title: PT4,Thymus_no_MG,CD45p, scRNA-seq

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

description:
Library name: PT4.S5.Thymus_no_MG.CD45p
10x Genomics

data_processing:
For scRNA-seq, raw reads were demultiplexed with Cell Ranger (v6.0.0 or v7.1.0) and mapped to the human genome (GRCh38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Quality control in Seurat excluded cells with <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content. For V(D)J sequencing, the djvdj (v0.1.0) package was utilized, retaining only cells with high-quality transcriptomic data. Samples with fewer than 10 cells were excluded for robustness. Clonotypes were defined by CDR3 amino acid sequences, and only those with exactly two chains were retained; cells without an assigned clonotype were removed. For Visium HD, images were aligned in Loupe Browser (v8.0.0), and Space Ranger (v3.1.0) was used for mapping. Bin2cell (v0.3.3) aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression at 0.5 μm per pixel resolution. Downstream analysis was performed in Scanpy, excluding cells with <100 or >40,000 features or >20% mitochondrial content.
Assembly: HG38
Supplementary files format and content: HDF5, csv and tsv of processed data

source_name: Thymus

extract_protocol:
Fresh thymus samples were obtained for scRNA-seq plus V(D)J sequencing and formalin-fixed, paraffin-embedded specimens were used for Visium HD spatial transcriptomics.
For scRNA-seq (3' v3) and scRNA-seq with V(D)J sequencing (5'), libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3 or Single Cell 5' Expression Assay and sequenced on NextSeq 1000/2000 or Illumina NovaSeq 6000 instruments. For Visium HD, samples were sectioned at 5 μm and processed at the Northwestern University NUSeq Core following the manufacturer’s protocol (Visium HD v1). These libraries were subsequently sequenced on an Illumina NovaSeq X Plus.

value: Thymus


title: PT4,Thymus_no_MG,CD45nEPCAMp, scRNA-seq

status: Public on Jul 31 2026

type: SRA

country: USA

description:
Library name: PT4.S5.Thymus_no_MG.CD45nEPCAMp
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue


title: Largemouth bass Spleen, 12h post-challenge, Av, biological replicate 3 [13E3S]

city: Auburn

first: Timothy

middle: James

last: Bruce

state: AL

address: 203 Swingle Hall

department: School of Fisheries, Aquaculture and Aquatic Sciences

institute: Auburn University

description:
Library name: 13E3S
Aeromonas veronii single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

library_source: transcriptomic

data_processing:
Raw reads assessed with FastQC/MultiQC; trimmed with fastp (Q20, 50 bp minimum length). Mean retention 97.9% across 7.1 billion reads.
Transcript quantification with Salmon (decoy-aware index GCF_014851395.1, k=31, --libType A, 30 bootstraps, seqBias/gcBias/posBias corrections). Mean mapping rate 82.84%.
Gene-level import with tximeta (lengthScaledTPM), rounded for DESeq2. Pre-filter: rowSums(counts>=10)>=2. Gill: 23,561 genes; Spleen: 22,152 genes.
DESeq2 differential expression: ~group design, reference=t0_Pre, ashr LFC shrinkage. 72 pairwise contrasts (36/tissue). Significance: padj<0.05, |log2FC|>=1 (BH correction).
Annotation: org.Msalmoides.eg.db v1.0.0 (NCBI RefSeq GFF3 + ZFIN GO GAF 2026-04-01 + OrthoDB v12.2 Actinopterygii). 68.9% of genes annotated with at least one GO term.
Please note that the three samples (11B3G, 15J2G, 29R3G) were intentionally excluded from the processed data files due to gDNA contamination, as indicated by mapping rates below 25% (21.4%, 20.9%, and 15.9%, respectively). These samples failed quality control and were not included in the DESeq2 model or any downstream analyses. Their raw FASTQ files are deposited for transparency and completeness, but they do not appear in the processed count matrices (raw_counts_gill.csv, vst_normalized_counts_gill.csv, DESeq2_all_contrasts_gill.csv) for this reason.
Assembly: GCF_014851395.1 (ASM1485139v1, Micropterus salmoides, NCBI RefSeq)
Supplementary files format and content: raw_counts_gill.csv / raw_counts_spleen.csv: CSV, raw gene count matrix (genes x samples); rows=NCBI gene IDs, columns=sample IDs.
Supplementary files format and content: vst_normalized_counts_gill.csv / vst_normalized_counts_spleen.csv: CSV, VST-normalized expression values from DESeq2.
Supplementary files format and content: DESeq2_all_contrasts_gill.csv / DESeq2_all_contrasts_spleen.csv: CSV, annotated DESeq2 results (gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, gene_symbol, contrast) for all 36 contrasts per tissue.
Supplementary files format and content: Stage5_DEG_summary.tsv: TSV, summary of significant DEGs (up/down/total) per contrast.
Supplementary files format and content: Msalmoides_master_annotation_GO.tsv: TSV, master gene annotation for GCF_014851395.1 (gene_id, gene_symbol, drerio_symbol, GO terms, ortholog information).

molecule: polyA RNA

organism: Micropterus salmoides

source_name: Spleen

growth_protocol: Largemouth bass were maintained in recirculating freshwater systems prior to challenge.

extract_protocol:
Total RNA was extracted from DNA/RNA Shield-preserved tissue at Azenta Inc. RNA quality assessed by TapeStation
Paired-end RNA-Seq libraries prepared from polyA-selected RNA using NEBNext Ultra II. Libraries sequenced on Illumina NovaSeq X (paired-end, 150 bp)

treatment_protocol: Fish were challenged by immersion with Aeromonas veronii, Aeromonas hydrophila, Flavobacterium columnare, or coinfections, or mock-challenged. Gill and spleen were dissected at 0h, 12h, and 24h post-challenge and preserved in DNA/RNA Shield (Zymo Research, Inc.).

value: Spleen

tag: treatment

value: Aeromonas veronii single infection

tag: sample group


title: c57-D10-lung-M2-R1

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

description: Library name: c57-D10-lung-M2

data_processing:
Raw FASTQ files (paired-end) were aligned/quantified using the BioJupies web platform (Ma'ayan Lab). Alignment was performed with the platform's default cloud alignment service (Elysium) against the mouse reference transcriptome/genome
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: .csv, normalized counts

organism: Mus musculus

source_name: Lung

extract_protocol:
Mouse tissue samples were collected, homogenize, and preserved in TRIzol reagent (Invitrogen/Thermo Fisher) by the submitter. Preserved samples were shipped to Azenta Life Sciences (GENEWIZ) on dry ice. Total RNA was then extracted by Azenta using a column-based purification method (Qiagen RNeasy or equivalent best-in-class silica-membrane kit with on-column DNase I treatment) according to the manufacturer’s instructions and Azenta’s optimized protocols for TRIzol-preserved samples.
Library preparation was performed by Azenta Life Sciences using a stranded polyA-enriched bulk RNA-seq protocol, based on Illumina or 10x Genomics-compatible reagents (confirm with Azenta report).

value: Lung

tag: genotype


title: Peripheral blood from patient with normal pubertal age [206909030058_R03C01]

type: genomic

city: London

first: Sasha

last: Howard

address: JVSC Charterhouse Square

department: Endocrinology

country: United Kingdom

institute: Queen Mary University London

hyb_protocol: Sequencing using the Illumina Infinium Methylation EPIC array BeadChip (850K) was carried out by the Epigenomic Services from Diagenode (Cat nr. G02090000).

scan_protocol: Standard Ilumina protocol

data_processing:
A pipeline following that of Barrett et al (Barrett et al. 2022) was used for a second round of quality control and normalisation of the samples. Quality control, annotation of CpG sites and differential methylation analysis was undertaken in R Studio using the dmpFinder function from the minfi package along with bumphunter.
*processed value definition: Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: Standard Ilumina protocol

extract_protocol: Genomic DNA was isolated from peripheral blood leukocytes from all patients and family members using standard procedures

value: Peripheral blood

value: patient with normal pubertal age


title: c57-D10-lung-M1-R1

description: Library name: c57-D10-lung-M1


title: PT4,Thymus_no_MG,CD45nEPCAMn, scRNA-seq

description:
Library name: PT4.S5.Thymus_no_MG.CD45nEPCAMn
10x Genomics


title: Largemouth bass Spleen, 12h post-challenge, Av, biological replicate 2 [13E2S]

description:
Library name: 13E2S
Aeromonas veronii single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with normal pubertal age [206909030058_R02C01]


title: Largemouth bass Spleen, 12h post-challenge, Av, biological replicate 1 [13E1S]

description:
Library name: 13E1S
Aeromonas veronii single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909030058_R01C01]

value: patient with delayed puberty


title: COCs, PCI, biol rep 3, 12h

first: Caroline

middle: Elisabeth

last: Kratka

address: 303 East Superior Street

department: OBGYN

description:
Library name: Sample 21
S12h_PCI_T3_S21

data_processing:
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Martin, 2011).
Trimmed reads were aligned to the Mus musculus genome (mm39) using STAR (Dobin et al., 2013).
Read counts for each gene were calculated using htseq-count (Anders et al., 2015) in conjunction with a gene annotation file for mm39 obtained from Ensembl (http://useast.ensembl.org/index.html).
Assembly: mm39
Supplementary files format and content: a count matrix that contains all samples

source_name: Ovary

growth_protocol: Mouse cumulus-oocyte-complexes (COCs) were cultured in ⍺-MEM (Thermo Fisher) supplemented with 5% (v/v) fetal bovine serum (Thermo Fisher), 20 mM HEPES buffer (Sigma), 0.25 mM pyruvate (Sigma), and 0.02% (v/v) mouse epidermal growth factor (Sigma) for 0h, 4h, 8h, or 12h at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using the RNeasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit following manufacturer's protocols without modifications.

treatment_protocol: COCs were treated with 10 µM proprotein convertase inhibitor (PCI) or DMSO (1/2000) control.

value: Ovary

value: cumulus-oocyte-complexes (COCs)

value: WT

value: Proprotein convertase inhibitor (PCI)

tag: time


title: PT4,Thymoma_no_MG,CD45p, scRNA-seq

description:
Library name: PT4.S4.Thymoma_no_MG.CD45p
10x Genomics


title: PT4,Thymoma_no_MG,CD45nEPCAMp, scRNA-seq

description:
Library name: PT4.S4.Thymoma_no_MG.CD45nEPCAMp
10x Genomics


title: Peripheral blood from patient with delayed puberty [206909030112_R08C01]


title: PT4,Thymoma_no_MG,CD45nEPCAMn, scRNA-seq

description:
Library name: PT4.S4.Thymoma_no_MG.CD45nEPCAMn
10x Genomics


title: Largemouth bass Gill, 12h post-challenge, Av, biological replicate 3 [13E3G]

description:
Library name: 13E3G
Aeromonas veronii single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

source_name: Gill

value: Gill


title: COCs, PCI, biol rep 3, 8h

description:
Library name: Sample 19
S8h_PCI_T3_S19


title: PT3,Thymus_no_MG,CD45p, scRNA-seq

description:
Library name: PT3.S3.Thymus_no_MG.CD45p
10x Genomics


title: COCs, CTL, biol rep 3, 12h

description:
Library name: Sample 20
S12h_CTL_T3_S20

value: None (DMSO control)


title: Largemouth bass Gill, 12h post-challenge, Av, biological replicate 1 [13E1G]

description:
Library name: 13E1G
Aeromonas veronii single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909030112_R07C01]


title: Peripheral blood from patient with delayed puberty [206909030112_R06C01]


title: PT3,Thymus_no_MG,CD45nEPCAMp, scRNA-seq

description:
Library name: PT3.S3.Thymus_no_MG.CD45nEPCAMp
10x Genomics


title: COCs, PCI, biol rep 3, 4h

description:
Library name: Sample 17
S4h_PCI_T3_S17


title: Peripheral blood from patient with delayed puberty [206909030112_R05C01]


title: PT3,Thymus_no_MG,CD45nEPCAMn, scRNA-seq

description:
Library name: PT3.S3.Thymus_no_MG.CD45nEPCAMn
10x Genomics


title: COCs, CTL, biol rep 3, 4h

description:
Library name: Sample 16
S4h_CTL_T3_S16


title: Largemouth bass Spleen, 12h post-challenge, Mock, biological replicate 2 [11B2S]

description:
Library name: 11B2S
Sham-injected control; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Sham-injected control


title: PT2,Thymus_MG,CD45p, scRNA-seq

description:
Library name: PT2.S2.Thymus_MG.CD45p
10x Genomics


title: Largemouth bass Spleen, 12h post-challenge, Mock, biological replicate 1 [11B1S]

description:
Library name: 11B1S
Sham-injected control; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with normal pubertal age [206909030112_R03C01]


title: COCs, biol rep 3, 0h

description:
Library name: Sample 15
S0h_T3_S15


title: Largemouth bass Gill, 12h post-challenge, Mock, biological replicate 3 [11B3G]

description:
Library name: 11B3G
Sham-injected control; 12h post-challenge; Gill; EXCLUDED from DESeq2 model — gDNA contamination (mapping rate <25%)
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: COCs, PCI, biol rep 2, 12h

description:
Library name: Sample 14
S12h_PCI_T2_S14


title: PT2,Thymus_MG,CD45nEPCAMn, scRNA-seq

description:
Library name: PT2.S2.Thymus_MG.CD45nEPCAMn
10x Genomics


title: COCs, CTL, biol rep 2, 12h

description:
Library name: Sample 13
S12h_CTL_T2_S13


title: Peripheral blood from patient with delayed puberty [206909030112_R01C01]


title: Largemouth bass Gill, 12h post-challenge, Mock, biological replicate 1 [11B1G]

description:
Library name: 11B1G
Sham-injected control; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909170094_R08C01]


title: PT1,Thymoma_no_MG,CD45p, scRNA-seq

description:
Library name: PT1.S1.Thymoma_no_MG.CD45p
10x Genomics


title: Largemouth bass Spleen, 12h post-challenge, Mock, biological replicate 3 [11A3S]

description:
Library name: 11A3S
Sham-injected control; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: COCs, CTL, biol rep 2, 8h

description:
Library name: Sample 11
S8h_CTL_T2_S11


title: PT1,Thymoma_no_MG,CD45nEPCAMp, scRNA-seq

description:
Library name: PT1.S1.Thymoma_no_MG.CD45nEPCAMp
10x Genomics


title: Peripheral blood from patient with delayed puberty [206909170094_R07C01]


title: PT1,Thymoma_no_MG,CD45nEPCAMn, scRNA-seq

description:
Library name: PT1.S1.Thymoma_no_MG.CD45nEPCAMn
10x Genomics


title: Largemouth bass Spleen, 12h post-challenge, Mock, biological replicate 2 [11A2S]

description:
Library name: 11A2S
Sham-injected control; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: PANC-1 TP53-KO, Ferroptocide, 2801

city: Verona

first: Alessandra

last: Fiore

state: VR

address: Str. le Grazie, 8

country: Italy

institute: University of Verona

description:
Library name: Sample 2801
Column name in raw_counts.csv: 2801

data_processing:
Base calling was performed using Illumina Real-Time Analysis (RTA) software v3.10.30 on an Illumina NextSeq 2000 platform.
Demultiplexing and FASTQ file generation were performed using Illumina bcl-convert v3.10.12 with dual-index barcodes (Index1 and Index2), allowing up to one mismatch per index; FASTQ files were compressed in gzip format.
Sequencing generated single-end reads of 76 bp with dual 8 bp index reads.
Reads were processed using the DRAGEN RNA pipeline v3.10.12 to generate BAM alignments and gene-level read counts.
Read alignment was performed against the human reference genome hg38 using the alt-aware reference bundle (hg38_alt_aware). A raw (unnormalized) gene-level read count matrix was generated by aggregating DRAGEN RNA outputs across all samples.
Assembly: GRCh38 (hg38), alt-aware reference genome.
Supplementary files format and content: raw_counts.csv: CSV file (comma-separated values) containing a raw, unnormalized gene-level read count matrix (rows = genes, columns = samples).
Supplementary files format and content: sample.txt: comma-separated file containing sample metadata describing sample identifiers, cell line, genotype (TP53 wild-type or TP53 knockout), treatment (DMSO, Erastin, RSL3, Ferroptocide).

source_name: PANC-1 TP53-KO

growth_protocol: PANC-1 and TP53 KO PANC-1 cells were maintaned in RPMI-1640 supplemented with 10% FBS and antibiotics in humified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherland, Cat. No. 74104) according to the manufactures’ instructions. The RNA was eluted in RNAse-free water and stored at – 80° C until quantification.
RNA-seq library preparation was performed starting from 1,000 ng high-quality total RNA using the “TruSeq Stranded mRNA library prep kit” (Illumina, San Diego, USA).

treatment_protocol: PANC-1 and TP53 KO PANC-1 cells were treated with RSL3 (0.5 μM) for 6 hours to induce ferroptosis

tag: cell line

value: PANC-1 TP53-KO

value: TP53 knockout

value: Ferroptocide

tag: batch

value: single sequencing run


title: Largemouth bass Spleen, 12h post-challenge, Mock, biological replicate 1 [11A1S]

description:
Library name: 11A1S
Sham-injected control; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: COCs, CTL, biol rep 2, 4h

description:
Library name: Sample 9
S4h_CTL_T2_S9


title: Peripheral blood from patient with delayed puberty [206909170094_R05C01]


title: COCs, biol rep 2, 0h

description:
Library name: Sample 8
S0h_T2_S8


title: Peripheral blood from patient with delayed puberty [206909170094_R04C01]


title: PANC-1 TP53-KO, Erastin, 2799

description:
Library name: Sample 2799
Column name in raw_counts.csv: 2799

value: Erastin


title: Largemouth bass Gill, 12h post-challenge, Mock, biological replicate 2 [11A2G]

description:
Library name: 11A2G
Sham-injected control; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: COCs, PCI, biol rep 1, 12h

description:
Library name: Sample 7
S12h_PCI_T1_S7


title: Largemouth bass Gill, 12h post-challenge, Av, biological replicate 1 [13F1G]

description:
Library name: 13F1G
Aeromonas veronii single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Aeromonas veronii single infection


title: Largemouth bass Gill, 12h post-challenge, Mock, biological replicate 1 [11A1G]

description:
Library name: 11A1G
Sham-injected control; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909170094_R02C01]

value: Peripheral blood


title: COCs, PCI, biol rep 1, 8h

description:
Library name: Sample 5
S8h_PCI_T1_S5


title: Peripheral blood from patient with delayed puberty [206909170094_R01C01]


title: PANC-1 TP53-KO, RSL3, 2796

description:
Library name: Sample 2796
Column name in raw_counts.csv: 2796


title: COCs, CTL, biol rep 1, 8h

description:
Library name: Sample 4
S8h_CTL_T1_S4


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 9

description:
Library name: 00S8S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Pre-challenge baseline (0h)


title: Peripheral blood from patient with delayed puberty [206909030112_R02C01]

value: patient with delayed puberty


title: COCs, PCI, biol rep 2, 8h

description:
Library name: Sample 12
S8h_PCI_T2_S12

value: Ovary


title: PANC-1 TP53-KO, Erastin, 2795

description:
Library name: Sample 2795
Column name in raw_counts.csv: 2795


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 8

description:
Library name: 00S7S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: COCs, PCI, biol rep 1, 4h

description:
Library name: Sample 3
S4h_PCI_T1_S3

value: cumulus-oocyte-complexes (COCs)


title: Peripheral blood from patient with delayed puberty [206909030005_R07C01]


title: PANC-1 TP53-KO, DMSO, 2794

description:
Library name: Sample 2794
Column name in raw_counts.csv: 2794

value: DMSO


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 7

description:
Library name: 00S6S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: COCs, CTL, biol rep 1, 4h

description:
Library name: Sample 2
S4h_CTL_T1_S2

value: WT


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 6

description:
Library name: 00S5S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: COCs, biol rep 1, 0h

description:
Library name: Sample 1
S0h_T1_S1


title: PANC-1 TP53-KO, Ferroptocide, 2793

description:
Library name: Sample 2793
Column name in raw_counts.csv: 2793


title: Peripheral blood from patient with delayed puberty [206909030005_R05C01]


title: PANC-1 TP53-KO, RSL3, 2792

description:
Library name: Sample 2792
Column name in raw_counts.csv: 2792


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 5

description:
Library name: 00S4S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: HCT116 cells, GIA treatment 3, hypoxia

city: Wenzhou

first: Ya

last: Zhang

state: Zhejiang

address: Fanhai road 101

country: China

institute: the first affiliated hospital of Wenzhou medical university

description: Library name: GIA3

data_processing:
FastQC v0.10.1 was used for raw data quality control
Clean reads were obtained by trimming adaptor sequences and low-quality reads using Cutadapt.
Trimmed reads were mapped to the human reference genome GRCh38/hg38 using Hisat2 v2.2.1.
Transcript assembly and quantification were performed using StringTie v2.1.6.
Differential expression analysis was performed using DESeq2 v1.22.2 with a threshold of |log2(fold change)| > 1 and adjusted p-value < 0.05.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files include gene expression values (FPKM and raw read counts) for each Sample.

growth_protocol: HCT116 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified atmosphere with 5% CO₂ at 37°C.

extract_protocol:
Total RNA was harvested using TRIzol reagent (Invitrogen, USA) according to the manufacturer's protocol. RNA integrity and purity were assessed using an Agilent 2100 Bioanalyzer.
RNA libraries for RNA-seq were prepared using the SMARTER mRNA-Seq Library Prep Kit following the manufacturer's protocols. Strand-specific libraries were constructed.

treatment_protocol: Cells were treated with 10 µM GIA or DMSO control under hypoxic conditions (1% O₂) for 24 hours.

value: colorectal cancer cells

value: GIA (10 µM) 24h


title: Peripheral blood from patient with delayed puberty [206909030005_R04C01]


title: PANC-1 TP53-KO, Erastin, 2791

description:
Library name: Sample 2791
Column name in raw_counts.csv: 2791


title: S6Te

city: San Juan

first: Elba

last: Caraballo Rivera

state: Puerto Rico

address: Av. Jose Kiko Custodio

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 12

data_processing:
Quality assessment of the raw FASTQ reads was conducted using FastQC to evaluate data integrity. Adapter trimming and low-quality base removal were performed using Trimmomatic, followed by alignment of the reads to the human reference genome GRCh38 (hg38) using the STAR. Gene-level quantification was carried out using RSEM, and the resulting expression data was imported into R/RStudio.
Assembly: hg38
Supplementary files format and content: rna-seq-normalized-counts_allSamples.csv-CSV file that contains gene-level raw read counts for each RNA-seq sample.
Supplementary files format and content: differential_gene_expression_te_me.csv-CSV file that contains differential gene expression results when comparing early-stage CRC tumors with adjacent mucosal tissue.
Supplementary files format and content: differential_gene_expression_ta_ma.csv-CSV file that contains differential gene expression results when comparing advanced-stage CRC tumors with adjacent mucosal tissue.

source_name: Early CRC

growth_protocol: This study was a secondary data analysis and uses previously collected tissue from PRH enrolled in the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR) IRB #2290034759. Tissue was stored at 80°C

extract_protocol:
RNA was extracted from frozen tumor and adjacent mucosal tissue samples using the Qiagen RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.  RNA quality and concentration were assessed prior to library preparation using a NanoDrop 2000 (Thermo Fisher Scientific).
RNA-seq libraries were prepared from total RNA using a poly(A)-selected library preparation kit according to the manufacturer’s protocol.

treatment_protocol: No in vitro treatment was applied. Samples represent primary early and advanced CRC tumors and adjacent mucosal tissue collected at the time of surgery.

value: Colorectal

value: Tumor tissue


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 4

description:
Library name: 00S3S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909030005_R03C01]


title: PANC-1 TP53-KO, DMSO, 2790

description:
Library name: Sample 2790
Column name in raw_counts.csv: 2790

value: PANC-1 TP53-KO

value: TP53 knockout


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 3

description:
Library name: 00S2S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: HCT116 cells, GIA treatment 1, hypoxia

description: Library name: GIA1


title: Peripheral blood from patient with delayed puberty [206909030005_R02C01]


title: Peripheral blood from patient with delayed puberty [206909030005_R06C01]


title: Splenic CD8+ T cells, rested, 24-hours, Dusp2 conditional knockout, mouse 2

city: Rochester

first: Emilia

middle: R

last: Dellacecca

state: MN

address: 200 First Street SW, Kellen Building 02-102

department: Immunology

institute: Mayo Clinic

description: Library name: 116C_R

data_processing:
Raw RNA sequencing paired-end reads were processed through Mayo RNA-Seq bioinformatics pipeline, MAP-Rseq (v3.1.5) to align to genome build mm39.
Variants were called using the RVBoost module from MAPR-seq.
Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM) reads.
FASTQC, MultiQC, and RSEQC tools were used for comprehensive quality control assessment of the aliqned reads.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file including raw counts and FPKM for each sample

growth_protocol: CD8+ T cells were maintained in RPMI 1640 + 10% fetal bovine serum, 20 mM HEPES buffer, and 1X penicillin/streptomycin at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Invitrogen), prior to inclusion in spin-column based isolation (Zymo Research). 100 ng of total RNA was used for construction of cDNA libraies.
Libraries were prepared with Illumina Stranded mRNA Prep kit following manufacturer's instructions. The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation's D1000 ScreenTape and Qubit fluorometry.

treatment_protocol: CD8+ T cells were activated with anti-CD3/CD28 beads (Gibco) for 24-hours, rested cells were maintained under the same conditions without addition of beads.

value: CD8+ T cells

tag: Sex

value: Male


title: PANC-1,Ferroptocide, 2789

description:
Library name: Sample 2789
Column name in raw_counts.csv: 2789

value: Ferroptocide

value: single sequencing run


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 2

description:
Library name: 00S1S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: HCT116 cells, DMSO control 3, hypoxia

description: Library name: Ctrl3


title: Peripheral blood from patient with delayed puberty [206909030005_R01C01]

value: Peripheral blood


title: Largemouth bass Gill, 12h post-challenge, Av, biological replicate 2 [13E2G]

description:
Library name: 13E2G
Aeromonas veronii single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill

value: Aeromonas veronii single infection


title: COCs, CTL, biol rep 3, 8h

description:
Library name: Sample 18
S8h_CTL_T3_S18

value: Ovary

value: cumulus-oocyte-complexes (COCs)

value: None (DMSO control)


title: PANC-1,RSL3, 2788

description:
Library name: Sample 2788
Column name in raw_counts.csv: 2788


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 1

description:
Library name: 00S0S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Pre-challenge baseline (0h)


title: Largemouth bass Spleen, 12h post-challenge, Mock, biological replicate 3 [11B3S]

description:
Library name: 11B3S
Sham-injected control; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Sham-injected control


title: HCT116 cells, DMSO control 2, hypoxia

description: Library name: Ctrl2

value: colorectal cancer cells

value: WT


title: Peripheral blood from patient with delayed puberty [206772660040_R08C01]

value: patient with delayed puberty


title: Peripheral blood from patient with delayed puberty [206909030112_R04C01]


title: PANC-1,Erastin, 2787

description:
Library name: Sample 2787
Column name in raw_counts.csv: 2787

value: Erastin


title: PT2,Thymus_MG,CD45nEPCAMp, scRNA-seq

description:
Library name: PT2.S2.Thymus_MG.CD45nEPCAMp
10x Genomics

value: Thymus


title: HCT116 cells, DMSO control 1, hypoxia

description: Library name: Ctrl1


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 10

description:
Library name: 00S9G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206772660040_R07C01]


title: PANC-1,DMSO, 2786

description:
Library name: Sample 2786
Column name in raw_counts.csv: 2786

value: DMSO


title: Largemouth bass Gill, 12h post-challenge, Mock, biological replicate 2 [11B2G]

description:
Library name: 11B2G
Sham-injected control; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 9

description:
Library name: 00S8G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: A549 cells, 1ng/ml of TGF-β1 for 24 h, (Input)

city: Kumamoto

first: Minoru

last: Terashima

state: Kumamoto

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

description: Library name: A549, plusTGFbeta, INPUT

library_source: genomic

data_processing:
Sequenced reads were mapped to the human genome using BWA with default parameters.
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS2.
broadPeak files were generated using MACS2 with broad option settings.
Assembly: hg19
Supplementary files format and content: bed, broadPeak

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor II ultrasonicator.
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).

treatment_protocol: For EMT induction, A549 cells were treated with 1 ng/ml TGF-β1 for 24 h.

value: lung adenocarcinoma cells


title: Peripheral blood from patient with normal pubertal age [206772660040_R06C01]

value: patient with normal pubertal age


title: PANC-1,Ferroptocide, 2785

description:
Library name: Sample 2785
Column name in raw_counts.csv: 2785

value: Ferroptocide

value: single sequencing run


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 8

description:
Library name: 00S7G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: Peripheral blood from patient with normal pubertal age [206772660040_R05C01]

value: Peripheral blood


title: PANC-1,RSL3, 2784

description:
Library name: Sample 2784
Column name in raw_counts.csv: 2784


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 7

description:
Library name: 00S6G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: A549 cells, (Input)

description: Library name: A549, minusTGFbeta, INPUT


title: HCT116 cells, GIA treatment 2, hypoxia

description: Library name: GIA2

value: GIA (10 µM) 24h


title: PANC-1,Erastin, 2783

description:
Library name: Sample 2783
Column name in raw_counts.csv: 2783


title: A549 cells, 1ng/ml of TGF-β1 for 24 h, H3K4me3 (ChIP)

description: Library name: A549, plusTGFbeta, H3K4me3ChIP

tag: antibody


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 6

description:
Library name: 00S5G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206772660040_R04C01]


title: A549 cells, H3K4me3 (ChIP)

description: Library name: A549, minusTGFbeta, H3K4me3ChIP


title: Peripheral blood from patient with delayed puberty [206909170094_R06C01]


title: COCs, PCI, biol rep 2, 4h

description:
Library name: Sample 10
S4h_PCI_T2_S10

value: Ovary

value: cumulus-oocyte-complexes (COCs)

value: Proprotein convertase inhibitor (PCI)


title: Peripheral blood from patient with delayed puberty [206772660040_R03C01]


title: PANC-1,DMSO, 2782

description:
Library name: Sample 2782
Column name in raw_counts.csv: 2782


title: plasma,gastric cancer patient,E3

city: Baotou

first: yunqi

last: hua

address: 18 Tuanjie Street, Qingshan District, Baotou City, Inner Mongolia Autonomous Region

department: 1.Medical oncology 2.Department of Public Health

institute: 1.Baotou Cancer Hospital2.International College, Krirk University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCh38
Supplementary files format and content: excel,expression profiles

source_name: tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: plasma

value: exosome isolation


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 5

description:
Library name: 00S4G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Pre-challenge baseline (0h)


title: Largemouth bass Gill, 12h post-challenge, Mock, biological replicate 3 [11A3G]

description:
Library name: 11A3G
Sham-injected control; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Sham-injected control


title: PANC-1 TP53-KO, RSL3, 2800

description:
Library name: Sample 2800
Column name in raw_counts.csv: 2800

value: PANC-1 TP53-KO

value: TP53 knockout


title: Peripheral blood from patient with delayed puberty [206772660040_R02C01]

value: patient with delayed puberty


title: PANC-1,Ferroptocide, 2781

description:
Library name: Sample 2781
Column name in raw_counts.csv: 2781


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 4

description:
Library name: 00S3G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with normal pubertal age [206772660040_R01C01]


title: plasma,treatment-resistant gastric cancer patient,N2


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 3

description:
Library name: 00S2G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: PANC-1,RSL3, 2780

description:
Library name: Sample 2780
Column name in raw_counts.csv: 2780


title: A549 cells, 1ng/ml of TGF-β1 for 24 h

description: Library name: A549, plusTGFbeta

data_processing:
Illumina bcl2fastq software used for basecalling.
The raw FASTQ files were assessed for quality using FastQC. Adapter sequences and low-quality bases were trimmed.
The trimmed reads were pseudoaligned to the reference transcriptome using kallisto.
Transcript-level abundance estimates were generated.
Assembly: GENCODE Release 43 (GRCh38.p13)
Supplementary files format and content: Gene-level counts matrix, CSV format

extract_protocol:
Total RNA from A549 cells was extracted using TRIzol reagent (Invitrogen). RNA was quantified using the Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Prep Kit and standard Illumina protocols.

value: lung adenocarcinoma cells


title: PANC-1,Erastin, 2779

description:
Library name: Sample 2779
Column name in raw_counts.csv: 2779

value: Erastin


title: plasma,treatment-resistant gastric cancer patient,N1


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 2

description:
Library name: 00S1G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909170094_R03C01]


title: plasma,gastric cancer patient,E2


title: PANC-1,DMSO, 2778

description:
Library name: Sample 2778
Column name in raw_counts.csv: 2778

value: DMSO


title: A549 cells

description: Library name: A549, minusTGFbeta


title: plasma,gastric cancer patient,E1


title: SJRHB071779_X1

status: Public on Jul 30 2026

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: SJRHB071779_X1
10x Genomics 3' RNA kit

data_processing:
Aligning and transcript counting were performed using 10x Genomics Cell Ranger version 7
Assembly: GRCh38
Supplementary files format and content: processed data reflect cell ranger output from the filter_bc_matrix folder, including feature names, cell barcode IDs, and expression count matrix (unnormalized)

source_name: tumor

extract_protocol:
cells or nuclei were extracting using protocols described in Slyper et al Nat Medicine 2020 (https://doi.org/10.1038/s41591-020-0844-1)
Libraries were generating using the 10x Genomics 3' gene expression kits version 3.1

value: tumor

tag: sample type

value: O-PDX

tag: disease

value: ERMS

tag: method

value: cell

tag: sjid

tag: age

tag: gender

value: F

tag: primary site

value: Retroperitoneum

tag: sample site

tag: timepoint

value: recurrence

tag: sample

value: primary

tag: treatment status

value: treated


title: SJRHB049188_X1_rep3

description:
Library name: SJRHB049188_X1_rep3
10x Genomics 3' RNA kit

tag: tissue

value: M

value: diagnostic


title: SJRHB049188_X1_rep1

description:
Library name: SJRHB049188_X1_rep1
10x Genomics 3' RNA kit


title: SJRHB030624_X1_rep2

description:
Library name: SJRHB030624_X1_rep2
10x Genomics 3' RNA kit

value: ARMS

value: unknown


title: SJRHB030624_X1_rep1

description:
Library name: SJRHB030624_X1_rep1
10x Genomics 3' RNA kit


title: SJRHB015720_X1

description:
Library name: SJRHB015720_X1
10x Genomics 3' RNA kit

value: SRMS

value: Sinus

value: Oropharynx


title: SJRHB015721_X1

description:
Library name: SJRHB015721_X1
10x Genomics 3' RNA kit

value: Paratesticular mass


title: SJRHB013_X_rep1

description:
Library name: SJRHB013_X_rep1
10x Genomics 3' RNA kit

value: tumor

value: abdominopelvic

value: untreated


title: SJRHB013_X_rep2

description:
Library name: SJRHB013_X_rep2
10x Genomics 3' RNA kit

value: O-PDX

value: ERMS

value: cell


title: SJRHB013759_X1_rep2

description:
Library name: SJRHB013759_X1_rep2
10x Genomics 3' RNA kit

value: Pelvis

value: Inguinal mass

value: recurrence

value: metastasis


title: SJRHB013759_X1_rep1

description:
Library name: SJRHB013759_X1_rep1
10x Genomics 3' RNA kit

value: M


title: SJRHB012_X_rep1

description:
Library name: SJRHB012_X_rep1
10x Genomics 3' RNA kit

value: Prostate

value: diagnostic

value: primary


title: SJRHB011_Y

description:
Library name: SJRHB011_Y
10x Genomics 3' RNA kit

value: Neck

value: treated


title: SJRHB010463_X16

description:
Library name: SJRHB010463_X16
10x Genomics 3' RNA kit

value: ARMS

value: Sinus

value: Lung


title: Exp_3_CB839_UK5099

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: Exp_3_CB839_UK5099

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: RPKM normalized expression values for all ENTREZ genes

source_name: Germinal Center B cell

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
RNA-seq libraries were generated at the Vanderbilt Vantage Genomics Core using the Tecan Ovation kit.

treatment_protocol: All cells were cultured with anti-CD40, BAFF, IL-4, and IL-5 for 3 days in the presence or absence of CB-839 (a GLS1 inhibitor) and UK-5099 (an MPC inhibitor).

tag: cell type

value: Germinal Center B cell

tag: strain

tag: treatment


title: Exp_3_CB839

description: Library name: Exp_3_CB839

tag: batch


title: SJRHB071779_R1

description:
Library name: SJRHB071779_R1
10x Genomics 3' RNA kit

value: tumor

value: Patient

value: F

value: Retroperitoneum


title: SJRHB010463_M1

description:
Library name: SJRHB010463_M1
10x Genomics 3' RNA kit

value: nucleus

value: untreated


title: SJRHB031412_M1

description:
Library name: SJRHB031412_M1
10x Genomics 3' RNA kit

value: ERMS

value: cell

value: Testes

value: Para-aortic lymph node

value: metastasis


title: Exp_2_CB839_UK5099

description: Library name: Exp_2_CB839_UK5099


title: SJRHB031412_D

description:
Library name: SJRHB031412_D
10x Genomics 3' RNA kit

value: M

value: diagnostic

value: primary


title: SJRB071938_D2

description:
Library name: SJRB071938_D2
10x Genomics 3' RNA kit

value: RB

value: unknown

value: eye


title: Exp_2_Veh

description: Library name: Exp_2_Veh

value: Germinal Center B cell

value: Vehicle Control


title: Exp_2_Unactivated

description: Library name: Exp_2_Unactivated

value: Unstimulated/Unactivated


title: SJRHB063825_X1

description:
Library name: SJRHB063825_X1
10X Genomics 3’ RNA kit

data_processing:
Aligning and transcript counting were performed using 10x Genomics Cell Ranger version 7
Assembly: Hg38 for patient samples. Combined Hg38 and mm10 for PDX samples
Supplementary files format and content: processed data reflect cell ranger output from the filter_bc_matrix folder, including feature names, cell barcode IDs, and expression count matrix (unnormalized)

source_name: ERMS

tag: group

value: O-PDX

value: male

value: Bladder/prostate

value: recurrence

value: treated


title: Exp_1_CB839_UK5099

description: Library name: Exp_1_CB839_UK5099


title: SJDSRCT046151_X1

description:
Library name: SJDSRCT046151_X1
10X Genomics 3’ RNA kit

source_name: DSRCT

value: DSRCT

value: nucleus

value: pelvis


title: SJOS001132_X1

description:
Library name: SJOS001132_X1
10X Genomics 3’ RNA kit

source_name: OS

value: OS

value: female

value: Bone

value: Lung

value: metastasis

value: untreated


title: Exp_1_UK5099

description: Library name: Exp_1_UK5099

value: Germinal Center B cell


title: SJOS063833_X2

description:
Library name: SJOS063833_X2
10X Genomics 3’ RNA kit

value: Femur

value: diagnostic

value: primary


title: Exp_1_CB839

description: Library name: Exp_1_CB839


title: SJMRT030873_X1

description:
Library name: SJMRT030873_X1
10X Genomics 3’ RNA kit

source_name: MRT

value: MRT

value: O-PDX

value: male

value: kidney


title: SJOS030272_X1

description:
Library name: SJOS030272_X1
10X Genomics 3’ RNA kit

value: recurrence

value: treated


title: Exp_1_Veh

description: Library name: Exp_1_Veh

value: Vehicle Control


title: Exp_1_Unactivated

description: Library name: Exp_1_Unactivated

value: Unstimulated/Unactivated


title: SJGIST030657_X1

description:
Library name: SJGIST030657_X1
10X Genomics 3’ RNA kit

source_name: GIST

value: GIST

value: nucleus

value: stomach


title: WT.NaiveB.3

description: Library name: WT.NaiveB.3

source_name: Naive B cell

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: Naive B cell

tag: genotype

value: Wild type


title: WT.NaiveB.2

description: Library name: WT.NaiveB.2


title: WT.NaiveB.1

description: Library name: WT.NaiveB.1


title: SJHGS015726_X1

description:
Library name: SJHGS015726_X1
10X Genomics 3’ RNA kit

source_name: HGS

value: HGS

value: thigh

value: recurrent


title: WT.GCB.3

description: Library name: WT.GCB.3

value: Germinal Center B cell

value: SRBC immunization


title: SJHGS012410_X1

description:
Library name: SJHGS012410_X1
10X Genomics 3’ RNA kit

value: O-PDX

value: female

value: unknown

value: lung

value: diagnosis

value: metastasis

value: untreated


title: SJOS001116_X2

description:
Library name: SJOS001116_X2
10X Genomics 3’ RNA kit

value: OS

value: Lung

value: recurrence


title: WT.GCB.2

description: Library name: WT.GCB.2


title: SJOS001107_X3

description:
Library name: SJOS001107_X3
10X Genomics 3’ RNA kit

value: nucleus

value: male

value: Humerus


title: SJDSRCT049192_X3

description:
Library name: SJDSRCT049192_X3
10X Genomics 3’ RNA kit

value: DSRCT

value: abdominopelvic

value: liver

value: metastatic

value: treated


title: Mpc2.cKOB.GCB.3

description: Library name: Mpc2.cKOB.GCB.3

value: Germinal Center B cell

value: SRBC immunization


title: Mpc2.cKOB.GCB.2

description: Library name: Mpc2.cKOB.GCB.2


title: SJRHB063823_X1

description:
Library name: SJRHB063823_X1
10X Genomics 3’ RNA kit

value: ERMS

value: O-PDX

value: Unknown

value: Back soft tissue

value: diagnostic

value: unknown


title: Mpc2.cKOB.GCB.1

description: Library name: Mpc2.cKOB.GCB.1


title: SJUESL03081_X1

description:
Library name: SJUESL03081_X1
10X Genomics 3’ RNA kit

source_name: EMBSARC

value: EMBSARC

value: female

value: primary

value: untreated


title: Gls1.Mpc2.dKOB.NaiveB.3

description: Library name: Gls1.Mpc2.dKOB.NaiveB.3

value: Gls1-KO, Mpc2-KO


title: SJHGS030131_X1

description:
Library name: SJHGS030131_X1
10X Genomics 3’ RNA kit

source_name: SCS

value: SCS

value: nucleus

value: male

value: femur


title: Gls1.Mpc2.dKOB.NaiveB.2

description: Library name: Gls1.Mpc2.dKOB.NaiveB.2

value: Germinal Center B cell


title: SJOS013768_X1

description:
Library name: SJOS013768_X1
10X Genomics 3’ RNA kit

value: OS

value: Femur

value: treated


title: Gls1.Mpc2.dKOB.NaiveB.1

description: Library name: Gls1.Mpc2.dKOB.NaiveB.1


title: SJOS001105_X1

description:
Library name: SJOS001105_X1
10X Genomics 3’ RNA kit

value: O-PDX

value: Bone

value: recurrence

value: metastasis


title: Gls1.Mpc2.dKOB.GCB.3

description: Library name: Gls1.Mpc2.dKOB.GCB.3

value: SRBC immunization


title: Gls1.Mpc2.dKOB.GCB.2

description: Library name: Gls1.Mpc2.dKOB.GCB.2


title: SJHGS015726_X2

description:
Library name: SJHGS015726_X2
10X Genomics 3’ RNA kit

value: HGS

value: thigh

value: recurrent


title: SJWLM046158_X1

description:
Library name: SJWLM046158_X1
10X Genomics 3’ RNA kit

source_name: WT

value: WT

value: female

value: kidney

value: diagnostic

value: primary

value: untreated


title: Gls1.cKOB.GCB.3

description: Library name: Gls1.cKOB.GCB.3

value: Germinal Center B cell


title: SJWLM046157_X1

description:
Library name: SJWLM046157_X1
10X Genomics 3’ RNA kit

value: nucleus


title: Gls1.cKOB.GCB.2

description: Library name: Gls1.cKOB.GCB.2


title: SJWLM046152_X1

description:
Library name: SJWLM046152_X1
10X Genomics 3’ RNA kit

value: male


title: Gls1.cKOB.GCB.1

description: Library name: Gls1.cKOB.GCB.1


title: SJWLM046146_X1

description:
Library name: SJWLM046146_X1
10X Genomics 3’ RNA kit

value: O-PDX


title: mES, dTAG_DGCR8, dTAG_3h, SPT5, rep2

city: Shanghai

first: ying

last: cai

address: Fudan University, 131 Dong'an Road, Shanghai

institute: Fudan University

description: Library name: mES, dTAG_DGCR8, dTAG_3h, SPT5, rep2

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 genome using Bowtie2 (v2.5.1). PCR duplicates were removed using samtools (v1.11) rmdup. Genome coverage bigwig files were generated by deeptools (v2.5.7) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: dTAG cells were treated with DMSO or 100 nM dTAG for 24 hours.

tag: cell line

value: Embryonic stem cells

tag: chip antibody

value: SPT5(Proteintech, Cat#16511-1-AP)


title: SJSTS030383_X1

description:
Library name: SJSTS030383_X1
10X Genomics 3’ RNA kit

source_name: URCS

value: URCS

tag: method

tag: sjid

value: neck

value: lymph node

value: metastasis

value: treated


title: mES, dTAG_DGCR8, dTAG_3h, ERH, rep2

description: Library name: mES, dTAG_DGCR8, dTAG_3h, ERH, rep2

value: ERH(Proteintech, Cat# 15974-1-AP)


title: SJSS063828_X1

description:
Library name: SJSS063828_X1
10X Genomics 3’ RNA kit

source_name: SS

value: SS

tag: age

tag: gender

value: female

value: femur


title: mES, dTAG_DGCR8, dTAG_3h, ERH, rep1

description: Library name: mES, dTAG_DGCR8, dTAG_3h, ERH, rep1


title: Her2(+)EpCAM(+) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep5

city: LYON

first: Amélien

last: SANLAVILLE

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample05

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.
Sequencing reads were mapped to the Mus musculus genome sequence and transcriptome annotations (as provided by GENCODE release M9) and converted to gene counts using STAR (Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21, 2013).
All statistical calculations were performed in R programming language (v. 3.5.3). DESeq2 (v. 1.22.2; Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550, 2014) was used to normalize raw counts
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Mammary tumor cells

growth_protocol: Her2-expressing E-A14 mouse mammary tumor cells were implanted into the fourth mammary fat pad of 6-8 week old FVB/N mice.

extract_protocol:
Tumors were collected at growth end-point (20 days post-injection of E-A14 tumor cells in CD4/CD8-depleted mice versus 47 days post-injection in control mice) and enzymatically digested in 10mg.mL-1 collagenase and 0.2mg.mL-1 DNAse I for 30min at 37°C. Red blood cells were then lysed 5min with Pharmlyse Buffer (BD Biosciences) at room temperature. These cells were labeled with fluorescence-conjugated CD90, CD105, CD45, Her2 and EpCAM antibodies and Zombie Fixable Viability Dye. Her2+EpCAM+ and Her2+EpCAM- cells were sorted by a FACSAria III cell sorter (BD Biosciences) after exclusion of dead cells, CD90(+), CD105(+) and CD45(+) cells. Total RNA was extracted from sorted cells and also from single cell suspensions of two replicates of in vitro cultured E-A14 tumor cells stabilized in RLT buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Micro Kit (Qiagen). The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories) was used to generate first strand cDNA from 0.1 to 1.0 ng total-RNA. Double stranded cDNA was amplified by LD PCR (10, 12 or 14 cycles) and purified via magnetic bead clean-up.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina). The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

treatment_protocol: Mice were depleted both for CD4 and CD8 T cells, via twice per week intraperitoneal injection of 100µg anti-CD4 and 100µg anti-CD8a antibodies, or injected twice per week with 100µg of rat IgG2a and 100µg of rat IgG2b as control. Both treatments started 2 weeks before tumor implantation and were maintained all along tumor growth.

value: tumor cells isolated from E-A14 tumors

value: FVB/N

value: CD4 and CD8 double depletion

tag: cell selection method

value: cell sorting based on Her2-positive and EpCAM-positive expression

tag: collection time points

value: 20 days after E-A14 tumor cell injection


title: Her2(+)EpCAM(+) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep4

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample04


title: Her2(+)EpCAM(+) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep6

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample06


title: SJWLM049191_X1

description:
Library name: SJWLM049191_X1
10X Genomics 3’ RNA kit

value: WT

value: O-PDX

value: nucleus

tag: primary site

value: kidney

tag: sample site

tag: timepoint

value: diagnostic

tag: sample

value: primary

value: untreated


title: SJSS049190_X1

description:
Library name: SJSS049190_X1
10X Genomics 3’ RNA kit

tag: tissue

value: male

value: unknown

value: lung

value: recurrence

value: metastasis

tag: treatment status

value: treated


title: Gls1.Mpc2.dKOB.GCB.1

description: Library name: Gls1.Mpc2.dKOB.GCB.1

tag: cell type

value: Germinal Center B cell

value: Gls1-KO, Mpc2-KO

tag: treatment

value: SRBC immunization

tag: batch


title: mES, dTAG_DGCR8, non_dTAG, SPT5, rep2

description: Library name: mES, dTAG_DGCR8, non_dTAG, SPT5, rep2

tag: cell line

value: Embryonic stem cells

tag: genotype

value: SPT5(Proteintech, Cat#16511-1-AP)


title: SJRHB046156_X2

description:
Library name: SJRHB046156_X2
10X Genomics 3’ RNA kit

source_name: ARMS

value: ARMS

tag: group

value: O-PDX

tag: method

value: female

value: Forearm

value: Breast


title: SJRHB030787_X1

description:
Library name: SJRHB030787_X1
10X Genomics 3’ RNA kit

value: nucleus

tag: sjid

tag: age

value: Unknown

value: Pancreas

value: untreated


title: mES, dTAG_DGCR8, non_dTAG, SPT5, rep1

description: Library name: mES, dTAG_DGCR8, non_dTAG, SPT5, rep1

tag: chip antibody


title: mES, dTAG_DGCR8, non_dTAG, ERH, rep2

description: Library name: mES, dTAG_DGCR8, non_dTAG, ERH, rep2

value: ERH(Proteintech, Cat# 15974-1-AP)


title: SJRHB030705_X1

description:
Library name: SJRHB030705_X1
10X Genomics 3’ RNA kit

tag: gender

value: unknown

value: Peritracheal node

value: diagnostic

value: metastasis


title: mES, dTAG_DGCR8, non_dTAG, ERH, rep1

description: Library name: mES, dTAG_DGCR8, non_dTAG, ERH, rep1


title: SJRB030281_X1

description:
Library name: SJRB030281_X1
10X Genomics 3’ RNA kit

source_name: RB

value: RB

tag: primary site

value: Eye

value: primary

value: treated


title: SJOS063824_X1

description:
Library name: SJOS063824_X1
10X Genomics 3’ RNA kit

value: OS

value: O-PDX

value: male

value: Femur

tag: sample site


title: mES, dTAG_DROSHA, dTAG_3h, SPT5, rep2

description: Library name: mES, dTAG_DROSHA, dTAG_3h, SPT5, rep2

value: Embryonic stem cells

value: SPT5(Proteintech, Cat#16511-1-AP)


title: SJOS063819_X1

description:
Library name: SJOS063819_X1
10X Genomics 3’ RNA kit

value: nucleus

value: female

tag: timepoint


title: mES, dTAG_DROSHA, dTAG_3h, ERH, rep2

description: Library name: mES, dTAG_DROSHA, dTAG_3h, ERH, rep2

value: ERH(Proteintech, Cat# 15974-1-AP)


title: mES, dTAG_DROSHA, dTAG_3h, SPT5, rep1

description: Library name: mES, dTAG_DROSHA, dTAG_3h, SPT5, rep1


title: SJOS046149_X1

description:
Library name: SJOS046149_X1
10X Genomics 3’ RNA kit

value: unknown

value: Back

value: recurrence

tag: sample

value: untreated


title: Largemouth bass Gill, 0h post-challenge, Pre, biological replicate 1

description:
Library name: 00S0G
Pre-challenge baseline (0h); 0h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

source_name: Gill

tag: tissue

value: Gill

value: Pre-challenge baseline (0h)

tag: sample group


title: Largemouth bass Gill, 24h post-challenge, AhFc, biological replicate 2 [29Q2G]

description:
Library name: 29Q2G
A. hydrophila + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: SJSTS030383_X2

description:
Library name: SJSTS030383_X2
10X Genomics 3’ RNA kit

value: URCS

value: neck

value: diagnostic

value: primary

tag: treatment status


title: mES, dTAG_DROSHA, dTAG_3h, ERH, rep1

description: Library name: mES, dTAG_DROSHA, dTAG_3h, ERH, rep1

tag: cell type

tag: treatment


title: SJRHB049188_X1_rep2

description:
Library name: SJRHB049188_X1_rep2
10x Genomics 3' RNA kit

source_name: tumor

value: tumor

tag: sample type

value: O-PDX

tag: disease

value: ERMS

value: cell

value: M

value: Retroperitoneum

value: treated


title: mES, dTAG_DGCR8, dTAG_3h, SPT5, rep1

description: Library name: mES, dTAG_DGCR8, dTAG_3h, SPT5, rep1

tag: cell line

value: Embryonic stem cells

tag: genotype

value: SPT5(Proteintech, Cat#16511-1-AP)


title: SJOS030441_X1

description:
Library name: SJOS030441_X1
10X Genomics 3’ RNA kit

value: OS

tag: group

tag: method

value: nucleus

tag: sjid

value: male

value: Bone

value: Lung

value: recurrence

value: metastasis


title: mES, dTAG_DROSHA, non_dTAG, SPT5, rep2

description: Library name: mES, dTAG_DROSHA, non_dTAG, SPT5, rep2

tag: chip antibody


title: SJRHB013759_X1_rep3

description:
Library name: SJRHB013759_X1_rep3
10x Genomics 3' RNA kit

value: ARMS

tag: age

tag: gender

tag: primary site

value: Pelvis

value: Inguinal mass

value: untreated


title: SJOS030279_X1

description:
Library name: SJOS030279_X1
10X Genomics 3’ RNA kit

value: O-PDX

value: female

value: Femur

tag: sample site

tag: timepoint

value: diagnostic

tag: sample

value: primary


title: mES, dTAG_DROSHA, non_dTAG, SPT5, rep1

description: Library name: mES, dTAG_DROSHA, non_dTAG, SPT5, rep1

value: Embryonic stem cells

value: SPT5(Proteintech, Cat#16511-1-AP)


title: SJOS030101_X1

description:
Library name: SJOS030101_X1
10X Genomics 3’ RNA kit

tag: tissue

value: OS

value: nucleus

tag: treatment status

value: treated


title: SJRHB012_X_rep2

description:
Library name: SJRHB012_X_rep2
10x Genomics 3' RNA kit

value: tumor

value: ERMS

value: cell

value: M

value: Prostate


title: mES, dTAG_DROSHA, non_dTAG, ERH, rep2

description: Library name: mES, dTAG_DROSHA, non_dTAG, ERH, rep2

tag: cell type

tag: treatment

value: ERH(Proteintech, Cat# 15974-1-AP)


title: SJOS016016_X1

description:
Library name: SJOS016016_X1
10X Genomics 3’ RNA kit

value: male

value: Tibia

value: recurrence


title: mES, dTAG_DROSHA, non_dTAG, ERH, rep1

description: Library name: mES, dTAG_DROSHA, non_dTAG, ERH, rep1


title: SJOS016015_X1

description:
Library name: SJOS016015_X1
10X Genomics 3’ RNA kit

value: O-PDX

value: Femur


title: Exp_3_UK5099

description: Library name: Exp_3_UK5099

source_name: Germinal Center B cell

value: Germinal Center B cell

tag: strain

tag: batch


title: mES, dTAG_ERH, dTAG_3h, SPT5, rep2

description: Library name: mES, dTAG_ERH, dTAG_3h, SPT5, rep2

tag: cell line

value: Embryonic stem cells

tag: genotype


title: mES, dTAG_ERH, non_dTAG, SPT5, rep2

description: Library name: mES, dTAG_ERH, non_dTAG, SPT5, rep2

value: SPT5(Proteintech, Cat#16511-1-AP)


title: Exp_3_Unactivated

description: Library name: Exp_3_Unactivated

value: Unstimulated/Unactivated


title: SJOS013769_X1

description:
Library name: SJOS013769_X1
10X Genomics 3’ RNA kit

value: OS

tag: group

tag: method

value: nucleus

value: diagnostic

value: primary


title: SJOS013768_X3

description:
Library name: SJOS013768_X3
10X Genomics 3’ RNA kit

tag: sjid

value: female

value: treated


title: Exp_3_Veh

description: Library name: Exp_3_Veh

value: Vehicle Control


title: mES, dTAG_ERH, dTAG_3h, SPT5, rep1

description: Library name: mES, dTAG_ERH, dTAG_3h, SPT5, rep1

tag: chip antibody


title: mES, dTAG_ERH, non_dTAG, SPT5, rep1

description: Library name: mES, dTAG_ERH, non_dTAG, SPT5, rep1


title: SJOS012409_X1

description:
Library name: SJOS012409_X1
10X Genomics 3’ RNA kit

tag: age

tag: gender


title: SJOS010929_X1

description:
Library name: SJOS010929_X1
10X Genomics 3’ RNA kit

tag: primary site

tag: sample site

value: untreated


title: F_KO_896

city: Jinan

first: Fei

last: Xie

address: 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province

institute: Qilu Hospital of Shandong University

description: Library name: Sample 6

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: epididymal white adipose tissue

growth_protocol: All mice were housed and maintained in a germ-free environment with an ad libitum supply of food and water, a 12-h light/dark cycle, an ambient temperature of 20–26°C and humidity of 40%–70%.

extract_protocol:
Total RNA was extracted with an RNA extraction kit (Fastagen Biotech Co., RNAfast200)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eight-week-old ILF3flox/flox and ILF3AKO mice were fed with either a HFD (60% fat) for 16 weeks.

value: epididymal white adipose tissue

value: KO

value: high fat diet


title: F_KO_895

description: Library name: Sample 5


title: SJOS003939_X1

description:
Library name: SJOS003939_X1
10X Genomics 3’ RNA kit

source_name: OS

value: O-PDX

value: male

value: Humerus

tag: timepoint

tag: sample


title: F_KO_894

description: Library name: Sample 4

tag: tissue


title: SJOS001112_X1

description:
Library name: SJOS001112_X1
10X Genomics 3’ RNA kit

value: Bone

value: Lung

value: recurrence

value: metastasis

tag: treatment status


title: SJOS001108_X1

description:
Library name: SJOS001108_X1
10X Genomics 3’ RNA kit

value: OS

value: nucleus

value: unknown


title: F_WT_1294

description: Library name: Sample 2

value: WT

tag: treatment


title: SJMRT063832_X1

description:
Library name: SJMRT063832_X1
10X Genomics 3’ RNA kit

source_name: MRT

value: MRT

value: paraspinal mass

value: diagnostic

value: primary

value: treated


title: Pdk4_Scrambled_sgRNA-Rep2

city: Nanjing

first: YIQIU

last: WU

state: Jiangsu

address: LongMian Road

institute: Nanjing medical university

description: Library name: Pdk4_Scrambled_sgRNA-Rep2

data_processing:
The raw bisulfite sequencing reads were trimmed to remove adaptors and low-quality bases by using trim_galore (v0.6.10) (parameters: -q 20 --phred33 --length 30 --stringency 3 --paired --clip_R1 10 --clip_R2 10). Next, Bismark (v0.24.2) was used to map clean reads to GRCm38/GRCh38 with single-end alignment mode (parameters: --non_directional --bowtie2 --bam --single_end). PCR duplicates were removed using deduplicate_bismark with default parameters. And only the high-quality reads (MAPQ > 10) were retained for further analysis. DNA methylation level estimation. The DNA methylation level of each cytosine site in the reference genome sequence was calculated as the percentage of reads supporting C (methylated). Unless otherwise specified, the DNA methylation level of CpG sites in a given sample or region refers to the average methylation level across that sample or region. Owing to the low number of input cells, CpG sites with read depths ≥3 were included for methylation analysis.
Assembly: GRCm39
Supplementary files format and content: BigWig including CG sites methylation values for each sample
Library strategy: EM-seq

source_name: oocyte

extract_protocol:
Collect 15 mouse oocytes
Whole-genome bisulfite sequencing (WGBS) was performed on mouse oocytes using 15 oocytes as input, whereas Enzymatic Methyl-seq (EM-seq) was applied to human oocytes starting from a single cell due to its high efficiency with minimal input. Library preparation and sequencing: Mouse metaphase II (MII) oocytes (n = 15 per replicate, two biological replicates per group) were used for WGBS. Briefly, cells were lysed in buffer (10 mM Tris-HCl, pH 7.4, 2% SDS), and genomic DNA was extracted and digested with proteinase K. Purified DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (ZYMO, D5008), followed by purification with Agencourt AMPure XP beads (Beckman). The converted DNA was end-repaired and dA-tailed, then ligated to Illumina sequencing adapters. Libraries were amplified for 13 cycles using Illumina universal PCR primer and indexed primers. For human samples, individual oocytes were lysed and genomic DNA were fragmented to ~ 300 bp using a DNA fragmentation device (Shanghai Jingxin, DNA Fragmentation Model 26A). Libraries were constructed using the NEBNext® Enzymatic Methyl-seq kit (NEB, E7120 L) and the Unique Dual Index Primer pairs (NEB, E7140L). Unmethylated lambda phage DNA and CpG-methylated plasmid pUC19 DNA were included as negative and positive controls. For single-oocyte libraries, amplification was performed for 18 cycles. Libraries were purified using the DNA Clean & Concentrator-5 kit (ZYMO, D4013). Finally, equimolar amounts of libraries were pooled and subjected to paired-end sequencing on an Illumina NovaSeq 6000 platform.

value: oocyte

tag: cell type


title: Pdk4_sgRNA-Rep1

description: Library name: Pdk4_sgRNA-Rep1


title: Pdk4_sgRNA-Rep2

description: Library name: Pdk4_sgRNA-Rep2


title: Hnf1a_sgRNA-Rep2

description: Library name: Hnf1a_sgRNA-Rep2


title: F_WT_1292

description: Library name: Sample 1

value: epididymal white adipose tissue

value: high fat diet


title: SJIFS030375_X1

description:
Library name: SJIFS030375_X1
10X Genomics 3’ RNA kit

source_name: IFS

value: IFS

value: O-PDX

value: male

value: thigh


title: Hnf1a_sgRNA-Rep1

description: Library name: Hnf1a_sgRNA-Rep1


title: SJMEL030083_X1

description:
Library name: SJMEL030083_X1
10X Genomics 3’ RNA kit

source_name: MEL

value: MEL

value: leg

value: recurrence

value: metastasis


title: SJEWS063834_X2

description:
Library name: SJEWS063834_X2
10X Genomics 3’ RNA kit

source_name: EWS

value: EWS

value: nucleus

value: female

value: unknown

value: lung

value: untreated


title: Hnf1a_Scrambled_sgRNA-Rep2

description: Library name: Hnf1a_Scrambled_sgRNA-Rep2

value: oocyte


title: F_WT_899

description: Library name: Sample 3

value: epididymal white adipose tissue

value: WT


title: Hnf1a_Scrambled_sgRNA-Rep1

description: Library name: Hnf1a_Scrambled_sgRNA-Rep1


title: SJEWS063826_X1

description:
Library name: SJEWS063826_X1
10X Genomics 3’ RNA kit

value: rib

value: axilla


title: KO, P0, rep4

first: YIYING

last: ZHANG

state: New York

address: 1150 St. Nicholas Ave

department: Pediatrics

institute: Columbia University

description: Library name: RG309

data_processing:
fastq files were aligned to the mouse reference genome GRCm39 using HISAT2 in Galaxy Version 21.01
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Assembly: mouse reference genome GRCm39
Supplementary files format and content: tab-delimited text file containing raw integer gene-level counts of all samples

source_name: pituitary

growth_protocol: Pituitaries were collected and flash-frozen in liquid nitrogen and stored at -80oC before RNA extraction

extract_protocol:
RNA was isolated using Total RNA Purification Plus Micro Kit  (Norgen Biotek) and processed as per manufacturer’s instructions.
libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold (Illumina) with Ribo-Zero Plus rRNA Depletion Kit  according to the manufacturer’s instructions.

treatment_protocol: no treatment

value: pituitary

tag: Sex

value: male

value: Snord116 KO


title: SJEWS049193_X2

description:
Library name: SJEWS049193_X2
10X Genomics 3’ RNA kit

value: O-PDX

value: ilium

value: treated


title: SJEWS049193_X1

description:
Library name: SJEWS049193_X1
10X Genomics 3’ RNA kit

value: EWS

value: recurrence

value: metastasis


title: KO, P0, rep3

description: Library name: RG308


title: KO, P0, rep2

description: Library name: RG307


title: SJEWS001321_X1

description:
Library name: SJEWS001321_X1
10X Genomics 3’ RNA kit

value: nucleus

value: tibia

value: diagnosis

value: primary


title: SJSTS046147_X1

description:
Library name: SJSTS046147_X1
10X Genomics 3’ RNA kit

source_name: EPSARC

value: EPSARC

value: spine

value: diagnostic

value: untreated


title: WT, P0, rep5

description: Library name: RG305

value: pituitary

value: wild-type


title: SJDSRCT030722_X1

description:
Library name: SJDSRCT030722_X1
10X Genomics 3’ RNA kit

source_name: DSRCT

value: DSRCT

value: male

value: unknown

value: thigh

value: metastatic


title: WT, P0, rep4

description: Library name: RG304


title: SJCCS030604_X1

description:
Library name: SJCCS030604_X1
10X Genomics 3’ RNA kit

source_name: CCSST

value: CCSST

value: O-PDX

value: female

value: thumb

value: recurrence

value: treated


title: SJCCS030167_X1

description:
Library name: SJCCS030167_X1
10X Genomics 3’ RNA kit

source_name: CCSK

value: CCSK

value: nucleus

value: kidney

value: primary


title: WT, P0, rep3

description: Library name: RG303

value: pituitary


title: WT, P0, rep2

description: Library name: RG302

value: wild-type


title: SJACT030812_X2

description:
Library name: SJACT030812_X2
10X Genomics 3’ RNA kit

source_name: ACT

value: ACT

value: Abdomen

value: Distal pancreas

value: diagnostic

value: no


title: SJACT030812_X1

description:
Library name: SJACT030812_X1
10X Genomics 3’ RNA kit

value: male

value: Adrenal mass


title: WT, W4, rep5

description: Library name: RG110

value: 4 week


title: KO, W4, rep5

description: Library name: RG109

value: Snord116 KO


title: SJWT046158_D1

description:
Library name: SJWT046158_D1
10X Genomics 3’ RNA kit

source_name: WT

value: WT

value: Patient

value: female

value: untreated


title: KO, W4, rep4

description: Library name: RG108


title: SJWT046152_D1

description:
Library name: SJWT046152_D1
10X Genomics 3’ RNA kit

value: nucleus

value: kidney


title: KO, W4, rep3

description: Library name: RG107

value: pituitary


title: KO, W4, rep2

description: Library name: RG106


title: SJWT049191_D1

description:
Library name: SJWT049191_D1
10X Genomics 3’ RNA kit

value: primary


title: WT, W4, rep4

description: Library name: RG105

value: wild-type


title: SJSTS030383_D2

description:
Library name: SJSTS030383_D2
10X Genomics 3’ RNA kit

source_name: URCS

value: URCS

value: neck

value: treated


title: SJSTS030383_D1

description:
Library name: SJSTS030383_D1
10X Genomics 3’ RNA kit

value: lymph node

value: diagnostic

value: metastasis


title: WT, W, rep3

description: Library name: RG104

value: male

value: 4 week


title: KO, W4, rep1

description: Library name: RG103

value: Snord116 KO


title: WT, W4, rep2

description: Library name: RG102


title: SJSS049190_R1

description:
Library name: SJSS049190_R1
10X Genomics 3’ RNA kit

source_name: SS

value: SS

value: Patient

value: unknown

value: lung

value: recurrence


title: WT, W4, rep1

description: Library name: RG101

value: pituitary


title: SJHGS030131_D1

description:
Library name: SJHGS030131_D1
10X Genomics 3’ RNA kit

source_name: SCS

value: SCS

value: nucleus

value: femur

value: primary

value: untreated


title: SJST030705_D1

description:
Library name: SJST030705_D1
10X Genomics 3’ RNA kit

source_name: ARMS

value: ARMS

value: female

value: Peritracheal node


title: DX.3_Normal bladder_mouse

city: Buffalo

first: Qiang

last: Li

address: Elm and Carlton Streets

department: Urology

institute: Roswell Park Comprehensive Cancer Center

description: Library name: DX-3

data_processing:
Bulk RNA-seq reads were first assessed for quality using fastqc and then mapped to the mouse GRCm38-mm10 genome using STAR and quantified with RSEM. Features were filtered if not expressed in more than 3 samples. Normalized counts were calculated within DESeq2 with variance stabilization.
Assembly: GRCm38-mm10
Supplementary files format and content: matrix of TPM counts per gene

source_name: bladder

extract_protocol:
Cells were scratched from the bladder lumen, centrifuged and stored as frozen pellet prior to RNA extraction. Total RNA was extracted from frozen bladder tumors (20 mg) using Qiazol reagent and miRNeasy Mini Kit (Qiagen).
The sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing Solutions), from 500 ng total RNA. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 following the manufacturer’s protocol.

value: bladder

value: no Cre Triple-floxed mice (Trp53 f/f, Pten f/f, Rb1f/f) from normal bladder


title: SJRHB063825_R1

description:
Library name: SJRHB063825_R1
10X Genomics 3’ RNA kit

source_name: ERMS

value: ERMS

value: male

value: Bladder/prostate

value: treated


title: DX.2_Normal bladder_mouse

description: Library name: DX-2


title: SJWT046146_D1

description:
Library name: SJWT046146_D1
10X Genomics 3’ RNA kit

value: WT

value: Patient

value: kidney

value: diagnostic


title: SJRHB063823_D1

description:
Library name: SJRHB063823_D1
10X Genomics 3’ RNA kit

value: nucleus

value: Unknown

value: Back soft tissue

value: unknown


title: DX.1_Normal bladder_mouse

description: Library name: DX-1


title: SJSS063828_D1

description:
Library name: SJSS063828_D1
10X Genomics 3’ RNA kit

value: SS

value: femur

value: primary


title: SJRHB049188_D1

description:
Library name: SJRHB049188_D1
10X Genomics 3’ RNA kit

value: Retroperitoneum


title: Normal bladder, mouse

description: Library name: UPTOM-Bladder-Normal

data_processing:
10x Cell Ranger Pipeline
aligned with modified mm10 genome with Egfp
Assembly: mm10
Supplementary files format and content: 10x Cell Ranger outs

extract_protocol:
Male bladder fundus tissues were collected from four Upk2-Cre;mT/mG mice and then cut into half pieces, and the bladder lumens were unfolded. These tissue pieces were placed in 5.0 mL of biopsy medium containing a 1:10 dilution of collagenase/hyaluronidase (STEMCELL Technologies) and incubated at 37 °C for 1 hour with shaking. Following digestion, the cell pellet was resuspended in 1 mL of TrypLE™ Express Enzyme for 5 minutes, then treated with 1 mL of ACK lysis buffer (Gibco) for 2 minutes. The suspension was filtered using a 40 μm strainer to obtain a single-cell suspension. The alive singlets were isolated via flow cytometry prior to single-cell RNA sequencing.
Single-cell libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1. Cell suspensions were first evaluated with Trypan Blue staining on a Countess FL automated cell counter (ThermoFisher) to assess concentration, viability, and the absence of cell clumps or debris that could interfere with single-cell encapsulation. Cells were then loaded into the Chromium Controller (10X Genomics), where they were partitioned into nanoliter-scale Gel Beads-in-Emulsion (GEMs), each containing a unique barcode for individual cells. Reverse transcription was carried out within the GEMs, followed by amplification of the resulting cDNA. Amplified full-length cDNA was used to construct gene expression libraries through enzymatic fragmentation, end-repair, A-tailing, adapter ligation, and PCR amplification to incorporate Illumina-compatible sequencing adapters. The final libraries were assessed using D1000 screentape on a TapeStation 4200 (Agilent Technologies) and quantified using the KAPA qPCR quantification kit for Illumina platforms (Kapa Biosystems). Libraries were pooled, denatured, and diluted to 300 pM with 1% PhiX control, then loaded onto a NovaSeq Reagent cartridge and sequenced on the NovaSeq 6000 system according to Illumina’s recommended protocol by the Roswell Park Comprehensive Cancer Center Genomics Shared Resource.

value: bladder


title: SJRHB046156_A2

description:
Library name: SJRHB046156_A2
10X Genomics 3’ RNA kit

value: ARMS

value: female

value: Forearm

value: Breast

value: recurrence

value: metastasis

value: untreated


title: s 3-3-2

city: Hangzhou

first: Zeyu

last: Ma

address: No. 3 Qingchun East Road

department: Department of Gastroenterology

institute: Sir Run Run Shaw Hospital, Medical School of Zhejiang University

description: Library name: sample6

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Assembly: GRCm39
Supplementary files format and content: tab-delimited tex file include FPKM values for each Sample

source_name: skin

extract_protocol:
Total RNA was extracted using the TRIzol reagent(Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instruction.

value: skin

value: Lenv-Treg


title: SJRHB030787_D1

description:
Library name: SJRHB030787_D1
10X Genomics 3’ RNA kit

value: Patient

value: nucleus

value: Unknown

value: Pancreas


title: DX.4_Normal bladder_mouse

description: Library name: DX-4

value: no Cre Triple-floxed mice (Trp53 f/f, Pten f/f, Rb1f/f) from normal bladder


title: s 3-2-2

description: Library name: sample5


title: SJRHB015721_D1

description:
Library name: SJRHB015721_D1
10X Genomics 3’ RNA kit

value: ERMS

value: male

value: Paratesticular mass

value: primary

value: treated


title: s 3-1-2

description: Library name: sample4


title: SJRHB015720_D1

description:
Library name: SJRHB015720_D1
10X Genomics 3’ RNA kit

source_name: SRMS

value: SRMS

value: female

value: Sinus

value: Oropharynx


title: s 1-3-2

description: Library name: sample3

value: Ctrl-Treg


title: SJRB030403_D1

description:
Library name: SJRB030403_D1
10X Genomics 3’ RNA kit

source_name: RB

value: RB

value: eye

value: diagnostic

value: untreated


title: s 1-2-2

description: Library name: sample2

value: skin


title: SJOS003939_X2_sn

description:
Library name: SJOS003939_X2_sn
10X Genomics 3’ RNA kit

source_name: OS

value: OS

value: O-PDX

value: nucleus

value: Humerus

value: Lung

value: recurrence

value: metastasis

value: unknown


title: SJRB030317_D1

description:
Library name: SJRB030317_D1
10X Genomics 3’ RNA kit

value: Patient

value: male

value: primary


title: s 1-1-2

description: Library name: sample1

value: Ctrl-Treg


title: SJOS003939_X2_sc

description:
Library name: SJOS003939_X2_sc
10X Genomics 3’ RNA kit

value: cell


title: SJMRT031055_X1

description:
Library name: SJMRT031055_X1
10X Genomics 3’ RNA kit

source_name: MRT

value: MRT

value: liver

value: Iiver


title: SJMRT015723_X1

description:
Library name: SJMRT015723_X1
10X Genomics 3’ RNA kit

value: chest wall

value: treated


title: SJRB030304_D1

description:
Library name: SJRB030304_D1
10X Genomics 3’ RNA kit

value: RB

value: eye

value: diagnostic

value: untreated


title: int 3-3

description: Library name: sample6

source_name: large intestine

value: large intestine


title: SJRB030281_D1

description:
Library name: SJRB030281_D1
10X Genomics 3’ RNA kit

value: nucleus

value: female


title: Pdk4_Scrambled_sgRNA-Rep1

description: Library name: Pdk4_Scrambled_sgRNA-Rep1

source_name: oocyte

value: oocyte


title: int 3-2

description: Library name: sample5


title: SJRB030252_D1

description:
Library name: SJRB030252_D1
10X Genomics 3’ RNA kit

value: Patient


title: int 3-1

description: Library name: sample4


title: SJRB030241_D1

description:
Library name: SJRB030241_D1
10X Genomics 3’ RNA kit

value: primary


title: SJRB030135_R1

description:
Library name: SJRB030135_R1
10X Genomics 3’ RNA kit

value: male

value: recurrence


title: int 2-2

description: Library name: sample2


title: int 2-3

description: Library name: sample3


title: SJOS063833_D2

description:
Library name: SJOS063833_D2
10X Genomics 3’ RNA kit

value: OS

value: Femur


title: int 2-1

description: Library name: sample1


title: SJEWS063829_X1

description:
Library name: SJEWS063829_X1
10X Genomics 3’ RNA kit

source_name: EWS

value: EWS

value: O-PDX

value: femur

value: diagnosis


title: SJOS063833_D1

description:
Library name: SJOS063833_D1
10X Genomics 3’ RNA kit

value: Lung

value: metastasis

value: treated


title: mES, dTAG_DROSHA, dTAG24h, ERH, rep2

description: Library name: mES, dTAG_DROSHA, dTAG24h, ERH, rep2

tag: cell line

value: Embryonic stem cells

value: dTAG 24h

value: ERH(Proteintech, Cat# 15974-1-AP)


title: KO, P0, rep5

description: Library name: RG310

source_name: pituitary

value: pituitary

tag: genotype

value: Snord116 KO


title: SJOS063822_A1

description:
Library name: SJOS063822_A1
10X Genomics 3’ RNA kit

tag: group

value: Patient

value: nucleus

value: Bone


title: mES, dTAG_DROSHA, DMSO, ERH, rep2

description: Library name: mES, dTAG_DROSHA, DMSO, ERH, rep2

value: DMSO 24h


title: SJOS063824_D1

description:
Library name: SJOS063824_D1
10X Genomics 3’ RNA kit

value: OS

tag: method

value: male

value: Femur

value: diagnostic

value: primary


title: KO, P0, rep1

description: Library name: RG306


title: SJOS063819_D2

description:
Library name: SJOS063819_D2
10X Genomics 3’ RNA kit

tag: sjid

value: female


title: mES, dTAG_DGCR8, dTAG24h, ERH, rep1

description: Library name: mES, dTAG_DGCR8, dTAG24h, ERH, rep1

tag: chip antibody


title: SJDSRCT049192_X1

description:
Library name: SJDSRCT049192_X1
10X Genomics 3’ RNA kit

source_name: DSRCT

value: DSRCT

value: O-PDX

tag: age

value: abdominopelvic


title: mES, dTAG_DGCR8, DMSO, ERH, rep1

description: Library name: mES, dTAG_DGCR8, DMSO, ERH, rep1

value: Embryonic stem cells


title: SJOS046149_R1

description:
Library name: SJOS046149_R1
10X Genomics 3’ RNA kit

tag: gender

value: unknown

value: Back

value: recurrence

value: metastasis

value: untreated


title: mES, dTAG_DROSHA, dTAG24h, FLAG, rep2

description: Library name: mES, dTAG_DROSHA, dTAG24h, FLAG, rep2

value: dTAG 24h


title: SJOS031478_D1

description:
Library name: SJOS031478_D1
10X Genomics 3’ RNA kit

value: Patient

value: nucleus

tag: primary site

value: Humerus

value: treated


title: mES, dTAG_DGCR8, dTAG24h, FLAG, rep2

description: Library name: mES, dTAG_DGCR8, dTAG24h, FLAG, rep2


title: SJOS030645_D2

description:
Library name: SJOS030645_D2
10X Genomics 3’ RNA kit

value: OS

value: male

value: Femur

tag: sample site

value: Lung


title: mES, dTAG_DROSHA, DMSO, FLAG, rep2

description: Library name: mES, dTAG_DROSHA, DMSO, FLAG, rep2

value: DMSO 24h


title: SJOS030605_D2

description:
Library name: SJOS030605_D2
10X Genomics 3’ RNA kit

value: female

tag: timepoint


title: mES, dTAG_DGCR8, DMSO, FLAG, rep2

description: Library name: mES, dTAG_DGCR8, DMSO, FLAG, rep2

value: Embryonic stem cells


title: SJOS030605_D1

description:
Library name: SJOS030605_D1
10X Genomics 3’ RNA kit

value: Chest wall

tag: sample

value: primary


title: mES, dTAG_DROSHA, dTAG24h, FLAG, rep1

description: Library name: mES, dTAG_DROSHA, dTAG24h, FLAG, rep1


title: SJOS030597_D1

description:
Library name: SJOS030597_D1
10X Genomics 3’ RNA kit

tag: tissue

value: recurrence


title: mES, dTAG_DROSHA, DMSO, FLAG, rep1

description: Library name: mES, dTAG_DROSHA, DMSO, FLAG, rep1


title: SJOS030441_D1

description:
Library name: SJOS030441_D1
10X Genomics 3’ RNA kit

value: Bone

value: metastasis

tag: treatment status


title: mES, dTAG_DGCR8, dTAG24h, FLAG, rep1

description: Library name: mES, dTAG_DGCR8, dTAG24h, FLAG, rep1

tag: treatment

value: dTAG 24h


title: SJOS030279_D1

description:
Library name: SJOS030279_D1
10X Genomics 3’ RNA kit

value: Patient

value: diagnostic


title: SJOS030272_D1

description:
Library name: SJOS030272_D1
10X Genomics 3’ RNA kit

value: nucleus


title: mES, dTAG_DROSHA, dTAG3h, PROseq, rep2

description: Library name: mES, dTAG_DROSHA, dTAG3h, PROseq, rep2

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with “-q 25”, remaining reads were mapped to mouse rDNA database using Bowtie (v2.5.1) with parameter “--very-sensitive-local” to remove rRNA contamination. Unmapped reads were aligned to mm10 genome and hg38 genome respectively, with default parameter. Samtools (v1.11) was used to filter and deduplicate SAM files. The counts of spike-in hg38 reads were used to generate normalization factors for coverage profiles.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files
Library strategy: PRO-seq

extract_protocol:
RNA was isolated with TRIzol.
Permeabilized cells were subjected to nuclear run-on reactions in the presence of biotin-labeled nucleotides. Biotinylated nascent RNA was extracted, fragmented by base hydrolysis, and enriched using streptavidin magnetic beads. Enriched RNA was ligated with a 3' RNA adaptor using T4 RNA ligase I, followed by another round of streptavidin bead enrichment. The 5' ends were then decapped with RNA 5' Pyrophosphohydrolase (RppH) and repaired with Polynucleotide Kinase (PNK) before ligation to a 5' RNA adaptor with T4 RNA ligase I. Adaptor-ligated RNA was enriched again with streptavidin beads. Reverse transcription (RT) was performed using Superscript IV (Thermo Fisher Scientific) with a custom RT primer. The reverse transcription products were proceeded to library amplification using Phusion polymerase (NEB) for 12-14 cycles. Libraries were sequenced on the Illumina NovaSeq platform in paired-end 60/50 bp cycle runs following the manufacturer's protocols.

treatment_protocol: dTAG Cells were treated with DMSO or dTAG-13 for 3h.

tag: cell type

value: dTAG 3h


title: mES, dTAG_DROSHA, DMSO, PROseq, rep2

description: Library name: mES, dTAG_DROSHA, DMSO, PROseq, rep2

value: DMSO 3h


title: SJOS030101_D1

description:
Library name: SJOS030101_D1
10X Genomics 3’ RNA kit

value: OS

value: male

value: treated


title: SJOS016016_D1

description:
Library name: SJOS016016_D1
10X Genomics 3’ RNA kit

value: Tibia


title: SJOS016015_D1

description:
Library name: SJOS016015_D1
10X Genomics 3’ RNA kit

value: Femur


title: mES, dTAG_DGCR8, dTAG3h, PROseq, rep2

description: Library name: mES, dTAG_DGCR8, dTAG3h, PROseq, rep2

value: Embryonic stem cells


title: mES, dTAG_DGCR8, DMSO, PROseq, rep2

description: Library name: mES, dTAG_DGCR8, DMSO, PROseq, rep2


title: mES, dTAG_DROSHA, dTAG3h, PROseq, rep1

description: Library name: mES, dTAG_DROSHA, dTAG3h, PROseq, rep1


title: SJOS013769_D1

description:
Library name: SJOS013769_D1
10X Genomics 3’ RNA kit


title: mES, dTAG_DROSHA, DMSO, PROseq, rep1

description: Library name: mES, dTAG_DROSHA, DMSO, PROseq, rep1


title: SJOS013768_M1

description:
Library name: SJOS013768_M1
10X Genomics 3’ RNA kit

value: female

value: Lung


title: SJOS013768_D1_repB

description:
Library name: SJOS013768_D1_repB
10X Genomics 3’ RNA kit

value: primary


title: SJOS013768_D1

description:
Library name: SJOS013768_D1
10X Genomics 3’ RNA kit


title: mES, dTAG_DGCR8, DMSO, PROseq, rep1

description: Library name: mES, dTAG_DGCR8, DMSO, PROseq, rep1


title: SJOS010930_D1

description:
Library name: SJOS010930_D1
10X Genomics 3’ RNA kit

value: Humerus


title: mES, dTAG_ERH, dTAG3h, TTseq, rep1

description: Library name: mES, dTAG_ERH, dTAG3h, TTseq, rep1

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with “-q 25”, remaining reads were mapped to mouse rDNA database using Bowtie (v2.5.1) with parameter “--very-sensitive-local” to remove rRNA contamination. Unmapped reads were aligned to mm10 genome and hg38 genome respectively, with default parameter. Samtools (v1.11) was used to filter and deduplicate SAM files. The counts of spike-in hg38 reads were used to generate normalization factors for coverage profiles.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.


title: mES, dTAG_ERH, DMSO, TTseq, rep2

description: Library name: mES, dTAG_ERH, DMSO, TTseq, rep2


title: SJOS001132_M1

description:
Library name: SJOS001132_M1
10X Genomics 3’ RNA kit

value: Bone

value: recurrence

value: metastasis

value: untreated


title: SJOS001127_M1

description:
Library name: SJOS001127_M1
10X Genomics 3’ RNA kit

value: Patient

value: nucleus


title: mES, dTAG_DROSHA, dTAG3h, TTseq, rep2

description: Library name: mES, dTAG_DROSHA, dTAG3h, TTseq, rep2

value: dTAG 3h


title: mES, dTAG_ERH, DMSO, TTseq, rep1

description: Library name: mES, dTAG_ERH, DMSO, TTseq, rep1

value: DMSO 3h


title: mES, dTAG_DROSHA, dTAG3h, TTseq, rep1

description: Library name: mES, dTAG_DROSHA, dTAG3h, TTseq, rep1


title: SJOS001112_M2

description:
Library name: SJOS001112_M2
10X Genomics 3’ RNA kit

value: OS

value: male


title: mES, dTAG_DROSHA, DMSO, TTseq, rep2

description: Library name: mES, dTAG_DROSHA, DMSO, TTseq, rep2


title: mES, dTAG_DROSHA, DMSO, TTseq, rep1

description: Library name: mES, dTAG_DROSHA, DMSO, TTseq, rep1


title: SJOS001107_M2

description:
Library name: SJOS001107_M2
10X Genomics 3’ RNA kit


title: SJOS001108_M1

description:
Library name: SJOS001108_M1
10X Genomics 3’ RNA kit

value: unknown


title: SJOS001105_M1

description:
Library name: SJOS001105_M1
10X Genomics 3’ RNA kit

value: Femur


title: mES, dTAG_DGCR8, dTAG3h, TTseq, rep2

description: Library name: mES, dTAG_DGCR8, dTAG3h, TTseq, rep2

value: Embryonic stem cells


title: mES, dTAG_DGCR8, dTAG3h, TTseq, rep1

description: Library name: mES, dTAG_DGCR8, dTAG3h, TTseq, rep1


title: SJNBL047443_R1_repB

description:
Library name: SJNBL047443_R1_repB
10X Genomics 3’ RNA kit

source_name: NB

value: NB

value: Paraspinal Mass

value: chemotherapy


title: mES, dTAG_DGCR8, DMSO, TTseq, rep2

description: Library name: mES, dTAG_DGCR8, DMSO, TTseq, rep2


title: SJNBL047443_R1

description:
Library name: SJNBL047443_R1
10X Genomics 3’ RNA kit


title: mES, dTAG_DGCR8, DMSO, TTseq, rep1

description: Library name: mES, dTAG_DGCR8, DMSO, TTseq, rep1


title: SJMRT031055_D1

description:
Library name: SJMRT031055_D1
10X Genomics 3’ RNA kit

value: MRT

value: liver

value: Iiver

value: diagnostic

value: primary


title: SJMRT063832_D1

description:
Library name: SJMRT063832_D1
10X Genomics 3’ RNA kit

value: Patient

value: paraspinal mass

value: treated