title: ocean, female, gonads #2

first: Michael

description:
Library name: F2G
ctm_female.csv

value: gonads

value: ocean


title: C556, scRNA-seq

status: Public on Jul 20 2026

type: SRA

city: Bunkyo-ku

first: Akiyasu

last: Iwase

state: Tokyo

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description:
Fluidigm C1
C556

library_source: transcriptomic single cell

data_processing:
Sequence reads from fastq files were mapped by HISAT2 version 2.1.0. Gene expression counts were calculated with the featureCounts function from the Rsubread version 1.34.7 package using R
Assembly: mm10
Supplementary files format and content: Fluidigm_raw_counts.txt. Tab-separated matrix files include raw counts for each single-cell
Supplementary files format and content: Fluidigm_SCT_counts.txt. Tab-separated matrix files include normalized counts by SCTransform from Seurat for each single-cell

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiac NCCs labeled by Wnt1-Cre; R26-EYFP mice at E11.5, 12.5, 14.5 and 17.5 around sub-region of aorticopulmonary septum were dissociated by using 0.25 w/v% trypsin / 1 mmol/L EDTA・4Na solution (Wako) at 37 °C, 15 minutes. Enzymes were neutralized with equal volume of DMEM (Wako) with 10% fetal bovine serum (FBS) (SIGMA). Cell suspensions were filtered through a 35 μm nylon mesh cell strainer（FALCON 352235.  Cells were kept on ice until cell sorting. Cell sorting was performed in a fluorescence-activated cell sorting (FACS) AriaⅡcell sorter (BD Biosciences).
EYFP-positive single cells were captured on the Fluidigm C1 Medium-cell (10-17 μm cell diameter) integrated fluidic circuit (IFC) for single cell cDNA libraries for mRNA sequencing. EYFP-positive cells were loaded on the IFC chips at concentration of 300 cells per μL. All captured cells were photographed to check whether cells were truly EYFP-positive and were dissociated for single cells by using KEYENCE BZ-X710. Single cell cDNAs were prepared on Fluidigm C1 system by using SMARTer v4 Ultra Input Low RNA kit for the Fluidigm C1 System (Clontech). Only single cell cDNAs confirmed by imaging data were performed quality check (QC) by using Agilent 2200 TapeStation system and quantified by Qubit (Thermo Fisher). High quality cDNAs were further constructed sequencing libraries by using Nextera XT DNA Sample Preparation Kit (Illumina). Each single cell cDNAs were sequenced 50 pair-end on the Illumina HiSeq 2500.

tag: tissue

value: heart

tag: cell line

tag: cell type

tag: genotype

value: Wnt1-Cre; R26-EYFP

tag: treatment


title: C555, scRNA-seq

description:
Fluidigm C1
C555


title: AML PDX TUH06 P1 bulk RNA-seq

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

description:
Library name: TUH06_P1
Model TUH06 timepoint P1

library_source: transcriptomic

data_processing:
Raw sequencing reads were quantified using Salmon. Transcript-level estimates were aggregated at the gene level to generate count and TPM matrices used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing gene-level raw counts for all samples.
Supplementary files format and content: Tab-delimited text files containing gene-level TPM values for all samples.

organism: Homo sapiens

source_name: xenografted human AML cells

growth_protocol: AML patient-derived xenograft cells were expanded in vivo through serial transplantation in immunodeficient mice and collected at passages P0, P1, and P2.

extract_protocol:
Total RNA was extracted from AML patient-derived xenograft cells using standard RNA extraction procedures.
RNA-seq libraries were prepared using Illumina-compatible protocols for poly(A)-selected RNA sequencing.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: xenografted human AML cells

value: AML cells


title: C552, scRNA-seq

description:
Fluidigm C1
C552


title: HEK293T, IFNg_12h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

first: JIANG

last: JIAYAO

address: 江苏省扬州市邗江区扬州大学文汇路校区

department: 扬州大学

country: China

institute: 扬州大学

description: Library name: 293T_IFNg_12h_1

data_processing:
Raw reads were trimmed with Trim Galore v0.6.5. Clean reads were aligned to the reference genome (GRCh38) using STAR v2.7.3. Obtaining gene-level read counts using the featureCount function from subread v2.0.0. Calculated TPM/FPKM value for each gene using RSEM v1.3.2. Differentially expressed genes were identified with FDR<0.05 and fold change>1 using DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited table, gene-level read counts

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, Nanjing, China).
RNA-seq libraries were construction by using DNBSEQ Eukaryotic Strand-specific mRNA library sample preparation kit (BGI), and sequenced as 150 bp paired-end reads with DNBSEQ platform (DNBSEQ Technology).

value: IFNg 12h


title: C551, scRNA-seq

description:
Fluidigm C1
C551


title: AML PDX TUH06 P0 bulk RNA-seq

description:
Library name: TUH06_P0
Model TUH06 timepoint P0

source_name: peripheral blood

value: peripheral blood


title: C546, scRNA-seq

description:
Fluidigm C1
C546


title: C540, scRNA-seq

description:
Fluidigm C1
C540


title: HEK293T, IFNg_6h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_06h_2

value: IFNg 6h


title: AML PDX TUH84 P1 bulk RNA-seq

description:
Library name: TUH84_P1
Model TUH84 timepoint P1


title: AML PDX PAR27 P2 bulk RNA-seq

description:
Library name: PAR27_P2
Model PAR27 timepoint P2


title: C531, scRNA-seq

description:
Fluidigm C1
C531


title: C534, scRNA-seq

description:
Fluidigm C1
C534


title: AML PDX PAR27 P1 bulk RNA-seq

description:
Library name: PAR27_P1
Model PAR27 timepoint P1


title: HEK293T, IFNg_6h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_06h_1


title: C527, scRNA-seq

description:
Fluidigm C1
C527


title: HEK293T, IFNg_3h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_03h_2

value: IFNg 3h


title: C618, scRNA-seq

description:
Fluidigm C1
C618


title: C525, scRNA-seq

description:
Fluidigm C1
C525


title: AML PDX PAR27 P0 bulk RNA-seq

description:
Library name: PAR27_P0
Model PAR27 timepoint P0

source_name: bone marrow

value: bone marrow


title: C524, scRNA-seq

description:
Fluidigm C1
C524


title: HEK293T, IFNg_3h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_03h_1


title: C605, scRNA-seq

description:
Fluidigm C1
C605


title: C519, scRNA-seq

description:
Fluidigm C1
C519


title: PID025_TM1_T1_1_1

city: Montréal

first: Hamed

last: Najafabadi

state: Québec

address: 740 Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: PID025_TM1_T1_1_1

data_processing:
Raw sequencing reads were aligned to reference genomes using the 10x Genomics CellRanger software (v3.0.2). For tumor samples, reads were aligned to the human reference genome (hg38). For PDX samples, a combined human (hg38) and mouse (mm10) reference was used. Unique molecular identifier (UMI) counts were generated by collapsing alignments using CellRanger. For PDX samples, multiplets and mouse cells were removed as identified by the CellRanger pipeline. Only cells with >95% of counts mapped to the human genome were retained.
Quality control metrics were computed using the scuttle (v.1.0.4) package. Cells were retained if they met the following criteria: log10 total counts >3, log10 total features >3, and percentage of mitochondrial reads per cell <20%. Doublet detection was performed using DoubletFinder (v.2.0.3). The doublet rate was estimated based on the number of cells recovered per sample, following the multiplet rate guidelines from the 10x Genomics v3 user guide. Other parameters remained as default, except that the top 50 principal components were used for dimensional reduction.
Assembly: GRCh38 and mm10
Supplementary files format and content: Single cell experiment object with counts and metadata in .rds format

molecule: polyA RNA

source_name: Tumor

extract_protocol:
Tumor specimens were dissociated into single-cell suspensions prior to single-cell RNA sequencing. Tumor tissue was washed two to three times with Dulbecco’s Phosphate-Buffered Saline (DPBS) and minced into 1–2 mm pieces using a scalpel. Tissue fragments were collected, washed with DPBS, and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Briefly, tissue pieces were incubated in enzyme solution composed of Enzymes H, R, and A prepared in RPMI 1640 medium and processed using the gentleMACS Octo Dissociator with Heaters (program 37_h_TDK_1). Following dissociation, cells were filtered through a 70 µm cell strainer to remove undigested material, washed with DPBS, and pelleted by centrifugation. Red blood cells were lysed using ACK lysis buffer, after which cells were washed and resuspended in DPBS supplemented with 1% bovine serum albumin. Cell suspensions were passed through a 40 µm filter to remove remaining debris. Viable cells were counted using Trypan Blue exclusion prior to downstream single-cell RNA sequencing library preparation.
Single-cell cDNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) according to the manufacturer’s instructions. Briefly, single-cell suspensions that passed quality control were loaded onto the Chromium Next GEM Chip along with reverse transcription reagents, gel beads, and partitioning oil, and processed using the Chromium Controller to generate gel bead–in–emulsions (GEMs). Reverse transcription was performed in GEMs, followed by GEM cleanup and cDNA recovery. Full-length cDNA was purified using silane magnetic beads and amplified by PCR. cDNA quality and size distribution were assessed prior to library construction. Amplified cDNA was fragmented, end-repaired, and A-tailed, followed by double-sided size selection using SPRIselect beads. Indexed sequencing libraries were generated by adaptor ligation and sample index PCR amplification. Final libraries were purified and quality controlled prior to sequencing. Libraries were sequenced to a targeted depth of approximately 20,000 reads per cell.

value: Tumor

tag: tumor type

tag: disease state

value: renal cell carcinoma

tag: renal cell_carcinoma_subtype

value: ccRCC

tag: tumor site

value: Lung metastasis

tag: group


title: C516, scRNA-seq

description:
Fluidigm C1
C516


title: HEK293T, IFNg_1h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_01h_2

value: IFNg 1h


title: PID024_TP1_T1_1_1

description: Library name: PID024_TP1_T1_1_1

value: pRCC

value: Primary


title: C515, scRNA-seq

description:
Fluidigm C1
C515


title: C513, scRNA-seq

description:
Fluidigm C1
C513


title: HEK293T, IFNg_1h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_01h_1


title: PID023_TP1_T1_1_1

description: Library name: PID023_TP1_T1_1_1


title: HEK293T, IFNg_30m, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_30m_2

value: IFNg 30m


title: C512, scRNA-seq

description:
Fluidigm C1
C512

value: heart


title: C510, scRNA-seq

description:
Fluidigm C1
C510

value: Wnt1-Cre; R26-EYFP


title: C511, scRNA-seq

description:
Fluidigm C1
C511


title: PID022_TM1_T1_1_1

description: Library name: PID022_TM1_T1_1_1


title: C507, scRNA-seq

description:
Fluidigm C1
C507


title: AML PDX TUH76 P2 bulk RNA-seq

description:
Library name: TUH76_P2
Model TUH76 timepoint P2

value: xenografted human AML cells


title: C503, scRNA-seq

description:
Fluidigm C1
C503


title: HEK293T, IFNg_30m, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_30m_1


title: C496, scRNA-seq

description:
Fluidigm C1
C496


title: HEK293T, IFNg_0m, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_00m_2

value: IFNg 0m


title: PID020_TP1_T1_1_1

description: Library name: PID020_TP1_T1_1_1


title: C492, scRNA-seq

description:
Fluidigm C1
C492


title: C489, scRNA-seq

description:
Fluidigm C1
C489


title: HEK293T, IFNg_0m, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_00m_1


title: PID019_TP1_T1_1_1

description: Library name: PID019_TP1_T1_1_1


title: C485, scRNA-seq

description:
Fluidigm C1
C485


title: HeLa, IFNg_24h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_24h_2

source_name: HeLa

value: HeLa

value: IFNg 24h


title: C468, scRNA-seq

description:
Fluidigm C1
C468


title: PID008_TP1_T1_1_1

description: Library name: PID008_TP1_T1_1_1

value: uRCC


title: mature DCs, 96h, control, rep1

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

description: Library name: Ctrl72_1

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42)human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13 (release 38)
Supplementary files format and content: Text file including the normalized counts for each sample.

growth_protocol: THP-1 human monocytic cells were maintained in 100-mm tissue culture dishes in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 50 µM 2-mercaptoethanol, and 10% heat-inactivated fetal bovine serum (FBS), hereafter referred to as cell culture medium. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂ and maintained according to the ATCC recommendations (TIB-202), being passaged twice weekly and reseeded at a density of 2–4×10⁵ viable cells/mL to maintain exponential growth. For differentiation, THP-1 cells were seeded at a density of 1x10^5 cells/mL in T-35 tissue culture flasks and cultured for five days in cell culture medium supplemented with rhIL-4 (1500 U/mL) and GM-CSF (1500 U/mL) to induce differentiation into immature dendritic cells (iDCs).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol, and total RNA was purified using RNeasy spin columns including on-column DNase digestion. RNA was eluted in RNase-free water and stored at −80 °C until use. RNA concentration and purity were assessed by measuring absorbance at 230, 260, and 280 nm using a NanoReady F-3100 spectrophotometer (Life Real, Zhejiang, China). The A260/A280 and A260/A230 ratios were used to evaluate RNA purity.
After poly(A) selection, library preparation was performed using the NEBNext Ultra RNA Library Preparation kit.

treatment_protocol: On day five of differentiation, iDCs were seeded at a density of 1×10⁶ cells/mL in 12-well plates containing complete treatment medium and exposed for 24 h to PFOA (10 µg/mL), PFOS (10 µg/mL), or vehicle control (0.1% DMSO, v/v). Following the initial 24-h exposure, a maturation cocktail consisting of rhIL-4 (3,000 IU/mL), rhGM-CSF (1,500 IU/mL), rhTNF-α (2,000 IU/mL), and ionomycin (200 ng/mL) was added to induce maturation into mature dendritic cells (mDCs). PFAS and control compounds remained present throughout the maturation period. Cells were harvested after 24 or 72 h of maturation, corresponding to total exposure times of 48 and 96 h, respectively.

value: 0.1% DMSO


title: HeLa, IFNg_24h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_24h_1


title: C466, scRNA-seq

description:
Fluidigm C1
C466


title: Liver, UI, biol rep 1

city: Seattle

first: Alexis

last: Kaushansky

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

country: USA

institute: Seattle Children’s Research Institute

description: Library name: sample 1

library_source: genomic

data_processing:
Data QC, alignment, and peak calling were conducted using the PEPATAC pipeline.
Assembly: mm10
Supplementary files format and content: narrowPeak files (one per sample) generated from peak caller MACS2 during the PEPATAC pipeline.

molecule: genomic DNA

source_name: Liver

extract_protocol:
Nuclei were isolated from frozen liver tissue and transposition conducted according to the protocol developed by Corces et al. 2017 Nat Methods.
Library preparation was performed as described by Buenrostro et al. 2015 Curr Protoc Mol Biol. and sequenced by Psomagen using the Illumina NovaSeq 6000 platform for 151-bp paired-end reads

value: Liver

tag: strain

value: Uninfected


title: PID005_TM1_T1_1_1

description: Library name: PID005_TM1_T1_1_1

value: Tumor

value: renal cell carcinoma

value: Brain metastasis


title: Donor 6 RINSC 2 Gy

city: Kingston

last: Antosh

state: RI

address: 2 Lippitt Rd

institute: University of Rhode Island

description: Library name: Sample 58

data_processing:
Alignment: HISAT2
Quality check: FastQC
Analysis: deseq2
Assembly: GRCh38 Reference Genome
Supplementary files format and content: normalized data,from deseq2 output (csv file)
Supplementary files format and content: read counts (csv file)

source_name: Whole blood

growth_protocol: Sampled from donors under IRB protocol IRB-AAAS5693 at Columbia University.

extract_protocol:
Blood samples preserved in PAXgene RNA stabilization reagent were sent to Azenta, where total RNA was extracted followed by globin reduction.
QIAGEN Fast Select rRNA HMR and Globin Kit, plus NEGNext Ultra II RNA Library preparation kit.  Note: sequencer model number listed may be incorrect.

treatment_protocol: Each sample was irradiated with 42% photons and 58% neutrons, at either the RINSC source or the RARAF source.

value: Whole blood

tag: irradiation site

value: RINSC

tag: radiation dose_(gy)

tag: age

tag: Sex

value: Female


title: HeLa, IFNg_12h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_12h_2

value: IFNg 12h


title: C465, scRNA-seq

description:
Fluidigm C1
C465

value: heart


title: C464, scRNA-seq

description:
Fluidigm C1
C464

value: Wnt1-Cre; R26-EYFP


title: HeLa, IFNg_12h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_12h_1


title: C461, scRNA-seq

description:
Fluidigm C1
C461


title: C459, scRNA-seq

description:
Fluidigm C1
C459


title: HeLa, IFNg_6h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_06h_2

value: IFNg 6h


title: C458, scRNA-seq

description:
Fluidigm C1
C458


title: C456, scRNA-seq

description:
Fluidigm C1
C456


title: Bulk_RNA-seq_siHIF2A_2

description: Library name: Bulk_RNA-seq_siHIF2A_2

data_processing:
Raw sequencing reads were aligned to the human reference genome (GRCh38) using HISAT2(v.2.2.1). Gene-level read counts were obtained using featureCounts (v.2.0.3).
Assembly: GRCh38
Supplementary files format and content: Raw RNA-seq counts in tab delimited format

growth_protocol: A498 cell line was purchased from ATCC and maintained in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted 48 hours post-transfection using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA quality and integrity were assessed using a Bioanalyzer. Samples with RNA Integrity Number (RIN) ≥ 8.0 were used for library preparation.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on an Illumina NovaSeq 6000 platform to generate 100 bp paired-end reads.

treatment_protocol: For knockdown of HIF1A and EPAS1, reverse siRNA transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions. Cells were transfected with siRNA targeting HIF1A, HIF2A (EPAS1), or a non-targeting control siRNA (Qiagen) at a final concentration of 10 nM. Transfection was carried out in 6-well plates with 2.5 × 10⁵ cells per well.


title: HeLa, IFNg_6h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_06h_1


title: C455, scRNA-seq

description:
Fluidigm C1
C455


title: C454, scRNA-seq

description:
Fluidigm C1
C454


title: HeLa, IFNg_3h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_03h_2

value: IFNg 3h


title: Bulk_RNA-seq_siHIF1A_siHIF2A_3

description: Library name: Bulk_RNA-seq_siHIF1A_siHIF2A_3


title: C451, scRNA-seq

description:
Fluidigm C1
C451


title: C447, scRNA-seq

description:
Fluidigm C1
C447


title: Bulk_RNA-seq_siHIF1A_siHIF2A_2

description: Library name: Bulk_RNA-seq_siHIF1A_siHIF2A_2


title: C446, scRNA-seq

description:
Fluidigm C1
C446


title: C442, scRNA-seq

description:
Fluidigm C1
C442


title: Bulk_RNA-seq_siHIF1A_siHIF2A_1

description: Library name: Bulk_RNA-seq_siHIF1A_siHIF2A_1


title: C441, scRNA-seq

description:
Fluidigm C1
C441


title: HeLa, IFNg_1h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_01h_1

value: HeLa

value: IFNg 1h


title: C444, scRNA-seq

description:
Fluidigm C1
C444


title: HeLa, IFNg_1h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_01h_2


title: C440, scRNA-seq

description:
Fluidigm C1
C440


title: Bulk_RNA-seq_siHIF1A_2

description: Library name: Bulk_RNA-seq_siHIF1A_2


title: HeLa, IFNg_30m, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_30m_1

value: IFNg 30m


title: C424, scRNA-seq

description:
Fluidigm C1
C424


title: C431, scRNA-seq

description:
Fluidigm C1
C431


title: Bulk_RNA-seq_siControl_3

description: Library name: Bulk_RNA-seq_siControl_3

value: siControl


title: C419, scRNA-seq

description:
Fluidigm C1
C419


title: C417, scRNA-seq

description:
Fluidigm C1
C417


title: Bulk_RNA-seq_siControl_2

description: Library name: Bulk_RNA-seq_siControl_2


title: PID021_TM1_T1_1_1

description: Library name: PID021_TM1_T1_1_1

value: ccRCC

value: Lung metastasis


title: HeLa, IFNg_0m, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_00m_2

value: IFNg 0m


title: C486, scRNA-seq

description:
Fluidigm C1
C486


title: C477, scRNA-seq

description:
Fluidigm C1
C477


title: Bulk_RNA-seq_siControl_1

description: Library name: Bulk_RNA-seq_siControl_1


title: HeLa, IFNg_0m, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_00m_1


title: C406, scRNA-seq

description:
Fluidigm C1
C406


title: Bulk_RNA-seq_siHIF2A_3

description: Library name: Bulk_RNA-seq_siHIF2A_3


title: Line 62 DP Replicate C

city: Langston

first: haji

last: akbar

address: 100 Success Drive Ag building

department: Agriculture Sciences

institute: Langston University

description:
Library name: HA9462_DP_C
FACS-purified late lytic (DP; mRFP+eGFP+) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate C.

data_processing:
Raw sequencing reads were quality assessed prior to downstream analyses.
Reads were quantified by quasi-mapping to a combined Gallus gallus and Marek's disease virus reference transcriptome using Salmon (v1.5.2).
Transcript abundances were summarized to gene-level counts using tximport.
Lowly expressed genes were filtered and count data were normalized using the trimmed mean of M-values (TMM) method in edgeR.
Normalized counts were transformed using the limma-voom workflow and adjusted for unwanted variation (RUV) before differential expression analysis.
Assembly: Gallus gallus GRCg7b (NCBI Annotation Release 106) together with the Marek's disease virus RB1B reference genome.
Supplementary files format and content: Gene-level raw count matrix for all 18 RNA-seq samples generated from Salmon transcript quantification and summarized using tximport.
Supplementary files format and content: Differential expression analyses were performed using edgeR and limma-voom.

organism: Gallus gallus

source_name: Lymphoblastoid cell line

growth_protocol: Recombinant Marek's disease virus (rMDV) strain v2001, expressing monomeric red fluorescent protein (mRFP) fused to the early viral gene RLORF4 and enhanced green fluorescent protein (eGFP) fused to the C-terminus of UL47, was used to generate lymphoblastoid cell lines (LCLs). Tumors were collected from Pure Columbian chickens infected with v2001 at 4 weeks post-infection. Mononuclear cells were isolated using Histopaque 1077 density-gradient centrifugation and cultured in LM medium (1:1 Leibovitz L-15 and McCoy 5A) supplemented with 10% fetal bovine serum (FBS), 8% chicken serum, 100 U/mL penicillin, and 100 µg/mL streptomycin at 41°C in 5% CO₂. After two weeks, cultures were gradually adapted to LM10 medium containing 10% FBS only. Four stable LCLs (Lines 59, 62, 82, and 94) were established and maintained for approximately 20 weeks before use in subsequent experiments.

extract_protocol:
Total RNA was isolated from FACS-purified cell populations using RNA Stat60 reagent according to the manufacturer's instructions. RNA quantity and integrity were assessed prior to library preparation.
Poly(A)-selected stranded mRNA libraries were prepared using the KAPA HyperPrep Stranded mRNA Library Preparation Kit following the manufacturer's protocol. Libraries were sequenced as single-end 100-bp reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: LCLs were incubated at 32°C to induce MDV reactivation. Cells were subsequently separated by fluorescence-activated cell sorting (FACS) into latent (Lo; mRFP⁻), early lytic (Hi; mRFP⁺), and late lytic (DP; mRFP⁺eGFP⁺) populations based on RLORF4-mRFP and UL47-eGFP reporter expression.

value: Lymphoblastoid cell line

value: Line 62

value: MDV-transformed CD4+ T lymphoblastoid cell

value: MDV recombinant reporter virus (RLORF4-mRFP/UL47-eGFP)

value: Low-temperature (32°C)-induced MDV reactivation; late lytic (DP) population


title: C403, scRNA-seq

description:
Fluidigm C1
C403


title: NK92MI, DMSO treated rep2

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

description:
Library name: DMSO-2
Count.Human.txt

data_processing:
Raw RNA-seq data were preprocessed using fastp (v0.23.4), an ultra-fast all-in-one FASTQ preprocessor, with default parameters to ensure high-quality reads. Processed reads were then aligned to the GRCm38/mm10 (for mouse) or GRCh38/hg38 (for human) reference genome using STAR (v2.7.11b), allowing a maximum of 2 mismatches per read alignment. Gene-level quantification was performed using HTSeq (v2.0.3) to generate raw read counts. Differentially expressed genes (DEGs) were identified using DESeq2 R package with the following thresholds: absolute log₂ fold change (|log₂FC|) > 0.5 and Benjamini-Hochberg (BH)-adjusted P value < 0.01.
Assembly: GRCh38/hg38 for Homo sapiens GRCm38/mm10 for Mus musculus
Supplementary files format and content: text format of the raw read count for each gene

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.

value: DMSO


title: C437, scRNA-seq

description:
Fluidigm C1
C437

value: heart


title: C386, scRNA-seq

description:
Fluidigm C1
C386

value: Wnt1-Cre; R26-EYFP


title: Line 62 DP Replicate B

description:
Library name: HA9462_DP_B
FACS-purified late lytic (DP; mRFP+eGFP+) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate B.


title: C382, scRNA-seq

description:
Fluidigm C1
C382


title: C420, scRNA-seq

description:
Fluidigm C1
C420


title: C380, scRNA-seq

description:
Fluidigm C1
C380


title: Line 62 DP Replicate A

description:
Library name: HA9462_DP_A
FACS-purified late lytic (DP; mRFP+eGFP+) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate A.


title: C377, scRNA-seq

description:
Fluidigm C1
C377


title: NK92MI, BIX-01294 treated rep3

description:
Library name: BIX-3
Count.Human.txt


title: C376, scRNA-seq

description:
Fluidigm C1
C376


title: C375, scRNA-seq

description:
Fluidigm C1
C375


title: NK92MI, BIX-01294 treated rep2

description:
Library name: BIX-2
Count.Human.txt


title: C409, scRNA-seq

description:
Fluidigm C1
C409


title: Line 62 Hi Replicate B

description:
Library name: HA9462_Hi_B
FACS-purified early lytic (Hi; mRFP+) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate B.

value: Low-temperature (32°C)-induced MDV reactivation; early lytic (Hi) population


title: C372, scRNA-seq

description:
Fluidigm C1
C372


title: NK92MI, BIX-01294 treated rep1

description:
Library name: BIX-1
Count.Human.txt


title: C371, scRNA-seq

description:
Fluidigm C1
C371


title: Line 62 Hi Replicate A

description:
Library name: HA9462_Hi_A
FACS-purified early lytic (Hi; mRFP+) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate A.


title: 24hpi VacV_dE3L PKRIP-2

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description: Library name: 9208-RZ-0012

data_processing:
trim raw reads by fastp
align the trimmed reads with STAR to combined genome of human and VACV
featurecount
Assembly: GRCh38
Supplementary files format and content: txt file containing the counts

growth_protocol: All cells were maintained in Dulbecco’s modified Eagle medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 U/ml Penicillin-Streptomycin (Pen/Strep; Gibco).

extract_protocol:
RNA for the RNAseq TRIzol and and the J2 RIPseq was extracted using TRIzol reagent, treated with DNase I, then purified with phenol:chloroform:isoamyl alcohol [25:24:1 (vol/vol)] and ethanol. RNA for the PKR fRIPseq was recovered with phenol:chloroform:isoamyl alcohol [25:24:1 (vol/vol)] followed by ethanol precipitation.
Strand-specific RNA-sequencing libraries were prepared using the Ultra II Directional RNA Library Prep Kit (NEBNext) and submitted for paired-end sequencing on an Illumina NovaSeq 6000 with 150 cycles at Vanderbilt Technologies for Advanced Genomics (VANTAGE).

value: lung carcinoma epithelial cells

value: 24hpi VacV_dE3L PKRIP


title: C369, scRNA-seq

description:
Fluidigm C1
C369


title: NK92MI, DMSO treated rep1

description:
Library name: DMSO-1
Count.Human.txt


title: Line 62 Lo Replicate C

description:
Library name: HA9462_Lo_C
FACS-purified latent (Lo; mRFP−) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate C.

value: Low-temperature (32°C)-induced MDV reactivation; latent (Lo) population


title: C368, scRNA-seq

description:
Fluidigm C1
C368


title: 24hpi VacV_dE3L PKRIP-1

description: Library name: 9208-RZ-0011


title: Line 62 Hi Replicate C

description:
Library name: HA9462_Hi_C
FACS-purified early lytic (Hi; mRFP+) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate C.


title: C366, scRNA-seq

description:
Fluidigm C1
C366


title: Line 62 Lo Replicate B

description:
Library name: HA9462_Lo_B
FACS-purified latent (Lo; mRFP−) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate B.


title: PID003_TP1_T1_1_1

description: Library name: PID003_TP1_T1_1_1

value: Tumor

value: renal cell carcinoma

value: Primary


title: C365, scRNA-seq

description:
Fluidigm C1
C365


title: 24hpi VacV PKRIP-2

description: Library name: 9208-RZ-0010

value: 24hpi VacV PKRIP


title: C374, scRNA-seq

description:
Fluidigm C1
C374


title: C364, scRNA-seq

description:
Fluidigm C1
C364


title: C457, scRNA-seq

description:
Fluidigm C1
C457


title: Bulk_RNA-seq_siHIF2A_1

description: Library name: Bulk_RNA-seq_siHIF2A_1


title: Line 62 Lo Replicate A

description:
Library name: HA9462_Lo_A
FACS-purified latent (Lo; mRFP−) population from MDV-transformed chicken lymphoblastoid cell line 62 following low-temperature-induced reactivation; biological replicate A.


title: C453, scRNA-seq

description:
Fluidigm C1
C453


title: C361, scRNA-seq

description:
Fluidigm C1
C361


title: 24hpi VacV PKRIP-1

description: Library name: 9208-RZ-0009


title: HeLa, IFNg_3h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_03h_1

value: HeLa

value: IFNg 3h


title: Line 82 DP Replicate C

description:
Library name: HA9482_DP_C
FACS-purified late lytic (DP; mRFP+eGFP+) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate C.

value: Lymphoblastoid cell line

value: Line 82


title: C360, scRNA-seq

description:
Fluidigm C1
C360


title: C358, scRNA-seq

description:
Fluidigm C1
C358


title: Uninfected PKRIP-2

description: Library name: 9208-RZ-0008

value: Uninfected PKRIP


title: C356, scRNA-seq

description:
Fluidigm C1
C356


title: Line 82 DP Replicate B

description:
Library name: HA9482_DP_B
FACS-purified late lytic (DP; mRFP+eGFP+) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate B.

value: MDV-transformed CD4+ T lymphoblastoid cell

value: MDV recombinant reporter virus (RLORF4-mRFP/UL47-eGFP)

value: Low-temperature (32°C)-induced MDV reactivation; late lytic (DP) population


title: Bulk_RNA-seq_siHIF1A_3

description: Library name: Bulk_RNA-seq_siHIF1A_3


title: HeLa, IFNg_30m, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_30m_2

value: IFNg 30m


title: C370, scRNA-seq

description:
Fluidigm C1
C370

value: heart

value: Wnt1-Cre; R26-EYFP


title: C355, scRNA-seq

description:
Fluidigm C1
C355


title: Uninfected PKRIP-1

description: Library name: 9208-RZ-0007

value: lung carcinoma epithelial cells


title: C354, scRNA-seq

description:
Fluidigm C1
C354


title: Line 82 DP Replicate A

description:
Library name: HA9482_DP_A
FACS-purified late lytic (DP; mRFP+eGFP+) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate A.


title: 24hpi VacV_dE3L PKR Input-2

description: Library name: 9208-RZ-0006

value: 24hpi VacV_dE3L PKR Input


title: C353, scRNA-seq

description:
Fluidigm C1
C353


title: C351, scRNA-seq

description:
Fluidigm C1
C351


title: C436, scRNA-seq

description:
Fluidigm C1
C436


title: Line 82 Hi Replicate C

description:
Library name: HA9482_Hi_C
FACS-purified early lytic (Hi; mRFP+) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate C.

value: Low-temperature (32°C)-induced MDV reactivation; early lytic (Hi) population


title: C350, scRNA-seq

description:
Fluidigm C1
C350


title: 24hpi VacV_dE3L PKR Input-1

description: Library name: 9208-RZ-0005


title: HeLa, IFNg_15m, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_15m_2

value: IFNg 15m


title: Bulk_RNA-seq_siHIF1A_1

description: Library name: Bulk_RNA-seq_siHIF1A_1


title: C346, scRNA-seq

description:
Fluidigm C1
C346


title: Line 82 Hi Replicate B

description:
Library name: HA9482_Hi_B
FACS-purified early lytic (Hi; mRFP+) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate B.


title: C344, scRNA-seq

description:
Fluidigm C1
C344


title: C339, scRNA-seq

description:
Fluidigm C1
C339


title: 24hpi VacV PKR Input-2

description: Library name: 9208-RZ-0004

value: 24hpi VacV PKR Input


title: Line 82 Hi Replicate A

description:
Library name: HA9482_Hi_A
FACS-purified early lytic (Hi; mRFP+) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate A.


title: C335, scRNA-seq

description:
Fluidigm C1
C335


title: 24hpi VacV PKR Input-1

description: Library name: 9208-RZ-0003


title: C333, scRNA-seq

description:
Fluidigm C1
C333


title: C327, scRNA-seq

description:
Fluidigm C1
C327


title: C326, scRNA-seq

description:
Fluidigm C1
C326


title: Uninfected PKR Input-2

description: Library name: 9208-RZ-0002

value: Uninfected PKR Input


title: Line 82 Lo Replicate C

description:
Library name: HA9482_Lo_C
FACS-purified latent (Lo; mRFP−) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate C.

value: Low-temperature (32°C)-induced MDV reactivation; latent (Lo) population


title: C416, scRNA-seq

description:
Fluidigm C1
C416


title: HeLa, IFNg_15m, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: Hela_IFNg_15m_1

value: HeLa


title: C321, scRNA-seq

description:
Fluidigm C1
C321


title: Line 82 Lo Replicate A

description:
Library name: HA9482_Lo_A
FACS-purified latent (Lo; mRFP−) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate A.

value: Lymphoblastoid cell line


title: Line 82 Lo Replicate B

description:
Library name: HA9482_Lo_B
FACS-purified latent (Lo; mRFP−) population from MDV-transformed chicken lymphoblastoid cell line 82 following low-temperature-induced reactivation; biological replicate B.

value: Line 82


title: 24hpi VacV_dE3L J2IP-2

description: Library name: 9221-YZ-12

value: 24hpi VacV_dE3L J2IP


title: C311, scRNA-seq

description:
Fluidigm C1
C311


title: whole fly, insulin ablated, old, 8hr post heat shock, climber

city: Chicago

first: Manuel

middle: Jospeh

last: Widuch

state: IL

address: 1040 West Granville Avenue, 1021

department: Molecular Biology Sciences

institute: Northwestern University

description:
Library name: MW109
Analyses done on Read 1 only

data_processing:
Quest
Trimmed reads were aligned to the Drosophila melanogaster reference genome (dm6; FlyBase release r6.61) using the STAR aligner (v2.7.5a). Alignment was performed using two-pass mapping (--twopassMode Basic) with a maximum mismatch threshold of 2 (--outFilterMismatchNmax 2), and alignments were output as coordinate-sorted BAM files (--outSAMtype BAM SortedByCoordinate).
Gene-level counts were generated using the STAR aligner (v2.7.5a) with the --quantMode GeneCounts option in a separate run. During this step, alignments were not written to files (--outSAMtype None). Per-sample count files (ReadsPerGene.out.tab) were aggregated into a gene-by-sample count matrix using a custom AWK script (build_count_table.awk).
The data was further analyzed in R Studio. Counts were normalized and z- scored before being put through PCA and sPCA.
Assembly: Trimmed reads were aligned to the Drosophila melanogaster reference genome (dm6; FlyBase release r6.61) using the STAR aligner (v2.7.5a).
Supplementary files format and content: Tab delimited text files were used for all samples in a counts table.
Supplementary files format and content: .csv file created to work with in R studio.

organism: Drosophila melanogaster

source_name: whole fly

extract_protocol:
Whole body fly RNA was extracted using the Trizol method and cleaned up using the 50µg Monarch RNA Clean-Up Kit.
250 ng of clean RNA was used to prepare libraries with the Lexogen Quant 3' mRNA-Seq V2 Prep Kit.

value: whole fly

value: Insulin ablated

value: Heat shock

tag: classification

value: climber

tag: batch


title: 24hpi VacV_dE3L J2IP-1

description: Library name: 9221-YZ-11


title: C309, scRNA-seq

description:
Fluidigm C1
C309

tag: tissue

value: heart


title: 24hpi VacV J2IP-2

description: Library name: 9221-YZ-10

tag: cell line

value: 24hpi VacV J2IP


title: C305, scRNA-seq

description:
Fluidigm C1
C305

tag: cell type

value: Wnt1-Cre; R26-EYFP


title: whole fly, insulin ablated, old, 6hr post heat shock, climber

description:
Library name: MW106
Analyses done on Read 1 only

tag: genotype


title: C293, scRNA-seq

description:
Fluidigm C1
C293

tag: treatment


title: 24hpi VacV J2IP-1

description: Library name: 9221-YZ-9

value: lung carcinoma epithelial cells


title: C281, scRNA-seq

description:
Fluidigm C1
C281


title: C278, scRNA-seq

description:
Fluidigm C1
C278


title: whole fly, insulin ablated, old, 4hr control, behavior not assessed

description:
Library name: MW104
Analyses done on Read 1 only

value: Control

value: behavior not assessed


title: Uninfected J2IP-2

description: Library name: 9221-YZ-8

value: Uninfected J2IP


title: C276, scRNA-seq

description:
Fluidigm C1
C276


title: whole fly, insulin ablated, old, 4hr post heat shock, climber

description:
Library name: MW102
Analyses done on Read 1 only


title: whole fly, insulin ablated, old, 2hr post heat shock, climber

description:
Library name: MW101
Analyses done on Read 1 only


title: whole fly, insulin ablated, old, 1hr post heat shock, climber

description:
Library name: MW99
Analyses done on Read 1 only


title: Uninfected J2IP-1

description: Library name: 9221-YZ-7


title: C262, scRNA-seq

description:
Fluidigm C1
C262


title: C265, scRNA-seq

description:
Fluidigm C1
C265


title: 6hpi VacV_dE3L Input-2

description: Library name: 9814-YZ-4

value: 6hpi VacV_dE3L Input


title: C260, scRNA-seq

description:
Fluidigm C1
C260


title: whole fly, insulin ablated, old, 0hr post heat shock, climber

description:
Library name: MW97
Analyses done on Read 1 only


title: C256, scRNA-seq

description:
Fluidigm C1
C256


title: C255, scRNA-seq

description:
Fluidigm C1
C255


title: whole fly, insulin ablated, young, 8hr post heat shock, climber

description:
Library name: MW53
Analyses done on Read 1 only


title: 6hpi VacV_dE3L Input-1

description: Library name: 9814-YZ-3


title: C254, scRNA-seq

description:
Fluidigm C1
C254


title: 6hpi VacV Input-2

description: Library name: 9814-YZ-2

value: 6hpi VacV Input


title: C253, scRNA-seq

description:
Fluidigm C1
C253


title: whole fly, insulin ablated, young, 6hr post heat shock, climber

description:
Library name: MW51
Analyses done on Read 1 only


title: C251, scRNA-seq

description:
Fluidigm C1
C251


title: 6hpi VacV Input-1

description: Library name: 9814-YZ-1


title: C250, scRNA-seq

description:
Fluidigm C1
C250


title: C249, scRNA-seq

description:
Fluidigm C1
C249


title: 24hpi VacV_dE3L Input-2

description: Library name: 9221-YZ-6

value: 24hpi VacV_dE3L Input


title: whole fly, insulin ablated, young, 4hr post heat shock, climber

description:
Library name: MW47
Analyses done on Read 1 only


title: 24hpi VacV_dE3L Input-1

description: Library name: 9221-YZ-5


title: whole fly, insulin ablated, young, 2hr post heat shock, climber

description:
Library name: MW45
Analyses done on Read 1 only


title: C243, scRNA-seq

description:
Fluidigm C1
C243


title: 24hpi VacV Input-2

description: Library name: 9221-YZ-4

value: 24hpi VacV Input


title: C240, scRNA-seq

description:
Fluidigm C1
C240


title: whole fly, insulin ablated, young, 1hr post heat shock, climber

description:
Library name: MW43
Analyses done on Read 1 only


title: 24hpi VacV Input-1

description: Library name: 9221-YZ-3


title: whole fly, insulin ablated, young, 0hr post heat shock, climber

description:
Library name: MW41
Analyses done on Read 1 only


title: C238, scRNA-seq

description:
Fluidigm C1
C238


title: Uninfected Input-2

description: Library name: 9221-YZ-2

value: Uninfected Input


title: C237, scRNA-seq

description:
Fluidigm C1
C237


title: whole fly, wildtype, old, 8hr post heat shock, non-climber

description:
Library name: MW28
Analyses done on Read 1 only

value: wildtype

value: non-climber


title: C236, scRNA-seq

description:
Fluidigm C1
C236


title: Uninfected Input-1

description: Library name: 9221-YZ-1


title: C234, scRNA-seq

description:
Fluidigm C1
C234


title: C233, scRNA-seq

description:
Fluidigm C1
C233


title: HeLa cells, Input-Vector

city: Shanghai

first: Shunyi

last: Li

state: Shanghai

address: 100 Haike Rd, Building 13

department: Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

description: Library name: HeLa_Input_Vector

data_processing:
Illumina platform are transformed to short reads by base calling and these short reads are recorded in FASTQ format.
For RNA-seq, FASTQ files were processed using RaNA-seq Version 1.0 (https://ranaseq.eu/).
For RNA-seq, reads were processed with Salmon software to obtain the expression quantification.
For RNA-seq, differential expression analysis was performed with limma.
For ChIP-seq, reads were quality controlled with Fastp (version 0.23.1).
For ChIP-seq, reads were aligned using Bowtie2 (2.2.5).
For ChIP-seq, reads were sorted and filtered using Samtools.
For ChIP-seq, the peak calling was done by MACS2 ( 2.2.7.1) in narrow peak calling mode with q-value (minimum false discovery rate) cutoff set to 0.05 for peak detection.
Assembly: hg38
Supplementary files format and content: For RNA-seq, XLSX files containing raw counts and limma-normalized abundance measurements for each sample were generated. For ChIP-seq, BED and bigWig (BW) files were produced for each sample, except for Input control.

source_name: Uterus; Cervix

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO₂ at 37°C. These conditions were used for both RNA-seq and ChIP-seq experiments.

extract_protocol:
For RNA-seq, total RNA was harvested using RNAiso Plus (TaKaRa) according to the manufacturer’s instructions. For ChIP-seq, cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented in a water bath using a Qsonica Q800R3 sonicator (55% amplitude, 20 s on/20 s off) for a total of 10 minutes.
For RNA-seq, sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer’s protocol. For ChIP-seq, the purified DNA was used to prepare libraries with the NEBNext Ultra II DNA Library Prep Kit (NEB, USA, Catalog #: E7645L) according to the manufacturer’s instructions.

value: Uterus; Cervix

value: HeLa

value: epithelial cells


title: C231, scRNA-seq

description:
Fluidigm C1
C231

value: heart


title: C227, scRNA-seq

description:
Fluidigm C1
C227


title: whole fly, wildtype, old, 6hr post heat shock, climber

description:
Library name: MW25
Analyses done on Read 1 only

value: whole fly

value: Heat shock

value: climber


title: C226, scRNA-seq

description:
Fluidigm C1
C226

value: Wnt1-Cre; R26-EYFP


title: HeLa cells, Input-CDC5L

description: Library name: HeLa_Input_CDC5L


title: C225, scRNA-seq

description:
Fluidigm C1
C225


title: whole fly, wildtype, old, 4hr control, behavior not assessed

description:
Library name: MW23
Analyses done on Read 1 only

value: Control

value: behavior not assessed


title: HeLa cells, CDC5L-HA

description: Library name: HeLa_CDC5L_HA_CST


title: whole fly, wildtype, old, 6hr post heat shock, non-climber

description:
Library name: MW26
Analyses done on Read 1 only


title: C221, scRNA-seq

description:
Fluidigm C1
C221


title: HeLa cells, Vector-HA

description: Library name: HeLa_Vector_HA_CST


title: whole fly, wildtype, old, 4hr post heat shock, non-climber

description:
Library name: MW22
Analyses done on Read 1 only


title: C220, scRNA-seq

description:
Fluidigm C1
C220


title: HeLa cells, siCDC5L, RNA-seq, biol rep 3

description: Library name: si_CDC5L_3

value: CDC5L knockdown


title: C218, scRNA-seq

description:
Fluidigm C1
C218


title: whole fly, wildtype, old, 4hr post heat shock, climber

description:
Library name: MW21
Analyses done on Read 1 only


title: C217, scRNA-seq

description:
Fluidigm C1
C217


title: C317, scRNA-seq

description:
Fluidigm C1
C317


title: Uninfected PKR Input-1

description: Library name: 9208-RZ-0001

value: lung carcinoma epithelial cells

value: Uninfected PKR Input


title: HeLa cells, siCDC5L, RNA-seq, biol rep 2

description: Library name: si_CDC5L_2


title: whole fly, wildtype, old, 2hr post heat shock, non-climber

description:
Library name: MW20
Analyses done on Read 1 only


title: C215, scRNA-seq

description:
Fluidigm C1
C215


title: C316, scRNA-seq

description:
Fluidigm C1
C316


title: C310, scRNA-seq

description:
Fluidigm C1
C310


title: C224, scRNA-seq

description:
Fluidigm C1
C224


title: C213, scRNA-seq

description:
Fluidigm C1
C213


title: HeLa cells, siCDC5L, RNA-seq, biol rep 1

description: Library name: si_CDC5L_1


title: C212, scRNA-seq

description:
Fluidigm C1
C212


title: C211, scRNA-seq

description:
Fluidigm C1
C211


title: HeLa cells, siControl, RNA-seq, biol rep 3

description: Library name: si_Ctrl_3

value: WT


title: whole fly, wildtype, old, 2hr post heat shock, climber

description:
Library name: MW19
Analyses done on Read 1 only


title: C271, scRNA-seq

description:
Fluidigm C1
C271


title: C210, scRNA-seq

description:
Fluidigm C1
C210


title: whole fly, wildtype, old, 1hr post heat shock, climber

description:
Library name: MW18
Analyses done on Read 1 only


title: C270, scRNA-seq

description:
Fluidigm C1
C270


title: C208, scRNA-seq

description:
Fluidigm C1
C208


title: C206, scRNA-seq

description:
Fluidigm C1
C206


title: HeLa cells, siControl, RNA-seq, biol rep 2

description: Library name: si_Ctrl_2


title: whole fly, wildtype, old, 1hr post heat shock, non-climber

description:
Library name: MW17
Analyses done on Read 1 only


title: C205, scRNA-seq

description:
Fluidigm C1
C205


title: HeLa cells, siControl, RNA-seq, biol rep 1

description: Library name: si_Ctrl_1


title: whole fly, wildtype, old, 0hr post heat shock, climber

description:
Library name: MW16
Analyses done on Read 1 only


title: C201, scRNA-seq

description:
Fluidigm C1
C201


title: C204, scRNA-seq

description:
Fluidigm C1
C204


title: C252, scRNA-seq

description:
Fluidigm C1
C252


title: STXBP1-3

city: Wulumuqi

first: Meng

last: Zhang

state: Xinjiang province

address: Affiliated Tumor Hospital of Xinjiang Medical University

description: Library name: Sampel 6

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
clean reads were aligned to the STXBP1 genome by HISAT2 allowing 4 mismatches
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified by using the ABLas pipeline as described previously
Assembly: STXBP1
Supplementary files format and content: reads counts for each Samples
Supplementary files format and content: FPKM values for each Samples

growth_protocol: MDA-MB-231 cells line (CL-0150B, Procell Life Science & Technology Co., Ltd., China) were cultured at 37℃ with 5% CO2 in DMEM (PM150210, Procell Life Science & Technology Co., Ltd., China) with 10% fetal bovine serum (FBS) (10091148, Gibco, China), 100 µg/mL streptomycin, 100 U/mL penicillin(SV30010, Hyclone, USA). Plasmid transfection of MDA-MB-231 cells was performed using Lipofectamine 3000 (L3000015, Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR and Western blotting analysis.

extract_protocol:
Total RNA extraction using TRIZOL (15596-018, Ambion, USA). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (M6101, Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Ultrafine spectrophotometer (N50 touch, IMPLEN, Germany). The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: RT-qPCR ,Western Blot,Cell proliferation assay and Annexin V apoptosis assay

value: STXBP1 overexpression


title: C196, scRNA-seq

description:
Fluidigm C1
C196


title: whole fly, wildtype, old, 0hr post heat shock, non-climber

description:
Library name: MW15
Analyses done on Read 1 only

value: wildtype


title: whole fly, insulin ablated, young, 4hr control, behavior not assessed

description:
Library name: MW49
Analyses done on Read 1 only

value: Insulin ablated


title: STXBP1-2

institute: Affiliated Tumor Hospital of Xinjiang Medical University

description: Library name: Sampel 5


title: C194, scRNA-seq

description:
Fluidigm C1
C194


title: C195, scRNA-seq

description:
Fluidigm C1
C195


title: whole fly, wildtype, young, 8hr post heat shock, climber

description:
Library name: MW14
Analyses done on Read 1 only


title: C245, scRNA-seq

description:
Fluidigm C1
C245


title: C193, scRNA-seq

description:
Fluidigm C1
C193


title: STXBP1-1

description: Library name: Sampel 4


title: C190, scRNA-seq

description:
Fluidigm C1
C190


title: C244, scRNA-seq

description:
Fluidigm C1
C244


title: C189, scRNA-seq

description:
Fluidigm C1
C189


title: NC-3

description: Library name: Sampel 3

value: NC plasmid


title: whole fly, wildtype, young, 8hr post heat shock, non-climber

description:
Library name: MW13
Analyses done on Read 1 only

value: non-climber


title: whole fly, wildtype, young, 6hr post heat shock, climber

description:
Library name: MW12
Analyses done on Read 1 only


title: C241, scRNA-seq

description:
Fluidigm C1
C241


title: C187, scRNA-seq

description:
Fluidigm C1
C187


title: C185, scRNA-seq

description:
Fluidigm C1
C185


title: NC-2

description: Library name: Sampel 2


title: C186, scRNA-seq

description:
Fluidigm C1
C186


title: C184, scRNA-seq

description:
Fluidigm C1
C184


title: whole fly, wildtype, young, 6hr post heat shock, non-climber

description:
Library name: MW11
Analyses done on Read 1 only


title: NC-1

description: Library name: Sampel 1


title: C177, scRNA-seq

description:
Fluidigm C1
C177


title: whole fly, wildtype, young, 4hr control, behavior not assessed

description:
Library name: MW09
Analyses done on Read 1 only


title: C239, scRNA-seq

description:
Fluidigm C1
C239


title: C174, scRNA-seq

description:
Fluidigm C1
C174


title: C172, scRNA-seq

description:
Fluidigm C1
C172


title: WI-38 cells, multi-fraction, 2200mGy, 5hmC, rep4

city: Chalk River

first: Richard

middle: B.

last: Richardson

state: Ontario

address: 286 Plant Rd

department: Radiobiology and Health

institute: Canadian Nuclear Laboratories

description: Library name: MF2200 H4

data_processing:
Quality control was conducted using FastQ Screen (v0.4.1) and FastQC (v0.11.9).
Trimming was performed using TrimGalore (v0.6.6) with parameters: --clip_R1 1; --clip_R2 1; --three_prime_clip_R1 1; - three_prime_clip_R2 1; --trim-n; --length 50; -q 20 and --stringency 5. Quality of trimmed filtered reads was revaluated using FastQC (v0.11.9).
Alignment to the human reference genome GRCh38 was conducted using BWA (v0.7.17) in the paired-end mode of the BWA-MEM algorithm with the default parameter settings.
Mapped read files (*.sam) were converted to sorted BAM files by SAMtools (v1.11). Unmapped reads were filtered out using SAMtools (v1.11).
Bioconductor package MEDIPS (v1.40.0) was used to identify differentially hydroxymethylated regions (DhMRs) between controls and irradiated cells for both regimens with ws=50 bp; shift=0 and uniq=1.
Differential coverage was calculated using the edgeR function in MEDIPS with minRowSum=5 and TMM normalization. P-values were adjusted for multiple testing using the FDR method. Statistically significant methylation coverage results were selected using the criteria of FDR<0.05.
Genomic annotation was carried out using HOMER (v4.11). Neighboring significant regions located within the same chromosome, and with the same annotation and Gene ID, were merged using an in-house Python script.
Assembly: GRCh38
Supplementary files format and content: Bam files include only mapped sorted reads for each sample
Supplementary files format and content: RData files include differential coverage results using the edgeR function (edgeR_control_treatment). When available, it also includes specific data extracted from the "edgeR_control_treatment" file as follows:  differential coverage results with unadjusted P value<0.05 (edgeR.sna_control_treatment), differential coverage results with FDR<0.1 (edgeR.s0.1_control_treatment), differential coverage results with FDR<0.05 (edgeR.s0.05_control_treatment), differential coverage results with FDR<0.05 of hyperDhMRs (hyper_control_treatment), differential coverage results with FDR<0.05 of hypoDhMRs (hypo_control_treatment)

growth_protocol: WI-38 cells were maintained in EMEM medium supplemented with 10% fetal bovine serum (FBS), 50 U/mL Penicillin, 50 µg/mL Streptomycin, and 2 mM L-Glutamine in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total DNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol with minor modifications.
Cell pellets were resuspended in PBS and treated with proteinase K and RNase A. The DNA-loaded spin columns were washed three times with buffer AW2. DNA was then eluted in Tris-EDTA (TE) buffer (low EDTA, pH 8.0) after 5 m at RT. DNA samples displayed A260/A280 ratios in the range of 1.8 to 2.0 and A260/A230 ratios higher than 2.1.
DNA was sheared into ~200 bp fragments using a Covaris S220 focused ultrasonicator. Libraries were constructed with 1.2 μg of DNA using a NEBNext Ultra II DNA library prep kit for Illumina following the manufacturer’s guidelines. Immunoprecipitation with a 5hmC antibody was conducted using a Diagenode hMeDIP kit as described in the manufacturer’s protocol with a starting volume of 15 µL. The immunoprecipitated adaptor-ligated DNA and Input fraction were purified with a Diagenode IPure kit v2 according to the manufacturer’s instructions.
The libraries from the Input fraction and IP DNA were linked to unique dual index primers (New England Biolabs) and amplified by PCR using a NEBNext Ultra II DNA library prep kit for Illumina with 7 cycles for the Input and 8 for the IP samples. The PCR products were further purified and size selected using NEBNext sample purification beads. Libraries were quantified using a KAPA library quantification kit.

treatment_protocol:
Cells were irradiated to seven doses of americium-241 α-sources ranging from 2.0 to 2,200 mGy using two exposure regimens, a single-fraction where the total dose was given at once, and a multi-fraction method, where the total dose was equally distributed over 14 consecutive days.
Cells in both exposure regimens were trypsinized and collected after the last irradiation following 1 h incubation at 37 °C in a 5% CO2 humidified atmosphere. Collected cells were immediately flash-frozen in liquid nitrogen and subsequently stored at -80 °C.

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

tag: dose (mgy)

tag: radiation regimen

value: multi-fraction

tag: total number_of_fractions

tag: antibody

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: C168, scRNA-seq

description:
Fluidigm C1
C168

value: heart


title: C170, scRNA-seq

description:
Fluidigm C1
C170

value: Wnt1-Cre; R26-EYFP


title: C167, scRNA-seq

description:
Fluidigm C1
C167


title: whole fly, wildtype, young, 4hr post heat shock, non-climber

description:
Library name: MW07
Analyses done on Read 1 only

value: whole fly

value: Heat shock


title: C166, scRNA-seq

description:
Fluidigm C1
C166


title: C165, scRNA-seq

description:
Fluidigm C1
C165


title: WI-38 cells, multi-fraction, 2200mGy, 5hmC, rep1

description: Library name: MF2200 H1


title: whole fly, wildtype, young, 2hr post heat shock, non-climber

description:
Library name: MW05
Analyses done on Read 1 only


title: C164, scRNA-seq

description:
Fluidigm C1
C164


title: C163, scRNA-seq

description:
Fluidigm C1
C163


title: WI-38 cells, multi-fraction, 1100mGy, 5hmC, rep4

description: Library name: MF1100 H4


title: C232, scRNA-seq

description:
Fluidigm C1
C232


title: C161, scRNA-seq

description:
Fluidigm C1
C161


title: C158, scRNA-seq

description:
Fluidigm C1
C158


title: WI-38 cells, multi-fraction, 1100mGy, 5hmC, rep3

description: Library name: MF1100 H3


title: whole fly, wildtype, young, 1hr post heat shock, non-climber

description:
Library name: MW04
Analyses done on Read 1 only


title: C157, scRNA-seq

description:
Fluidigm C1
C157


title: C156, scRNA-seq

description:
Fluidigm C1
C156


title: WI-38 cells, multi-fraction, 1100mGy, 5hmC, rep2

description: Library name: MF1100 H2


title: C155, scRNA-seq

description:
Fluidigm C1
C155


title: PID001_TP1_P1_1_1

description: Library name: PID001_TP1_P1_1_1

organism:
Homo sapiens
Mus musculus

value: Tumor

tag: tumor type

tag: disease state

value: renal cell carcinoma

tag: renal cell_carcinoma_subtype

value: ccRCC

tag: tumor site

value: Primary

tag: group

value: Patient-derived xenograft model


title: WI-38 cells, multi-fraction, 1100mGy, 5hmC, rep1

description: Library name: MF1100 H1


title: whole fly, wildtype, young, 0hr post heat shock, non-climber

description:
Library name: MW01
Analyses done on Read 1 only

value: wildtype


title: WI-38 cells, multi-fraction, 220mGy, 5hmC, rep4

description: Library name: MF220 H4


title: oligodendrocyte,0.01mM water‑soluble cholesterol,Treat 12hours,rep3

first: Zhang

last: Jiannan

address: cangqian street

institute: Hangzhou normal university

description:
Library name: Treat3
B3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: rn6
Supplementary files format and content: FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Total RNA was extracted using RNAiso plus reagent (TAKARA, 9108) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Brain

value: oligodendrocyte

value: Cholesterol


title: C150, scRNA-seq

description:
Fluidigm C1
C150


title: Control_Rep4

city: Wenzhou

first: Binbin

last: Deng

state: -- Select --

address: 0 Chashan Street, Ouhai District, Wenzhou City,

institute: wenzhou medical university

description: Library name: SOD1_VEH_4

data_processing:
Raw sequencing reads were subjected to quality control using fastp to remove adapter sequences, low-quality bases (quality score < 20), and reads containing >10% unknown bases (N).
High-quality clean reads were aligned to the mouse reference genome using HiSat2.
Gene expression levels were quantified as read counts using RSEM.
Assembly: GRCm39
Supplementary files format and content: The processed data files are provided in tabular format (.xls). They include raw read count matrices (e.g., transcript.count.matrix.xls), as well as normalized expression matrices calculating FPKM and TPM (e.g., gene.tpm.matrix.xls, gene.fpkm.matrix.xls) at both the gene and transcript levels across all samples.

growth_protocol: NSC-34 cells were cultured in standard incubator conditions and grown to the logarithmic growth phase.

extract_protocol:
Total RNA was extracted from samples, and its concentration and purity were assessed using Nanodrop2000. RNA integrity was evaluated using agarose gel electrophoresis and the Agilent 5300 system.
Sequencing libraries were generated using the Illumina® Stranded mRNA Prep, Ligation kit. Briefly, mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, and reverse-transcribed into double-stranded cDNA. The cDNA underwent end-repair, 'A'-tailing, adapter ligation, and PCR amplification. The final libraries were sequenced on the Illumina NovaSeq X Plus platform.

treatment_protocol: Cells were transfected with SOD1G93A plasmid. After reaching the logarithmic growth phase, cells were treated with PF4 (100ng/ml) or vehicle for 24 hours.

value: motor neuron-like cells

value: SOD1G93A transfected

value: Vehicle


title: oligodendrocyte,0.01mM water‑soluble cholesterol,Treat 12hours,rep2

description:
Library name: Treat2
B2


title: WI-38 cells, multi-fraction, 220mGy, 5hmC, rep3

description: Library name: MF220 H3

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

value: multi-fraction

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: C148, scRNA-seq

description:
Fluidigm C1
C148

data_processing:
Sequence reads from fastq files were mapped by HISAT2 version 2.1.0. Gene expression counts were calculated with the featureCounts function from the Rsubread version 1.34.7 package using R
Assembly: mm10
Supplementary files format and content: Fluidigm_raw_counts.txt. Tab-separated matrix files include raw counts for each single-cell
Supplementary files format and content: Fluidigm_SCT_counts.txt. Tab-separated matrix files include normalized counts by SCTransform from Seurat for each single-cell

extract_protocol:
Cardiac NCCs labeled by Wnt1-Cre; R26-EYFP mice at E11.5, 12.5, 14.5 and 17.5 around sub-region of aorticopulmonary septum were dissociated by using 0.25 w/v% trypsin / 1 mmol/L EDTA・4Na solution (Wako) at 37 °C, 15 minutes. Enzymes were neutralized with equal volume of DMEM (Wako) with 10% fetal bovine serum (FBS) (SIGMA). Cell suspensions were filtered through a 35 μm nylon mesh cell strainer（FALCON 352235.  Cells were kept on ice until cell sorting. Cell sorting was performed in a fluorescence-activated cell sorting (FACS) AriaⅡcell sorter (BD Biosciences).
EYFP-positive single cells were captured on the Fluidigm C1 Medium-cell (10-17 μm cell diameter) integrated fluidic circuit (IFC) for single cell cDNA libraries for mRNA sequencing. EYFP-positive cells were loaded on the IFC chips at concentration of 300 cells per μL. All captured cells were photographed to check whether cells were truly EYFP-positive and were dissociated for single cells by using KEYENCE BZ-X710. Single cell cDNAs were prepared on Fluidigm C1 system by using SMARTer v4 Ultra Input Low RNA kit for the Fluidigm C1 System (Clontech). Only single cell cDNAs confirmed by imaging data were performed quality check (QC) by using Agilent 2200 TapeStation system and quantified by Qubit (Thermo Fisher). High quality cDNAs were further constructed sequencing libraries by using Nextera XT DNA Sample Preparation Kit (Illumina). Each single cell cDNAs were sequenced 50 pair-end on the Illumina HiSeq 2500.

value: heart

value: Wnt1-Cre; R26-EYFP


title: Control_Rep3

description: Library name: SOD1_VEH_3


title: oligodendrocyte,0.01mM water‑soluble cholesterol,Treat 12hours,rep1

description:
Library name: Treat1
B1


title: WI-38 cells, multi-fraction, 220mGy, 5hmC, rep2

description: Library name: MF220 H2


title: C147, scRNA-seq

description:
Fluidigm C1
C147


title: Control_Rep2

description: Library name: SOD1_VEH_2


title: oligodendrocyte,pbs,Treat 12hours,rep3

description:
Library name: control3
A3

value: PBS


title: WI-38 cells, multi-fraction, 220mGy, 5hmC, rep1

description: Library name: MF220 H1


title: Control_Rep1

description: Library name: SOD1_VEH_1


title: oligodendrocyte,pbs,Treat 12hours,rep2

description:
Library name: control2
A2


title: Treated_Rep4

description: Library name: SOD1_PF4_4


title: C144, scRNA-seq

description:
Fluidigm C1
C144


title: oligodendrocyte,pbs,Treat 12hours,rep1

description:
Library name: control1
A1


title: WI-38 cells, multi-fraction, 110mGy, 5hmC, rep3

description: Library name: MF110 H3


title: C143, scRNA-seq

description:
Fluidigm C1
C143


title: Treated_Rep3

description: Library name: SOD1_PF4_3


title: WI-38 cells, multi-fraction, 110mGy, 5hmC, rep2

description: Library name: MF110 H2


title: Sftpc-ND1 DP 3

city: beijing

last: Ryan

address: panjiayuan chaoyang china

institute: Chinese Academy of Medical Sciences  AND Peking Union Medical College

description:
Library name: sample 6
Column name in Processed data .xlsx: Sftpc-ND1-DP25

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to the reference genome using HISAT2, and gene expression was normalized to FPKM.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using DESeq2.
Functional enrichment analyses (GO and KEGG) were conducted using R software to identify significantly enriched pathways. The ggplot2 package was used for creating graphics in R software (R version 4.3.3).
Assembly: After reads ressembled by StringTie2, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
Supplementary files format and content: Processed data .xlsx

source_name: Lung

growth_protocol: All animals were maintained on an SD genetic background under standard housing conditions: temperature range of 20–26°C, relative humidity of 40–60%, and a 12-hour light/dark cycle. Food and water were provided ad libitum.

extract_protocol:
Total RNA Extraction Kit 2.0 Plus (R411-C3, Vazyme, China)
Libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit

value: Lung

value: ND1 cKO


title: C142, scRNA-seq

last: Iwase

institute: The University of Tokyo

description:
Fluidigm C1
C142


title: C141, scRNA-seq

description:
Fluidigm C1
C141


title: Treated_Rep1

description: Library name: SOD1_PF4_1


title: WI-38 cells, multi-fraction, 110mGy, 5hmC, rep1

description: Library name: MF110 H1


title: WI-38 cells, multi-fraction, 23mGy, 5hmC, rep4

description: Library name: MF23 H4


title: Sftpc-ND1 DP 1

description:
Library name: sample 4
Column name in Processed data .xlsx: Sftpc-ND1-DP4


title: C139, scRNA-seq

description:
Fluidigm C1
C139


title: Sftpc-ND1 Control 3

description:
Library name: sample 3
Column name in Processed data .xlsx: Sftpc-ND1-Control19

value: WT


title: WI-38 cells, multi-fraction, 23mGy, 5hmC, rep3

description: Library name: MF23 H3


title: Liver, Pc day 20 + Py 44hpi, biol rep 4

description: Library name: Sample 38

data_processing:
Sequences were aligned and raw gene counts acquired using the BioJupies platform (https://maayanlab.cloud/biojupies/) with default parameters.
Assembly: mm10
Supplementary files format and content: xls file containing raw gene counts for all samples

source_name: liver

extract_protocol:
RNA was extracted from homogenized livers using trizol and chloroform.
Library construction and sequencing  were conducted by Novogene using paired-end sequencing using the NovaSeq X Plus platform.

value: liver

value: Pc blood-stage + Py liver-stage

tag: time

value: 20 dpi + 44 hpi

tag: strain


title: Sftpc-ND1 Control 2

description:
Library name: sample 2
Column name in Processed data .xlsx: Sftpc-ND1-Control11


title: C135, scRNA-seq

description:
Fluidigm C1
C135


title: WI-38 cells, multi-fraction, 23mGy, 5hmC, rep2

description: Library name: MF23 H2


title: Sftpc-ND1 Control 1

description:
Library name: sample 1
Column name in Processed data .xlsx: Sftpc-ND1-Control7


title: C134, scRNA-seq

description:
Fluidigm C1
C134


title: Liver, Pc day 20 + Py 44hpi, biol rep 2

description: Library name: Sample 36


title: PAVSMCs, non-IP control, Total RNA

city: Fuzhou

first: Cheng

last: Yu

state: Fujian

address: 29 Xinquan Road, Gulou District, Fuzhou City, Fujian Province

institute: Affiliated Union Hospital of Fujian Medical University

data_processing:
For acRIP-seq: cutadapt (v2.5) was used to trim adapters and filter sequences. The remaining reads were aligned to the mouse Ensemble genome GRCm38 using the Hisat2 aligner (v2.1.0) with the parameter “--rna-strandness RF”. Ac4C peaks were identified using the exomePeak R package (v2.13.2) with the parameters “PEAK_CUTOFF_PVALUE=0.05”, “PEAK_CUTOFF_FDR=NA”, and “ FRAGMENT_LENGTH=200”. Differential ac4C peaks were identified using the exomePeak R package with the same parameters. GO and KEGG analysis were performed using the clusterprofile R package (v3.6.0). ac4C-RNA-related genomic features were visualized using the Guitar R package (v1.16.0). The identified ac4C peaks with a p-value <0.05 were chosen for de novo motif analysis using homer (v4.10.4) with the parameters “-len 12 -rna”. For RNA-seq: Cutadapt (v2.5) was used to trim adapters and filter for sequences. Reads were aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3). Differential gene expression analysis was performed using the DESeq2 R-package.  For NAT10-RIP-seq: exomePeak2 software was used to identify read-enriched regions from RIP-seq data. A region was considered a peak if the p-value was less than 0.05, and peaks with over 50% overlap were retained for further analysis.
Assembly: rn6
Supplementary files format and content: bed, peaks, tab-delimited text file includes FPKM values for each Sample

source_name: primary aortic vascular smooth muscle cell (PAVSMC)

growth_protocol: primary aortic vascular smoothn muscle cells were cultured in medium consisting of DMEM/F12 medium, 20% fetal bovine serum, and 1% penicillin/streptomycin in humidified atmosphere woth 5% CO2 at 37 ℃

extract_protocol:
For acRIP-seq: Total RNA was extracted and fragmented into 100-200 nt RNA fragments. The fragmented RNA was purified using a Zymo RNA Clean and Concentrator-25 Kit (Zymo Research, R1017) and was incubated for 4 hours at 4 °C with anti-ac4C monoclonal antibody (Abcam, ab25221, 1:50), followed by protein A/G magnetic beads (Invitrogen, 10004D) at 4 °C for an additional 2 hours to obtain immunoprecipitated RNA fragments using EpiTM ac4C Immunoprecipitation Kit (Epibiotek, R1815). The ac4C-enriched RNA was extracted by HiPure cell miRNA Kit (Magen, R4311) after high salt washing. Both the input samples without IP and the ac4C IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer. For NAT10-RIP-seq: Cells were resuspended in NP40 lysis buffer and then treated with 2 U/mL DNase I. For each immunoprecipitation (IP), 2.5 μg of polyclonal anti-NAT10 antibody (Proteintech, 13365-1-AP, rabbit) or 2.5 μg of rabbit polyclonal IgG control (Cell Signaling Technology, 2729S, rabbit) were pre-coupled to 900 μg of Protein G Dynabeads for 1 hour at room temperature. The cell lysates were then immunoprecipitated overnight at 4 ℃ in 500 mL of NP40 lysis buffer.After total RNA was extracted, the enriched mRNAs and ncRNAs were fragmented and reverse transcribed into cDNA with random primers. The resulting cDNA fragments were purified using the QiaQuick PCR extraction kit, subjected to end repair, poly(A) addition, and ligation to Illumina NovaSeq 6000 sequencer. Uracil-N-Glycosylase (UNG) was then utilized to digest the second-strand cDNA. The digested products were size-selected through agarose gel electrophoresis, PCR amplified, and finally sequenced using the Illumina NovaSeq 6000 sequencer.
For acRIP-seq: the library was prepared using the smart-seq method with EpiTM mini longRNA-seq kit (Epibiotek, E1802).  For RNA-seq: the VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme Biotech, NR612-02) was used for library preparation. For NAT10-RIP seq:  the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).
acRIP-seq, RNA-seq, NAT10-RIP-seq

treatment_protocol: Adenovirus-control or Adenovirus-shRNA-NAT10 were added into primary aortic vascular smoothn muscle cells culture in full medium for 48 hours

value: wild type


title: WI-38 cells, multi-fraction, 11mGy, 5hmC, rep4

description: Library name: MF11 H4


title: C133, scRNA-seq

description:
Fluidigm C1
C133


title: Liver, Pc day 20 + Py 44hpi, biol rep 1

description: Library name: Sample 35


title: Liver, Pc day 20 + Py 44hpi, biol rep 5

description: Library name: Sample 39


title: PAVSMCs, NAT10-RIP-3

value: primary aortic vascular smooth muscle cell (PAVSMC)


title: C136, scRNA-seq

description:
Fluidigm C1
C136


title: WI-38 cells, multi-fraction, 11mGy, 5hmC, rep3

description: Library name: MF11 H3


title: C132, scRNA-seq

description:
Fluidigm C1
C132


title: Liver, Pc day 20 + Py 24hpi, biol rep 5

description: Library name: Sample 34

value: 20 dpi + 24 hpi


title: PAVSMCs, NAT10-RIP-2


title: WI-38 cells, multi-fraction, 11mGy, 5hmC, rep2

description: Library name: MF11 H2


title: Liver, Pc day 20 + Py 44hpi, biol rep 3

description: Library name: Sample 37


title: C131, scRNA-seq

description:
Fluidigm C1
C131


title: Liver, Pc day 20 + Py 24hpi, biol rep 4

description: Library name: Sample 33


title: WI-38 cells, multi-fraction, 23mGy, 5hmC, rep1

description: Library name: MF23 H1


title: PAVSMCs, NAT10-RIP-1


title: C130, scRNA-seq

description:
Fluidigm C1
C130


title: WI-38 cells, multi-fraction, 11mGy, 5hmC, rep1

description: Library name: MF11 H1


title: Liver, Pc day 20 + Py 24hpi, biol rep 3

description: Library name: Sample 32


title: PAVSMCs, Adsh-3-IP

value: acRIP-seq

value: NAT10 knockdown

value: Adenovirus


title: WI-38 cells, multi-fraction, 2mGy, 5hmC, rep4

description: Library name: MF2 H4

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

value: multi-fraction


title: C129, scRNA-seq

description:
Fluidigm C1
C129

value: heart

value: Wnt1-Cre; R26-EYFP


title: Liver, Pc day 20 + Py 24hpi, biol rep 2

description: Library name: Sample 31


title: PAVSMCs, Adsh-2-IP


title: WI-38 cells, multi-fraction, 2200mGy, 5hmC, rep3

description: Library name: MF2200 H3

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: whole fly, wildtype, young, 4hr post heat shock, climber

description:
Library name: MW08
Analyses done on Read 1 only

value: whole fly

value: wildtype

value: Heat shock

tag: classification

value: climber

tag: batch


title: WI-38 cells, multi-fraction, 2mGy, 5hmC, rep3

description: Library name: MF2 H3

tag: cell line


title: WI-38 cells, multi-fraction, 2200mGy, 5hmC, rep2

description: Library name: MF2200 H2

tag: cell type


title: C128, scRNA-seq

description:
Fluidigm C1
C128

tag: tissue

tag: genotype


title: Liver, Pc day 20 + Py 24hpi, biol rep 1

description: Library name: Sample 30

value: liver

value: Pc blood-stage + Py liver-stage


title: whole fly, wildtype, young, 2hr post heat shock, climber

description:
Library name: MW06
Analyses done on Read 1 only

tag: treatment


title: WI-38 cells, multi-fraction, 2mGy, 5hmC, rep2

description: Library name: MF2 H2

tag: dose (mgy)

tag: radiation regimen


title: PAVSMCs, Adsh-1-IP

value: primary aortic vascular smooth muscle cell (PAVSMC)


title: C126, scRNA-seq

description:
Fluidigm C1
C126


title: PAVSMCs, Adcon-3-IP

value: wild type


title: WI-38 cells, multi-fraction, 2mGy, 5hmC, rep1

description: Library name: MF2 H1

tag: total number_of_fractions

tag: antibody


title: whole fly, wildtype, young, 1hr post heat shock, climber

description:
Library name: MW03
Analyses done on Read 1 only


title: PAVSMCs, Adcon-2-IP

value: acRIP-seq


title: Liver, Pc day 20 + Py 6hpi, biol rep 4

description: Library name: Sample 28

tag: disease state

value: 20 dpi + 6 hpi


title: C125, scRNA-seq

description:
Fluidigm C1
C125


title: WI-38 cells, multi-fraction, 0mGy, 5hmC, rep4

description: Library name: MF0 H4

value: Sham


title: C124, scRNA-seq

description:
Fluidigm C1
C124


title: Liver, Pc day 20 + Py 6hpi, biol rep 3

description: Library name: Sample 27


title: whole fly, wildtype, young, 0hr post heat shock, climber

description:
Library name: MW02
Analyses done on Read 1 only


title: C154, scRNA-seq

description:
Fluidigm C1
C154


title: PAVSMCs, Adcon-1-IP

value: Adenovirus


title: WI-38 cells, multi-fraction, 0mGy, 5hmC, rep3

description: Library name: MF0 H3

value: Human fibroblast from 3-month-old female lung tissue


title: C122, scRNA-seq

description:
Fluidigm C1
C122


title: Liver, Pc day 20 + Py 6hpi, biol rep 2

description: Library name: Sample 26


title: WI-38 cells, multi-fraction, 0mGy, 5hmC, rep2

description: Library name: MF0 H2

value: multi-fraction


title: PAVSMCs, Adsh-3-Input

description: All.fpkm.anno.txt

value: RNA-seq

value: NAT10 knockdown


title: C121, scRNA-seq

description:
Fluidigm C1
C121

value: heart

value: Wnt1-Cre; R26-EYFP


title: Liver, Pc day 20 + Py 6hpi, biol rep 1

description: Library name: Sample 25


title: WI-38 cells, multi-fraction, 0mGy, 5hmC, rep1

description: Library name: MF0 H1

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: C120, scRNA-seq

description:
Fluidigm C1
C120


title: PAVSMCs, Adsh-2-Input

description: All.fpkm.anno.txt


title: PAVSMCs, Adsh-1-Input

description: All.fpkm.anno.txt


title: WI-38 cells, single-fraction, 2200mGy, 5hmC, rep4

description: Library name: SF2200 H4

value: alpha-irradiation

value: single-fraction


title: Liver, Py 44hpi, biol rep 5

description: Library name: Sample 24

value: liver

value: Py liver-stage

value: 44 hpi


title: C119, scRNA-seq

description:
Fluidigm C1
C119


title: Liver, Py 44hpi, biol rep 4

description: Library name: Sample 23


title: PAVSMCs, Adcon-3-Input

description: All.fpkm.anno.txt

value: primary aortic vascular smooth muscle cell (PAVSMC)

value: wild type


title: WI-38 cells, single-fraction, 2200mGy, 5hmC, rep3

description: Library name: SF2200 H3


title: C146, scRNA-seq

description:
Fluidigm C1
C146


title: C118, scRNA-seq

description:
Fluidigm C1
C118


title: Liver, Py 44hpi, biol rep 3

description: Library name: Sample 22


title: WI-38 cells, multi-fraction, 110mGy, 5hmC, rep4

description: Library name: MF110 H4


title: PAVSMCs, Adcon-2-Input

description: All.fpkm.anno.txt


title: WI-38 cells, single-fraction, 2200mGy, 5hmC, rep2

description: Library name: SF2200 H2


title: C116, scRNA-seq

description:
Fluidigm C1
C116


title: Liver, Py 44hpi, biol rep 2

description: Library name: Sample 21


title: PAVSMCs, Adcon-1-Input

description: All.fpkm.anno.txt


title: WI-38 cells, single-fraction, 2200mGy, 5hmC, rep1

description: Library name: SF2200 H1


title: C112, scRNA-seq

description:
Fluidigm C1
C112


title: Liver, Py 44hpi, biol rep 1

description: Library name: Sample 20


title: sample_818_GLU, Oxford Nanopore methylation

city: La Jolla

first: Eran

middle: A

last: Mukamel

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

description:
Library name: sample_818_GLU
sample ID=sample_818_GLU; donor=818; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing

data_processing:
Pod5 files generated with Oxford Nanopore PromethION were used as the input for basecalling using Dorado (v.0.9.1). Modified basecalling mode that can recognize both 5mC and 5hmC was activated using the Super Accurate (SUP) modified basecalling model “dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v3” in the Dorado “basecaller” subcommand (simplex mode), with “--modified-bases-threshold” set to 0.05 and “--min_qscore” set to 9. Basecalled sequences were saved in unmapped BAM files, where the modification information was saved in the MM and ML tags. These reads were then aligned to the hg38 human reference genome with minimap2 (v2.28-r1209) with the “-ayx lr:hq” parameters. Modkit (v0.4.1) “pileup” subcommand was then used to create bedMethyl files for all cytosines, CG or CH sites with “--max-depth” set to 100000 and “--sampling-frac” set to 0.01. Summarized statistics of 5mC or 5hmC in gene body or 100kb genomic bins were computed using the Modkit “stats” subcommand with “--min-coverage” set to 1.
Assembly: GRCh38
Supplementary files format and content: bedMethyl files contain genomic positions, coverage, and native DNA methylation calls generated with modkit; .tbi files are tabix indexes.
Supplementary files format and content: Processed data file 2 is the tabix index (.tbi) for the corresponding bedMethyl file.

source_name: human prefrontal cortex

growth_protocol: Not applicable; postmortem human brain tissue was used.

extract_protocol:
Genomic DNA was isolated from sorted Glu or MGE-GABA nuclei from human prefrontal cortex.
Native genomic DNA ligation libraries were prepared for Oxford Nanopore sequencing.

treatment_protocol: None.

value: human prefrontal cortex

value: Glu


title: WI-38 cells, single-fraction, 1100mGy, 5hmC, rep4

description: Library name: SF1100 H4


title: C110, scRNA-seq

city: Bunkyo-ku

first: Akiyasu

description:
Fluidigm C1
C110


title: Liver, Py 24hpi, biol rep 5

description: Library name: Sample 19

value: 24 hpi


title: sample_5977_GLU, Oxford Nanopore methylation

description:
Library name: sample_5977_GLU
sample ID=sample_5977_GLU; donor=5977; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing


title: Treated_Rep2

description: Library name: SOD1_PF4_2

value: motor neuron-like cells

value: SOD1G93A transfected


title: WI-38 cells, single-fraction, 1100mGy, 5hmC, rep3

description: Library name: SF1100 H3

value: Human fibroblast from 3-month-old female lung tissue


title: Liver, Py 24hpi, biol rep 4

description: Library name: Sample 18


title: C108, scRNA-seq

description:
Fluidigm C1
C108


title: Sftpc-ND1 DP 2

description:
Library name: sample 5
Column name in Processed data .xlsx: Sftpc-ND1-DP9

value: Lung

value: ND1 cKO


title: sample_5977_GABA, Oxford Nanopore methylation

description:
Library name: sample_5977_GABA
sample ID=sample_5977_GABA; donor=5977; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing

value: MGE-GABA


title: WI-38 cells, single-fraction, 1100mGy, 5hmC, rep2

description: Library name: SF1100 H2

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: Liver, Py 24hpi, biol rep 3

description: Library name: Sample 17


title: C103, scRNA-seq

description:
Fluidigm C1
C103

value: heart

value: Wnt1-Cre; R26-EYFP


title: WI-38 cells, single-fraction, 1100mGy, 5hmC, rep1

description: Library name: SF1100 H1

value: alpha-irradiation

value: single-fraction


title: sample_5697_GLU, Oxford Nanopore methylation

description:
Library name: sample_5697_GLU
sample ID=sample_5697_GLU; donor=5697; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing


title: Liver, Py 24hpi, biol rep 2

description: Library name: Sample 16

value: liver

value: Py liver-stage


title: WI-38 cells, single-fraction, 220mGy, 5hmC, rep4

description: Library name: SF220 H4


title: sample_5697_GABA, Oxford Nanopore methylation

description:
Library name: sample_5697_GABA
sample ID=sample_5697_GABA; donor=5697; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing


title: C101, scRNA-seq

description:
Fluidigm C1
C101


title: whole fly, wildtype, old, 8hr post heat shock, climber

description:
Library name: MW27
Analyses done on Read 1 only

value: whole fly

value: wildtype

value: Heat shock

value: climber


title: PID007_TM1_P1_2_1

last: Najafabadi

institute: McGill University

description: Library name: PID007_TM1_P1_2_1

data_processing:
Raw sequencing reads were aligned to reference genomes using the 10x Genomics CellRanger software (v3.0.2). For tumor samples, reads were aligned to the human reference genome (hg38). For PDX samples, a combined human (hg38) and mouse (mm10) reference was used. Unique molecular identifier (UMI) counts were generated by collapsing alignments using CellRanger. For PDX samples, multiplets and mouse cells were removed as identified by the CellRanger pipeline. Only cells with >95% of counts mapped to the human genome were retained.
Quality control metrics were computed using the scuttle (v.1.0.4) package. Cells were retained if they met the following criteria: log10 total counts >3, log10 total features >3, and percentage of mitochondrial reads per cell <20%. Doublet detection was performed using DoubletFinder (v.2.0.3). The doublet rate was estimated based on the number of cells recovered per sample, following the multiplet rate guidelines from the 10x Genomics v3 user guide. Other parameters remained as default, except that the top 50 principal components were used for dimensional reduction.
Assembly: GRCh38 and mm10
Supplementary files format and content: Single cell experiment object with counts and metadata in .rds format

extract_protocol:
Tumor specimens were dissociated into single-cell suspensions prior to single-cell RNA sequencing. Tumor tissue was washed two to three times with Dulbecco’s Phosphate-Buffered Saline (DPBS) and minced into 1–2 mm pieces using a scalpel. Tissue fragments were collected, washed with DPBS, and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Briefly, tissue pieces were incubated in enzyme solution composed of Enzymes H, R, and A prepared in RPMI 1640 medium and processed using the gentleMACS Octo Dissociator with Heaters (program 37_h_TDK_1). Following dissociation, cells were filtered through a 70 µm cell strainer to remove undigested material, washed with DPBS, and pelleted by centrifugation. Red blood cells were lysed using ACK lysis buffer, after which cells were washed and resuspended in DPBS supplemented with 1% bovine serum albumin. Cell suspensions were passed through a 40 µm filter to remove remaining debris. Viable cells were counted using Trypan Blue exclusion prior to downstream single-cell RNA sequencing library preparation.
Single-cell cDNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) according to the manufacturer’s instructions. Briefly, single-cell suspensions that passed quality control were loaded onto the Chromium Next GEM Chip along with reverse transcription reagents, gel beads, and partitioning oil, and processed using the Chromium Controller to generate gel bead–in–emulsions (GEMs). Reverse transcription was performed in GEMs, followed by GEM cleanup and cDNA recovery. Full-length cDNA was purified using silane magnetic beads and amplified by PCR. cDNA quality and size distribution were assessed prior to library construction. Amplified cDNA was fragmented, end-repaired, and A-tailed, followed by double-sided size selection using SPRIselect beads. Indexed sequencing libraries were generated by adaptor ligation and sample index PCR amplification. Final libraries were purified and quality controlled prior to sequencing. Libraries were sequenced to a targeted depth of approximately 20,000 reads per cell.

value: Tumor

tag: tumor type

value: renal cell carcinoma

tag: renal cell_carcinoma_subtype

value: ccRCC

value: Brain metastasis

value: Patient-derived xenograft model


title: Liver, Py 24hpi, biol rep 1

description: Library name: Sample 15

value: 24 hpi


title: sample_5652_GLU, Oxford Nanopore methylation

description:
Library name: sample_5652_GLU
sample ID=sample_5652_GLU; donor=5652; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing

value: human prefrontal cortex

value: Glu


title: PID006_TM1_P1_2_1

description: Library name: PID006_TM1_P1_2_1

tag: tumor site

tag: group


title: WI-38 cells, single-fraction, 220mGy, 5hmC, rep3

description: Library name: SF220 H3

value: Human fibroblast from 3-month-old female lung tissue

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: Liver, Pc day 20 + Py 6hpi, biol rep 5

description: Library name: Sample 29

value: Pc blood-stage + Py liver-stage

tag: time

value: 20 dpi + 6 hpi

tag: strain


title: Liver, Py 6hpi, biol rep5

description: Library name: Sample 14

value: liver

value: Py liver-stage

value: 6 hpi


title: sample_5652_GABA, Oxford Nanopore methylation

description:
Library name: sample_5652_GABA
sample ID=sample_5652_GABA; donor=5652; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing

value: MGE-GABA


title: PID002_TP1_P1_1_1

description: Library name: PID002_TP1_P1_1_1

value: Primary


title: Liver, Py 6hpi, biol rep4

description: Library name: Sample 13


title: WI-38 cells, single-fraction, 220mGy, 5hmC, rep1

description: Library name: SF220 H1

value: alpha-irradiation

value: single-fraction


title: sample_510_GLU, Oxford Nanopore methylation

description:
Library name: sample_510_GLU
sample ID=sample_510_GLU; donor=510; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing