicate11 (miRNA)

description:
miRNA expression in plasma of MM patient
SM78


title: I10R026c18_400/10 ; Nervous system

source_name: non-radiated sporadic associated tumors from the nervous system

value: sporadic


title: 24.D50.NLAD8.SIV_VPX

description: exp3_HIV1_HIV2_and_innate_agonists_expression_matrix.txt


title: I10R026c17_380/09 ; Nervous system


title: I10R026c19_403/10 ; Nervous system


title: SL-137 chronic hepatitis C


title: 24.D493.NLAD8


title: SL-121 chronic hepatitis C


title: I10R026a05_185/07 ; Nervous system


title: Multiple Myeloma Replicate9 (miRNA)

description:
miRNA expression in plasma of MM patient
SM47


title: Multiple Myeloma Replicate8 (miRNA)

description:
miRNA expression in plasma of MM patient
SM77


title: I10R026c16_373/09 ; Nervous system


title: 24.D51.NLAD8


title: SR-23 chronic hepatitis C


title: I10R026c15_371/09 ; Nervous system


title: Multiple Myeloma Replicate10 (miRNA)

description:
miRNA expression in plasma of MM patient
SM64


title: SL-46 chronic hepatitis C


title: SL-15 chronic hepatitis C


title: Control Replicate1 (miRNA)

description:
miRNA expression in plasma of healthy controls
HD Pooled1

value: Control

value: Mononuclear cells


title: Multiple Myeloma Replicate7 (miRNA)

description:
miRNA expression in plasma of MM patient
SM98


title: 24.D493.JK7312AS


title: Multiple Myeloma Replicate6 (miRNA)

description:
miRNA expression in plasma of MM patient
SM18


title: I10R026c14_362/09 ; Nervous system


title: Multiple Myeloma Replicate5 (miRNA)

description:
miRNA expression in plasma of MM patient
SM91


title: Multiple Myeloma Replicate12 (miRNA)

description:
miRNA expression in plasma of MM patient
SM34


title: I10R026f01_435/10 ; Nervous system


title: 24.D493.NLAD8.SIV_VPX


title: 24.D51.HIV2_WT


title: AD-138 chronic hepatitis C


title: I10R026c12_315/09 ; Nervous system


title: 24.D50.NLAD8


title: AD-148 chronic hepatitis C


title: 24.D51.JK7312AS


title: I10R026c11_313/09 ; Nervous system


title: I10R026c10_305/08 ; Nervous system


title: 24.D51.NLAD8.SIV_VPX


title: AD-106 chronic hepatitis C


title: I10R026c09_287/08 ; Nervous system


title: Multiple Myeloma Replicate4 (miRNA)

description:
miRNA expression in plasma of MM patient
SM94


title: AD-75 chronic hepatitis C


title: AD-24 chronic hepatitis C


title: AD-47 chronic hepatitis C


title: AD-57 chronic hepatitis C


title: 24.D50.HIV2_WT


title: Multiple Myeloma Replicate3 (miRNA)

description:
miRNA expression in plasma of MM patient
SM52


title: 24.D493.HIV2_WT


title: 24.D50.JK7312AS


title: Multiple Myeloma Replicate2 (miRNA)

description:
miRNA expression in plasma of MM patient
SM19


title: AD-22 chronic hepatitis C


title: SR-158 chronic hepatitis C


title: I10R026c07_260/08 ; Nervous system


title: I10R026c08_286/08 ; Nervous system


title: 24.D493.HIV2_P86HA.CsA


title: Multiple Myeloma Replicate34 (miRNA)

description:
miRNA expression in plasma of MM patient
SM226


title: I10R026c05_245/08 ; Nervous system


title: I10R026c04_230/08 ; Nervous system


title: SR-6 chronic hepatitis C


title: I10R026c06_250/08 ; Nervous system


title: Multiple Myeloma Replicate1 (miRNA)

description:
miRNA expression in plasma of MM patient
SM7


title: I10R026c02_210/08 ; Nervous system


title: I10R026c03_222/08 ; Nervous system


title: 24.D51.HIV2_P86HA.CsA


title: SL-252 chronic hepatitis C


title: SL-248 chronic hepatitis C


title: EU-B039H UCB positive Blood

city: Braunschweig

first: Ayssar

middle: A.

last: Elamin

state: Nds

address: Salzdahlumer Str. 196

department: Research & Development

institute: LIONEX GmbH

description: UCB positive Blood

hyb_protocol: Finally the biotinylated single stranded cDNA was hybridized onto the whole transcript Affymetrix® Human Gene 2.1 ST arrays, which cover a total of 40.716 annotated transcripts.

scan_protocol: After labeling with a streptavidin phycoerythrin conjugate the strips were washed and scanned by the Washing Station and the Imaging Station from the GeneAtlas®System (Affymetrix)

data_processing: The probe cell intensity data (CEL) files were generated using the Command ConsoleTM software (Affymetrix). The CEL files were imported into Partek Genomics Suite version 6.6 (Partek Inc., St. Louis, MO, USA) for the gene and exon expression analysis using the Robust Multi-array Average (RMA) settings for normalization. A batch removal was performed to minimize the influence of external factors on the data. The lists of differentially expressed genes were created using analysis of variance (ANOVA) with an fdr (false discovery rate) corrected p-value <0.05 and a fold change > 1.5

source_name: UCB positive Male

label_protocol: The RNA samples were processed using the GeneChip® WT Plus Reagent Kit (Affymetrix) according to the manufacturer’s protocol. In brief, the total RNA was first transcribed to double stranded cDNA, which was transcribed to cRNA. The cRNA was then synthesized into single stranded cDNA, which was fragmented and biotinylated

growth_protocol: The selection of patients was based on the following inclusion criteria: the patient was diagnosed with urothelial carcinoma of the urinary bladder (cystoscopic and histological evidence of Bladder Cancer). Recurrence-negative patients are defined as showing no cystoscopic or histological evidence of bladder cancer during monitoring. Recurrence-positive patients are defined as showing cystoscopic and histological evidence of bladder cancer during monitoring after treatment of de novo Bladder Cancer. New patients are bladder cancer patients with no previous history of bladder cancer. Healthy volunteers with no previous history of bladder cancer or any other cancer (Table 1). Average Age of positive cancer patients is 75.4 years. Average Age of recurrence-negative patients is 70.5 years. Average Age of new Bladder Cancer patients is 76.7 years. Average Age of Healthy volunteers is 68 years.

extract_protocol: Isolation of total RNA from clinical whole blood samples was performed according to the manufacturer’s protocol using the PAXgene® Blood RNA-Kit (PreAnalytiX). The total RNA was quantified by a QubitTM Assay (Invitrogen) based on the manufacturer’s standard protocols. The RNA integrity was determined by agarose gel electrophoresis.

treatment_protocol: All individuals gave informed consent for sample donation and the collection was approved by local ethical committee (ref. 3/LO/0739). Plasma from blood samples was collected from the same cohort patients except 4 patients and one healthy volunteer were missed. Plasma was obtained from cohort participant blood using BD Vacutainer® Plasma Tubes (Heparin). Tubes containing 8-10 mL of blood were mixed for 30min at RT and centrifuged at 1600g for 10min at RT. Plasma was added to a fresh tube and centrifuged again at 1400g for 10min at RT. Plasma was then transferred to cryo-vials and stored at -80°C. Whole blood was collected using BD PAXgene™ Blood RNA Tubes. After the patient was bled the PAXgene™ Blood RNA Tubes were incubated at RT for 2hrs and then chilled on ice for 10mins. The tubes were then incubated at -20°C overnight and then transferred to a storage box at -80°C.

tag: stage at sample (histology after turbt)

tag: grade at sample (histology after turbt)

value: pTa


title: EU-B042H UCB positive Blood

description: UCB positive Blood

tag: age


title: I10R026c01_205/08 ; Nervous system

value: non-radiated


title: EU-B049H UCB positive Blood

description: UCB positive Blood


title: EU-B045H UCB positive Blood

description: UCB positive Blood

source_name: UCB positive Female


title: EU-B052H UCB positive Blood

description: UCB positive Blood


title: EU-B046H UCB positive Blood

description: UCB positive Blood


title: 24.D50.HIV2_P86HA.CsA

tag: time


title: AD-151 chronic hepatitis C


title: 24.D493.HIV2_P86HA


title: 24.D51.HIV2_P86HA


title: AD-54 chronic hepatitis C


title: 24.D50.HIV2_P86HA


title: SL-167 chronic hepatitis C


title: EU-B016H UCB positive Blood

description: UCB positive Blood


title: I10R026a35_392/09 ; Nervous system


title: SL-158 chronic hepatitis C


title: EU-B004H UCB positive Blood

description: UCB positive Blood


title: 24.D51.NS.CsA

value: NS+CsA


title: 24.D493.NS.CsA


title: I10R026a34_356/09 ; Nervous system


title: 24.D50.NS.CsA


title: I10R026a33_349/09 ; Nervous system


title: EU-B014H UCB positive Blood

description: UCB positive Blood


title: SR-168 chronic hepatitis C


title: I10R026a31_345/09 ; Nervous system


title: 24.D493.NS

value: NS


title: I10R026a30_335/09 ; Nervous system


title: SL-301 chronic hepatitis C


title: EU-B013H UCB positive Blood

description: UCB positive Blood


title: 24.D50.NS


title: SL-323 chronic hepatitis C


title: I10R026a32_346/09 ; Nervous system


title: B062P UCB positive Blood

description: UCB positive Blood

value: pTa (new)


title: SR-53 chronic hepatitis C


title: I10R026a25_263/08 ; Nervous system


title: SR-88 chronic hepatitis C


title: B061P UCB positive Blood

description: UCB positive Blood

value: Neg


title: 24.D51.NS


title: SL-263 chronic hepatitis C


title: SL-272 chronic hepatitis C


title: I10R026a24_253/08 ; Nervous system


title: B046P UCB positive Blood

description: UCB positive Blood

value: No speciment received


title: B050P UCB positive Blood

description: UCB positive Blood


title: I10R026a23_238/08 ; Nervous system


title: 24.D235.pIC

value: poly iC


title: 24.D235.pLKO1.SIV_VPX.GFP_NEG

value: GFP- (G)plko.1GFP + VPX


title: 24.D235.pLKO1.SIV_VPX.GFP_POS

value: GFP+ (G)plko.1GFP + VPX


title: 24.D235.NL4_3.SIV_VPX.GFP_NEG

value: GFP- (G)HIVGFP + VPX


title: I10R026a17_213/08 ; Nervous system


title: B058P UCB positive Blood

description: UCB positive Blood

value: Basingstoke sample, no histology sent


title: 24.D235.LPS

value: lps


title: B037P UCB positive Blood

description: UCB positive Blood


title: B038P UCB positive Blood

description: UCB positive Blood


title: SL-228 chronic hepatitis C

value: chronic hepatitis C


title: SL-224 chronic hepatitis C


title: SL-234 chronic hepatitis C


title: B032P UCB positive Blood

description: UCB positive Blood


title: 24.D235.NL4_3.SIV_VPX.GFP_POS

value: GFP+ (G)HIVGFP + VPX


title: SL-257 chronic hepatitis C


title: I10R026a18_217/08 ; Nervous system

value: Vestibular schwannoma WHO grade I

value: Vestibular schwannoma tumor

value: sporadic


title: B051P UCB positive Blood

description: UCB positive Blood


title: I10R026a19_218/08 ; Nervous system

value: non-radiated


title: B031P UCB positive Blood

description: UCB positive Blood


title: I10R026a06_189/07 ; Nervous system


title: B060P UCB positive Blood

description: UCB positive Blood


title: B030P UCB positive Blood

description: UCB positive Blood


title: I10R026a15_204/08 ; Nervous system


title: 24.D234.pLKO1.SIV_VPX.GFP_NEG


title: shAsh2l-Med1_ChIPSeq

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

data_processing:
quality trim: trimmomatic-0.39
sequence alignment: bowtie2 ver. 2.3.4.1
alignment data processing: samtools ver. 1.7
bigWig files generation: bamCoverage 3.3.0
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files generation: bamCoverage 3.3.0

organism: Mus musculus

growth_protocol: ES-D3 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 20% FBS, GlutaMAX (Gibco), MEM Non-Essential Amino Acids (Gibco), Leukemia inhibitory factor, 1 mM sodium pyruvate, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 and 1 mM PD0325901. Cells were cultured at 37 °C under 5% CO2 in air.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Anti Oct4, Sox2, Nanog, Wdr5, H3K27ac, and Med1 were used to capture protein-DNA complex. Protein A/G magnetic beads (Dynabeads) were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column. ChIP-seq libraries were prepared using the NEBNext® Ultra™II DNA Library Prep Kit. Libraries were sequenced on the Illumina X system following the manufacturer's protocols.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

tag: passage

tag: knockdown

tag: chip target

value: Med1 (Biorbyt, Cat #orb393103, lot 1)

tag: developmental stage

value: Embryo

tag: strain


title: 24.D234.NL4_3.SIV_VPX.GFP_NEG


title: shCtrl-Med1_ChIPSeq

value: shCtrl


title: shAsh2l-H3K27ac_ChIPSeq

value: H3K27ac (Cell Signaling Technology, Cat #8173, lot 1)


title: I10R026a04_182/07 ; Nervous system


title: 24.D234.NL4_3.SIV_VPX.GFP_POS


title: SL-20 chronic hepatitis C


title: SL-205 chronic hepatitis C


title: SL-161 chronic hepatitis C


title: SL-152 chronic hepatitis C


title: input DNA

value: none (input)


title: I10R026a03_173/07 ; Nervous system


title: SL-198 chronic hepatitis C


title: 24.D234.pIC

value: poly iC


title: 24.D234.pLKO1.SIV_VPX.GFP_POS


title: shAsh2l-Wdr5_ChIPSeq

value: Wdr5 (Cell Signaling Technology, Cat #13105, lot 1)


title: B027P UCB positive Blood

description: UCB positive Blood

value: pTa


title: 24.D234.LPS


title: SL-117 chronic hepatitis C


title: shCtrl-Wdr5_ChIPSeq


title: B024P UCB positive Blood

description: UCB positive Blood

value: Neg


title: 24.D234.NS

value: NS


title: 24.D225.pLKO1.SIV_VPX.GFP_POS

value: GFP+ (G)plko.1GFP + VPX


title: B028P UCB positive Blood

description: UCB positive Blood


title: SL-106 chronic hepatitis C

value: chronic hepatitis C


title: B029P UCB positive Blood

description: UCB positive Blood


title: B023P UCB positive Blood

description: UCB positive Blood


title: shCtrl-Nanog_ChIPSeq

value: Nanog (Cell Signaling Technology, Cat #8822S, lot 1)


title: 24.D225.pLKO1.SIV_VPX.GFP_NEG

value: GFP- (G)plko.1GFP + VPX


title: SL-132 chronic hepatitis C


title: 24.D225.NL4_3.SIV_VPX.GFP_POS

value: GFP+ (G)HIVGFP + VPX


title: 24.D225.NL4_3.SIV_VPX.GFP_NEG

value: GFP- (G)HIVGFP + VPX


title: SL-87 chronic hepatitis C


title: 24.D225.pIC


title: B021P UCB positive Blood

description: UCB positive Blood


title: SL-90 chronic hepatitis C


title: shAsh2l-Oct4_ChIPSeq

value: Oct4 (Cell Signaling Technology, Cat #83932, lot 1)


title: SL-101 chronic hepatitis C


title: 24.D225.LPS

value: lps


title: SL-82 chronic hepatitis C


title: SL-6 chronic hepatitis C


title: 24.D225.NS


title: JH53_WT_retina_scRNAseq_R4

city: Baltimore

first: Jacob

middle: S

last: Heng

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Dissociated retinal cells

data_processing:
scRNA-seq data were pre-processed using the Cell Ranger pipeline (v2.2.0; 10x Genomics) with default settings.  Cell barcodes were determined using the DropletUtils R/Bioconductor package. The normalized gene x cell matrix was used as input for the Monocle R/Bioconductor package (Trapnell et al., 2014).  Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis.  For preliminary cell clustering, PCA was performed on the high variance genes, and appropriate components were visualized in two dimensions using UMAP.  Initial clusters were identified from the 2-D embedding using k-means clustering.  Cell type identity was determined by cross-referencing clusters with expression of multiple known cell type markers.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: adult dissociated WT retina

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Dissociated single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip, and Library Kits (10X Genomics, Pleasanton) as per the manufacturer’s protocol.  In brief, single cells were sorted into 0.4% BSA–DPBS.  Approximately 14,000 single retinal cells were added to a channel.  The cells were then partitioned into Gel Beads in Emulsion in the 10x Genomics Chromium Controller, where cell lysis occurred
Cell lysis was followed by barcoded oligo-DT priming and reverse transcription of poly-adenylated RNA, amplification, shearing and 5′ adaptor and sample index attachment.

tag: genotype

value: WT

tag: disease grade

value: 11 weeks

tag: Sex

value: Female

value: retina

tag: treatment protocol


title: SL-40 chronic hepatitis C

tag: disease state


title: shCtrl-Oct4_ChIPSeq

value: shCtrl

value: Embryo


title: I10R026a21_232/08 ; Nervous system

tag: diagnosis

value: Vestibular schwannoma WHO grade I

value: Vestibular schwannoma tumor

tag: vs type

value: sporadic

tag: radiation

value: non-radiated


title: B017P UCB positive Blood

description: UCB positive Blood

tag: stage at sample (histology after turbt)

tag: grade at sample (histology after turbt)

value: pTa


title: B018P UCB positive Blood

description: UCB positive Blood

tag: age


title: JH52_AireKO_retina_scRNAseq_R3

description: Dissociated retinal cells

source_name: adult dissociated AireKO retina

value: AireKO

tag: tissue


title: B014P UCB positive Blood

description: UCB positive Blood

value: Neg


title: B016P UCB positive Blood

description: UCB positive Blood


title: 24.D235.NS

tag: time

value: NS


title: B012P UCB positive Blood

description: UCB positive Blood


title: SL-52 chronic hepatitis C

value: chronic hepatitis C


title: SL-92 chronic hepatitis C


title: 24.D223.pLKO1.SIV_VPX.GFP_NEG

value: GFP- (G)plko.1GFP + VPX


title: SL-294 chronic hepatitis C


title: JH51_WT_retina_scRNAseq_R3

description: Dissociated retinal cells


title: 24.D223.NL4_3.SIV_VPX.GFP_POS

value: GFP+ (G)HIVGFP + VPX


title: JH32_AireKO_retina_scRNAseq_R2

description: Dissociated retinal cells

value: 12 weeks


title: 24.D223.NL4_3.SIV_VPX.GFP_NEG

value: GFP- (G)HIVGFP + VPX


title: JH31_WT_retina_scRNAseq_R2

description: Dissociated retinal cells

value: WT

value: Female


title: AD-150 chronic hepatitis C


title: VTC35_78_S383

city: San Antonio

first: Chun-Lin

last: Lin

state: Texas

address: 7703 Floyd Curl Dr., MC8257, 233 STRF

institute: University of Texas Health Science Center at San Antonio

data_processing:
Illumina Real-Time Analysis software used for basecalling.
Sequenced reads were mapped to GRCh38 human genome using STAR-2.5.3a
Fragments Per Kilobase of transcript per Million mapped reads were calculated for each sample using RSEM software
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: CTCs from prostate patients' blood sample

growth_protocol: Patients CTCs were isolated from blood sample by using Ficoll and cultured in Prime-EX tumorsphere SFM medium for a week.

extract_protocol:
single cell cDNA generation with Fluidigm C1 Single-Cell Auto Prep System
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit with Nextera XT Index Kit v2 Set A and B index primers.
single cell RNA-seq

tag: cell type

value: circulating tumor cells from prostate cancer patients


title: B008P UCB positive Blood

description: UCB positive Blood


title: SL-2 chronic hepatitis C


title: 24.D223.pIC

value: poly iC


title: VTC35_70_S382


title: AD-120 chronic hepatitis C


title: B025p UCB positive Blood

description: UCB positive Blood


title: AD-117 chronic hepatitis C


title: B010P UCB positive Blood

description: UCB positive Blood


title: 24.D223.NS


title: B011P UCB positive Blood

description: UCB positive Blood

value: G2 pTa


title: B005P UCB positive Blood

description: UCB positive Blood


title: B006P UCB positive Blood

description: UCB positive Blood


title: VTC35_68_S368


title: JH54_AireKO_retina_scRNAseq_R4

description: Dissociated retinal cells

value: 11 weeks

value: retina


title: B002P UCB positive Blood

description: UCB positive Blood


title: AD-111 chronic hepatitis C


title: B004P UCB positive Blood

description: UCB positive Blood


title: 8.D235.NL4_3.SIV_VPX

value: (G)HIVGFP + VPX


title: VTC35_45_S365


title: VTC35_64_S381


title: AD-109 chronic hepatitis C


title: VTC35_37_S363


title: AD-92 chronic hepatitis C


title: VTC35_36_S379


title: AD-67 chronic hepatitis C


title: AD-53 chronic hepatitis C


title: B001P UCB positive Blood

description: UCB positive Blood


title: B072 Health volunteer Blood

description: Health volunteer Blood

source_name: Health volunteer Female

value: Healthy


title: VTC35_35_S376


title: VTC35_28_S372


title: 8.D234.pLKO1.SIV_VPX

value: (G)plko.1GFP + VPX


title: 8.D235.NS


title: AD-50 chronic hepatitis C


title: 8.D235.LPS

value: lps


title: B062 Health volunteer Blood

description: Health volunteer Blood


title: AD-49 chronic hepatitis C


title: B056 Health volunteer Blood

description: Health volunteer Blood


title: shAsh2l-Sox2_ChIPSeq

tag: cell line

tag: passage

tag: knockdown

tag: chip target

value: Sox2 (Cell Signaling Technology, Cat #23064, lot 3)

value: Embryo


title: B063* Health volunteer Blood

description: Health volunteer Blood


title: shAsh2l-Nanog_ChIPSeq

value: Nanog (Cell Signaling Technology, Cat #8822S, lot 1)

tag: developmental stage

tag: strain


title: VTC35_17_S374


title: 8.D234.NL4_3.SIV_VPX


title: B052 Health volunteer Blood

description: Health volunteer Blood


title: VTC35_14_S364


title: VTC35_12_S371


title: AD-45 chronic hepatitis C

value: chronic hepatitis C


title: 8.D234.pIC


title: 8.D234.LPS


title: B045 Health volunteer Blood

description: Health volunteer Blood


title: 8.D235.pLKO1.SIV_VPX


title: 8.D234.NS

value: NS


title: AD-40 chronic hepatitis C


title: 8.D225.pLKO1.SIV_VPX


title: VTC34_96_S316


title: AD-44 chronic hepatitis C


title: B038 Health volunteer Blood

description: Health volunteer Blood


title: AD-10 chronic hepatitis C


title: shCtrl-H3K27ac_ChIPSeq

value: shCtrl

value: H3K27ac (Cell Signaling Technology, Cat #8173, lot 1)


title: SL-341 chronic hepatitis C


title: VTC34_86_S300


title: 8.D225.NL4_3.SIV_VPX


title: VTC34_75_S298


title: VTC34_70_S314


title: VTC34_64_S313


title: SL-153 chronic hepatitis C


title: B015P UCB positive Blood

description: UCB positive Blood

value: Neg


title: B020 Health volunteer Blood

description: Health volunteer Blood

source_name: Health volunteer Male


title: 8.D225.LPS


title: SL-48 chronic hepatitis C


title: B036 Health volunteer Blood

description: Health volunteer Blood


title: 8.D223.pLKO1.SIV_VPX


title: VTC34_58_S312

value: circulating tumor cells from prostate cancer patients


title: VTC34_47_S307


title: 8.D225.pIC

value: poly iC


title: B007P UCB positive Blood

description: UCB positive Blood


title: B019 Health volunteer Blood

description: Health volunteer Blood


title: shCtrl-Sox2_ChIPSeq


title: AD-136 chronic hepatitis C


title: B034 Health volunteer Blood

description: Health volunteer Blood


title: SR-16 chronic hepatitis C


title: B018 Health volunteer Blood

description: Health volunteer Blood


title: SR-3 chronic hepatitis C


title: B016 Health volunteer Blood

description: Health volunteer Blood


title: SL-293 chronic hepatitis C


title: B015 Health volunteer Blood

description: Health volunteer Blood


title: B017 Health volunteer Blood

description: Health volunteer Blood


title: B013P UCB positive Blood

description: UCB positive Blood

value: G1 pTa

value: pTa


title: 24.D223.LPS


title: 8.D223.NL4_3.SIV_VPX


title: 8.D225.NS


title: 24.D223.pLKO1.SIV_VPX.GFP_POS

value: GFP+ (G)plko.1GFP + VPX


title: VTC34_36_S311


title: VTC34_40_S304


title: 8.D223.pIC


title: 8.D223.NS


title: 8.D223.LPS


title: B014 Health volunteer Blood

description: Health volunteer Blood


title: VTC34_17_S306


title: 6.D51.R_IFN


title: SL-192 chronic hepatitis C


title: 8.D235.pIC


title: 6.D50.R848


title: VTC34_11_S305


title: 6.D51.cGAMP


title: SL-173 chronic hepatitis C


title: SL-44 chronic hepatitis C


title: VTC34_26_S291


title: AD-59 chronic hepatitis C


title: B013 Health volunteer Blood

description: Health volunteer Blood


title: SL-35 chronic hepatitis C


title: B012 Health volunteer Blood

description: Health volunteer Blood


title: AD-1 chronic hepatitis C


title: B010 Health volunteer Blood

description: Health volunteer Blood


title: B011 Health volunteer Blood

description: Health volunteer Blood


title: VTC27_95_S357


title: B020P UCB positive Blood

description: UCB positive Blood


title: 6.D493.pdCdG


title: 6.D51.pdCdG


title: VTC27_83_S341


title: VTC34_16_S310


title: VTC27_96_S354


title: 6.D493.pIC

value: pIC


title: AD-7 chronic hepatitis C


title: AD-116 chronic hepatitis C


title: B009 Health volunteer Blood

description: Health volunteer Blood

value: Healthy


title: B008 Health volunteer Blood

description: Health volunteer Blood


title: B006 Health volunteer Blood

description: Health volunteer Blood


title: 6.D51.pIC


title: B007 Health volunteer Blood

description: Health volunteer Blood


title: 6.D50.pdCdG


title: VTC27_76_S360


title: VTC27_62_S331


title: VTC27_58_S350


title: SL-165 chronic hepatitis C


title: SL-168 chronic hepatitis C


title: SL-160 chronic hepatitis C


title: 6.D50.pIC


title: VTC27_42_S349


title: VTC27_36_S348


title: B005 Health volunteer Blood

description: Health volunteer Blood


title: B002 Health volunteer Blood

description: Health volunteer Blood


title: 6.D50.R_IFN


title: B003 Health volunteer Blood

description: Health volunteer Blood


title: SL-159 chronic hepatitis C


title: AD-26 chronic hepatitis C


title: VTC27_34_S340


title: SL-163 chronic hepatitis C


title: 6.D493.R848


title: VTC27_24_S339


title: 1919_L

city: Raleigh

first: Chelsea

middle: Adele

last: Phillips

state: NC

address: 2711 Founders Drive

department: Prestage Department of Poultry Science

institute: NC State University

data_processing:
Illumina software used for basecalling.
Using CLC 10  RNA-Seq Analysis Toolbox and default parameters
Genome_build: Reference genome was Gal gal 5
Supplementary_files_format_and_content: Processed data files are those that were used for the WEKA machine learning analysis in the paper. The gene values for these files are unique exon reads.

organism: Gallus gallus

source_name: Moderate to Severe WB

extract_protocol:
Qiagen RNEasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Moderate to Severe WB

value: Liver

value: 45 days

tag: Sex

value: male

value: broilers


title: VTC27_19_S322


title: SL-166 chronic hepatitis C

tag: disease state

value: chronic hepatitis C


title: 6.D493.cGAMP

source_name: PBMCs


title: 6.D50.cGAMP


title: 3004_L


title: 3039_L


title: 3104_L


title: 6.D51.R848


title: SL-155 chronic hepatitis C


title: SL-154 chronic hepatitis C


title: VTC27_16_S346


title: VTC27_18_S338


title: B001 Health volunteer Blood

description: Health volunteer Blood


title: SL-157 chronic hepatitis C


title: 1976_L


title: 1975_L


title: B004 Health volunteer Blood

description: Health volunteer Blood


title: 2.D235.pLKO1.SIV_VPX

value: (G)plko.1GFP + VPX


title: VTC27_13_S321


title: 1930_L


title: 2.D235.NL4_3.SIV_VPX

value: (G)HIVGFP + VPX


title: SR-81 chronic hepatitis C


title: VTC048_58_S78


title: SR-59 chronic hepatitis C


title: 1929_L


title: SR-8 chronic hepatitis C


title: 1906_L


title: VTC048_45_S74


title: VTC048_44_S73


title: 2.D235.pIC


title: 2.D235.LPS

value: lps


title: 1879_L


title: VTC048_42_S77


title: 3090_L

source_name: Normal WB

value: normal


title: 6.D493.R_IFN


title: 2.D235.NS

value: NS


title: 2.D234.pLKO1.SIV_VPX


title: 3072_L


title: 2.D234.NL4_3.SIV_VPX


title: 3074_L


title: 2.D234.pIC

value: poly iC


title: 3071_L


title: VTC048_37_S71

value: circulating tumor cells from prostate cancer patients


title: 2.D234.LPS


title: VTC048_25_S70


title: VTC047_9_S17


title: VTC047_50_S21


title: SL-226 chronic hepatitis C


title: SL-208 chronic hepatitis C


title: 2.D234.NS


title: VTC047_39_S20


title: SL-220 chronic hepatitis C


title: SL-162 chronic hepatitis C


title: 3029_L


title: SL-284 chronic hepatitis C


title: SL-268 chronic hepatitis C


title: 3108_M

value: Pectoralis Major muscle


title: 2.D223.NL4_3.SIV_VPX


title: VTC047_33_S19


title: 2.D223.pIC


title: 1975_M


title: VTC047_30_S36


title: SL-108 chronic hepatitis C


title: 2995_M


title: VTC047_22_S35


title: 2.D223.LPS


title: SL-99 chronic hepatitis C


title: 2.D223.NS


title: SL-49 chronic hepatitis C


title: 1908_M


title: 2.D225.pLKO1.SIV_VPX


title: VTC047_20_S14


title: VTC047_1_S24


title: AD-154 chronic hepatitis C


title: 1863_M


title: 3104_M


title: 2.D225.pIC


title: 3039_M


title: VTC046_88_S13


title: VTC046_60_S207


title: 2.D225.NL4_3.SIV_VPX


title: 1919_M


title: VTC046_18_S7


title: 2.D225.NS


title: 2.D225.LPS


title: 2.D223.pLKO1.SIV_VPX


title: VTC046_14_S4


title: AD-129 chronic hepatitis C


title: VTC046_12_S204


title: 0.D51.NS


title: VTC046_51_S203


title: SL-65 chronic hepatitis C


title: VTC046_05_S206


title: AD-142 chronic hepatitis C


title: 0.D50.NS


title: VTC043_95_S255


title: VTC043_79_S213


title: 0.D493.NS


title: 1874_M


title: 1976_M


title: 3004_M


title: 1906_M


title: 1929_M


title: 2990_M


title: 1930_M


title: VTC043_71_S253


title: AD-113 chronic hepatitis C


title: AD-132 chronic hepatitis C


title: AD-137 chronic hepatitis C


title: AD-122 chronic hepatitis C


title: AD-123 chronic hepatitis C


title: VTC043_64_S249


title: SL-27 chronic hepatitis C


title: 3074_M


title: AD-105 chronic hepatitis C


title: AD-97 chronic hepatitis C


title: AD-104 chronic hepatitis C


title: AD-96 chronic hepatitis C


title: UMM065_single cell RNAseq

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

institute: University of Miami Miller School of Medicine

data_processing:
CellRanger (2.3.4) “mkfastq” command was used to generate fastq files from Illumina bcl files
CellRanger (2.3.4) “count” command was used to generate bam files and raw gene-barcode matrices aligned to the GRCh38 Ensembl build 93 genome.
Genome_build: GRCh38 Ensembl build 93

source_name: human uveal melanoma_primary

extract_protocol:
Single cell suspensions from primary and metastatic uveal melanoma were generated and run on the 10X genomics Chromium instrument using the 3' single cell RNA-seq v2 and and 5' single cell RNA-seq
10X genomics 3' single cell RNA-seq v2 and 5' single cell RNA-seq

value: human uveal melanoma

tag: sample type

value: primary

tag: gep class

tag: age at diagnosis

value: F


title: VTC043_63_S211


title: UMM067L_single cell RNAseq

source_name: human uveal melanoma_metastatic

value: metastatic

value: M


title: UMM069_single cell RNAseq


title: 3072_M

value: 45 days


title: AD-94 chronic hepatitis C


title: UMM064_single cell RNAseq


title: 3071_M

value: male


title: VTC043_50_S232


title: 3029_M

value: broilers


title: VTC043_58_S248


title: VTC043_57_S210


title: UMM063_single cell RNAseq


title: UMM061_single cell RNAseq


title: 3090_M


title: VTC043_47_S242


title: AD-82 chronic hepatitis C

value: chronic hepatitis C


title: UMM066_single cell RNAseq


title: AD-84 chronic hepatitis C


title: UMM059_single cell RNAseq


title: UMM041L_single cell RNAseq


title: VTC043_46_S235


title: VTC043_42_S246


title: AD-58 chronic hepatitis C


title: UMM062_single cell RNAseq


title: AD-70 chronic hepatitis C


title: shDes-3_S62_R1_001.fastq.gz

city: Philadelphia

first: Julie

last: Heffler

state: PA

address: 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

description:
RJ_Desmin_RNAseq_RJBP_differentialexpression.xls
RJ_Desmin_RNAseq_RJBP_log2cpm.xls

data_processing:
ChIP seq: Trimmomatic and aligned with bwa (aln  -q 5 -l 32 -k 2) to the Rn6 genome. PCR duplicates were removed with Picard tools (VALIDATION_STRINGENCY=LENIENT ChIP seq: ASSUME_SORTED=true REMOVE_DUPLICATES=true), multimapping reads and reads with a MAPQ score of < 30 were removed using samtools (-F 1804 -q 30).
ChIP seq: Bam files were used as input into Deeptools bamCoverage and converted to bigwig format (--normalizeUsing RPGC --effectiveGenomeSize 2729860805 -bs 10 -e 200).  These bigwig files were then input into Deeptools multiBigwigSummary using default settings and region limited to chr1. Resulting data matrix was input into Deeptools plotHeatmap.
ChIP seq: After confirming high correlation among input and LB ChIP-seq replicates from control samples, three replicates of input and ChIP from control were merged separately to create a unionized/merged dataset. shDesmin input and ChIP replicates were also merged separately to create an shDesmin unionized/merged dataset. Control LB ChIP and Input libraries were sampled to approximately even depth using samtools. Control LB and Input bam files were sampled to ~40 million reads. shDesmin LB and Input bam files were set to ~8 million reads due to low sequencing depth of shDesmin LB. Resulting bam files were converted to bed format using bedtools  bamtobed and extended to 200bp using bedtools slop.  Bed files were then input to epic and ran with window 600, gap 4 and fdr <0.05, rn6 genome, -fs 200 parameters. Resulting peaks within 50kb were merged using bedtools merge, and all peaks less than 50kb in size were removed. Control LADs and the Rn6 ENSEMBL gtf file were input to bedtools intersect to identify all features that are contained in LADs, with a minimum of 1bp of any exon/CDS in a LAD.
RNAseq: RNAseq data processing:Raw reads were trimmed with Trimmomatic v0.32 and then aligned to hg19 genome using STAR(version 2.6.0c) ’ and then filtered using samtools view with ‘-F 4 -q 10’ parameters. Rsubread featureCounts quantified the number of reads per feature of Ensembl hg19 gene annotation file. For differential gene expression analysis, genes with <1 count per million (CPM) in less than 25% of samples were removed from differential expression analysis. For analyses using all genes, no cpm filter was applied.  EdgeR’s calcNormFactors was used to calculate library size normalization factors. Limma voom function was used to log2 transform and quantile normalize the CPM matrix. For differential expression analysis, Limma lmFit, contrast.fit and eBayes functions were used to fit the linear model, compute coefficients and standard error, and then perform differential expression calculation with Benjamini–Hochberg multiple correction adjusted P-values (Benjamini and Hochberg, 1995). Cutoffs of FDR≤0.05 and log2 fold change ≥1.5 or ≤−1.5 were used for differentially upregulated or downregulated genes.
Genome_build: rn6
Supplementary_files_format_and_content: BigWig files were generated for unionized control and shDesmin datasets; BED File of control LADs is also included. XLS  for differential expression and log2cpm included for RNAseq

organism: Rattus norvegicus

source_name: Cardiac Myocytes

growth_protocol: Cardiomyocytes isolated from adult rat hearts were cultured for 48 hrs in M199 media containing insulin transferrin selenium (ITS), additional HEPES and primocin at 5% CO2 37 C

extract_protocol:
ChIP: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNAseq: mRNA was isolated using trizol extraction from pelleted snap-frozen adult CMs using a standard protocol.
Libraries were prepared using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for multiplex sequencing. Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems). Libraries were pooled for multiplex sequencing, requantified, and sequenced on the Illumina NextSeq500 platform (vII; 75bp single end sequencing; Illumina) Illumina)

treatment_protocol: Isolaged adult rat cardiomyocytes were treated with adenovirus encoding shRNA targeted toward desmin or a scrambled control

value: 6-8 months

tag: replicate

tag: treatment

value: shDesmin AdV


title: Null-3_S59_R1_001.fastq.gz

tag: age

value: Null AdV


title: ShDes-2_S61_R1_001.fastq.gz


title: AD-52 chronic hepatitis C


title: VTC043_41_S241


title: BSSR0022_single cell RNAseq

tag: tissue


title: Null-2_S58_R1_001.fastq.gz


title: VTC043_39_S228


title: 233_DES_LB_octrun.fastq.gz

tag: chip antibody

value: Lamin B (ab16048)


title: VTC043_36_S245

tag: cell type


title: ShDes-1_S60_R1_001.fastq.gz


title: AD-56 chronic hepatitis C


title: 30 ppb ATZ Replicate 3

city: West Lafayette

first: Chongli

last: Yuan

state: IN

address: 480 Stadium Mall Drive

institute: Purdue University

data_processing:
Quality Control
FastQC
Alignment
Bowtie2
Methylation Calling
Bismarkv0.21.0
A minimum alignment score function (f(x) = 0 + -0.6x, where x is the read length) was used. Reads aligned to identical positions on the genome were removed and bases that have more than 99.9th percentile of coverage in each sample were discarded to account for excessive PCR amplifications. In addition, reads with coverage below 10x were removed to increase the power of statistical tests.
Genome_build: GRCz11
Supplementary_files_format_and_content: cov
Supplementary_files_format_and_content: col1: chromosome, col2: start, col3: end, col4: proportion CpG methylation col5: methylated cytosines col6: unmethylated cytosines

source_name: Brain

extract_protocol:
gDNA was collected from nine mpf female zebrafish brain following a standard protocol modified for brain samples(27, 31). Zebrafish brains were homogenized in lysis buffer (50 mM Tris, 100 mM EDTA, 100 mM NaCl, 1% SDS, 100 µg/mL Proteinase K) and incubated overnight at 55°C with rocking agitation. The next day, samples were transferred to 1.5 Phase Lock Gel (PLG; QuantaBio, Beverly, MA) tubes, and phenol (phenol-Tris saturated, pH 8; Roche, Indianapolis, IN) and chloroform:isoamyl alcohol (American Bioanalytical, Natick, MA) were added before the samples were centrifuged at room temperature for 5 minutes at 1500 rcf. The upper aqueous phase was transferred to a new PLG tube and the previous steps repeated. The upper aqueous phase was transferred to a 2 ml screw top microcentrifuge tube (Fisher Scientific, Hampton, NH) and 0.1X volume of 3M sodium acetate and 1X volume of isopropanol were added and the tube inverted until DNA aggregation. Samples were incubated at room temperature and then centrifuged at 4°C for 10 minutes at 800 rcf to form a DNA pellet. The pellet was washed in 70% ethanol twice, centrifuging at 4°C for 10 minutes at 800 rcf between washes. After the second wash, the pellet was centrifuged again and dried to remove remaining ethanol. The sample was rehydrated in 1xTLE buffer and incubated overnight at 55°C with rocking agitation. The following morning, the DNA quality and concentration was checked with a NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE) and stored at 4°C until further analysis.
For bisulfite conversions, ~500 ng of gDNA were bisulfite-converted using EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA) following the manufacturer’s protocol. Bisulfite-converted gDNA were eluted to a final concentration of ~ 100 – 200 ng/μl and stored at -20°C prior to sequencing. The quality of BS-converted samples, such as fragment size, were further examined via a Picochip (Agilent Bioanalyzer, U.S.). The fragment size was found to peak at ~ 1000 nt as expected.

tag: dose (ppb atz)

value: Brain

tag: agent

value: Atrazine


title: VTC043_35_S240

value: circulating tumor cells from prostate cancer patients


title: 232_CTL_IN_octrun.fastq.gz

description:
CTRL_LB.sort.ds40M.mergebl.bigWig
600.g4.merge50.filter50.bed

value: Input

value: shScrambled AdV


title: AD-39 chronic hepatitis C


title: 231_CTL_LB_octrun.fastq.gz


title: 3 ppb ATZ Replicate 3


title: 30 ppb ATZ Replicate 1


title: VTC043_32_S224


title: AD-36 chronic hepatitis C


title: VTC043_29_S239


title: 3 ppb ATZ Replicate 2


title: 3 ppb ATZ Replicate 1


title: 162_DES_LB_octrun.fastq.gz


title: VTC043_28_S233


title: AD-33 chronic hepatitis C


title: 161_DES_IN_octrun.fastq.gz


title: AD-38 chronic hepatitis C


title: Null-1_S57_R1_001.fastq.gz


title: 0.3 ppb ATZ Replicate 3


title: 30 ppb ATZ Replicate 2


title: AD-27 chronic hepatitis C


title: AD-51 chronic hepatitis C


title: VTC043_27_S227


title: AD-12 chronic hepatitis C


title: 160_DES_LB_octrun.fastq.gz


title: 0.3 ppb ATZ Replicate 2


title: AD-11 chronic hepatitis C


title: 118_CTL_IN_octrun.fastq.gz


title: 117_CTL_LB_octrun.fastq.gz


title: 0 ppb ATZ Replicate 3


title: VTC043_14_S222


title: VTC043_01_S226


title: VTC043_05_S236


title: 0.3 ppb ATZ Replicate 1


title: 0 ppb ATZ Replicate 2


title: 233_DES_LB.fastq.gz


title: 116_CTL_IN_octrun.fastq.gz


title: AD-5 chronic hepatitis C


title: 115_CTL_LB_octrun.fastq.gz


title: 0 ppb ATZ Replicate 1


title: 234_DES_IN.fastq.gz


title: AD-6 chronic hepatitis C


title: OCH458 chronic hepatitis C

source_name: liver tissue

growth_protocol: Liver tissue was obtained by liver biopsy.

treatment_protocol: Liver tissue sample was obtained before anti-viral treatment.


title: VTC034_82_S69


title: VTC043_21_S219


title: AD-3 chronic hepatitis C

source_name: exosome


title: NC-32-D

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

description:
genome Putnam et al. (2007)
North Carolina, 32 C,replicate D
S142

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

source_name: whole-organism

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
RNA was extracted from whole organisms using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: MA animals were exposed to 20C or 30C; ME animals were exposed to 20C, 28C, or 30C;  NC animals were exposed to 20C , 30C or 32C; NS animals were exposed to 20C, 28C, or 30C; SC animals were exposed to 20C, 30C or 32C. Sample sizes: nTotal=52; nMA = 8; nME = 10; nNC = 11; nNS = 11; nSC = 12

value: adult

tag: geographic location

value: USA:North Carolina

tag: temperature


title: SC-30-B

description:
genome Putnam et al. (2007)
South Carolina, 30 C, replicate B
S141

tag: developmental stage

value: USA:South Carolina


title: AD-2 chronic hepatitis C


title: OCH-328 chronic hepatitis C


title: VTC034_62_S64


title: NS-30-D

description:
genome Putnam et al. (2007)
Nova Scotia, 30 C, replicate D
S140

value: Canada:Nova Scotia


title: AD-131 chronic hepatitis C


title: VTC034_48_S68


title: VTC034_57_S65


title: NS-20-D

description:
genome Putnam et al. (2007)
Nova Scotia, 20 C, replicate D
S139


title: 231_CTL_LB.fastq.gz


title: VTC034_28_S67


title: OCH-125 chronic hepatitis C


title: OCH-207 chronic hepatitis C


title: 161_DES_IN.fastq.gz


title: VTC034_24_S66


title: SC-30-A

description:
genome Putnam et al. (2007)
South Carolina, 30 C, replicate A
S133


title: 160_DES_LB.fastq.gz


title: VTC010_2_86_S280


title: VTC010_2_87_S276


title: 163_DES_IN.fastq.gz


title: OCH-192 chronic hepatitis C


title: NC-32-C

description:
genome Putnam et al. (2007)
North Carolina, 32 C,replicate C
S134


title: NS-30-C

description:
genome Putnam et al. (2007)
Nova Scotia, 30 C, replicate C
S132


title: OCH-123 chronic hepatitis C


title: OCH-118 chronic hepatitis C


title: 162_DES_LB.fastq.gz


title: NS-20-C

description:
genome Putnam et al. (2007)
Nova Scotia, 20 C, replicate C
S131


title: VTC010_2_84_S89


title: 118_CTL_IN.fastq.gz


title: OCH455 chronic hepatitis C


title: VTC010_2_79_S283


title: NC-32-B

description:
genome Putnam et al. (2007)
North Carolina, 32 C,replicate B
S126


title: OCH432 chronic hepatitis C


title: 117_CTL_LB.fastq.gz


title: 116_CTL_IN.fastq.gz


title: OCH-248 chronic hepatitis C


title: VTC010_2_78_S88


title: NC-30-C

description:
genome Putnam et al. (2007)
North Carolina, 30 C, replicate C
S125


title: VTC010_2_67_S274


title: NS-20-B

description:
genome Putnam et al. (2007)
Nova Scotia, 20 C, replicate B
S123


title: VTC010_2_77_S93


title: VTC010_2_75_S275


title: NS-20-A

description:
genome Putnam et al. (2007)
Nova Scotia, 20 C, replicate A
S115


title: ME-28-D

description:
genome Putnam et al. (2007)
Maine, 28 C,replicate D
S110


title: 115_CTL_LB.fastq.gz


title: OCH-165 chronic hepatitis C


title: OCH357 chronic hepatitis C


title: NC-32-A

description:
genome Putnam et al. (2007)
North Carolina, 32 C,replicate A
S118


title: NS-30-B

description:
genome Putnam et al. (2007)
Nova Scotia, 30 C, replicate B
S124


title: OCH-217 chronic hepatitis C


title: OCH-221 chronic hepatitis C


title: NC-30-B

description:
genome Putnam et al. (2007)
North Carolina, 30 C, replicate B
S117


title: OCH-259 chronic hepatitis C


title: VTC010_2_65_S92


title: NS-30-A

description:
genome Putnam et al. (2007)
Nova Scotia, 30 C, replicate A
S116


title: VTC010_2_74_S278


title: VTC010_2_69_S282


title: OCH-159 chronic hepatitis C


title: OCH-214 chronic hepatitis C


title: OCH-171 chronic hepatitis C


title: NC-30-A

description:
genome Putnam et al. (2007)
North Carolina, 30 C, replicate A
S109


title: VTC010_2_58_S87


title: SC-20-D

description:
genome Putnam et al. (2007)
South Carolina, 20 C, replicate D
S108


title: OCH-129 chronic hepatitis C


title: VTC010_2_47_S81


title: VTC010_2_45_S271


title: ME-28-B

description:
genome Putnam et al. (2007)
Maine, 28 C,replicate B
S102


title: OCH-127 chronic hepatitis C


title: MA-30-D

description:
genome Putnam et al. (2007)
Massachusetts, 30 C, replicate D
S101


title: VTC010_2_34_S287


title: VTC010_2_51_S281


title: SC-20-C

description:
genome Putnam et al. (2007)
South Carolina, 20 C, replicate C
S100


title: OCH-317 chronic hepatitis C


title: T24_sCD40L_24h_rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Gene expression data from T24 cells treated with sCD40L (1 µg/ml) for  24 hours

hyb_protocol: The cDNA was hybridized to Human Gene 1.0 ST v1 arrays

scan_protocol: Affymetrix Standard protocol

data_processing:
Gene level analysis was performed using the Affymetrix® Expression Console™ software with the default settings of the RMA-sketch workflow.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: T24 treated with sCD40L (1 µg/ml) for 24 hrs

label_protocol: Fragmentation and labeling was performed using the Affymetrix GeneChip WT terminal Labeling Kit.

growth_protocol: T24 bladder carcinoma cells were maintained in DMEM supplemented with 2mM glutamine and 10% FCS

extract_protocol: Total RNA was extracted using EZ-RNA total isolation kit (Biological Industries, Israel)

treatment_protocol: T24 cells were transfected with 50 MOI of either RAdMock or RAdnCD40L (RAd expressing membrane-bound noncleavable CD40L) for 24 hours or treated with soluble CD40L (1µg/ml) for 24 hours or left as untreated control

tag: cell line

value: bladder carcinoma cells

tag: treated/infected with

value: sCD40L (1 µg/ml) for  24 hrs


title: OCH376 chronic hepatitis C

tag: disease state


title: VTC010_2_31_S258


title: OCH-262 chronic hepatitis C


title: VTC010_2_30_S84


title: ME-20-C

description:
genome Putnam et al. (2007)
Maine, 20 C, replicate C
S99


title: T24_sCD40L_24h_rep3


title: ME-20-D

description:
genome Putnam et al. (2007)
Maine, 20 C, replicate D
S107


title: OCH-216 chronic hepatitis C


title: T24_GFP_rep3

description: Gene expression data from T24 cells expressing GFP

source_name: T24 infected with 50 MOI RAdMock  for 24 hrs

value: 50 MOI RAdMock (RAd expressing GFP) for 24 hrs


title: OCH-215 chronic hepatitis C

value: chronic hepatitis C


title: ME-28-A

description:
genome Putnam et al. (2007)
Maine, 28 C,replicate A
S94


title: VTC010_2_28_S286


title: T24_GFP_rep1


title: T24_sCD40L_24h_rep1


title: T24_GFP_rep2


title: T24_mCD40L_rep3

description: Gene expression data from T24 cells expressing mCD40L

source_name: T24 infected with 50 MOI RAdnCD40L for 24 hrs

value: 50 MOI RAdnCD40L (RAd expressing noncleavable version of human CD40L) for 24 hrs


title: OCH-213 chronic hepatitis C


title: MA-30-C

description:
genome Putnam et al. (2007)
Massachusetts, 30 C, replicate C
S93


title: T24_mCD40L_rep2


title: T24_mCD40L_rep1


title: VTC010_2_22_S83


title: SC-20-B

description:
genome Putnam et al. (2007)
South Carolina, 20 C, replicate B
S92


title: VTC010_2_20_S262


title: VTC010_2_19_S268


title: ME-20-B

description:
genome Putnam et al. (2007)
Maine, 20 C, replicate B
S91


title: OCH-152 chronic hepatitis C


title: VTC010_2_14_S261


title: VTC010_2_10_S82


title: MA-30-B

description:
genome Putnam et al. (2007)
Massachusetts, 30 C, replicate B
S85


title: OCH-151 chronic hepatitis C


title: 232_CTL_IN.fastq.gz

description:
CTRL_LB.sort.ds40M.mergebl.bigWig
600.g4.merge50.filter50.bed

value: 6-8 months


title: SC-20-A

description:
genome Putnam et al. (2007)
South Carolina, 20 C, replicate A
S84


title: VTC010_2_09_S257


title: ME-20-A

description:
genome Putnam et al. (2007)
Maine, 20 C, replicate A
S83


title: VTC010_2_08_S260


title: OCH-128 chronic hepatitis C


title: OCH-133 chronic hepatitis C


title: OCH-188 chronic hepatitis C


title: SC-32-D

description:
genome Putnam et al. (2007)
South Carolina, 32 C,replicate D
S79


title: NS-28-D

description:
genome Putnam et al. (2007)
Nova Scotia, 28 C,replicate D
S86


title: OCH-120 chronic hepatitis C


title: VTC010_2_06_S285


title: OCH-115 chronic hepatitis C


title: NS-28-B

description:
genome Putnam et al. (2007)
Nova Scotia, 28 C,replicate B
S78


title: VTC010_2_44_S265


title: VTC010_2_01_S266


title: MA-30-A

description:
genome Putnam et al. (2007)
Massachusetts, 30 C, replicate A
S77


title: OCH-113 chronic hepatitis C


title: NC-20-D

description:
genome Putnam et al. (2007)
North Carolina, 20 C, replicate D
S76


title: VTC004_2_81_S45


title: VTC004_2_75_S199


title: T24_Control_rep3

description: Gene expression data from untreated T24 cells

source_name: T24 untreated for 24 hrs

value: none (untreated)