title: RBM20 homo with correction, scRNAseq

city: Dallas

first: Miao

last: Cui

state: Texas

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
For data quality filtering, we removed cells that had more than 6000 or fewer than 200 detected genes or cells that had a percent of mitochondrial genes > 10%.
We then normalized the data by the total expression, multiplied by a scale factor of 10,000 and log-transformed the result. IntegrateData function implemented in Seurat V4 was used to correct batch effects between samples and to merge samples into one Seurat object. Briefly, we performed standard preprocessing (log-normalization), and identified the top 2000 variable features for each individual dataset. We then identified integration anchors using the FindIntegrationAnchors function. We used default parameters and dimension 30 to find anchors. We then passed these anchors to the IntegrateData function to generate an integrated Seurat object
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
6-month old mice were used for snRNA-seq. Three hearts were pooled for each condition. Total cardaic nuclei were used to generate single-nucleus RNA-seq libraries.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, CD45+ immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: cardaic nuclei

value: Heart

tag: age


title: A22 MI

status: Public on Aug 14 2022

type: SRA

city: fort valley

first: phaneendra

last: batchu

state: georgia

address: 1005 State univerity drive

department: Animal Science

country: USA

institute: fort valley state university

description: Blood samples collected after 30 minutes of transportation

library_source: transcriptomic

data_processing:
Data processing was done by Novagene
Methods uploaded

molecule: total RNA

organism: Capra hircus

source_name: Blood

extract_protocol:
Blood RNA was extracted using a MagMAX™ Stabilized Blood Tubes RNA Isolation Kit by applied biosystems (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s instructions. Muscle RNA was extracted by using RNeasy® Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) according to manufacturer’s procedures
NEBNext® UltraTM  RNA Library Prep kit from Illumina® (NEB, USA) were used to generate the sequencing libraries

tag: tissue

value: Blood

tag: group

value: MI

tag: treatment

value: 30 minutes of transportation


title: Microdissected Mice Renal PT-S1, UNx1_24h, RNA-Seq, Transcriptome 01 [24h_PT_unx1_1]

city: Bethesda

first: Hiroaki

last: Kikuchi

state: MD

address: 10 CENTER DR

department: Epithelial Systems Biology Laboratory, Systems Biology Center

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm39.103) using STAR v2.7.61
Transcript abundances in TPM were caculated by  RSEM/1.3.3
Assembly: GRCm39 (Ensembl)
Supplementary files format and content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney

growth_protocol: Pathogen-free male C57BL/6 mice (Taconic) weighing 20-30 g had free access to ad libitum drinking water and normal rodent chow before experiment. The mice were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 3 days before the experimental procedures.

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seven-week-old mice were assigned to two groups with sham operation or with unilateral nephrectomy (UNx). UNx was performed by the surgical excision method.

value: Kidney

tag: genotype

value: WT

value: UNx


title: n=1, T3, Kon LN 03

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

description:
5
5_Kon_LN_03_S5

data_processing:
Data was processed with Lexogen QuantSeq data analysis pipeline on BlueBee Genomics platform.
Assembly: hg38
Supplementary files format and content: RNA_counts.csv: Expression counts retrieved from Quantseq software as semicolon-separated table.

organism: Homo sapiens

source_name: LNCaP

extract_protocol:
RNA was extracted with miRNeasy Mini Kit (Qiagen).
Libraries were constructed with Lexogen Quantseq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.

tag: cell line

value: LNCaP

tag: cell type

value: prostate adenocarcinoma cells

tag: condition

value: control co-culture

tag: time point

value: three days


title: RBM20 homo, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

tag: strain


title: Microdissected Mice Renal PT-S1, Sham1_24h, RNA-Seq, Transcriptome 02 [24h_PT_sham1_2]

value: Sham


title: RBM20 het, scRNAseq

description: 10x Genomics


title: B2 CL

description: Muscle samples collected from non transported goats

source_name: Muscle

value: Muscle

value: CL

value: non transported goats


title: A17 MO

description: Blood samples collected after 180 minutes of transportation

value: MO

value: 180 minutes of transportation


title: B1 CL


title: WT, scRNAseq

description: 10x Genomics

value: cardaic nuclei

value: Heart


title: Microdissected Mice Renal PT-S1, Sham1_24h, RNA-Seq, Transcriptome 01 [24h_PT_sham1_1]


title: A16 MO

value: Blood


title: ATAC_WT_rep2

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

description: Genome-wide library of tagmented fragments

library_source: genomic

data_processing:
Mapping : bowtie -m 2 --maxIns 350, mm9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualization
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: mm9
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsing RPKM --minMappingQuality 30)

molecule: genomic DNA

source_name: Embryoid body (differentiated embryonic stem cells)

growth_protocol: E14-TG2a.IV mouse embryonic stem cells were cultured and differentiated as described previously (Francis et al., 2020, Jeziorska et al., 2017, Nichols et al., 1990, Smith, 1991). Embryoid bodies were harvested after 7 days of differentiation and cells released by trypsin-mediated disaggregation and CD71+ Ter119+ cells were selected for using magnetic column purification (Miltenyi)

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 75000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

tag: Sex

value: Male

value: Erythroid (CD71+ Ter119+)

tag: time

value: differentiation day 7


title: 56R_BCR

city: Shanghai

first: Ying

last: Wang

state: Shanghai

address: 130 Dong’an Road

department: Immunology

country: China

institute: fudan university

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
-> MT% < 20%;
-> Cell Gene Number < Median Gene Number * 2;
-> Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes;  csv file contain BCR clonotypes.

source_name: Bone marrow B lineage cells

growth_protocol: BM B220+ cells were purified using BD IMag™ Mouse B Lymphocyte Enrichment Set-DM and were processed using the 10x Genomic Chromium Single Cell Platform

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: C57BL/6, 56R heterozygous

value: 10 Week

value: Bone marrow B lineage cells


title: SCVI-111_hiPSC_CM_Reporter_10

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

state: CA

address: 265 Campus Dr.

department: Cardiovascular Institute

institute: Stanford University

description:
Human induced pluripotent stem cells containing a TBX5-lineage tracing system consisting of a TBX5-Cre and CMV Drive lox-stop-lox-TurboGFP construct were differentiated to day 15 hiPSC cardiomyocytes. Cells were dissociated and processed for scRNA-seq using the ICELL8 system.
111_ICELL8_D15_barcodes.tsv.gz
111_ICELL8_D15_features.tsv.gz
111_ICELL8_D15_matrix.mtx.gz

data_processing:
All single cell ibraries were sequenced with the Illumina NovaSeq 6000 platform.
Droplet Based Sequencing: Data generated using the 10X Genomics 3' scRNA-seq v3.1 kit  were processed using CellRanger v6.0.0 (10X Genomics). Default parameters were used for alignment. The reference genomes used were refdata-gex-GRCh38-2020-A  for Human alignment and refdata-gex-mm10-2020-A for mouse data. References were obtained from the 10X Genomics website.
Samples (SCVI-111_hiPSC-Derived Cardiomyocytes_Day7-30) were multiplexed using the 10X Genomics CellPlex kit were demultiplexed using the CellRanger multi configuration. 10X Genomics cell multiplexing oligos used for each individual sample were as follow: Day7-CMO306, Day11-CMO307, Day13-CMO308, Day15-CMO309, Day30-CMO310.
Smartseq2 Based Sequencing: Data generated using the ICELL8 Takara Smartseq2 kit were processed using STARSolo aligner v2.7.9a software developed by Alexander Dobin. Reference genome used was a custom reference from GRCh38-2020-A (10X Genomics) containing added TurboGFP sequence. Parameters used were:  --soloType SmartSeq --soloStrand Unstranded.
GRCh38 (for Human) and mm10 (for Mouse)
Genome_build: Samples containing tab-delimited files contain output from CellRanger or STARSolo containing file with gene ensembl ID and gene symbols, cell barcodes, and matrix file containing raw counts.

source_name: hiPSC-derived Cardiomyocytes

extract_protocol:
Droplet based extraction: HiPSC-derived cardiomyocyte or mouse embryonic heart derived single cells were dissociated and captured and lysed using 10X Genomics Chromium Next GEM Single Cell 3' v3.1 Kit. mRNA was reverse transcribed to cDNA, and cDNA pre-amplification was conducted following manufacturer's protocol.    Smart-seq2 based extraction: HiPSC-derived cardiomyocytes were dissociated into single cell suspensions and captured using the ICELL8 Smartseq2 TAKARA system. mRNA was reverse transcribed to cDNA and cDNA pre-amplification was conducted per manufacturer’s protocol on an ICELL8 nanowell chip.
Droplet based library construction: Libraries for samples processed using 10X Genomics Single Cell 3' v3.1 kit were prepared from pre-amplified cDNA according to manufactrer's protocol. Gene expression libraries were generated for all 10X samples, and CellPlex multiplexing libraries were generated for running hiPSC-CM samples (Day 7, 11, 13,15, 30). Individual library index primers were used for multiplexing libraries on flow cell during sequencing.     Smart-seq2 library construction: Following Takara Smartseq2 ICELL8 protocol, pre-amplified and tagmented cDNA from individual single cells in ICELL8 nanowells received individual index sequencing barcodes for demultiplexing cells during downstream analysis.

value: hiPSC-derived cardiomyocytes

tag: developmental stage

value: Day 15

value: SCVI-111 TBX5-Lineage Reporter Line


title: ATAC_WT_rep1

value: WT


title: A15 MO


title: SCVI-111_hiPSC_CM_Reporter_14


title: SCVI-111_hiPSC_CM_Reporter_09


title: ATAC_PP7_rep2


title: Laptm5KO56R_BCR

value: C57BL/6, Laptm5KO56R heterozygous


title: SCVI-111_hiPSC_CM_Reporter_13


title: SCVI-111_hiPSC_CM_Reporter_11


title: A13 MO


title: A14 MO


title: A21 MI

value: MI

value: 30 minutes of transportation


title: ATAC_PP7_rep1


title: Laptm5KO56R

source_name: B220+ bone marrow cells

value: B220+ bone marrow cells


title: SCVI-111_hiPSC_CM_Reporter_07


title: SCVI-111_hiPSC_CM_Reporter_12


title: ATAC_PCP_C12

value: PCP C12 clone


title: A11 MO

value: MO

value: 180 minutes of transportation


title: SCVI-111_hiPSC_CM_Reporter_08


title: 56R

value: Male


title: A10 MO

value: Blood


title: ATAC_PCP_B11

value: Erythroid (CD71+ Ter119+)

value: PCP B11 clone

value: differentiation day 7


title: A9 CL

description: Blood samples collected from non transported goats

value: CL

value: non transported goats


title: SCVI-111_hiPSC_CM_Reporter_05

value: hiPSC-derived cardiomyocytes

value: Day 15


title: ATAC_PCP_B7

value: PCP B7 clone


title: Embryonic Day 10.5 Mouse Hearts

description: Whole mouse E10.5 embryonic hearts were dissected and dissociated for scRNA-seq.

source_name: Embryonic Mouse Hearts

value: Embryonic Mouse Heart Cells

value: Embryonic Day 10.5


title: SCVI-111_hiPSC_CM_Reporter_06

value: SCVI-111 TBX5-Lineage Reporter Line


title: Dll1- control tumor

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

description: n=1, Dll1- control tumor was harvested; live CD45- cells FACS sorted.

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, single indexing run. We had a mean of about 22,000 reads per cell. Data was then processed using the Cellranger pipeline (10x genomics, v.4.0.0) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome and creation of feature-barcode matrices. Libraries were normalized for sequencing depth across all libraries during aggregation.
Genome_build: mm10
Supplementary_files_format_and_content: barcode, feature, matrix tsv files

source_name: Mouse mammary tumor

extract_protocol:
Single cell suspensions were generated by digestion with collagenase type IA and hyaluronidase  for 55 minutes at 37oC. Post-whole tumor tissue digestion, tumor cells were brought to single cells using 0.25% trypsin EDTA and Dispase/DNAse solution sequentially. Red blood cells were removed using 0.64% sterile ammonium chloride solution for 5 min at 37 °C. Tumor cells were further passed through a 0.45-μm strainer to obtain single cells. Single cells were stained with a combination of antibodies (biotynated CD31, CD45 and Ter 119), followed by streaptavidin PEcy7. Cells were sorted on Aria II at the Upenn Flow Cytometry Core Laboratory.
Dataset consists of a total of two single-cell datasets generated using the 10x Genomics Chromium platform. Prior to GEM generation, the sample’s concentration (cells/ul) and viability (%) were determined by staining the cells with trypan blue and by manually counting using an inverted microscope. Next-generation sequencing libraries were prepared following the 10X Single Cell v3 protocol without modification. Sample quality was evaluated using Agilent’s Bioanalyzer High Sensitivity reagent kit following cDNA amplification and library construction. The completed libraries were quantified using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were diluted to 2nM and sequenced in a paired-end, single-indexed format on the Illumina NovaSeq SP using the Rapid Run v3 chemistry.

treatment_protocol: Untreated control tumors

value: Dll1- CD45-

value: Untreated tumor


title: 24h APF wing, H3K27me3, 75 wings, supernatant

city: Ann Arbor

first: Elizabeth

last: Fogarty

state: MI

address: 1105 N. University Ave

institute: University of Michigan

description: 24h H3K27me3 75 wings

data_processing:
library strategy: CUT&RUN
Raw sequencing files assessed using FastQC
Trimmomatic-0.39 used to trim adaptors and low-quality bases
Reads aligned to dm6 genome using Bowtie2.4.1 with --local --very-sensitive parameters. Max fragment size set to 1000.
Duplicates marked using picard-tools2.8.1 MarkDuplicates, and BAM files generated using samtools1.5.
Peaks called using macs2 version 2.1.2. Bigwigs and heatmaps generated using DeepTools.
Assembly: dm6
Supplementary files format and content: BigWig

organism: Drosophila melanogaster

source_name: pupa wing

extract_protocol:
Tissues were dissected in CUT&RUN wash buffer, then dissociated in collagenase/dispase solution for 40 minutes
Libraries were prepared using Takara ThruPLEX DNA-seq and Dual Index kits. Libraries were amplified using 14-19 PCR cycles, then cleaned up using AMPure XP beads from Beckman Coulter. Library quality was assessed using an Agilent Tape Station.

value: pupa wing

value: mixture of y,w/w;+;+ and y,w/y,w;+;+

value: pooled male and female

tag: cut&run antibody

value: Rabbit Anti-H3K27me3, Cell Signaling, cat#9733


title: 24h APF wing, H3K27me3, 45 wings, supernatant

description: 24h H3K27me3 45 wings


title: SCVI-111_hiPSC_CM_Reporter_04


title: SCVI-111_hiPSC_CM_Reporter_03


title: cKO-AOM-DSS_rep3

first: Ji-Xuan

last: Han

address: 145 Middle Shandong Road

institute: Renji Hospital, Shanghai Jiao-Tong University School of Medicine

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: mm9
Supplementary_files_format_and_content: FPKM_with_gene_exp_significant_with_symbol

source_name: Colon epithliem cells

growth_protocol: 6-8-week-old male Zfp90fl/fl and Zfp90△IEC mice were housed in laminar flow cabinets under specific pathogen-free conditions with food and water provided ad libitum

extract_protocol:
Colonic epithelium cells were isolated by incubating in HBSS with 2.5mM EDTA and 1mM DTT for 20min at 37℃ under slow rotation. RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

treatment_protocol: Zfp90fl/fl and Zfp90△IEC mice were injected intraperitoneally with AOM (10 mg/kg). After 5 days, 2% DSS was added to the drinking water for 7 consecutive days, then followed by 14 days of regular water. Three cycles of DSS treatment were used. After induction of tumorigenesis, mice were euthanized on day 80.

value: colon


title: L3 wing, IgG, rep2

description: L3 wing IgG rep2

source_name: third instar larval wing

value: third instar larval wing

value: female

value: Rabbit Anti-Mouse IgG, Abcam,Cat#Ab46540


title: SCVI-111_hiPSC_CM_Reporter_02


title: cKO-AOM-DSS_rep1


title: A7 CL

value: Blood

value: CL

value: non transported goats


title: A6 CL


title: Control-AOM-DSS_rep3


title: A4 CL


title: L3 wing, H3K27me3, rep2

description: L3 wing H3K27me3 rep2


title: A3 CL


title: SCVI-111_hiPSC-Derived Cardiomyocytes_Day50

description: Human induced pluripotent stem cells were differentiated into cardiomyocytes and frozen at day 7 of differentiation. Time thaws were conducted to synchronize collection of cells for scRNA seq at Day 7, 11, 13, 15, 30, and 50 of differentiation.  This sample represents day 50 hiPSC-CMs.

value: hiPSC-derived cardiomyocytes

value: Days 50


title: A1 CL


title: L3 wing, H3K27me3, rep1

description: L3 wing H3K27me3 rep1


title: Control-AOM-DSS_rep1


title: SCVI-111_hiPSC-Derived Cardiomyocytes_Day7-30

description: Human induced pluripotent stem cells were differentiated into cardiomyocytes and frozen at day 7 of differentiation. Time thaws were conducted to synchronize collection of cells for scRNA seq at Day 7, 11, 13, 15, 30, and 50 of differentiation.  This sample represents Day 7, 11, 13, 15, and 30.


title: Dll1+ control tumor

description: n=1, Dll1+ control tumor was harvested; live CD45- cells FACS sorted.

value: Dll1+ CD45-


title: A8 CL


title: CHO_1

status: Public on Aug 13 2022

city: Guangzhou

first: fei

middle: peng

last: li

address: Zhongshan second road

institute: Sun Yat-Sen University

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity  or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM)were calculated using protocol from Chepelev et al.Nucleic Acids Research, 2019.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mature chondrocytes isolated replicate 1

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bone Marrow

value: mesenchymal stem cells


title: C21_3

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 21 days replicate 3


title: C21_2

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 21 days replicate 2


title: cKO-AOM-DSS_rep2


title: C21_1

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 21 days replicate 1


title: SCVI-111_hiPSC_CM_Reporter_01

value: Day 15

value: SCVI-111 TBX5-Lineage Reporter Line


title: C7_3

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 7 days replicate 3


title: C14_2

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 14 days replicate 2


title: C14_3

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 14 days replicate 3


title: C14_1

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 14 days replicate 1


title: C7_2

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 7 days replicate 2


title: C7_1

source_name: Mesenchymal stem cells subjected to TGF-β induced micromass chondrogenic differentiation for 7 days replicate 1


title: MSC_2

source_name: Mesenchymal stem cells not subjected to TGF-β induced chondrogenic differentiation replicate 2


title: MSC_1

source_name: Mesenchymal stem cells not subjected to TGF-β induced chondrogenic differentiation replicate 1


title: MSC_3

source_name: Mesenchymal stem cells not subjected to TGF-β induced chondrogenic differentiation replicate 3


title: Control-AOM-DSS_rep2


title: lib59573

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts_MUPPITS2_nasal_samples.csv is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
RNA quality was assessed using RNA electrophoresis (Agilent). All samples had RIN values ≥7. Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina)

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

value: Placebo

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib59577

tag: treatment


title: lib59575


title: lib59568


title: lib59580


title: CHO_2

source_name: Mature chondrocytes isolated replicate 2

tag: tissue

tag: cell type


title: CHO_3

source_name: Mature chondrocytes isolated replicate 3


title: lib59546

value: Mepolizumab

value: Discontinued Study


title: lib59552


title: lib59537


title: lib59542


title: lib59528


title: lib59512


title: lib59535


title: lib59524


title: lib59507


title: lib59498


title: lib59506


title: lib59502


title: lib59496


title: lib59480


title: lib59484


title: lib59504


title: lib59469


title: lib59457


title: lib59461


title: lib59443


title: lib59437


title: L3 wing, IgG, rep1

description: L3 wing IgG rep1

value: third instar larval wing

tag: genotype

tag: Sex

value: female

value: Rabbit Anti-Mouse IgG, Abcam,Cat#Ab46540


title: lib59449


title: lib59562

value: Visit 14


title: lib59550


title: lib59551


title: lib59549


title: lib59556


title: lib59547


title: lib59539


title: lib59531


title: lib59530


title: lib59538


title: lib59532


title: lib59526


title: lib59522


title: lib59520


title: lib59486


title: lib59517


title: lib59513


title: lib59439


title: lib59450


title: lib59483


title: lib59463


title: lib59438


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title: lib59579

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title: lib59581


title: lib59561


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title: lib59564


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title: lib59553


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title: lib42399


title: lib42416


title: lib42428


title: lib42409


title: lib59960


title: lib42566


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title: lib42407


title: lib42415


title: lib42471


title: lib42523


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title: lib42522


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title: lib42519


title: lib42516


title: lib42510


title: lib42517


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title: lib42509


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title: lib42531


title: lib42496


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title: lib42486


title: lib42470


title: B73, leaf, Hour60 [Cg60_2]

city: Beijing

first: Xinyao

last: Xia

address: West Yuanmingyuan Road, Haidian District, Beijing

institute: caas

data_processing:
Fragments per kilobase of exon model per million mapped reads (FPKM) of maize genes were calculated. The heatmap was created by R package pheatmap based on the transformed FPKM with Z-score standardization
Assembly: B73 v 4.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

source_name: maize leaf cells

extract_protocol:
Total RNA was extracted from leaf samples using Trizol method. Then, the RNA was analyzed by agrose gel electrophoresis
RNA-seq libraries was finally constructed with the Illumina standard mRNASeq Prep Kit (TruSeq RNA and DNA Sample Preparation Kits)

value: maize leaf cells

value: Colletotrichum graminicola

tag: time

value: Hour 60


title: B73, leaf, Hour96 [Cg96_2]

value: Hour 96


title: lib42480

tag: source tissue


title: B73, leaf, Hour96 [Cg96_3]


title: B73, leaf, Hour60 [Cg60_1]


title: B73, leaf, Hour60 [Cg60_3]


title: lib42484

tag: flowcell id


title: lib42485

tag: visit


title: B73, leaf, Hour40 [Cg40_3]

value: Hour 40


title: B73, leaf, Hour24 [Cg24_3]

value: Hour 24


title: lib42443

value: Nasal Lavage

tag: study id


title: lib42458

tag: fastq total reads


title: B73, leaf, Hour24 [Cg24_2]


title: B73, leaf, Hour40 [Cg40_2]


title: B73, leaf, Hour40 [Cg40_1]


title: lib42427

tag: percent aligned

value: Placebo


title: lib42426

tag: aligned counts in millions

value: Completed Study


title: lib42420

tag: median cv coverage


title: B73, leaf, Hour0 [Control3]

value: water

value: Hour 0


title: B73, leaf, Hour24 [Cg24_1]


title: B73, leaf, Hour96 [Cg96_1]


title: lib42418

value: Mepolizumab

tag: time in study in years

value: Discontinued Study


title: B73, leaf, Hour0 [Control1]


title: lib42417

tag: status


title: B73, leaf, Hour0 [Control2]


title: lib42414

tag: exacerbation number


title: lib42405

tag: treatment


title: lib42401


title: lib42404


title: lib42396


title: lib42437


title: lib42400


title: ZXD_3

city: Fuzhou

first: wenjin

last: Lin

address: Road 54

institute: Fujian Academy of Medical Sciences

data_processing:
Sequencing reads were mapped to reference sequence by the SOAPaligner/soap2, a tool designed for short sequences alignment. Coverage of reads in one gene was used to calculate expression level of this gene. Using this method we obtained the expression levels of all genes detected.Reads that could be uniquely mapped to a gene were used to calculate the expression level. The gene expression level was measured by the number of uniquely mapped reads per kilobase of exon region per million mappable reads (RPKM). All expression data statistic and visualization was conduction with R package (http://www.r-project.org/).
After the expression level of each gene was calculated, differential expression analysis was conducted using edgeR. The false discovery rate (FDR) was used to determine the threshold of the p value in multiple tests, and for the analysis, a threshold of the FDR≤0.01 and an absolute value of log2Ratio≥1 were used to judge the significance of the gene expression differences. The differentially expressed genes were used for GO and KEGG enrichment analyses according to a method similar to that described by Zhang[3] .Both GO terms and KEGG pathways with a Q-value ≤0.05 are significantly enriched in DEGs.
Genome_build: Rattus norvegicus
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was purified using the Trizol Kit (Invitrogen Life Technologies, NY, USA) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The rats were fed a standard chow for an acclimatization period of one week after their arrival. Then, some rats were fed normal chow as the normal control group (CON group, n=10), and others were orally administered irradiated HFD composed of 2% cholesterol, 8.3% yolk, 7% lard, 0.3% sodium cholate, 16.7% sucrose, 0.2% propylthiouracil and 66% base forage. After 4 weeks, the rats fed a HFD were randomly divided into three groups: one group was administered saline as a high-fat control (HFD group, n=10), while the other two groups were orally administered simvastatin at 2.1mg/(kg•d) (SVT group, n=10) or ZXD at 2.2g/(kg•d) (ZXD group, n=10) for another 4 weeks. All rats had free access to diet and water during the experiment.

tag: strain

value: Sprague-Dawley

value: male

value: Zexie Decoction group

tag: tissue

value: liver


title: HFD_4

value: high-fat control group


title: lib42330

value: Visit 3


title: ZXD_5


title: ZXD_1


title: HFD_2


title: ZXD_4


title: HFD_5


title: HFD_3


title: lib42319


title: lib42320


title: lib42406

value: CDNDKANXX

value: Randomization


title: lib42313


title: lib42316


title: CON_5

value: normal control group


title: CON_4


title: CON_3


title: CON_2


title: ZXD_2


title: lib42309


title: lib42247


title: lib42233


title: CON_1


title: lib42232


title: lib42387

value: Visit 14


title: lib42223

value: Nasal Lavage


title: HFD_1


title: lib42383


title: Patient 65 non-ulcerated melanoma  [NU65 mRNA]

type: RNA

city: Columbus

first: William

middle: E.

last: Carson III

state: OH

institute: The Ohio State University

hyb_protocol: RNA samples were hybridized overnight with nCounter reporter probes (8 μL) in hybridization buffer and in excess of nCounter capture probes (2 μL) at 65 °C for 18 h.  After overnight hybridization, excess probes were removed using two-step magnetic beads based purification on an automated fluidic handling system (nCounter Prep Station).  Biotinylated capture probe-bound samples were immobilized and recovered on a streptavidin-coated cartridge.

scan_protocol: The abundance of specific target molecules was then quantified using the nCounter digital analyzer.  Individual fluorescent barcodes and target molecules present in each sample were recorded with a CCD camera by performing a high-density scan (325 fields of view).  Images were processed internally into a digital format and exported as Reporter Code Count (RCC).

data_processing: Both ulcerated and non-ulcerated samples were included on each cartridge. Two standard control RNA samples supplied by the manufacturer were included in the assay to permit normalization of mRNA expression in samples across multiple cartridges. Six positive and eight negative control targets were included on each cartridge to assess background hybridization and filter out target mRNAs with low expression. The upper quartile normalization method was then used to normalize across biological samples. Linear models and a moderated t-test were employed to detect differential expression between ulcerated and non-ulcerated tumors while considering cartridge effect. Significance was adjusted using a Bonferroni procedure to control the mean number of false positives.  Statistical software SAS 9.4 and R 3.6 were used for analysis with an α of 0.01 and a fold change of at least 1.5 used to identify differentially expressed miRs.

source_name: non-ulcerated primary cutaneous melanoma

extract_protocol: RNA isolated from four 20 um thick scrolls of formalin fixed, paraffin embedded human biopsy tissue using the Invitrogen RecoverAll total nucleic acid isolation kit for FFPE (#AM1975). For FFPE samples the RNA concentration was determined using Qubit High Sensitive RNA Assay (Thermo Fisher Scientific).  The correct quantity of RNA to be used for the nCounter® Tumor Signaling 360 Panel was determined using the DV200.  The DV200 is the percentage of RNA fragments that are larger than 200 nucleotides in size and was determined with a 2200 Tapestation (Agilent) with an RNA Screentape kit.  For DV200 > 65% 100ng of RNA is recommended; for DV200 between 25% to 65%, 200 ng of RNA is recommended; for DV200 < 25%, 300 ng of RNA is recommended.


title: lib42385

value: Placebo


title: lib42382

value: Completed Study


title: lib42227


title: lib42252


title: lib42380


title: Patient 63 non-ulcerated melanoma  [NU63 mRNA]

value: non-ulcerated primary cutaneous melanoma


title: lib42374


title: lib42386


title: lib42375


title: Patient 73 ulcerated melanoma [UC73 mRNA]

source_name: ulcerated primary cutaneous melanoma

value: ulcerated primary cutaneous melanoma


title: Patient 72 ulcerated melanoma [UC72 mRNA]


title: lib42373

value: Mepolizumab


title: Patient 61 non-ulcerated melanoma  [NU61 mRNA]


title: Patient 62 non-ulcerated melanoma  [NU62 mRNA]


title: lib42372


title: Patient 67 ulcerated melanoma [UC67 mRNA]


title: lib42371


title: Patient 60 non-ulcerated melanoma  [NU60 mRNA]


title: Patient 70 ulcerated melanoma [UC70 mRNA]


title: lib42370


title: Patient 50 non-ulcerated melanoma  [NU50 mRNA]


title: Patient 52 non-ulcerated melanoma  [NU52 mRNA]


title: Patient 49 non-ulcerated melanoma  [NU49 mRNA]


title: Patient 68 ulcerated melanoma [UC68 mRNA]


title: Patient 69 ulcerated melanoma [UC69 mRNA]


title: lib42366


title: lib42367


title: lib42365


title: lib42364


title: Patient 47 non-ulcerated melanoma  [NU47 mRNA]


title: Patient 36 non-ulcerated melanoma  [NU36 mRNA]


title: Patient 59 ulcerated melanoma [UC59 mRNA]


title: Patient 2 non-ulcerated melanoma  [NU2 mRNA]


title: Patient 51 non-ulcerated melanoma  [NU51 mRNA]


title: Patient 58 ulcerated melanoma [UC58 mRNA]


title: lib42356


title: lib42358


title: lib42355


title: lib42353


title: Patient 57 ulcerated melanoma [UC57 mRNA]


title: Patient 56 ulcerated melanoma [UC56 mRNA]


title: CSF_SAH_057

city: BARCELONA

first: Leire

last: Pedrosa

state: Barcelona

address: Carrer del Villarroel 170

country: Spain

institute: IDIBAPS

hyb_protocol: Three microliters of extracted RNA were processed according to the manufacturer’s recommendations for the nCounter Human v3 miRNA Expression Assay Kit (CSO-MIR3-12, NanoString Technologies, Seattle).

scan_protocol: Each sample was scanned for 555 FOV on the nCounter Digital Analyzer. nCounter Prep Station using nCounter Analysis System User Manual (MAN-C0035), nSolver software.

data_processing: Quality control, normalization, and data analysis were performed using nSolver 4.0 Analysis Software (NanoString Technologies). For each gene, count data was processed as follows: (a) normalization to the geometric mean of both spikes (reference genes), (b) geometric mean of negative control and (c) considering only the miRNA with more of the negative mean and which were express over this threshold in >20% of all samples.

source_name: cerebrocerebrospinal fluid (CSF)

extract_protocol: Total RNA was isolated from 200 μL of each sample of CSF according to the manufacturer’s protocol (Total RNA isolation kit, Appendix B; Norgen Biotek, Thorold, Canada). MS2 carrier RNA (Roche, Switzerland) and spike-ins (cel-miR-254 and osa-miR414, Integrated DNA Technologies (IDT), USA) were added according to the protocol to improve the miRNA extraction and evaluate the efficacy of the process

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

value: Female

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ACoA

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h

tag: moca at 3-months

tag: molecule

value: miRNA


title: lib42297

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: lib42369


title: CSF_SAH_056

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ICAD

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Poor


title: lib42296

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

value: Visit 14

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: Patient 54 ulcerated melanoma [UC54 mRNA]

tag: tissue


title: lib42295

value: Completed Study


title: Patient 6 non-ulcerated melanoma  [NU6 mRNA]

value: non-ulcerated primary cutaneous melanoma


title: CSF_SAH_055

tag: subject status

tag: Sex

value: Male

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: glycemia

tag: glycemia at 72h

tag: moca at 3-months

tag: molecule


title: lib42292

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Placebo

tag: time in study in years

tag: status

tag: exacerbation number


title: lib42357


title: lib42291


title: lib42293


title: lib42354


title: CSF_SAH_054

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: PICA

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2


title: lib42290

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: Patient 49 ulcerated melanoma [UC49 mRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: lib42289


title: CSF_SAH_053

tag: subject status

tag: Sex

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ACoA

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

value: No

tag: dci

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: Patient 55 ulcerated melanoma [UC55 mRNA]


title: Patient 48 ulcerated melanoma [UC48 mRNA]


title: lib42288

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: lib42287


title: lib42286

value: Mepolizumab


title: CSF_SAH_052

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: moca at 3-months

value: miRNA


title: Patient 47 ulcerated melanoma [UC47 mRNA]

tag: tissue


title: Patient 46 ulcerated melanoma [UC46 mRNA]


title: lib42284

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

value: Visit 14

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: CSF_SAH_051

tag: subject status

tag: Sex

value: Male

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMD

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: Patient 45 ulcerated melanoma [UC45 mRNA]

tag: tissue


title: CSF_SAH_050

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

value: no aneurysms

value: No treatment

tag: rankin at 3-months

tag: rankin at 3-months (0-2


title: lib42283

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: lib42282

value: Placebo


title: Patient 3 ulcerated melanoma [UC3 mRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: CSF_SAH_049

tag: subject status

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ACMI

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

value: No

tag: symptomathic vasospasm

tag: dci

tag: evd

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: lib42281

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

tag: exacerbation number


title: lib42280


title: Patient 2 ulcerated melanoma [UC2 mRNA]

tag: tissue


title: lib42276


title: CSF_SAH_048

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoA

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Poor

tag: moca at 3-months

value: miRNA


title: CSF_SAH_047

tag: subject status

value: Embolization (intravascular coiling)

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: Patient 1 ulcerated melanoma [UC1 mRNA]

tag: tissue


title: lib42275

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

value: Visit 14

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib42285


title: Patient 65 non-ulcerated melanoma  [NU65 miRNA]

hyb_protocol: Tagged microRNAs were hybridized to capture and reporter probes at 64°C for 18 hours. Hybridized probes were immobilized onto a streptavidin-coated cartridge via nCounter Prep Station (Nanostring).

scan_protocol: Fluorescence of each hybridized miR-probe complex was analyzed by an nCounter Digital analyzer (Nanostring Technologies, Seattle, WA) via high density scan with 600 fields of view.

data_processing: Both ulcerated and non-ulcerated samples were included on each cartridge.  5 positive, 5 negative and 5 housekeeping genes were included in the panel by the manufacturer. Negative controls were used to assess background hybridization and filter out target miRs with expression below the mean of the highest detected negative control sample. The upper quartile normalization method was then used to normalize across biological samples. Linear models and a moderated t-test were employed to detect differential expression between ulcerated and non-ulcerated tumors while considering cartridge effect. Significance was adjusted using a Bonferroni procedure to control the mean number of false positives.  Statistical software SAS 9.4 and R 3.6 were used for analysis with an α of 0.05 and a fold change of at least 1.5 used to identify differentially expressed miRs.

label: not provided

label_protocol: 100 ng of RNA per sample was loaded onto a Nanostring nCounter cartridge. Individual miRs were ligated to DNA tags provided by the manufacturer. Excess tags were washed away.

extract_protocol: RNA isolated from four 20 um thick scrolls of formalin fixed, paraffin embedded human biopsy tissue using the Invitrogen RecoverAll total nucleic acid isolation kit for FFPE (#AM1975). RNA concentration was determined using a Nanodrop spectrophotometer and Qubit analysis.

value: non-ulcerated primary cutaneous melanoma


title: lib42268


title: lib42269


title: CSF_SAH_046

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMD

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: moca at 3-months


title: lib42267

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: Patient 63 non-ulcerated melanoma  [NU63 miRNA]

tag: tissue


title: lib42266

value: Placebo


title: lib42265


title: lib42264


title: Patient 62 non-ulcerated melanoma  [NU62 miRNA]


title: Patient 61 non-ulcerated melanoma  [NU61 miRNA]


title: lib42331

value: Randomization


title: lib42352


title: Patient 60 non-ulcerated melanoma  [NU60 miRNA]


title: lib42321


title: CSF_SAH_042

tag: subject status

tag: Sex

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ICAD

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: CSF_SAH_044

tag: subject status

value: Male

value: No

value: ACoA

value: Yes

tag: rankin at 3-months

tag: rankin at 3-months (0-2


title: lib42270

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_043

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dci

tag: evd

tag: glycemia

tag: glycemia at 72h

value: miRNA


title: lib42312

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

value: Completed Study


title: lib42311

tag: status

tag: exacerbation number


title: lib42310


title: CSF_SAH_041

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoPi

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: moca at 3-months

tag: molecule


title: CSF_SAH_045

tag: dci

tag: evd

tag: glycemia

tag: glycemia at 72h


title: Patient 73 ulcerated melanoma [UC73 miRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: lib42263

tag: source tissue

tag: flowcell id

tag: visit

value: Visit 14

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Placebo

tag: time in study in years

tag: status

tag: exacerbation number


title: lib42234

value: Randomization


title: lib42231


title: CSF_SAH_040

tag: subject status

tag: Sex

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: moca at 3-months

tag: molecule


title: lib42226

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: Patient 70 ulcerated melanoma [UC70 miRNA]

tag: tissue


title: lib42308


title: lib42224


title: lib42222


title: CSF_SAH_038

tag: subject status

tag: Sex

value: Male

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMD

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

value: good; 3-5:poor):Poor

tag: glycemia

tag: glycemia at 72h


title: Patient 59 non-ulcerated melanoma  [NU59 miRNA]

tag: tissue

value: non-ulcerated primary cutaneous melanoma


title: Patient 72 ulcerated melanoma [UC72 miRNA]


title: CSF_SAH_039

tag: subject status

tag: Sex

value: Yes

value: Posterior circulation Aneurysm treatment, n (%)

value: AVD

value: Embolization (intravascular coiling)

value: No

tag: molecule


title: Patient 69 ulcerated melanoma [UC69 miRNA]


title: lib42221

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28722

value: CCHDTANXX

value: Visit 3

value: Placebo

value: Discontinued Study


title: lib28717


title: lib28720


title: Patient 67 ulcerated melanoma [UC67 miRNA]

value: ulcerated primary cutaneous melanoma


title: CSF_SAH_037

value: spontaneous subarachnoid hemorrhage (SAH)

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ACMD

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h

tag: moca at 3-months

value: miRNA


title: Patient 52 non-ulcerated melanoma  [NU52 miRNA]

tag: tissue

value: non-ulcerated primary cutaneous melanoma


title: lib28715

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_034

tag: subject status

tag: Sex

value: Male

tag: age

tag: exitus

value: Yes

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMI

tag: treatment of aneurysm

value: No treatment

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dci

tag: evd

tag: molecule


title: CSF_SAH_036

value: No

value: ACoA

value: Embolization (intravascular coiling)

tag: dvp

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Poor

tag: glycemia

tag: glycemia at 72h


title: lib28709

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: CSF_SAH_035

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: PICA

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: moca at 3-months

tag: molecule


title: lib28704

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_033

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ICAD

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h

value: miRNA


title: Patient 51 non-ulcerated melanoma  [NU51 miRNA]

tag: tissue

value: non-ulcerated primary cutaneous melanoma


title: lib28701

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Placebo

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28687


title: lib28698


title: Patient 50 non-ulcerated melanoma  [NU50 miRNA]


title: lib42220

value: Randomization


title: CSF_SAH_032

tag: subject status

tag: Sex

value: Male

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoA

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: moca at 3-months

tag: molecule


title: lib28689

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: Patient 49 non-ulcerated melanoma  [NU49 miRNA]

tag: tissue


title: lib28685

value: Mepolizumab

value: Discontinued Study


title: lib28680


title: Patient 68 ulcerated melanoma [UC68 miRNA]

value: ulcerated primary cutaneous melanoma


title: CSF_SAH_031

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h


title: CSF_SAH_030

tag: subject status

value: Female

value: no aneurysms

value: No treatment

tag: rankin at 3-months

value: good; 3-5:poor):Poor

tag: molecule

value: miRNA


title: lib28669

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Placebo

tag: time in study in years

tag: status

tag: exacerbation number


title: Patient 43 non-ulcerated melanoma  [NU43 miRNA]

tag: tissue

value: non-ulcerated primary cutaneous melanoma


title: Patient 41 non-ulcerated melanoma  [NU41 miRNA]


title: CSF_SAH_029

tag: Sex

value: Male

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoPd

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months (0-2

tag: glycemia

tag: glycemia at 72h

tag: moca at 3-months


title: CSF_SAH_028

tag: subject status

tag: Sex

value: ACoA

tag: rankin at 3-months

tag: molecule


title: lib28665

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28666

value: Mepolizumab


title: lib28661


title: Patient 12 non-ulcerated melanoma  [NU12 miRNA]

tag: tissue


title: lib28656


title: lib28682


title: lib28650


title: lib28646


title: Patient 36 non-ulcerated melanoma  [NU36 miRNA]


title: lib28654


title: Patient 47 non-ulcerated melanoma  [NU47 miRNA]


title: lib28672


title: lib28645


title: lib28642


title: Patient 9 non-ulcerated melanoma  [NU9 miRNA]


title: CSF_SAH_025

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h


title: CSF_SAH_024

tag: Sex

tag: rankin at 3-months

tag: moca at 3-months

tag: molecule

value: miRNA


title: CSF_SAH_023

tag: subject status

tag: age

tag: exitus

tag: wfns

value: no aneurysms

value: No treatment


title: CSF_SAH_026

value: Female

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: AB

tag: treatment of aneurysm

tag: mfisher

value: good; 3-5:poor):Poor


title: lib28638

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28668


title: Patient 8 non-ulcerated melanoma  [NU8 miRNA]

tag: tissue

value: non-ulcerated primary cutaneous melanoma


title: Patient 5 non-ulcerated melanoma  [NU5 miRNA]


title: Patient 6 non-ulcerated melanoma  [NU6 miRNA]


title: lib28632

value: Placebo


title: CSF_SAH_027

tag: subject status

tag: Sex

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

value: ICAI

value: Embolization (intravascular coiling)

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: glycemia

tag: glycemia at 72h

tag: moca at 3-months

tag: molecule


title: CSF_SAH_022

tag: subject status

tag: aneurysms location

value: ACoPi

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher


title: lib28633

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28626


title: lib28625

value: Mepolizumab


title: Patient 2 non-ulcerated melanoma  [NU2 miRNA]

tag: tissue


title: lib28611


title: lib28618


title: lib28609


title: CSF_SAH_021

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: PICA

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dci

tag: evd

tag: glycemia

tag: glycemia at 72h

tag: molecule

value: miRNA


title: lib28607

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years


title: lib28605

tag: status

tag: exacerbation number


title: lib28596


title: lib28603


title: Patient 1 non-ulcerated melanoma [NU1 miRNA]

tag: tissue

value: non-ulcerated primary cutaneous melanoma


title: Patient 58 ulcerated melanoma [UC58 miRNA]

value: ulcerated primary cutaneous melanoma


title: lib28594


title: lib28629

value: Placebo


title: Patient 59 ulcerated melanoma [UC59 miRNA]


title: lib28593


title: CSF_SAH_018

tag: subject status

tag: Sex

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ACMI

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Poor

tag: moca at 3-months


title: CSF_SAH_019

tag: subject status

value: ACoA

value: Embolization (intravascular coiling)

value: Yes

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: Patient 3 non-ulcerated melanoma  [NU3 miRNA]

tag: tissue


title: lib28589

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Discontinued Study

tag: exacerbation number


title: Patient 57 ulcerated melanoma [UC57 miRNA]


title: Patient 56 ulcerated melanoma [UC56 miRNA]


title: lib28586

value: Mepolizumab

value: Completed Study


title: CSF_SAH_016

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

value: Female

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMD

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: moca at 3-months

value: miRNA


title: CSF_SAH_017

tag: subject status

value: No

value: Anterior circulation

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: CSF_SAH_015

tag: Sex

tag: age

tag: exitus

tag: wfns

value: Posterior circulation Aneurysm treatment, n (%)

value: AVI

value: No treatment


title: Patient 55 ulcerated melanoma [UC55 miRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: lib28583

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_014

tag: subject status

tag: Sex

value: Male

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoPi

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Poor

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: Patient 54 ulcerated melanoma [UC54 miRNA]

tag: tissue


title: lib28579

tag: source tissue

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Placebo

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28580


title: CSF_SAH_020

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMI

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: moca at 3-months

value: miRNA


title: lib28575

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28571


title: lib28566

value: Discontinued Study


title: CSF_SAH_013

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: AVD

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

value: No

tag: symptomathic vasospasm

tag: dci

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: lib28564

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status


title: CSF_SAH_012

tag: subject status

tag: Sex

value: Male

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: AB

tag: treatment of aneurysm

value: No treatment

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: dvp

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: moca at 3-months


title: Patient 49 ulcerated melanoma [UC49 miRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: Patient 48 ulcerated melanoma [UC48 miRNA]


title: lib28561

tag: source tissue

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Visit 3

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28550


title: lib28554

value: Placebo


title: lib28556


title: CSF_SAH_009

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

value: ICAD

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

value: good; 3-5:poor):Poor

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: lib28552

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_010

tag: subject status

tag: Sex

value: Female

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: PICA

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Good

tag: moca at 3-months

value: miRNA


title: Patient 47 ulcerated melanoma [UC47 miRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: CSF_SAH_011

tag: subject status

value: AB

value: Yes

tag: evd

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: lib28724

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Randomization

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: Patient 45 ulcerated melanoma [UC45 miRNA]

tag: tissue


title: Patient 20 ulcerated melanoma [UC20 miRNA]


title: Patient 46 ulcerated melanoma [UC46 miRNA]


title: lib28713

value: Placebo


title: lib28710


title: lib28719


title: CSF_SAH_006

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: no aneurysms

tag: aneurysms location

tag: treatment of aneurysm

value: No treatment

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2


title: CSF_SAH_007

value: Female

value: No

value: Anterior circulation

value: ACoPi

tag: glycemia

tag: glycemia at 72h

tag: moca at 3-months

tag: molecule


title: lib28705

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_008

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: PICA

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dci

tag: evd

value: miRNA


title: lib28707

tag: source tissue

value: Nasal Lavage

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Discontinued Study


title: Patient 14 ulcerated melanoma [UC14 miRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: lib28703

value: CCHDTANXX

value: Randomization

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28702

value: Placebo


title: lib28697


title: Patient 10 ulcerated melanoma [UC10 miRNA]


title: CSF_SAH_005

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

value: Yes

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoA

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: lib28688

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment


title: lib28692

tag: time in study in years

tag: status

tag: exacerbation number


title: CSF_SAH_004

tag: subject status

tag: Sex

value: Female

tag: age

tag: exitus

value: No

tag: wfns

tag: aneurysms location (ciruclation)

value: Anterior circulation

tag: aneurysms location

tag: treatment of aneurysm

tag: mfisher

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

value: good; 3-5:poor):Poor

tag: moca at 3-months


title: lib28716

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: Patient 4 ulcerated melanoma [UC4 miRNA]

tag: tissue


title: CSF_SAH_003

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACoPi

tag: treatment of aneurysm

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

value: good; 3-5:poor):Good

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: lib28684

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28686

value: Nasal Lavage


title: lib28681


title: Patient 2 ulcerated melanoma [UC2 miRNA]

tag: tissue


title: CSF_SAH_002

tag: subject status

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

value: Posterior circulation Aneurysm treatment, n (%)

tag: aneurysms location

value: AB

tag: treatment of aneurysm

value: Embolization (intravascular coiling)

tag: mfisher

tag: angiographic vasospasm

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: rankin at 3-months

tag: rankin at 3-months (0-2

tag: moca at 3-months

value: miRNA


title: lib28678

tag: source tissue

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Randomization

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: Patient 3 ulcerated melanoma [UC3 miRNA]

tag: tissue

value: ulcerated primary cutaneous melanoma


title: lib28679


title: lib28663


title: Patient 13 ulcerated melanoma [UC13 miRNA]


title: CSF_SAH_001

tag: subject status

value: spontaneous subarachnoid hemorrhage (SAH)

tag: Sex

tag: age

tag: exitus

tag: wfns

tag: aneurysms location (ciruclation)

tag: aneurysms location

value: ACMD

tag: treatment of aneurysm

value: Clipping (open surgery)

tag: mfisher

tag: angiographic vasospasm

value: Yes

tag: symptomathic vasospasm

tag: dvp

tag: dci

tag: evd

tag: glycemia

tag: glycemia at 72h

tag: molecule


title: Patient 1 ulcerated melanoma [UC1 miRNA]

tag: tissue


title: CSF_Control_010

tag: subject status

value: healthy


title: lib28653

tag: source tissue

tag: flowcell id

tag: visit

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28649

value: Placebo


title: lib28643


title: FNLN01_01_ATAC

city: Urbana

first: Dr. Gregory

last: Underhill

address: 1406 West Green Street

institute: University of Illinois at Urbana Champaign

data_processing:
https://www.encodeproject.org/atac-seq/
Assembly: hg19
Supplementary files format and content: csv files include FPKM values for entrez geneids for each sample

source_name: Primary Human HSCs

growth_protocol: HSCs were cultured on the cellular microarrays with defined ECM and stiffness composition in DMEM, 10% FBS, 1%Pen-Strep, 1% L-Glutamine for 72 hours

extract_protocol:
Cells were harvested and nuclie were isolated.
The libraries were prepared with the  ATAC-seq  library construction kit from Active Motif. https://www.activemotif.com/catalog/1301/atac-seq-kit

tag: cell line

value: Primary Human HSCs

tag: cell type

value: Hepatic Stellate Cells

tag: substrate stiffness

tag: ecm compositions

value: Fibronectin, Laminin

tag: time

value: 72 hours


title: lib28662

tag: source tissue

value: Nasal Lavage


title: FNLN01_02_ATAC


title: lib28637

tag: flowcell id


title: C4TC01_02_ATAC

value: Collagen 4, Tenascin C


title: FNLN01_03_ATAC


title: lib28657

tag: visit


title: lib28659

tag: study id


title: lib28660

tag: fastq total reads


title: lib28636

tag: percent aligned


title: CSF_Control_009

tag: subject status

tag: molecule

value: miRNA


title: C4TC01_01_ATAC


title: CSF_Control_007


title: CSF_Control_008


title: lib28622

value: CCHDTANXX

tag: aligned counts in millions

tag: median cv coverage

tag: treatment

value: Mepolizumab


title: lib28635

value: Randomization

tag: time in study in years

tag: status

value: Completed Study

tag: exacerbation number


title: lib28620


title: C1FN01_02_ATAC

tag: cell line

tag: cell type

tag: substrate stiffness

value: Collagen 1, Fibronectin


title: C1FN01_03_ATAC

tag: ecm compositions

tag: time


title: CSF_Control_006


title: lib28619

tag: source tissue

tag: flowcell id

tag: visit


title: lib28617

tag: study id

tag: fastq total reads

tag: percent aligned


title: CSF_Control_005

tag: subject status

tag: molecule


title: CSF_Control_003


title: C4TC01_03_ATAC


title: lib28639

tag: aligned counts in millions

tag: median cv coverage

tag: treatment


title: C1FN01_01_ATAC


title: lib28615

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28602


title: lib28604


title: FNLN25_02_ATAC

tag: cell line

tag: cell type

tag: substrate stiffness


title: CSF_Control_002


title: lib28613

tag: source tissue


title: lib28595

tag: flowcell id


title: EpiLC_input

city: New York

first: Abderhman

last: Abuhashem

state: NY

address: Rockefeller Research Labs, 430 E 67th St

department: Developmental Biology Program

institute: Sloan-Kettering Institute for Cancer Research

data_processing:
Reads are aligned to mm10 and hg38 combined reference using Bowtie2. mm10 read kept, and hg38 used for spike-in count
Alignments were filtrered for MAPQ >30 and mm10 blacklisted regions excluded
BigWig files generated using bamCoverage in R (DeepTools), normalized to human spike-in
Visualized using WashU genome browser
Assembly: mm10
Supplementary files format and content: BigWig files

source_name: 20 x 10^6 mouse embryonic stem cells

growth_protocol: Culture in serum/LIF at 37C and 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
nonstranded, generated using KAPA HTP Library Prep Kit

tag: antibody

tag: genotype

value: Nelfb deg


title: 2i_input


title: CSF_Control_001


title: lib28592

tag: visit

tag: study id

tag: fastq total reads


title: Sample_RNA-Lib_enGFP+Yki+Aac11-IR

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS
Single-read 50 bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.
Reads were aligned using Tophat2 v2.0.12
RPKM expression values from different conditions were extracted and compared by cuffdiff v2.2.1 using Refseq gene models [2].
Assembly: dm6 Drosophila

source_name: Larval wing disc cells

growth_protocol: Drosophila of the relevant genotypes were cultured under standard conditions at 25 degrees Celsius in humidity-controlled incubators with 12hr light:dark cycles

extract_protocol:
Wandering stage (L3 instar) larvae were sorted for GFP expression under a dissecting microscope equipped with a Zeiss HBO lamp and a GFP filter. Larvae were rinsed in 1x PBS and then  immediately ground and  dissolved in Trizol (TM) kept on ice. Tissue+Trizol mixtures were frozen at -80 degrees Celsius. This was repeated until 10-20 larvae per genotype (Act>Aac11-RNAi or Act>control) had been collected. Samples were then pooled within genotypes as needed, and total RNA was extracted according the manufacturer's instructions and depleted for rRNA prior to analysis.
4 µg of total RNA was rRNA depleted and utilized for library construction with the Illumina TruSeq RNA Sample Preparation Kit v2 following the manufacturer's instructions. Libraries were sequenced with an Illumina HiScan platform.

value: Larval wing disc cells


title: lib28601

tag: percent aligned


title: C4TC25_03_ATAC

tag: ecm compositions

tag: time


title: FNLN25_03_ATAC


title: FNLN25_01_ATAC


title: lib28584

tag: aligned counts in millions

tag: median cv coverage

tag: treatment


title: lib28597

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28582


title: EpiLC_NELFE_2

tag: cell line

value: Anti-NELFe abcam (ab170104)


title: lib28578

tag: source tissue


title: C4TC25_01_ATAC

tag: cell type

tag: substrate stiffness


title: lib28574

tag: flowcell id


title: CSF_Control_004

tag: subject status

value: healthy

tag: molecule


title: C4TC25_02_ATAC


title: lib28614

tag: visit

tag: study id

tag: fastq total reads

value: Placebo


title: lib28610

tag: percent aligned


title: lib28573

tag: aligned counts in millions


title: EpiLC_NELFB:HA_2

tag: antibody

value: HA-Tag CST (C29F4)

tag: genotype


title: C1FN25_03_ATAC

value: Primary Human HSCs

value: Hepatic Stellate Cells

tag: ecm compositions

tag: time


title: lib28572

tag: median cv coverage

tag: treatment

tag: time in study in years

tag: status

tag: exacerbation number


title: lib28570

tag: source tissue

tag: flowcell id

value: Discontinued Study


title: C1FN25_02_ATAC

tag: cell line

tag: cell type

tag: substrate stiffness

value: 72 hours


title: EpiLC_NELFE_1


title: lib28557

value: Nasal Lavage

tag: visit

tag: study id

tag: fastq total reads


title: lib28560

tag: percent aligned

tag: aligned counts in millions


title: naïve_NELFE_2

tag: antibody

tag: genotype


title: lib28555

tag: median cv coverage


title: naïve_NELFE_1

tag: treatment


title: naïve_NELFB:HA_2


title: C1FN25_01_ATAC

tag: ecm compositions

tag: time


title: lib28551

tag: time in study in years

tag: status

tag: exacerbation number


title: FNLN01_03_RNA

data_processing:
https://www.encodeproject.org/data-standards/rna-seq/small-rnas/
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for entrez geneids for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

tag: cell line

value: Fibronectin, Laminin


title: FNLN01_02_RNA

tag: cell type


title: lib28553

tag: source tissue

tag: flowcell id

value: CCHDTANXX


title: naïve_NELFB:HA_1


title: FOXA2 WT, Mature Hepatocytes, Samp11

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

data_processing:
Illumina sequencing and conventional base calling
Sequenced reads were quality-controlled by FASTQC and trimmed by Trimmomatic v.0.36 for adaptor sequence (if present).
Clean sequences were mapped to the GRCh38 whole genome using STAR v2.7.2b
The uniquely-mapped reads aligned to exons were counted with HTSeq v.0.9.1 , then tested for the presence of differentially expressed genes (DEGs) by the DESeq2 R package v.1.26.0
Genome_build: Homo Sapiens GRCh38
Supplementary_files_format_and_content: tab-delimited files with the raw counts for each sample

source_name: FOXA2 WT, Mature Hepatocytes

growth_protocol: iPSC were grown on matrigel coated plates and allowed to undergo differentiation using a previously published protocol (Ang et al., Cell Reports 2018)

extract_protocol:
Cells were collected using TRIzol reagent (Cat Number.15596026) and RNA was extracted using Norgen rna extraction kit (Cat Number. 47700)
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library(Cat # 20020594, for Hepatic Progenitors) and NEBNext Ultra Directional Library Prep Kit (NEB, E7420L, for Mature Hepatocytes) following the manufacturer’s protocol

treatment_protocol: No chemical treatment was carried out. CRISPR-CAS9 was used to create deletion in FOXA2 gene in iPSC generated from two healthy controls.

value: Mature hepatocytes

value: FOXA2 wild type


title: C4TC01_03_RNA

tag: substrate stiffness

value: Collagen 4, Tenascin C


title: FNLN01_01_RNA


title: FOXA2 WT, Mature Hepatocytes, Samp9


title: FOXA2 KO, Hepatic Progenitor, HP1

source_name: FOXA2 KO, Hepatic Progenitor

value: Hepatic progenitors

value: FOXA2 knock out


title: Epidermal LC Tfam-KO rep2

first: Jun

last: Zhang

address: No.2 Lujing road

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava software was used for basecalling.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. Mouse reference genome (mm10) annotation files were used.
Gene expression levels of all of the transcripts as fragments per kilobase of exon per million mapped fragments (FPKM) were calculated by cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: skin

extract_protocol:
LCs were sorted from epidermal cells suspension. Total RNA was extracted with Trizol reagent. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.
RNA libraries were prepared for sequencing by standard Illumina protocols.

tag: tissue

value: skin

value: primary cells

value: Langerhans cells

value: Tfam cKO


title: FOXA2 KO, Mature Hepatocytes, Samp12

source_name: FOXA2 KO, Mature Hepatocytes


title: FOXA2 KO, Mature Hepatocytes, Samp10


title: FOXA2 KO, Hepatic Progenitor, HP3


title: FOXA2 WT, Hepatic Progenitor, HP4

source_name: FOXA2 WT, Hepatic Progenitor


title: EpiLC_NELFB:HA_1

value: HA-Tag CST (C29F4)

value: Nelfb deg


title: FOXA2 WT, Hepatic Progenitor, HP2


title: C4TC01_02_RNA

value: Primary Human HSCs

value: Hepatic Stellate Cells


title: Epidermal LC WT rep2

value: WT


title: Epidermal LC Tfam-KO rep1


title: Epidermal LC WT rep1