title: HPR_45_input

description: Library name: Sample 148


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_173

status: Public on Mar 06 2025

type: SRA

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road, Weill Hall 301

department: Biomedical Engineering

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, sequencing data from the Illumina NextSeq 500 and Novaseq 6000 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts30 (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts30 (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap31 (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 3, if a sample had less than 75000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 3 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma seprated values .csv file contain gene counts for each sample in this study

molecule: total RNA

organism: Homo sapiens

source_name: plasma from HSCT cohort

extract_protocol:
Before cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from the plasma supernatant (250-1500 μl) using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Urine samples were thawed at room temperature and centrifuged at 16,000 x g for 10 minutes at 4 °C. cfRNA was extracted from (450-2000 μl) supernatant using QIAamp Circulating Nucleic Acid Kit -Purification of Circulating microRNA in serum/plasma/urine protocol (Qiagen, product #55114).  Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

tag: tissue

value: Plasma, extracted cell-free RNA

tag: cell type

tag: treatment

value: Hematopoietic Stem Cell Transplantation

tag: time

tag: diagnosis


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-115

source_name: urine from the HSCT cohort

value: Urine, extracted cell-free RNA


title: HPR_174_H3K27ac

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

description: Library name: Sample 147

library_source: genomic

data_processing:
Single-end or paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800), and for paired-end read to retain only paired reads in a proper pair (flags: 0x1, 0x2)          .
Reads were filtered to retain only individual reads (single-end) or read-pairs (paired-end) mapping to <=2 sites genome-wide (X0 tag <=2 for single-end or both paired-end reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

molecule: genomic DNA

source_name: Mass, base of tongue

extract_protocol:
For frozen lymphoma tumor samples, tumor cellularity from the frozen block was confirmed by H&E-frozen section by a board-certified hematopathologist (R.J.H. Ryan), and the block was trimmed as needed. Twenty-five–micron sections were then cut to a total of approximately 50 mg of tissue for each ChIP-Seq chromatin prep. Frozen sections were resuspended and dissociated in PBS + protease inhibitors + 10 mmol/L sodium butyrate. Formaldehyde was added to 1% and cells were cross-linked for 10 minutes at room temperature, quenched with 1/20th volume of 2.5M glycine, washed twice in cold PBS with protease inhibitors, and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g, and resuspended in cold SDS lysis buffer (0.3% SDS for H3K27ac and 1% SDS for TFs, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes. Nuclei were fragmented on a Q800R2 Sonifier (QSonica) as follows: three cycles of amplitude = 50, pulse times: 30s on / 30s off, total on time = 3:20 m, temperature = 80C. Samples were diluted 1:3 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4°C overnight with 2-5 ug of antibody. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After reversal of cross-linking, RNase and proteinase K treatment were performed and DNA was purified with Ampure XP beads for library preparation. Input sample was prepared by the same approach without immunoprecipitation.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated (Quick T4 DNA ligase, NEB) to barcoded illumina adaptors (Single-Indexed Adapter Kit, KAPA, #KK8700). Each reaction was followed by clean-up with AMPure XP beads. Ligation products were amplified by PCR for 14-18 cycles with illumina indexing primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection.

value: Mass, base of tongue

value: Diffuse large B-cell lymphoma

tag: chip antibody

value: H3K27ac (Active Motif, Cat #39133)


title: HPR_129_input

description: Library name: Sample 149

source_name: Mass, orbital soft tissue

value: Mass, orbital soft tissue


title: Pool of cortices and hippocampi samples (2620, 2771 and 2790 mice)

city: Rehovot

first: Rafael

last: Valdés Mas

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description: Library name: Batch_10

data_processing:
Ilumina output files were demultiplexed with bcl2fastq v.2.17. Resulting FASTQ files were analyzed using the zUMIs pipeline. Reads were aligned with STAR (v.2.5.3a) to the reference genome and unique molecular identifier (UMI) counts were used for downstream analysis.
the samples_description_barcode.tsv describes the barcodes for each sample in each batch
Assembly: Gencode_H34 or Gencode_M24/
Supplementary files format and content: tab delimited file including all gene counts across samples

organism: Mus musculus

source_name: Cortex, hippocampus

extract_protocol:
RNA was purified using standard chloroform extraction
Bulk mcSCRB-seq

value: Cortex, hippocampus

tag: cell line

value: bulk

tag: genotype

value: FAD/WT

tag: batch


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-104


title: Pool of cortices and hippocampi samples (2601, 2603, 2618 and 2756 mice)

description: Library name: Batch_8


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-103

value: E


title: HPR_131_H3K27ac

description: Library name: Sample 145

source_name: Lymph node, cervical

value: Lymph node, cervical


title: resolution_3

city: Atlanta

first: Pallavi

last: Bhattaram

address: 21 Ortho Ln

institute: Emory University

description:
Library name: Sample 11
DOX OFF_3

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Sequenced reads were mapped to the mus musculus GRCm38.p3 genome assembly using DNASTAR software, normalization was performed by RPKM on ArrayStar software.
Assembly: GRCm38.p3
Supplementary files format and content: Matrix table - delimited text files include normalized expression levels for each sample

source_name: Fibroblast-like synoviocytes

extract_protocol:
Synovial fibroblasts from TNF-induced inflammatory arthritis mice were cultured and RNA was harvested using Trizol reagent.
Human mRNA Sequencing (WOBI) was used to perform RNA sample QC. Poly A enrichment was implemented for mRNA library preparation. NovaSeq PE150 was used to generate 6 G raw data per sample.

value: Fibroblast-like synoviocytes

value: 1mg/ml Doxycycline + 5% sucrose water for 3 weeks and then stopped


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-098


title: HPR_171_H3K27ac

description: Library name: Sample 146

source_name: Mass, nasopharynx

value: Mass, nasopharynx


title: resolution_4

description:
Library name: Sample 12
DOX OFF_4


title: resolution_2

description:
Library name: Sample 10
DOX OFF_2


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-108


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-101


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-107


title: HPR_129_H3K27ac

description: Library name: Sample 144


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-110


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-130

value: PR


title: HPR_45_H3K27ac

description: Library name: Sample 143


title: resolution_1

description:
Library name: Sample 9
DOX OFF_1


title: inflammation_4

description:
Library name: Sample 8
DOX ON_4

value: 1mg/ml Doxycycline + 5% sucrose water for 3 weeks


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-094


title: MGE-derived neuron, PT2C, replicate3

city: Cardiff

first: Zongze

last: Li

country: United Kingdom

library_source: transcriptomic single cell

data_processing:
FastQC for as first Quality Control step and MultiQC for summarization
Raw sequencing data were converted into FASTQ files containing all indices for each chip which were then demultiplexed using the cogent demux command and analysed using the cogent analyze command with default settings, as part of the Cogent NGS Analysis Pipeline software 2.0.0 (Takara).
Assembly: Homo sapiens GRCh38.94
Supplementary files format and content: raw gene count matrix as csv files

source_name: cell line

extract_protocol:
Day 80 neuronal cultures were dissociated with Accutase containing 10 units/mL of papain (Sigma-Aldrich) for 8 minutes at 37°C, resuspended in DPBS (Gibco), mixed with 0.5% bovine serum albumin (Sigma Aldrich) and 50 units/mL DNase I (Sigma Aldrich), and passed through a 35 µm mesh cell strainer. Cells were stained with ReadyProbes™ Cell Viability Imaging Kit, Blue/Red (Invitrogen) following manufacturer’s guidance, and then dispensed into the nano-well plates of the ICELL8® cx Single-Cell System (Takara). Wells containing a single nucleus were automatically and manually selected using the ICELL8 cx CellSelect v2.5 Software (Takara).
The sequencing library was prepared using the SMART-Seq ICELL8 application kit (Takara) following manufacturer’s instructions.

value: cell line

value: iPSC differentiated into MGE-patterned neurons

value: CRISPR-Cas9 correction of SGCE mutation

value: Untreated


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-075

value: Urine, extracted cell-free RNA

value: Hematopoietic Stem Cell Transplantation


title: inflammation_3

description:
Library name: Sample 7
DOX ON_3


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-070


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-061


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-150


title: MGE-derived neuron, PT2, replicate3

value: SGCE Exon 5 c.622G > A, p.Gly221Asp


title: inflammation_2

description:
Library name: Sample 6
DOX ON_2


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-118


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-100


title: MGE-derived neuron, PT2, replicate1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-092


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-062


title: MGE-derived neuron, PT2C, replicate1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-122


title: inflammation_1

description:
Library name: Sample 5
DOX ON_1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-123


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-125


title: homeostasis_2

description:
Library name: Sample 2
WT_2

value: 5% sucrose water for 3 weeks


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-052


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-137


title: MGE-derived neuron, PT2, replicate2


title: homeostasis_1

description:
Library name: Sample 1
WT_1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-129


title: homeostasis_3

description:
Library name: Sample 3
WT_3


title: P18

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

data_processing:
Utilizing CellRanger (10X Genomics), raw reads were demultiplexed and aligned against the human reference genome (GRCh38.p14) prior to quantification of single-cell gene expression (UIC Research Informatics Core).
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated barcode files, genes files, and matrix files.

molecule: polyA RNA

source_name: Lymph nodes

growth_protocol: Bronchoscopy and EBUS-TBNA were performed following the standard medical guidelines utilizing an Olympus ViziShot system (Olympus Ltd, Japan) equipped with an ultrasonic 7.5-mHz longitudinal transducer. A 21-gauge needle was used for 3 to 5 needle passes for each lymph node to establish clinical diagnosis and one or two needle passes were collected for research.  Intrathoracic EBUS-TBNA samples were washed twice in PBS, and tissue was gently digested with Dispase (5 U/ml, STEMCELL Technologies) at 37°C for 30 minutes. Cells were then centrifuged at 300g for 5 minutes and treated with RBC lysis buffer (Roche) per the manufacturer’s instructions to remove red blood cells, followed by filtration through a 40-μm strainer. The cells were washed twice with PBS and prepared for scRNA-seq

extract_protocol:
Prepared single-cell suspensions with cell viability >80% were used to generate single-cell 3’ transcriptomes targeting 10000 cells/subject. Cells were loaded at a concentration of 1000 cells/µL and captured with barcoded oligo-dT containing gel beads using the Chromium controller (10X Genomics) according to the manufacturer’s instructions.
The transcriptomic library was prepared using a 10X Chromium v3 kit (10X Genomics) and sequenced on a Novaseq 6000 instrument using an S4 lane with 2x150nt cycles (University of Illinois Urbana-Champaign DNA Services Lab).

value: Lymph nodes

tag: age

tag: Sex

value: M

tag: race

value: White, Hispanic or Latino

tag: pathology

value: Poorly differentiated carcinoma


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-067


title: P17

value: F

value: White, Not Hispanic or Latino

value: Non-small cell carcinoma


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-127

value: E


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-033


title: P16

value: Black, Not Hispanic or Latino

value: Squamous cell carcinoma


title: scRNA-seq_E14.5 WT,rep 2

city: Durham

first: Jing

last: Liu

state: NC

address: 218 CARL buildling

department: Molecular Genetics and Microbiology

institute: Duke University

description:
Library name: sample3
10x Genomics

data_processing:
The 10x Genomics cell ranger count command version 6.1.2 was used to process fastq files and generate filtered count matrices . The count matrices were further processed using the Seurat R package version 4.0.5. Normalization was performed using the SCTransform function, with the number of variable features = 5000, and regression of mitochondrial genes. The datasets were integrated using the IntegrateData function. A PCA was obtained with the RunPCA function with the number of principal components = 300. UMAP was generated with the RunUMAP function based on the top 20 principal components. Clusters were obtained using the integrated counts with the FindNeighbors function, based on the 20 principal components. The function FindClusters was used with resolution = 1.1. Marker genes were obtained using the FindConservedMarkers function. The percentage of counts derived from MALAT1 transcripts were calculated, as high percentages are indicative of damaged neurons. Cells were considered damaged and removed if >5% of their counts were derived from MALAT1. To obtain cluster-specific differentially expressed genes between WT and HARE5 Hs/Hs , a pseudo-bulk approach was used. The pseudo BulkDGE function from the scran R package version 1.22.1, which performs the edgeR approach for each cluster, was used. The design used for the model was “y ~ batch + genotype”, and the contrast used was Mm-HARE5 Hs/Hs over control. An FDR threshold of 0.05 was used to obtain differentially expressed genes.
Assembly: mm10
Supplementary files format and content: rds files with Seurat objects

source_name: Mouse cerebral cortex

extract_protocol:
Two biological replicates from 2 different litters were used per genotype. E14.5 cortices were dissected in cold PBS, and dissociated using 0.25% Trypsin  (Thermo,69825200056) for 5 mins at 37°C ,cells finally resuspended in  PBS supplemented with 0.04% BSA. Cell viability and number were counted by a Cell Counter (Thermo). The scRNA seq experiment aimed to recover 8,000–10,000 cells from each embryo.
cDNA was amplification and library construction were performed following 10x Genomics Chromium Single Cell 3’ v3.1701 kit. cDNA libraries were quantified using the Agilent High Sensitivity DNA Kit (Agilent, 5067-702 4626) and were sequenced on an Illumina NovaSeq6000(PE150). Samples were sequenced to a depth of 40,000-70,000 reads per cell. A total number of 22,695 cells from two WT samples and 21,211 cells from two HARE5Hs/Hs sample were used for analysis, with an average of 2,110 genes detected per cell.

value: Mouse cerebral cortex

value: WT


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-037


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-044


title: scRNA-seq_E14.5 HARE5Hs/Hs ,rep 1

description:
Library name: sample2
10x Genomics


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-041


title: P15

value: small cell carcinoma


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-143

value: Urine, extracted cell-free RNA


title: P14


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-082

value: Hematopoietic Stem Cell Transplantation

value: PR


title: scRNA-seq_E14.5 WT,rep 1

description:
Library name: sample1
10x Genomics


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-063


title: MGE-derived neuron, PT2C, replicate2

value: cell line

value: iPSC differentiated into MGE-patterned neurons

value: CRISPR-Cas9 correction of SGCE mutation

value: Untreated


title: P13

value: Lymph nodes

value: M

value: White, Hispanic or Latino

value: small cell lung cancer


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-093


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-113


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-068

value: E


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-050


title: P12

value: F

value: White, Not Hispanic or Latino


title: scRNA-seq_E14.5 HARE5Hs/Hs ,rep 2

description:
Library name: sample4
10x Genomics

value: Mouse cerebral cortex


title: P11

value: Black, Not Hispanic or Latino

value: Squamous cell carcinoma


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-043

value: Urine, extracted cell-free RNA


title: E14.5 HARE5Hs/Hs ,rep 1

description: Library name: sample10

data_processing:
Read quality was assessed with Read orientation, quality distribution, base distribution and GC distribution for all reads. Reads were aligned to the mm39 genome using STAR.  Differential expression from E12.5 to E14.5  of WT and  HARE5Hs/Hs was determined using DESeq2.
Assembly: mm39
Supplementary files format and content: excel files include gene list compare E14.5 to E12.5 for both WT and HARE5Hs/Hs, average log2FC, Padj ,raw counts and FPKM of each gene are included for each sample.

extract_protocol:
E12.5 and E14.5 embryos were dissected in cold PBS and cortical tissue from single embryos were microdissected and flash frozen on dry ice. Three biological replicates were used per genotype. Tissue was homogenized  and RNA was  purified from Trizol method.
Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's instructions,library QC was performed by Qubit fluorometric quantitation, tapestation bioanalyzer.


title: P10

value: Adenocarcinoma


title: homeostasis_4

description:
Library name: Sample 4
WT_4

value: Fibroblast-like synoviocytes

value: 5% sucrose water for 3 weeks


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-083

value: Hematopoietic Stem Cell Transplantation


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-089


title: P9


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-065


title: E14.5 WT,rep 2

description: Library name: sample8

value: WT


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-064


title: E14.5 WT,rep 3

description: Library name: sample9


title: E14.5 WT,rep 1

description: Library name: sample7


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-079


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-060


title: E12.5 HARE5Hs/Hs ,rep 3

description: Library name: sample6


title: P7


title: P8


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-076


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-071


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-086


title: E14.5 HARE5Hs/Hs ,rep 3

description: Library name: sample12


title: E14.5 HARE5Hs/Hs ,rep 2

description: Library name: sample11


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-049


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-087


title: E12.5 HARE5Hs/Hs ,rep 2

description: Library name: sample5


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-078

value: PR


title: P5

value: Lymph nodes


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-112


title: P4

value: M


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-090


title: E12.5 WT,rep 3

description: Library name: sample3


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-066


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-023


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-001


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-016


title: E12.5 WT,rep 2

description: Library name: sample2


title: P2

value: Asian


title: P3


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-006


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-055


title: P1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-053


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-047


title: RA_R5

city: Toronto

first: Clinton

last: Robbins

state: ON

address: 101 College Street

country: Canada

institute: UHN

description: Library name: RA_R5

data_processing:
RNA-seq reads were quality filtered and mapped using STAR aligner (version 2.7.9a) against the mouse genome (mm10)
Uniquely mapped reads were quantified with HTSeq (version 0.11.0) and protein-coding genes with non-zero read count were included for downstream analysis
Gene expression read counts were analyzed to identify differentially expressed genes using Bioconductor package DESeq2 (version 1.36.0)
Genes with adjusted P value <0.05 and fold change >0.5 were considered having a significant altered expression.
Unsupervised clustering was used to generate the heatmap using heatmap.2 function.
GO enrichment analysis was performed on differentially expressed genes using enrichGO as implemented in clusterProfiler package (version 4.4.4)
Assembly: mm10
Supplementary files format and content: htseq counts

source_name: Aorta

extract_protocol:
Abdominal aortae were collected and snap frozen in liquid nitrogen, frozen aortae were digested according to the manufacturers protocol for the RNeasy Mini Kit (Qiagen, catalog#74104)
Libraries were prepared with 100ng of total RNA using Stranded Total RNA prep with Ribo-Zero Plus kit (Illumina) with 13 cycles of amplification used. Final cDNA libraries were size validated using Agilent Bioanalyzer or Tapestation and concentration validated by qPCR (Kapa Biosystems/Roche). All libraries were normalized and pooled, denatured with 0.2N NaOH and diluted to a final concentration of 250 pM.
Pooled libraries were loaded onto an Illumina Novaseq V1.5 cartridge for cluster generation and sequencing on an Illumina Novaseq 6000 instrument (Illumina) Paired-end 101 bp protocol to achieve approximately 30-40 million reads per sample.

treatment_protocol: ApoE-/- mice were exposed to cigarette smoke or room air and high fat fed for 16 weeks, aortae were collected upon euthanasia

value: Aorta

tag: strain

value: ApoE-/-

value: RNA sequencing


title: RA_R4

description: Library name: RA_R4


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-035


title: N3

value: non metastatic control


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-036

value: E


title: E12.5 HARE5Hs/Hs ,rep 1

description: Library name: sample4

value: Mouse cerebral cortex


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-051


title: RA_R2

description: Library name: RA_R2


title: N2

value: White, Not Hispanic or Latino


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-042

value: Urine, extracted cell-free RNA


title: N1

value: Black, Not Hispanic or Latino


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-032


title: RA_R1

description: Library name: RA_R1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-045


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-038


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-039


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-074


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-034


title: E12.5 WT,rep 1

description: Library name: sample1


title: P6

value: F

value: Adenocarcinoma


title: CD3 T cells, in vitro cell culture Day2, 7am replicate3

city: Hefei

first: Liang

last: Wang

state: Anhui

address: 96 Jinzhai Road

country: China

institute: University of Science and Technology of China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release111
Supplementary files format and content: tab-delimited text files include tpm values for each Sample

source_name: peripheral blood

growth_protocol: CD3+ T cells were removed from fresh PBMCs by immunomagnetic depletion using CD3 microbeads (Miltenyi Biotech, #130-050-101) and cultured in AIMV (Gibco) medium at 2 × 105 cells/ml supplemented with 100 IU/ml human IL-2 and 10% FBS and cultured in a 37°C humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.After total RNA was extracted, eukaryotic mRNA was enriched with oligo (dT) beads.
The enriched mRNA was subsequently fragmented into short fragments via fragmentation buffer and reverse transcribed into cDNA via the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, poly(A) was added, and the fragments were ligated to Illumina sequencing adapters. The ligation reaction mixture was purified with AMPure XP beads (1.0X), and polymerase chain reaction (PCR) amplification was performed.

treatment_protocol: Patients' serum collected at 7 am (7am group) or 4 pm (4pm group) (20 µl/well) from the same patient at the end of the myeloablative conditioning regimen  was added to CD3+ cells (4 × 105 cells/well) and cultured in vitro for  2 days

value: peripheral blood

value: CD3+ T cells

value: cultured with patients' serum collected at 7 am


title: CS_R6

description: Library name: CS_R6


title: CS_R5

description: Library name: CS_R5


title: CD3 T cells, in vitro cell culture Day2, 7am replicate2


title: N4

value: Lymph nodes

value: White, Hispanic or Latino


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-056

value: Hematopoietic Stem Cell Transplantation


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-054


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-072

value: PR


title: CS_R3

description: Library name: CS_R3

value: Aorta

value: ApoE-/-


title: CD3 T cells, in vitro cell culture Day2, 7am replicate1


title: RA_R3

description: Library name: RA_R3

value: RNA sequencing


title: CS_R4

description: Library name: CS_R4


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-058


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-091

value: E


title: CS_R2

description: Library name: CS_R2


title: CD3 T cells, in vitro cell culture Day2, 4pm replicate4

value: cultured with patients' serum collected at 4 pm


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-026


title: CD3 T cells, in vitro cell culture Day2, 4pm replicate3


title: CS_R1

description: Library name: CS_R1


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-030


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-004


title: CD3 T cells, in vitro cell culture Day2, 4pm replicate2


title: AAA_R2

description: Library name: AAA_R2


title: CD3 T cells, in vitro cell culture Day2, 7am replicate4


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-046


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-018


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-088


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-095


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-012


title: AAA_R1

description: Library name: AAA_R1


title: CD3 T cells, in vitro cell culture Day2, 4pm replicate1


title: Sample44

city: Dallas

first: Todd

last: Aguilera

state: TX

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

description: resected tissue

data_processing:
Raw reads were quality-controlled with FastQC (version 0.12.0), trimmed using Trimmomatic (version 0.32)
Counts quantified with Kallisto (version 0.46.0) and imported to R using tximport (version 1.30.0)
Assembly: GRCh38
Supplementary files format and content: tab delimited text file includes raw count for each Sample

source_name: PDAC

extract_protocol:
RNA from surgically resected tumor samples stored in RNAlater at -80C was extracted using Qiagen RNeasy Plus Kits, and RNA quality was assessed with a Nanodrop 2000 and Agilent 2100 Bioanalyzer. Samples with RNA integrity numbers (RIN) >7.0 were used
Libraries were prepared using Illumina Stranded mRNA Prep kit according to manufacturer protocol

value: PDAC


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-135

value: Urine, extracted cell-free RNA


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-117


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-102


title: vILC3, 72 hours post Pa infection, 8

city: New York

first: Yuefeng

last: Huang

state: NY

address: 701W 168th Street

department: Microbiology & Immunology

institute: Columbia University

data_processing:
TrimGalore V0.6.6
HISAT2 V2.2.1
Samtools V1.2
featureCounts V2.0.3
DESeq2 V1.38.3
Assembly: mm10
Supplementary files format and content: bw

source_name: vascular ILC3

extract_protocol:
RNA was harvested using miRNeasy Micro plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep kit for Illumina protocol.

value: vascular ILC3

value: RORgt-eGFP

value: Pa infection (Pa)


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-109


title: vILC3, 72 hours post Pa infection, 7


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-111


title: Sample42

description: resected tissue


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-099


title: Sample43

description: resected tissue


title: tILC3, 72 hours post Pa infection, 6

source_name: tissue ILC3

value: tissue ILC3


title: Sample41

description: resected tissue


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-144


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-114


title: tILC3, 72 hours post Pa infection, 5


title: Sample40

description: resected tissue


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-131


title: Plasma cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-7-A

source_name: plasma from healthy volunteer

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-3-A


title: Plasma cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-2-A

source_name: plasma from healthy volunteers


title: Sample38

description: resected tissue


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-133

source_name: urine from the HSCT cohort


title: vILC3, steady state no treatment control, 3

value: no treatment (NT)


title: Sample39

description: resected tissue


title: tILC3, steady state no treatment control, 2


title: Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-7-A

source_name: urine from healthy volunteer

value: healthy


title: tILC3, steady state no treatment control, 1


title: Sample37

description: resected tissue


title: Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-3-A


title: Sample36

description: resected tissue


title: ATAC-seq_heart_E115_mm39_WT_Rep2

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

country: Germany

institute: Berlin Institute of Health

data_processing:
Tn5 adaptor sequences were trimmed using cutadapt (--minimum-length 20 --quality-cutoff 20)
Reads were aligned to appropriate genome builds using bowtie2 ( --very-sensitive -X 1000)
Duplicates were removed using Picard v2.23.4. Unmapped, low quality reads (MAPQ < 10), and chromosomal reads were removed with samtools
bigWig profiles of normalized counts (CPM) were generated using deeptools v3.5.4 (Ramírez, Fidel, et al., 2016).
Assembly: mouse: mm39, chicken: galGal6
Supplementary files format and content: bigWig

source_name: heart

extract_protocol:
50.000 cells were lysed for nuclei, and used for each reaction of tagmentation as previously described for Omni-ATAC (Corces, M., Trevino, A., Hamilton, E. et al. 2017). Tagmented DNA were purified using MinElute Reaction Cleanup kit.
Libraries were amplified with dual indexing Nextera primers, followed by purification and double size-selection using AmPureXP beads

treatment_protocol: dissected embryonic hearts are dissociated with Trypsin/EDTA for 10 minutes (FL) or 15 minutes (heart) to get single-cell suspension. dissociated cells were filtered through a 100µm (embryonic heart) or 70µm (limb) MACS® SmartStrainer

value: heart

tag: developmental stage

value: WT


title: Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-2-A


title: Sample35

description: resected tissue


title: ATAC-seq_heart_E115_mm39_WT_Rep1


title: Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-1-A


title: spleen, 24 h experimental treatment S. iniae challenge, white bass, rep6

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description:
wb_strep_t24h_6
wb-strep-counts.txt

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using  FastQC (v.0.11.9) and Trimmomatic (v.0.38). This was used to trim low-quality ends from reads and for Illumina adapter removal.
All reads were filtered for the removal of 18S, 5.8S, and 28S sequences using the STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) for alignment of sequences to the Morone 18S, 5.8S, and 28S sequences available on GenBank and output of unaligned reads used for subsequent analysis. This was completed as QC indicated the sequence reads for WB_t01h_5 had high alignment (44.46%) to these sequences. This individual was dropped from subsequent analysis.
The STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) were used to align all filtered reads generated for the other 47 samples to the respective SB or WB reference transcriptomes using default parameters.
Read-counts were generated using the default parameters of HTSeq (v.0.9.0).
Gene expression fold-changes were determined between groups were determined in a pairwise fashion using edgeR (v.4.0.16) with TMM (Weighted trimmed mean of M-values) as the normalization method, Generalized Linear Model (GLM) Quasi Likelihood F-Test,  and “robust” filter to strengthen estimations against potential outliers.
Assembly: The reference SB transcriptome was built from the protein-coding sequences available on NCBI associated with the current reference genome (GCF_004916995.1; NCSU_SB_2.0). The WB reference transcriptome is a shotgun assembly built from the sequence data available in GenBank GAZY00000000.1 (GAZY01000001-GAZY01183659).
Supplementary files format and content: tab-deliminated text files of read counts representing the total number of reads aligned to each genomic feature for striped bass (sb-strep-counts.txt) and white bass (wb-strep-counts.txt).

organism: Morone chrysops

source_name: spleen

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
RNA library preparation, sequencing and data analysis were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis match was allowed for index sequence identification.

treatment_protocol: Striped bass (SB) and white bass (WB) in the control group (t00h) were given a mock saline treatment via intraperitoneal (IP) injection and sampled immediately prior to fish in experimental aquaria being challenged with 100 uL of Streptococcus iniae isolate ARS 98-60 via IP injection. Fish were observed twice daily for the recording and removal of any dead or moribund fish, and fish were formally sampled at three timepoints after the challenge had been initiated, 1 hour post treatment (t01h), 4 hours post treatment (t04h), and 24 hours post treatment (t24h).

tag: animal

value: white bass (WB)

value: spleen

value: Streptococcus iniae intraperitoneal injection

value: 24 h after bacteria treatment


title: Sample34

description: resected tissue


title: Plasma cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-8-A


title: spleen, 24 h experimental treatment S. iniae challenge, white bass, rep5

description:
wb_strep_t24h_5
wb-strep-counts.txt


title: ATAC-seq_heart_E105_mm39_WT_Rep2


title: vILC3, steady state no treatment control, 4


title: spleen, 24 h experimental treatment S. iniae challenge, white bass, rep3

description:
wb_strep_t24h_3
wb-strep-counts.txt


title: Sample33

description: resected tissue


title: ATAC-seq_heart_E105_mm39_WT_Rep1


title: spleen, 24 h experimental treatment S. iniae challenge, white bass, rep1

description:
wb_strep_t24h_1
wb-strep-counts.txt


title: Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-8-A


title: Sample32

description: resected tissue


title: Sample31

description: resected tissue


title: spleen, 4 h experimental treatment S. iniae challenge, white bass, rep6

description:
wb_strep_t04h_6
wb-strep-counts.txt

value: 4 h after bacteria treatment


title: spleen, 4 h experimental treatment S. iniae challenge, white bass, rep5

description:
wb_strep_t04h_5
wb-strep-counts.txt


title: Sample30

description: resected tissue


title: Plasma cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-1-A


title: spleen, 4 h experimental treatment S. iniae challenge, white bass, rep3

description:
wb_strep_t04h_3
wb-strep-counts.txt


title: spleen, 4 h experimental treatment S. iniae challenge, white bass, rep4

description:
wb_strep_t04h_4
wb-strep-counts.txt


title: spleen, 24 h experimental treatment S. iniae challenge, white bass, rep2

description:
wb_strep_t24h_2
wb-strep-counts.txt


title: Sample29

description: resected tissue


title: spleen, 4 h experimental treatment S. iniae challenge, white bass, rep1

description:
wb_strep_t04h_1
wb-strep-counts.txt


title: Liver, untreated r1

city: Boston

first: Kevin

last: Haigis

state: MA

address: 450 Brookline Avenue, LC 8303

institute: Dana Farber Cancer Institute

data_processing:
Raw read counts (fastq) were processed using in-house perl scripts. Specifically, low-quality reads (Base Quality < 5 comprise over 50% of read) and reads containing adapter and poly-N (N > 10%) were removed.
Clean paired-end reads were mapped to the mm39 reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to determine the number of read counts for each gene.
Assembly: mm39
Supplementary files format and content: tab-delimited text file contains raw read counts for each sample

source_name: Liver

growth_protocol: Mice were housed in a barrier facility within a temperature-controlled environment and twelve-hour light/dark cycle and fed ad libitum.

extract_protocol:
Tissues were pulverized and RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA quality control, non-directional library preparation, and sequencing were performed by Novogene according to their standard practice.

treatment_protocol: Mice were treated with either 1 mg/kg Egf (Thermo Fisher Scientific) dissolved in phosphate buffered saline (PBS) or  50 - 60 uL o f PBS alone via retro-orbital injection. All treatments were administered under isofluorane anesthesia. At 2 and 6 hours after treatment, organs were collected for RNA-seq analysis and rapidly flash-frozen. All harvests were performed in under 4 minutes. Three additional mice were included as untreated controls.

value: Liver

value: wild-type

value: untreated


title: Liver, veh, 6h r3

value: vehicle


title: Sample28

description: resected tissue

value: PDAC


title: spleen, 24 h experimental treatment S. iniae challenge, white bass, rep4

description:
wb_strep_t24h_4
wb-strep-counts.txt


title: spleen, 1 h experimental treatment S. iniae challenge, white bass, rep6

description:
wb_strep_t01h_6
wb-strep-counts.txt

value: 1 h after bacteria treatment


title: spleen, 1 h experimental treatment S. iniae challenge, white bass, rep5

description:
wb_strep_t01h_5
wb-strep-counts.txt


title: spleen, 1 h experimental treatment S. iniae challenge, white bass, rep4

description:
wb_strep_t01h_4
wb-strep-counts.txt


title: spleen, 1 h experimental treatment S. iniae challenge, white bass, rep3

description:
wb_strep_t01h_3
wb-strep-counts.txt


title: Liver, veh, 6h r1


title: Sample27

description: resected tissue


title: spleen, 1 h experimental treatment S. iniae challenge, white bass, rep2

description:
wb_strep_t01h_2
wb-strep-counts.txt


title: Liver, veh, 6h r2


title: Liver, untreated r3


title: spleen, 1 h experimental treatment S. iniae challenge, white bass, rep1

description:
wb_strep_t01h_1
wb-strep-counts.txt


title: Sample26

description: resected tissue


title: spleen, 4 h experimental treatment S. iniae challenge, white bass, rep2

description:
wb_strep_t04h_2
wb-strep-counts.txt


title: Sample25

description: resected tissue


title: spleen, 0 h control treatment S. iniae challenge, white bass, rep6

description:
wb_strep_t00h_6
wb-strep-counts.txt

value: control saline intraperitoneal injection

value: 0 hr after control treatment


title: Liver, Egf, 6h r3

value: Egf


title: spleen, 0 h control treatment S. iniae challenge, white bass, rep4

description:
wb_strep_t00h_4
wb-strep-counts.txt


title: Liver, Egf, 6h r4


title: Liver, untreated r2


title: spleen, 0 h control treatment S. iniae challenge, white bass, rep5

description:
wb_strep_t00h_5
wb-strep-counts.txt


title: spleen, 0 h control treatment S. iniae challenge, white bass, rep3

description:
wb_strep_t00h_3
wb-strep-counts.txt


title: Sample24

description: resected tissue


title: Liver, Egf, 6h r2


title: spleen, 0 h control treatment S. iniae challenge, white bass, rep2

description:
wb_strep_t00h_2
wb-strep-counts.txt


title: Sample23

description: resected tissue


title: Liver, Egf, 6h r1


title: spleen, 0 h control treatment S. iniae challenge, white bass, rep1

description:
wb_strep_t00h_1
wb-strep-counts.txt


title: E0771_10, Liver, 29°C

city: Vienna

first: Tamina

last: Österreicher

state: Vienna

address: Währingerstraße 10

department: Institute of Medical Chemistry and Pathobiochemistry

country: Austria

institute: Medical University of Vienna

description:
Library name: RO02010
raw_gene_counts_all_samples.tsv RO02010 29°C

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403) incl. trimming of the sequencing adapters.
Reads in fastq format were aligned to the mouse reference genome version GRCm38 (Gencode) with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode
Raw reads per gene were counted by STAR. Differential gene expression was analyzed using DESeq2 version 1.44.0
Assembly: GRCm38
Supplementary files format and content: tab-delimited tsv file containes raw counts for each sample

growth_protocol: 0.5 x 106 E0771 cells were implanted orthotopically into the second mammary fat pad of Balb/C or C57Bl6/J mice, respectively, under isofluorane anesthesia. Tumor growth was monitored for 21 days.

extract_protocol:
Mouse tissues were homogenized in Trizol reagent (1 ml per 50 mg) and phase separation was performed by the addition of 0.2 ml chloroform per ml of Trizol reagent. The aequous phase was further processed using the Relia Prep RNA Tissue Miniprep reagent. The aequous phase was further processed using the Relia Prep RNA Tissue Miniprep System.
Sequencing libraries from total RNA of the samples were prepared at the Core Facility Genomics, Medical University of Vienna, using the NEBNext UltraExpress rRNA depletion kits (NEB #E3330) for Illumina with Unique Dual Indices (UDIs) according to manufacturer's protocols (New England Biolabs

treatment_protocol: To compare tumor growth kinetics in WT mice housed at different temperatures (6°C, 22°C, 29°C), mice were acclimatized for one week at indicated temperatures in HPP750 life climate chambers (Memmert) with ad libitum access to food and water and a 12 h light – 12 h dark cycle.

value: E0771 Tumor, 29°C


title: E0771_12, Liver, 29°C

description:
Library name: RO02012
raw_gene_counts_all_samples.tsv RO02012  29°C


title: Sample21

description: resected tissue


title: Liver, veh, 2h r3


title: Sample22

description: resected tissue


title: E0771_11, Liver, 29°C

description:
Library name: RO02011
raw_gene_counts_all_samples.tsv RO02011 29°C


title: E0771_9, Liver, 29°C

description:
Library name: RO02009
raw_gene_counts_all_samples.tsv  RO02009 29°C


title: E0771_8, Liver, 22°C

description:
Library name: RO02008
raw_gene_counts_all_samples.tsv RO02008 22°C

value: E0771 Tumor, 22°C


title: Sample20

description: resected tissue


title: Liver, veh, 2h r1


title: E0771_6, Liver, 22°C

description:
Library name: RO02006
raw_gene_counts_all_samples.tsv RO02006 22°C

value: WT


title: E0771_7, Liver, 22°C

description:
Library name: RO02007
raw_gene_counts_all_samples.tsv RO02007 22°C


title: E0771_5, Liver, 22°C

description:
Library name: RO02005
raw_gene_counts_all_samples.tsv RO02005 22°C


title: Liver, Egf, 2h r4


title: Sample18

description: resected tissue


title: E0771_4, Liver, 6°C

description:
Library name: RO02004
raw_gene_counts_all_samples.tsv  RO02004 6°C

value: E0771 Tumor, 6°C


title: E0771_2, Liver, 6°C

description:
Library name: RO02002
raw_gene_counts_all_samples.tsv RO02002 6°C


title: Sample17

description: resected tissue


title: Liver, Egf, 2h r2


title: Sample15

description: resected tissue


title: E0771_1, Liver, 6°C

description:
Library name: RO02001
raw_gene_counts_all_samples.tsv RO02001  6°C


title: Liver, Egf, 2h r1


title: Sample16

description: resected tissue


title: Liver, veh, 2h r2


title: E0771_3, Liver, 6°C

description:
Library name: RO02003
raw_gene_counts_all_samples.tsv  RO02003 6°C


title: Sample14

description: resected tissue


title: Kidney, untreated r2

source_name: Kidney

value: Kidney


title: Sample19

description: resected tissue


title: Sample12

description: resected tissue


title: Sample13

description: resected tissue


title: Kidney, untreated r3


title: Sample11

description: resected tissue


title: Kidney, untreated r1


title: Kidney, veh, 6h r3


title: Kidney, veh, 6h r2


title: Liver, Egf, 2h r3


title: Sample10

description: resected tissue


title: Sample9

description: resected tissue


title: Kidney, veh, 6h r1


title: 7-17 mouse 1 BAL

type: RNA

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from flow-sorted neutrophils isolated from lavaged alveolar space (BAL).

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.60.0), using R version 3.5.1 and the Brainarray mogene20stmmentrezgcdf R package (version 23.0.0).

label: biotin

source_name: flow-sorted neutrophils

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Female C57BL/6J mice were obtained from Jackson Laboratories at 6-7 weeks of age. Prior to infection, they were housed at the Boston University animal facility and provided with an ad libitum supply of standard chow. Mice were infected at 10-12 weeks of age. All animal protocols were approved by the BU Institutional Animal Care and Use Committee (IACUC).

extract_protocol: RNA was isolated from frozen neutrophils using the RNeasy micro kit (Qiagen), following the manufacturer’s instructions. RNA was eluted in 14µl RNase-free water.

treatment_protocol: After anesthetization with ketamine and xylazine, the left lung lobes of C57BL/6J mice were intratracheally infected with 1.0 x 1E6 CFU S. Pneumoniae. Just prior to euthanasia, CD45-FITC was administered IV (CD45-IV). Mice were euthanized, CD45-APC was  administered IT (CD45-IT). BALF performed to wash CD45-IT and harvest BALF neutrophils. Single cell suspensions of left lobe were generated using a gentleMACS tissue dissociator (Miltenyi Biotec), following manufacturer's instruction. Cells were stained with Ly6G, CD45.2 and Zombie Aqua. Neutrophils (CD45.2+/Ly6G+) from BALF, and lung digest  vasculature (CD45-IV+ CD45IT-), interstitium (CD45-IV- CD45-IT-) and alveolar space (CD45-IV- CD-45IT+) were isolated by FACS. Sorted cells were washed and re-suspended in RNAProtect (Qiagen) and frozen at -80C.

tag: location

value: lavaged alveolar space (BAL)

value: flow-sorted neutrophils


title: 7-18 mouse 1 BAL


title: 7-17 mouse 2 BAL


title: 7-18 mouse 4 alveolar

description: Gene expression data from flow-sorted neutrophils isolated from non-lavaged alveolar space.

value: non-lavaged alveolar space


title: 7-18 mouse 1 interstitial

description: Gene expression data from flow-sorted neutrophils isolated from the lung interstitium.

value: lung interstitium


title: 7-17 mouse 2 alveolar


title: Kidney, Egf, 6h r4

tag: tissue

value: wild-type


title: 7-18 mouse 4 BAL

tag: cell type


title: 7-17 mouse 1 alveolar


title: 7-18 mouse 4 interstitial


title: 7-18 mouse 4 vascular

description: Gene expression data from flow-sorted neutrophils isolated from the lung vasculature.

value: lung vasculature


title: 7-17 mouse 2 vascular


title: 7-17 mouse 2 interstitial


title: 7-18 mouse 1 vascular


title: 7-18 mouse 1 alveolar


title: Sample7

description: resected tissue


title: Kidney, Egf, 6h r3

tag: treatment


title: Kidney, Egf, 6h r2

tag: time


title: Sample6

description: resected tissue


title: 7-17 mouse 1 vascular


title: Sample8

description: resected tissue


title: IA 12-12-17 3

description: Gene expression data from flow-sorted neutrophils isolated from the BALF of an infected animal.

treatment_protocol: After anesthetization with ketamine and xylazine, the left lung lobes of C57BL/6J mice were intratracheally infected with 1.0 x 1E6 CFU S. Pneumoniae or saline control. After 24 hours of infection, peripheral blood and BALF was harvested. Red cells were lysed using osmotic lysis. Remaining cells were stained with 7AAD, CD45 and Ly6G to identify neutrophils, which were then isolated using FACS. Sorted cells were washed and re-suspended in RNAProtect (Qiagen) and frozen at -80C.

tag: infection

value: S. pneumoniae infected

value: alveolar

value: batch 2


title: Kidney, Egf, 6h r1


title: Sample5

description: resected tissue

value: PDAC


title: IP 11-14-17 5

description: Gene expression data from flow-sorted neutrophils isolated from the peripheral blood of an infected animal.

value: peripheral

value: batch 1


title: Kidney, veh, 2h r3

value: vehicle


title: Sample4

description: resected tissue


title: IA 11-14-17 1


title: Kidney, veh, 2h r2


title: Sample3

description: resected tissue


title: IP 12-12-17 3


title: eCLIP_SMI_ZAP_HA_3

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description: Library name: eCLIP_SMI_ZAP_HA_3

library_source: other

data_processing:
Paired-end sequencing reads were adapter- and quality trimmed by cutadapt (v1.18) in two runs according to the ENCODE eCLIP-seq processing pipeline v. 2.2 (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)). In the first run 5' and 3' adapters were clipped from both reads using the parameters: --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
In the second run 3' adapters of read 2 were clipped to control for double ligation events. Cutadapt clipping was performed with the parameters:  --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
RNA-seq reads were aligned to the concatenated genomes of hg38 (ensembl) with either HIV-2 or SIVsmm using STAR version 2.7.10a with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterType Normal --alignSoftClipAtReferenceEnds No --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --scoreDelOpen -1 --alignIntronMin 20 --alignIntronMax 3000 --alignMatesGapMax 3000 --alignEndsType EndToEnd
Using the python package pyBigWig, bigWig files were generated based on the HIV-2 and SIVsmm RNAs. Only reads mapped in to positive sense RNA were further analyzed. Score represents the information content of IP over SMI of positive sense RNA fragments at a given genomic coordinate normalized over all mapped reads for each library.
Assembly: hg38, HIV-2 (GenBank: L36874.1), SIVsmm (GenBank: KU182922.1)
Supplementary files format and content: bigWig files, containing raw read coverage in IP and SMI
Supplementary files format and content: bigWig files, containing relative information content in IP over SMI

molecule: other

organism:
Homo sapiens
Simian immunodeficiency virus

source_name: HEK293T ZAP KO

growth_protocol: Cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 2.5% (during virus production) or 10% (at all other times) heat-inactivated foetal calf serum (FCS), 2 mM l-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin. Jurkat cells were cultured in RPMI supplemented with 10% FCS, 2 mM l-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Immunoprecipitation and cDNA library preparation was performed as described in the eCLIP method (PMID: 27018577), including the following modifications: immunoprecipitates were washed two times in 1 ml CLIP lysis buffer and two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% [vol/vol] NP-40, 0.5% sodium deoxycholate, 0.25 mM TCEP), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, and 0.5% (vol/vol) NP-40. All other steps were carried out as described in the eCLIP method.
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

value: HEK293T ZAP KO

value: SIVsmm infected HEK293T ZAP KO cells


title: Kidney, veh, 2h r1


title: eCLIP_IP_ZAP_HA_3

description: Library name: eCLIP_IP_ZAP_HA_3


title: eCLIP_SMI_ZAP_HA_2

description: Library name: eCLIP_SMI_ZAP_HA_2

organism:
Homo sapiens
Human immunodeficiency virus 2

value: HIV-2 infected HEK293T ZAP KO cells


title: eCLIP_IP_ZAP_HA_2

description: Library name: eCLIP_IP_ZAP_HA_2


title: IP 11-14-17 1


title: Sample2

description: resected tissue


title: SUDHL4_4Cseq_DpnII_CviQI_BCL6p_rep1

data_processing:
library strategy: 4C-seq
Interaction frequency heatmaps for the MYC locus and fused MYC and BCL6 loci were generated with 4CSeq pipe, using a DpnII-CviQIF-digested hg19 reference or a custom reference containing a chr8 / chr3 fusion chromosome
Bedgraphs of interaction fragment counts were generated with FourCSeq, using a DpnII-CviQIF-digested hg19 reference
Assembly: hg19
Supplementary files format and content: Bedgraph of read counts mapped to genomic locations with appropriate restriction sites

growth_protocol: All cell lines were cultured in RPMI 1640 + Glutamax supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1 mM sodium pyruvate, and 55 micromolar 2-mercaptoethanol.

extract_protocol:
Cells were crosslinked with 2% formaldehyde in PBS at room temperature for 10 minutes, followed by glycine quenching, washing in PBS, isolation of nuclei by hypotonic buffer lysis, and resuspension in primary restriction enzyme buffer. Primary digestion was accomplished by sequential addition of SDS, Triton-X100, and primary restriction enzyme while mixing at 37°C, followed by heat inactivation at 65°C. Ligation was performed after sample dilution in T4 ligase buffer by addition of T4 ligase at 16°C. Ligated DNA was isolated by proteinase K and RNAase A digestion, phenol-chloroform extraction, and ethanol precipitation. DNA was then digested with secondary restriction enzyme, heat inactivated, ligated with T4 ligase, and isolated by ethanol precipitation and QIAquick PCR purification columns.
PCR (ExTaq, Takara) with barcoded illumina adaptors was used to amplify sgRNA sequences from genomic DNA corresponding to 500 cell equivalents per library sgRNA, aliquoted into 50 uL PCR reactions (6ug DNA per reaction). All reactions from each replicate were pooled, and 100 ul was gel-purified with E-gel size-select II.
To generate each 4C-Seq library, a total of 3.2 micrograms of 4C DNA was amplified across 16 separate 50-microliter PCR reactions containing Q5 high-fidelity polymerase mix (NEB) and oligonucleotides pairs consisting of universal illumina adaptor sequences, sample-specific barcodes, and viewpoint-specific primer sequences. Equal portions of each reaction were pooled and the PCR-amplified library was purified with 0.8 volumes of Ampure XP per volume of PCR product.

value: Diffuse large B-cell lymphoma cell line


title: Kidney, Egf, 2h r4

value: Kidney

value: Egf


title: 7-17 mouse 1 interstitial

value: flow-sorted neutrophils


title: IA 11-14-17 5


title: SUDHL4_4Cseq_DpnII_CviQI_MYCp_rep1


title: UP 12-12-17 4

description: Gene expression data from flow-sorted neutrophils isolated from the peripheral blood of an uninfected animal.

value: uninfected


title: UP 11-14-17 4


title: DB_4Cseq_DpnII_CviQI_BCL6enh_rep2

source_name: DB

value: DB


title: Sample1

description: resected tissue


title: Kidney, Egf, 2h r3

value: wild-type


title: Ark1 cells, siGATA2, replicate 4

city: Madison

middle: Rusch

last: Matson

state: WI

address: WIMR Room 1761 - 1111 Highland Avenue

department: Pathology and Laboratory Medicine

institute: University of Wisconsin - Madison

data_processing:
The trimming software skewer (Jiang et al. 2014) was used to preprocess raw fastq files.
To improve further the quality of the sequence reads, skewer also trims the 3’ end of the fragment until a Phred quality of 20 is reached.
The trimmed single- or paired-end reads were aligned against the selected reference genome sequence using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013).
Mapped paired-end reads for both genes and transcripts (isoforms) were counted in each sample using RSEM (RNASeq by Expectation Maximization), described in Li and Dewey (2011).
Assembly: hg38
Supplementary files format and content: csv file, tab delineated gene names and raw counts for each sample
Supplementary files format and content: txt file, tab delineated gene identifier and TPM for each sample

growth_protocol: Cells were grown in RPMI-1640 media with 10% fetal bovine serum (FBS) and 1% pen/strep antibiotics in a humidified tissue culture incubator at 37 degrees Celsius and 5% CO2

extract_protocol:
Total RNA extraction using TRIZOL
Each RNA was assayed on NanoDrop One Spectrophotometer and Agilent 4200Tapestaion, to assess purity and integrity.   RNA samples that met Illumina’s “TruSeq Stranded mRNA Reference Guide (Document# 1000000040498 v00, October 2017) quality criteria were prepared for sequencing.  Briefly, 1ug total RNA sample was enriched for mRNA by oligo (dT) selection followed by fragmentation using divalent cations under elevated temperature.  Double-stranded cDNA was synthesized using SuperScript II RT (Invitrogen, Carlsbad, California) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and RNAse H for removal of mRNA.  Double-stranded cDNA was purified with SPRI beads (Beckman Coulter Genomics, CA), followed by incubation with Klenow DNA Polymerase and Adenine to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments.  DNA fragments were  ligated to Illumina unique molecular index (UMI) adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end.  Following ligation, cDNA was purified with SPRI beads, and PCR-amplified (11 cycles) with PhusionTM DNA Polymerase using Illumina's genomic DNA primer set and purified with SPRI beads.   Quality and quantity of the finished libraries were assayed on Agilent 4200Tapestation using D1000 Screentape and  Qubit HS Quantification Kit (Invitrogen, Carlsbad, CA), respectively.

treatment_protocol: Cells were treated with either 20 nM siScramble siRNA or 20 nM siGATA2 siRNA pool and incubated for 48 hours

value: endometrial serous carcinoma

value: GATA2 KD

value: GATA2 siRNA


title: DB_4Cseq_DpnII_CviQI_BCL6enh_rep1

last: Ryan


title: UP 11-14-17 2


title: Kidney, Egf, 2h r2


title: DB_4Cseq_DpnII_CviQI_BCL6p_rep2


title: DB_4Cseq_DpnII_CviQI_BCL6p_rep1


title: Kidney, Egf, 2h r1


title: DB_4Cseq_DpnII_CviQI_MYCp_rep2


title: Ark1 cells, siGATA2, replicate 3


title: Lung, untreated r3

source_name: Lung

value: Lung

value: untreated


title: Ark1 cells, siGATA2, replicate 2


title: Karpas422_4Cseq_DpnII_CviQI_BCL6enh_rep2


title: SUDHL4_4Cseq_DpnII_CviQI_MYCp_rep2


title: Ark1 cells, siGATA2, replicate 1


title: Lung, untreated r2


title: Karpas422_4Cseq_DpnII_CviQI_BCL6enh_rep1


title: Ark1 cells, siScramble, replicate 4

value: WT

value: Scramble siRNA


title: Karpas422_4Cseq_DpnII_CviQI_BCL6p_rep2


title: Karpas422_4Cseq_DpnII_CviQI_BCL6p_rep1


title: Lung, untreated r1


title: Karpas422_4Cseq_DpnII_CviQI_MYCp_rep2


title: Ark1 cells, siScramble, replicate 3


title: SUDHL4_OCT2_ChIP-Seq

data_processing:
Single-end or paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800), and for paired-end read to retain only paired reads in a proper pair (flags: 0x1, 0x2)          .
Reads were filtered to retain only individual reads (single-end) or read-pairs (paired-end) mapping to <=2 sites genome-wide (X0 tag <=2 for single-end or both paired-end reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

growth_protocol: All cell lines were cultured in RPMI 1640 + Glutamax supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1 mM sodium pyruvate, and 55 micromolar 2-mercaptoethanol

extract_protocol:
Five to twenty million cells were cross-linked in PBS + 1% formaldehyde for 10 minutes at room temperature (histone marks) or 37C (TFs), quenched with 1/20th volume of 2.5M glycine, washed twice in cold PBS with protease inhibitors, and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g, and resuspended in cold SDS lysis buffer (0.3% SDS for H3K27ac and 1% SDS for TFs, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes. Nuclei were fragmented on a Q800R2 Sonifier (QSonica) as follows: three cycles of amplitude = 50, pulse times: 30s on / 30s off, total on time = 3:20 m, temperature = 80C (histone marks) or two cycles of amplitude = 70, pulse times: 45s on / 15s off, total on time = 8:50 m, temperature = 40C (TFs). Samples were diluted 1:3 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4°C overnight with 2-5 ug of antibody. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After reversal of cross-linking, RNase and proteinase K treatment were performed and DNA was purified with Ampure XP beads for library preparation. Input sample was prepared by the same approach without immunoprecipitation.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated (Quick T4 DNA ligase, NEB) to barcoded illumina adaptors (Single-Indexed Adapter Kit, KAPA, #KK8700). Each reaction was followed by clean-up with AMPure XP beads. Ligation products were amplified by PCR for 14-18 cycles with illumina indexing primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection.

tag: chip antibody

value: OCT2 ChIP-Seq (Santa Cruz, Cat #sc-233)


title: Lung, veh, 6h r3

value: vehicle


title: Karpas422_4Cseq_DpnII_CviQI_MYCp_rep1

tag: cell line


title: Ark1 cells, siScramble, replicate 2

tag: genotype


title: Lung, veh, 6h r2


title: DB_OCT2_ChIP-Seq


title: Karpas422_p300_ChIP-Seq

value: p300 ChIP-Seq (Bethyl, Cat #A300-358A)


title: Ark1 cells, siScramble, replicate 1


title: Karpas422_OCA-B_ChIP-Seq

value: Diffuse large B-cell lymphoma cell line

value: OCA-B (POU2AF1 / Bob.1) ChIP-Seq (Santa Cruz, Cat #sc-955)


title: Lung, veh, 6h r1


title: Karpas422_OCT2_ChIP-Seq


title: DB_4Cseq_DpnII_CviQI_MYCp_rep1


title: 37T

city: Taipei

first: Wen-Hsuan

last: Yu

address: No.7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: 10x Genomics

data_processing:
Cell Ranger software pipeline (version 7.2.0, 10x Genomics) was used for cellular barcode demultiplexing and align reads.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human metaplastic breast cancer (MBC)

extract_protocol:
Total RNA was extracted from indicated cell lines using TRIzol reagent (Thermo Fischer Scientific, Waltham, MA, USA according to the manufacturer's instructions.
RNA library was performed according to Chromium Next GEM Single Cell 3' Reagent Kits.

value: human metaplastic breast cancer (MBC)

tag: histological subtype

value: squamous metaplasia

tag: library preparation_kit

value: Chromium Next GEM Single Cell 3' Reagent Kits v3.1


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_77-trimmed

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road, Weill Hall 301

institute: Cornell University

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, sequencing data from the Illumina NextSeq 500 and Novaseq 6000 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts30 (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts30 (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap31 (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 3, if a sample had less than 75000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 3 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma seprated values .csv file contain gene counts for each sample in this study

source_name: plasma from the AKI cohort

extract_protocol:
Before cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from the plasma supernatant (250-1500 μl) using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Urine samples were thawed at room temperature and centrifuged at 16,000 x g for 10 minutes at 4 °C. cfRNA was extracted from (450-2000 μl) supernatant using QIAamp Circulating Nucleic Acid Kit -Purification of Circulating microRNA in serum/plasma/urine protocol (Qiagen, product #55114).  Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

value: Plasma, extracted cell-free RNA

value: Immune checkpoint inhibitor therapy

tag: diagnosis

value: Acute Kidney Injury


title: Ctrl-Exo RPT2

city: Nanjing

first: Chen

state: Jiangsu

address: 163 Xianlin Avenue

department: Life Sciences

institute: Nanjing University

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to pre-miRNA sequence in miRBase_v21
Sequenced reads with no more than 1 mismatch and 2nt shift in mature miRNA position were identified as mature miRNAs.
Genome_build: miRBase_v21
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, sequences and counts in each sample

source_name: 293T cells

growth_protocol: MRSA strain was grown in tryptic soy broth (TSB). E. coli BL21 (DE3) was grown in Luria Bertani (LB) broth.

extract_protocol:
Total RNA from bacteria was extracted using TRIzol Reagent (Invitrogen). Total RNA from exosomes was extracted using the miRNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Typically, overnight cultures of bacteria were diluted in fresh culture medium to an optical density (OD600) of 0.1. Exosomes were then added to the bacterial culture and incubated for indicated time in a shaking incubator at 37℃.

value: kidney

tag: sirna

value: Ctrl-Exo


title: Ctrl-Exo RPT1


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_74-trimmed


title: Lung, Egf, 6h r3

value: Lung

value: wild-type

value: Egf


title: E. coli mock

organism: Escherichia coli

source_name: E. coli

value: mock


title: E. coli + Ctrl-Exo


title: E. coli + siAda-Exo

value: siAda-Exo


title: siAda-Exo


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_101-trimmed


title: Lung, Egf, 6h r2


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_58-trimmed


title: Lung, veh, 2h r3

value: vehicle


title: MRSA + siMecA-Exo

organism: Staphylococcus aureus

source_name: MRSA


title: Lung, Egf, 6h r1


title: MRSA + Ctrl-Exo


title: Lung, veh, 2h r2


title: RA-155 GBM 385 RNA-seq Alexidine

city: Cincinnati

first: Matthew

last: Garrett

state: Ohio

address: 5061 myerdale drive

institute: Kettering Health

description: Library name: RA-155

data_processing:
Quality control check performed with FastQC v0.11.7
Adapter sequences and quality trimming with Trim Galore! v0.6.6
Trimmed reads aligned to GRCh38/hg38 using bowtie2 v2.5.1 with 'verysensitive' setting
Mitochondrial and duplicate reads removed using samtools v.1.17
Peak calling performed using MACS2 v2.2.9
Assembly: GRCh38/hg38
Supplementary files format and content: "Normalized Gene Expression after Drug Treatment.csv" Comma separated values; Log2-transformed, library size normalized expression data using rlog() function from DESeq2 v1.26.0
Supplementary files format and content: "RNA_SEQ_countMatrix.csv" Raw read counts per gene generated by featureCounts v1.6.2 using NCBI RefSeq annotations

source_name: Brain tumor

growth_protocol: Initial cell numbers were plated to maximize the number of viable cells at the target time point without over-growth. Additional drug and growth factor were added on a weekly basis.

extract_protocol:
50,000 cells were spun down at 500 x g for 5 minutes at 4°C, resuspended in ATAC-resuspension buffer (0.1% NP40, 0.1% tween-20, 0.01% digitonin), incubated on ice for 3 minutes and washed. Nuclei were pelleted at 500 x g at 4C for 10 minutes.
ATAC-seq libraries were created using 50,000 cells, cells were resuspended in ATAC-resuspension buffer, transposed using Illumina Nextera Tn5 Transposase, DNA purified with Qiagen MinElute PCR Purification Kit and amplified for 12 cycles.

treatment_protocol: Cells were treated at 500nM (in some cases reduced to 250nM to obtain enough viable material) for 7 days.

value: Brain tumor

value: Glioblastoma

value: Alexidine

tag: alive (c/ml)

tag: acutal cell_count

tag: %alive

tag: batch


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_100-trimmed


title: Lung, Egf, 6h r4


title: RA-154 GBM 385 RNA-seq GSK591

description: Library name: RA-154


title: siMecA-Exo

value: siMecA-Exo


title: Lung, veh, 2h r1


title: RA-152 GBM 385 RNA-seq Gavinostat

description: Library name: RA-152

value: Gavinostat


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_79-trimmed


title: RA-153 GBM 385 RNA-seq Rucaporib

description: Library name: RA-153

value: Rucaporib


title: Lung, Egf, 2h r4


title: RA-151 GBM 385 RNA-seq SirReal2

description: Library name: RA-151


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_103-trimmed

value: Plasma, extracted cell-free RNA


title: RA-149 GBM 385 RNA-seq ML228

description: Library name: RA-149


title: Lung, Egf, 2h r3


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_81-trimmed

value: Immune checkpoint inhibitor therapy


title: RA-150 GBM 385 RNA-seq CPI203

description: Library name: RA-150


title: Lung, Egf, 2h r2


title: RA-147 GBM 385 RNA-seq A485

description: Library name: RA-147


title: RA-146 GBM 385 RNA-seq Decitabine

description: Library name: RA-146

value: Decitabine


title: RA-148 GBM 385 RNA-seq Ciclopirox

description: Library name: RA-148

value: Ciclopirox


title: MRSA mock

tag: strain


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_102-trimmed

tag: tissue

value: Acute Kidney Injury


title: Lung, Egf, 2h r1

value: Lung


title: RA-145 GBM 385 RNA-seq PF06726304

description: Library name: RA-145

tag: cell type


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_56-trimmed

tag: treatment


title: RA-156 GBM 385 RNA-seq Hesperadin

description: Library name: RA-156

value: Hesperadin


title: RA-143 GBM 357 RNA-seq Hesperadin

description: Library name: RA-143


title: RA-144 GBM 385 RNA-seq Control

description: Library name: RA-144

value: Control


title: Heart, untreated r3

source_name: Heart

value: Heart

value: wild-type

value: untreated

tag: time


title: RA-142 GBM 357 RNA-seq Alexidine

description: Library name: RA-142

value: Brain tumor


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_97-trimmed


title: Heart, untreated r2


title: RA-141 GBM 357 RNA-seq GSK591

description: Library name: RA-141

value: Glioblastoma


title: RA-139 GBM 357 RNA-seq Gavinostat

description: Library name: RA-139


title: Heart, untreated r1


title: RA-140 GBM 357 RNA-seq Rucaporib

description: Library name: RA-140


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_99-trimmed


title: Heart, veh, 6h r3

value: vehicle


title: RA-137 GBM 357 RNA-seq CPI203

description: Library name: RA-137


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_61-trimmed


title: RA-136 GBM 357 RNA-seq ML228

description: Library name: RA-136


title: RA-134 GBM 357 RNA-seq A485

description: Library name: RA-134


title: Heart, veh, 6h r1


title: RA-135 GBM 357 RNA-seq Ciclopirox

description: Library name: RA-135


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_37-trimmed


title: RA-132 GBM 357 RNA-seq PF06726304

description: Library name: RA-132


title: Heart, Egf, 6h r4

value: Egf


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_92-trimmed


title: RA-131 GBM 357 RNA-seq Control

description: Library name: RA-131


title: RA-133 GBM 357 RNA-seq Decitabine

description: Library name: RA-133


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_65-trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_63-trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_86-trimmed


title: Heart, Egf, 6h r3


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_106-trimmed


title: RA-130 GBM MGG-119 RNA-seq Hesperadin

description: Library name: RA-130


title: RA-129 GBM MGG-119 RNA-seq Alexidine

description: Library name: RA-129

value: Alexidine


title: RA-128 GBM MGG-119 RNA-seq GSK591

description: Library name: RA-128


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_67-trimmed


title: RA-138 GBM 357 RNA-seq SirReal2

description: Library name: RA-138


title: Heart, Egf, 6h r2


title: RA-126 GBM MGG-119 RNA-seq Gavinostat

description: Library name: RA-126

value: Gavinostat


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_76-trimmed

value: Plasma, extracted cell-free RNA


title: Heart, Egf, 6h r1


title: RA-127 GBM MGG-119 RNA-seq Rucaporib

description: Library name: RA-127

value: Rucaporib


title: Heart, veh, 6h r2


title: RA-124 GBM MGG-119 RNA-seq CPI203

description: Library name: RA-124


title: Heart, veh, 2h r3


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_104-trimmed

value: Immune checkpoint inhibitor therapy


title: RA-123 GBM MGG-119 RNA-seq ML228

description: Library name: RA-123


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_68-trimmed


title: Heart, veh, 2h r2


title: RA-121 GBM MGG-119 RNA-seq A485

description: Library name: RA-121


title: Heart, veh, 2h r1


title: RA-120 GBM MGG-119 RNA-seq Decitabine

description: Library name: RA-120

value: Decitabine


title: RA-119 GBM MGG-119 RNA-seq PF06726304

description: Library name: RA-119


title: RA-116 GBM 252 RNA-seq Alexidine

description: Library name: RA-116


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_80-trimmed

value: Acute Kidney Injury


title: Heart, Egf, 2h r3


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_78-trimmed


title: RA-117 GBM 252 RNA-seq Hesperadin

description: Library name: RA-117


title: RA-114 GBM 252 RNA-seq Rucaporib

description: Library name: RA-114


title: RA-113 GBM 252 RNA-seq Gavinostat

description: Library name: RA-113


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_33-trimmed


title: RA-125 GBM MGG-119 RNA-seq SirReal2

description: Library name: RA-125


title: Heart, Egf, 2h r2


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_59-trimmed


title: Heart, Egf, 2h r1


title: RA-115 GBM 252 RNA-seq GSK591

description: Library name: RA-115


title: RA-111 GBM 252 RNA-seq CPI203

description: Library name: RA-111


title: RA-112 GBM 252 RNA-seq SirReal2

description: Library name: RA-112


title: RA-110 GBM 252 RNA-seq ML228

description: Library name: RA-110


title: Liver, XY7.F

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

institute: McGill University

data_processing:
Data preprocessing and alignment was performed using the GenPipes RNA-seq pipeline
Reads were trimmed and filtered for quality, then aligned to the mouse reference genome (GRCm38) using STAR
Alignment bam files were used to generate bedGraph files with genomeCoverageBed and bedGraph files were converted to bigwig files with bedGraphToBigWig
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
Total RNA was extracted from mouse organs using Trizol Reagent (Thermo Fisher Scientific, MA, US) and purified using the RNeasy MinElute Cleanup Kit (Qiagen, NL).
Library preparation and RNA-sequencing (RNA-seq) were performed at the McGill University and Genome Quebec Innovation Centre for the liver, and at the McGill Genome Centre for the brain, lung, and heart tissues.

value: Liver

tag: sex chromosome complement

value: XY

tag: gonadal sex

value: Female

tag: age

value: 8 weeks

tag: library type

value: rRNA depleted


title: RA-109 GBM 252 RNA-seq Ciclopirox

description: Library name: RA-109

tag: cell line

value: Ciclopirox


title: RA-122 GBM MGG-119 RNA-seq Ciclopirox

description: Library name: RA-122

value: Brain tumor


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_39-trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_57-trimmed


title: RA-118 GBM MGG-119 RNA-seq Control

description: Library name: RA-118

value: Glioblastoma

value: Control


title: RA-108 GBM 252 RNA-seq A485

description: Library name: RA-108


title: Liver, XY6.F


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_72-trimmed


title: Heart, Egf, 2h r4

value: Heart

tag: genotype

value: wild-type

value: Egf


title: RA-107 GBM 252 RNA-seq Decitabine

description: Library name: RA-107


title: Liver, XY4.F


title: RA-106 GBM 252 RNA-seq PF06726304

description: Library name: RA-106


title: RA-105 GBM 252 RNA-seq Control

description: Library name: RA-105


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_75-trimmed

value: Plasma, extracted cell-free RNA

tag: diagnosis


title: RA-104 GBM BT142 RNA-seq Hesperadin

description: Library name: RA-104

value: Hesperadin


title: RA-103 GBM BT142 RNA-seq Alexidine

description: Library name: RA-103

value: Alexidine


title: Liver, XY3.F


title: RA-102 GBM BT142 RNA-seq GSK591

description: Library name: RA-102


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_91-trimmed

value: Immune checkpoint inhibitor therapy


title: RA-101 GBM BT142 RNA-seq Rucaporib

description: Library name: RA-101

value: Rucaporib


title: Liver, XY15.M

value: Liver

value: Male


title: RA-100 GBM BT142 RNA-seq Gavinostat

description: Library name: RA-100

value: Gavinostat


title: RA-99 GBM BT142 RNA-seq SirReal2

description: Library name: RA-99


title: Liver, XY14.M

value: XY

value: 8 weeks


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_52-trimmed

value: Acute Kidney Injury


title: RA-98 GBM BT142 RNA-seq CPI203

description: Library name: RA-98

value: Brain tumor


title: RA-97 GBM BT142 RNA-seq ML228

description: Library name: RA-97

value: Glioblastoma


title: Liver, XY13.M

value: rRNA depleted


title: RA-96 GBM BT142 RNA-seq Ciclopirox

description: Library name: RA-96

value: Ciclopirox


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_44_61bp

source_name: urine from the AKI cohort

value: Urine, extracted cell-free RNA


title: RA-95 GBM BT142 RNA-seq A485

description: Library name: RA-95


title: Liver, XY10.M


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_43_61bp


title: RA-94 GBM BT142 RNA-seq Decitabine

description: Library name: RA-94

value: Decitabine


title: Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_90-trimmed

value: Plasma, extracted cell-free RNA


title: RA-91 GBM TS1156 RNA-seq Hesperadin

description: Library name: RA-91

value: Hesperadin


title: RA-92 GBM BT142 RNA-seq Control

description: Library name: RA-92

value: Control


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_41_61bp

value: Immune checkpoint inhibitor therapy


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_40_61bp


title: RA-90 GBM TS1156 RNA-seq Alexidine

description: Library name: RA-90

value: Alexidine


title: Liver, XX14.F

value: Liver

value: XX

value: Female


title: Liver, XX13.F


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_39_61bp


title: RA-88 GBM TS1156 RNA-seq Rucaporib

description: Library name: RA-88

value: Rucaporib


title: Liver, XX8.F

value: 8 weeks


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_36_61bp

value: Acute Kidney Injury


title: RA-85 GBM TS1156 RNA-seq CPI203

description: Library name: RA-85

value: Brain tumor


title: RA-87 GBM TS1156 RNA-seq Gavinostat

description: Library name: RA-87

value: Glioblastoma

value: Gavinostat


title: Liver, XX17.F

value: XPaf

value: rRNA depleted


title: RA-86 GBM TS1156 RNA-seq SirReal2

description: Library name: RA-86


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_35_61bp

value: Urine, extracted cell-free RNA


title: RA-83 GBM TS1156 RNA-seq Ciclopirox

description: Library name: RA-83

value: Ciclopirox


title: RA-84 GBM TS1156 RNA-seq ML228

description: Library name: RA-84


title: Liver, XX16.F


title: RA-82 GBM TS1156 RNA-seq A485

description: Library name: RA-82


title: RA-81 GBM TS1156 RNA-seq Decitabine

description: Library name: RA-81

value: Decitabine


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_42_61bp


title: RA-93 GBM BT142 RNA-seq PF06726304

description: Library name: RA-93


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_33_61bp


title: RA-80 GBM TS1156 RNA-seq PF06726304

description: Library name: RA-80


title: Liver, XX15.F


title: Liver, XX10.F


title: RA-79 GBM TS1156 RNA-seq Control

description: Library name: RA-79

value: Control


title: RA-89 GBM TS1156 RNA-seq GSK591

description: Library name: RA-89


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_31_61bp

value: Immune checkpoint inhibitor therapy


title: RA-78 GBM TS600 RNA-seq Hesperadin

description: Library name: RA-78

value: Hesperadin


title: Liver, XX5.F

value: Liver


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_30_61bp


title: RA-77 GBM TS600 RNA-seq Alexidine

description: Library name: RA-77

value: Alexidine


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_29_61bp


title: Liver, XO7.F

value: XX

value: Female


title: RA-75 GBM TS600 RNA-seq Rucaporib

description: Library name: RA-75

value: Rucaporib


title: RA-72 GBM TS600 RNA-seq CPI203

description: Library name: RA-72


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_26_61bp

value: Acute Kidney Injury


title: RA-74 GBM TS600 RNA-seq Gavinostat

description: Library name: RA-74

value: Brain tumor


title: Liver, XX11.F

value: 8 weeks


title: RA-70 GBM TS600 RNA-seq Ciclopirox

description: Library name: RA-70

value: Glioblastoma


title: Liver, XO4.F

value: XPaf

value: XO


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_27_61bp

value: Urine, extracted cell-free RNA


title: Liver, XO6.F

value: rRNA depleted


title: Liver, XO5.F


title: RA-69 GBM TS600 RNA-seq A485

description: Library name: RA-69


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_25_61bp


title: RA-73 GBM TS600 RNA-seq SirReal2

description: Library name: RA-73


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_24_61bp


title: RA-68 GBM TS600 RNA-seq Decitabine

description: Library name: RA-68

value: Decitabine


title: RA-66 GBM TS600 RNA-seq Control

description: Library name: RA-66

value: Control


title: RA-67 GBM TS600 RNA-seq PF06726304

description: Library name: RA-67


title: Lung, XY4.F

value: Lung

value: XY


title: Lung, XY3.F


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_23_61bp

value: Immune checkpoint inhibitor therapy


title: RA-65 GBM PDX59 RNA-seq Hesperadin

description: Library name: RA-65

value: Hesperadin


title: RA-64 GBM PDX59 RNA-seq Alexidine

description: Library name: RA-64

value: Alexidine


title: Lung, XY2.F

value: Female


title: RA-63 GBM PDX59 RNA-seq GSK591

description: Library name: RA-63


title: RA-76 GBM TS600 RNA-seq GSK591

description: Library name: RA-76


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_21_61bp


title: RA-62 GBM PDX59 RNA-seq Rucaporib

description: Library name: RA-62

value: Rucaporib


title: RA-61 GBM PDX59 RNA-seq Gavinostat

description: Library name: RA-61

value: Gavinostat


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_19_61bp

value: Acute Kidney Injury


title: Lung, XY1.F

value: 8 weeks


title: RA-71 GBM TS600 RNA-seq ML228

description: Library name: RA-71

value: Brain tumor

value: Glioblastoma


title: Lung, XY13.M

value: Male


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_18_61bp

value: Urine, extracted cell-free RNA


title: Lung, XY11.M

value: rRNA depleted


title: RA-58 GBM PDX59 RNA-seq ML228

description: Library name: RA-58


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_17_61bp