title: MDA231 cells, ENL-T2-3A, Flag-ChIP, ChIP

first: Liling

last: Wan

address: 421 Curie Blvd

department: Cancer Biology

description: Library name: MDA231-ENL-T2-3A-Flag-ChIP

data_processing:
ChIP-seq, RNA-seq and CLAP-seq samples were sequenced using Illumina NextSeq 2000.
Assembly: ChIP-seq, human RNA-seq samples were mapped to human reference genome (hg19). Mouse RNA-seq samples were mapped to mouse reference genome (mm10). CLAP-seq samples were mapped to human reference genome (hg38).
Supplementary files format and content: bigWig files are in an indexed binary format
Supplementary files format and content: tab-delimited text files include TPM for each sample

growth_protocol: LSK cells were sorted from mouse bone marrow.LSK cells were cultured in IMDM + GlutaMAX supplemented with 10% FBS, 100 U/mL penicillin-streptomycin, 20 ng/mL mFlt3L, 20 ng/mL mIL6, 100 ng/mL mSCF, 20 ng/mL mTPO, 1:1000 0.1M betamercaptoethanol, 1:100 200mM L-glutamine. HEK293 cells were procured from ATCC and were cultured in EMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin. MDA-231 cells were shared by the labs of Dr. Junwei Shi and Dr. Yibin Kang, respectively, and cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin.

extract_protocol:
RNeasy plus mini kit (Qiagen, #74136) was used to extract total RNA and remove genomic DNA.
ChIP-seq libraries were constructed with VAHTS Universal DNA Library Prep Kit for Illumina V4 from Vazyme (ND610-01). RNA-seq libraries were constructed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina from Vazyme (NR605-02).

value: epithelial cell


title: MDA231 cells, ENL-T1-3A, Flag-ChIP, ChIP

status: Public on Nov 28 2025

type: SRA

city: Philadelphia

state: PA

country: USA

institute: University of Pennsylvania

description: Library name: MDA231-ENL-T1-3A-Flag-ChIP

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: iWAT ADAR1 -/-, Ifih1 -/-,high fat diet, rep 2

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

library_source: transcriptomic

data_processing:
Fastq files were aligned to mouse mm10  reference genome using STAR alignment(v2.5.0a) .
Based on GTF annotation files from GENCODE GRCm38 M16, quantification of gene expression was determined using fragments counting mode by FeatureCounts.
Gene expression was normalized to RPKM (Reads Per Kilobase Million).
Assembly: mm10
Supplementary files format and content: txt
Supplementary files format and content: tab-delimited text files include log2(RPKM+1) values for each Sample.

molecule: polyA RNA

organism: Mus musculus

source_name: iWAT

extract_protocol:
Total RNA was extracted from adipose tissues with miRNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: iWAT


title: DMSO

city: Guangzhou

first: yang

last: zhou

address: South Shatai Road, Baiyun District

country: China

institute: Southern Medical University

description: Library name: sample1

data_processing:
Raw FASTQ sequencing data underwent quality control processing using Trim Galore to ensure optimal sequence integrity. The resulting high-quality sequences were aligned to the GRCm38 mouse reference genome using Bowtie2. To enhance data quality, mitochondrial reads and low-quality alignments were filtered out using SAMtools, while PCR duplicates were eliminated using Sambamba. ENCODE blacklist regions were subsequently removed using BEDtools to minimize potential artifacts. Read coordinates were adjusted using alignmentSieve, followed by sorting and indexing with SAMtools to generate BAM files. Finally, peak calling was performed using MACS3 to identify regions of significant enrichment.
Assembly: GRCm38
Supplementary files format and content: DMSO.bw and Epa.bw

source_name: splenocytes

extract_protocol:
cold lysis buffer was used to get crude nuclei.
40,000 nuclei are subjected to a transposase reaction using Tn5 enzyme (Illumina). The transposed DNA fragments are recovered using the MinElute PCR Purification Kit (Qiagen).PCR amplification is carried out using 1X NEBNext High - Fidelity PCR Master Mix (New England Biolabs, MA). The amplified products are recovered using the MinElute PCR Purification Kit (Qiagen).

value: splenocytes

tag: strain

value: T cell

tag: treatment

value: DMSO


title: iWAT ADAR1 -/-, Ifih1 -/-,high fat diet, rep 1


title: MDA231 cells, ENL-T1, Flag-ChIP, ChIP

description: Library name: MDA231-ENL-T1-Flag-ChIP


title: P1-H12

city: Toronto

first: Steven

last: Dupas

address: 160 College St.

country: Canada

institute: University of Toronto

description: Library name: Sample96

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed based on i5/i7 PCR barcodes and processed using a modified pipeline from (Cao et al. 2019) implemented in a Snakemake framework. First, barcodes and unique molecular identifiers (UMIs) were extracted from read1 of FASTQ files followed by trimming of read 2. Reads were then aligned to the mouse genome (mm10) with STAR short-read aligner (v 2.6.1d) using Gencode vM12 gene annotations and quality filtered. Reads were deduplicated based on UMIs, and summarized into a count matrix of M genes x N nuclei, which was converted into AnnData object in Scanpy (v1.9.3).
Doublets were removed with Scrublet (Wolock, Lopez et al. 2019) and cells with a detected number of genes, total RNA counts, or mapping rate greater than five absolute deviations from the median were discarded, as were cells with > 1% mitochondrial RNA. Total counts per cell was normalized and log transformed.
The top 2,000 most variable genes were extracted and used in principal component analysis (PCA) to reduce the dimensionality of the data. Neighborhood graphs were constructed using 30 principal components and data were visualized with Uniform Manifold Approximation and Projection (UMAP). Clustering was performed using the Leiden algorithm (leidenalg v 0.10.2) with a resolution of 0.1 to identify broad cell clusters and 0.8 to identify subclusters. A specific subcluster (‘15’) was noted to have aberrantly high RNA counts, and expression signatures consistent with doublets, and therefore was excluded from downstream analysis. Clusters were manually annotated based on expression of known cell type marker genes and label transfer using an embryonic mouse dataset and named accordingly
Sequencing data from hgRNA libraries were processed using a Snakemake pipeline. Raw FASTQ files were processed to attach UMIs using custom scripts (Cao, Spielmann et al. 2019), incorporating ligation and reverse transcription barcodes. Reads were aligned to a non-redundant hgRNA index using Bowtie (Langmead, Trapnell et al. 2009). Aligned reads were filtered to retain high-quality mappings. hgRNA-UMI pairings were considered chimeric if they represented less than 80% of the reads for a given hgRNA-UMI paring within a given cell, and were removed using a custom Python script, and the resulting non-chimeric BAM files were indexed. Deduplication was performed using UMI-tools (Smith, Heger et al. 2017) to retain unique molecules. Aligned reads with UMIs were processed to assign guides to individual cells. Reads were grouped by cell and guide, and UMIs were counted to determine the number of unique reads per cell and guide. Guides were assigned to cells by prioritizing the guide pair with the highest combined UMI counts or, for non-redundant guides, where possible, the single guide with the highest UMI count. Perturbation targets were annotated based on guide metadata, and final assignments were compiled.
Assembly: mm10
Supplementary files format and content: h5ad anndata object of quality filtered guide assigned single-cells.

growth_protocol: CGR8 mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in GMEM supplemented with 100 μM β-mercaptoethanol, 0.1 mM nonessential amino acids, 2 mM sodium pyruvate, 5 000 units ml–1 of penicillin/streptomycin, 1,000 units ml–1 of recombinant mouse LIF (all Life Technologies) and 10% ES fetal calf serum (Wisent). Cells were passaged using Trypsin (Life Technologies) and maintained at subconfluent conditions at 37 °C and 5% CO2. Cells were regularly monitored for mycoplasma infection. CGR8 mESCs were transduced with a lentiviral library of hybrid guide (hg) RNAs and selected with puromycin for 3 days. In vitro differentiation of CGR8 mESCs into neurons was performed as previously described (Gueroussov et al., 2015; Hubbard et al., 2013). At day in vitro (DIV) -8, 5.1x106 cells were seeded on 15cm non-tissue-culture-treated plates containing 30mL of serum-free differentiation media (GMEM containing 5% KnockOut Serum replacement (Thermo Fisher Scientific), 0.1 mM nonessential amino acids, 1mM sodium pyruvate, 5 000 units ml–1 of penicillin/streptomycin and 100mM b-mercaptoethanol). Cells were incubated for 3 days undisturbed. 50% media changes were conducted every 48 hours. At DIV -5 the media was supplemented with 6mM retinoic acid (RA) with subsequent media changes also contained 6mM RA. At DIV 0, cellular aggregates were dissociated with TrypLE Express (Gibco) for 5 minutes at 37°C. Trypsinization was halted with soybean trypsin inhibitor (Thermo Fisher Scientific) and aggregates were homogenized by trituration with a micropipette. Cells were pelleted for 5 minutes at 300xg. Neural progenitors were washed in N2 medium (Neurobasal-A medium [Gibco] with 1x N2 supplement: 2 mM glutamine and 5 000 units ml–1 of penicillin/streptomycin [Gibco]), counted using a hemocytometer, and plated at a density of 1.5x105cells/cm2 onto poly-D-Lysine and Laminin-coated dishes. The plated neural progenitors were washed with N2 medium after 24 hours to remove residual serum and non-adherent cells. At DIV2, the N2 medium was replaced with B27 medium (Neurobasal-A supplemented with antibiotics, 2mM glutamine and 1xB27 supplement [Gibco]). Subsequently, differentiating neurons were provided with full medium changes with B27 on DIV4, and every 3 days onward.

extract_protocol:
DIV7 neurons were harvested with Hank’s Balanced Salt Solution (Gibco) supplemented with 20 Uml-1 Papain (Worthington), 5 mM MgCl2 and 5 mgmL-1 DNase I (Worthington), counted and pelleted and immediately snap-frozen in liquid nitrogen and then stored at -80°C. Nuclei extraction and fixation were performed as previously described (Cao et al. 2019), except for the use of a modified CST lysis buffer (Slyper et al. 2020) plus 1% of SUPERase In RNase Inhibitor (AM2696). Nuclei quality was checked with DAPI and Wheat Germ Agglutinin (WGA) staining.
Sci-RNA-Seq3 libraries were generated as previously described (Martin et al. 2023) using three-level combinatorial indexing. The final libraries were sequenced on an Illumina NovaSeq with read cycles as follows: read 1: 34bp, read 2: 69bp, index 1: 10bp, index 2: 10bp.

value: In vitro differentiated neurons

tag: timepoint

value: day in vitro 7


title: iWAT ADAR1 flox/flox, Ifih1 -/-, high fat diet, rep 3


title: MDA231 cells, ENL-T2, Flag-ChIP, ChIP

description: Library name: MDA231-ENL-T2-Flag-ChIP


title: eWAT ADAR1 flox/flox, Ifih1 -/-, high fat diet, rep 3

source_name: eWAT

value: eWAT


title: iWAT ADAR1 flox/flox, Ifih1 -/-, high fat diet, rep 2


title: HEK293 cells, ENL-T2-3A, Flag-ChIP, batch2, ChIP

description: Library name: HEK293-ENL-T2-3A-Flag-ChIP

value: embryonic kidney cell


title: HEK293 cells, ENL-T2, Flag-ChIP, batch2, ChIP

description: Library name: HEK293-ENL-T2-Flag-ChIP


title: MDA231 cells, ENL-WT, input, ChIP

description: Library name: MDA231-ENL-WT-Flag-Input


title: iWAT ADAR1 flox/flox, Ifih1 -/-, high fat diet, rep 1


title: P1-H09

description: Library name: Sample93


title: HEK293 cells, ENL-T1-3A, Flag-ChIP, batch1 ChIP

description: Library name: HEK293-T1-3A-FLAG-ENL-ChIP


title: HEK293 cells, ENL-WT, Flag-ChIP, batch1, ChIP

description:
Library name: HEK293-WT-FLAG-ENL-ChIP-1
ENL-WT-bacth1 for HEK293 ENL-WT-T1-T13A ChIP


title: HEK293 cells, ENL-WT, input, batch2, ChIP

description:
Library name: HEK293-ENL-WT-input-2
Input-batch2 for HEK293 ENL-WT-T2-T23A ChIP


title: eWAT ADAR1 -/-, Ifih1 -/-,chow diet, rep 3


title: P1-H07

description: Library name: Sample91


title: P1-H08

description: Library name: Sample92


title: HEK293 cells, ENL-T1-3A, input, replicate1, CLAP

description: Library name: HEK293-ENL-T1-3A-input-1-CLAP

molecule: nuclear RNA

extract_protocol:
RNeasy plus mini kit (Qiagen, #74136) was used to extract total RNA and remove genomic DNA.
ChIP-seq libraries were constructed with VAHTS Universal DNA Library Prep Kit for Illumina V4 from Vazyme (ND610-01). RNA-seq libraries were constructed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina from Vazyme (NR605-02).
CLAP-seq uses a Halo ligand affinity resin to pull down our Halo-tagged proteins.


title: eWAT ADAR1 -/-, Ifih1 -/-,chow diet, rep 2


title: MDA231 cells, ENL-WT, Flag-ChIP, ChIP

description: Library name: MDA231-ENL-WT-Flag-ChIP


title: HEK293 cells, ENL-T1-3A, IP, replicate1, CLAP

description: Library name: HEK293-ENL-T1-3A-IP-1-CLAP


title: eWAT ADAR1 -/-, Ifih1 -/-,chow diet, rep 1


title: P1-H06

description: Library name: Sample90


title: eWAT ADAR1 flox/flox, Ifih1 -/-, chow diet, rep 3


title: P1-H11

description: Library name: Sample95


title: P1-H10

description: Library name: Sample94


title: P1-H05

description: Library name: Sample89


title: HEK293 cells, ENL-T1, input, replicate1, CLAP

description: Library name: HEK293-ENL-T1-input-1-CLAP


title: HEK293 cells, ENL-WT, IP, replicate1, CLAP

description: Library name: HEK293-ENL-WT-IP-1-CLAP


title: HEK293 cells, ENL-WT, input, replicate1, CLAP

description: Library name: HEK293-ENL-WT-input-1-CLAP


title: HEK293 cells, ENL-WT, Flag-ChIP, batch2, ChIP

description:
Library name: HEK293-ENL-WT-Flag-ChIP-2
ENL-WT-bacth2 for HEK293 ENL-WT-T2-T23A ChIP


title: P1-H04

description: Library name: Sample88


title: HEK293 cells, ENL-T1-3A, replicate2, RNA-seq

description:
Library name: HEK293-ENL-T1-3A-rep2-RNAseq
HEK293_RNAseq_T1_TPM.txt

molecule: total RNA

source_name: cell line

value: cell line


title: eWAT ADAR1 flox/flox, Ifih1 -/-, chow diet, rep 1


title: P1-H03

description: Library name: Sample87


title: HEK293 cells, ENL-T1-3A, replicate1, RNA-seq

description:
Library name: HEK293-ENL-T1-3A-rep1-RNAseq
HEK293_RNAseq_T1_TPM.txt


title: iWAT ADAR1 -/-, Ifih1 -/-,chow diet, rep 3


title: HEK293 cells, ENL-WT, replicate4, RNA-seq

description:
Library name: HEK293-ENL-WT-rep4-RNAseq-2
HEK293_RNAseq_T1_TPM.txt


title: HEK293 cells, ENL-T1, replicate1, RNA-seq

description:
Library name: HEK293-ENL-T1-rep1-RNAseq
HEK293_RNAseq_T1_TPM.txt


title: HEK293 cells, ENL-T1, replicate2, RNA-seq

description:
Library name: HEK293-ENL-T1-rep2-RNAseq
HEK293_RNAseq_T1_TPM.txt


title: iWAT ADAR1 -/-, Ifih1 -/-,chow diet, rep 2


title: HEK293 cells, ENL-WT, replicate3, RNA-seq

description:
Library name: HEK293-ENL-WT-rep3-RNAseq-2
HEK293_RNAseq_T1_TPM.txt


title: P1-H02

description: Library name: Sample86


title: HEK293 cells, ENL-T1, IP, replicate1, CLAP

description: Library name: HEK293-ENL-T1-IP-1-CLAP


title: iWAT ADAR1 -/-, Ifih1 -/-,chow diet, rep 1


title: P1-G12

description: Library name: Sample84


title: HEK293 cells, ENL-T2, replicate2, RNA-seq

description:
Library name: HEK293-ENL-T2-rep2-RNAseq
HEK293_RNAseq_T2_TPM.txt


title: HEK293 cells, ENL-T2-3A, replicate2, RNA-seq

description:
Library name: HEK293-ENL-T2-3A-rep2-RNAseq
HEK293_RNAseq_T2_TPM.txt


title: HEK293 cells, ENL-T2-3A, replicate1, RNA-seq

description:
Library name: HEK293-ENL-T2-3A-rep1-RNAseq
HEK293_RNAseq_T2_TPM.txt


title: P1-G11

description: Library name: Sample83


title: P1-G10

description: Library name: Sample82


title: HEK293 cells, ENL-T2, replicate1, RNA-seq

description:
Library name: HEK293-ENL-T2-rep1-RNAseq
HEK293_RNAseq_T2_TPM.txt


title: HEK293 cells, ENL-WT, replicate2, RNA-seq

description:
Library name: HEK293-ENL-WT-rep2-RNAseq
HEK293_RNAseq_T2_TPM.txt


title: eWAT ADAR1 flox/flox, Ifih1 -/-, chow diet, rep 2


title: MDA231 cells, ENL-T2, replicate1, RNA-seq

description:
Library name: MDA231-ENL-T2-rep1-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: HEK293 cells, ENL-WT, replicate1, RNA-seq

description:
Library name: HEK293-ENL-WT-rep1-RNAseq
HEK293_RNAseq_T2_TPM.txt


title: iWAT ADAR1 KO, rep 1


title: MDA231 cells, ENL-T2-3A, replicate2, RNA-seq

description:
Library name: MDA231-ENL-T2-3A-rep2-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: iWAT ADAR1 flox/flox, Ifih1 -/-, chow diet, rep 1


title: iWAT ADAR1 flox/flox, Ifih1 -/-, chow diet, rep 3


title: P1-G06

description: Library name: Sample78


title: MDA231 cells, ENL-WT, replicate2, RNA-seq

description:
Library name: MDA231-ENL-WT-rep2-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: MDA231 cells, ENL-WT, replicate1, RNA-seq

description:
Library name: MDA231-ENL-WT-rep1-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: MDA231 cells, ENL-T2-3A, replicate1, RNA-seq

description:
Library name: MDA231-ENL-T2-3A-rep1-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: P1-G09

description: Library name: Sample81


title: iWAT WT, rep 1


title: MDA231 cells, ENL-T2, replicate2, RNA-seq

description:
Library name: MDA231-ENL-T2-rep2-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: P1-G08

description: Library name: Sample80


title: MDA231 cells, ENL-T1-3A, replicate2, RNA-seq

description:
Library name: MDA231-ENL-T1-3A-rep2-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: iWAT ADAR1 KO, rep 2


title: P1-G04

description: Library name: Sample76


title: P1-H01

description: Library name: Sample85


title: P1-G07

description: Library name: Sample79


title: MDA231 cells, ENL-T1-3A, replicate1, RNA-seq

description:
Library name: MDA231-ENL-T1-3A-rep1-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: MDA231 cells, ENL-T1, replicate2, RNA-seq

description:
Library name: MDA231-ENL-T1-rep2-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: eWAT WT, rep 2


title: IMOK infected with E. coli (no T-cell coculture) – replicate 4

city: Seoul

first: Min Gyu

last: Kang

address: Daehak-ro

country: South Korea

institute: Seoul national university

description:
Library name: IMOKonly_4
Column name in gene_counts_matrix.txt: Th17IMOKonly3

data_processing:
Reads were trimmed and filtered using fastp to remove adapter sequences and low-quality bases.
Trimmed reads were aligned to the mouse GRCm39 genome using STAR with default parameters.
Transcript-level quantification was performed using Salmon in alignment-based mode, using STAR-generated BAM files as input.
Gene-level count matrices were generated using the tximport package in R.
Normalization, dispersion estimation, and differential expression analysis were performed using DESeq2.
Assembly: Mouse genome reference GRCm39 with GENCODE M27 annotations was used.
Supplementary files format and content: The processed data file is a tab-delimited text file containing gene-level differential expression results generated by DESeq2, including baseMean, log2FoldChange, p-value, adjusted p-value, gene symbol, and TPM values for each sample.

source_name: IMOK

growth_protocol: IMOK cells were maintained in CnT medium (CELLnTEC) supplemented with 1% penicillin-streptomycin and cultured at 37°C in a humidified incubator with 5% CO2. Cells were expanded according to standard procedures and used for experiments at approximately 70–80% confluence.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Cells were lysed directly in TRIzol, followed by phase separation with chloroform and centrifugation. The aqueous phase containing RNA was collected, and RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in RNase-free water. RNA concentration and purity were measured using a NanoDrop spectrophotometer, and RNA integrity was assessed by TapeStation.
RNA-seq libraries were generated using the 3′ mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices (12 nt) following the manufacturer’s instructions. Libraries were indexed and amplified according to kit guidelines.

treatment_protocol: IMOK cells were infected with an oral lichen planus–derived Escherichia coli strain at a multiplicity of infection (MOI) of 500 and incubated for 2 hours. Prior to infection, cells were washed and cultured in antibiotic-free medium to prevent inhibition of bacterial uptake. After the 2-hour infection period, the medium was replaced with gentamicin-containing medium to eliminate extracellular bacteria. Following antibiotic treatment, cells were either cocultured with Th17 cells placed in 0.4 μm Transwell inserts (no direct contact), or maintained without T cells as controls.

value: IMOK

value: keratinocytes

tag: genotype

value: WT

value: E. coli infection only


title: P1-G02

description: Library name: Sample74


title: iWAT WT, rep 2


title: IMOK infected with E. coli (no T-cell coculture) – replicate 2

description:
Library name: IMOKonly_2
Column name in gene_counts_matrix.txt: Th17IMOKonly1re


title: IMOK infected with E. coli + Th17 coculture (Transwell) – replicate 1

description:
Library name: Th17Coculture_1
Column name in gene_counts_matrix.txt: Th17coculture1

value: E. coli infection + Th17 coculture (Transwell)


title: MDA231 cells, ENL-T1, replicate1, RNA-seq

description:
Library name: MDA231-ENL-T1-rep1-RNAseq
MDA-MB-231_RNAseq_TPM.txt


title: iWAT ADAR1 flox/flox, Ifih1 -/-, chow diet, rep 2


title: eWAT ADAR1 KO, rep 1


title: P1-G05

description: Library name: Sample77


title: IMOK infected with E. coli + Th17 coculture (Transwell) – replicate 4

description:
Library name: Th17Coculture_4
Column name in gene_counts_matrix.txt: Th17coculture3re


title: eWAT ADAR1 KO, rep 2


title: P1-F12

description: Library name: Sample72


title: IMOK infected with E. coli + Th17 coculture (Transwell) – replicate 3

description:
Library name: Th17Coculture_3
Column name in gene_counts_matrix.txt: Th17coculture3


title: IMOK infected with E. coli + Th17 coculture (Transwell) – replicate 2

description:
Library name: Th17Coculture_2
Column name in gene_counts_matrix.txt: Th17coculture2


title: Murine colonic fibroblasts

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Colon fibroblast dataset

data_processing:
barcode/feature matrices  generated using count function from cellranger v3 with default parameter.
Assembly: Mouse mm10 genome with Mouse FAST DB 2018_1 annotations and Human EGFP sequence
Supplementary files format and content: murinMyofibColon_filteredCounts.csv: count data
Supplementary files format and content: 2018_1_mm10_gene_annots.txt: gene  annotations
Supplementary files format and content: epithelial_clustering_reso0.1_clusterCellsList.txt: barcode/cluster for epithelial cells
Supplementary files format and content: fibroblast_2_clustering_resolution0.6_clusterCellsList.txt: barcode/cluster for fibroblast cells

source_name: intestine- colon

extract_protocol:
After colon separation, it has been washed 3 times with ice-cold PBS and cut open longitidually. Then, mucosal and muscle layers have been separated with a help of glass-slide scraping. Mucosal sample was mechanically disssociated using 2 scalpels and digested with collagenase I solution, enriched with growth factors (DMEM-Glutamax with  0.25 U/mL insulin, 100 µg/mL transferrin, 10 ng/mL murine EGF and 1% antibiotic-antimycotic, collagenase I, 100U/mL) and incubated for 1h at 37C with constant agitation with magnetic stirrer. GFP positive cells were enriched by FACS sorting.
Chromium Single Cell 3’ Library Kit V3 (10X Genomics)

treatment_protocol: Mouse have been injected 5 consecutive days with Tamoxifen (50 mg/kg) and killed 2 days after

value: intestine- colon

value: fibroblasts

value: aSmaCre mTmG


title: P1-G03

description: Library name: Sample75


title: P1-F11

description: Library name: Sample71


title: HEK293 cells, ENL-T1, Flag-ChIP, batch1, ChIP

description: Library name: HEK293-T1-FLAG-ENL-ChIP


title: P1-F10

description: Library name: Sample70


title: IMOK infected with E. coli (no T-cell coculture) – replicate 5

description:
Library name: IMOKonly_5
Column name in gene_counts_matrix.txt: Th17IMOKonly3re


title: P1-F09

description: Library name: Sample69


title: 12_SNAT3_cKO_S7

city: Haifa

first: Inna

last: Radzishevsky

address: Oren 13

department: Biochemistry

country: Israel

institute: Inna Radzishevsky

description: Library name: sample 6

data_processing:
Quality control was assessed using Fastqc (v0.12.1). Reads were trimmed for adapters, minimum quality Phred score of 20 and minimum length of 35 using CUTADAPT (v4.4).
Single reads (100 bp) were aligned to Mus musculus (GRCm39) reference genome and annotation file using STAR (v2.7.10b) with mismatch ratio allowed < 0.2, the minimum and maximum intron sizes were set to 21 and 1,000,000, respectively. The number of reads per gene was counted using STAR “--quantMode GeneCounts” (v2.7.10b) with ‘reverse’ mode.
Normalization and differential expression analyses were conducted using DESeq2 R package (v1.41.8). The threshold for significantly differentially expressed genes is determined by two factors: adjusted p-value ≤ 0.05 and the ‘base-mean independent filtering’ threshold, which is calculated by the DESeq2 algorithm for each comparison. FDR was calculated using the default approach of DESeq2, Benjamini-Hochberg.
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: csv file of normalized count table containg all samples
Supplementary files format and content: Excel file with differential gene expression comparisons including log fold-change and FDR values.

source_name: hippocampus

extract_protocol:
Total RNA was extracted from 9 tissue samples using the RNeasy mini kit (Qiagen, cat no. 74106). 600 ul of RLT buffer was added to each sample and the samples were disrupted and homogenized using the Polytron PT3000 Homogenizer (Kinematica). After homogenization, samples were centrifuged for 3 min at 13000g and the supernatant was transferred to a new tube for automated extraction using the QIAcube Connect (Qiagen). The RINe value of all samples was in the range of 9.7-9.9, indicating very high quality.
RNA-seq libraries were constructed simultaneously using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7760), according to the manufacturer’s protocol.

treatment_protocol: Hippocampi of 11-day-old1-days-old mice were dissected, flash-frozen in liquid nitrogen and stored at −80°C until further analysis

value: hippocampus

tag: age

value: 11 days

value: Slc38a3 cKO

tag: Sex

value: male


title: 6_SNAT3_cKO_S3

description: Library name: Sample 3

value: female


title: 2_SNAT3_wt_S2

description: Library name: Sample 2

value: wt


title: IMOK infected with E. coli (no T-cell coculture) – replicate 1

description:
Library name: IMOKonly_1
Column name in gene_counts_matrix.txt: Th17IMOKonly1


title: 14_SNAT3_wt_S9

description: Library name: Sample 8


title: P1-G01

description: Library name: Sample73

value: In vitro differentiated neurons

value: day in vitro 7


title: eWAT WT, rep 1

value: eWAT


title: 13_SNAT3_cKO_S8

description: Library name: Sample 7


title: P1-F08

description: Library name: Sample68


title: LSK cells, ENL-T1, replicate2, RNA-seq

description:
Library name: LSK-MSCV-ENL-T1-rep2-RNAseq
LSK_RNAseq_TPM.txt

source_name: Blood

value: Blood

value: LSK

value: hematopoietic stem cell


title: LSK cells, ENL-T1-3A, replicate2, RNA-seq

description:
Library name: LSK-MSCV-ENL-T1-3A-rep2-RNAseq
LSK_RNAseq_TPM.txt


title: 7_SNAT3_wt_S4

description: Library name: Sample 4


title: 9_SNAT3_wt_S6

description: Library name: Sample 5


title: 1_SNAT3_cKO_S1

description: Library name: Sample 1


title: P1-F07

description: Library name: Sample67


title: K52Q_1

city: Boston

first: Renato

last: Santos

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: K52Q_1

data_processing:
For ChIP: Sequencing reads were aligned to the Vibrio cholerae reference genome (NC_002505.1 and NC_002506.1) using Bowtie2 v2.4.1. Fragments ≤ 400 bp were retained. Peaks were called with QuEST v2.4.24 using an untagged V5 mock strain as background, with a >2-fold enrichment threshold. For RNA-seq: Reads were demultiplexed using barcode sequences with up to one allowed mismatch that did not cause barcode reassignment. Terminal G residues from template switching and adapter sequences were removed before alignment.
Assembly: Vibrio cholerae N16961 reference genome from NCBI RefSeq: NC_002505.1 and NC_002506.1.
Supplementary files format and content: Processed files consist of BED peak-calling output (MACS/QuEST-style enriched regions) for each ChIP-seq sample. Processed data consist of a gene-level count matrix (all_counts.tsv) containing raw read counts for all annotated V. cholerae transcripts.

organism: Vibrio cholerae

source_name: Vibrio cholerae C6706

extract_protocol:
ChIP DNA libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7645S) following the manufacturer’s instructions. Libraries were amplified for 10 PCR cycles without size selection and sequenced at the Harvard Biopolymers Facility on an Illumina NovaSeq 6000. Total RNA was extracted from 5 mL exponential-phase cultures using the Direct-zol RNA MiniPrep Plus kit (Zymo Research #R2072), including on-column DNase digestion to remove genomic DNA.
ChIP DNA libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7645S) following the manufacturer’s instructions. Libraries were amplified for 10 PCR cycles without size selection and sequenced at the Harvard Biopolymers Facility on an Illumina NovaSeq 6000 (paired-end). Illumina cDNA libraries were prepared using a modified RNAtag-Seq protocol (Shishkin et al., 2015). Briefly, 500 ng–1 µg total RNA was fragmented, DNA-depleted, dephosphorylated, and ligated to barcoded 5′-AN₈-3′ adapters. Barcoded RNAs were pooled and rRNA-depleted with the RiboZero rRNA Removal Kit (Epicentre). cDNA synthesis used a template-switching primer (SMARTScribe RT, Clontech), followed by PCR amplification with Illumina P5/P7 primers. Libraries were sequenced on an Illumina NextSeq 500 (paired-end 75 bp).

value: Vibrio cholerae C6706


title: K52Q_3

description: Library name: K52Q_3


title: 4xR_3

description: Library name: 4xR_3


title: 4xR_2

description: Library name: 4xR_2


title: 4xR_1

description: Library name: 4xR_1


title: LSK cells, ENL-WT, replicate2, RNA-seq

description:
Library name: LSK-MSCV-ENL-WT-rep2-RNAseq
LSK_RNAseq_TPM.txt


title: 4xQ_3

description: Library name: 4xQ_3


title: LSK cells, ENL-T1, replicate1, RNA-seq

description:
Library name: LSK-MSCV-ENL-T1-rep1-RNAseq
LSK_RNAseq_TPM.txt


title: LSK cells, ENL-WT, replicate1, RNA-seq

description:
Library name: LSK-MSCV-ENL-WT-rep1-RNAseq
LSK_RNAseq_TPM.txt


title: P1-F06

description: Library name: Sample66


title: P1-F04

description: Library name: Sample64


title: K52Q_2

description: Library name: K52Q_2


title: P1-F05

description: Library name: Sample65


title: LSK cells, ENL-T1-3A, replicate1, RNA-seq

description:
Library name: LSK-MSCV-ENL-T1-3A-rep1-RNAseq
LSK_RNAseq_TPM.txt


title: 4xQ_2

description: Library name: 4xQ_2


title: 4xQ_1

description: Library name: 4xQ_1


title: P1-F03

description: Library name: Sample63


title: 3xQ_3

description: Library name: 3xQ_3


title: P1-F02

description: Library name: Sample62


title: IMOK infected with E. coli (no T-cell coculture) – replicate 3

description:
Library name: IMOKonly_3
Column name in gene_counts_matrix.txt: Th17IMOKonly2

value: IMOK

value: keratinocytes

value: WT

value: E. coli infection only


title: 3xQ_1

description: Library name: 3xQ_1


title: CRPV5_3

description: Library name: CRPV5_3


title: P1-F01

description: Library name: Sample61


title: 19_SNAT3_wt_S10

description: Library name: Sample 9

value: hippocampus


title: HEK293 cells, ENL-WT, input, batch1, ChIP

description:
Library name: HEK293-WT-FLAG-ENL-input-1
Input-batch1 for HEK293 ENL-WT-T1-T13A ChIP

value: embryonic kidney cell


title: P1-E10

description: Library name: Sample58


title: CRPV5_2

description: Library name: CRPV5_2


title: P1-E12

description: Library name: Sample60


title: CRPV5_1

description: Library name: CRPV5_1


title: P1-E09

description: Library name: Sample57


title: 3xQ_2

description: Library name: 3xQ_2


title: P1-E11

description: Library name: Sample59


title: DCRP_3

description: Library name: DCRP_3


title: P1-E08

description: Library name: Sample56


title: DCRP_2

description: Library name: DCRP_2


title: P1-E07

description: Library name: Sample55


title: P1-E05

description: Library name: Sample53


title: P1-E06

description: Library name: Sample54


title: WT_3

description: Library name: WT_3


title: DCRP_1

description: Library name: DCRP_1


title: PDX527_1095_20_CNTL_1L

type: RNA

city: Barcelona

first: Andreu

last: Òdena

state: Please Select

address: C/ Natzaret, 115-117 CELLEX CENTER

country: Spain

institute: VHIO

hyb_protocol: Hybridation was performed as per manufacturer's protocol

scan_protocol: Analysed in the nCounter FLEX Digital Analyzer

data_processing: Expression counts were then normalized using custom scripts in R 3.6.3.

organism:
Homo sapiens
Mus musculus

source_name: Breast Cancer Patient Derived Xenograft

label_protocol: Fluorescent barcode

extract_protocol: RNA was extracted using the High Pure FFPET RNA isolation kit (Roche, Indianapolis, IN, USA) following manufacturer’s protocol. One to five 10-μm FFPE slides depending on tumor cellularity were used for each tumor sample, and macrodissection was performed, when needed, to avoid normal tissue contamination. A minimum of 100 ng of total RNA was analyzed at the nCounter platform using a customized nCounter Elements 72-gene panel.

value: Untreated

tag: her3-dxd 10mg-kg sensitivity (relapsed or non-relapsed)

value: Relapsed


title: PDX060_1347_22_U3_24h_11L

value: HER3-DXd 10mg-kg

value: Non-relapsed


title: PDX098_1056_20_CNTL_1R_rep2


title: PDX060_1059_20_CNTL_2R


title: PDX060_1059_20_CNTL_1R


title: PDX533_1205_21_CNTL_2R


title: PDX533_1043_20_CNTL_1L


title: PDX098_1056_20_CNTL_5R


title: PDX583.2_1456_23_CNTL_1R


title: PDX512_1374_22_CNTL_1R


title: PDX509_1016_20_CNTL_1L


title: PDX098_1260_21_U3_24h_11L


title: PDX098_1061_20_U3_7d_11L


title: PDX098_1056_20_CNTL_1R_rep1


title: PDX476.2_CNTL_passage_3_BEDC


title: PDX527_1042_20_CNTL_1L


title: PDX476.2_1367_22_CNTL_1R


title: PDX509_1070_20_CNTL_1L


title: PDX509_1070_20_CNTL_2L


title: PDX491_1366_22_U3_7d_11R


title: PDX060_1059_20_U3_7d_11R


title: PDX509_1070_20_U3_7d_11R


title: PDX491_1250_21_CNTL_1L_rep1


title: PDX509_1231_21_U3_24h_11R


title: PDX491_1250_21_CNTL_1L_rep2


title: WT_2

description: Library name: WT_2


title: PDX491_1041_20_CNTL_1L


title: PDX491_CNTL_passage_0_6F7C


title: P1-E04

description: Library name: Sample52

value: In vitro differentiated neurons


title: P1-E02

description: Library name: Sample50

value: day in vitro 7


title: P1-E01

description: Library name: Sample49


title: P1-D12

description: Library name: Sample48


title: WT_1

description: Library name: WT_1


title: P1-E03

description: Library name: Sample51


title: PDX490_1272_21_U3_7d_11L


title: PDX490_CNTL_passage_1_603F


title: PDX490_1040_20_CNTL_1L


title: PDX491_1250_21_U3_24h_11L_rep2


title: PDX491_1250_21_U3_24h_11L_rep1


title: P1-D11

description: Library name: Sample47


title: PDX490_1181_21_CNTL_3R


title: PDX479_CNTL_passage_1_6E98


title: PDX490_1475_24_U3_24h_11L


title: PDX474.7_passsage_1_9E7E


title: P1-D09

description: Library name: Sample45


title: P1-D10

description: Library name: Sample46


title: PDX479_1079_20_CNTL_1L_rep1


title: PDX474.7_1252_21_CNTL_1R


title: PDX479_1079_20_CNTL_1L_rep2


title: SC5314-3

city: Shanghai

first: Jianchen

last: Peng

address: 2005 Songhu Road

institute: Fudan University

description: Library name: SC5314-3

data_processing:
Raw sequencing data were quality-assessed with FastQC (v0.11.9).
Reads were aligned to the human reference genome (GRCh38 Ensembl99) using STAR (2.7.1a) with default parameters.
Resulting Bam files were sorted with Samtools, and count matrices were produced using featureCounts (v2.0.1).
Differential gene expression analysis was performed using DESeq2 (v1.38.3) in R.
Assembly: 10x Genomics refdata-gex-GRCh38-2020-A
Supplementary files format and content: A file in CSV format containing RNA expression counts of all groups.

source_name: vaginal epithelium

extract_protocol:
Total RNA was extracted from organoids using the RNAprep Pure Micro Kit (Tiangen Biochemical Technology)
RNA-seq libraries were constructed on the Illumina Novaseq 6000.

value: vaginal epithelium


title: C1

description: Library name: C1


title: PDX474.7_1252_21_U3_7d_13L


title: C3

description: Library name: C3


title: C2

description: Library name: C2


title: 83P-3

description: Library name: 83P-3


title: SC5314-2

description: Library name: SC5314-2


title: SC5314-1

description: Library name: SC5314-1


title: PDX474.7_1251_21_U3_24h_11L


title: P1-D08

description: Library name: Sample44


title: PDX474.2_1262_21_CNTL_1L


title: 83P-2

description: Library name: 83P-2


title: PDX474.2_1055_20_CNTL_1L_rep2


title: P1-D07

description: Library name: Sample43


title: PDX474.2_1055_20_CNTL_1L_rep1


title: P1-D06

description: Library name: Sample42


title: PDX474.2_CNTL_passage_1_56B1


title: PDX474.2_1262_21_U3_24h_11R


title: PDX474.1_1062_20_CNTL_1R


title: 48T-1

description: Library name: 48T-1


title: P1-D05

description: Library name: Sample41


title: P1-D02

description: Library name: Sample38


title: 48T-2

description: Library name: 48T-2


title: 39A-2

description: Library name: 39A-2


title: P1-D04

description: Library name: Sample40


title: 48T-3

description: Library name: 48T-3


title: PDX474.1_CNTL_passage_3_E755


title: P1-D01

description: Library name: Sample37


title: PDX457_1039_20_CNTL_1R


title: PDX456.2_1355_22_CNTL_1L


title: 39A-3

description: Library name: 39A-3


title: 39A-1

description: Library name: 39A-1


title: PDX457_1223_21_CNTL_1R


title: PDX474.1_1015_20_CNTL_1L


title: P1-C12

description: Library name: Sample36


title: 83P-1

description: Library name: 83P-1


title: 27G-3

description: Library name: 27G-3


title: PDX474.2_1100_20_U3_7d_11L


title: P1-D03

description: Library name: Sample39


title: P1-C11

description: Library name: Sample35


title: PDX044_1010_20_CNTL_1L


title: PDX044_1060_20_CNTL_1R


title: PDX456.2_CNTL_passage_X_X


title: PDX457_CNTL_passage_1_73DB


title: 27G-2

description: Library name: 27G-2


title: P1-C10

description: Library name: Sample34


title: 27G-1

description: Library name: 27G-1


title: P1-C09

description: Library name: Sample33


title: P1-C07

description: Library name: Sample31


title: P05

city: Beijing

first: Xin

last: Hong

address: No.1 Life Garden Road, Zhongguancun Life Science Park

department: Urology

institute: Peking University International Hospital

description: Library name: HIGH S08

data_processing:
The  reads were alternative alignment with RNASeQC，The raw data were filtered to exclude low-quality reads.
Qualified reads were mapped to the human reference genome(GRCh38) by using STAR
Caculate  the count of each gene
Estimate the RNA expression level by TPM
Ensembl primary assembly, version GRCh38
Assembly: tab-delimited CSV files include raw counts for all Samples
Supplementary files format and content: tab.deimited CSV file includes TPM values for all Samples

source_name: tumor tissue

growth_protocol: Bladder cancer tissue samples were surgically resected from patients diagnosed with bladder cancer during their clinical surgical procedures, serving as the primary material for subsequent molecular and pathological analyses.

extract_protocol:
Frozen tissues were homogenized using liquid nitrogen-cooled grinders. Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, cat#74104, Germany), followed by DNase treatment to eliminate genomic DNA. RNA quality was assessed by spectrophotometry (A260/A280 ratio ≥1.8) and a bioanalyzer (RNA Integrity Number,RIN ≥7)
Libraries were amplified using TruSeq™ RNA and DNA Library Preparation Kits v2 (Illumina, cat# RS-122-2001, USA),and RNA sequencing.

treatment_protocol: The collected  tissues were immediately placed into 1.5 mL RNA-later buffer for RNA stabilization, sealed, and cryopreserved at -20 °C.

value: tumor tissue

value: high grade


title: P01

description: Library name: HIGH S07


title: P1-C08

description: Library name: Sample32


title: P08

description: Library name: control06

value: low grade


title: P1-C06

description: Library name: Sample30


title: PDX044_1060_20_U3_7d_11R


title: PDX404_1036_20_CNTL_1R


title: PDX039_1107_20_CNTL_1R


title: PDX404_1080_20_CNTL_1R


title: PDX039_1107_20_U3_7d_11L


title: P07

description: Library name: control05


title: PDX039_1183_21_U3_24h_11L


title: PDX039_1029_20_CNTL_1L


title: P1-C05

description: Library name: Sample29


title: PDX044_1269_21_U3_24h_11R


title: PDX044_1010_20_CNTL_1R


title: PDX044_1269_21_CNTL_1R


title: PDX350.2_1038_20_CNTL_1R


title: P06

description: Library name: control04


title: P04

description: Library name: control03


title: PDX350.2_1234_21_CNTL_3R


title: P1-C04

description: Library name: Sample28


title: PDX350.2_CNTL_passage_3_6406


title: PDX346_1089_20_CNTL_2R


title: PDX039_1183_20_CNTL_1L


title: PDX346_990_20_CNTL_2L


title: PDX346_1089_20_U3_7d_12R


title: P1-C03

description: Library name: Sample27


title: PDX346_1261_21_U3_24h_11R


title: P1-C02

description: Library name: Sample26


title: PDX343_1283_21_CNTL_1L


title: PDX343_1012_20_CNTL_1L


title: P03

description: Library name: control02


title: Patient 8, GBM, Sample 1, Enhancing

city: Ann Arbor

first: Wajd

middle: N.

last: Al-Holou

state: MI

address: 1500 E Medical Center Dr

department: Neurosurgery

institute: University of Michigan

description:
Library name: 6473_SS_1
10X Genomics

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files and the Cell Ranger Pipeline (version 7.1.0) was used to align reads and generate count matrices.
Assembly: Human reference transcriptome from Cell Ranger, 10X Genomics (GRCh38-2020-A)
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Brain tumor

extract_protocol:
Human tumor samples were dissociated into single cells utilizing Accutase dissociation reagent (Gibco, NH). Cells were passed through a 70µm strainer (Alkali Inc), centrifuged, and resuspended followed by application of RBC lysis buffer (Biolegend).
Single cell suspensions were subjected to counting on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 1000 cells/µL. Single cell 3’ gene expression libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol. In brief, suspensions were loaded onto the 10x chip along with reverse transcription (RT) master mix and appropriate gel beads. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed, and the resulting Post GEM-RT product was cleaned up and the cDNA amplified. cDNA was subjected to enzymatic fragmentation and size selection to optimize the cDNA size prior to final library construction following the manufacturer’s protocol (10x Genomics; 3’ v3 (patient). Final library quality was assessed using the LabChip GX (PerkinElmer). Pooled libraries were then subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000).

value: Brain tumor

tag: diagnosis

value: GBM

value: IDH WT

value: Male


title: PDX343_1283_22_U3_7d_11L


title: Patient 7, GBM, Sample 1, Non-Enhancing

description:
Library name: 6369_SS_1
10X Genomics


title: Patient 7, GBM, Sample 2, Enhancing

description:
Library name: 6369_SS_2
10X Genomics


title: P1-B12

description: Library name: Sample24


title: PDX343_1365_22_U3_24h_11L


title: PDX341_1369_22_CNTL_3L


title: P1-B11

description: Library name: Sample23


title: Patient 6, H3G34 Mutant HGG, Sample 2, Non-Enhancing

description:
Library name: 6025_SS_2
10X Genomics

value: Diffuse hemispheric glioma, IDH wild-type, WHO Grade 4


title: PDX288_1069_20_CNTL_1R


title: P1-B09

description: Library name: Sample21


title: PDX313_1028_20_CNTL_1L


title: PDX313_1168_21_CNTL_1L_NOOVX


title: PDX288_1101_20_CNTL_1L


title: PDX288_1069_20_U3_7d_11R


title: Patient 6, H3G34 Mutant HGG, Sample 1, Enhancing

description:
Library name: 6025_SS_1
10X Genomics


title: Patient 4, Oligodendroglioma, Sample 2, Non-Enhancing

description:
Library name: 5675_SS_2
10X Genomics

value: Oligodendroglioma, IDH mutant, 1p/19q codeleted, WHO Grade 3

value: IDH mutant

value: Female


title: PDX244_1052_20_CNTL_1L

value: Untreated

value: Relapsed


title: PDX288_1361_22_U3_24h_11L

value: HER3-DXd 10mg-kg

value: Non-relapsed


title: PDX244_1058_20_U3_7d_7DD6R


title: PDX244_1058_20_CNTL_7F54L


title: P1-B07

description: Library name: Sample19

value: In vitro differentiated neurons

value: day in vitro 7


title: P1-B08

description: Library name: Sample20


title: Patient 4, Oligodendroglioma, Sample 1, Enhancing

description:
Library name: 5675_SS_1
10X Genomics


title: PDX244_1150_21_U3_24h_11R


title: P1-C01

description: Library name: Sample25


title: PDX225_1220_21_CNTL_2L


title: PDX225_1011_20_CNTL_1L


title: PDX225_1011_20_CNTL_1R


title: P1-B06

description: Library name: Sample18


title: P02

description: Library name: control01

value: tumor tissue


title: P1-B10

description: Library name: Sample22


title: Patient 2, GBM, Sample 2, Enhancing

description:
Library name: 5363_SR_2
10X Genomics


title: Patient 2, GBM, Sample 1, Enhancing

description:
Library name: 5363_SR_1
10X Genomics


title: P1-B04

description: Library name: Sample16


title: PDX179_1323_23_U3_7d_11L


title: Patient 1, GBM, Sample 3, Enhancing

description:
Library name: 4554_DH_3
10X Genomics


title: PDX131_1264_21_CNTL_1R


title: Patient 1, GBM, Sample 2, Enhancing

description:
Library name: 4554_DH_2
10X Genomics


title: P1-B02

description: Library name: Sample14


title: P1-B03

description: Library name: Sample15


title: PDX131_1025_20_CNTL_4L


title: PDX131_1025_20_CNTL_2L


title: PDX179_1401_23_U3_24h_11R


title: Patient 1, GBM, Sample 1, Non-Enhancing

description:
Library name: 4554_DH_1
10X Genomics


title: PDX131_1086_20_U3_7d_12R


title: PDX131_1264_21_U3_24h_11L


title: PDX127_1073_20_CNTL_1L


title: P1-B01

description: Library name: Sample13


title: PDX127_1156_21_CNTL_74DDL


title: PDX127_1085_20_CNTL_2L


title: P1-A12

description: Library name: Sample12


title: Vascular fraction, AD, donor 40

city: Cardiff

first: Gabriel Mateus

last: Bernardo Harrington

address: 52 Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

description: Library name: V_40

data_processing:
The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
Assembly: GRCh38
Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata

source_name: Prefrontal cortex

extract_protocol:
1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).

value: Prefrontal cortex

tag: batch


title: P1-B05

description: Library name: Sample17


title: P1-A11

description: Library name: Sample11


title: Vascular fraction, AD, donor 39

description: Library name: V_39


title: PDX179_1401_23_CNTL_1L


title: Parenchymal fraction, AD, donor 40

description: Library name: P_40


title: PDX124_1057_20_CNTL_1L


title: PDX124_1141_20_CNTL_3L


title: PDX124_1051_20_CNTL_1L


title: PDX124_1057_20_U3_7d_11R


title: PDX124_1148_21_U3_24h_11L


title: P1-A09

description: Library name: Sample09


title: Vascular fraction, Control, donor 38

description: Library name: V_38


title: FTA-23-Plasma-Long-RNA

city: Chengdu

first: Genpeng

state: AA

address: Guoxuexiang 37

institute: West china hospital

description:
Long RNA-seq of homo sapiens: follicular thyroid adenoma patient's plasma RNA; Provided by West China Hospital;  Constructed by SMARTer Stranded Total RNA-seq Kit v3; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
Plasma RNA

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remained reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences, and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off. Read pairs with an average quality score below 30 in either read were removed.
STAR (version 2.5.4a) was used to map clean reads to the hg38 genome index built with the GENCODE v38 annotation
Duplicates in the aligned reads were removed using umi_tools(v1.1.2)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v38 annotation, circular RNA annotation from circBase, intron, and intergenic regions from UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: plasma

extract_protocol:
Small cell-free RNA was extracted using miRNeasy Serum/Plasma Kit (Qiagen) while long RNA was extracted with a QIAzol (Qiagen) lysis, phenol-chloroform extraction, and isopropanol precipitation approach.
Small RNA libraries were prepared with a QIAseq miRNA Library Kit (Qiagen) while long RNA libraries were prepared using a SMARTer Stranded Total RNA-seq Kit v3 - Pico Input Mammalian Components (Takara).

value: plasma

tag: disease

value: follicular thyroid adenoma

tag: gender

value: male

tag: Stage


title: Parenchymal fraction, Control, donor 38

description: Library name: P_38


title: FTA-20-Plasma-Long-RNA


title: FTA-24-Plasma-Long-RNA

value: female


title: FTA-18-Plasma-Long-RNA


title: P1-A08

description: Library name: Sample08


title: P1-A07

description: Library name: Sample07


title: FTA-17-Plasma-Long-RNA


title: FTA-16-Plasma-Long-RNA


title: FTA-13-Plasma-Long-RNA


title: Vascular fraction, AD, donor 37

description: Library name: V_37


title: FTA-15-Plasma-Long-RNA


title: FTA-12-Plasma-Long-RNA


title: P1-A10

description: Library name: Sample10


title: Vascular fraction, Control, donor 36

description: Library name: V_36


title: FTA-9-Plasma-Long-RNA


title: P1-A05

description: Library name: Sample05


title: FTA-10-Plasma-Long-RNA


title: Parenchymal fraction, AD, donor 37

description: Library name: P_37


title: Parenchymal fraction, Control, donor 36

description: Library name: P_36


title: FTA-5-Plasma-Long-RNA


title: FTA-6-Plasma-Long-RNA


title: Vascular fraction, Control, donor 35

description: Library name: V_35


title: P1-A04

description: Library name: Sample04


title: FTA-4-Plasma-Long-RNA


title: P1-A06

description: Library name: Sample06


title: Parenchymal fraction, Control, donor 35

description: Library name: P_35


title: FTA-2-Plasma-Long-RNA


title: P1-A02

description: Library name: Sample02


title: P1-A03

description: Library name: Sample03


title: FTA-1-Plasma-Long-RNA


title: FTC-20-Plasma-Long-RNA

description:
Long RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma RNA; Provided by West China Hospital;  Constructed by SMARTer Stranded Total RNA-seq Kit v3; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
Plasma RNA

value: follicular thyroid carcinoma

value: I


title: FTC-22-Plasma-Long-RNA

value: IV


title: FTC-21-Plasma-Long-RNA

value: II


title: P1-A01

description: Library name: Sample01


title: FTA-11-Plasma-Long-RNA


title: Vascular fraction, AD, donor 33

description: Library name: V_33


title: FTC-18-Plasma-Long-RNA


title: FTC-17-Plasma-Long-RNA

value: III


title: Parenchymal fraction, Control, donor 34

description: Library name: P_34


title: FTC-16-Plasma-Long-RNA


title: Parenchymal fraction, AD, donor 33

description: Library name: P_33


title: Clasp1-A_EX_ESC_rep2

description: Library name: Sample26

data_processing:
Paired-end sequencing reads were quality-trimmed using Trimmomatic v0.33 (Bolger et al. 2014). The trimming pipeline utilized the TruSeq2 adapter sequences for clipping (ILLUMINACLIP:2:30:10), removed trailing bases with quality scores below 3 (TRAILING:3), and discarded reads shorter than 36 bp (MINLEN:36).
Transcript quantification was performed using Salmon (v1.10.3) (Patro et al. 2018) with an index built from the GCvM21 transcriptome. Read pairs were mapped to the reference index with sequence and GC bias correction (--seqBias --gcBias), and mappings were validated (--validateMappings).
Assembly: mm10
Supplementary files format and content: Gene-level quantifications output from Salmon (v1.10.3)

source_name: CGR8 mouse embryonic stem cells

growth_protocol: CGR8 mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in GMEM supplemented with 100 μM β-mercaptoethanol, 0.1 mM nonessential amino acids, 2 mM sodium pyruvate, 5 000 units ml–1 of penicillin/streptomycin, 1,000 units ml–1 of recombinant mouse LIF (all Life Technologies) and 10% ES fetal calf serum (Wisent). Cells were passaged using Trypsin (Life Technologies) and maintained at subconfluent conditions at 37 °C and 5% CO2. Cells were regularly monitored for mycoplasma infection. In vitro differentiation of CGR8 mESCs into neurons was performed as previously described (Gueroussov et al., 2015; Hubbard et al., 2013). At day in vitro (DIV) -8, 5.1x106 cells were seeded on 15cm non-tissue-culture-treated plates containing 30mL of serum-free differentiation media (GMEM containing 5% KnockOut Serum replacement (Thermo Fisher Scientific), 0.1 mM nonessential amino acids, 1mM sodium pyruvate, 5 000 units ml–1 of penicillin/streptomycin and 100mM b-mercaptoethanol). Cells were incubated for 3 days undisturbed. 50% media changes were conducted every 48 hours. At DIV -5 the media was supplemented with 6mM retinoic acid (RA) with subsequent media changes also contained 6mM RA. At DIV 0, cellular aggregates were dissociated with TrypLE Express (Gibco) for 5 minutes at 37°C. Trypsinization was halted with soybean trypsin inhibitor (Thermo Fisher Scientific) and aggregates were homogenized by trituration with a micropipette. Cells were pelleted for 5 minutes at 300xg. Neural progenitors were washed in N2 medium (Neurobasal-A medium [Gibco] with 1x N2 supplement: 2 mM glutamine and 5 000 units ml–1 of penicillin/streptomycin [Gibco]), counted using a hemocytometer, and plated at a density of 1.5x105cells/cm2 onto poly-D-Lysine and Laminin-coated dishes. The plated neural progenitors were washed with N2 medium after 24 hours to remove residual serum and non-adherent cells. At DIV2, the N2 medium was replaced with B27 medium (Neurobasal-A supplemented with antibiotics, 2mM glutamine and 1xB27 supplement [Gibco]). Subsequently, differentiating neurons were provided with full medium changes with B27 on DIV4, and every 3 days onward.

extract_protocol:
Total RNA was extracted with the Qiagen RNasy Mini kit with on-column DNAse treatment.
500 ng of total RNA was used to generate  polyA+ stranded RNA-seq libraries with the NEB Next Ultra II Directional kit. 150 nucleotide paired end reads were sequenced on an Illumina NovaSeq 6000 at an average depth of 25 million reads.

value: CGR8 mouse embryonic stem cells

value: mouse embryonic stem cells

value: Exclusion of Clasp1-A microexon by dCasRx-RBM25

value: mESC


title: Clasp1-A_INC_ESC_rep1

description: Library name: Sample27

value: Inclusion of Clasp1-A microexon by dCasRx-RBM25


title: FTC-13-Plasma-Long-RNA


title: Clasp1-A_EX_ESC_rep1

description: Library name: Sample25


title: FTA-3-Plasma-Long-RNA


title: Vascular fraction, AD, donor 32

description: Library name: V_32


title: Parenchymal fraction, AD, donor 32

description: Library name: P_32


title: Vascular fraction, Control, donor 34

description: Library name: V_34


title: Camta1_INC_ESC_rep2

description: Library name: Sample24

value: Inclusion of Camta1 microexon by dCasRx-RBM25


title: FTC-14-Plasma-Long-RNA


title: FTC-12-Plasma-Long-RNA


title: FTC-10-Plasma-Long-RNA


title: Clasp1-A_INC_ESC_rep2

description: Library name: Sample28


title: Parenchymal fraction, Control, donor 31

description: Library name: P_31


title: FTC-7-Plasma-Long-RNA


title: FTC-8-Plasma-Long-RNA


title: FTC-19-Plasma-Long-RNA


title: Camta1_INC_ESC_rep1

description: Library name: Sample23


title: FTC-6-Plasma-Long-RNA


title: Vascular fraction, Control, donor 30

description: Library name: V_30


title: Camta1_EX_ESC_rep1

description: Library name: Sample21

value: Exclusion of Camta1 microexon by dCasRx-RBM25


title: FTC-15-Plasma-Long-RNA


title: FTC-5-Plasma-Long-RNA


title: FTC-4-Plasma-Long-RNA


title: FTC-3-Plasma-Long-RNA


title: WT_wt_DIV7_b1

description: Library name: Sample20

source_name: Neurons derived in vitro from mouse embryonic stem cells

value: In vitro differentiated neurons

value: WT

value: day in vitro (DIV) 7


title: Parenchymal fraction, Control, donor 30

description: Library name: P_30

value: Prefrontal cortex


title: FTC-2-Plasma-Long-RNA

value: plasma

value: female


title: FTC-1-Plasma-Long-RNA

value: follicular thyroid carcinoma

value: I


title: Parenchymal fraction, Control, donor 29

description: Library name: P_29


title: FTA-24-Plasma-Small-RNA

description:
Small RNA-seq of homo sapiens: follicular thyroid adenoma patient's plasma RNA; Provided by West China Hospital;  Constructed by QIAseq miRNA Library Kit; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
Plasma RNA

value: follicular thyroid adenoma


title: FTA-23-Plasma-Small-RNA

value: male


title: Gfra1_Hom_DIV7_c13

description: Library name: Sample18

value: Neurons derived in vitro from mouse embryonic stem cells

value: Gfra1 micrexon homozygous deletion

value: Homozygous deletion of Gfra1 microexon with Cas9


title: FTC-11-Plasma-Long-RNA

value: IV


title: Vascular fraction, AD, donor 28

description: Library name: V_28


title: Camta1_EX_ESC_rep2

description: Library name: Sample22

value: CGR8 mouse embryonic stem cells

value: mouse embryonic stem cells

value: mESC


title: FTA-20-Plasma-Small-RNA


title: FTA-17-Plasma-Small-RNA


title: Gfra1_Hom_DIV7_c5

description: Library name: Sample17

value: In vitro differentiated neurons


title: Vascular fraction, AD, donor 27

description: Library name: V_27


title: FTA-15-Plasma-Small-RNA


title: Ptprf-A_INC_DIV7_rep2

description: Library name: Sample16

value: Inclusion of Ptprf-A microexon by dCasRx-RBM25


title: FTA-13-Plasma-Small-RNA


title: Parenchymal fraction, AD, donor 28

description: Library name: P_28


title: FTA-16-Plasma-Small-RNA


title: Ptprf-A_INC_DIV7_rep1

description: Library name: Sample15

value: day in vitro (DIV) 7


title: Parenchymal fraction, AD, donor 27

description: Library name: P_27

value: Prefrontal cortex


title: Vascular fraction, Control, donor 29

description: Library name: V_29


title: Ptprf-A_EX_DIV7_rep2

description: Library name: Sample14

value: Exclusion of Ptprf-A microexon by dCasRx-RBM25


title: FTA-11-Plasma-Small-RNA

value: plasma

value: female


title: FTA-12-Plasma-Small-RNA


title: WT_wt_DIV7_e5

description: Library name: Sample19

value: WT


title: FTA-10-Plasma-Small-RNA

value: follicular thyroid adenoma


title: Vascular fraction, AD, donor 26

description: Library name: V_26


title: FTA-9-Plasma-Small-RNA


title: Ptprf-A_EX_DIV7_rep1

description: Library name: Sample13


title: Parenchymal fraction, AD, donor 26

description: Library name: P_26


title: FTA-5-Plasma-Small-RNA


title: Vascular fraction, Control, donor 31

description: Library name: V_31


title: FTA-18-Plasma-Small-RNA


title: Vascular fraction, Control, donor 25

description: Library name: V_25


title: Ptk2-A_INC_DIV7_rep2

description: Library name: Sample12

value: Inclusion of Ptk2-A microexon by dCasRx-RBM25


title: FTA-1-Plasma-Small-RNA


title: Ptk2-A_INC_DIV7_rep1

description: Library name: Sample11

value: Neurons derived in vitro from mouse embryonic stem cells


title: FTC-22-Plasma-Small-RNA

description:
Small RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma RNA; Provided by West China Hospital;  Constructed by QIAseq miRNA Library Kit; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
Plasma RNA

value: follicular thyroid carcinoma


title: FTA-2-Plasma-Small-RNA

value: male


title: FTA-4-Plasma-Small-RNA


title: FTC-20-Plasma-Small-RNA

value: I


title: FTA-3-Plasma-Small-RNA


title: Ptk2-A_EX_DIV7_rep2

description: Library name: Sample10

value: Exclusion of Ptk2-A microexon by dCasRx-RBM25


title: FTC-21-Plasma-Small-RNA

value: II


title: Parenchymal fraction, Control, donor 25

description: Library name: P_25


title: FTC-19-Plasma-Small-RNA


title: Vascular fraction, AD, donor 24

description: Library name: V_24


title: FTA-6-Plasma-Small-RNA


title: Clasp1-A_INC_DIV7_rep1

description: Library name: Sample07

value: Inclusion of Clasp1-A microexon by dCasRx-RBM25


title: FTC-18-Plasma-Small-RNA


title: Parenchymal fraction, AD, donor 24

description: Library name: P_24


title: Clasp1-A_INC_DIV7_rep2

description: Library name: Sample08

value: In vitro differentiated neurons


title: FTC-17-Plasma-Small-RNA

value: III


title: Vascular fraction, Control, donor 23

description: Library name: V_23


title: FTC-16-Plasma-Small-RNA


title: FTC-15-Plasma-Small-RNA


title: Vascular fraction, AD, donor 22

description: Library name: V_22


title: FTC-13-Plasma-Small-RNA


title: Parenchymal fraction, Control, donor 23

description: Library name: P_23


title: Clasp1-A_EX_DIV7_rep2

description: Library name: Sample06

value: Exclusion of Clasp1-A microexon by dCasRx-RBM25

value: day in vitro (DIV) 7


title: Clasp1-A_EX_DIV7_rep1

description: Library name: Sample05


title: FTC-12-Plasma-Small-RNA


title: FTC-14-Plasma-Small-RNA


title: Parenchymal fraction, AD, donor 22

description: Library name: P_22

value: Prefrontal cortex


title: Ptk2-A_EX_DIV7_rep1

description: Library name: Sample09


title: Camta1_INC_DIV7_rep2

description: Library name: Sample04

value: Inclusion of Camta1 microexon by dCasRx-RBM25


title: FTC-10-Plasma-Small-RNA

value: plasma

value: female

value: IV


title: FTC-11-Plasma-Small-RNA


title: Vascular fraction, Control, donor 21

description: Library name: V_21


title: FTC-8-Plasma-Small-RNA


title: Camta1_INC_DIV7_rep1

description: Library name: Sample03


title: FTC-7-Plasma-Small-RNA


title: Parenchymal fraction, Control, donor 21

description: Library name: P_21


title: FTC-6-Plasma-Small-RNA


title: FTC-5-Plasma-Small-RNA


title: Camta1_EX_DIV7_rep2

description: Library name: Sample02

value: Exclusion of Camta1 microexon by dCasRx-RBM25


title: FTC-4-Plasma-Small-RNA


title: FTC-3-Plasma-Small-RNA


title: PDX044_1060_20_CNTL_1R

description:
Library name: AV8844
PDX044_1060_20_CNTL_1R

data_processing:
Raw RNA-seq data was mapped against human reference genome of human (GRCh38) using STAR 2.7.10a using ENCODE parameters.
Quantification of annotated genes was conducted using human GENCODE v39 with software RSEM version 1.3.0 and default parameters.
Assembly: GRCh38
Supplementary files format and content: Raw counts for each sample in Excel xlsx format

source_name: Breast Cancer Patient Derived Mouse Xenograft

extract_protocol:
RNeasy Mini Kit (#74106, Qiagen)
KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche)

value: Untreated


title: FTC-2-Plasma-Small-RNA

value: follicular thyroid carcinoma


title: Camta1_EX_DIV7_rep1

description: Library name: Sample01

value: Neurons derived in vitro from mouse embryonic stem cells


title: FTC-1-Plasma-Small-RNA

value: I


title: BMDM_LPS+CS+Torin_03

city: Memphis

first: Thirumala-Devi

last: Kanneganti

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Read trimming was done by TrimGalore, and read alignment to the mouse genome (gencode vM22) was performed with STAR (version 2.7) software81. Strand specific gene level read count was determined using RSEM (version 1.3.1) software82. The transcript count table was normalized and log-transformed by DEseq2 packages79 for further differential expression analysis in R.
Assembly: gencode vM22
Supplementary files format and content: csv, raw count table

source_name: BMDM

extract_protocol:
The RNA extraction was done using TRIzol reagent (Invitrogen, 15596026) following the manufacturer’s protocol from BMDMs stimulated by indicated stimulations for 9 h.
RNA was quantified using the Quant-iT RiboGreen RNA assay (Thermo Fisher Scientific) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.  Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina PN 20020595). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Thermo Fisher Scientific ) or by low pass sequencing with a MiSeq nano kit (Illumina).

value: BMDM

value: WT

value: LPS+CS+Torin


title: PDX127_1134_21_CNTL_1R

description:
Library name: ABA41389
PDX127_1134_21_CNTL_1R

value: Breast Cancer Patient Derived Mouse Xenograft


title: PDX288_1069_20_CNTL_1R

description:
Library name: AV8847
PDX288_1069_20_CNTL_1R


title: FTA-23-EV-Long-RNA

description:
Long RNA-seq of homo sapiens: follicular thyroid adenoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by SMARTer Stranded Total RNA-seq Kit v3; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA

value: follicular thyroid adenoma

value: male


title: FTA-20-EV-Long-RNA


title: BMDM_LPS+CS+Torin_01


title: PDX098_1056_20_CNTL_2R

description:
Library name: AV8846
PDX098_1056_20_CNTL_2R


title: FTA-19-EV-Long-RNA


title: BMDM_LPS+CS+Torin_02


title: FTA-18-EV-Long-RNA


title: BMDM_LPS+CS_03

value: LPS+CS


title: FTA-16-EV-Long-RNA


title: BMDM_LPS+CS_02


title: PDX060_1096_21_CNTL_2L

description:
Library name: AV8845
PDX060_1096_21_CNTL_2L


title: FTA-17-EV-Long-RNA


title: PDX491_1209_21_CNTL_1L

description:
Library name: AW0250
PDX491_1209_21_CNTL_1L


title: FTA-14-EV-Long-RNA


title: FTA-15-EV-Long-RNA


title: BMDM_LPS+CS_01


title: PDX225_491_16_CNTL_1R

description:
Library name: AW0261
PDX225_491_16_CNTL_1R


title: FTA-12-EV-Long-RNA


title: FTA-11-EV-Long-RNA


title: FTA-24-EV-Long-RNA


title: FTA-13-EV-Long-RNA


title: PDX474.7_969_20_CNTL_1R

description:
Library name: AV8840
PDX474.7_969_20_CNTL_1R


title: BMDM_CS_03

value: CS


title: BMDM_CS_02


title: FTA-10-EV-Long-RNA


title: FTA-9-EV-Long-RNA


title: FTA-6-EV-Long-RNA


title: BMDM_CS_01


title: FTA-5-EV-Long-RNA


title: BMDM_LPS_03

value: LPS


title: FTA-4-EV-Long-RNA

value: plasma


title: PDX583.2_passage_3_83B0

description:
Library name: ABA41564
PDX583.2_passage_3_83B0


title: FTA-3-EV-Long-RNA


title: FTA-2-EV-Long-RNA


title: PDX527_1236_21_CNTL_1R

description:
Library name: AW0253
PDX527_1236_21_CNTL_1R


title: BMDM_LPS_02


title: PDX509_1070_20_CNTL_1L

description:
Library name: AV8850
PDX509_1070_20_CNTL_1L


title: FTC-22-EV-Long-RNA

description:
Long RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by SMARTer Stranded Total RNA-seq Kit v3; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA

value: female


title: PDX313_1068_20_CNTL_1R

description:
Library name: AV8861
PDX313_1068_20_CNTL_1R


title: FTC-20-EV-Long-RNA


title: BMDM_LPS_01


title: BMDM_Media_03

value: Media


title: FTC-19-EV-Long-RNA


title: PDX474.1_1067_20_CNT_1L

description:
Library name: AV8834
PDX474.1_1067_20_CNT_1L


title: PDX244_1058_20_CNTL_1L

description:
Library name: AW0227
PDX244_1058_20_CNTL_1L


title: PDX474.2_1031_20_CNTL_1L

description:
Library name: AV8836
PDX474.2_1031_20_CNTL_1L


title: BMDM_Media_01


title: FTC-15-EV-Long-RNA

value: II


title: FTC-16-EV-Long-RNA


title: BMDM_Media_02


title: PDX124_236_15_2R

description:
Library name: AV8780
PDX124_236_15_2R

value: Untreated


title: PDX343_passage_6_8F65

description:
Library name: AW0232
PDX343_passage_6_8F65


title: FTC-13-EV-Long-RNA

value: follicular thyroid carcinoma


title: FTC-12-EV-Long-RNA


title: FTC-14-EV-Long-RNA


title: PDX512_1248_21_CNTL_1L

description:
Library name: AW0252
PDX512_1248_21_CNTL_1L


title: iPS 3D CD4-/CD8-/CD5+ iNKT #2

city: Kyoto

first: Shin

last: Kaneko

state: Kyoto

address: 53 shogoin Kawaharacho Sakyo-ku

country: Japan

institute: Kyoto University

description: Library name: IonCode_0129

data_processing:
From the sequencing output, quality control, alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts and the normalization (counts per million, CPM) for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1
Data scaling of AmpliSeq count data were performed by using Transcriptome Analysis Console.
Assembly: hg19
Supplementary files format and content: csv file

source_name: iPSC-derived iNKT cells

growth_protocol: iPSCs were first induced to differentiate into hematopoietic progenitor cells, generating CD4SP cells, CD4-/CD8-/CD5+ cells, and CD4-/CD8-/CD5- cells in 3D culture, and CD4-/CD8-/CD5- cells in 2D culture. These induced cells were expanded on αGalCer-pulsed PBMCs in the presence of IL-2. Primary iNKT cells were FACS-sorted from human PBMCs and stimulated as described above.

extract_protocol:
RNA was extracted from up to 100K  cells using Nucleospin XS and cRNA was prepared using SuperScript® VILO™ cDNA Synthesis Kit   ( Lifetechnologies  11754050 or 11754250)
Libraries were preprared using Ion AmpliSeq™ Transcriptome Human Gene Expression Core Panel as manufacturer's instruction by ThermoFischer Scientific targeted RNA-sequencing

treatment_protocol: primary iNKT cells and 3D culture or 2D culture of defferentiation from iPSCs

value: iPSC-derived iNKT cells

value: iPSC line

value: 3D culture


title: FTC-21-EV-Long-RNA


title: FTC-11-EV-Long-RNA

value: IV


title: iPS 3D CD4-/CD8-/CD5+ iNKT #3

description: Library name: IonCode_0130


title: FTC-10-EV-Long-RNA


title: PDX350.2_1038_20_CNTL_1R

description:
Library name: AW0239
PDX350.2_1038_20_CNTL_1R


title: FTA-1-EV-Long-RNA

description:
Long RNA-seq of homo sapiens: follicular thyroid adenoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by SMARTer Stranded Total RNA-seq Kit v3; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA


title: PDX039_1176_21_CNTL_1R

description:
Library name: AW0223
PDX039_1176_21_CNTL_1R


title: iPS 3D CD4-/CD8-/CD5+ iNKT #1

description: Library name: IonCode_0128


title: FTC-6-EV-Long-RNA

value: I


title: PDX456.2_1157_21_CNTL_2L

description:
Library name: AW0256
PDX456.2_1157_21_CNTL_2L

value: Breast Cancer Patient Derived Mouse Xenograft


title: FTC-18-EV-Long-RNA


title: FTC-17-EV-Long-RNA

value: III


title: PBMC CD4-/CD8- iNKT #3

description: Library name: IonCode_0127

source_name: human iNKT cells

value: human iNKT cells

value: primary tissue


title: FTC-8-EV-Long-RNA

value: male


title: FTC-5-EV-Long-RNA


title: PBMC CD4-/CD8- iNKT #2

description: Library name: IonCode_0126


title: FTC-4-EV-Long-RNA


title: PBMC CD4-/CD8- iNKT #1

description: Library name: IonCode_0125


title: FTC-2-EV-Long-RNA


title: PDX490_1181_21_CNTL_2L

description:
Library name: AW0249
PDX490_1181_21_CNTL_2L


title: FTC-3-EV-Long-RNA


title: FTA-24-EV-Small-RNA

description:
Small RNA-seq of homo sapiens: follicular thyroid adenoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by QIAseq miRNA Library Kit; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA

value: follicular thyroid adenoma


title: PDX533_1205_21_CNTL_2L

description:
Library name: AV8851
PDX533_1205_21_CNTL_2L


title: iPS 3D CD4-/CD8-/CD5- iNKT #3

description: Library name: IonCode_0123


title: FTA-19-EV-Small-RNA

value: plasma


title: iPS 3D CD4-/CD8-/CD5- iNKT #1

description: Library name: IonCode_0121


title: FTA-18-EV-Small-RNA

value: female


title: iPS 3D CD4-/CD8-/CD5- iNKT #2

description: Library name: IonCode_0122


title: FTC-7-EV-Long-RNA


title: FTA-20-EV-Small-RNA


title: PDX131_passage_19_5767

description:
Library name: AW0224
PDX131_passage_19_5767


title: iPS 2D iNKT #2

description: Library name: IonCode_0118


title: PDX476.2_passage_5_5423

description:
Library name: AW0251
PDX476.2_passage_5_5423


title: PDX346_1187_21_CNTL_1R

description:
Library name: AW0233
PDX346_1187_21_CNTL_1R


title: FTA-16-EV-Small-RNA


title: FTA-14-EV-Small-RNA


title: FTA-17-EV-Small-RNA


title: PDX404_1195_21_CNTL_1L

description:
Library name: AW0237
PDX404_1195_21_CNTL_1L


title: FTA-15-EV-Small-RNA


title: iPS 2D iNKT #1

description: Library name: IonCode_0117


title: FTA-12-EV-Small-RNA


title: FTC-1-EV-Long-RNA

description:
Long RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by SMARTer Stranded Total RNA-seq Kit v3; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA


title: PDX341_1481_24_U3_3_11L

description:
Library name: ABA41555
PDX341_1481_24_U3_3_11L

value: HER3-DXd 3mg-kg

tag: time


title: FTA-11-EV-Small-RNA


title: iPS 3D CD4+ iNKT #3

description: Library name: IonCode_0106


title: PDX341_1476_24_U3_3_11L

description:
Library name: ABA41554
PDX341_1476_24_U3_3_11L


title: PDX479_1078_20_CNTL_62R

description:
Library name: AW0248
PDX479_1078_20_CNTL_62R


title: FTA-10-EV-Small-RNA


title: FTA-23-EV-Small-RNA


title: iPS 3D CD4+ iNKT #2

description: Library name: IonCode_0105


title: FTA-6-EV-Small-RNA


title: FTA-9-EV-Small-RNA


title: iPS 2D iNKT #3

description: Library name: IonCode_0119


title: PDX341_1476_24_CNTL_1R

description:
Library name: ABA41553
PDX341_1476_24_CNTL_1R


title: FTA-3-EV-Small-RNA


title: FTA-4-EV-Small-RNA


title: FTA-13-EV-Small-RNA


title: FTA-2-EV-Small-RNA


title: FTA-1-EV-Small-RNA


title: iPS 3D CD4+ iNKT #1

description: Library name: IonCode_0104


title: PBMC CD4+ iNKT #3

description: Library name: IonCode_0103


title: PDX179_1401_23_CNTL_3R

description:
Library name: ABA41548
PDX179_1401_23_CNTL_3R


title: PDX179_1323_22_U3_3_21L

description:
Library name: ABA41550
PDX179_1323_22_U3_3_21L


title: FTC-22-EV-Small-RNA

description:
Small RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by QIAseq miRNA Library Kit; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA


title: FTC-21-EV-Small-RNA

value: II


title: PBMC CD4+ iNKT #2

description: Library name: IonCode_0102


title: PDX474.7_1252_21_U3_3_22R

description:
Library name: ABA41547
PDX474.7_1252_21_U3_3_22R


title: FTC-20-EV-Small-RNA


title: PDX474.7_1251_21_U3_3_22L

description:
Library name: ABA41545
PDX474.7_1251_21_U3_3_22L


title: Fibro/adipogenic progenitor (FAP) cells, 1

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

description: Library name: Sample 40

data_processing:
Count data were analyzed in Rstudio version 4.2. After filtering genes with low expression levels (mean ≤ 10), 13448 genes remained. The raw counts were then normalized and stabilized according to Anders and Huber (2010) [7580], who first introduced VST, which is recommended for medium-to-large datasets (e.g., more than 30 samples). Normalized counts were used for further analysis
Assembly: Human (Homo sapiens) GRCh38 / hg38
Supplementary files format and content: .csv

source_name: Adipose tissue

growth_protocol: iPSCs and their intermediate derivatives, along with the corresponding expanded cells, were generated and cultured as described in the Methods section.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) and treated with the DNase I kit (Qiagen) to remove any residual genomic DNA following producer's protocols. Then, 10 ng of total RNA was reverse-transcribed into single-stranded cDNA using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific)
For NGS library construction targeting the Ion AmpliSeq Transcriptome, we utilized the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (Thermo Fisher Scientific), and the Ion Chef (Thermo Fisher Scientific) instruments, following the manufacturer's protocol. Briefly, a reverse transcription master mix was prepared by combining 5X VILO Reaction Mix and 10X SuperScript III Enzyme Mix. The mix was then aliquoted into reaction plates, with 10 ng of total RNA added to each. The plates were loaded into a thermal cycler and subjected to incubation at 42°C for 30 min, followed by 85°C for 5 min, and then held at 10°C. During library preparation on the Ion Chef instruments, the following consumables and cartridges were loaded: Ion AmpliSeq Chef Solutions DL8 cartridge, Ion AmpliSeq Chef Reagents DL8 cartridge, Ion AmpliSeq Tip Cartridge L8, PCR Frame Seal, IonCode 96 Well PCR Plate, PCR Plate Frame, Empty Tip Cartridge L8, and Enrichment Cartridge. Notably, IonCode 96 Well PCR Plates used for reverse transcription reactions contained an IonCode barcode adapter. Additionally, the tube containing the Ion AmpliSeq Transcriptome Human Gene Expression Panel was inserted into an Ion AmpliSeq Chef Reagents DL8 cartridge. Multiplex PCR was performed in the thermal cycler within the Ion Chef, with 13 cycles of 16-minute annealing/extension reactions. Subsequent steps involved primer digestion with FUPA reagents, ligation of IonCode barcode adapters, library purification using magnetic beads, equalization of library concentrations, and mixing in a single tube

treatment_protocol: Both iMSCs and tMSCs were cultured on fibronectin (Millipore, Bedford, CA, USA)-coated six-well plates in PRIME-XV MSC Expansion XSFM medium (FUJIFILM Irvine Scientific, Tokyo, Japan). The cells were passaged every 3 days or when they reached 80% confluence. At each passage, iMSCs were assessed by Trypan Blue in triplicate; only cultures with ≥90% viability proceeded to downstream assays, and all lineages met this criterion.

value: Adipose tissue

value: Mesenchymal stem cells


title: FTA-5-EV-Small-RNA


title: PDX474.7_1251_21_CNTL_2R

description:
Library name: ABA41544
PDX474.7_1251_21_CNTL_2R

value: Untreated


title: Dental pulp-derived mesenchymal stem cells, 1

description: Library name: Sample 39

source_name: Dental pulp

value: Dental pulp


title: FTC-18-EV-Small-RNA

value: follicular thyroid carcinoma


title: FTC-19-EV-Small-RNA


title: PDX457_1092_20_U3_3_22R

description:
Library name: ABA41407
PDX457_1092_20_U3_3_22R


title: PDX179_1401_23_U3_3_21L

description:
Library name: ABA41549
PDX179_1401_23_U3_3_21L


title: Re-AML-MSCs#8

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from AML-MSCs of Sample 8 with CaV1.2 overexpression

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using RMA

label: biotin

source_name: Mesenchymal Stromal Cells

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher 3'IVT KIT

growth_protocol: Cells were cultured in StemMACS XF MSC expansion Media (Miltenyi Biotec).

extract_protocol: RNA was extracted after 14 days from transduction using Trizol reagent (Invitrogen, Thermo Fisher Scientific)

treatment_protocol: Cells were exposed to lentiviral particles (Vector Builder) for 18 hours with protamine sulfate (100 µg/mL in DMEM, Sigma-Aldrich-Merck).

value: AML-MSCs

value: CAV1.2 overexpressed

tag: sample

value: Re-AML-MSCs


title: PDX457_1223_21_U3_3_32L

description:
Library name: ABA41542
PDX457_1223_21_U3_3_32L

value: Breast Cancer Patient Derived Mouse Xenograft


title: FTC-17-EV-Small-RNA

value: III


title: Adipose tissue-derived mesenchymal stem cells, 1

description: Library name: Sample 36

tag: cell line


title: Re-AML-MSCs#7

description: Gene expression data from AML-MSCs of Sample 7 with CaV1.2 overexpression

tag: cell type


title: Re-AML-MSCs#6

description: Gene expression data from AML-MSCs of Sample 6 with CaV1.2 overexpression


title: PDX457_1092_20_CNTL_3R

description:
Library name: ABA41541
PDX457_1092_20_CNTL_3R

tag: tissue


title: FTC-16-EV-Small-RNA

value: I


title: Bone marrow-derived mesenchymal stem cells, 3

description: Library name: Sample 35

source_name: Bone marrow

value: Bone marrow


title: AML-MSCs#6

description: Gene expression data from AML-MSCs of Sample 6 with eGFP-mCherry control

value: control (eGFP-mCherry)


title: AML-MSCs#5

description: Gene expression data from AML-MSCs of Sample 5 with eGFP-mCherry control


title: FTC-15-EV-Small-RNA

value: plasma


title: PDX288_1069_20_U3_3_22L

description:
Library name: ABA41537
PDX288_1069_20_U3_3_22L


title: Bone marrow-derived mesenchymal stem cells, 2

description: Library name: Sample 34


title: Re-AML-MSCs#4

description: Gene expression data from AML-MSCs of Sample 4 with CaV1.2 overexpression


title: Adipose tissue-derived mesenchymal stem cells, 3

description: Library name: Sample 38


title: Re-AML-MSCs#5

description: Gene expression data from AML-MSCs of Sample 5 with CaV1.2 overexpression


title: PDX288_1361_22_U3_3_21L

description:
Library name: ABA41536
PDX288_1361_22_U3_3_21L


title: FTC-14-EV-Small-RNA

description:
Small RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by QIAseq miRNA Library Kit; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA

value: female


title: PDX288_1361_22_CNTL_2R

description:
Library name: ABA41535
PDX288_1361_22_CNTL_2R


title: PDX098_1061_20_U3_3_31L

description:
Library name: ABA41531
PDX098_1061_20_U3_3_31L

value: HER3-DXd 3mg-kg


title: Adipose tissue-derived mesenchymal stem cells, 2

description: Library name: Sample 37


title: FTC-13-EV-Small-RNA


title: Limb mesenchyme-derived mesenchymal stem cells, 2

description: Library name: Sample 32

source_name: Somatic mesoderm (Lateral plate-derived)

value: Mesoderm


title: Re-AML-MSCs#3

description: Gene expression data from AML-MSCs of Sample 3 with CaV1.2 overexpression


title: FTC-12-EV-Small-RNA


title: Limb mesenchyme-derived mesenchymal stem cells, 1

description: Library name: Sample 31

value: Somatic mesoderm (Lateral plate-derived)


title: Bone marrow-derived mesenchymal stem cells, 1

description: Library name: Sample 33

value: Mesenchymal stem cells


title: PDX098_1260_21_U3_3_22L

description:
Library name: ABA41530
PDX098_1260_21_U3_3_22L


title: Re-AML-MSCs#2

description: Gene expression data from AML-MSCs of Sample 2 with CaV1.2 overexpression


title: PDX098_1260_21_CNTL_3L

description:
Library name: ABA41529
PDX098_1260_21_CNTL_3L

value: Untreated


title: Expanded limb mesenchymal cells, 2

description: Library name: Sample 30


title: Re-AML-MSCs#1

description: Gene expression data from AML-MSCs of Sample 1 with CaV1.2 overexpression


title: FTC-10-EV-Small-RNA

value: IV


title: Expanded limb mesenchymal cells, 1

description: Library name: Sample 29


title: Placenta-derived exosomal miRNA, 1 μg/mL LPS-treated, replicate 3

city: Hangzhou

first: Yongqing

last: Zhang

state: Zhejiang

address: 1st, xueshi Road,hangzhou,zhejiang

department: Obstetrics and gynecology

institute: women's hospital school of medicine, zhejiang university

description:
Library name: Exo_lps_3
Exosomal RNA from placenta-derived exosomes (1-LPS-Pd-Exos) isolated from term placental explants cultured for 18 h in complete medium containing 1 μg/mL LPS, replicate 3.

data_processing:
Raw reads were subjected to quality control, including adaptor removal, trimming of low-quality bases, and exclusion of reads below the minimum length threshold.
Clean reads were aligned to the human reference genome and miRNA reference sequences (e.g., miRBase) using a standard small RNA analysis pipeline to obtain miRNA-level read counts.
Expression matrices were generated by summarizing mapped reads for each annotated miRNA across all libraries.
Assembly: GRCh38 (hg38)
Supplementary files format and content: No processed data files are included in this submission. All sequencing data are deposited as raw FASTQ files, which can be reprocessed using standard small RNA analysis pipelines to obtain miRNA-level counts.

source_name: placenta

growth_protocol: Term placental villous explants were cultured ex vivo in complete medium at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA enriched for small RNAs was extracted from placenta-derived exosomes using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and RNA quality and small RNA integrity were evaluated using an Agilent Bioanalyzer or an equivalent platform.
Small RNA libraries were constructed following the manufacturer’s protocol for miRNA sequencing. Briefly, 3′ and 5′ adapters were ligated to small RNAs, followed by reverse transcription and PCR amplification to generate cDNA libraries enriched for miRNAs. Size selection of library fragments corresponding to mature miRNA inserts was performed using gel- or bead-based purification. The final libraries were quantified, quality-controlled, and sequenced on an Illumina platform.

treatment_protocol: Explants were incubated either in complete medium without LPS (control) or in medium containing 1 μg/mL LPS for 18 hours prior to exosome isolation.

value: placenta

value: term placenta from uncomplicated pregnancy

value: 1 μg/mL LPS, 18 h


title: Placenta-derived exosomal miRNA, 1 μg/mL LPS-treated, replicate 4

description:
Library name: Exo_lps_4
Exosomal RNA from placenta-derived exosomes (1-LPS-Pd-Exos) isolated from term placental explants cultured for 18 h in complete medium containing 1 μg/mL LPS, replicate 4.


title: Placenta-derived exosomal miRNA, 1 μg/mL LPS-treated, replicate 2

description:
Library name: Exo_lps_2
Exosomal RNA from placenta-derived exosomes (1-LPS-Pd-Exos) isolated from term placental explants cultured for 18 h in complete medium containing 1 μg/mL LPS, replicate 2.


title: FTC-8-EV-Small-RNA

last: Li

value: follicular thyroid carcinoma

value: male

value: II


title: PDX060_1059_22_U3_3_21L

description:
Library name: ABA41528
PDX060_1059_22_U3_3_21L

value: Breast Cancer Patient Derived Mouse Xenograft


title: Placenta-derived exosomal miRNA, 1 μg/mL LPS-treated, replicate 1

description:
Library name: Exo_lps_1
Exosomal RNA from placenta-derived exosomes (1-LPS-Pd-Exos) isolated from term placental explants cultured for 18 h in complete medium containing 1 μg/mL LPS, replicate 1.


title: Limb mesenchymal cells, 2

description: Library name: Sample 28


title: PDX060_1347_22_U3_3_21R

description:
Library name: ABA41401
PDX060_1347_22_U3_3_21R


title: Placenta-derived exosomal miRNA, control, replicate 4

description:
Library name: Exo_con_4
Exosomal RNA from placenta-derived exosomes isolated from term placental explants cultured for 18 h in complete medium without LPS (control), replicate 4.

value: no LPS (complete medium only), 18h


title: FTC-7-EV-Small-RNA

value: I


title: PDX060_1347_22_CNTL_2R

description:
Library name: ABA41525
PDX060_1347_22_CNTL_2R


title: FTC-6-EV-Small-RNA

value: plasma


title: Lateral plate mesoderm-derived mesenchymal stem cells, 2

description: Library name: Sample 26

source_name: Lateral plate mesoderm

value: Lateral plate mesoderm


title: PDX044_1269_21_U3_3_22R

description:
Library name: ABA41523
PDX044_1269_21_U3_3_22R

value: HER3-DXd 3mg-kg


title: Placenta-derived exosomal miRNA, control, replicate 1

description:
Library name: Exo_con_1
Exosomal RNA from placenta-derived exosomes isolated from term placental explants cultured for 18 h in complete medium without LPS (control), replicate 1.


title: FTC-5-EV-Small-RNA

description:
Small RNA-seq of homo sapiens: follicular thyroid carcinoma patient's plasma EV RNA; Provided by West China Hospital;  Constructed by QIAseq miRNA Library Kit; Purpose: To explore novel plasma and extracellular RNA biomarkers for the diagnosis of follicular thyroid carcinoma
EV RNA


title: FTC-4-EV-Small-RNA

value: female


title: Placenta-derived exosomal miRNA, control, replicate 2

description:
Library name: Exo_con_2
Exosomal RNA from placenta-derived exosomes isolated from term placental explants cultured for 18 h in complete medium without LPS (control), replicate 2.


title: FTC-11-EV-Small-RNA


title: PDX044_1060_20_U3_3_32R

description:
Library name: ABA41524
PDX044_1060_20_U3_3_32R


title: Expanded lateral plate mesoderm cells, 2

description: Library name: Sample 24

value: Mesoderm


title: PDX044_1269_21_CNTL_2L

description:
Library name: ABA41522
PDX044_1269_21_CNTL_2L


title: Expanded lateral plate mesoderm cells, 1

description: Library name: Sample 23


title: FTC-3-EV-Small-RNA


title: Limb mesenchymal cells, 1

description: Library name: Sample 27

value: Somatic mesoderm (Lateral plate-derived)


title: PDX313_1068_20_U3_3_21L

description:
Library name: ABA41406
PDX313_1068_20_U3_3_21L


title: Lateral plate mesoderm cells, 2

description: Library name: Sample 22


title: PDX313_1149_21_U3_3_31L

description:
Library name: ABA41405
PDX313_1149_21_U3_3_31L


title: FTC-2-EV-Small-RNA


title: FTC-1-EV-Small-RNA


title: Placenta-derived exosomal miRNA, control, replicate 3

description:
Library name: Exo_con_3
Exosomal RNA from placenta-derived exosomes isolated from term placental explants cultured for 18 h in complete medium without LPS (control), replicate 3.


title: Fed 3, 24hr,  ATAC-seq

city: Pittsburgh

first: Greg

last: Delgoffe

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

institute: University of Pittsburgh

description: 10x Genomics

data_processing:
The raw sequence reads were mapped to mm10 after trimming and aligned using default parameters in bowtie2(v2.4.5)
were called using MACS2 and quantified using R package Diffbind
Assembly: mm10
Supplementary files format and content: Tab-separated bed files

source_name: CD8 T cells

growth_protocol: Mice were fasted or ad libitum for 12hr and next day sacrificed, spleen and peripheral lymph nodes harvested. CD8 purified from mix of lymph nodes and spleen single cell suspension; for ex vivo, cells were processed for ATAC-seq sample preparation using H3K27Ac antibody following kit manual (Active motif). For 24hr group, cells were given TCR stimulation for 24hr in the presence of mIL2 (50 IU/mL). Post stimulation cells were collected and processed for ATAC-seq sample preparation using H3K27Ac antibody followiing kit manual (Active motif).

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8 T cells

value: Fed T cells given TCR stimulation for 24hr and collected for ATAC-sequencing

tag: strain

value: 6-8 weeks old


title: PBMC CD4+ iNKT #1

description: Library name: IonCode_0101

value: human iNKT cells

value: primary tissue


title: Somite-derived mesenchymal stem cells, 2

description: Library name: Sample 20

source_name: Paraxial mesoderm

value: Paraxial mesoderm


title: Lateral plate mesoderm-derived mesenchymal stem cells, 1

description: Library name: Sample 25


title: PDX127_1085_20_U3_3_21L

description:
Library name: ABA41404
PDX127_1085_20_U3_3_21L

tag: treatment


title: Somite-derived mesenchymal stem cells, 1

description: Library name: Sample 19


title: PDX127_1156_21_U3_3_31L

description:
Library name: ABA41403
PDX127_1156_21_U3_3_31L


title: Expanded somite cells, 2

description: Library name: Sample 18


title: Fed 2, 24hr,  ATAC-seq

description: 10x Genomics


title: PDX127_1027_20_CNTL_4L

description:
Library name: ABA41402
PDX127_1027_20_CNTL_4L

value: Untreated


title: Fasted 3, 24hr,  ATAC-seq

description: 10x Genomics

value: Fasted T cells given TCR stimulation for 24hr and collected for ATAC-sequencing


title: Expanded somite cells, 1

description: Library name: Sample 17


title: Fasted 2, 24hr,  ATAC-seq

description: 10x Genomics


title: WT_R4

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: 10

data_processing:
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter using the auto detection mode.
Then reads were mapped to the mouse Ensembl GRCh38 transcriptome index using salmon (v.1.5.0).
Gene-level normalization and differential gene expression analysis were performed with Bioconductor (Gentleman et al., 2004; Huber et al., 2015) package DESeq2 v.1.28 (Love et al., 2014) using the R environment v.4.0 (R Core Team, 2015).
The Wald test was used for significance testing and the resulting false discovery rate (FDR) p-values were adjusted for multiple comparisons using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) and genes were considered differentially expressed (DEGs) only at FDR < 0.05
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was isolated with the RNeasy Plus Mini Kit Qiagen (Cat. 74134) from at least 4x10^6 PBMCs
RNA-Seq library for mRNA sequencing was prepared with Truseq Stranded mRNA Prep Kit. All extracted RNA samples were quality controlled for integrity with a 2100 Bioanalyzer system (Agilent Technologies) and libraries were sequenced on a NovaSeq 6000 System (Illumina)

value: peripheral blood mononuclear cells

value: M

value: Ctrl


title: Lateral plate mesoderm cells, 1

description: Library name: Sample 21


title: PDX313_1149_21_CNTL_4R

description:
Library name: ABA41538
PDX313_1149_21_CNTL_4R

value: Breast Cancer Patient Derived Mouse Xenograft


title: Somite, 1

description: Library name: Sample 15


title: Fasted 1, 24hr,  ATAC-seq

description: 10x Genomics


title: WT_R2

description: Library name: 8

value: F


title: Fed 1, 24hr,  ATAC-seq

description: 10x Genomics