title: RCC PBMC CD8-sorted single cell TCR-seq

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave. N.

department: Immunotherapy Integrated Research Center

institute: Fred Hutchinson Cancer Center

description:
Library name: Kidney_PBMC_CD8_TCR
10x Genomics

data_processing:
After 10X sequencing data was processed through the Cell Ranger pipeline (version 3.0.2, hg38 genome assembly) with default settings, filtered gene-barcode matrices for single cells were analyzed using the scanpy toolkit. Genes that were detected in less than three cells were filtered out, and cells were filtered out with greater than ten percent of mitochondrial genes and with fewer than 100 or greater than 2500 detected genes. Cells that were annotated as red blood cells (HBB) or macrophage (CD14, CD68, CD163) were also excluded from downstream analyses. The gene expression values were log2 plus one transformed and normalized to 10,000 counts per cell. The resulting matrix was batch corrected by regressing out total UMI counts and percent mitochondrial genes using the built-in scanpy function followed by using the scanpy implementation of Harmony with each cell sorted biospecimen acting as a batch (12 biospecimens total). The adjusted matrix was scaled to a mean of zero and variance of 1. Highly variable genes were selected using the embedded scanpy function followed by principal component analysis (PCA), leiden clustering and uniform manifold approximation and projection (UMAP) plotting with default settings. This yielded 20 clusters which were collapsed to 7 cell phenotypes based on manual annotation.  To characterize each cluster to individual cell types, we applied the rank_genes_group procedure in scanpy, which identifies markers using log fold changes of mean expression up-regulated in each cluster relative to the combination of all other single cells (regardless of tissue or cell type). We compared the gene lists to known literature to manually label the clusters.  TCR-seq data for each sample was processed using Cell Ranger software with the command ‘cellranger vdj’ using the default reference set of genes, based on human reference genome GRCh38 and RefSeq gene models. For each sample, Cell Ranger generated an output file, filtered_contig_annotations.csv, containing TCR α-chain and β-chain CDR3 nucleotide sequences for single cells that were identified by barcodes. Patient origins for TRA and TRB clonotypes were inferred by matching 10X barcodes from demultiplex paired single cell RNA sequence via demuxlet 57. Furthermore, for any given 10X barcode, the most abundant TRA or TRB clonotype was accepted for further analysis; if 2 TRA or TRB clonotypes were equally abundant for a given 10X barcode, the clonotype with the highest sequence alignment score was used for further analysis. Detailed sequencing statistics and saturation analysis are provided in (Supplementary Table 6). Only cells with paired TRA and TRB with identifiable patient origins were used for further downstream analysis.
Assembly: GRCh37/hg38
Supplementary files format and content: filtered single cell scanpy and TCR matrix used for downstream analysis. Included are also individual single cell TCR csv files from cellranger vdj
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
For single cell RNA and TCR-sequencing, resected surgical specimens were dissected and grossly identified as tumor or as “non-malignant” kidney. Once received, these tissues were immediately digested with DNAse I and Collagenase IV in RPMI media with mechanical dissociation at 37°C with 5% CO2 for 1 hour. Residual erythrocytes were lysed with ACK lysing buffer (Thermofisher) for 5 minutes and quenched with 10-fold excess PBS. Single cell suspensions were then strained through a 100um filter and counted for viability before downstream experiments such as flow cytometry or scRNAseq. Patient and healthy donor blood were collected in parallel. Peripheral blood mononuclear cells (PBMCs) were processed with Ficoll (Cytiva), isolated by gradient centrifugation and cryopreserved to be later thawed for validation experiments.
Sample processing for single-cell gene expression (scRNA-seq) and T cell receptor V(D)J clonotypes (scTCR-seq) was done using the Chromium Single Cell 5′ Library and Gel Bead Kit (10x Genomics), following the manufacturer’s user guide. CD3+CD4+, CD3+CD8+, and CD3+CD4+CD8+ T cells were sorted from digested tumor and non-malignant tissues, or Ficoll-purified and previously cryopreserved PBMCs, into 500 ul of PSA/0.04% BSA for loading onto 10X. After Gel Bead-in-Emulsion reverse transcription (GEM-RT) reaction and clean-up, a total of 13 cycles of PCR amplification were performed to obtain sufficient cDNAs used for both RNA-seq library generation and TCR V(D)J targeted enrichment followed by V(D)J library generation. TCR V(D)J enrichment was done per manufacturer’s user guide using Chromium Single Cell V(D)J Enrichment Kit, Human T cell (10x Genomics). Following library preparation, sequencing was performed on an Illumina NovaSeq 6000 on S4 flow cells. Patient samples were processed and pooled by sorted T cell populations in parallel during library preparation and sequenced on the same flowcell to minimize batch effects.

tag: tissue

value: PBMC

value: CD8+ T cells

tag: treatment

value: renal cell carcinoma


title: KYSE150-hypoxia-oxamate-rep2

status: Public on Jan 01 2026

type: SRA

city: Beijing

first: Ji

last: Cong

address: No.17, Panjiayuan Nanli, South Huawei Road

country: China

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Library name: Sample 6
Column name in gene_count_mat.txt:hypoxia-so-rep2

library_source: transcriptomic

data_processing:
Read quality was calculated for all samples by using FastQC (v0.11.9) (Andrews.2010) software with the default parameters.
Fastp(v0.20.1) (Chen S, el at. 2018) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed.
RNA-seq reads were aligned to the human genome hg38 using STAR (v2.7.8a), and the number of reads mapped to each gene was calculated by RSEM (v1.3.3).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: KYSE150 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA purification, reverse transcription, library construction and sequencing were performed in Mingma Technologies at Shanghai according to the manufacturer's instructions. The agarose gel electrophoresis was used to detect the integrity of the extracted RNA. And NanoDrop was used to measure the concentration of RNA.
The mRNAs containing oligoDT were enriched from the total RNA by magnetic beads, and the captured mRNAs were fragmented, then the reverse transcriptase was used to synthesize the strands of cDNA and repair the end of the transcripts product. An “A” base was added to the 3’ end of the product and the sequencing adapters were connected to the ends. The incomplete ligation products and empty linker self-ligation products were removed by the ligation products purification, and the primers complementary to the linker sequence were used for PCR amplification. Finally, the sequencing library was purified by magnetic beads.

treatment_protocol: KYSE150 cells were cultured under normoxia or hypoxia condition and treated with sodium oxamate or sodium lactate.

tag: cell line

tag: cell type

value: esophageal squamous cell carcinoma

value: hypoxia+oxamate


title: MUT7_Condition C

type: RNA

city: Avaino

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: DRDAT

country: Italy

institute: Centro di Riferimento Oncologico Aviano IRCCS

hyb_protocol: The hybridization was performed at 55°C for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides. Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green.

data_processing: Threshold: 1.0   Logbase: 2. Technology: Agilent.miRNA.70156_v21_0. Normalization: Quantile. Baseline Transformation: median of all samples

source_name: Peripheral Blood, control beads, agonist mix

label_protocol: The microarray was performed according to miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent). A total of 100ng of total RNA for each condition was used and labelled with Cyanine 3-pCp molecule.

extract_protocol: RNA was extracted with miRNeasy tissue/cell Advance kit (Quiagen), according to manufacturer's instruction, and RNA was quantified using a NanoDrop1000 spectrophotometer .

treatment_protocol: CLL cells were stimulated with agonist mix in presence of anti-IgM and Ibrutinib 1 uM (Condition D) or with DMSO and control beads (Condition C) vs CLL cells treated only with anti-IgM and Ibrutinib 1 uM (Condition B) or with DMSO and control beads (Condition A). Condition A: DMSO+control beads; Condition B: Anti-IgM beads+Ibrutinib 1uM; Condition C: DMSO+control beads+agonist mix (IL-10; CpG; CD40L); Condition D: Anti-IgM beads+Ibrutinib 1uM+agonist mix (IL-10; CpG; CD40L)

tag: peripheral blood cd19 purity (%)

tag: FISH analysis (% of deletion)

tag: tp53 mutation (%)


title: PBS_01

city: Chicago

first: DUY BINH

last: TRAN

state: IL

address: 840 S. Wood St

department: Surgery

country: USA

institute: University of Illinois Chicago

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_1

hyb_protocol: A cartridge containing a hybridization reaction for each sample was set up using the following components: 3 μl Reporter CodeSet, 5 μl Hybridization Buffer, 5 μl (50 ng) sample RNA, and 2 μl Capture ProbeSet at room temperature. Samples were hybridized to target-specific reporter and capture probes overnight at 65 °C in a thermocycler.

data_processing:
Following hybridization, 35 μL of each hybridized product was pipetted to the nCounter cartridge, sealed, and loaded into the drawer of the SPRINT Profiler.
Reporter code counts (RCC) and reporter library file (RLF) obtained from the nCounter SPRINT Profiler were utilized for gene expression analysis though the nSolver Advanced Analysis Software v4.0. Background correction, quality assessment, and inter-sample normalization was performed in accordance with the Gene Expression Data Analysis Guidelines (MAN-C0011–04). Imaging quality control measurements were set to flag any lane failing to have a registered FOV above 75%. Binding density was flagged if any lane recorded an optical feature per square micron outside the range of 0.1 to 1.8. Positive control linearity, used to assess the efficiency of hybridization, was flagged if any resulting count was below a correlation of 0.95. Positive control limit of detection flagged any sample if the 0.5 fM positive control counts were ≤ 2 SD above the mean of the negative controls. Background thresholds were set to the mean of the manufactured negative controls plus two standard deviations. Positive control normalization was performed using the geometric mean to compute normalization factors for each sample; lanes with a normalization factor outside of the 0.3–3.0 range were flagged. Codeset content normalization was performed with the geometric mean of the twenty housekeeping genes, flagging lanes if the normalization factor was outside of the 0.1–10.0 range. Normalized mRNA counts were analyzed for differential expression in four comparative analyses: aurB vs. PBS, Combination vs. IR, IR vs. PBS, and Combination vs. IR. Differential expression analysis was performed via the nSolver Advanced Analysis module.

source_name: tibial tumor

growth_protocol: DU145 cells were cultured in MEM-E supplemented with 10% FBS, 100 units/ml penicillin, and 100 μg/ml streptomycin. DU145 cells stably expressing the luciferase gene (pGL4.51[luc2/CMV/Neo], Promega) were generated through chemical transfection using FuGENE HD (Promega) in the presence of G418 antibiotics (GoldBio). The DU145-luc cell line was maintained at 70% confluency and regularly monitored for luminescence activity. DU145-luc cells were resuspended in Matrigel Growth Factor Reduced (Sigma) at a concentration of 5 × 105 cells/20 µl. Intratibial bone injections were performed on 4- to 5-week-old athymic female mice. Briefly, the proximal end of the left tibia was surgically exposed, the knee was flexed, and 20 µl of Matrigel containing DU145-luc cells were injected into the bone marrow space using a 26-gauge needle.

extract_protocol: RNA from tumor tissues was extracted by RNeasy Mini Kit (Qiagen).

treatment_protocol: After 2 weeks, the mice injected with DU145-luc cells were randomly divided into groups receiving PBS, irradiation (focal radiation at 2.0 Gy, X-Rad320, Precision X-Ray Inc, Madison, CT), aAurB (10 mg/kg, i.p., three times per week), or a combination of irradiation (2.0 Gy) and aAurB (10 mg/kg, i.p., three times per week) (N=5). Irradiation was targeted to the proximal end of the left tibia and administered in a single fraction of 2.0 Gy. The day of irradiation was designated as day 0 of treatment.

value: tibial tumor


title: Normal_Fib_3D_Norm02_1

type: genomic

city: Lebanon

first: Rezvan

last: Parvizi

state: NH

address: 1 Medical Center Drive

department: Biomedical Data Science

institute: Dartmouth College

hyb_protocol: MethylationEPIC microarray slides are prepared and conditioned according to manufacturer specifications.

scan_protocol: High-resolution images were generated for each slide, with the scanner recording intensity values for both the methylated (red) and unmethylated (green) fluorescent signals at each probe. The scanning generated raw intensity data files (IDAT files) that contain the fluorescence intensities for all probes on each sample.

data_processing:
Methylated and unmethylated signal intensities were obtained for each sample. Data were normalized using the minfi::preprocessQuantile function, which generated normalized beta values and detection p-values for each sample. The results are provided in tab-delimited text file format.
The minfi package from bioconductor was used to process the data.

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Between 500 ng and 1 µg of DNA from these 2D and 3D samples were bisulfite converted and processed according to the Illumina Infinium MethylationEPIC array protocols.

growth_protocol: Isolated fibroblasts were cultured in either 2D monolayer or 3D tissue culture systems.

extract_protocol: Genomic DNA was extracted using the Qiagen QIAcube by QIAamp DNA Mini Kit.

tag: disease state

value: Normal

tag: culture

tag: biopsy

value: forarm


title: MUT6_Condition D

source_name: Peripheral Blood, anti-IgM beads, Ibrutinib, agonist mix


title: MUT9_Condition D


title: RCC normal DP-sorted single cell TCR-seq

description:
Library name: Kidney_Normal_DP_TCR
10x Genomics

source_name: Adjacent-Normal

value: Adjacent-Normal

value: CD4+CD8+ T cells


title: NoMoMa3

city: St. Paul

first: Nicole

last: Marquez Reyes

state: Minnesota

address: 1445 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota - Twin Cities

description: Library name: Sample 6

data_processing:
Using Kbase (https://www.kbase.us/), paired - end reads raw data was trimmed (Trimmomatic (v.0.36))
Using Kbase (https://www.kbase.us/), we then mapped the genome of R. palustris CGA009 (HISAT2 (v.2.1.0)).
Using Kbase (https://www.kbase.us/), transcripts were assembled from the aligned reads by using StringTie (v.2.1.5).
Using Kbase (https://www.kbase.us/), assembled transcripts were used to do differential expression analysis matrix with DESeq2 (v.1.20.0)
Transcript regulation was further analyzed through heat and volcano plots in R.
Assembly: NZ_CP116810.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rhodopseudomonas palustris CGA009

source_name: Prokaryote

growth_protocol: WT cells were maintained in anaerobic hungate tubes with 10mL of either PM or Low Sulfate PM or Low Sulfate PM with No Molybdenum supplemented with 10mM Malate as carbon source. These anaerobic media was prepared using an anaerobic chamber with an atmosphere of 98%N2, 2%H2, <10ppm O2.

extract_protocol:
QIAgen miRNeasy Mini Kit (QIAgen, Hilden, Germany). ~1ug of total RNA was used to send to Azenta
Library preparation done by Azenta with Illumina 2x150bp, RNA with rRNA depletion, ~350M PE reads (~105GB), single index

treatment_protocol: Only the samples stating they have MT-EtOH were added 1mM MT-EtOH as sulfur source

tag: strain

value: Prokaryote

tag: genotype

value: WT


title: KYSE150-normoxia-rep2

description:
Library name: Sample 2
Column name in gene_count_mat.txt:normoxia-rep2

value: normoxia


title: RCC PBMC DP-sorted single cell TCR-seq

description:
Library name: Kidney_PBMC_DP_TCR
10x Genomics


title: MUT7_Condition B

source_name: Peripheral Blood, anti-IgM beads, Ibrutinib


title: KYSE150-hypoxia-rep2

description:
Library name: Sample 4
Column name in gene_count_mat.txt:hypoxia-rep2

value: hypoxia


title: MUT6_Condition B


title: MUT7_Condition A

source_name: Peripheral Blood, control beads


title: MUT9_Condition C


title: MUT9_Condition A


title: MUT9_Condition B


title: RCC PBMC CD4-sorted single cell TCR-seq

description:
Library name: Kidney_PBMC_CD4_TCR
10x Genomics

value: CD4+ T cells


title: MUT4_Condition B


title: RCC tumor CD4-sorted single cell TCR-seq

description:
Library name: Kidney_Tumor_CD4_TCR
10x Genomics

source_name: Tumor

value: Tumor


title: healthy donor DP-sorted single cell TCR-seq

description:
Library name: HealthyPBMC_DP_TCR
10x Genomics

value: healthy donor


title: MUT4_Condition A


title: RCC normal CD4-sorted single cell TCR-seq

description:
Library name: Kidney_Normal_CD4_TCR
10x Genomics


title: MUT3_Condition D


title: KYSE150-hypoxia-so

description: Library name: Sample 3

library_source: genomic

data_processing:
Raw reads were quality checked with FastQC v0.11.9 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg38) genome with Bowtie2 v2.5.0 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.6.
Peaks were called using macs2 2.2.7.1 with the default setting. Visualization of detected peaks was performed using deeptools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
For ATAC-seq experiment, 50,000 KYSE30 cells were collected for ATAC-seq followed commercial manual ATAC kit (cat. #N248, Novoprotein Inc.).
DNA libraries were prepared through PCR using a commercial ATAC kit (cat. #N248, Novoprotein Inc.) according to the manufacture’s protocol. The sequencing libraries were qualified with Qubit 2.0 and Agilent 2100, and sequenced on an Illumina NovaSeq 6000 platform for each library.


title: MUT6_Condition A


title: RCC tumor DP-sorted single cell TCR-seq

description:
Library name: Kidney_Tumor_DP_TCR
10x Genomics


title: RCC normal CD8-sorted single cell TCR-seq

description:
Library name: Kidney_Normal_CD8_TCR
10x Genomics


title: MUT3_Condition B


title: RCC PBMC CD8-sorted single cell RNA-seq

description:
Library name: Kidney_PBMC_CD8
10x Genomics

library_source: transcriptomic single cell

data_processing:
After 10X sequencing data was processed through the Cell Ranger pipeline (version 3.0.2, hg38 genome assembly) with default settings, filtered gene-barcode matrices for single cells were analyzed using the scanpy toolkit. Genes that were detected in less than three cells were filtered out, and cells were filtered out with greater than ten percent of mitochondrial genes and with fewer than 100 or greater than 2500 detected genes. Cells that were annotated as red blood cells (HBB) or macrophage (CD14, CD68, CD163) were also excluded from downstream analyses. The gene expression values were log2 plus one transformed and normalized to 10,000 counts per cell. The resulting matrix was batch corrected by regressing out total UMI counts and percent mitochondrial genes using the built-in scanpy function followed by using the scanpy implementation of Harmony with each cell sorted biospecimen acting as a batch (12 biospecimens total). The adjusted matrix was scaled to a mean of zero and variance of 1. Highly variable genes were selected using the embedded scanpy function followed by principal component analysis (PCA), leiden clustering and uniform manifold approximation and projection (UMAP) plotting with default settings. This yielded 20 clusters which were collapsed to 7 cell phenotypes based on manual annotation.  To characterize each cluster to individual cell types, we applied the rank_genes_group procedure in scanpy, which identifies markers using log fold changes of mean expression up-regulated in each cluster relative to the combination of all other single cells (regardless of tissue or cell type). We compared the gene lists to known literature to manually label the clusters.  TCR-seq data for each sample was processed using Cell Ranger software with the command ‘cellranger vdj’ using the default reference set of genes, based on human reference genome GRCh38 and RefSeq gene models. For each sample, Cell Ranger generated an output file, filtered_contig_annotations.csv, containing TCR α-chain and β-chain CDR3 nucleotide sequences for single cells that were identified by barcodes. Patient origins for TRA and TRB clonotypes were inferred by matching 10X barcodes from demultiplex paired single cell RNA sequence via demuxlet 57. Furthermore, for any given 10X barcode, the most abundant TRA or TRB clonotype was accepted for further analysis; if 2 TRA or TRB clonotypes were equally abundant for a given 10X barcode, the clonotype with the highest sequence alignment score was used for further analysis. Detailed sequencing statistics and saturation analysis are provided in (Supplementary Table 6). Only cells with paired TRA and TRB with identifiable patient origins were used for further downstream analysis.
Assembly: GRCh37/hg38
Supplementary files format and content: filtered single cell scanpy and TCR matrix used for downstream analysis. Included are also individual single cell TCR csv files from cellranger vdj

value: PBMC


title: healthy donor CD4-sorted single cell TCR-seq

description:
Library name: HealthyPBMC_CD4_TCR
10x Genomics


title: MUT3_Condition A


title: RCC tumor CD8-sorted single cell TCR-seq

description:
Library name: Kidney_Tumor_CD8_TCR
10x Genomics

value: CD8+ T cells


title: RCC normal CD8-sorted single cell RNA-seq

description:
Library name: Kidney_Normal_CD8
10x Genomics

value: renal cell carcinoma


title: MUT4_Condition D


title: healthy donor CD8-sorted single cell TCR-seq

description:
Library name: HealthyPBMC_CD8_TCR
10x Genomics


title: RCC PBMC DP-sorted single cell RNA-seq

description:
Library name: Kidney_PBMC_DP
10x Genomics


title: RCC PBMC CD4-sorted single cell RNA-seq

description:
Library name: Kidney_PBMC_CD4
10x Genomics


title: MUT1_Condition C


title: MUT4_Condition C


title: RCC normal DP-sorted single cell RNA-seq

description:
Library name: Kidney_Normal_DP
10x Genomics


title: MUT6_Condition C


title: MUT1_Condition D


title: MUT3_Condition C


title: MUT1_Condition B


title: RCC normal CD4-sorted single cell RNA-seq

description:
Library name: Kidney_Normal_CD4
10x Genomics


title: RCC tumor CD8-sorted single cell RNA-seq

description:
Library name: Kidney_Tumor_CD8
10x Genomics


title: RCC tumor DP-sorted single cell RNA-seq

description:
Library name: Kidney_Tumor_DP
10x Genomics


title: RCC tumor CD4-sorted single cell RNA-seq

description:
Library name: Kidney_Tumor_CD4
10x Genomics


title: WT8_Condition A

value: NORM


title: healthy donor CD8-sorted single cell RNA-seq

description:
Library name: HealthyPBMC_CD8
10x Genomics


title: WT8_Condition B


title: MUT1_Condition A


title: WT8_Condition C


title: WT8_Condition D


title: healthy donor DP-sorted single cell RNA-seq

description:
Library name: HealthyPBMC_DP
10x Genomics


title: WT7_Condition D


title: 241018_SSc_FB_siRNA_RUNX1_12

description:
Library name: 12146-JF-12
241018_SSc_FB_ siRNA_RUNX1_12

data_processing:
Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10X Cell Ranger software. The samples were then merged into a single expression matrix using the Cell Ranger aggr pipeline.
Assembly: human hg38
Supplementary files format and content: includes barcodes, features, and alignments

source_name: Isolated skin fibroblasts

growth_protocol: Cells were grown in RPMI-1640 media and were cultured at 37°C with of 5% CO2 and maintained by sub-culturing twice a week.

extract_protocol:
Cell pellet was resuspended in 1X PBS+0.04% BSA, and cell viability was assessed with 0.4% Trypan Blue.
Cells were fixed and permeabilized with 10X Genomics fix/perm buffer for 16 hours at 4°C, followed by incubation with quenching and enhancer buffer on ice, as per the instructions in Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics, catalog number PN-1000414). Samples were stored in 10% glycerol until sequencing. Sequencing was performed at the University of Michigan Advanced Genomics Core.

treatment_protocol: Approximately 7.5 x104 cells were seeded into each well of a 6-well plate in 5 ml complete tissue culture media. Fibroblasts were incubated with RUNX1 siRNA or NC (1µM each in 1.3 ml Accell siRNA delivery media) for 72 hours, after which they were detached with 0.25% Trypsin-EDTA and centrifuged.

value: Isolated skin fibroblasts

value: fibroblast

tag: batch


title: 241018_SSc_FB_siRNA_NTC_11

description:
Library name: 12146-JF-11
241018_SSc_FB_ siRNA_NTC_11


title: WT7_Condition A


title: WT7_Condition B


title: WT7_Condition C


title: WT6_Condition A


title: WT6_Condition B


title: WT6_Condition C


title: 241018_SSc_FB_siRNA_RUNX1_5

description:
Library name: 12146-JF-5
241018_SSc_FB_ siRNA_RUNX1_5


title: Rheumatoid arthritis-3

city: Hefei

first: Shu

last: Li

state: Anhui

address: No. 117, Meishan Road, Shushan District

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: Library name: RA3

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated,Sequencing data contains a number of connectors,low-quality Reads, so we use fastp(0,22.0)software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .After quality control, sequence data was processed with STAR to generate read alignments with hg38. Raw read counts for annotated genes were obtained with featureCounts with default settings, normalized and analyzed using DEseq2.
Assembly: hg38
Supplementary files format and content: csv file including Reads count for each sample

molecule: polyA RNA

source_name: Synovial tissue

extract_protocol:
Total RNA was extracted from the Synovial tissue used for mRNA-seq by Trizol regent (Thermo Fisher Scientific)
RNA-seq libraries were prepared with 1ug of total RNA using VAHTS mRNA-seq V3 Library Prep Kit (Vazyme Biotech) according to manufacturer’s instruction: mRNA was enriched with oligo-dT magnetic beads, followed by fragmentation, end repair, adapter ligation and PCR amplification. Final libraries quality assessment was performed using BioAnalyzer and Qubit.

value: Synovial tissue

tag: subject group

value: Rheumatoid arthritis


title: healthy volunteer-3

description: Library name: NC3

value: healthy volunteer


title: WT6_Condition D


title: WT5_Condition D


title: Rheumatoid arthritis-2

description: Library name: RA2


title: Rheumatoid arthritis-1

description: Library name: RA1


title: healthy volunteer-2

description: Library name: NC2


title: WT5_Condition C


title: healthy volunteer-1

description: Library name: NC1


title: healthy donor CD4-sorted single cell RNA-seq

description:
Library name: HealthyPBMC_CD4
10x Genomics


title: WT5_Condition B


title: WT5_Condition A


title: WT4_Condition B


title: WT4_Condition D


title: WT4_Condition C


title: siMFAP2-2

city: Hohhot

first: Xiaobo

last: Cui

address: No. 1, Tongdao North Street

department: Department of Otolaryngology

institute: the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia

description: Library name: Sample5

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GRCh38
Supplementary files format and content: Matrix table with FPKM and TPM values for each gene and each sample.

source_name: Cell line

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: Cell line

value: FaDu

value: MFAP2 knockdown


title: siCtrl-1

description: Library name: Sample1

value: MFAP2 wild type


title: siMFAP2-1

description: Library name: Sample4


title: Colonoid, pre and post-differentiation pooled 24hr, 48hr, 72hr growth media, 24hr, 48hr, 72hr differentiation media

first: Sonia

middle: S

last: Kupfer

department: Human Genetics

institute: University of Chicago

description:
Library name: SK1abcd
10X Genomics

data_processing:
The cell ranger count pipeline (v8.1.0) was used to process raw fastq files.
Assembly: transcriptome reference refdata-gex-GRCh38-2020-A
Supplementary files format and content: Cell Ranger output feature and barcode files in compressed tsv format and counts file in compressed mtx format

source_name: colonic stem/colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
Organoids were cultured on Biolite Multidish (Fisher Scientific, IL), embedded in six 30 µL droplets of Matrigel, cultured in 1.5 mL of the organoid media in an incubator at 37°C and 5% CO2. Prior to treatments organoids were incubated in basal media for 24, 48, and 72 hours to enable differentiation.
After culturing, the MULTI-Seq barcoding and library preparation protocol of McGinnis et al. (2019) was followed that utilizes the Single Cell 3’ reagent kit (10x Genomics). Briefly, single cell suspensions were prepared and barcoded by sequentially adding anchor:barcode solution, incubating on ice, followed by the addition of co-anchor solution and further incubation. Cell samples were transferred to individual wells and washed by centrifugation with 1% BSA in PBS. Barcoded cells were pooled, filtered through a cell strainer, and counted.

value: colonic stem/colonic organoid


title: siCtrl-2

description: Library name: Sample2


title: WT3_Condition D


title: Control-F

city: Jinan

first: Kailiang

last: Zhang

state: Shandong

address: 25 Shifan Raod

institute: the 960th Hospital of Joint Logistic Support Force

description:
Library name: Sample 8
Column name in all.counts.xls: Control-F

data_processing:
Analysis workflow established on a local server v 1.1
Clean reads were acquired after qualification of raw reads using FastQC software. The the adaptor sequences and low-quality reads were removed.
Assembly: hg38
Supplementary files format and content: xls files includes raw counts for eachSample
Supplementary files format and content: xls files include FPKM values for eachSample

source_name: Osteosarcoma

extract_protocol:
Total RNA was extracted from sample by Trizol reagent (Invitrogen).
The cDNA libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions

value: Osteosarcoma

tag: tissue type

value: adjacent normal bone tissues


title: Cancer-F

description:
Library name: Sample 7
Column name in all.counts.xls: Cancer-F

value: human osteosarcoma tissues


title: siMFAP2-3

description: Library name: Sample6


title: Cancer-H

description:
Library name: Sample 9
Column name in all.counts.xls: Cancer-H


title: Control-H

description:
Library name: Sample 10
Column name in all.counts.xls: Control-H


title: WT3_Condition C


title: Control-E

description:
Library name: Sample 6
Column name in all.counts.xls: Control-E


title: WT4_Condition A


title: Treat_3 FSS_imDCs

city: Guiyang

first: Peng

last: Yu

state: Guizhou

address: Guizhou Medical University, 6 Ankang Avenue, GUI 'an New District, Guizhou Province, China

institute: Guizhou Medical University

data_processing:
BGISEQ-500
clean reads were compared to the reference genome sequence using HISAT
Bowtie2 was used to compare clean reads to reference gene sequences to obtain comparison results
Supplementary files format and content: tab-deliminted text file includes raw couts for each sample

organism: Mus musculus

source_name: bone marrow

growth_protocol: Briefly, bone marrow cells were extracted from the femurs and tibias of 7-week-old male C57BL/6 mice immediately after dissection. The remaining cells were cultured in complete RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 0.1% β-mercaptoethanol, 20 ng/ml rmGM-CSF and 10 ng/mlrmIL-4 for a duration of 7 days to generate imDCs. Suspension cells were collected and isolated using a CD11c isolation kit to achieve high purity imDCs.

extract_protocol:
Add 600μL Buffer RLT Plus, homogenize the grinding machine, and let it stand at room temperature for 5 min; At room temperature, centrifuge at 12,000×g for 3 min; All supernatants were transferred to AllPrep DNA spin column; Centrifuge at room temperature of 10,000×g for 30 s, and the liquid in the collection tube was purified and collected for RNA
The DNBs obtained were added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced by combined probe anchoring polymerization (cPAS)

treatment_protocol: The imDCs were cultured in a 6-cm Corning petri dish and positioned within a cone-plate shearing system at a concentration of 2×10^6 cells/mL.

value: bone marrow

tag: cell

value: Immature dendritic cells

value: primary cell

value: 10 dyn/cm2 FSS treatment


title: Treat_1 FSS_imDCs


title: Treat_2 FSS_imDCs


title: siCtrl-3

description: Library name: Sample3


title: WT3_Condition A

value: NORM


title: Cancer-E

description:
Library name: Sample 5
Column name in all.counts.xls: Cancer-E


title: Control_2 Static_imDCs

value: Static cultured


title: WT3_Condition B


title: Control_3 Static_imDCs


title: Control_1 Static_imDCs


title: Control-D

description:
Library name: Sample 2
Column name in all.counts.xls: Control-D


title: Cancer-B

description:
Library name: Sample 3
Column name in all.counts.xls: Cancer-B


title: 241018_SSc_FB_siRNA_NTC_4

description:
Library name: 12146-JF-4
241018_SSc_FB_ siRNA_NTC_4

value: Isolated skin fibroblasts

value: fibroblast


title: SH-NTA_, replicate 2

city: Brescia

first: Roberto

last: Ronca

address: viale Europa 11

department: Molecular and Translational medicine

institute: University of Brescia

description: Total RNA extracted from DAOY shNT cells using TRIzol, hybridized on Clariom D array- Replicate 2

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific), starting from 100 ng of total RNA. After hybridization, arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: Arrays were washed and stained using the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000 7G. Data acquisition was performed using GeneChip Operating Software (GCOS).

data_processing: Raw data (CEL files) were generated using the GeneChip Scanner 3000 7G in conjunction with GeneChip Operating Software (ThermoFisher Scientific). Quality control was performed according to the manufacturer’s instructions. Expression values were obtained using Affymetrix Expression Console software with robust multi-array average (RMA) normalization. Statistical analysis was performed using ANOVA to compare gene expression profiles between DAOY shNT and DAOY shPTX3 cells.

label: biotin

source_name: Medulloblastoma DAOY cell line

label_protocol: Labeling was performed using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) starting from 100 ng of total RNA, according to the manufacturer’s instructions. The resulting cDNA was labeled with biotin for hybridization to the Clariom D Assay Human arrays.

growth_protocol: DAOY shNT and shPTX3 cells were growth in complete medium before total RNA extraction

extract_protocol: Trizol reagent

treatment_protocol: no treatment

tag: cell ine

value: SHH Medulloblastoma cell line

value: shNT


title: Cancer-D

description:
Library name: Sample 1
Column name in all.counts.xls: Cancer-D

tag: tissue


title: Control-B

description:
Library name: Sample 4
Column name in all.counts.xls: Control-B


title: SH-NT_, replicate 1

description: Total RNA extracted from DAOY shNT cells using TRIzol, hybridized on Clariom D array- Replicate 1

tag: treatment


title: Lv_NC_1

description:
Library name: Sample 4
Column name in CPMs_all_Samples.xlsx: Lv_NC_1

data_processing:
Analysis workflow established on a local server v 1.1
Assembly: hg38
Supplementary files format and content: CPMs for each Sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen)
Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Inc.) according to the manufacturer's instructions.

tag: cell line

value: osteosarcoma cell line

value: NC


title: Lv_NC_2

description:
Library name: Sample 5
Column name in CPMs_all_Samples.xlsx: Lv_NC_2

tag: cell type


title: SH-20A_, replicate 2

description: Total RNA extracted from DAOY shPTX3 cells using TRIzol, hybridized on Clariom D array- Replicate 2


title: Lv_Lin_3

description:
Library name: Sample 3
Column name in CPMs_all_Samples.xlsx: Lv_Lin_3


title: SH-20_, replicate 1

description: Total RNA extracted from DAOY shPTX3 cells using TRIzol, hybridized on Clariom D array- Replicate 1


title: PBMC，SLE_rep2

first: lili

last: cheng

state: Anhui Province

address: No. 117, Meishan Road

description:
Library name: Sample5
10X Genomics

data_processing:
Reads were processed using the Cell Ranger 3.0.1 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version hg38, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes.Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.0.2) R toolkit for quality control and downstream analysis of our single cell RNAseq data. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package. To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression.
Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package . Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain Method after computing a shared nearest neighbor graph. For sub-clustering, we applied the same procedure of scaled, dimensionality reduction, and clustering to the specific set of data (usually restricted to one type of cell.) For each cluster, we used the Wilcoxon Rank-Sum Test to find significant deferentially expressed genes comparing the remaining clusters. SingleR and known marker genes were used to identify cell type.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
PBMC cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57) . Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess庐 II Automated Cell Counter (Thermo Fisher).
Using a Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10X Genomics),cell were immediately loaded onto a Chromium Single Cell Processor(10X Genomics) for barcoding of RNA from single cell. Sequencing libraries were constructed according to the manufacturer’s instructions (10× Genomics) and then sequenced in a NovaSeq 6000 sequencing system (Illumina, 20012866).

value: Blood

value: CD4+ T lymphocytes, B lymphocytes

value: SLE

value: Immunosuppressant


title: SH-NTB_, replicate 3

description: Total RNA extracted from DAOY shNT cells using TRIzol, hybridized on Clariom D array- Replicate 3


title: Lv_NC_3

description:
Library name: Sample 6
Column name in CPMs_all_Samples.xlsx: Lv_NC_3

value: Osteosarcoma


title: SH-20B_, replicate 1

description: Total RNA extracted from DAOY shPTX3 cells using TRIzol, hybridized on Clariom D array- Replicate 3


title: Lv_Lin_1

description:
Library name: Sample 1
Column name in CPMs_all_Samples.xlsx: Lv_Lin_1


title: PBMC，SLE_rep3

description:
Library name: Sample6
10X Genomics


title: Patient 17

city: Guangzhou

first: Yuqi

last: Zheng

address: Sanyuanli

institute: Guangzhou University of Chinese Medicine

description: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package.Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: POI group

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

value: plasma in POI group

tag: Sex

value: Female

tag: age

value: under 40 years old


title: Patient 26

source_name: control group

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

value: plasma in control group


title: Lv_Lin_2

description:
Library name: Sample 2
Column name in CPMs_all_Samples.xlsx: Lv_Lin_2


title: Patient 24


title: Patient 22


title: Patient 14


title: PBMC，SLE_rep1

description:
Library name: Sample4
10X Genomics

source_name: PBMC


title: PBMC，N_rep1

description:
Library name: Sample1
10X Genomics

value: NORMAL


title: Patient 13


title: IgG

first: shoupei

last: liu

address: 9th Floor, Building b, Huanyu 2nd Road, Haizhu District

department: Institute of Clinical Medicine

institute: Guangzhou First People's Hospital

description: Library name: Sample 3

data_processing:
Raw reads were trimmed with Trimmomatic (v0.39) to remove adapters and low-quality bases. Cleaned reads were aligned to the GRCh38 genome using STAR (v2.7.10a), and gene counts were quantified with featureCounts (v2.0.3) against GENCODE v44 annotation. Normalization was performed using DESeq2’s median-of-ratios method.
Assembly: All analyses were based on the GRCh38.p14 genome assembly with GENCODE v44 gene annotations.
Supplementary files format and content: gene_counts.csv (raw counts matrix, gene × sample)
Library strategy: CUT&Tag

source_name: human embryonic stem cells

extract_protocol:
Total RNAs were extracted using Trizol reagent (Takara), and RNA-Seq was performed by Novogene (Beijing).
Sequencing libraries were constructed using Illumina mRNA-Seq Prep Kit. Fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 4000.

tag: induvidual

value: IgG

value: human embryonic stem cells

value: hEH_10d cells

tag: cut&tag antibody

value: IgG (Beyotime, A7028)


title: Patient 25


title: Mfffl/fl; Gdf9-Cre  ovulated oocyte-CKO2

city: Shenzhen

first: Renwu

last: Hua

address: Haiyuan 1st Road

institute: HKU-SZH

description:
Library name: SAMPLE 13
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: MFF_CKO2 Read Count/MFF_CKO2 FRKM

data_processing:
Related bioinformatic analyses were carried out on the Dr.Tom system (https://biosys.bgi.com).
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FRKM for each Sample

source_name: Ovulated oocyte

extract_protocol:
Delivered single-cell samples, which are stored in cell lysis buffer, are processed to cell lysis by PCR instrument.
The reaction system is configured for reverse transcription. First-strand cDNA is synthesized with SMART-SeqII. The reaction system is configured for PCR amplification to process preamplification of cDNAs.

value: Ovulated oocyte

value: Mfffl/fl; Gdf9-Cre

value: MFF conditional knockout


title: PBMC，N_rep2

description:
Library name: Sample2
10X Genomics

value: Blood


title: CEBPB_OE

description: Library name: Sample 1

value: CEBPB overexpression

value: CEBPB (Santa Cruz, sc-7962X)


title: DAC

first: Zhewei

last: Lin

address: No. 33 Zhongyuan Road, Buji Subdistrict, Longgang District, Shenzhen City, Guangdong Province; Luohe Hospital Group Medical Center

institute: Medical Laboratory of the third affiliated hospital of Shenzhen university

description:
Library name: Sample 3
10X Genomics

data_processing:
The scRNA-seq sequencing data were compared with the reference genome using R package CellRanger (version 7.1.0) , and cells and single-cell 3' end transcripts were identified and counted in the sequenced samples.We loaded the output CellRanger expression matrix into Seurat (version 4.1.1) for filtering low-quality cells from scRNA-seq data, and the filtered data were downscaled and clustered. Filtering low-quality cell thresholds: the number of genes expressed per cell >500, and mitochondrial genes expressed in <25% of each cell's transcriptome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor tissue

extract_protocol:
Fresh tumor tissue samples (≥ 0.2g) were obtained through surgical resection or endoscopic nasal biopsy. The samples were rinsed with 0.9% normal saline and the fat, visible blood vessels and surrounding necrotic areas were removed.Then, the tumor tissue samples were cleaned, minced, and enzymatically digested to generate a cell suspension. Following filtration and centrifugation, red blood cells in the cell suspension were lysed by using a lysis buffer and washed out. The remaining cells were resuspended in RPMI 1640 medium and adjusted to a concentration of 700-1200 cells per microliter.
Single-cell suspensions were loaded onto the 10x Chromium chip according to the instructions for the 10x Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells.cDNA amplification and library construction were prepared according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: Tumor tissue

value: 69 years old

value: female


title: PBMC，N_rep3

description:
Library name: Sample3
10X Genomics

value: CD4+ T lymphocytes, B lymphocytes

value: Immunosuppressant


title: Mfffl/fl; Gdf9-Cre  GV oocyte-CKO4

description:
Library name: SAMPLE 8
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_CKO4 Read Count/MFF_CKO4 FRKM

source_name: GV oocyte

value: GV oocyte


title: Mfffl/fl ovulated oocyte-WT3

description:
Library name: SAMPLE 11
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: MFF_WT3 Read Count/MFF_WT3 FRKM

value: Mfffl/fl

value: WT


title: adult testicular cells

city: nanjing

first: Liyong

last: He

state: Not US or Canada

address: 南京市玄武区东南大学

institute: State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering

description:
Library name: Sample 1-192
for all 192 single-cells data

data_processing:
The sequencing data was processed using the SSH (Secure Shell) client MobaXterm within a Linux operating system. The overall processing workflow was performed according to the following:
1) Quality control: FastQC was used to assess the quality of the sequencing data fastq.gz format. Indicators such as “Per base sequence quality,” “Per base sequence content,” and “Sequence Duplication Levels” were used to make a preliminary judgment of the quality of the sequencing library.
2) Barcode B and UMI swapping: The fastq.gz files were decompressed using the zcat command to convert them into “fq” files. Following the process shown in Supplementary Fig. 15, a Python script was written to swap the Barcode B and UMI from Read 2 to the beginning of Read 1. Additionally, 33 bp from the 5’ end of Read 2 was deleted. The Final_R1/R2.fq.gz files were then compressed.
3) Data preprocessing: The FastqToSam function in Picard tools were invoked to convert the “fq” file into query-name sorted bam file. Run the TagBamWithReadSequenceExtended function from Drop-seq_tools-3.0.2-0 twice to extract Barcode and UMI sequences at different locations, then invoke FilterBam function to filter low-quality Barcode and UMI sequences, and finally use the PolyATrimmer function to remove the Poly A sequence at the capture end. After preprocessing, the SamToFastq function from Picard tools was used to convert the bam files back into fastq files for subsequent sequence alignment.
4) Sequence alignment: Reference genome indices for mouse GRCm38 (https://www.ncbi.nlm.nih.gov/grc/mouse) and human GRCh38 (https://www.ncbi.nlm.nih.gov/grc/human) were constructed from NCBI Genome Reference Consortium, respectively. Sequence alignment was then performed using STAR software (version 2.7.11b).
5) Expression matrix: After alignment, the SortSam and MergeBamAlignment functions in Picard were called to sort and integrate the results. Finally, the DigitalExpression function in Drop-seq_tools-3.0.2-0 was employed with specified filtering conditions to select the digital expression matrix corresponding to the specified Barcode.
Assembly: GRCh38
Supplementary files format and content: matrixed files

source_name: Sample 1-192

extract_protocol:
All patients have provided written informed consent. Testicular tissues of patients with OA were minced with sterilized scissors after washing three times with PBS, then were digested in collagenase type and trypsin at 37 °C for 30 min. The digestion process was stopped with DMEM containing 10% FBS. After centrifugation and resuspension, single testicular cells were randomly selected into the prepared lysis buffer through a mouth pipette and stored at −80 °C for further analysis.
Sorted single-cell or microregion tissue samples were removed from the −80 °C storage and thawed at room temperature for 10 min to facilitate sample lysis and RNA release, then transferred to a preheated PCR thermocycler, incubated for 3 min at 72 °C and immediately placed on ice afterwards. Next, 10 µl of RT-PCR mix containing 1.2 µL dNTP mix (10 mM), 0.252 µL RNase Inhibitor (40 U/µl), 0.1 µL DTT (100 mM), 0.328 µL MgCl2 (279 mM), 0.18 µL dCTP (100 mM), 2 µL Betaine (5 M), 0.368 µL CBTi-TSO (50 µM), 0.172 µL of Superscript Ⅳ / Maxima H (200 U/µL, ThermoFisher Scientific) and 5 µL of KAPA HiFi HotStart Ready Mix (2×, Roche) were added to synthesis full-length dsDNA. The following RT-PCR program was set to: 60 min at 50 °C, 98 °C for 3 min, then 20 cycles of (98 °C for 20 s, 67 °C for 20 s, 72 °C for 6 min). The cDNA concentration was quantified using the Qubit 4.0 fluorimeter, and size distribution was assessed using capillary electrophoresis on a Fragment Analyzer system (Agilent Bioanalyzer). 1 μl unpurified amplified cDNA working dilution (5 ng/µl) of each sample was transferred to a new plate before adding tagmentation reaction mix as described above. Of note, each sample used unique combination barcoding. Samples were incubated for 10 min at 55 °C. Then, all tagmented products were mixed into 1.5- or 2 ml PCR tube, purified with 1.5× AMPure XP beads for termination of the tagmented reaction and collection, followed by elution with 20 µl nuclease-free water.

value: testis

value: spermatogenic cells


title: VECTOR

description: Library name: Sample 2

value: VECTOR

value: human embryonic stem cells

value: hEH_10d cells

value: VECTOR control


title: Patient 11

value: plasma in POI group

value: Female

value: under 40 years old


title: Patient 103, control SVZ

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description: Library name: sample791

data_processing:
First, the raw FASTQ files were run with FastQC (v0.11.9) to assess the overall sequencing quality and possible adapter sequence contamination
Skewer (v0.11.9) was used to remove Illumina TruSeq adapter sequences (read 1: 5’-AGATCGGAAGAGCACACGTCTGAACTC-CAGTCA-3’, read 2: 5’-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’) from the read files.
Followingly, the reads were aligned to the GRCh38 (hg38) reference genome using STAR aligner (v2.7.10a) to generate coordinate-sorted BAM files.
FeatureCounts (v2.0.3) was used to generate the gene expression count table, which is further normalized in transcripts per million (TPM) criterion with R (v4.3.3).
Differential expression (DE) analyses were performed using the DESeq2 R package, and the genes that met the following threshold were considered significant: |Log2 fold change| > 0.5 & BH-adjusted P-value < 0.05.
Pathway enrichment analyses for GO Biological Process were then conducted using the clusterProfiler R package.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

source_name: control subventricular zone

extract_protocol:
RNA was extracted with Rneasy mini plus kit (Qiagen).
The samples for RNAseq were processed with Aglient SureSelect Human Alll Exon v6 + UTR kit to build sequence libraries under maufacturer's protocols.

value: control subventricular zone


title: Mfffl/fl; Gdf9-Cre  ovulated oocyte-CKO1

description:
Library name: SAMPLE 12
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: MFF_CKO1 Read Count/MFF_CKO1 FRKM

value: Ovulated oocyte

value: Mfffl/fl; Gdf9-Cre

value: MFF conditional knockout


title: Mfffl/fl; Gdf9-Cre  GV oocyte-CKO3

description:
Library name: SAMPLE 7
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_CKO3 Read Count/MFF_CKO3 FRKM


title: Mfffl/fl; Gdf9-Cre  ovulated oocyte-CKO3

description:
Library name: SAMPLE 14
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: MFF_CKO3 Read Count/MFF_CKO3 FRKM


title: Patient 15


title: Patient 99, control SVZ

description: Library name: sample579


title: Mfffl/fl ovulated oocyte-WT1

description:
Library name: SAMPLE 9
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: MFF_WT1 Read Count/MFF_WT1 FRKM


title: Mfffl/fl ovulated oocyte-WT2

description:
Library name: SAMPLE 10
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: MFF_WT2 Read Count/MFF_WT2 FRKM


title: Patient 102, control SVZ

description: Library name: sample937


title: Patient 98, control SVZ

description: Library name: sample941


title: Mfffl/fl GV oocyte-WT4

description:
Library name: SAMPLE 4
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_WT4 Read Count/MFF_WT4 FRKM


title: Mfffl/fl; Gdf9-Cre  GV oocyte-CKO1

description:
Library name: SAMPLE 5
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_CKO1 Read Count/MFF_CKO1 FRKM


title: ITAC

description:
Library name: Sample 1
10X Genomics

value: Tumor tissue

value: 73 years old

value: male


title: Mfffl/fl; Gdf9-Cre  GV oocyte-CKO2

description:
Library name: SAMPLE 6
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_CKO2 Read Count/MFF_CKO2 FRKM

value: GV oocyte


title: Mfffl/fl GV oocyte-WT1

description:
Library name: SAMPLE 1
Column name in  GV oocyte RNA read count.txt GV oocyte RNA FRKM.txt : MFF_WT1 Read Count/MFF_WT1 FRKM

value: Mfffl/fl

value: WT


title: Patient 95, GBM, replicate 1

description: Library name: sample1055

source_name: Glioblastoma tissue

value: Glioblastoma tissue


title: Non-ITAC

description:
Library name: Sample 2
10X Genomics

value: 59 years old

value: female


title: Nemo_NEMOF_L19

city: Minneapolis

first: Paul

middle: D.

last: Robbins

address: 312 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: UNIVERSITY OF MINNESOTA

description: Library name: Nemo_NEMOF_L19

data_processing:
Quality control on raw sequence data for each sample was performed with FastQC
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (GRCm38) as reference
Gene quantification was done via Feature Counts for raw read counts
Assembly: GRCm38/mm10
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Liver

extract_protocol:
Trizol RNA extraction
Illumina TruSeq Stranded Total RNA Library Prep kit

value: Liver

value: NEMO DK; Ercc1-/D

tag: age (weeks)


title: Nemo_ERCC1F_L12

description: Library name: Nemo_ERCC1F_L12

value: Ercc1 -/D

value: Female


title: Patient 94, Tumor-free SVZ, replicate 1

description: Library name: sample936

source_name: Tumor-free subventricular zone

value: Tumor-free subventricular zone


title: Patient 100, control SVZ

description: Library name: sample404

value: control subventricular zone


title: Mfffl/fl GV oocyte-WT2

description:
Library name: SAMPLE 2
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_WT2 Read Count/MFF_WT2 FRKM


title: Patient 97, control SVZ

description: Library name: sample948


title: Kif13b knock down aorta scRNA-seq

city: 海淀区

first: YiRan

last: Liu

state: 北京市

department: Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, China

institute: PKU

description:
Library name: KIF13B KO
10x Genomics

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
Assembly: Mouse mm10
Supplementary files format and content: H5/HDF5 archives

source_name: aorta

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).
Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).

value: aorta


title: Nemo_WTF_L3

description: Library name: Nemo_WTF_L3


title: Nemo_WTF_L2

description: Library name: Nemo_WTF_L2


title: Patient 96, control SVZ

description: Library name: sample396


title: wild type aorta scRNA-seq

description:
Library name: WT
10x Genomics

value: Wild type


title: Patient 21

value: plasma in control group

value: under 40 years old


title: Patient 101, control SVZ

description: Library name: sample942


title: Mfffl/fl GV oocyte-WT3

description:
Library name: SAMPLE 3
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : MFF_WT3 Read Count/MFF_WT3 FRKM


title: Patient 93, GBM, replicate 1

description: Library name: sample882


title: Nemo_WTF_L1

description: Library name: Nemo_WTF_L1


title: Nemo_NEMOF_L18

description: Library name: Nemo_NEMOF_L18


title: PB_4_PBS_ZT18_BioL rep 4

city: Rehovot

first: Montaser

last: Haddad

address: Herzl St 234

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Ex_149_PB_2

data_processing:
Analysis was performed using the bioinformatics analysis pipeline User Friendly Transcriptomic Analysis Pipeline (UTAP)
Assembly: mm10
Supplementary files format and content: excel file includes read counts and differential gene expression analysis

source_name: Peripheral blood

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen). Cells underwent tapestation and QUBIT and 30 ng were taken for library prep.
MARS-Seq was performed per Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019

value: Peripheral blood

value: Male

value: PBS


title: Patient 89, GBM, replicate 1

description: Library name: sample574


title: PB_3_LPS_ZT18_BioL rep 3

description: Library name: Ex_149_PB_3

value: LPS


title: Patient 92, GBM, replicate 2

description: Library name: sample722

value: Glioblastoma tissue


title: PB_4_LPS_ZT18_BioL rep 4

description: Library name: Ex_149_PB_4


title: Nemo_ERCC1F_L11

description: Library name: Nemo_ERCC1F_L11


title: Patient 94, GBM, replicate 1

description: Library name: sample935


title: Patient 91, GBM, replicate 1

description: Library name: sample608


title: Patient 91, GBM, replicate 2

description: Library name: sample623


title: Nemo_WTF_L4

description: Library name: Nemo_WTF_L4

value: WT


title: Patient 90, GBM, replicate 2

description: Library name: sample541


title: Patient 89, GBM, replicate 2

description: Library name: sample540


title: BM_4_LPS_ZT18_BioL rep 4

description: Library name: Ex_149_BM_4

source_name: Bone marrow

value: Bone marrow


title: BM_3_LPS_ZT18_BioL rep 3

description: Library name: Ex_149_BM_3


title: BM_4_PBS_ZT18_BioL rep 4

description: Library name: Ex_149_BM_2


title: Patient 87, Tumor-free SVZ, replicate 1

description: Library name: sample408


title: Patient 86, GBM, replicate 1

description: Library name: sample389


title: Patient 92, GBM, replicate 1

description: Library name: sample718


title: Patient 87, GBM, replicate 1

description: Library name: sample407


title: Patient 85, Tumor-free SVZ, replicate 1

description: Library name: sample392


title: Patient 90, GBM, replicate 1

description: Library name: sample414


title: Patient 88, Tumor-free SVZ, replicate 1

description: Library name: sample632


title: Patient 88, GBM, replicate 1

description: Library name: sample614


title: BM_4_LPS_ZT18_BioL rep 2

description: Library name: Ex_147_BM_4


title: PB_1_PBS_ZT18_BioL rep 1

description: Library name: Ex_147_PB_1


title: PB_3_PBS_ZT18_BioL rep 3

description: Library name: Ex_149_PB_1


title: BM_2_PBS_ZT18_BioL rep 2

description: Library name: Ex_147_BM_2


title: Patient 84, GBM, replicate 1

description: Library name: sample340


title: PB_4_LPS_ZT18_BioL rep 2

description: Library name: Ex_147_PB_4


title: BM_1_PBS_ZT18_BioL rep 1

description: Library name: Ex_147_BM_1


title: Patient 83, Tumor-free SVZ, replicate 1

description: Library name: sample383


title: Patient 85, GBM, replicate 1

description: Library name: sample391


title: Patient 82, GBM, replicate 1

description: Library name: sample364


title: Patient 81, GBM, replicate 1

description: Library name: sample203


title: PB_4_PBS_ZT10_BioL rep 4

description: Library name: Ex_144_PB_2


title: PB_3_LPS_ZT18_BioL rep 1

description: Library name: Ex_147_PB_3


title: Patient 83, GBM, replicate 2

description: Library name: sample381


title: Patient 83, Cortex, replicate 2

description: Library name: sample386

source_name: Brain cortex

value: Brain cortex


title: BM_3_LPS_ZT10_BioL rep 3

description: Library name: Ex_144_BM_3


title: Patient 79, GBM, replicate 1

description: Library name: sample378


title: BM_4_PBS_ZT10_BioL rep 4

description: Library name: Ex_144_BM_2


title: PB_2_PBS_ZT18_BioL rep 2

description: Library name: Ex_147_PB_2


title: Patient 78, GBM, replicate 1

description: Library name: sample199


title: BM_3_PBS_ZT10_BioL rep 3

description: Library name: Ex_144_BM_1


title: Patient 83, Cortex, replicate 1

description: Library name: sample384


title: Patient 83, GBM, replicate 1

description: Library name: sample380


title: BM_3_LPS_ZT18_BioL rep 1

description: Library name: Ex_147_BM_3


title: Patient 80, GBM, replicate 1

description: Library name: sample335


title: Patient 82, GBM, replicate 2

description: Library name: sample282


title: Patient 77, GBM, replicate 1

description: Library name: sample195


title: BM_3_PBS_ZT18_BioL rep 3

description: Library name: Ex_149_BM_1


title: PB_3_PBS_ZT10_BioL rep 3

description: Library name: Ex_144_PB_1


title: BM_4_LPS_ZT10_BioL rep 2

description: Library name: Ex_143_BM_4


title: PB_2_PBS_ZT10_BioL rep 2

description: Library name: Ex_143_PB_2


title: BM_4_LPS_ZT10_BioL rep 4

description: Library name: Ex_144_BM_4


title: PB_4_LPS_ZT10_BioL rep 4

description: Library name: Ex_144_PB_4


title: Patient 82, Cortex, replicate 1

description: Library name: sample362


title: Patient 74, GBM, replicate 1

description: Library name: sample180


title: PB_4_LPS_ZT10_BioL rep 2

description: Library name: Ex_143_PB_4


title: PB_3_LPS_ZT10_BioL rep 3

description: Library name: Ex_144_PB_3


title: Patient 76, GBM, replicate 1

description: Library name: sample11


title: Patient 71, GBM, replicate 2

description: Library name: sample877


title: Patient 80, Tumor-free SVZ, replicate 1

description: Library name: sample336


title: PB_3_LPS_ZT10_BioL rep 1

description: Library name: Ex_143_PB_3


title: PB_1_PBS_ZT10_BioL rep 1

description: Library name: Ex_143_PB_1


title: BM_3_LPS_ZT10_BioL rep 1

description: Library name: Ex_143_BM_3


title: KO_4week_3

city: 广东省

first: YU

middle: ansheng and southern medical

last: HU

state: 广东广东

address: 广东省广州市白云区京溪街道

institute: Nanfang Hospital

description: Library name: Sample18

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0).
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in reference genome alignment and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a reference based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release109
Supplementary files format and content: csv files includes FPKM and Counts values for each sample

source_name: Kidney

extract_protocol:
Trizol reagent was used to extract total RNA directly from tissues.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the Illumina Novaseq X Plus.

value: Kidney


title: KO_4week_2

address: 广东省广州市白云区京溪街道

description: Library name: Sample17


title: BM_1_PBS_ZT10_BioL rep 1

description: Library name: Ex_143_BM_1


title: Patient 72, GBM, replicate 1

description: Library name: sample172


title: Patient 75, GBM, replicate 1

description: Library name: sample192


title: Patient 71, Cortex, replicate 2

description: Library name: sample876


title: Patient 70, GBM, replicate 1

description: Library name: sample109


title: Patient 73, GBM, replicate 1

description: Library name: sample174


title: Patient 75, GBM, replicate 2

description: Library name: sample186


title: Patient 70, Tumor-free SVZ, replicate 1

description: Library name: sample110


title: KO_4week_1

address: 广东省广州市白云区京溪街道

description: Library name: Sample16


title: WT_4week_1

address: 广东省广州市白云区京溪街道

description: Library name: Sample13


title: KO_2week_1

address: 广东省广州市白云区京溪街道

description: Library name: Sample10


title: Patient 69, GBM, replicate 2

description: Library name: sample106


title: Patient 67, GBM, replicate 2

description: Library name: sample402


title: Patient 71, Cortex, replicate 1

description: Library name: sample111


title: WT_4week_2

address: 广东省广州市白云区京溪街道

description: Library name: Sample14


title: BM_2_PBS_ZT10_BioL rep 2

description: Library name: Ex_143_BM_2


title: WT_4week_3

address: 广东省广州市白云区京溪街道

description: Library name: Sample15


title: KO_2week_3

address: 广东省广州市白云区京溪街道

description: Library name: Sample12


title: WT_2week_2

address: 广东省广州市白云区京溪街道

description: Library name: Sample8


title: Patient 68, GBM, replicate 1

description: Library name: sample10


title: Patient 69, GBM, replicate 1

description: Library name: sample886


title: Patient 71, Tumor-free SVZ, replicate 1

description: Library name: sample113


title: Patient 64, GBM, replicate 2

description: Library name: sample95


title: KO_2week_2

address: 广东省广州市白云区京溪街道

description: Library name: Sample11


title: Patient 67, GBM, replicate 1

description: Library name: sample337


title: Patient 65, GBM, replicate 1

description: Library name: sample97


title: KO_1week_1

address: 广东省广州市白云区京溪街道

description: Library name: Sample4


title: KO_1week_2

address: 广东省广州市白云区京溪街道

description: Library name: Sample5


title: KO_1week_3

address: 广东省广州市白云区京溪街道

description: Library name: Sample6


title: WT_2week_3

address: 广东省广州市白云区京溪街道

description: Library name: Sample9


title: Patient 63, GBM, replicate 2

description: Library name: sample289


title: Patient 66, GBM, replicate 1

description: Library name: sample393


title: WT_2week_1

address: 广东省广州市白云区京溪街道

description: Library name: Sample7


title: Patient 64, GBM, replicate 1

description: Library name: sample50


title: WT_1week_3

address: 广东省广州市白云区京溪街道

description: Library name: Sample3


title: Patient 71, GBM, replicate 1

description: Library name: sample112


title: WT_1week_2

address: 广东省广州市白云区京溪街道

description: Library name: Sample2


title: Patient 63, Tumor-free SVZ, replicate 1

description: Library name: sample89


title: Inf_20

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

description: Library name: Inf_20

data_processing:
Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to mouse genome mm10 using STAR (v2.6.1d, mismatch=2).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including read counts of genes for each sample

source_name: Aorta

extract_protocol:
RNA was extracted using Rneasy fibrous tissue mini kits (Qiagen, #74704). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA library prep kits for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: Aortic samples were harvested from the ascending, descending, suprarenal abdominal, and infrarenal abdominal regions of male and female C57BL/6J mice administered saline or AngII (1,000 ng/kg/min) for 3 days.

value: Aorta

tag: region

value: Infrarenal

value: AngII


title: Patient 63, GBM, replicate 1

description: Library name: sample88


title: Patient 62, Tumor-free SVZ, replicate 1

description: Library name: sample87

value: Tumor-free subventricular zone


title: Patient 61, GBM, replicate 1

description: Library name: sample165


title: Patient 62, GBM, replicate 1

description: Library name: sample86


title: Inf_17

description: Library name: Inf_17

value: Female

value: Saline


title: Patient 59, GBM, replicate 1

description: Library name: sample125


title: Inf_15

description: Library name: Inf_15


title: Patient 60, GBM, replicate 1

description: Library name: sample167


title: Inf_12

description: Library name: Inf_12


title: Inf_11

description: Library name: Inf_11


title: Inf_10

description: Library name: Inf_10


title: WT_1week_1

address: 广东省广州市白云区京溪街道

description: Library name: Sample1


title: Patient 59, Cortex, replicate 1

description: Library name: sample123


title: Inf_08

description: Library name: Inf_08


title: Patient 58, GBM, replicate 5

description: Library name: sample374


title: Inf_07

description: Library name: Inf_07


title: Patient 58, GBM, replicate 4

description: Library name: sample189


title: Inf_05

description: Library name: Inf_05


title: Patient 58, Tumor-free SVZ, replicate 1

description: Library name: sample8


title: Patient 58, GBM, replicate 1

description: Library name: sample279


title: Patient 59, Tumor-free SVZ, replicate 1

description: Library name: sample126


title: Inf_01

description: Library name: Inf_01


title: Patient 58, GBM, replicate 6

description: Library name: sample376


title: Patient 57, Cortex, replicate 1

description: Library name: sample127


title: Patient 58, GBM, replicate 2

description: Library name: sample280


title: Inf_06

description: Library name: Inf_06


title: Inf_04

description: Library name: Inf_04


title: Sup_24

description: Library name: Sup_24

value: Suprarenal


title: Patient 58, GBM, replicate 3

description: Library name: sample188


title: Patient 57, Tumor-free SVZ, replicate 1

description: Library name: sample129


title: Sup_23

description: Library name: Sup_23


title: Patient 57, GBM, replicate 1

description: Library name: sample128


title: Patient 56, GBM, replicate 3

description: Library name: sample599


title: Inf_09

description: Library name: Inf_09


title: Inf_02

description: Library name: Inf_02


title: Patient 56, GBM, replicate 2

description: Library name: sample938


title: Sup_22

description: Library name: Sup_22


title: Sup_21

description: Library name: Sup_21


title: Sup_20

description: Library name: Sup_20


title: Patient 56, Tumor-free SVZ, replicate 2

description: Library name: sample600


title: Patient 56, Tumor-free SVZ, replicate 1

description: Library name: sample939


title: Sup_19

description: Library name: Sup_19


title: Sup_18

description: Library name: Sup_18


title: Patient 52, GBM, replicate 2

description: Library name: sample262


title: Patient 55, GBM, replicate 1

description: Library name: sample211


title: Patient 56, GBM, replicate 1

description: Library name: sample918


title: Patient 52, GBM, replicate 1

description: Library name: sample22


title: Patient 52, Tumor-free SVZ, replicate 1

description: Library name: sample23


title: Sup_17

description: Library name: Sup_17


title: Patient 52, Tumor-free SVZ, replicate 2

description: Library name: sample24


title: Sup_12

description: Library name: Sup_12


title: Sup_15

description: Library name: Sup_15


title: Sup_11

description: Library name: Sup_11


title: Patient 51, GBM, replicate 2

description: Library name: sample896


title: Patient 51, GBM, replicate 1

description: Library name: sample929


title: Patient 50, GBM, replicate 1

description: Library name: sample602


title: Sup_16

description: Library name: Sup_16


title: Sup_14

description: Library name: Sup_14


title: Sup_07

description: Library name: Sup_07


title: Inf_03

description: Library name: Inf_03


title: Patient 53, GBM, replicate 1

description: Library name: sample341


title: Patient 54, GBM, replicate 1

description: Library name: sample1050


title: Patient 49, GBM, replicate 1

description: Library name: sample176


title: Sup_09

description: Library name: Sup_09


title: Sup_13

description: Library name: Sup_13


title: Sup_03

description: Library name: Sup_03


title: Sup_08

description: Library name: Sup_08


title: Patient 54, GBM, replicate 2

description: Library name: sample1051


title: Sup_04

description: Library name: Sup_04


title: Patient 49, GBM, replicate 2

description: Library name: sample290


title: Patient 48, GBM, replicate 1

description: Library name: sample265


title: Sup_06

description: Library name: Sup_06


title: Patient 48, GBM, replicate 3

description: Library name: sample267


title: Patient 48, GBM, replicate 4

description: Library name: sample85


title: Patient 47, GBM, replicate 1

description: Library name: sample919


title: Patient 48, GBM, replicate 2

description: Library name: sample84


title: Patient 48, Tumor-free SVZ, replicate 1

description: Library name: sample68


title: Sup_10

description: Library name: Sup_10


title: Patient 46, GBM, replicate 1

description: Library name: sample101


title: Sup_02

description: Library name: Sup_02


title: Dsc_23

description: Library name: Dsc_23

value: Descending


title: Dsc_22

description: Library name: Dsc_22


title: Dsc_24

description: Library name: Dsc_24


title: Sup_01

description: Library name: Sup_01


title: Patient 45, GBM, replicate 1

description: Library name: sample898


title: Dsc_21

description: Library name: Dsc_21


title: Dsc_19

description: Library name: Dsc_19


title: Patient 43, GBM, replicate 2

description: Library name: sample274


title: Patient 44, GBM, replicate 1

description: Library name: sample933


title: Patient 43, GBM, replicate 1

description: Library name: sample83


title: Dsc_20

description: Library name: Dsc_20


title: Dsc_18

description: Library name: Dsc_18


title: Patient 42, GBM, replicate 2

description: Library name: sample93


title: Dsc_16

description: Library name: Dsc_16


title: Dsc_17

description: Library name: Dsc_17


title: Patient 42, GBM, replicate 1

description: Library name: sample674


title: Dsc_12

description: Library name: Dsc_12


title: Dsc_10

description: Library name: Dsc_10


title: Dsc_15

description: Library name: Dsc_15


title: Patient 40, GBM, replicate 1

description: Library name: sample924


title: Patient 39, GBM, replicate 1

description: Library name: sample365


title: Patient 40, GBM, replicate 3

description: Library name: sample923


title: Dsc_08

description: Library name: Dsc_08


title: Patient 38, Tumor-free SVZ, replicate 2

description: Library name: sample584


title: Dsc_07

description: Library name: Dsc_07


title: Dsc_13

description: Library name: Dsc_13


title: Dsc_05

description: Library name: Dsc_05


title: Dsc_09

description: Library name: Dsc_09


title: Patient 41, GBM, replicate 2

description: Library name: sample1053


title: Patient 38, GBM, replicate 2

description: Library name: sample548


title: Dsc_11

description: Library name: Dsc_11


title: Dsc_04

description: Library name: Dsc_04


title: Dsc_02

description: Library name: Dsc_02


title: Patient 37, GBM, replicate 2

description: Library name: sample240


title: Patient 41, GBM, replicate 1

description: Library name: sample1052


title: Patient 38, Tumor-free SVZ, replicate 1

description: Library name: sample549


title: Patient 37, GBM, replicate 4

description: Library name: sample30


title: Asc_24

description: Library name: Asc_24

value: Ascending


title: Patient 37, GBM, replicate 3

description: Library name: sample29


title: Patient 37, Cortex, replicate 1

description: Library name: sample169


title: Patient 42, Tumor-free SVZ, replicate 1

description: Library name: sample94


title: Dsc_14

description: Library name: Dsc_14


title: Patient 37, Tumor-free SVZ, replicate 2

description: Library name: sample31


title: Patient 37, Tumor-free SVZ, replicate 1

description: Library name: sample241


title: Patient 40, GBM, replicate 2

description: Library name: sample555


title: Patient 38, GBM, replicate 1

description: Library name: sample897


title: Patient 35, GBM, replicate 1

description: Library name: sample294


title: Asc_23

description: Library name: Asc_23


title: Dsc_01

description: Library name: Dsc_01

value: Male


title: Asc_16

description: Library name: Asc_16


title: Asc_22

description: Library name: Asc_22


title: Dsc_03

description: Library name: Dsc_03


title: Patient 34, GBM, replicate 2

description: Library name: sample910


title: Patient 37, Cortex, replicate 3

description: Library name: sample239


title: Asc_19

description: Library name: Asc_19


title: Patient 33, GBM, replicate 2

description: Library name: sample903


title: Patient 36, GBM, replicate 1

description: Library name: sample884


title: Patient 33, GBM, replicate 1

description: Library name: sample902


title: Patient 37, Cortex, replicate 2

description: Library name: sample28


title: Patient 34, Tumor-free SVZ, replicate 1

description: Library name: sample907


title: Patient 32, GBM, replicate 1

description: Library name: sample909


title: Asc_21

description: Library name: Asc_21


title: Asc_20

description: Library name: Asc_20


title: Patient 31, GBM, replicate 2

description: Library name: sample219


title: Patient 37, GBM, replicate 1

description: Library name: sample171


title: Asc_07

description: Library name: Asc_07


title: Asc_08

description: Library name: Asc_08


title: Asc_18

description: Library name: Asc_18


title: Asc_14

description: Library name: Asc_14


title: Patient 30, GBM, replicate 2

description: Library name: sample230


title: Asc_13

description: Library name: Asc_13


title: Patient 35, Cortex, replicate 1

description: Library name: sample668


title: Patient 31, Cortex, replicate 2

description: Library name: sample218


title: Asc_05

description: Library name: Asc_05


title: Asc_17

description: Library name: Asc_17


title: Asc_15

description: Library name: Asc_15


title: Patient 34, GBM, replicate 1

description: Library name: sample906


title: Dsc_06

description: Library name: Dsc_06


title: Patient 31, GBM, replicate 1

description: Library name: sample19


title: Asc_12

description: Library name: Asc_12


title: Patient 30, Tumor-free SVZ, replicate 2

description: Library name: sample231


title: Asc_09

description: Library name: Asc_09


title: Asc_03

description: Library name: Asc_03


title: Patient 31, Tumor-free SVZ, replicate 1

description: Library name: sample20


title: Asc_10

description: Library name: Asc_10


title: Asc_06

description: Library name: Asc_06


title: Patient 30, Tumor-free SVZ, replicate 1

description: Library name: sample1


title: Patient 29, GBM, replicate 1

description: Library name: sample916


title: Patient 30, GBM, replicate 1

description: Library name: sample47


title: Patient 31, Cortex, replicate 1

description: Library name: sample18


title: Asc_04

description: Library name: Asc_04


title: Asc_11

description: Library name: Asc_11


title: Heart left ventricle_GSK_S14_rep4

city: Rouen

first: Sylvain

last: Fraineau

address: 22 Boulevard Gambetta

country: France

institute: Unversity of Rouen Normandy

description: Library name: S_14

data_processing:
Reads were aligned to the mouse genome build mm10 using Hisat2 version 2.0.541
mm10
Assembly: Transcript quantification was performed with feature Counts from the subread package42. Differential analysis, including normalization, was performed with DESeq2 bioconductor package version 1.22.143 using R version 3.5.1.
Supplementary files format and content: gene_fpkm.xls contains FPKM counts far all samples

source_name: Heart left ventricle

growth_protocol: Commercial C57BL/6JRj (Janvier Labs)female mice, 20–22 g (12–18 weeks), were maintained at the EU0477 animal care facility in ventilated cages with softly lit, environmental enrichment, ad libitum access to normal chow diet (Altromin International Cat#1310) and water (automated watering system), subjected to a standard 12-hour light-dark cycle at a constant temperature of 22 °C and a relative humidity kept between 45 and 65%. A two-week acclimatization period was observed for mice provided by Janvier Laboratories.

extract_protocol:
total RNA isolated from left ventricles of 5 independent sham or MI mice previously treated either with GSK-343 (20 mg/kg, Interchim Cat# XLR94D) or vehicle (20% captisol), 8 days post-MI using NucleoSpin RNA XS kit (Macherley-Nagel Cat# 740902)
1 000 ng of total RNA with a concentration >20 ng/ml and a RIN ratio >8 were used for Poly-A mRNA-seq, sequencing length of 150 nt paired end (PE150) with the Illumina NovaSeq 6000

treatment_protocol: Left ventricular (LV) MI was induced in 20–22 g (12–18 weeks) C57BL/6JRj (Janvier Labs) female mice by permanent ligation of the left descending coronary artery. GSK-343 (20 mg/kg, Interchim Cat# XLR94D) was dissolved in cyclodextrin-based Captisol® as a solubilization vehicle at 20% final concentration, as advised by the manufacturer to perform daily intraperitoneal injections starting from 6 h after surgery and daily until 7 days post-MI. Control mice received a vehicle solution (Captisol® 20%) injection of the same volume at the same time as treated mice.

value: Heart left ventricle


title: Heart left ventricle_GSK_S15_rep5

description: Library name: S_15


title: Patient 28, GBM, replicate 1

description: Library name: sample914


title: Asc_01

description: Library name: Asc_01


title: Patient 28, Tumor-free SVZ, replicate 1

description: Library name: sample915


title: Asc_02

description: Library name: Asc_02


title: Patient 27, GBM, replicate 1

description: Library name: sample77


title: Patient 27, Cortex, replicate 1

description: Library name: sample75


title: Heart left ventricle_GSK_G20_rep1

description: Library name: G_20


title: Heart left ventricle_MI_S22_rep4

description: Library name: S_22


title: Patient 26, Tumor-free SVZ, replicate 2

description: Library name: sample947


title: Patient 26, Tumor-free SVZ, replicate 1

description: Library name: sample928


title: Heart left ventricle_MI_S32_rep5

description: Library name: S_32


title: Heart left ventricle_MI_S5_rep3

description: Library name: S_5


title: Patient 24, GBM, replicate 1

description: Library name: sample917


title: Patient 24, GBM, replicate 2

description: Library name: sample253


title: Heart left ventricle_MI_S2_rep1

description: Library name: S_2


title: Heart left ventricle_GSK_S12_rep3

description: Library name: S_12


title: Heart left ventricle_Sham_S10_rep4

description: Library name: S_10


title: Heart left ventricle_Sham_S5_S7_mixed_rep2

description: Library name: S5_S7_mixed


title: Patient 23, Cortex, replicate 1

description: Library name: sample245


title: Heart left ventricle_GSK_G21_rep2

description: Library name: G_21


title: Patient 23, GBM, replicate 1

description: Library name: sample246


title: Patient 23, GBM, replicate 2

description: Library name: sample114


title: Patient 22, Tumor-free SVZ, replicate 2

description: Library name: sample252


title: Heart left ventricle_Sham_S9_rep3

description: Library name: S_9


title: Patient 22, GBM, replicate 2

description: Library name: sample249


title: Patient 22, GBM, replicate 1

description: Library name: sample56


title: Patient 25, GBM, replicate 1

description: Library name: sample930


title: Heart left ventricle_MI_S4_rep2

description: Library name: S_4


title: L929 cells, 3' knock groups

description: Library name: knock-250425

data_processing:
The sequencing data was processed using the SSH (Secure Shell) client MobaXterm within a Linux operating system. The overall processing workflow was performed according to the following:
1) Quality control: FastQC was used to assess the quality of the sequencing data fastq.gz format. Indicators such as “Per base sequence quality,” “Per base sequence content,” and “Sequence Duplication Levels” were used to make a preliminary judgment of the quality of the sequencing library.
2) Barcode B and UMI swapping: The fastq.gz files were decompressed using the zcat command to convert them into “fq” files. Following the process shown in Supplementary Fig. 15, a Python script was written to swap the Barcode B and UMI from Read 2 to the beginning of Read 1. Additionally, 33 bp from the 5’ end of Read 2 was deleted. The Final_R1/R2.fq.gz files were then compressed.
3) Data preprocessing: The FastqToSam function in Picard tools were invoked to convert the “fq” file into query-name sorted bam file. Run the TagBamWithReadSequenceExtended function from Drop-seq_tools-3.0.2-0 twice to extract Barcode and UMI sequences at different locations, then invoke FilterBam function to filter low-quality Barcode and UMI sequences, and finally use the PolyATrimmer function to remove the Poly A sequence at the capture end. After preprocessing, the SamToFastq function from Picard tools was used to convert the bam files back into fastq files for subsequent sequence alignment.
4) Sequence alignment: Reference genome indices for mouse GRCm38 (https://www.ncbi.nlm.nih.gov/grc/mouse) and human GRCh38 (https://www.ncbi.nlm.nih.gov/grc/human) were constructed from NCBI Genome Reference Consortium, respectively. Sequence alignment was then performed using STAR software (version 2.7.11b).
5) Expression matrix: After alignment, the SortSam and MergeBamAlignment functions in Picard were called to sort and integrate the results. Finally, the DigitalExpression function in Drop-seq_tools-3.0.2-0 was employed with specified filtering conditions to select the digital expression matrix corresponding to the specified Barcode.
Assembly: GRCm38
Supplementary files format and content: matrixed files

source_name: connective tissue

extract_protocol:
cells were detached with trypsin treatment after the supernatant was removed. Perform cell aggregate dissociation with strong pipetting. Cells were then rinsed three times with ice-cold phosphate buffer solution (PBS), pelleted by centrifugation at 500 ×g for 10 min at 4 °C to remove the supernatant containing excess trypsin and culture media thoroughly. The home-built microneedle capturing system described above was employed for picking up single cells into 8- or 96-well plates containing lysis buffer. Specifically, under the optimized diameter of the capillary tip (30 μm), the conical tip of the capillary probe was controlled to be aligned with the target cells, and the target cell was sucked into the probe under capillary force. The CBTi-seq lysis buffer consisted of 0.13 µl recombinant RNase inhibitor (40 U/µl, Takara), 0.25 µl of Takara lysis buffer (10 ×) and 0.5 µl CBTi-Oligo dT primer (10 µM), and ddH2O to 2.5 µl final volume. The plates were centrifuged at 1000 ×g immediately after sorting and stored at −80 °C until use.
Sorted single-cell or microregion tissue samples were removed from the −80 °C storage and thawed at room temperature for 10 min to facilitate sample lysis and RNA release, then transferred to a preheated PCR thermocycler, incubated for 3 min at 72 °C and immediately placed on ice afterwards. Next, 10 µl of RT-PCR mix containing 1.2 µL dNTP mix (10 mM), 0.252 µL RNase Inhibitor (40 U/µl), 0.1 µL DTT (100 mM), 0.328 µL MgCl2 (279 mM), 0.18 µL dCTP (100 mM), 2 µL Betaine (5 M), 0.368 µL CBTi-TSO (50 µM), 0.172 µL of Superscript Ⅳ / Maxima H (200 U/µL, ThermoFisher Scientific) and 5 µL of KAPA HiFi HotStart Ready Mix (2×, Roche) were added to synthesis full-length dsDNA. The following RT-PCR program was set to: 60 min at 50 °C, 98 °C for 3 min, then 20 cycles of (98 °C for 20 s, 67 °C for 20 s, 72 °C for 6 min). The cDNA concentration was quantified using the Qubit 4.0 fluorimeter, and size distribution was assessed using capillary electrophoresis on a Fragment Analyzer system (Agilent Bioanalyzer). 1 μl unpurified amplified cDNA working dilution (5 ng/µl) of each sample was transferred to a new plate before adding tagmentation reaction mix as described above. Of note, each sample used unique combination barcoding. Samples were incubated for 10 min at 55 °C. Then, all tagmented products were mixed into 1.5- or 2 ml PCR tube, purified with 1.5× AMPure XP beads for termination of the tagmented reaction and collection, followed by elution with 20 µl nuclease-free water.

value: connective tissue

value: fibroblasts


title: Patient 22, Tumor-free SVZ, replicate 1

description: Library name: sample2