title: PsA4954_CD4, HiC

description: Library name: PsA4954_CD4


title: H3.2-K4R 16-18hr  embryo, rep2

status: Public on Dec 18 2024

type: SRA

city: Chapel Hill

first: Daniel

middle: J.

last: McKay

state: NC

address: 250 Bell Tower Drive

country: USA

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Adapter sequences were removed using bbmap (v38.67) using parameters ktrim=r ref=adapters rcomp=t tbo=t tpe=t hdist=1 mink=11
Sequenced reads were aligned to the genome using STAR (v2.7.7a)
Bam file was indexed and sorted using samtools (v1.9)
subread (v2.0.6) was used to count reads mapping to genes
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes feature counts for each Sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: 16-18hr embryo

growth_protocol: Eggs were collected at 25°C for two hours on apple agar plates and then aged for 16 hours at 25°C. Homozygous histone locus deletion embryos were positively selected via GFP expression.

extract_protocol:
RNA was harvested using RNeasy plus Mini Kit (QIAGEN). Approximately 0.25µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Universal RNA-Seq with NuQuant, Drosophila AnyDeplete kit (Tecan Genomics) following manufacturer's protocols.

tag: tissue

value: 16-18hr embryo

tag: genotype

value: deltaHisC; 12xH3.2-K4R


title: H3.2-K4R 16-18hr  embryo, rep1


title: PsA4962CD8, ATAC

city: Manchester

first: Jake

last: Butler

address: AV Hill Building, The University of Manchester, Acker Street

country: United Kingdom

institute: University of Manchester

description: Library name: PsA4962CD8

library_source: genomic

data_processing:
ATAC-seq reads were quality filtered and trimmed and adapters were removed using fastp v0.20.1 (Chen et al. 2018). Reads were then mapped using bowtie2 v2.4.4 (Langmead and Salzberg 2012) using the very-sensitive pre-set. Duplicates were removed using the MarkDuplicates functionality of picard tools (Institute 2019) and mitochondrial reads were removed, as well as removing low quality alignments (MAPQ<30) and keeping only properly paired reads. Coverages were generated from cleaned alignments using the bamCoverage functionality from DeepTools2 (Ramírez et al. 2016). Peaks were called using macs2 v2.2.7.1 (Zhang et al. 2008). The ATAC-seq processing pipeline is available on GitHub (https://github.com/ChenfuShi/ATAC_ChIP_pipeline). Data for all samples was then analysed in R using DiffBind (Stark and Brown 2011). A consensus peakset was generated using peaks that were present in at least 5 samples. Peak size was set to 500bp. Cross library normalization was performed using the DESeq2 normalization method (DBA_NORM_NATIVE) but using only reads in peaks (DBA_LIBSIZE_PEAKREADS), as different samples had significantly different proportion of reads in peaks, which would bias the default normalization method. Counts were extracted at this point for further analysis, except for differential binding analysis, which was performed within DiffBind, using the DESeq2 method. No batch effect correction was found to be necessary. We found that quantile normalization slightly improved results, such as separation of cell types on the PCA plot and correlation between expression and peak height of promoter peaks, and as such we used quantile normalized counts for all downstream analysis.
Assembly: hg38
Supplementary files format and content: Narrow peak file,in bed format, showing locations of Macs2 called peaks on narrow mode

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Between 40ml and 100ml of peripheral blood was collected following informed consent from 55 PsA patients and 19 healthy controls and processed on the same day. Patients and healthy controls were recruited under the National Repository study ethics approval number IRAS 32231, MREC 99/8/084. PBMCs were isolated using Ficoll density gradient centrifugation. EasySep Human CD4+ and CD8+ T cell negative selection kits (StemCell technologies #17952 and #17953) were used to isolate CD4+ and CD8+ T cells respectively. Cells were then aliquoted and prepared for long-term storage separately for each technique used. Synovial fluid extracted from patients with PsA was first treated with hyaluronidase enzyme (Sigma Aldrich #H3884) and then processed in a similar way as the peripheral blood samples.
Approximately 500 thousand cells were frozen in RecoveryTM Cell Culture Freezing Medium (Thermofisher #12648010) and stored at -80°C. An aliquot of 50 thousand cells was then used for ATAC-seq library preparation following the Omni-ATAC protocol as released by the Kaersten lab (Corces et al. 2017; Amanda Ackermann 2019). Library size was checked by TapeStation 4200 (Agilent) and QC was done by quantstudio (Life technologies) using the NEBNext® Library Quant Kit for Illumina (E7630). Sequencing was performed on the NextSeq2000 platform at a target depth of 50 million reads per library and generating 50bp paired-end reads.

value: Blood

tag: cell type

value: CD8 + T-cell

tag: treatment

value: Patient


title: PSA4951CD8SF, HiC

description: Library name: PSA4951CD8SF

data_processing:
Hi-C reads were quality filtered and trimmed and adapters were removed using fastp v0.20.1 (Chen et al. 2018). Reads were then processed and mapped to the GRCh38 genome using HiC-pro v3.0.0 (Servant et al. 2015), using default settings. Hic juicebox files for visualization and analysis were generated using the hicpro2juicebox.sh script using juicer tools v1.22.01. Cool files were generated from the juicebox files using hic2cool (https://github.com/4dn- dcic/hic2cool). TAD calling was done using onTAD (An et al. 2019) with default settings and ICE normalized 40kb resolution maps.
Assembly: hg38
Supplementary files format and content: .hic files that can be used for visualisation. These files can be converted to cool files.

source_name: Synovial fluid

extract_protocol:
Between 40ml and 100ml of peripheral blood was collected following informed consent from 55 PsA patients and 19 healthy controls and processed on the same day. Patients and healthy controls were recruited under the National Repository study ethics approval number IRAS 32231, MREC 99/8/084. PBMCs were isolated using Ficoll density gradient centrifugation. EasySep Human CD4+ and CD8+ T cell negative selection kits (StemCell technologies #17952 and #17953) were used to isolate CD4+ and CD8+ T cells respectively. Cells were then aliquoted and prepared for long-term storage separately for each technique used. Synovial fluid extracted from patients with PsA was first treated with hyaluronidase enzyme (Sigma Aldrich #H3884) and then processed in a similar way as the peripheral blood samples.
Approximately 3-5 million cells were crosslinked in 2% formaldehyde for 10 minutes at room temperature and the reaction was then quenched using a solution glycine + BSA. Samples were then washed in PBS and snap frozen on dry ice and then transferred to -80°C for long- term storage. 2 million cells were then used for library preparation following the two-restriction enzyme Arima Hi-C kit (Arima Genomics) and the KAPA HyperPrep kit (Roche #KK8504) manufacturer’s protocol using Illumina TruSeq dual indexes. Library size was checked by TapeStation 4200 (Agilent) and QC was done by quantstudio (Life technologies) using the NEBNext® Library Quant Kit for Illumina (E7630). Sequencing was performed on the NovaSeq6000 platform using NovaSeq S4 flow cells at a target depth of 350 million reads per library and generating 150bp paired-end reads.

value: Synovial fluid


title: NRK-52E cells, TGF-beta1 + 2D-EVs-3

city: Guangzhou

first: Qiang

last: Guo

state: Guangdong

address: No. 26, Erheng Road, Yuancun, Tianhe District

country: China

institute: Sun-Yat Sen university, The sixth affiliated Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(parameter;default)
Clean reads were mapped to  Rattus_norvegicus  genome using by Hisat2（v2.2.0）
The expression level of genes were calculated by StringTie （v2.1.2） and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads.
DEseq2（1.26.0） was used to detect DEGs (Different expressed genes), and DEGs with fold change > 2 and adjusted P value <= 0.05 were considered to be significantly different expressed genes.
GO enrichment analysis and KEGG enrichment analysis were performed using clusterProfiler, a function of R. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value < 0.05)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Rattus norvegicus

growth_protocol: NRK-52E cells were maintained in DMEM supplemented 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the treated NRK-52E cells using TRIzol Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
The RNA samples were processed for RNA-seq library construction using the Hieff NGS® RNA Lib Prep Primer Mix for Illumina® (Yeasen, 13335ES96).

treatment_protocol: NRK-52E cells were incubated in DMEM with 10% FBS until 80% convergence, and treated with 10ug/ml TGF-beta1 24h to induced renal fibrosis,and then treated with 2D- or 3D-EVs(5*10^8 particles/ml) for another 48h.

tag: cell line

value: Tubular epithelial cells

value: WT

tag: phenotype

value: Renal fibrosis

value: TGF-beta1 + 2D-EVs


title: H3.2-WT 16-18hr  embryo, rep2

value: deltaHisC; 12xH3.2-WT


title: NRK-52E cells, TGF-beta1 + 2D-EVs-2


title: NRK-52E cells, TGF-beta1 + 3D-EVs-2

value: TGF-beta1 + 3D-EVs


title: PsA4951_CD8, HiC

description: Library name: PsA4951_CD8


title: NRK-52E cells, TGF-beta1 + 2D-EVs-1


title: H3.2-WT 16-18hr  embryo, rep1


title: Control_1

city: Shanghai

first: Shujing

last: Feng

address: Qingyuan ring road

institute: Shanghai university of sport

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: xls file includes TPM for each sample

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were examined using Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RQN values were determined by Agilent5300. The requirements for a single library were 1 μg of total RNA, concentration ≥ 30 ng/μL, RQN > 6.5, and OD260/280 between 1.8 and 2.2.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

value: skeletal muscle

tag: group

value: Control


title: PSA4962CD4, ATAC

description: Library name: PSA4962CD4

value: CD4 + T-cell


title: PsA4961_CD8, ATAC

description: Library name: PsA4961_CD8


title: femur, GIOP, 5

city: Saitama

first: Nagahiro

last: Ochiai

address: Yoshino-cho 1-403, Kita-ku

country: Japan

institute: Taisho Pharmaceutical, Co., Ltd

data_processing:
Sequenced reads were mapped and quantified using the RSEM v 1.2.28 in conjunction with the STAR aligner v 2.7.10a.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text-file includes read counts for each sample

source_name: femur

extract_protocol:
The frozen bone tissue was pulverized under liquid nitrogen using a Freezer/Mill 6775 (SPEX). For the extraction of RNA, TRIzol reagent was applied to the crushed tissue, followed by chloroform addition for phase separation. The RNA-containing aqueous phase was isolated and purified using the Direct-zol MicroPrep kit.
Total RNA was extracted from mouse tibiae and used for library construction using the SMARTer Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara Bio, 634412).

value: femur

tag: bone

value: cortical bone

tag: Sex

value: female

tag: age


title: NRK-52E cells, TGF-beta1-3


title: PsA4950_CD8, HiC

description: Library name: PsA4950_CD8


title: NRK-52E cells, TGF-beta1-2


title: PsA4959CD4, ATAC

description: Library name: PsA4959CD4


title: PSA4959_CD8, ATAC

description: Library name: PSA4959_CD8


title: PsA4950_CD4, HiC

description: Library name: PsA4950_CD4


title: PsA4946CD8, HiC

description: Library name: PsA4946CD8


title: femur, GIOP, 2


title: NRK-52E cells, Control-3

value: control


title: femur, GIOP, 3


title: PSA4958CD8SF, ATAC

description: Library name: PSA4958CD8SF


title: PSA4945CD4, HiC

description: Library name: PSA4945CD4

value: Blood


title: NRK-52E cells, Control-2


title: femur, GIOP, 1


title: psa4944CD8, HiC

description: Library name: psa4944CD8

value: CD8 + T-cell


title: PsA4958CD8, ATAC

description: Library name: PsA4958CD8

value: Patient


title: PsA4951_CD4, HiC

description: Library name: PsA4951_CD4


title: NRK-52E cells, Control-1


title: PSA4944_CD4, HiC

description: Library name: PSA4944_CD4


title: PsA4960_CD8, ATAC

description: Library name: PsA4960_CD8


title: femur, Non-GIOP, 3


title: PsA4958CD4, ATAC

description: Library name: PsA4958CD4


title: femur, Non-GIOP, 4


title: PSA4943_CD8, HiC

description: Library name: PSA4943_CD8


title: NRK-52E cells, TGF-beta1-1


title: PSA4958CD4SF, ATAC

description: Library name: PSA4958CD4SF

value: Synovial fluid


title: femur, GIOP, 4


title: Spinalcord WT 6 early stage

city: Beijing

first: Kexin

last: Li

address: No. 15, Datun Road, Chaoyang District, Beijing, China

institute: Peking Union Medical College

data_processing:
For data analysis, raw data were processed by first removing the 3′ Illumina universal adaptor sequence using Cutadapt (https://cutadapt.readthedocs.io/en/stable/). Next, clean reads were aligned to the rat reference genome (mRatBN7.2) downloaded from Ensembl (https://ftp.ensembl.org/pub/release-108/fasta/rattus_norvegicus/dna/) and read counts were quantified using featureCounts. Differential expression analysis was performed using R package DESeq2 and the batch effect was removed by using R package sva.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited file includes raw counts for each samples

source_name: Spinalcord

extract_protocol:
Total RNA was isolated using Trizol from indicated tissues and C6 cells. Only samples with a 260/280 nm ratio within 1.8 to 2.1 and the intensity of a 28S/18S ratio between 1.5 to 2 were further processed.
Briefly, rRNA depletion and RNA fragmentation were performed on total RNA samples (2 μg). Next, the RNA was reverse-transcribed into double-stranded cDNA with random primers. cDNA samples were end-repaired and polyadenylated before ligation of Y-shaped adapters containing the index for multiplexing, followed by dUTP strand degradation. Fragments containing Y-shaped adapters on both ends were enriched by PCR. The quantity of the cDNA library was validated using Qubit dsDNA HS Assay Kit (Invitrogen). The purity of the libraries was analyzed by a fragment analyzer automated CE system (Advanced Analytical) and the sequencing was further performed only when the libraries had a size of 300 to 400 bp and no adaptor dimer contamination. PE150 sequencing was performed on the Illumina NovaSeq 6000.

value: Spinalcord


title: femur, Non-GIOP, 1


title: Spinalcord WT 5 early stage

value: WT


title: PsA4956CD8, ATAC

description: Library name: PsA4956CD8


title: Spinalcord WT 3 early stage


title: PSA4942_CD4, HiC

description: Library name: PSA4942_CD4


title: femur, Non-GIOP, 2


title: PsA4957CD4, ATAC

description: Library name: PsA4957CD4


title: Spinalcord WT 4 early stage


title: control, R23671

city: New York City

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNA sequences were aligned to the hg38 reference genome from Ensembl via the STAR algorithm.
Quality control checks, including assessments of GC content, duplication rates, gene body coverage, and library complexity, were carried out using RSeQC30 and Picard tools (https://broadinstitute.github.io/picard/). Gene expression levels were quantified with featureCounts and the resulting expression matrix was curated to retain genes present in at least one-third of our sample set. This matrix was then normalized through the VOOM method.
Assembly: hg38
Supplementary files format and content: Raw count data were generated with featureCounts and are provided as a separate matrix.

source_name: Caudate

extract_protocol:
Total RNA was extracted from all tissue samples using AllPrep DNA/RNA Mini Kit (Qiagen Cat No./ID: 80204).
Paired-end strand-specific sequencing libraries were prepared from 300ng total RNA using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero Gold ribosomal RNA depletion which removes rRNA and mtRNA. The libraries were then sequenced on an Illumina HiSeq 3000 at the Promega Sequencing Facility, producing a median of 46.9 million reads per sample.

value: Caudate

value: Postmortem brain tissue

value: F

tag: group/disease

tag: rin


title: PsA4956CD4, ATAC

description: Library name: PsA4956CD4


title: PSA4941_CD8, HiC

description: Library name: PSA4941_CD8

value: Healthy


title: Spinalcord WT 2 early stage


title: control, R22843


title: control, R22842

value: M


title: Spinalcord WT 1 early stage


title: PSA4920_CD8, HiC

description: Library name: PSA4920_CD8


title: PSA4955CD8, ATAC

description: Library name: PSA4955CD8


title: PsA4954CD4, ATAC

description: Library name: PsA4954CD4


title: PSA4920_CD4, HiC

description: Library name: PSA4920_CD4


title: PSA4942_CD8, HiC

description: Library name: PSA4942_CD8


title: Spinalcord mtCO3mut 6 early stage


title: control, R22840


title: NRSF055CD8SF, HiC

description: Library name: NRSF055CD8SF


title: PsA4954_CD8, ATAC

description: Library name: PsA4954_CD8


title: ED, R22839

value: ED


title: NRHV332CD8, HiC

description: Library name: NRHV332CD8


title: control, R22838


title: PsA4953_CD8, ATAC

description: Library name: PsA4953_CD8


title: Spinalcord mtCO3mut 3 early stage


title: Spinalcord mtCO3mut 5 early stage


title: Spinalcord mtCO3mut 4 early stage


title: control, R22837


title: Spinalcord mtCO3mut 2 early stage


title: PsA4952_CD8, ATAC

description: Library name: PsA4952_CD8


title: NRHV332CD4, HiC

description: Library name: NRHV332CD4

value: CD4 + T-cell


title: OCD, R22836

value: OCD


title: NRHV326CD8, HiC

description: Library name: NRHV326CD8


title: PSA4951CD4SF, ATAC

description: Library name: PSA4951CD4SF


title: PsA4952CD4, ATAC

description: Library name: PsA4952CD4


title: NRHV326CD4, HiC

description: Library name: NRHV326CD4


title: Spinalcord mtCO3mut 1 early stage


title: OCD, R22835


title: NRHV325CD8, HiC

description: Library name: NRHV325CD8


title: psa4951_CD8, ATAC

description: Library name: psa4951_CD8


title: psa4951_CD4, ATAC

description: Library name: psa4951_CD4


title: ED, R22834


title: NRHV325CD4, HiC

description: Library name: NRHV325CD4


title: Brain WT 3

source_name: Brain

value: Brain


title: control, R22833


title: Brain WT 2


title: PsA4950_CD4, ATAC

description: Library name: PsA4950_CD4


title: NRHV324CD8, HiC

description: Library name: NRHV324CD8


title: NRHV324CD4, HiC

description: Library name: NRHV324CD4


title: ED, R22832


title: OCD, R22830


title: ED, R22831


title: Brain WT 1


title: Brain mtCO3mut 4


title: Brain mtCO3mut 3


title: NRHV322_CD8, HiC

description: Library name: NRHV322_CD8


title: control, R22828


title: NRHV321_CD8, HiC

description: Library name: NRHV321_CD8


title: PSA4947CD4, ATAC

description: Library name: PSA4947CD4


title: NRHV322_CD4, HiC

description: Library name: NRHV322_CD4


title: PSA4949_CD8, ATAC

description: Library name: PSA4949_CD8


title: OCD, R22829


title: NRHV321_CD4, HiC

description: Library name: NRHV321_CD4


title: Brain mtCO3mut 1


title: control, R22827


title: Brain WT 4


title: PsA4947_CD8, ATAC

description: Library name: PsA4947_CD8


title: PsA4950CD8, ATAC

description: Library name: PsA4950CD8


title: NRHV295CD8, HiC

description: Library name: NRHV295CD8


title: Brain mtCO3mut 2


title: PSA4946CD8, ATAC

description: Library name: PSA4946CD8


title: Spinalcord WT 4


title: control, R22826


title: OCD, R22825


title: NRHV295CD4, HiC

description: Library name: NRHV295CD4


title: PsA4949_CD4, ATAC

description: Library name: PsA4949_CD4


title: Spinalcord WT 3


title: PsA4948_CD8, ATAC

description: Library name: PsA4948_CD8


title: Spinalcord WT 2


title: PsA4945_CD8, ATAC

description: Library name: PsA4945_CD8


title: NRHV290CD4, HiC

description: Library name: NRHV290CD4


title: PSA4945_CD4, ATAC

description: Library name: PSA4945_CD4


title: control, R22824


title: NRHV290CD8, HiC

description: Library name: NRHV290CD8


title: Spinalcord WT 1


title: control, R22823


title: NRHV238_CD4, HiC

description: Library name: NRHV238_CD4


title: PsA4944_CD4, ATAC

description: Library name: PsA4944_CD4


title: control, R22821


title: NRHV171CD8, HiC

description: Library name: NRHV171CD8


title: control, R22820


title: Spinalcord mtCO3mut 2


title: PsA4941CD8, ATAC

description: Library name: PsA4941CD8


title: NRHV171CD4, HiC

description: Library name: NRHV171CD4


title: control, R22819


title: Spinalcord mtCO3mut 1


title: PsA4920_CD8, ATAC

description: Library name: PsA4920_CD8


title: control, R22818


title: NRHV168CD8, HiC

description: Library name: NRHV168CD8


title: Scale S3

city: Oklahoma City

first: John

middle: Kimble

last: Frazer

state: Oklahoma

address: 941 Stanton L Young Blvd

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
After conversion to fastq files, reads for each sample were processed and aggregated using the 10x Genomics Cell Ranger (v.6.0.0) pipeline (no normalization, default settings) and processed in the Seurat R package (v.4.3.0). We obtained transcriptomes for 6,359 cells after Cell Ranger processing.
SoupX (v.1.6.2) was used to model and remove ambient RNA contamination per sample, and scDblFinder (v.1.12.0) was used to detect potential multiplets (default settings, per individual tissue type). Additional QC filtering was performed to remove potential dead or dying cells along with cells exhibiting abnormal read/gene counts and high levels of mitochondrial transcripts, resulting in 1,890 usable cells for our analysis.
Using fastMNN, cells were normalized and integrated, and then clustered within Seurat (Leiden algorithm). Clustering resolution was optimized using the clustree package (v.0.5.0). Cluster boundaries were manually examined and fine-tuned to optimize biological interpretation. Collective diagnostic gene signatures corresponding to published gene lists and our own sc-qRT-PCR results were explored using Seurat and UCell (v.2.2.0). Preferential gene markers were determined for each distinct population using the FindAllMarkers function within Seurat, to aid in cell type assignment (p.adj ≤ 0.05, min.pct = 0.25).
Assembly: GRCz11
Supplementary files format and content: Tab-delimited value files and matrices.

organism: Danio rerio

source_name: Scale

extract_protocol:
For procedures, zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus, kidney marrow and scale samples were dissected and placed in 500 ul cell media (RPMI + 1% FBS + 1% Pen/Strep). Single-cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD-FACSJazz Instrument (analysis performed in FlowJo softare).
Following creation of single-cell emulsions, uniquely-identifiable 1st-strand template single-cell cDNA libraries were generated from each cell by emulsion PCR. 2nd-strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced, using read lengths of 28 bp for the first read, 120 bp for the second read, and 8 base index reads.

value: Scale

value: Lymphocytes


title: NRHV168CD4, HiC

description: Library name: NRHV168CD4

value: Blood


title: PsA4944CD8, ATAC

description: Library name: PsA4944CD8

value: CD8 + T-cell


title: PsA4920_CD4, ATAC

description: Library name: PsA4920_CD4

value: Patient


title: Kidney Marrow S2

description: 10X Genomics

source_name: Kidney Marrow

value: Kidney Marrow


title: NRHV238_CD8, HiC

description: Library name: NRHV238_CD8


title: Spinalcord mtCO3mut 4

value: Spinalcord


title: control, R22822

value: control


title: ED, R22680

value: Caudate


title: Thymus S1

description: 10X Genomics

source_name: Thymus

value: Thymus


title: NRSF056CD8SF, ATAC

description: Library name: NRSF056CD8SF

value: Synovial fluid


title: PSA4942CD8SF, ATAC

description: Library name: PSA4942CD8SF


title: control, R22682

value: Postmortem brain tissue


title: Spinalcord mtCO3mut 3


title: NRHV121_CD8, HiC

description: Library name: NRHV121_CD8

value: Healthy


title: NRHV151CD4, HiC

description: Library name: NRHV151CD4


title: OCD, R22679

value: M


title: Tube, HR, S70

city: Tucson

first: Michelle

last: Wei

state: AZ

address: 1200 E University Blvd

institute: University of Arizona

library_source: other

data_processing:
For data processing, sequencing adapters and low-quality bases were trimmed using Cutadapt. Reads with 18~26-nt in length were kept, and the paired-end reads were merged using fastq-join.
Reads mapping and miRNA quantification were performed using miRMaster with the default parameter settings
Assembly: human miRNA precursors (in mirBase database)
Supplementary files format and content: Comma-delimited file with raw counts

molecule: other

source_name: Tube

extract_protocol:
Small RNAs were extrated from an average of 10 sections per sample using the miRNeasy FFPE kit (Qiagen). Quality tests, including qRT-PCR and gel electrophoresis, were used to confirm successful miRNA isolation without contamination.
Libraries were prepared using the TruSeq Small RNA library Prep Kit (Illumina, San Diego, CA), validated on the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: Tube

tag: patient group

value: HR


title: NRHV121_CD4, HiC

description: Library name: NRHV121_CD4

value: CD4 + T-cell


title: Ovary, HR, S69

source_name: Ovary

value: Ovary


title: NRHV332CD8, ATAC

description: Library name: NRHV332CD8


title: NRHV086CD8, HiC

description: Library name: NRHV086CD8


title: Tube, HR, S68


title: OCD, R22677

value: OCD


title: NRHV332_CD4, ATAC

description: Library name: NRHV332_CD4

value: Blood


title: Ovary, HR, S67


title: OCD, R22676


title: NRHV086CD4, HiC

description: Library name: NRHV086CD4


title: NRSF055CD8SF, ATAC

description: Library name: NRSF055CD8SF


title: NRHV326CD4, ATAC

description: Library name: NRHV326CD4


title: NRHV079CD8, HiC

description: Library name: NRHV079CD8

value: CD8 + T-cell


title: Tube, LR, S66

value: LR


title: NRHV079CD4, HiC

description: Library name: NRHV079CD4


title: Ovary, LR, S65


title: NRHV326_CD8, ATAC

description: Library name: NRHV326_CD8


title: control, R22674

value: F


title: Ovary, LR, S63


title: NRHV073_CD8, HiC

description: Library name: NRHV073_CD8


title: control, R22671


title: ED, R22678

value: ED


title: NRHV073_CD4, HiC

description: Library name: NRHV073_CD4


title: NRHV325_CD8, ATAC

description: Library name: NRHV325_CD8


title: Tube, LR, S64


title: NRSF055CD4SF, ATAC

description: Library name: NRSF055CD4SF


title: NRHV325_CD4, ATAC

description: Library name: NRHV325_CD4


title: OCD, R22672


title: NRHV056CD8SF, HiC

description: Library name: NRHV056CD8SF


title: OCD, R22663


title: NRHV324CD8, ATAC

description: Library name: NRHV324CD8


title: Tube, HR, S62


title: NRHV324CD4, ATAC

description: Library name: NRHV324CD4


title: Ovary, HR, S61


title: NRHV014XCD8, HiC

description: Library name: NRHV014XCD8


title: control, R22661

value: control


title: NRHV014XCD4, HiC

description: Library name: NRHV014XCD4


title: Tube, HR, S60


title: NRHV322CD8, ATAC

description: Library name: NRHV322CD8


title: NRHV322CD4, ATAC

description: Library name: NRHV322CD4


title: HeLa, DDX39B knockout, HU treatment, input group, input

first: Jiadong

last: Wang

address: 38 College Road, Haidian District

department: Department of Radiation Medicine

institute: Peking University Health Science Center

data_processing:
For analysis of REFORC data acquired under crosslinking conditions, the raw reads were trimmed with Fastp version 0.20.1 (parameters: --trim_poly_g --poly_g_min_len 6 --trim_poly_x --poly_x_min_len 6 --cut_front --cut_tail --cut_window_size 4 --qualified_quality_phred 15 --low_complexity_filter --complexity_threshold 30 --length_required 4). For analysis of data acquired via REFORC without crosslinking, the raw reads were trimmed with Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
For analysis of REFORC data acquired under crosslinking conditions, the cleaned reads were aligned to the genome with STAR version 2.7.10b (parameters: --outFilterMismatchNmax 10 --outFilterMatchNminutes 10 --seedSearchLmax 10 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0), we removed the reads near the rDNA loci on chromosome 21 as nonspecific signals. For analysis of data acquired via REFORC without crosslinking, the cleaned reads were aligned to the genome with HISAT2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
The duplicated reads were removed with Sambamba version 0.8.2, and mapped reads were sorted with SAMtools version 1.17 and converted to generate bigWig files via the bamCoverage function of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
For peak calling, the untreated group and mock group were used as controls to obtain HU group-specific peaks with MACS2 version 2.1.0.20150731 for analysis of data acquired via REFORC with crosslinking or with Piranha for analysis of data acquired via REFORC version 1.2.1 without crosslinking. The false discovery rate (FDR) cutoff was set as 0.2 in MACS2. In Piranha, the parameters were set as follows: -s -p 0.05 -b 20 -l -n -i 20.
Assembly: hg38
Supplementary files format and content: bigWig, BED, narrowPeak
Library strategy: REFORC

molecule: nuclear RNA

source_name: HeLa cell line

growth_protocol: HeLa cells, HeLa DDX39A-Tet-On stable cells and DDX39A/DDX39B knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
The cells were harvested by scraping, washed twice with prechilled PBS and then fixed or collected directly without fixation for further processing. When fixation was performed, the cells were subjected to crosslinking at room temperature for 10 minutes with 1% paraformaldehyde diluted in PBS, and the reaction was then quenched with 0.125 M glycine. The cells were then washed twice with prechilled DEPC-treated PBS and subsequently permeabilized with DEPC-treated PBS containing 0.25% Triton X-100 and 80 U/Ml RNase inhibitor (Biosharp, BL780B) on a rotator at room temperature for 30 minutes. After centrifugation, the cell pellets were washed once with DEPC-treated PBS. Then, fresh click reaction mixture (in DEPC-treated PBS with sequential addition and mixture of 25 μM biotin-PEG3-azide, 100 mM sodium ascorbate, 100 mM CuSO4 and 80 U/mL RNase inhibitor) was added to the pellets, which were incubated on a rotator at room temperature for 2 hours. The cell pellets were then washed once with DEPC-treated PBS and lysed on ice in lysis buffer (DEPC-treated double-distilled water (ddH2O) containing 1% SDS, 50 mM Tris-HCl (pH 8.0), and 80 U/mL RNase inhibitor) for 10 minutes. A noncontact ultrasonic disruptor (Covaris M220 focused ultrasonicator) was subsequently used to sonicate the pellets for 3 minutes to obtain smeared DNA‒RNA fragments of 100-300 bp. After sonication, the samples were centrifuged at 15000 rpm at 4°C for 10 minutes, after which the supernatant was collected. Part of the supernatant was taken as the input sample (as Total-RNA group), while the remaining portion was used as the immunoprecipitation (IP) fraction (as REFORC-RNA group). The input samples were directly extracted for RNA components and prepared for cDNA library building. The IP fraction was diluted with an equal volume of DEPC-treated PBS supplemented with cocktail and RNase inhibitor. Two hundred microliters of streptavidin beads (GE) were added to each group, and the mixtures were incubated on a rotator at 4°C for 14-16 hours. The beads were washed with DEPC-treated PBS four times. Two hundred microliters of NT2 buffer (DEPC-treated ddH2O containing 50 mM HEPES (pH 7.5), 150 mM KCl, 1 mM MgCl2, 0.05% NP-40 and 80 U of RNase inhibitor) was added to the beads in each group, which were incubated at 95°C for 5 minutes and then immediately placed on ice for 2 minutes. The beads were treated with 10 U of RQ1 RNase-Free DNase I (Promega, M6101) and 80 U of RNase inhibitor and incubated in a Thermo Mixer-Heat with rotation at 1200 rpm at 37°C for 2 hours. For the RNase H treatment group, 25 U of RNase H (NEB, M0297S) was added, and the mixture was incubated with rotation at 1200 rpm at 37°C for 1 h before DNase I treatment. Finally, 500 μL of TRIzol was added to the bead mixture, which was incubated at room temperature for 5 minutes and centrifuged at 15000 rpm for 5 minutes. Phenol–chloroform was added to the supernatant for extraction. Then, 10 μL of glycogen (20 mg/mL) and 40 μL of NaCl (5 M) were added to the RNA-containing supernatant, followed by the addition of equal volume of isopropanol. The mixture was thoroughly mixed and incubated at -80°C overnight. The next day, the mixture was centrifuged at 15000 rpm for 30 minutes at 4°C. We then washed the RNA pellet once with 75% ethanol. Finally, we resuspended the pellet in 12 μL of DEPC-treated water to prepare the sample for DNA library preparation.
We used rRNA probes for rRNA cleanup. The RNA samples (no more than 2 μg) were mixed with 1 μL of rRNA probes (1 μM) and 2 μL of probe hybridization buffer (750 mM Tris-HCl, pH 8.0; 750 mM NaCl) and incubated at 95°C for 2 minutes, cooled to 22°C at a rate of 0.1°C/s and incubated at 22°C for 5 minutes. Then, 2 μL of Thermostable RNase H (NEB, M0523S), 2 μL of 10x RNase H buffer and 1 μL of ddH2O were added to the mixture, which was incubated at 50°C for 30 minutes. The RNA samples were further incubated with 2.5 μL of DNase I (NEB, M0303S), 2.5 μL of 10x DNase I buffer and 4.5 μL of ddH2O at 37°C for 30 minutes. After cleaning the rRNA, we constructed strand-specific cDNA libraries with the Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen) according to the instructions. However, we did not further fragment RNA with the reagent provided in the kit because the RNA was fragmented during sonication. The cDNA libraries were sequenced by Novogene on an Illumina platform.

treatment_protocol: DDX39A overexpression was induced with Dox (1 µg/mL). HeLa cells were transfected with SMRCAL1 siRNA to knock down its expression before synchronization. First, the cells were synchronized by a double thymidine block. The cells were treated with 2 mM thymidine for 18 h, the block was released for 9 h, and the cells were then treated again with thymidine for 18 h. This process allowed the cells to be synchronized at the G1/S boundary, and the block was released for 1 h. Then, the cells were incubated with preheated 20 μM EdU for 10 min in a 37°C incubator. For the untreated group, cells were collected directly; for the HU group, cells were further treated with 4 mM HU for 1 h without EdU washout.

value: HeLa cell line

value: DDX39B knockout

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, after sonication the supernatant was taken as input


title: ED, R22658

value: Caudate

value: Postmortem brain tissue


title: control, R22668


title: HeLa, DDX39B knockout, without HU treatment, input group, input

value: incubated with 20 μM EdU at 37°C for 10 min, after sonication the supernatant was taken as input


title: ED, R22656


title: ED, R22660

value: M


title: Tube, LR, S58

value: Tube


title: Ovary, LR, S57


title: ED, R22655


title: NRHV295CD8, ATAC

description: Library name: NRHV295CD8

value: Healthy


title: NRHV321_CD8, ATAC

description: Library name: NRHV321_CD8


title: HeLa, DDX39A knockout, HU treatment, input group, input

value: DDX39A knockout


title: HeLa, DDX39A knockout, without HU treatment, input group, input


title: NRHV321_CD4, ATAC

description: Library name: NRHV321_CD4

value: CD4 + T-cell


title: Tube, HR, S56

value: HR


title: ED, R22650


title: HeLa, HU treatment, input group, rep2

value: Wild type


title: control, R22645


title: NRHV290CD4, ATAC

description: Library name: NRHV290CD4

value: Blood


title: Tube, Flu, S54

value: Flu


title: ED, R22647

value: F

value: ED


title: Ovary, HR, S59

value: Ovary


title: Ovary, HR, S55


title: NRHV290_CD8, ATAC

description: Library name: NRHV290_CD8

value: CD8 + T-cell


title: HeLa, without HU treatment, input group, rep2

value: HeLa cell line


title: HeLa, HU treatment, input group, rep1

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, after sonication the supernatant was taken as input


title: Ovary, Flu, S53


title: control, R22644

value: Caudate

value: Postmortem brain tissue

value: control


title: nrhv238_CD8_, ATAC

description: Library name: nrhv238_CD8_


title: NRHV295CD4, ATAC

description: Library name: NRHV295CD4


title: NRHV238_CD4, ATAC

description: Library name: NRHV238_CD4


title: HeLa, without HU treatment, input group, rep1

value: incubated with 20 μM EdU at 37°C for 10 min, after sonication the supernatant was taken as input


title: Tube, Flu, S52

value: Tube


title: HeLa, SMARCAL1 knockdown, HU treatment, fixed with paraformaldehyde, without replicate

value: SMARCAL1 knockdown

value: transfected with SMARCAL1 siRNA, then incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis


title: Tube, Flu, S50


title: ED, R22641


title: control, R22640


title: OCD, R22642

value: OCD


title: NRHV171CD8, ATAC

description: Library name: NRHV171CD8

value: Healthy


title: NRHV171CD4, ATAC

description: Library name: NRHV171CD4

value: Blood

value: CD4 + T-cell


title: HeLa, SMARCAL1 knockdown, without HU treatment, fixed with paraformaldehyde, without replicate

value: transfected with SMARCAL1 siRNA, then incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis


title: Ovary, Flu, S51

value: Flu


title: Ovary, Flu, S49

value: Ovary


title: Ovary, Flu, S48


title: HeLa, SMARCAL1 knockdown, without HU treatment, fixed with paraformaldehyde, input group, input

value: transfected with SMARCAL1 siRNA, then incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: NRHV168_CD8, ATAC

description: Library name: NRHV168_CD8

value: CD8 + T-cell


title: HeLa DDX39A-Tet-On cells, DOX treatment, HU treatment, fixed with paraformaldehyde, input group, input

value: HeLa cell line

value: DDX39A-Tet-On stable

value: doxycycline (Dox) treatment, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: NRHV151_CD8, ATAC

description: Library name: NRHV151_CD8


title: NRHV168CD4, ATAC

description: Library name: NRHV168CD4


title: control, R22636

value: Caudate

value: Postmortem brain tissue

value: M

value: control


title: OCD, R22634


title: Tube, Flu, S46

value: Tube


title: ED, R22639

value: ED


title: HeLa, SMARCAL1 knockdown, HU treatment, fixed with paraformaldehyde, input group, input

value: SMARCAL1 knockdown

value: transfected with SMARCAL1 siRNA, then incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: Ovary, Flu, S47


title: HeLa DDX39A-Tet-On cells, DOX treatment, without HU treatment, fixed with paraformaldehyde, without replicate

value: doxycycline (Dox) treatment, incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis


title: Ovary, Flu, S45


title: NRHV151_CD4, ATAC

description: Library name: NRHV151_CD4

value: Blood

value: CD4 + T-cell

value: Healthy


title: ED, R22632


title: NRHV121CD4, ATAC

description: Library name: NRHV121CD4


title: control, R22631


title: Tube, HR, S44

value: HR


title: HeLa DDX39A-Tet-On cells, DOX treatment, without HU treatment, fixed with paraformaldehyde, input group, input

value: doxycycline (Dox) treatment, incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: HeLa DDX39A-Tet-On cells,  HU treatment, fixed with paraformaldehyde, without replicate

value: HeLa cell line

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis


title: NRHV121CD8, ATAC

description: Library name: NRHV121CD8

value: CD8 + T-cell


title: Ovary, HR, S43

value: Ovary


title: Tube, HR, S42


title: HeLa DDX39A-Tet-On cells,  HU treatment, fixed with paraformaldehyde, input group, input

value: DDX39A-Tet-On stable

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: OCD, R22630

value: Caudate

value: Postmortem brain tissue

value: M

value: OCD


title: control, R22629

value: control


title: control, R22633


title: NRHV086CD8, ATAC

description: Library name: NRHV086CD8


title: HeLa DDX39A-Tet-On cells, DOX treatment, HU treatment, fixed with paraformaldehyde, without replicate

value: doxycycline (Dox) treatment, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis


title: NRHV086CD4, ATAC

description: Library name: NRHV086CD4

value: Blood


title: Ovary, HR, S41


title: HeLa DDX39A-Tet-On cells, without HU treatment, fixed with paraformaldehyde, without replicate

value: incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis


title: OCD, R22628

value: F


title: Tube, Flu, S40

value: Tube

value: Flu


title: NRHV079CD4, ATAC

description: Library name: NRHV079CD4

value: CD4 + T-cell

value: Healthy


title: OCD, R22626


title: Ovary, Flu, S39


title: OCD, R22625


title: HeLa, HU treatment, fixed with paraformaldehyde, input group, rep2

value: HeLa cell line

value: Wild type


title: NRHV073CD8, ATAC

description: Library name: NRHV073CD8

value: CD8 + T-cell


title: HeLa, without HU treatment, fixed with paraformaldehyde, input group, rep1

value: incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: NRHV014XCD8, ATAC

description: Library name: NRHV014XCD8


title: OCD, R22624

value: Caudate


title: HeLa, HU treatment, fixed with paraformaldehyde, input group, rep1

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, after sonication the supernatant was taken as input


title: Ovary, Flu, S35

value: Ovary


title: ED, R22622

value: Postmortem brain tissue

value: M

value: ED


title: HeLa, without HU treatment, fixed with paraformaldehyde, input group, rep2


title: HeLa DDX39A-Tet-On cells, without HU treatment, fixed with paraformaldehyde, input group, input

value: DDX39A-Tet-On stable


title: NRHV014XCD4, ATAC

description: Library name: NRHV014XCD4

value: Blood


title: UM-SCC-74B tumor, SX-682, 3

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
6 mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded mRNA Prep and paired-end sequencing.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt v1.18.
Alignment with the reference genome (hg38) and the annotated transcripts using STAR v2.7.0f in 2-pass mode.
Gene expression quantification analysis was performed for all samples using RSEM v1.3.1 and the gene annotation GENCODE_30 GTF.
Assembly: hg38 / GENCODE_30
Supplementary files format and content: Raw counts provided in tab-delimited .txt format.

source_name: Xenograft

growth_protocol: UM-SCC-74B cells (1e6) were implanted subcutaneously in a 3:1 suspension of PBS and Matrigel in the flank of female NSG-MHC I/II KO mice (day 0). Mice were randomized based on tumor size at the start of drug treatment to equalize the average tumor volume in each group.

extract_protocol:
Total RNA from tumors was prepared using a Qiagen RNeasy Mini Kit and analyzed on an Agilent TapeStation.
RNA libraries were prepared using Illumina® Stranded mRNA Prep

treatment_protocol: Control diet feed or SX-682-containing feed (200 mg/kg body weight/day) was administered to mice starting on day 7.

value: Xenograft

value: Tumor

value: WT


title: OCD, R22623

value: F

value: OCD


title: Tube, Flu, S38

value: Tube

value: Flu


title: HeLa, DDX39A knockout, HU treatment, rep2

data_processing:
The raw reads were trimmed with Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
The cleaned reads were aligned to the genome with HISAT2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
Duplicate reads were removed with Sambamba version 0.8.2, mapped reads were sorted with SAMtools version 1.17, and converted to generate bigWig files via the bamCoverage function of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
The called peaks and narrowPeak files were generated with MACS2 version 2.1.0.20150731 (parameters: -q 0.2).
We used SAMtools version 1.17 view function to separate the strand-specific EdU-seq BAM files into reads from the minus (rev) and plus (fwd) strands. The parameters were set as ‘-f 128 -F 16’ and ‘-f 80’ to get two sets of reads, which are then merged to get the minus-strand reads. The parameters are set to ‘-f 144’ and ‘-f 64 -F 16’ to obtain two sets of reads, which are then merged to get the plus-strand reads.
Assembly: hg38
Supplementary files format and content: bigWig and narrowPeak files
Library strategy: EdU-seq

growth_protocol: HeLa cells, HeLa DDX39A-Tet-On stable cells, and DDX39A knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
The cells were harvested by scraping, washed twice with prechilled PBS and then fixed with 90% methanol at 4°C overnight. The cells were then washed twice with PBS, permeabilized with PBS containing 0.25% Triton-X 100 on a rotator at room temperature for 30 minutes. After centrifugation, the cell pellets were washed once with PBS. Then, fresh click reaction mixture (PBS with sequential addition and mixture of 25 μM biotin-PEG3-azide, 100 mM sodium ascorbate, 100 mM CuSO4) was added to the pellets, which were incubated on a rotator at room temperature for 2 hours. The cell pellets were then washed once with PBS and lysed on ice in lysis buffer (double-distilled water (ddH2O) containing 1% SDS, 50 mM Tris-HCl (pH 8.0)) for 10 minutes. A noncontact ultrasonic disruptor (Covaris M220 focused ultrasonicator) was subsequently used to sonicate the pellets for 3 minutes to obtain smeared DNA fragments of 100-300 bp. After sonication, the samples were centrifuged at 15000 rpm at 4°C for 10 minutes, after which the supernatant was collected. Part of the supernatant was taken as the input sample, while the remaining portion was used as the immunoprecipitation (IP) fraction. 100 μL of streptavidin beads was added to the supernatant of each IP group, and the mixture was incubated on a rotator at room temperature for 2 hours. The beads were subsequently washed successively with the following solutions: lysis buffer, 1 M NaCl, lysis buffer, 1 M NaCl, lysis buffer, and TE buffer (1 mM EDTA, pH 8.0; and 10 mM Tris-HCl, pH 8.0). Then, 300 μL of 2% β-mercaptoethanol was added to the beads, and the mixture was incubated with rotation at room temperature for 1 hour. The samples were subsequently centrifuged at 15000 rpm for 2 minutes, the supernatants were collected and extracted with phenol-chloroform. Then, 10 μL of glycogen (20 mg/mL), 100 μL of ammonium acetate (7.5 M), 40 μL of NaCl (5 M), and a 5x volume of ethanol were added to each supernatant and mixed, and the mixtures were incubated at -20°C overnight. The next day, the samples were centrifuged at 15000 rpm for 30 minutes at 4°C. We washed each pellet once with 75% ethanol and then centrifuged the sample and removed the supernatant. Finally, we resuspended the pellet in nuclease-free water to prepare the sample for sequencing.
The purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645L) for library preparation. As for strand-specific groups, the DNA libraries were building with the Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen), DNA samples are started directly from the second cDNA synthesis step, skipping the first cDNA synthesis step.

treatment_protocol: DDX39A overexpression was induced with Dox (1 µg/mL)  before synchronization. First, the cells were synchronized by a double thymidine block. The cells were treated with 2 mM thymidine for 18 h, the block was released for 9 h, and the cells were then treated again with thymidine for 18 h. This process allowed the cells to be synchronized at the G1/S boundary, and the block was released for 1 h. Then, the cells were incubated with preheated 20 μM EdU for 10 min in a 37°C incubator. For the untreated group, cells were collected directly; for the HU group, cells were further treated with 4 mM HU for 1 h without EdU washout.

value: HeLa cell line

value: DDX39A knockout

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, prepared for strand-specific library


title: HeLa, HU treatment, without replicate

value: Wild type


title: NRHV079CD8, ATAC

description: Library name: NRHV079CD8

value: CD8 + T-cell

value: Healthy


title: Tube, HR, S34

value: HR


title: control, R22627

value: Caudate

value: Postmortem brain tissue

value: M

value: control


title: ED, R22621

value: ED


title: Tube, Flu, S36


title: UM-SCC-74B tumor, SX-682, 2

value: Xenograft

value: Tumor

value: WT


title: Ovary, HR, S33

value: Ovary


title: Ovary, Flu, S37

value: Flu


title: NRHV073CD4, ATAC

description: Library name: NRHV073CD4

value: Blood

value: CD4 + T-cell


title: UM-SCC-74B tumor, SX-682, 1


title: HeLa DDX39A-Tet-On cells, doxycycline treatment, HU treatment, without replicate

value: HeLa cell line

value: DDX39A-Tet-On stable

value: doxycycline (Dox) treatment, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h


title: ED, R22619

value: F


title: UM-SCC-74B tumor, Control, 3

value: Control


title: Ovary, HR, S31

value: HR


title: Tube, HR, S32

value: Tube


title: HeLa DDX39A-Tet-On cells, doxycycline treatment, HU treatment, input


title: UM-SCC-74B tumor, Control, 2


title: control, R22618

value: Caudate

value: Postmortem brain tissue

value: M


title: HeLa DDX39A-Tet-On cells, doxycycline treatment, without HU treatment, without replicate

value: doxycycline (Dox) treatment, incubated with 20 μM EdU at 37°C for 10 min


title: T35B

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

description: Freshbiopsies.rds

data_processing:
Demultiplexing of sequencing results, barcode processing, read alignment, and UMI counting were performed using the Illumina 10x Cell Ranger analysis pipeline v6.1.1 with default parameters. Raw reads for each sample were aligned to GRCh38 reference genome, refdata-gex-GRCh38-2020-A.tar.gz, which was provided by 10X Genomics, using Cell Ranger. Cell hashing was used to pool cultured samples. Cells with detected genes < 500, fraction of mitochondrially-encoded reads > 0.5, or detected genes > 3x median for each sample as well as Scrublet73 predicted doublets (expected doublet rate 0.095) were removed. The threshold for mitochondrially-encoded reads was used to allow for the high mitochondrial content in renal tubular epithelial cells and was consistent with an observed bimodal distribution and with previous scRNA-seq analysis of renal tissue. For the pooled, hash tagged, cultured cells, a previously described hashing-based doublet detection strategy, implemented in HTODemux78 was employed to identify doublets.
Assembly: GRCh38
Supplementary files format and content: Seurat objects in rds format

molecule: polyA RNA

source_name: Kidney

growth_protocol: Cultured cells were maintained in growth medium in a humidified incubator or hypoxia chamber with 5%CO2 at 37degreesC.

extract_protocol:
For primary cultures, cells were detached using TrypleExpress and labelled with TotalSeq-A ‘hashtag’ antibodies (Biolegend) prior to analysis. For freshly-biopsied samples, single cell suspensions were generated using MACS Tumor Dissociation Kit enzymes in addition to Collagenase II, DNase I and trypsin prior to analysis.
10x Genomics 3' GEX v3.1

treatment_protocol: For physoxia and hypoxia conditions, an 'In Vivo2 400' Hypoxia Work Station (Ruskinn Technology) was used to obtain the desired ambient oxygen concentration. For PT2385 (Belzutifan) treatments, cells were treated with 1uM drug in growth medium, or DMSO (vehicle only control) for 16 hours.

tag: patient

value: Patient 35

value: Kidney

tag: tissue type

value: Unclassified RCC tumor

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

value: Patient underwent chemoimmunotherapy

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: Tube, HR, S30

tag: tissue


title: Tube, LR, S28

value: LR


title: UM-SCC-74B tumor, Control, 1

value: Xenograft

tag: cell line

tag: cell type

value: Tumor

tag: genotype

value: WT

tag: treatment


title: control, R22612

tag: Sex

value: F

tag: group/disease

value: control


title: HeLa DDX39A-Tet-On cells, doxycycline treatment, without HU treatment, input

value: HeLa cell line

value: DDX39A-Tet-On stable


title: OCD, R22620

value: Caudate

value: OCD

tag: rin


title: HeLa DDX39A-Tet-On cells, HU treatment, without replicate

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h


title: N35

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds

tag: patient

value: Background normal kidney


title: Tube, LR, S27

value: Tube

tag: patient group


title: HeLa, DDX39A knockout, HU treatment, rep1

value: DDX39A knockout

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, prepared for strand-specific library


title: HeLa DDX39A-Tet-On cells, without HU treatment, without replicate

value: incubated with 20 μM EdU at 37°C for 10 min


title: control, R22610

value: Postmortem brain tissue

value: M


title: HeLa DDX39A-Tet-On cells, HU treatment, input


title: control, R22608


title: Ovary, LR, S26

value: Ovary

value: LR


title: control, R22613


title: RCC4 HIF1A siRNA and HIF2A siRNA rep3

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3)
Reads were aligned to Genome Reference Consortium GRCh37 (hg19) using HISAT2 (2.05) (http://daehwankimlab.github.io/hisat2/) and non-uniquely mapped fragments were excluded using Picard tools (2.0.1) (http://broadinstitute.github.io/picard/)
Total read counts for each UCSC defined gene were extracted using HTSeq (0.5.4p3) with ‘intersection-strict’ mode
Significantly regulated genes were identified using DESeq2, pairing conditions by biological replicate.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text files from htseq with raw counts

growth_protocol: Cells were maintained in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich, D6429) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich F7524) and 1% 100X penicillin-streptomycin antibiotics (Gibco 15140122) in a humidified incubator with 21%O2 and 5%CO2 at 37degreesC.

extract_protocol:
Total RNA was prepared using the RNeasy Plus Mini kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) according to manufacturer’s instructions.
PolyA + RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Cells were reverse transfected with HIF-1a (HIF1A), HIF-2a (EPAS1), and control siPOOLs (siTOOLS Biotech) using Lipofectamine RNAiMAX Transfection Reagent (Thermofisher Scientific, 13778075) according to manufacturer’s instructions. For transfection, 200,000 cells were seeded on each 6cm dish in 3.5ml of DMEM (Sigma-Aldrich, D6429) containing 10% FBS (without antibiotic) and the final siRNA concentration for each condition was 2nM (control = 2nM controlSi; HIF-1a knockdown = 1nM HIF1Asi + 1nM controlSi; HIF-2a knockdown = 1nM HIF2Asi + 1nM controlSi; double knockdown = 1nM HIF1Asi + 1nM HIF2Asi; although the latter condition was not analyzed for the purpose of this study). After 24h, medium was replaced to fresh antibiotic-free medium. After a further 24h (48h-post transfection), cells were harvested for RNA-seq.

value: Kidney

tag: cancer type

value: ccRCC

value: Epithelial

value: HIF1A siRNA + HIF2A siRNA

tag: treatment duration

value: 48 hours


title: HeLa DDX39A-Tet-On cells, without HU treatment, input

value: HeLa cell line

value: DDX39A-Tet-On stable


title: control, R22607

value: Caudate

value: control


title: Ovary, HR, S29

value: HR


title: RCC4 HIF1A siRNA and HIF2A siRNA rep2


title: HS Skin 6

city: Birmingham

first: Mohammad

last: Athar

state: AL

address: 1670 University Blvd

department: Dermatology

institute: University of Alabama at Birmingham

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger count.
Assembly: GRCh38-2020-A
Supplementary files format and content: H5

source_name: Female; African American; Axilla; Hurley III

extract_protocol:
Skin (3x3 cm) was placed in 5 ml of medium 154 supplemented with human keratinocyte growth supplement and cut into small pieces. Freshly prepared 100µl Liberase TL (2mg/mL stock, Roche Diagnostics) + 700μl of Tyrode’s solution was added to the tissues and incubated for 15 min at 37°C and tissue was dispersed through a 70μm cell strainer (Falcon). Cells were then re-suspended in 300-500 μl of sterile PBS with 0.04% BSA  and centrifuged at 2000 rpm for 5 minutes. Cell viability was checked using 7-AAD Cells. Cells were processed for SingleCell RNA sequence.
Single cells were loaded into 10xcontroller and individual cells were be captured into oil droplets to form Gel Bead-In-EMulsions (GEMs). The single cell cDNA libraries were constructed according to manufacturer’s protocol provided by the Chromium NextGEM single cell 3’ reagent kit (10XGenomics, version 3.1).

value: Whole skin

value: female

tag: diagnosis

value: Hidradenitis suppurativa (HS)

tag: disease stage

value: Hurley III


title: Tube, Flu, S24

value: Tube

value: Flu


title: OCD, R22603

value: Postmortem brain tissue

value: M

value: OCD


title: RCC4 HIF1A siRNA and HIF2A siRNA rep1

value: Kidney

value: ccRCC

value: Epithelial


title: T35A

description: Freshbiopsies.rds

value: Patient 35

tag: tissue type

value: Unclassified RCC tumor

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

value: Patient underwent chemoimmunotherapy

tag: culture maintenance_conditions


title: OCD, R22602

tag: tissue

value: Caudate

tag: cell type


title: HS Skin 4

description: 10X Genomics

source_name: Female; African American; gluteal; Hurley II

value: Whole skin

tag: Sex

value: Hurley II


title: RCC4 HIF2A siRNA rep3

tag: cell line

tag: treatment

value: HIF2A siRNA + control siRNA

value: 48 hours


title: ED, R22611

tag: group/disease

value: ED

tag: rin


title: OCD, R22601

value: F


title: Tube, Flu, S22

value: Tube

tag: patient group

value: Flu


title: Ovary, Flu, S21

value: Ovary


title: RCC4 HIF2A siRNA rep2

value: Kidney

tag: cancer type

tag: treatment duration


title: HS Skin 3

description: 10X Genomics

value: female

tag: diagnosis

value: Hidradenitis suppurativa (HS)

tag: disease stage

value: Hurley III


title: RCC4 HIF2A siRNA rep1

value: ccRCC

value: Epithelial


title: HS Skin 2

description: 10X Genomics


title: Tube, LR, S20

value: LR


title: RCC4 HIF1A siRNA rep3

value: HIF1A siRNA + control siRNA


title: OCD, R22599

value: Caudate

value: Postmortem brain tissue

value: OCD


title: HS Skin 1

description: 10X Genomics

source_name: Male; African American; Axilla; Hurlry III

value: Whole skin

value: male


title: Ovary, LR, S19


title: control, R21743

value: F

value: control


title: control, R17974


title: Ovary, Flu, S23

value: Flu


title: Tube, LR, S25

value: Tube


title: Normal Skin 2

description: 10X Genomics

source_name: Female; African American; healthy skin

value: healthy


title: Normal Skin 1

description: 10X Genomics

value: female


title: Tube, Flu, S18


title: HS Skin 5

description: 10X Genomics

source_name: Female; African American; Axilla; Hurley II

value: Hidradenitis suppurativa (HS)

value: Hurley II


title: RCC4 HIF1A siRNA rep2

value: Kidney

value: ccRCC

value: 48 hours


title: control, R17464


title: RCC4 HIF1A siRNA rep1

value: Epithelial

value: HIF1A siRNA + control siRNA


title: ED, R22600

value: Caudate

value: Postmortem brain tissue

value: M

value: ED


title: control, R17463

value: F


title: Ovary, Flu, S17

value: Ovary


title: RCC4 control siRNA rep2

value: control (non-targeting) siRNA


title: RCC4 control siRNA rep3


title: Tube, LR, S16

value: Tube

value: LR


title: control, R17462

value: control


title: RCC4 control siRNA rep1


title: Ovary, LR, S15


title: Tube, HR, S14

value: HR


title: Ovary, HR, S13


title: control, R17459


title: ED, R17460


title: ED, R17454


title: 28-11-0040-7_pre_0

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 38.91, using STAR v.2.4.2a. Duplicate filtering, QC and metrics analysis was performed using the Picard 1.134 family of tools[ref]. For quality control, samples were kept that had human aligned counts > 250,0001 million mapped reads and median coefficient of variation (CV) coverage < 0.956. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1.20.8 in at least 23 samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights using voomWithQualityWeights from the limma R package version 3.5.1.(Ritchie ME et al. Nucleic Acids Res. 2015;20;43(7):e47) Sequencing was performed in 3 sample batches and a batch correction was done using limma removeBatcheffects.
Differentially expressed genes were then coassociated into modules using weighted gene correlation network analysis (WGCNA)
Assembly: GRCh38
Supplementary files format and content: csv file voom normalized counts

source_name: nasal lavage sample

extract_protocol:
Total RNA was isolated from pre- and post NAC nasal lavage samples.  Cell pellets were collected in RNAprotect Saliva Reagent (Qiagen) with extraction using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. Total RNA was isolated from nasal cell pellets in RNAprotect Saliva Reagent (Qiagen). Samples were centrifuged for 10 minutes at 10,000g, supernatant was removed, and the cell pellet was resuspended in 350μl RLT Buffer + 1% beta mercaptoethanol. The sample was vortexed for 1-2 seconds, sonicated for 30 seconds, spun through a Qiashredder column (Qiagen) and then extracted using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. RNA quality was assessed using RNA electrophoresis (Agilent) and NanoDrop 1000 (NanoDrop Products, Thermo Fisher Scientific).
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina)

tag: participant id

value: Male

value: SCIT

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv

value: nasal lavage sample


title: Tube, LR, S12

tag: tissue


title: 28-11-0040-7_post_0

tag: Sex

tag: treatment

value: post


title: Ovary, LR, S11

tag: patient group


title: Tube, LR, S10


title: 28-11-0039-4_pre_12


title: 28-11-0039-4_post_12


title: 28-11-0039-4_post_0


title: Ovary, LR, S09


title: ED, R17450

tag: cell type

tag: group/disease

tag: rin


title: control, R17452


title: ED, R17451


title: Tube, HR, S08


title: ED, R17448


title: 28-11-0039-4_pre_0

tag: participant id


title: 28-11-0021-5_post_0

value: Placebo

tag: age


title: ED, R17446

value: Caudate


title: Ovary, HR, S07


title: 28-11-0021-5_pre_0

tag: month


title: Ovary, LR, S05


title: 28-11-0012-7_post_12

value: Female

tag: nac


title: Tube, LR, S06


title: 28-11-0012-7_pre_12

tag: tnss


title: ED, R17443

value: Postmortem brain tissue


title: ED, R17442

value: ED


title: Ovary, LR, S03


title: control, R17438

value: F


title: 28-11-0004-5_pre_0

tag: tsneez


title: ED, R17439


title: Tube, LR, S02


title: ED, R17437


title: 28-09-0066-0_post_12

tag: dose


title: 28-09-0066-0_post_0

tag: batch


title: Ovary, LR, S01

value: Ovary


title: control, R17431


title: 28-11-0004-5_post_0

tag: pct reads


title: Tube, LR, S04


title: 28-09-0066-0_pre_0

tag: median cv


title: ED, R17428

tag: tissue


title: ED, R17426

tag: Sex


title: mammary, WT, D0, rep1 resequenced

city: New York

first: Hexiao

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description:
WT_D0_11
resequenced together with ATLD samples to correct batch effect

data_processing:
50bp paired-end reads were aligned to the mm10 mouse reference genome using STATaligner
Quantification of genes annoted in Gencode vM2 was performed using FeatureCounts.
Batch effects were corrected using RUVSeq if samples were submitted at multiple times.
Differential expression analysis was done using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: mammary

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen catalog # 217004)
Libraries were prepared using TruSeq library preparetion according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122- 2102)

value: mammary

tag: cell line

value: primary mammary organoid

value: mammary epithelia

tag: genotype

value: WT

tag: treatment

value: day 0


title: 28-09-0064-8_post_12

value: Male


title: mammary, ATLD, D28, rep3

tag: cell type

value: ATLD

value: day 28


title: mammary, WT, D14, rep1 resequenced

description:
WT_D14_11
resequenced together with ATLD samples to correct batch effect

value: day 14


title: 28-09-0064-8_pre_12

value: SCIT

value: pre

value: nasal lavage sample


title: control, R17421

source_name: Caudate

value: Caudate

tag: group/disease

value: control

tag: rin


title: 28-09-0064-8_post_0

tag: participant id

tag: age

value: post


title: control, R17419

value: Postmortem brain tissue

value: F


title: mammary, ATLD, D28, rep2

value: mammary


title: control, R17414


title: 28-09-0064-8_pre_0

tag: month

tag: nac


title: mammary, WT, D28, rep1 resequenced

description:
WT_D28_11
resequenced together with ATLD samples to correct batch effect

value: primary mammary organoid


title: 28-09-0061-5_post_0

value: Placebo

tag: tnss

tag: tsneez


title: mammary, ATLD, D28, rep1

value: mammary epithelia


title: 28-09-0057-2_post_0

tag: dose

tag: batch


title: mammary, ATLD, D14, rep3


title: 28-09-0061-5_pre_0

tag: pct reads

tag: median cv


title: mammary, ATLD, D14, rep2

tag: tissue


title: control, R17410

tag: Sex


title: RSL3+DIPY-3

city: Hefei

first: yun

middle: xiao

last: Fan

address: 218 Jixi Road, Shushan District

institute: Department of Geriatric Respiratory and Critical Care, the First Affiliated Hospital of Anhui Medical University

description:
RSL3+DIPY_raw_FPKM.txt
R+D3

data_processing:
rstudio. 3.5.0
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% FBS , 100 units/mL penicillin, and 100 μg/mL streptomycin in a 5% CO2 incubator at 37 °C.

extract_protocol:
Total RNA samples were isolated from A549 cells using the TRIzol® Reagent Kit. 1~2 μg of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using a KAPA Stranded RNA-Seq Library Prep kit according to the manufacturer’s protocol.

treatment_protocol: A549 cells were treated with DMSO, RSL3 (5 μM), and RSL3 plus DIPY  (10 μM) for 8 hours.

value: Lung

tag: cell line

value: human alveolar epithelial cell line

tag: genotype

value: WT


title: ED, R17408

tag: cell type

value: ED


title: mammary, ATLD, D14, rep1

value: ATLD

tag: treatment

value: day 14


title: OCD, R17405

tag: group/disease

value: OCD

tag: rin


title: control, R17398


title: mammary, ATLD, D0, rep3

value: day 0


title: 28-09-0043-2_post_12

tag: participant id

value: Female

value: SCIT

tag: age

value: nasal lavage sample


title: control, R17416

value: Caudate

value: Postmortem brain tissue

value: control


title: RSL3+DIPY-2

description:
RSL3+DIPY_raw_FPKM.txt
R+D2


title: ED, R17400

value: F


title: 28-09-0043-2_pre_12

tag: month

tag: nac

value: pre


title: RSL3+DIPY-1

description:
RSL3+DIPY_raw_FPKM.txt
R+D1


title: 28-09-0043-2_pre_0

tag: tnss

tag: tsneez


title: RSL3-3

description:
RSL3_raw_FPKM.txt
R3


title: ED, R17396


title: RSL3-2

description:
RSL3_raw_FPKM.txt
R2


title: mammary, WT, D28, rep2

value: mammary

value: primary mammary organoid

value: mammary epithelia

value: day 28


title: RSL3-1

description:
RSL3_raw_FPKM.txt
R1

value: Lung

value: human alveolar epithelial cell line

value: WT


title: control, R17394


title: control, R17392


title: DMSO-3

description:
DMSO_raw_FPKM.txt
C3

value: DMSO


title: mammary, ATLD, D0, rep2

value: ATLD

value: day 0


title: 28-09-0057-2_pre_0

value: Male

value: Placebo

tag: dose

tag: batch


title: ED, R17391

value: Caudate

value: ED


title: 28-09-0037-5_post_0

value: SCIT

value: post

tag: pct reads

tag: median cv

value: nasal lavage sample


title: 28-09-0037-5_pre_0

tag: Sex

value: pre

tag: tissue


title: mammary, WT, D28, rep1

value: mammary

tag: cell line

value: primary mammary organoid

tag: genotype


title: control, R17390

tag: cell type

value: Postmortem brain tissue

value: F

value: control


title: mammary, ATLD, D0, rep1

value: mammary epithelia

tag: treatment


title: mammary, WT, D14, rep3

value: WT

value: day 14


title: 28-09-0032-2_post_12


title: 28-09-0043-2_post_0

value: Female


title: mammary, WT, D28, rep3

value: day 28


title: 28-09-0032-2_pre_12

value: Male

value: Placebo


title: DMSO-2

description:
DMSO_raw_FPKM.txt
C2

value: Lung

value: human alveolar epithelial cell line

value: DMSO


title: mammary, WT, D14, rep2


title: DMSO-1

description:
DMSO_raw_FPKM.txt
C1


title: mammary, WT, D14, rep1


title: 28-09-0029-6_post_12

value: SCIT

value: post

value: nasal lavage sample


title: ED, R17388

value: Caudate

tag: group/disease

value: ED

tag: rin


title: mammary, WT, D0, rep2

value: mammary

value: primary mammary organoid

value: day 0


title: mammary, WT, D0, rep3

value: mammary epithelia

value: WT


title: ED, R17379

value: Postmortem brain tissue

value: F


title: CEA_scRNAseq_12

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics, v2.1.1 or v3.1.0) was used to performalignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: carotid plaque

extract_protocol:
Briefly, plaques were washed, minced and digested in DMEM supplemented with 10% vol/vol FBS, 1 mg ml−1 collagenase type IV (Sigma, C5138) and 0.3 mg ml–1 DNase I (Sigma, DN25), hyaluronidase (Sigma, H3506), collagenase type XI (Sigma, C7657) and collagenase type II (Sigma, C6885) in a gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) set to 0–25 rpm in five spin cycles at 37 °C for 40 min. Digested specimens were sequentially filtered through 70-μm and 40-μm cell strainers (Fisher Scientific, 22363547 and 22363548, respectively), then centrifuged at 300 g for 8 min. Dead cells were removed using an EasySep Dead Cell Removal (Annexin V) kit (StemCell Technologies, 17899) and then a leukocyte enrichment assay was carried out using an EasySep Release Human CD45 positive selection kit (StemCell Technologies, 100-0105), following the manufacturers’ instructions, respectively. Live, CD45+ cells were counted using a Cellometer Auto 2000 (Nexcellom) and loaded onto the Chromium Controller (10x Genomics)
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively) according to the manufacturer’s instructions.

value: carotid plaque

value: CD45+ Immune cells

tag: subject status

value: patients undergoing carotid endarterectomy


title: ED, R17384


title: mammary, WT, D0, rep1


title: 28-09-0029-6_pre_12

tag: participant id

value: Male

tag: age

tag: month

value: pre


title: control, R17385

value: control


title: 28-09-0026-8_pre_0

value: Placebo

tag: nac

tag: tnss

tag: tsneez


title: CEA_scRNAseq_11

description: 10x Genomics


title: ED, R17378


title: CEA_scRNAseq_9

description: 10x Genomics


title: 28-09-0026-8_pre_12

tag: dose

tag: batch

tag: pct reads

value: nasal lavage sample


title: 28-09-0026-8_post_12

tag: Sex

value: post

tag: median cv

tag: tissue


title: CEA_scRNAseq_7

description: 10x Genomics

tag: cell type


title: Mtm1KO_Liver_4

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1 with annotations from Ensembl version 96 and “union" mode. Only non-ambiguously assigned reads have been retained for further analyses.
Assembly: mm10
Supplementary files format and content: CSV file containing raw counts for each sample

source_name: LIVER

extract_protocol:
RNA was extracted from heart, liver, diaphragm and gastrocnemius samples using TRI Reagent (Molecular Research Center, Cincinnati, OH, USA), and precipitated in a mix of sodium acetate (0,1 vol) and ethanol (2,5 vol).
RNA-Seq libraries were generated from 350 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter (IDT for IlluminaXTruSeq RNA UD Indexes) on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: LIVER

tag: genotype


title: ED, R17374

value: Caudate

tag: group/disease

value: ED


title: Mtm1KO_Dia_4

source_name: DIAPHRAGM

value: DIAPHRAGM


title: control, R17376

tag: rin


title: 28-09-0018-9_post_12

tag: treatment

value: SCIT


title: CEA_scRNAseq_8

description: 10x Genomics

tag: subject status


title: Mtm1KO_Liver_2


title: CEA_scRNAseq_10

description: 10x Genomics


title: ED, R17373


title: Mtm1KO_Heart_4

source_name: HEART

value: HEART


title: CEA_scRNAseq_6

description: 10x Genomics


title: CEA_scRNAseq_4

description: 10x Genomics


title: 28-09-0018-9_pre_12

tag: participant id

tag: age


title: CEA_scRNAseq_5

description: 10x Genomics


title: ED, R17365

value: Postmortem brain tissue


title: Mtm1KO_Heart_3


title: 28-09-0012-4_pre_12

tag: month

tag: nac


title: Mtm1KO_Heart_2


title: CEA_scRNAseq_3

description: 10x Genomics


title: 28-09-0011-3_post_12

value: Female

tag: tnss

tag: tsneez


title: 28-09-0009-9_post_12

tag: dose

tag: batch


title: ED, R17362

tag: Sex

value: F


title: CEA_scRNAseq_2

description: 10x Genomics

value: carotid plaque

value: CD45+ Immune cells


title: control, R17364


title: control, R17349


title: Mtm1KO_Heart_1


title: WT_Heart_4

value: WT


title: 28-09-0012-4_post_12

value: Male

tag: pct reads

tag: median cv


title: Mtm1KO_Liver_3

tag: tissue


title: T33E

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T33_ccRCC_reclustered.rds

tag: patient

value: Patient 33

value: Kidney

tag: tissue type

value: ccRCC tumor

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R17371

tag: cell type

tag: group/disease

value: control

tag: rin


title: T33D


title: 28-09-0007-7_pre_0

tag: participant id

tag: treatment

value: Placebo

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

tag: dose

tag: batch

value: nasal lavage sample


title: T33B

tag: patient

tag: tissue

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia


title: 28-09-0009-9_pre_0

tag: Sex

tag: pct reads

tag: median cv


title: WT_Heart_2

tag: genotype


title: 28-09-0009-9_pre_12

tag: participant id

tag: treatment

tag: age


title: WT_Heart_3


title: 28-08-0005-6_post_12

tag: month

tag: nac

value: post

tag: tnss


title: ED, R17338

value: Caudate

tag: cell type

tag: group/disease

value: ED

tag: rin


title: Mtm1KO_Dia_2

tag: tissue

value: DIAPHRAGM


title: control, R17334

value: Postmortem brain tissue

value: F


title: T33A

tag: patient

tag: tissue type

tag: sample type

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R17329

tag: Sex


title: ED, R17348


title: WT_Heart_1

value: HEART

tag: genotype


title: Mtm1KO_Dia_1


title: ED, R17332


title: control, R17328


title: N33

value: Background normal kidney

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia


title: 28-08-0005-6_pre_12

tag: participant id

value: Male

tag: treatment

tag: age

tag: month

tag: nac

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: T32H

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T32_ccRCC_reclustered.rds

tag: patient

value: Patient 32

tag: tissue

tag: tissue type

tag: sample type

tag: drug treatment

tag: culture maintenance_conditions


title: 28-09-0007-7_post_0

tag: Sex

value: Female

tag: tnss


title: T32G

value: Kidney

value: ccRCC tumor

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: T33C

value: Patient 33

value: Freshly-dissociated biopsy


title: WT_Dia_4

tag: genotype

value: WT


title: 28-07-0041-3_post_0

tag: participant id

tag: treatment

value: SCIT

tag: age

tag: month

tag: nac

tag: tsneez

tag: dose

value: nasal lavage sample


title: 28-07-0041-3_post_12

value: post

tag: batch

tag: pct reads

tag: median cv

tag: tissue


title: WT_Dia_3


title: 28-07-0041-3_pre_0

tag: Sex

value: pre

tag: tnss


title: T32D

tag: patient

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: WT_Dia_2

value: DIAPHRAGM

tag: genotype


title: 28-07-0038-8_post_12

tag: participant id

tag: treatment

value: Placebo

tag: age

tag: month

tag: nac


title: ED, R15785

value: Caudate

tag: cell type

value: Postmortem brain tissue

value: F

tag: group/disease

value: ED

tag: rin


title: ED, R15786

tag: tissue

tag: Sex


title: WT_Dia_1


title: T32C

tag: patient

value: Patient 32

tag: tissue type

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: ED, R15783


title: 28-07-0038-8_pre_12

value: Male

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: T32B

value: Kidney

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: ED, R15782

tag: tissue

tag: cell type

tag: group/disease

tag: rin


title: Mtm1KO_Gas_4

source_name: GASTROCNEMIUS

value: GASTROCNEMIUS

tag: genotype


title: 28-07-0038-8_post_0

tag: participant id

tag: Sex

tag: treatment

tag: age

tag: month

tag: nac


title: ED, R15781


title: T32A

tag: patient

tag: tissue type

value: ccRCC tumor

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-07-0032-0_post_12

value: Female

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: control, R17326

tag: tissue

tag: cell type

tag: group/disease

value: control

tag: rin


title: ED, R15780

tag: Sex


title: N32B

value: Background normal kidney

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: Mtm1KO_Gas_2

tag: genotype


title: 28-07-0032-0_pre_12

tag: participant id

tag: treatment

tag: age

tag: month

tag: nac

tag: tnss

value: nasal lavage sample


title: T32E

tag: patient

tag: tissue

tag: tissue type

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: N32A

tag: sample type


title: 28-07-0032-0_post_0

tag: Sex

value: post

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: WT_Gas_4

tag: genotype

value: WT


title: Mtm1KO_Gas_1


title: ED, R15776

tag: cell type

tag: group/disease

tag: rin


title: Mtm1KO_Gas_3


title: T31D

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T31_ccRCC_reclustered.rds

value: Patient 31

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: 28-07-0032-0_pre_0

tag: participant id

tag: treatment

value: Placebo

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tissue


title: ED, R15771

value: Caudate

value: Postmortem brain tissue

tag: Sex

value: F


title: ED, R15772

value: ED


title: WT_Gas_3


title: T31C

tag: patient

value: Kidney

tag: tissue type

tag: sample type

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: WT_Gas_2

value: GASTROCNEMIUS

tag: genotype


title: 28-07-0031-4_pre_12

value: SCIT

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: T31B

value: ccRCC tumor

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: WT_Gas_1

tag: tissue


title: control, R13503

tag: cell type

tag: Sex

value: M

tag: group/disease

value: control

tag: rin


title: ED, R15770


title: 28-07-0031-4_post_0

tag: participant id

value: Female

tag: treatment

tag: age

tag: month

tag: nac

tag: tnss


title: T31A

tag: patient

tag: tissue type

tag: sample type

value: Freshly-dissociated biopsy

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: Mtm1KO_Liver_1

value: LIVER

tag: genotype


title: T30C

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T30_ccRCC_reclustered.rds

value: Patient 30

tag: tissue

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: N31

value: Patient 31

value: Background normal kidney


title: 28-07-0031-4_pre_0

tag: participant id

tag: Sex

value: pre

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv

value: nasal lavage sample


title: control, R13481

value: Caudate

tag: cell type

value: Postmortem brain tissue

tag: group/disease

tag: rin


title: T30D

tag: patient

tag: tissue type

tag: sample type

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-07-0027-6_post_0

tag: treatment

tag: age

tag: month

tag: nac

value: post

tag: tnss

tag: tissue


title: control, R13478

tag: Sex

value: F


title: WT_Liver_2

tag: genotype

value: WT


title: 28-07-0027-6_pre_12

tag: participant id

value: SCIT

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: 28-07-0027-6_post_12


title: control, R13497

tag: cell type

tag: group/disease

tag: rin


title: T30A

tag: patient

value: Kidney

tag: tissue type

value: ccRCC tumor

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R13431

tag: tissue

tag: Sex

value: M

value: control


title: T30B

value: Freshly-dissociated biopsy


title: WT_Liver_3

value: LIVER

tag: genotype


title: N30

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_N30_proximal_reclustered.rds

value: Patient 30


title: 28-07-0026-5_post_12

tag: participant id

value: Male

tag: treatment

value: Placebo

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: control, R13422

tag: cell type

tag: group/disease

tag: rin


title: Huh7 cells, T_3

city: Zhengzhou

first: wenzhi

last: guo

address: Zhengzhou, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: Sample 6

data_processing:
Raw reads of fastq format were firstly processed using fastp.
The low quality reads were removed to obtain the clean reads.
The clean reads were mapped toGRCm39 using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.Differential expression analysis was performed using the DESeq2. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: GRCm39
Supplementary files format and content: xls files include RPKM values for each Sample

source_name: Huh 7

growth_protocol: Huh7 cells were cultured in 6-well plates and subsequently treated with DMSO or carfilzomib for 24 h before collecting the cells for RNA extraction

extract_protocol:
Total RNA was isolated using mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Huh7 cells subjected toDMSO or Carfilzomib treatment

tag: cell line

value: Huh 7

value: Human HCC cell

value: Carfilzomib


title: control, R13401

tag: tissue

value: Caudate

value: Postmortem brain tissue


title: Huh7 cells, T_1

description: Library name: Sample 4


title: Huh7 cells, T_2

description: Library name: Sample 5


title: 28-07-0031-4_post_12

tag: Sex

value: Female

value: post

tag: median cv

value: nasal lavage sample


title: 28-07-0026-5_pre_12

tag: participant id

value: pre


title: WT_Liver_1

tag: genotype

value: WT


title: control, R13458

value: M


title: control, R13388

value: control


title: Huh7 cells, C3

description: Library name: Sample 3

tag: treatment

value: DMSO


title: C26B

description: Freshbiopsies.rds

tag: patient

value: Patient 26

value: Kidney

tag: tissue type

value: Background cystic kidney

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome

value: VHL syndrome


title: Huh7 cells, C1

description: Library name: Sample 1

value: Huh 7

tag: cell type

value: Human HCC cell


title: T26A

value: ccRCC tumor


title: 28-07-0026-5_pre_0

value: Male

value: Placebo

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: C26A

description: Freshbiopsies.rds

tag: patient

tag: tissue

tag: tissue type


title: 28-07-0027-6_pre_0

tag: participant id

tag: Sex

value: Female

tag: treatment

value: SCIT

tag: median cv


title: control, R13344

value: Caudate

value: Postmortem brain tissue

value: F

tag: group/disease

tag: rin


title: 28-07-0019-7_post_12

tag: age

value: post

value: nasal lavage sample


title: T25F

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T25_ccRCC_reclustered.rds

value: Patient 25

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: N29

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_N29_proximal_reclustered.rds

tag: patient

value: Patient 29

value: Kidney

value: Background normal kidney


title: OCD, R13225

tag: tissue

tag: cell type

value: M

value: OCD


title: control, R13305

value: control


title: 28-07-0010-0_pre_12

tag: participant id

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: 28-09-0007-7_post_12

tag: Sex

tag: treatment

tag: age

tag: median cv


title: control, R13340

tag: group/disease

tag: rin


title: 28-09-0032-2_post_0

value: Male


title: 28-07-0010-0_post_12


title: 28-09-0007-7_pre_12

value: Placebo


title: 28-07-0002-3_pre_0

value: Female


title: T25E

tag: patient

tag: tissue type

value: ccRCC tumor

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: OCD, R13194

tag: tissue

value: Caudate

tag: cell type

value: Postmortem brain tissue


title: 28-07-0007-9_post_12

tag: participant id

tag: Sex

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: T29

tag: patient

tag: tissue type

tag: sample type

tag: ambient o2_concentration


title: 28-07-0026-5_post_0

tag: treatment

tag: age

tag: median cv

value: nasal lavage sample


title: Huh7 cells, C2

description: Library name: Sample 2

tag: cell line

value: Huh 7

tag: cell type

value: Human HCC cell

tag: genotype

value: WT

value: DMSO


title: T25D

value: Patient 25

tag: tissue

value: Kidney

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-09-0032-2_pre_0

tag: participant id

tag: Sex

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: OCD, R13191

tag: cell type

value: M

tag: group/disease

value: OCD

tag: rin


title: T25C

tag: patient

tag: tissue

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia


title: 28-07-0019-7_pre_12

tag: participant id

tag: Sex

tag: treatment

tag: age

value: pre

tag: median cv


title: 28-09-0006-6_post_0

value: Male

value: SCIT

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose


title: 28-07-0007-9_pre_12

value: Placebo

tag: batch

tag: pct reads


title: control, R13287

tag: tissue

tag: cell type

tag: group/disease

value: control

tag: rin


title: 28-05-0006-5_post_12

value: Female


title: 28-09-0006-6_pre_0


title: T25A

tag: patient

tag: tissue type

value: ccRCC tumor

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: T25B


title: N25

value: Background normal kidney


title: control, R13125

value: Caudate

value: Postmortem brain tissue

tag: Sex


title: 28-08-0018-5_post_0

tag: participant id

tag: treatment

tag: age

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: median cv

value: nasal lavage sample


title: control, R13139

tag: tissue

tag: cell type

value: F

tag: group/disease

tag: rin


title: 28-05-0005-9_post_12

tag: batch

tag: pct reads


title: 28-08-0017-9_post_0


title: 28-05-0005-9_pre_12


title: 28-05-0006-5_pre_12


title: T24B

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T24_ccRCC_reclustered.rds

tag: patient

value: Patient 24

value: Kidney

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-08-0017-9_pre_0

tag: participant id

tag: Sex

tag: treatment

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose


title: 28-04-0012-6_pre_12

tag: batch

tag: pct reads

tag: median cv

tag: tissue


title: control, R13119

tag: cell type

tag: group/disease

tag: rin