title: Cell_0612

data_processing:
Raw fastq files were obtained by bcltoFastq conversion (version 2.20.0.422)
Fastq files were aligned to the mm10 reference genome using STAR aligner (version 2.7.9a) with the argument ‘STARsolo’. This argument allowed simultaneous mapping of reads and quantification of gene expression. The reference genome and gene transfer format (GTF) file were downloaded from 10x genomic webpage at (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz).
The output of ‘STARsolo’ was loaded into R (version 4.1.0) using the Bioconducter package DropletUtils (version 1.12.1).
Downstream analyses were done in R using SingleCellExperiment (version 5271.14.1) and Seurat (version 4.0.6).
Cells with <2000 detected genes, >15% mitochondrial content and > 10% hemoglobin percentage were excluded.
For isoform analysis, fastq files of selected 432 cells (46 cells from HE-HSC (AGM), 198 from HE-LMP (YSm), and 188 cells from HE-EMP (YSb)) were aligned and quantifed using Salmon 1.4.0  in Mapping mode. GRCm39 M32 mouse reference genome, transcriptome, and GTF file were downloaded from GENCODE website. Resulting quant.sf files were fed into IsoformSwitchAnalyzer  2.01.07 where importIsoformExpression function was used to give TMM normalized abundance values.
Assembly: GRCm39 M32 Gencode reference for Isoform Analysis and mm10 10X genomics reference for gene level analysis
Supplementary files format and content: RDS file having log normalized counts for each sample-gene level analyses (1494 cells)
Supplementary files format and content: RDS file having TMM normalized abundance for each sample used for isoform analyses (432 cells)

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol.
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)


title: Cell_1825

status: Public on Sep 19 2025

type: SRA

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: SmartSeq2_Gene_log_normalized_counts.rds

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: sequencing run


title: Cell_1828


title: Cell_0611


title: 11441 HIGH FAT DIET MALE baseline urothelium

city: Columbus

first: John

middle: David

last: Spencer

state: OH

address: 700 Children's Drive

country: USA

institute: Nationwide Children's Hospital

data_processing:
Individual FASTQ files were trimmed for adapter sequences and filtered for a minimum quality score of Q20 using AdapterRemoval v2.2.0
Preliminary alignment using HISAT2 v2.0.6 (48) was performed to a composite reference of rRNA, mtDNA, and PhiX bacteriophage sequences obtained from NCBI RefSeq (49). Reads aligning to these references were excluded in subsequent analyses. Primary alignment was performed against the mouse genome reference GRCm38p4 using HISAT2.
Gene expression values for genes described by the GENCODE (50, 51) Gene Transfer Format (GTF) release M14 (mouse) were quantified using the featureCounts tool of the Subread package v1.5.1 (52, 53) in unstranded mode.
Quality control was performed using a modification of the QuaCRS custom workflow (54). In brief, aligned read quality was verified using RNA-SeQC (55) and RSeQC (56). The exonic rate (the percentage of reads aligning to exons), intronic rate (the percentage of reads aligning to introns), and duplication rate (the percentage of reads that were identified as PCR duplicates) were evaluated.
Coverage depths across the aligned reference were calculated with a per-base resolution using the ‘genomecov’ utility tool of Bedtools v2.27.0 (57) in BedGraph format. These files were used as input into CLEAR: a gene-by-gene analysis workflow to identify robust genes in ultra-low input RNA-seq data for downstream analyses. Determination of analysis-ready CLEAR transcripts was done as outlined in (58).
Assembly: mm10
Supplementary files format and content: comma-separated values file include CLEAR count values for each sample
Supplementary files format and content: n/a

molecule: total RNA

source_name: bladder urothelium

growth_protocol: Mice were maintained on low fat or high fat rodent chow ad libitum with free access to water under controlled temperature and humidity with twelve-hour light and dark cycles.

extract_protocol:
The NucleoSpin RNA Plus XS Kit was used to extract RNA on enriched IC and PC fractions following the manufacturer’s instruction, with one modification: DNase digestion was performed in solution using DNase I. Urothelium samples were isolated mechanically from mouse bladders and RNA was isolated using Qiagen RNeasy Miniprep kit. RNA integrity was measured using Agilent 2100 Bioanalyzer with RNA pico chip. Samples with RNA integrity scores > 7 were used for RNA sequencing.
1 ng of RNA was preamplified using the Takara Clontech SMARTer v4 kit and RNA sequencing libraries were generated with the Illumina Nextera XT DNA Library Prep Kit. Samples were sequenced to a depth of 15–20 million 2 × 150 bp clusters on the Illumina HiSeq 4000 platform.

treatment_protocol: Mice were anesthetized with isoflurane prior to transurethral infection with 10^8 CFU UTI89 suspended in 50 uL sterile PBS, or sham infected with 50 uL sterile PBS. Following infection, mice were euthanized at 6 hours post infection.

value: bladder urothelium

tag: Sex

value: MALE

tag: cell type

value: urothelial cell

tag: genotype

tag: treatment

value: high fat diet, sham infection with sterile PBS

tag: timepoint

value: baseline


title: 11444 HIGH FAT DIET MALE baseline urothelium


title: Cell_1824


title: HFD2 HIGH FAT DIET FEMALE baseline urothelium

value: FEMALE


title: 205333490028_R02C02, Primarytumor, Foxr2_Trp53KO

type: genomic

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

country: Germany

institute: Research Institute Childrens Cancer Center Hamburg

hyb_protocol: DNA was bisulfite conversed by the EZ DNA Methylation Kit (Zymo Research)

scan_protocol: The samples were hybridized in the Infinium Mouse Methylation BeadChip microarray following the manufacturer’s instructions.

data_processing:
idat files were processed using the OpenSesame pipeline from the Sesame package
openSesame normalized beta values (see Supplementary file Geo_mset.txt at the foot of the GSE record)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Primarytumor

label_protocol: Standard Illumina label protocol

extract_protocol: extraction of DNA by Maxwell DNA isolation

value: Primarytumor


title: 205333490028_R01C02, Primarytumor, Foxr2_Trp53KO


title: Cell_0599


title: Cell_1820

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_0598


title: 11529 LOW FAT DIET MALE baseline urothelium

value: low fat diet, sham infection with sterile PBS


title: Cell_1819


title: 205333480132_R06C02, Cerebralcortex, Wildtype_P7

source_name: Cerebralcortex

value: Cerebralcortex


title: Cell_0597


title: Cell_1818


title: Cell_1817


title: 205333480132_R04C02, Cerebralcortex, Wildtype_P7


title: 11524 HIGH FAT DIET MALE baseline urothelium


title: 205333490028_R06C01, Primarytumor, Foxr2_Trp53KO


title: 204887840026_R06C02, Cerebralcortex, Wildtype_P7


title: Cell_0610


title: 11606 HIGH FAT DIET FEMALE baseline urothelium


title: 204887840026_R05C02, Cerebralcortex, Wildtype_P7


title: Cell_0587


title: 11616 LOW FAT DIET FEMALE baseline urothelium


title: Cell_1810


title: Cell_1807


title: 11614 LOW FAT DIET FEMALE baseline urothelium


title: HFD1 HIGH FAT DIET FEMALE baseline urothelium


title: 204887840026_R04C02, Cerebralcortex, Wildtype_P7


title: Cell_0583


title: 11613 LOW FAT DIET FEMALE baseline urothelium


title: 205333480135_R06C02, Cerebralcortex, Wildtype_P28


title: Cell_1803


title: 205333480132_R05C02, Cerebralcortex, Wildtype_P7


title: 11528 LOW FAT DIET MALE baseline urothelium


title: 205333480135_R05C02, Cerebralcortex, Wildtype_P28


title: Cell_0596


title: male LFD urothelium 4

value: male

tag: strain

value: high fat diet


title: Cell_1802


title: Cell_0582


title: Cell_0588


title: Cell_1801


title: Cell_1811


title: Cell_0581


title: 205333480135_R04C02, Cerebralcortex, Wildtype_P28


title: Cell_0580


title: Cell_0586


title: Cell_1800


title: 205291550082_R06C02, Cerebralcortex, Wildtype_P28


title: male LFD urothelium 2


title: Cell_1794


title: 205291550082_R05C02, Cerebralcortex, Wildtype_P28


title: male LFD urothelium 1


title: Cell_0575


title: male HFD urothelium 4

value: low fat diet


title: 205291550082_R04C02, Cerebralcortex, Wildtype_P28


title: Cell_0574


title: 205333480092_R06C02, Cerebralcortex, Wildtype_P21


title: Cell_0573


title: Cell_0361


title: 205333480092_R05C02, Cerebralcortex, Wildtype_P21


title: Cell_1793


title: male HFD urothelium 3


title: male HFD urothelium 2


title: Cell_1790


title: Cell_1791


title: Cell_1786


title: Cell_0360


title: 205333480092_R04C02, Cerebralcortex, Wildtype_P21


title: Cell_0359


title: male HFD urothelium 1


title: 205291550061_R06C02, Cerebralcortex, Wildtype_P21


title: Cell_1785


title: female HFD urothelium 4

value: female


title: Cell_0358


title: 205291550061_R05C02, Cerebralcortex, Wildtype_P21


title: Cell_1784


title: Cell_0357


title: male LFD urothelium 3


title: female HFD urothelium 3


title: Cell_1783


title: female HFD urothelium 2


title: 205291550061_R04C02, Cerebralcortex, Wildtype_P21


title: Cell_0356


title: Cell_1782


title: 205537640002_R06C02, Cerebralcortex, Wildtype_P14


title: female LFD urothelium 4


title: Cell_1780


title: 205537640002_R04C02, Cerebralcortex, Wildtype_P14


title: Cell_0354


title: 205537640002_R05C02, Cerebralcortex, Wildtype_P14


title: Cell_0355


title: Cell_1781


title: female LFD urothelium 3


title: Cell_0353


title: Cell_1779


title: female LFD urothelium 2


title: Cell_0352


title: Cell_1776


title: 205333490001_R05C02, Cerebralcortex, Wildtype_P14


title: 205333490001_R06C02, Cerebralcortex, Wildtype_P14


title: Cell_0351


title: MEP diploid Pgpd SAK1 overexpression, 48h, rep3

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: SAK1-3-48H

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.48.1
Assembly: R64-1-1
Supplementary files format and content: Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.

extract_protocol:
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit. 150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

value: whole organism

value: Pgpd SAK1 overexpression

tag: batch


title: 205333490001_R04C02, Cerebralcortex, Wildtype_P14


title: Cell_0350


title: female LFD urothelium 1


title: Cell_1775


title: MEP diploid Pgpd SAK1 overexpression, 48h, rep2

description: Library name: SAK1-2-48H


title: female HFD urothelium 1


title: 205291550098_R06C02, Cerebralcortex, Wildtype_P0


title: Cell_0349


title: Cell_1771


title: 205291550098_R05C02, Cerebralcortex, Wildtype_P0


title: Cell_1773


title: 205291550098_R04C02, Cerebralcortex, Wildtype_P0


title: Cell_1766


title: MEP diploid wild type, 48h, rep 3

description: Library name: WT-3-48H

value: wild type


title: MEP diploid wild type, 48h, rep 2

description: Library name: WT-2-48H


title: Cell_1759


title: 205291550084_R06C02, Cerebralcortex, Wildtype_P0


title: 205291550084_R05C02, Cerebralcortex, Wildtype_P0


title: Cell_1757


title: MEP diploid wild type, 48h, rep 1

description: Library name: WT-1-48H


title: MEP diploid Pgpd SAK1 overexpression, 24h, rep3

description: Library name: SAK1-3-24h


title: 205333480132_R03C01, Cerebellum, Wildtype_P7

source_name: Cerebellum

value: Cerebellum


title: MEP diploid Pgpd SAK1 overexpression, 24h, rep2

description: Library name: SAK1-2-24h


title: Cell_0346


title: Cell_1754


title: Cell_0343


title: MEP diploid Pgpd SAK1 overexpression, 48h, rep1

description: Library name: SAK1-1-48H


title: Cell_1755


title: 205333480132_R02C01, Cerebellum, Wildtype_P7


title: Cell_0342


title: Cell_1753


title: 205333480132_R01C01, Cerebellum, Wildtype_P7


title: MEP diploid wild type, 24h, rep 3

description: Library name: WT-3-24h


title: Cell_0341


title: Cell_0348


title: Cell_0347


title: Cell_1758


title: Cell_1750


title: 204887840026_R03C01, Cerebellum, Wildtype_P7


title: Cell_0340


title: Cell_1748


title: MEP diploid wild type, 24h, rep 2

description: Library name: WT-2-24h


title: Cell_0345


title: 204887840026_R02C01, Cerebellum, Wildtype_P7


title: Cell_0344


title: Cell_0339


title: MEP diploid Pgpd SAK1 overexpression, log, rep3

description: Library name: SAK1-3-LOG

value: log


title: Cell_1747


title: 204887840026_R01C01, Cerebellum, Wildtype_P7


title: MEP diploid Pgpd SAK1 overexpression, 24h, rep1

description: Library name: SAK1-1-24h


title: MEP diploid Pgpd SAK1 overexpression, log, rep2

description: Library name: SAK1-2-LOG


title: 205291550084_R04C02, Cerebralcortex, Wildtype_P0


title: Cell_0338


title: Cell_0337


title: 205333480135_R03C01, Cerebellum, Wildtype_P28


title: Cell_1746


title: Cell_1744


title: Cell_0336


title: 205333480135_R01C01, Cerebellum, Wildtype_P28


title: 205333480135_R02C01, Cerebellum, Wildtype_P28


title: MEP diploid Pgpd SAK1 overexpression, log, rep1

description: Library name: SAK1-1-LOG


title: Cell_0335


title: Cell_1743


title: Cell_1741


title: 205291550082_R03C01, Cerebellum, Wildtype_P28


title: MEP diploid wild type, log, rep 2

description: Library name: WT-2-LOG


title: 205291550082_R02C01, Cerebellum, Wildtype_P28


title: Cell_1740


title: MEP diploid wild type, log, rep 1

description: Library name: WT-1-LOG


title: Cell_0333


title: HaCaT cells, over-ATF4

city: Shanghai

first: Qiqi

last: Yang

address: dongchuan road

department: School of Biomedical Engineering

country: China

institute: Shanghai Jiao Tong University

description:
Library name: Sample 4
Column name in all.fpkm.xls: over-ATF4

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data. Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1). Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: GRCh38.p13
Supplementary files format and content: Column shControl and column shATF4 in all.fpkm.xls represent raw counts, and column shControl_FPKM and column shATF4_FPKM represent associated FPKM.

organism: Homo sapiens

source_name: HaCaT

growth_protocol: HaCaT cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted from HaCaT cells using a TRIzol Reagent (YaMei) according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using Asenta‘s protocols

tag: cell line

value: HaCaT

value: keratinocyte

value: ATF4 overexpression


title: Cell_1736


title: Cell_0332


title: HaCaT cells, over-NC

description:
Library name: Sample 3
Column name in all.fpkm.xls: over-NC

value: WT

value: over-NC


title: 205333480092_R03C01, Cerebellum, Wildtype_P21


title: MEP diploid wild type, log, rep 3

description: Library name: WT-3-LOG


title: Cell_1734


title: Cell_0330


title: 205333480092_R02C01, Cerebellum, Wildtype_P21


title: Cell_1731


title: Treg HD - 6

city: Daejeon

first: So-Young

last: Kim

state: Daejeon

address: GSMSE, 291, Daehak-ro, Yuseong-gu, Daejeon, Rep, E18-1

country: South Korea

institute: KAIST

library_source: genomic

data_processing:
Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 2.8).
Adaptor and primer sequences were trimmed using Cutadapt (v1.8.1) in the raw fastq files. Filtered reads were aligned on a reference genome using Bowtie2 (v2.2.9), with a maximum insert size of 1,000 and the “--very-sensitive” parameter.
The aligned reads were sorted, and mitochondrial reads were removed using samtools (v1.3). All of the samples were assessed for library quality according to the ENCODE guidelines and standards (https://www.encodeproject.org/atac-seq/).
Assembly: hg38
Supplementary files format and content: Peak file

source_name: Peripheral blood

extract_protocol:
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Nat Methods. 2017, 14:959; Curr Protoc Mol Biol 2015, 109:21)

treatment_protocol: Thawed PBMCs were isolated from the gate of viable CD4+CD25+CD127− T cells using a FACS Aria II cell sorter (BD Biosciences).

value: Peripheral blood

tag: group

value: Healthy donor


title: Treg HD - 5


title: 205333480092_R01C01, Cerebellum, Wildtype_P21


title: 205291550061_R03C01, Cerebellum, Wildtype_P21


title: Cell_0331


title: MEP diploid wild type, 24h, rep 1

description: Library name: WT-1-24h


title: Cell_0334


title: Cell_1729


title: Cell_0328


title: Treg HD - 4


title: Treg HD - 7


title: 205291550061_R02C01, Cerebellum, Wildtype_P21


title: Cell_0327


title: 205291550082_R01C01, Cerebellum, Wildtype_P28


title: Cell_1728


title: 205291550061_R01C01, Cerebellum, Wildtype_P21


title: Treg HD - 3


title: Cell_1735


title: Cell_1727


title: Cell_0326


title: Treg HD - 2


title: 205537640002_R03C01, Cerebellum, Wildtype_P14


title: Cell_0325


title: Cell_0329


title: Cell_1730


title: Treg HD - 1


title: Treg HCV LTFU - 7

value: HCV patients long term follow up after SVR12


title: 205537640002_R02C01, Cerebellum, Wildtype_P14


title: Cell_1725


title: Cell_1726


title: Cell_0324


title: Cell_0323


title: 205333490001_R03C01, Cerebellum, Wildtype_P14


title: 205537640002_R01C01, Cerebellum, Wildtype_P14


title: Cell_0322


title: Cell_1724


title: Cell_1723


title: Treg HCV LTFU - 6


title: Treg HCV LTFU - 5


title: 205333490001_R02C01, Cerebellum, Wildtype_P14


title: Cell_0321


title: Cell_0319


title: Cell_1721


title: 205333490001_R01C01, Cerebellum, Wildtype_P14


title: Cell_0320


title: Treg HCV SVR12 - 5


title: Treg HCV LTFU - 4


title: Cell_0318


title: Cell_1720


title: Cell_1718


title: Treg HCV Pre - 5


title: Cell_1719


title: 205291550098_R02C01, Cerebellum, Wildtype_P0


title: 205291550098_R03C01, Cerebellum, Wildtype_P0


title: Cell_0317


title: 205291550098_R01C01, Cerebellum, Wildtype_P0


title: Treg HCV SVR12 - 4


title: 205291550084_R03C01, Cerebellum, Wildtype_P0


title: Cell_0316


title: 205291550084_R02C01, Cerebellum, Wildtype_P0


title: Treg HCV LTFU - 3

value: HCV patients before at SVR12


title: 205291550084_R01C01, Cerebellum, Wildtype_P0


title: Cell_1715


title: Treg HCV SVR12 - 3


title: Cell_0315


title: Cell_0314


title: 205333480081_R03C02, Cerebellum, P7


title: Treg HCV Pre - 3


title: Cell_1712


title: 205333480081_R02C02, Cerebellum, P7


title: Cell_0313


title: Cell_1713


title: Cell_0312


title: Treg HCV Pre - 4


title: 205333480081_R01C02, Cerebellum, P7


title: Cell_1717


title: Cell_1710


title: Cell_1706


title: Cell_1716


title: Cell_0311


title: 205659810062_R05C01, Cerebellum, CtrlCBE16


title: Treg HCV Pre - 2

value: HCV patients before DAA treatment


title: Treg HCV SVR12 - 2


title: 205659810062_R03C01, Cerebellum, CtrlCBE16


title: Treg HCV LTFU - 1


title: Cell_1705


title: Cell_0309


title: Cell_1702


title: 205659810062_R01C01, Cerebellum, CtrlCBE16


title: Cell_0308


title: Treg HCV SVR12 - 1


title: Treg HCV Pre - 1


title: Cell_1701


title: Treg HCV LTFU - 2


title: 205333480132_R06C01, Brainstem, Wildtype_P7

source_name: Brainstem

value: Brainstem


title: Cell_1695


title: 205333480132_R05C01, Brainstem, Wildtype_P7


title: Cell_0306


title: Cell_1693


title: Porcine VEC cultured in growth medium, replicate 4

city: shanghai

first: Binglin

last: Li

state: 上海

address: 241 Huaihai West Road, Xuhui District, Shanghai, China

institute: shanghai chest hospital

description: Library name: pVEC_4

data_processing:
Trim Galore (v0.6.4): adapter trimming and removal of low-quality or short reads.
Bowtie2 (v2.4.2): alignment to rRNA databases of the corresponding species to remove rRNA reads.
HISAT2 (v2.2.0): alignment to reference genomes (Human: GRCh38.104; Mouse: GRCm39.104; Rat: Rnor_6.0).
HTSeq-count (v0.13.5): quantification of RNA expression.
edgeR: differential expression analysis.
Assembly: Pig: Sscrofa11.1 (Ensembl release 104)
Supplementary files format and content: Processed data are provided as tab-delimited text files.  Each file contains gene-level expression values for all samples.Columns include:Gene ID (Ensembl annotation) , Raw counts (HTSeq-count output) , Normalized expression values (FPKM)

organism: Sus scrofa

source_name: aortic valve tissue

extract_protocol:
Total RNA was extracted using the RNeasy RNA extraction kit (Qiagen) following the manufacturer’s instructions. RNA integrity was assessed using Agilent 4200 TapeStation (Agilent, Cat# G2991A), and RNA quantity was measured using Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Cat# Q33216) and NanoDrop One spectrophotometer (Thermo Fisher Scientific, ND-ONE). Only RNA samples passing quality control were used for library preparation.
mRNA-seq libraries were prepared using the VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme, Cat# NR602) according to the manufacturer’s instructions. Library quality and concentration were assessed using Qubit Fluorometer (Thermo Fisher Scientific, Cat# Q33216) and Agilent 4200 TapeStation (Agilent, Cat# G2991A). Sequencing was performed on the Illumina platform.
ualified libraries were subjected to Illumina sequencing with a paired-end 150 bp (PE150) strategy. Sequencing was based on the Sequencing by Synthesis (SBS) method: clusters on the flow cell were exposed to four fluorescently labeled dNTPs, DNA polymerase, and sequencing primers. During extension, the incorporation of each labeled dNTP released a specific fluorescent signal, which was captured by the sequencer and converted into sequence information through computational analysis.

value: aortic valve tissue

value: primary cells

value: valvular endothelial cell (VEC)


title: Porcine VEC cultured in growth medium, replicate 3

description: Library name: pVEC_3


title: 205333480132_R04C01, Brainstem, Wildtype_P7


title: Cell_0310


title: Cell_1692


title: Cell_0305


title: 204887840026_R06C01, Brainstem, Wildtype_P7


title: Cell_0304


title: 204887840026_R05C01, Brainstem, Wildtype_P7


title: Porcine VEC cultured in growth medium, replicate 1

description: Library name: pVEC_1


title: Cell_0303


title: Cell_1690


title: Porcine VEC cultured in growth medium, replicate 2

description: Library name: pVEC_2


title: 204887840026_R04C01, Brainstem, Wildtype_P7


title: Porcine VIC cultured in osteogenic medium for 8 days, replicate 4

description: Library name: pVIC_OM8d_4

value: valvular interstitial cell (VIC)


title: Cell_1689


title: Cell_0302


title: Cell_1688


title: Porcine VIC cultured in osteogenic medium for 8 days, replicate 3

description: Library name: pVIC_OM8d_3


title: Porcine VIC cultured in osteogenic medium for 8 days, replicate 2

description: Library name: pVIC_OM8d_2


title: 205333480135_R06C01, Brainstem, Wildtype_P28


title: Cell_0307


title: Cell_0301


title: Cell_1686


title: 205333480135_R05C01, Brainstem, Wildtype_P28


title: Cell_0300


title: Cell_1685


title: Porcine VIC cultured in osteogenic medium for 8 days, replicate 1

description: Library name: pVIC_OM8d_1


title: 205333480135_R04C01, Brainstem, Wildtype_P28


title: Porcine VIC cultured in growth medium, replicate 4

description: Library name: pVIC_GM_Ctr4


title: Cell_1684


title: 205291550082_R05C01, Brainstem, Wildtype_P28


title: 205291550082_R06C01, Brainstem, Wildtype_P28


title: Cell_0298


title: 205291550082_R04C01, Brainstem, Wildtype_P28


title: WT24L_liver

city: Badalona

first: David

last: Corujo

address: Ctra de Can Ruti, Camí de les Escoles

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Sequencing reads were trimmed for adapter sequence removal using TrimGalore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed reads were aligned with STAR (Dobin et al., 2013) to mouse genome annotation GRCm38
Aligned reads were quantified with FeatureCounts (Liao et al., 2014) to produce a count table at gene level
Differential gene expression analysis was performed with the R package DESeq2 (Love et al., 2014)
Assembly: GRCm38
Supplementary files format and content: .tsv, tab-separated table of raw counts with ensembl gene identifiers

source_name: liver

growth_protocol: Animal housing was performed in strict accordance with directive 2010/63/EU and the local and federal government. All mice were housed in individually ventilated caging (IVC) systems (Sealsafe plus, GM 500, Tecniplast, Buggugiate, Italy) under speciﬁc pathogen-free conditions with a maximum cage density of ﬁve adult mice per cage. IVC systems operate with positive pressure. All mice received autoclaved wood chips (Lignocel select ﬁne, J. Rettenmaier & Soehne GmbH, Rosenberg, Germany) and paper stripes (Arbocel crinclets natural Rettenmaier & Soehne GmbH) as bedding and nesting material, irradiated standard diet (#1314) or ketogenic diet (ketogenic diet, #C1084) for rodents (Altromin Spezialfutter GmbH, Lage, Germany) and sterile-ﬁltered tap water ad libitum. The light was adjusted to a 12 h/12 h light/dark cycle with a 10 min period of dimmed light to simulate sunrise/sunset; temperature and relative humidity are regulated to 22 ± 2°C and 55 ± 10 %. Health monitoring was based on quarterly exhaust air dust PCR analysis for all FELASA-listed agents. Autonomic functions including urination and defecation was tested during a modified SHIRPA protocol with a test duration of approximately 3 minutes (Rogers et al., 1997).

extract_protocol:
RNA was isolated from at least 20 mg of homogenized tissue using an automatic purification platform (Maxwell® RSC Instruments, Promega, Madison, WI, USA) and the corresponding Maxwell® RSC simplyRNA Tissue Kit (Promega) according to the manufacturer's recommendations.
Libraries for Illumina sequencing were constructed at Novogene (UK) Company Limited with mRNA-enrichment by poly(A) selection

treatment_protocol: A mouse model to generate isoform-specific KO of macroH2A1 was established by introducing loxP and Rox sites into the alternative exons 6 of the encoding gene (Bereshchenko et al., 2019). Specifically, macroH2A1.1 heterozygous mice were generated via in vitro fertilization with sperm carrying the floxed exon 6b and wild-type oocytes. Then, zygotes were treated with 0.3 µM soluble Cre enzyme (cat#RP-7-S, Excellgen, Rockville, MD, US) for 30 min to generate heterozygous embryos which were transferred to previously prepared foster mothers. Genotypic quality control has been carried out by PCR on blastocysts to check Cre-mediated deletion in embryos and ear clip-derived genomic DNA. Exon 6a was excised by mating of mice carrying Rox sites in the alternative exon 6a with the Dre deleter strain B6.Cg-Pvalbtm3.1(dreo)Hze/J (Anastassiadis et al., 2009), generating macroH2A1.2-specific KO mice. Wild-type and homozygous KO mice for macroH2A1.1 and macroH2A1.2 were obtained by mating of heterozygous KO mice for macroH2A1.1 and macroH2A1.2, respectively. The mice had been backcrossed for at least 10 generations on a C57BL/6J background.

value: liver

value: whole tissue


title: Porcine VIC cultured in growth medium, replicate 2

description: Library name: pVIC_GM_Ctr2


title: Porcine VIC cultured in growth medium, replicate 3

description: Library name: pVIC_GM_Ctr3


title: Cell_0297


title: Cell_0296


title: 205333480092_R06C01, Brainstem, Wildtype_P21


title: WT20L_liver


title: Cell_0295


title: WT19L_liver


title: Day8

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

data_processing:
The command-line version of the ICELL8 mappa analysis pipeline (demuxer and analyzer v0.92 with STAR v2.7.2a) was used for data pre-processing and read mapping. Mappa_demuxer assigned the reads to the cell barcodes present in a pre-defined list of barcode sequences. Read trimming, genome alignment (A. thaliana reference genome: TAIR10), counting, and summarization were performed by mappa_analyzer with default parameters
Assembly: TAIR10
Supplementary files format and content: The files *selection_WellList.txt contain the barcode sequences used for each well, and the quality associated to each of them.
Supplementary files format and content: A matrix generated by mappa_analyzer, where rows representing genes and columns barcodes/nuclei

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: For sterilization, all plant seeds used were frozen at -20 ℃ overnight, and the chlorine gas method was applied to the surface of the seeds under a fume hood through the reaction between NaClO and HCl. To synchronize and promote germination, after sterilization, seeds were stratified on soil and incubated at 4℃ for 2 days in the dark before moving to the growth chamber. Then, plants were grown in the growth chamber under long-day conditions (16hr light, 8hr dark) at 21 ℃, with the humidity around 60%.

extract_protocol:
Frozen inflorescences were crushed into small pieces manually and transferred to a gentleMACS M tube. Inflorescences were then dissociated by gentleMACS in Honda buffer (2.5% Ficoll 400, 5% Dextran T40, 0.4 M sucrose, 10 mM MgCl2, 1 µM DTT, 0.5% Triton X-100, 0.4 U/ µl RiboLock RNase inhibitor and cOmplete protease inhibitor). The homogenized plant tissue was filtered through a 70 µm strainer and nuclei were pelleted at 1000 xg for 6 min at 4°C. Most Honda buffer was removed nuclei pellet was resuspended in the remaining 500 µl Honda buffer. Nuclei were filtered again through a 35-µm strainer and stained with DAPI. Single and intact nuclei were sorted using a BD FACS Aria III gating on the DAPI signal
Single nuclei libraries were prepared using the SMARTer ICELL8 single-cell systems. Nuclei were double stained with NucBlue and dispensed into a barcoded SMARTer ICELL8 30 DE Chip by the NanoDispenser. Single nuclei wells were selected using the ICELL8 Imaging Station manually with the support of CellSelect software. Nuclei were selected for library preparation. RT-PCR reaction was done with the SMARTer ICELL8 30 DE Reagent Kit and cDNA was pooled from the chip and concentrated using the Zymo DNA Clean & Concentrator kit. cDNA was then used to construct the DNA libraries using the Illumina Nextera XT kit, followed by AMPure XP bead purification. A Qubit dsDNA HS Assay Kit and a KAPA Library Quantification Kit were used for library DNA quantification, and the Agilent High Sensitivity D1000 ScreenTape Assay was used for library DNA size assessment.

treatment_protocol: Plants were daily induced by Dex solution (2 μM Dexamethasone and 0.016% Silwet L-77) after bolting 0.5 cm to 3 cm tall, then inflorescences from the main stem were collected before DEX-induction (0 day), at 2 days, 4 days, and 8 days after the first induction. Around 20 inflorescences were collected for each sample and used for nuclei isolation.

value: floral tissue

tag: ecotype

value: Ler

tag: age

value: 3-4 weeks after germination

value: pAP1:AP1-GR ap1-1 cal-1

value: 8 days after DEX-induction


title: Cell_0294


title: Porcine VIC cultured in growth medium, replicate 1

description: Library name: pVIC_GM_Ctr1


title: 205333480092_R04C01, Brainstem, Wildtype_P21


title: KO18L_liver


title: Day4

value: 4 days after DEX-induction


title: Cell_0293


title: 205291550061_R06C01, Brainstem, Wildtype_P21


title: KO15L_liver


title: KO16L_liver


title: 205291550061_R05C01, Brainstem, Wildtype_P21


title: Cell_0291


title: WT22L_liver

value: WT


title: KO14L_liver


title: 205291550061_R04C01, Brainstem, Wildtype_P21


title: Cell_0290


title: 205537640002_R06C01, Brainstem, Wildtype_P14


title: 205333480092_R05C01, Brainstem, Wildtype_P21


title: KO13L_liver


title: Cell_0299


title: 205537640002_R05C01, Brainstem, Wildtype_P14


title: WT_24_kidney

source_name: kidney

value: kidney


title: WT_23_kidney


title: WT L1 noUV CPD Damage-seq Rep1

city: Chapel Hill

first: Cansu

last: Kose

state: NC

address: 120 Mason Farm Rd.

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

description: Library name: WT L1 noUV CPD Damage-seq Rep1

data_processing:
Damage-seq reads were trimmed to remove adaptor sequences by Cutadapt, paired-end reads were aligned with Bowtie with parameters ‐‐nomaqround, ‐‐phred33-quals, -m 4, -X 1000, ‐‐seed123. For each sample, duplicated reads were reduced to a single read. Damage sites were identified as the two nucleotides upstream of each fragment. Using custom scripts, reads were trimmed to the first 4 nucleotides from the 5’ end and slopped 6 nucleotides upstream to generate 10 nucleotide-long genomic regions with the damaged nucleotide in the middle. Processed bed files include the Damage-seq reads with dipyrimidines at the expected damage position.
Assembly: Caenorhabditis elegans (ce11)
Supplementary files format and content: dipyrimidine selected bed files

organism: Caenorhabditis elegans

source_name: whole-organism

growth_protocol: L1 worms were grown on NGM plates and fed with E. coli bacteria

extract_protocol:
L1 stage worms were irradiated with 4 kJ/m2 UVB at collected in M9 buffer at indicated repair times. Worms were washed 3 times with M9 buffer and then, genomic DNAs were isolated with QIamp DNA Mini Kit/tissue protocol. Ultrasonic fragmented genomic DNAs were purified using an equal volume of HighPrep PCR beads (MagBio). Purified DNA (~1 µg) was used for end-repair and dA-tailing and adaptor ligation (NEBNext Ultra II DNA Library Prep Kit) following manufacturer’s instructions. Damage-containing DNA fragments were purified with either anti-(6-4)PP (Cosmo Bio, cat. no. CAC-NM-DND-002) or Anti-CPD (Cosmo Bio, cat. no. CAC-NM-DND-001).
The purified DNA was primer extended in the presence of 30 pmol Bio3U (biotin elongation primer, 5′-bio-AGAGTG/dU/GACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′) using NEBNext Q5 Hot Start HiFi PCR Master Mix. Next, undamaged DNA strands were captured by 20 pmol (2 µL) of SH oligo (SH, Subtractive hybridization, 5′-bio-NNGACTGGTTCCAATTGAAAGTGCTCTTCCG-SpC-3′), DNAs were purified using phenol-chloroform extraction and ethanol precipitation. The DNA was then ligated to a second adaptor ligation using T4 DNA ligase HC (Thermo) at 16 °C overnight. After quality check, the DNA samples were purified with HighPrep PCR beads, and ligated DNAs were PCR amplified by NEBNext Ultra II PCR Master Mix with NEBNext Multiplex Oligos for Illumina (New England Biolabs). The PCR libraries were purified with HighPrep PCR beads. Libraries were sequenced by an Illumina NextSeq2000P2 with 50-bp.

value: whole-organism

value: wildtype

tag: antibody

value: anti-CPD


title: Cell_0288


title: Day2

value: 2 days after DEX-induction


title: Cell_0287


title: Cell_0292


title: WT_22_kidney


title: 205333490001_R06C01, Brainstem, Wildtype_P14

value: Brainstem


title: 205537640002_R04C01, Brainstem, Wildtype_P14


title: WT L1 noUV 64 Damage-seq Rep1

description: Library name: WT L1 noUV 64 Damage-seq Rep1


title: UdRPC_UM30_OSN

type: RNA

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

label: biotin

source_name: Urine-derived renal progenitor cells (UdRPCs) with episomal reprogramming

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The iPSCs were cultured on Matrigel coated culture dishes using StemMacs medium.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: Episomal transfection of combination plasmids containing POU5F1/SOX2/NANOG.

value: UdRPCs supplemented with POU5F1(OCT4)/SOX2/NANOG


title: WT_20_kidney


title: WT L1 noUV CPD Damage-seq Rep2

description: Library name: WT L1 noUV CPD Damage-seq Rep2


title: Day0

value: no induction


title: UM51_iPSCs

description: replicate 1

source_name: induced pluripotent stem cells (iPSCs) derived from UdRPCs

value: UM51 iPSCs


title: Cell_0285


title: 205333490001_R05C01, Brainstem, Wildtype_P14


title: 205333490001_R04C01, Brainstem, Wildtype_P14


title: Cell_0289


title: Cell_0284


title: WT L1 nak CPD Damage-seq Rep2

description: Library name: WT L1 nak CPD Damage-seq Rep2

value: nak


title: 205291550098_R06C01, Brainstem, Wildtype_P0


title: WT_19_kidney

value: whole tissue


title: WT L1 noUV 64 Damage-seq Rep2

description: Library name: WT L1 noUV 64 Damage-seq Rep2


title: KO_18_kidney


title: KO_16_kidney


title: 205291550098_R05C01, Brainstem, Wildtype_P0


title: UdRPC_UM30

description: replicate 1

source_name: Urine-derived renal progenitor cells (UdRPCs)

value: UdRPCs ctrl


title: WT L1 nak 64 Damage-seq Rep2

description: Library name: WT L1 nak 64 Damage-seq Rep2


title: KO_15_kidney


title: WT L1 nak CPD Damage-seq Rep1

description: Library name: WT L1 nak CPD Damage-seq Rep1


title: 205291550098_R04C01, Brainstem, Wildtype_P0


title: Cell_0286


title: Cell_0281


title: Cell_0282


title: KO_14_kidney


title: Cell_0280


title: WT L1 nak 64 Damage-seq Rep1

description: Library name: WT L1 nak 64 Damage-seq Rep1


title: 205291550084_R05C01, Brainstem, Wildtype_P0


title: KO_13_kidney


title: xpc-1 L1 48 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed

library_source: other

data_processing:
XR-seq reads were trimmed to remove adaptor sequences by Cutadapt, and then duplicated reads were removed by fastx_toolkit / 0.0.14. Trimmed reads were aligned to the C. elegans (ce11 ENSEMBL (WBcel235, Gen Bank assembly accession: GCA_000002985.3) genomes using Bowtie2 with arguments -f -very-sensitive. We only keep reads that: (i) have mapping quality greater than 20; (ii) are from chromosome I, II, III, IV, V, and X; and (iii) are of length 21-28 bp for downstream analysis after plotting nucleotide distribution and read length distribution of all mapped reads.
genome build/assembly: Caenorhabditis elegans (ce11)
processed data files format and content: stranded bedGraph

molecule: other

extract_protocol:
L1 stage worms were irradiated with 4 kJ/m2 UVB at collected in M9 buffer at indicated repair times. Worms were washed 3 times with M9 buffer and then, the pelleted worms were then incubated for 2 h at 62 °C with 450 μl of Worm Hirt Lysis Buffer (0.15M Tris pH 8.5, 0.1M NaCl, 5mM EDTA, 1% SDS) and 20 μl of Proteinase K (NEB, cat. no. P8107S). Subsequently, 120 μl of 5M NaCl was added, and the mixture was inverted to ensure proper mixing, followed by an overnight incubation and one hour centrifugation at 4 °C. Supernatant was treated with Ribonuclease A (Sigma-Aldrich, cat. no. R4642) and Proteinase K. Next, DNA is precipitated using phenol-chloroform extraction and ethanol precipitation, resolved in TE and incubated with anti-(6-4)PP (Cosmo Bio, cat. no. CAC-NM-DND-002) or anti-CPD (Cosmo Bio, cat. no. CAC-NM-DND-001), antibodies at 4°C overnight. Purified excised oligonucleotide containing either (6-4)PP or CPDs were processed for XR-seq libraries.
Purified excised oligomers were ligated with adaptors. Ligation products were subjected to immunoprecipitation with anti-CPD or anti-(6-4)PP antibodies. Purified DNA were repaired by (6-4)PP photolyase or CPD photolyase. Repaired DNA were PCR-amplified by Kapa Hifi HotStart ReadyMix with RP1 and RPIn (n means different indexsequences, compatible with Illumina TrueSeq small RNA kit) for 15 cycles. The PCR products were  subjected to electrophoresis in a 10% native polyacrylamide gel in 1x TBE. Gel slices corresponding to 130-to 155-nt fragments were excised. The DNA was eluted. Libraries were pooled together and sequenced in a NextSeq 2000 platform.

tag: time after_uvb

value: 48 hours


title: Cell_0279


title: 205537640001_R05C02, Primarytumor, Rosa26_creERT2_Smarcb1

value: Primarytumor


title: Cell_0153


title: 205291550084_R04C01, Brainstem, Wildtype_P0


title: Cell_0283


title: xpc-1 L1 24 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed

data_processing:
XR-seq reads were trimmed to remove adaptor sequences by Cutadapt, and then duplicated reads were removed by fastx_toolkit / 0.0.14. Trimmed reads were aligned to the  C. elegans (ce11 ENSEMBL (WBcel235, Gen Bank assembly accession: GCA_000002985.3) genomes using Bowtie2 with arguments -f -very-sensitive. We only keep reads that: (i) have mapping quality greater than 20; (ii) are from chromosome I, II, III, IV, V, and X; and (iii) are of length 21-28 bp for downstream analysis after plotting nucleotide distribution and read length distribution of all mapped reads.
Assembly: Caenorhabditis elegans (ce11)
Supplementary files format and content: stranded bedGraph

value: 24 hours


title: infected mice, replicate2, ScRNAseq

city: Jinan

first: Yaxiao

last: Liu

state: Shandong

address: Wenhuaxi Road 107

institute: Qilu hospital of Shandong University

library_source: transcriptomic single cell

data_processing:
Then Seurat v2.3 was used for dimension-reduction and clustering.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: bladder

extract_protocol:
Mice were sacrificed by cervical vertebra dislocation and bladder was removed. The fresh bladders were washed with cold phosphate buffered saline (PBS), dissected, minced, and incubated in 20 mg/ml dispase II (sigma D4693), 1 mg/ml DNaseI (solarbio D8071) and 0.5 mg/ml Liberase TL (roche 5401020001) solution at 37°C for 2 hours. The digested tissue was homogenized by vigorous shaking and filtered through 100 μm cell strainer. Mononuclear cells were then harvested from the interphase of an 80% and 40% Percoll gradient after a spin at 2500 rpm for 20 min at room temperature. CD16/32 antibody (eBioscience) was used to block the non-specific binding to Fc receptors before CD45.2 (1:200, Biolegend 109808) antibody staining. The live and dead cells were discriminated by Live and Dead violet viability kit (Invitrogen). Fluorescent cell sorting was used to attain living CD45+ single-cell suspensions.
Single-cell suspensions were loaded onto microfluidic devices, and single-cell RNA-sequencing (scRNA-seq) libraries were constructed according to the Singleron GEXSCOPE™ protocol in the GEXSCOPE™ Single-Cell RNA Library Kit (Singleron Biotechnologies). Pools were sequenced on Illumina novaseq6000 with 150 bp paired end reads. Raw reads were processed with fastQC and fastp to remove low-quality reads. Unique molecular identifiers (UMI) and cell barcodes were extracted after filtering out reads without poly-A tails. Poly-A tails and adapter sequences were then trimmed by cutadapt, and the reads that met quality control standards were matched to the reference genome mm10 using STAR.

value: bladder

value: CD45+ immune cell

tag: infection

value: UPEC


title: xpc-1 L1 48 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed

value: whole-organism


title: infected mice, replicate1, ScRNAseq


title: 205307790110_R04C01, Primarytumor, Rosa26_creERT2_Smarcb1


title: 205307790110_R02C01, Primarytumor, Rosa26_creERT2_Smarcb1


title: Cell_0152


title: Cell_0151


title: xpc-1 L1 8 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed

value: 8 hours


title: xpc-1 L1 24 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed

value: anti-CPD


title: Cell_0150


title: normal mice, replicate2, ScRNAseq

value: control


title: 205291550084_R06C01, Brainstem, Wildtype_P0

value: Brainstem


title: Cell_0149


title: xpc-1 L1 8 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: xpc-1 L1 1 hr CPD XR-seq Rep2

description: raw files are adaptor-trimmed

value: 1 hour


title: MCAO-QO-83-2, replicate2, snRNA-seq

city: Shijiazhuang

first: Huiran

last: Zhang

state: Hebei

address: 361 Zhongshan East road

institute: Hebei Medical University

description: 10x Genomics

data_processing:
For each sample, the quality of produced Fastq data was checked by FastQC v0.11.9. Raw scRNA-seq data was passed to the Cell Ranger 'count' pipeline v7.0.0 to generate the expression matrix with default settings.
Seurat v4.0.6 was used for processing the expression matrix generated by the Cell Ranger software. Processes included logarithmic normalization, picking out variable genes for PCA, non-linear reduction of dimensionality and clustering of cells. Integration of datasets was completed by the harmony algorithm v0.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

growth_protocol: Adult male C57BL/6 mice (6–8 weeks) were purchased from Liaoning Changsheng biotechnology (Liaoning, China). They were housed in groups of five per cage in a controlled animal facility maintained at a temperature of 23°C ± 2°C and a humidity range of 30–50%. The mice followed a 12-hour light/dark cycle and had ad libitum access to food and water. Mice weighing 21 ± 0.5 g were randomly assigned to different experimental groups in a blinded manner with regards to the administrated treatments. All animal procedures were conducted in accordance with the guidelines set by the Animal Care and Use Committee of Hebei Medical University and approved by the Animal Ethics Committee of Hebei Medical University.

extract_protocol:
For single-nucleus RNA sequencing experiments, we dissected the nuclei from frozen tissues (mouse) with Lysis buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2) plus RNase inhibitor, liberated cellular nuclei by mechanical force with a glass dounce tissue grinder. Nuclei were resuspended in a Nuclei Wash & Resuspension Buffer (1% BSA Solution, 0.2U/μL RNase Inhibitor, 1XPBS). Trypan blue and the Countess II FL Automated Cell Counter/microscopy were used to assess nucleus viability and concentration. Lastly, target nuclei concentration of 700-1,200 nuclei/µL was achieved for loading onto the chromium controller of the 10xGenomics platform. Approximately, 1.6x104 isolated nuclei and enzyme gel-beads were packed into a single oil droplet for single-cell RNA-seq library construction.
Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 700-1200cells/uL (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol.

treatment_protocol: A synthesized quantity of 3 mg of QO-83 was dissolved in 10 μl DMSO and then diluted with 1 ml βCD. The resulting mixture was subjected to ultrasonication at 40 Hz for 5 min until QO-83 is completely dissolved. Subsequently, 9 ml of βCD was added to achieve a solution of QO-83 with a concentration of 0.3 mg/ml. This stock solution was then further diluted to the desired concentration as per experimental requirements. QO-83 was administered intraperitoneally (i.p) at 0.2 ml/20 g body weight. Male C57BL/6 mice were anesthetized with 0.2 ml 1% sodium pentobarbital administrated intraperitoneally. Following anesthesia, a midline ventral neck incision was made to expose and isolate the right common carotid artery as well as the external carotid artery. Both arteries were subsequently ligated. Ischemic conditions were induced by gently inserting a silicone-coated monofilament (0.19 mm, 7–0; Doccol, USA) through the external carotid artery into the internal carotid artery. The monofilament was advanced until a slight resistance was encountered, signifying occlusion of the middle cerebral artery (MCA). After a duration of 90 min of induced ischemia, the monofilament was removed to allow for reperfusion. In the case of sham-operated mice, only the neck skin was incised and blood vessels were exposed, without any manipulation of the vasculature.

value: Brain

value: Male

value: c57 wide type mouse

value: ischemic model with QO-83


title: MCAO-QO-83-1, replicate1, snRNA-seq

description: 10x Genomics


title: 207017570061_R06C02, Primarytumor, R26_SHH

source_name: Primarytumor


title: Cell_0148


title: 207017570061_R05C02, Primarytumor, R26_SHH


title: MCAO-βCD-2, replicate2, snRNA-seq

description: 10x Genomics

value: ischemic model with vehicle


title: 207017570061_R04C02, Primarytumor, R26_SHH


title: xpc-1 L1 1 hr CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: Cell_0147


title: 205537640001_R04C02, Primarytumor, Sox2_creERT2_Smarcb1


title: 205537640001_R06C02, Primarytumor, Rosa26_creERT2_Smarcb1


title: Cell_0146


title: MCAO-βCD-1, replicate1, snRNA-seq

description: 10x Genomics


title: sham, replicate1, snRNA-seq

description: 10x Genomics

value: sham


title: xpc-1 L1 5 min CPD XR-seq Rep1

description: raw files are adaptor-trimmed

value: 5 minutes


title: xpc-1 L1 5 min CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: Cell_0145


title: normal mice, replicate1, ScRNAseq


title: scATAC-seq (10X Multiome) 4

city: La Jolla

first: Ferhat

last: Ay

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: 10x Genomics Multiome

data_processing:
mm10
Assembly: Filtered feature-barcode gene expression matrix in HDF5 format. Contains the raw count matrix in a "sparse matrix format", as well as cell barcodes and gene names.
Supplementary files format and content: ATAC-seq fragment file generated from the multi-omics data.
Supplementary files format and content: Index of the ATAC-seq fragment file.
Supplementary files format and content: Cell barcodes.
Supplementary files format and content: Contains feature names (gene names and peaks). Gene name is defined by the reference GTF. Peaks are denoted as "contig:start-end". The third column identifies the type of feature, which will be one of Gene Expression or Peaks
Supplementary files format and content: Feature-barcode matrix using sparse formats.

source_name: Joints

extract_protocol:
Nuclei suspensions are incubated in a Transposition Mix that includes a Transposase. The Transposase enters the nuclei and preferentially fragments the DNA in open regions of the chromatin. Simultaneously, adapter sequences are added to the ends of the DNA fragments. Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression (GEX) library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library.  GEMs are generated by combining barcoded Gel Beads, transposed nuclei, a Master Mix, and Partitioning Oil on a Chromium Next GEM Chip J.
Chromium Single Cell Multiome ATAC libraries comprise double stranded DNA with standard Illumina® paired-end constructs which begin with P5 and end with P7. Sequencing these libraries produces a standard Illumina® BCL data output folder that includes paired-end Read 1N and Read 2N used for sequencing the DNA insert, 8 bp sample index in the i7 read, and 24 bp in the i5 read to cover the 16 bp 10x Barcode and 8 bp Spacer.
Chromium Single Cell Multiome Gene Expression libraries comprise cDNA insert with standard Illumina® paired-end constructs which begin with P5 and end with P7. Sequencing these libraries produces a standard Illumina® BCL data output folder. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI, while 10 bp i5 and i7 sample index sequences are the sample index reads. TruSeq Read 2 is used to sequence the insert
RNA-Seq and ATAC-seq
We processed the 10x Multiome datasets using cellranger-arc (version 2.0.1) routines mkfastq, count and aggr, with respect to the reference genome mm10. The cellranger-arc output gene expression matrices and chromatin accessibility fragment files were then exported to Signac (version 1.6.0). We used mm10 reference genome and EnsDb.Mmusculus.v79 annotation in Signac. To remove any low-quality cells, we only retained the cells having RNA count between 1000 and 25,000, ATAC count between 1000 and 100,000, nucleosome signal < 2 and TSS enrichment > 1. We also removed any ATAC-seq signal from non-standard chromosomes, and inferred the ATAC-seq peaks by MACS2. Gene expression (RNA) was normalized using the routine SCTransform. ATAC-seq data was normalized by the routines RunTFIDF and RunSVD.

treatment_protocol: CD4 cell were isolated from TriTh17 mice and adoptive transferred in Rag2-KO mice (now Rag2-KO-CD4). Arthitis was triggered with 20mg of mannan. After arthitis plateaued, IL17a caputure assay was performed to capture Th17 cells (IL-17a APC positive and IL-17aCre tdTomato positive) and exTh17 cells (IL-17a APC negative and IL-17aCre tdTomato positive). Cells were stimulated with PMA-Ionomycin and then cell sorted from arthitic mice from    joints for 10X Multiome

value: Joints

value: TriTh17 - Rag2-KO

value: 12 weeks


title: scATAC-seq (10X Multiome) 3

description: 10x Genomics Multiome


title: 205307790110_R03C01, Primarytumor, Rosa26_creERT2_Smarcb1

value: Primarytumor


title: xpc-1 L1 48 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed

value: whole-organism

value: 48 hours


title: Cell_0144


title: scATAC-seq (10X Multiome) 2

description: 10x Genomics Multiome


title: Cell_0143


title: xpc-1 L1 24 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed

value: 24 hours


title: xpc-1 L1 48 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: 207097260046_R02C01, Primarytumor, R26_Myc


title: scATAC-seq (10X Multiome) 1

description: 10x Genomics Multiome


title: 207097260046_R03C01, Primarytumor, R26_Myc


title: Cell_0141


title: xpc-1 L1 8 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed

value: 8 hours


title: Cell_0139


title: Lymph nodes exTh17_Sample 14

data_processing:
RNA-seq data was processed by our custom pipeline (https://github.com/ay-lab/RNA_SEQ_PIPELINE). Input fastq files were processed by fastp for QC analysis. Paired-end RNA-seq reads were aligned with respect to the mm10 reference genome using the default parameters of STAR (version 2.7.3a). GENCODE v23 GTF annotation file was used as reference. STAR quantMode geneCounts was used to estimate the gene counts. The raw gene counts from individual samples were used with DESeq2 (version 1.34.0) to identify differentially expressed (DE) genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: CD4 subset

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA kit
Nextera XT DNA Library Prep

treatment_protocol: CD4 cell were isolated from TriTh17 mice and adoptive transferred in Rag2-KO mice (now Rag2-KO-CD4). Arthitis was triggered with 20mg of mannan. After arthitis plateaued, IL17a caputure assay was performed to capture Th17 cells (IL-17a APC positive and IL-17aCre tdTomato positive) and exTh17 cells (IL-17a APC negative and IL-17aCre tdTomato positive). Cells were stimulated with PMA-Ionomycin and then cell sorted from arthiticmice from lymph nodes and  joints for Bulk RNA-Seq

value: CD4 subset

value: PMA-Iono stimulation on T cell

tag: time

value: day 61  to 69 days post arthitis


title: xpc-1 L1 8 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: 206448030020_R04C01, Primarytumor, ASP_TFE_P53

tag: tissue


title: Joint Th17_Sample 15


title: Cell_0138

data_processing:
Raw fastq files were obtained by bcltoFastq conversion (version 2.20.0.422)
Fastq files were aligned to the mm10 reference genome using STAR aligner (version 2.7.9a) with the argument ‘STARsolo’. This argument allowed simultaneous mapping of reads and quantification of gene expression. The reference genome and gene transfer format (GTF) file were downloaded from 10x genomic webpage at (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz).
The output of ‘STARsolo’ was loaded into R (version 4.1.0) using the Bioconducter package DropletUtils (version 1.12.1).
Downstream analyses were done in R using SingleCellExperiment (version 5271.14.1) and Seurat (version 4.0.6).
Cells with <2000 detected genes, >15% mitochondrial content and > 10% hemoglobin percentage were excluded.
For isoform analysis, fastq files of selected 432 cells (46 cells from HE-HSC (AGM), 198 from HE-LMP (YSm), and 188 cells from HE-EMP (YSb)) were aligned and quantifed using Salmon 1.4.0  in Mapping mode. GRCm39 M32 mouse reference genome, transcriptome, and GTF file were downloaded from GENCODE website. Resulting quant.sf files were fed into IsoformSwitchAnalyzer  2.01.07 where importIsoformExpression function was used to give TMM normalized abundance values.
Assembly: GRCm39 M32 Gencode reference for Isoform Analysis and mm10 10X genomics reference for gene level analysis
Supplementary files format and content: RDS file having log normalized counts for each sample-gene level analyses (1494 cells)
Supplementary files format and content: RDS file having TMM normalized abundance for each sample used for isoform analyses (432 cells)

tag: sequencing run


title: scRNAseq (10X Multiome)

description: 10x Genomics Multiome


title: 206448030020_R03C01, Primarytumor, ASP_TFE_P53


title: xpc-1 L1 1 hr (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed

value: 1 hour


title: xpc-1 L1 1 hr (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: xpc-1 L1 24 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: 205307790110_R01C01, Primarytumor, Rosa26_creERT2_Smarcb1


title: Joint exTh17_Sample 16


title: Cell_0134


title: Joint Th17_Sample 11


title: Cell_0133


title: 206448030020_R02C01, Primarytumor, ASP_TFE_P53


title: Cell_0142


title: Lymph nodes Th17_Sample 13


title: Cell_0135


title: xpc-1 L1 5 min (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: Cell_0137


title: Cell_0136


title: Joint exTh17_Sample 12


title: csb-1 L1 48 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed

value: anti-CPD


title: xpc-1 L1 5 min (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: Lymph nodes Th17_Sample 9


title: csb-1 L1 24 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: Cell_0131


title: 206448030020_R06C02, Primarytumor, ASP_TFE_p53_Neo_1


title: 207097260046_R01C01, Primarytumor, R26_Myc


title: 206448030020_R06C01, Primarytumor, Pax3_Foxo1


title: csb-1 L1 8 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: csb-1 L1 48 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: 206448030014_R05C02, SAMprimarycells, Pax3_Foxo1

source_name: SAMprimarycells

value: SAMprimarycells


title: 206448030020_R05C01, Primarytumor, ASP_TFE_P53


title: 206448030020_R02C02, Primarytumor, Pax3_Foxo1


title: Lymph nodes exTh17_Sample 10


title: Cell_0132


title: 206448030014_R04C02, 3Dcellline, Pax3_Foxo1


title: csb-1 L1 24 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: 206448030020_R01C02, Primarytumor, Pax3_Foxo1


title: Cell_0128


title: Joint exTh17_Sample 8


title: Cell_0127


title: 206448030014_R06C02, SAMprimaryfragments, Pax3_Foxo1

source_name: SAMprimaryfragments

value: SAMprimaryfragments


title: Cell_0130


title: Joint Th17_Sample 7


title: Cell_0126


title: Joint Th17_Sample 3


title: csb-1 L1 5 min CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: 206448030002_R03C02, 2Dcellline, Pax3_Foxo1


title: Lymph nodes exTh17_Sample 2


title: Cell_0129


title: 206448030001_R02C01, Primarytumor, Pax3_Foxo1


title: Cell_0124


title: 206448030014_R03C02, Primarytumor, Pax3_Foxo1


title: csb-1 L1 8 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: aP2-Cre tdTomato HL

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: ATom hindlimb tom+ -2122760

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38(mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: FACS sorted Tomato positive endothelilal cells

extract_protocol:
SCM or hindlimb muscles were dissected and manually dissociated and digested for 1 hour at 37 C in 2 U/mL collagenase B (Roche, #11088831001), Dispase II (Roche, #04942078001), 50 mM HEPES/KOH pH 7.4, 150 mM NaCl. Cells were then resuspended in 2x volume 10% FBS  in PBS to inactivate digestion enzymes. Samples were filtered through 70 uM filter, spun and supernatant spun again. Then filtered through a 40 uM filter to yield a single cell suspension. Cells were spun again and resuspended on 0.04% BSA in PBS prior to FACS. Live tdTomato+ cells were isolated for downstream single cell RNA sequencing. DAPI was used as a live/dead marker. Data were aquired on FACS Aria cell sorter and analyzed with FACSDIva and FlowJo software.
Single cell GEMM isolation, cDNA preparation and library preparation was performed according to manufacturer's instructions for single cell 3' v3.1 10X Genomics kit.


title: csb-1 L1 1 hr CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: csb-1 L1 48 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: Joint exTh17_Sample 4


title: csb-1 L1 1 hr CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: Lymph nodes Th17_Sample 5


title: Cell_0122

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol.
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)


title: Cdh5-Cre tdTomato SCM

description: CTom SCM tom+ -2234779

value: FACS sorted Tomato positive endothelilal cells


title: 206448030002_R04C02, 3Dcellline, Pax3_Foxo1

data_processing:
idat files were processed using the OpenSesame pipeline from the Sesame package
openSesame normalized beta values (see Supplementary file Geo_mset.txt at the foot of the GSE record)


title: 206448030001_R01C01, Primarytumor, Pax3_Foxo1


title: Lymph nodes exTh17_Sample 6


title: csb-1 L1 48 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: Cell_0120


title: PDR, CD31high, sample7

city: Chicago

first: Andrius

last: Kazlauskas

state: IL

address: 1855 W Taylor Street

department: Ophthalmology & Visual Sciences

institute: University of Illinois Chicago

description:
Library name: H7
Column name in PDR_CD31cells_counts.txt: H7

data_processing:
Data processing consisted of general quality-control using FastQC before reads were aligned to the v.hg38 human reference genome in a splice-aware manner using STAR.
The abundance of genomic features (e.g., genes) were quantified as raw counts based on read alignments using featureCounts.
Gene isoforms were quantified using Kallisto, using k-mer based pseudo-alignment and expectation maximization to probabilistically assign reads to isoforms.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: PDR CD31+ cells

extract_protocol:
Cells expressing the endothelial marker CD31 were isolated from vitrectomy cassette specimens collected from patients with end-stage proliferative diabetic retinopathy (PDR). Vitrectomy cassettes were collected following pars planar vitrectomy surgery performed as standard of care. To isolate the CD31+ populations, the material within the vitrectomy cassette was pelleted by centrifuging conical tubes at 1000xg for 5 min @ 4° C. The tubes were rotated 180° and spun again in all centrifugation steps. The red blood cells (RBC) were then lysed in RBC buffer (150mM ammonium chloride, 100mM sodium bicarbonate, 10mM EDTA disodium) for 10 minutes at room temperature. The pellet was then washed in cold PBS and centrifuged as before. The pellet was then digested using a cocktail of type II collagenase (3000U/mL, 100502 MP Biomedicals), DNase (600U/mL, 18047019 Thermo Fisher Scientific), and hyaluronidase (0.3%, 02100740 MP Biomedicals) in Buffer 1 (PBS + 1% BSA) for 50 min @ 37° C. The pellet was then washed in cold PBS and centrifuged as before. The pellet was reconstituted in Buffer 1 and passed over a 35 µm cell strainer (352235 Corning Life Sciences) to generate a single-cell suspension. The single-cell suspension was then mixed with magnetic Dynabeads coated with anti-CD31 antibody (4x107 beads, 11155D Invitrogen) and rotated for 20 min @ 4° C. The CD31+ cells were pulled down using a magnetic tube stand and washed three times with cold PBS. The isolated cells were then lysed with buffer RT+ (Qiagen), vortexed, and frozen for batch RNA isolation. RNA was isolated from the entire batch of samples simultaneously. Each sample underwent further homogenization using QIAshredder columns (79656 Qiagen) before being loaded onto a gDNA eliminator column (Qiagen). RNA was then extracted from the samples using the RNeasy Plus Micro Kit (74034 Qiagen).
Libraries were prepared and sequenced by the University of Chicago Genomics Facility.

value: PDR CD31+ cells

tag: cell subset

value: bevacizumab


title: csb-1 L1 24 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed

tag: cell type


title: csb-1 L1 5 min CPD XR-seq Rep1

description: raw files are adaptor-trimmed

tag: genotype

value: 5 minutes


title: csb-1 L1 24 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed

tag: treatment


title: Cell_0125


title: Cell_0121


title: C3

first: miaomiao

last: zheng

address: No. 168 Changhai Road, Yangpu District

institute: Changhai Hospital

description:
Library name: sample 9
Received daily intraperitoneal injections of 200 μl of the STING activator SR-717 solution (30 mg/kg) for one week, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: gene counts for each sample

source_name: bone

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: bone

value: 7 weeks

tag: Sex

value: male


title: PDR, CD31high, sample6

description:
Library name: H6
Column name in PDR_CD31cells_counts.txt: H6


title: Cell_0119

first: Georges

last: Lacaud

address: Wilmslow Raod

institute: Cancer Research UK Manchester Institute


title: C2

description:
Library name: sample 8
Received daily intraperitoneal injections of 200 μl of the STING activator SR-717 solution (30 mg/kg) for one week, replicate biosample 2


title: Cdh5-Cre tdTomato HL

description: CTom hindlimb tom+ -2234878


title: Cell_0123


title: csb-1 L1 8 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed

value: whole-organism


title: PDR, CD31high, sample4

description:
Library name: H4
Column name in PDR_CD31cells_counts.txt: H4

value: no anti-VEGF


title: Lymph nodes Th17_Sample 1

tag: strain

value: TriTh17 - Rag2-KO


title: csb-1 L1 8 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed

value: 8 hours


title: PDR, CD31high, sample3

description:
Library name: H3
Column name in PDR_CD31cells_counts.txt: H3


title: csb-1 L1 1 hr (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: PDR, CD31high, sample2

description:
Library name: H2
Column name in PDR_CD31cells_counts.txt: H2


title: csb-1 L1 1 hr (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: B3

description:
Library name: sample 6
Received an equal volume of 200 μl of PBS buffer as a control for one week, replicate biosample 3


title: PDR, CD31high, sample1

description:
Library name: H1
Column name in PDR_CD31cells_counts.txt: H1


title: C1

description:
Library name: sample 7
Received daily intraperitoneal injections of 200 μl of the STING activator SR-717 solution (30 mg/kg) for one week, replicate biosample 1


title: Cell_0118

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: PDR, CD31high, sample5

description:
Library name: H5
Column name in PDR_CD31cells_counts.txt: H5


title: Cell_0117


title: Cell_0116

description: SmartSeq2_Gene_log_normalized_counts.rds


title: B2

description:
Library name: sample 5
Received an equal volume of 200 μl of PBS buffer as a control for one week, replicate biosample 2


title: PDR, CD31low, sample5

description:
Library name: L5
Column name in PDR_CD31cells_counts.txt: L5

value: aflibercept


title: Cell_0115


title: csb-1 L1 5 min (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: PDR, CD31low, sample4

description:
Library name: L4
Column name in PDR_CD31cells_counts.txt: L4


title: Cell_0114


title: WT L1 48 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed

value: 48 hours


title: A3

description:
Library name: sample 3
Received daily intraperitoneal injections of 200 μl of the STING inhibitor H-151 solution (750 nmol) for one week, replicate biosample 3


title: PDR, CD31low, sample3

description:
Library name: L3
Column name in PDR_CD31cells_counts.txt: L3


title: Cell_0113


title: A2

description:
Library name: sample 2
Received daily intraperitoneal injections of 200 μl of the STING inhibitor H-151 solution (750 nmol) for one week, replicate biosample 2


title: PDR, CD31low, sample2

description:
Library name: L2
Column name in PDR_CD31cells_counts.txt: L2


title: A1

description:
Library name: sample 1
Received daily intraperitoneal injections of 200 μl of the STING inhibitor H-151 solution (750 nmol) for one week, replicate biosample 1


title: Cell_0112


title: PDR, CD31low, sample1

description:
Library name: L1
Column name in PDR_CD31cells_counts.txt: L1


title: Cell_0110


title: WT L1 24 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed

value: 24 hours


title: B1

description:
Library name: sample 4
Received an equal volume of 200 μl of PBS buffer as a control for one week, replicate biosample 1


title: WT L1 8 hrs CPD XR-seq Rep2

description: raw files are adaptor-trimmed

value: anti-CPD


title: Cell_0111


title: WT L1 24 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: SF10602, SHP099,2

first: Shi-yuan

last: Cheng

state: Illinois

address: 303 E. Superior Street, The Robert H. Lurie Cancer Center

institute: Northwestern Univeristy

description: treatment

data_processing:
Data were aligned to the human genome reference hg38 using HISAT2 v2.0.4.
Assembly: hg38
Supplementary files format and content: Count

growth_protocol: SF10602 cells were cultured in medium composed of 50% DMEM/F12 medium (Thermo Fisher Scientific, 11320-033), 50% Neurobasal medium (Thermo Fisher Scientific, 21103-049), supplemented with 50X B27 supplement (Thermo Fisher Scientific, 17504-044), 100X N2 supplement (Thermo Fisher Scientific, 17502-048), 1X antibiotic-antimycotic (Thermo Fisher Scientific, 15240062), 5 mg/mL heparin (Sigma-Aldrich, 9041-08-1), 20 ng/mL EGF (Peprotech, 100-15R), and 20 ng/mL bFGF (Peprotech, 100-18B).

extract_protocol:
RNA was isolated using a Qiagen RNeasy Mini Kit following the manufacturer’s instructions.
We followed the manufacturer’s instructions for preparing the library using the NEBNext Poly(A) mRNA Magnetic Isolation Module, Ultra II RNA Library Prep Kit, and Multiplex Oligos (NEB, Cat #E7490, E7775, E6609).

treatment_protocol: SF10602 cells are treated with SHP099 (15 μM) or DMSO for 7 days.

value: IDH-mutant

value: WT


title: Cell_0109


title: astR-3-Orn/NH4

first: Lauren

middle: D

last: Palmer

address: 835 S Wolcott Ave

department: Microbiology and Immunology

description:
Library name: 3817-16
Ribo-zero depleted RNA-seq

data_processing:
Sequencing was performed on the Illumina NextSeq2000 platform using a 300 cycle flow cell kit to produce 2x150 bp paired reads. Read demultiplexing, read trimming, and run analytics were performed using DRAGEN v3.10.12, an on-board analysis software on the NextSeq2000.
Assembly: NCBI accession numbers: CP012004.1, CP012005.1
Supplementary files format and content: tab delimited file includes: Geneid, Chromosome, Start, End, Strand, Length, FeatureCounts

organism: Acinetobacter baumannii

source_name: ATCC 17978VU

growth_protocol: Overnight cultures were started from a single colony inoculated in 3 mL LB and grown with shaking at 37 degrees. Overnight cultures were diluted 1:1000 into 10 mL LB and grown for 3.5 h at 37 degrees with shaking.

extract_protocol:
Pellets were thawed on ice and resuspended in 100 µL of RNAse free TE Buffer pH 8.0. The samples were lysed and homogenized in a Yellow Bullet Blender tube (MidSci) at Bullet Blender (NextAdvance) speed 8 for 3 minutes. The Qiagen RNeasy was used to isolate and purify the RNA from the samples, following the manufacturer’s protocol.
Samples were prepared for sequencing using an Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Microbiome and unique dual indexes.

treatment_protocol: After 3.5 h of growth at 37ºC with shaking, cells were centrifuged at 4,137 x g for 5 minutes and washed twice with no-nitrogen 1X M9 salts59. Samples were resuspended in 1 mL of the 1X M9 salts with No Nitrogen and added to 9 mL of M9 media (CSHL protocols) containing 16.5 mM concentrations of carbon sources (ornithine or succinate) and 18.6 mM of nitrogen sources (ornithine or NH4), as well as 0.1X Vishniac trace minerals (Vishniac and Santer, 1957). The resuspended cells were incubated in the media for 1 h at 37ºC. Cells were harvested by centrifugation at 4,137 x g for 10 min. Supernatant was discarded and residual liquid was pipetted out from the pellets. Pellets were stored at -80ºC until RNA extraction.

value: ATCC 17978VU


title: SF10602, SHP099,1

description: treatment


title: SF10602, Vehicle,2

description: control

value: DMSO


title: astR-3-Orn/Succ

description:
Library name: 3817-18
Ribo-zero depleted RNA-seq

value: Orn/Succ


title: WT L1 8 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: SF10602, Vehicle,1

description: control


title: Cell_0108


title: csb-1 L1 5 min (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed

value: 5 minutes


title: astR-2-Succ/NH4

description:
Library name: 3817-14
Ribo-zero depleted RNA-seq


title: Cell_0107


title: astR-2-Orn/Succ

description:
Library name: 3817-15
Ribo-zero depleted RNA-seq


title: astR-2-Orn/NH4

description:
Library name: 3817-13
Ribo-zero depleted RNA-seq


title: WT L1 1 hr CPD XR-seq Rep2

description: raw files are adaptor-trimmed

value: 1 hour


title: WT L1 48 hrs CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: WT L1 5 min CPD XR-seq Rep2

description: raw files are adaptor-trimmed


title: WT L1 1 hr CPD XR-seq Rep1

description: raw files are adaptor-trimmed


title: Cell_0106


title: 0905-TAZ B3

first: Thomas

middle: Kieran

last: Sears

address: 303 E. Superior St.

department: Neurological Surgery

institute: Northwestern University

description: Library name: 0905-TAZ B3

data_processing:
Raw reads were assessed for quality using FastQC and trimmed using Trim Galore v0.4.4 and Cutadapt v 1.14.
Aligned BAM files were generated using STAR and normalized TPM gene counts were generated using the Salmon algorithm
Assembly: hg38
Supplementary files format and content: Processed data files are presented as normalized TPMs

growth_protocol: Serum-free, non-adherent gliomasphere cultures in Glioma Stem Cell Media (GSCM)

extract_protocol:
RNA was extracted using Qiagen's RNEasy Plus Mini Kit
RNA libraries were constructed using Complete Genomics' DNBSEQ Fast RNA Library Preparation Kit

treatment_protocol: 500 nM belinostat for 24 hours in IDH1/2 mutant glioma cultures with lentivirus-mediated overexpression of YAP 5SA or TAZ 4SA

value: glioma stem-like cells

value: TAZ 4SA

value: 500 nM belinostat for 24 hours


title: 0905-TAZ B2

description: Library name: 0905-TAZ B2


title: astR-3-Succ/NH4

description:
Library name: 3817-17
Ribo-zero depleted RNA-seq


title: 0905-TAZ B1

description: Library name: 0905-TAZ B1


title: WT L1 5 min CPD XR-seq Rep1

description: raw files are adaptor-trimmed

value: whole-organism


title: astR-1-Orn/Succ

description:
Library name: 3817-12
Ribo-zero depleted RNA-seq


title: Cell_0103

description: SmartSeq2_Gene_log_normalized_counts.rds


title: astR-1-Orn/NH4

description:
Library name: 3817-10
Ribo-zero depleted RNA-seq


title: WT L1 48 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: Cell_0104


title: astR-1-Succ/NH4

description:
Library name: 3817-11
Ribo-zero depleted RNA-seq


title: 0905-TAZ V2

description: Library name: 0905-TAZ V2

value: DMSO vehicle for 24 hours


title: Cell_0102


title: WT L1 48 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: WT-3-Orn/Succ

description:
Library name: 3817-9
Ribo-zero depleted RNA-seq


title: WT L1 24 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: 0905-TAZ V3

description: Library name: 0905-TAZ V3


title: Cell_0105


title: 0905-TAZ V1

description: Library name: 0905-TAZ V1


title: Cell_0100


title: Cell_0097


title: WT-2-Orn/Succ

description:
Library name: 3817-6
Ribo-zero depleted RNA-seq


title: WT-3-Orn/NH4

description:
Library name: 3817-7
Ribo-zero depleted RNA-seq


title: 0905-YAP B1

description: Library name: 0905-YAP B1

value: YAP 5SA


title: WT L1 8 hrs (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed

value: 8 hours


title: WT-3-Succ/NH4

description:
Library name: 3817-8
Ribo-zero depleted RNA-seq


title: 0905-YAP B3

description: Library name: 0905-YAP B3


title: WT L1 24 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: Cell_0099


title: 0905-YAP B2

description: Library name: 0905-YAP B2


title: WT-2-Succ/NH4

description:
Library name: 3817-5
Ribo-zero depleted RNA-seq


title: WT L1 1 hr (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: WT L1 8 hrs (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: Cell_0096


title: 0905-YAP V3

description: Library name: 0905-YAP V3


title: Cell_0095


title: 0905-YAP V2

description: Library name: 0905-YAP V2


title: WT-2-Orn/NH4

description:
Library name: 3817-4
Ribo-zero depleted RNA-seq


title: Cell_0094


title: WT L1 1 hr (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed


title: WT L1 5 min (6-4)PP XR-seq Rep2

description: raw files are adaptor-trimmed


title: 0905-YAP V1

description: Library name: 0905-YAP V1


title: WT-1-Succ/NH4

description:
Library name: 3817-2
Ribo-zero depleted RNA-seq


title: Cell_0093


title: WT-1-Orn/NH4

description:
Library name: 3817-1
Ribo-zero depleted RNA-seq


title: WT L1 48 hrs CPD Damage-seq Rep2

data_processing:
Damage-seq reads were trimmed to remove adaptor sequences by Cutadapt, paired-end reads were aligned with Bowtie with parameters ‐‐nomaqround, ‐‐phred33-quals, -m 4, -X 1000, ‐‐seed123. For each sample, duplicated reads were reduced to a single read. Damage sites were identified as the two nucleotides upstream of each fragment. Using custom scripts, reads were trimmed to the first 4 nucleotides from the 5’ end and slopped 6 nucleotides upstream to generate 10 nucleotide-long genomic regions with the . Processed bed files include the Damage-seq reads with dipyrimidines at the expected damage position.
Assembly: Caenorhabditis elegans (ce11)
Assembly: Caenorhabditis elegans (ce11)
Supplementary files format and content: dipyrimidine selected bed files

value: 48 hours


title: 0905-GFP B3

description: Library name: 0905-GFP B3

value: GFP


title: C. Elegans, 4th generation Hypoxia, replicate 3

city: St. Louis

first: Eric

middle: Lieberman

last: Greer

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: 4th expo H3

data_processing:
Fastq files were checked for quality using FastQC before being filtered out with a Q score of 30 or above and trimmed for adapters using CutAdapt 4.0.
The trimmed reads were then aligned to the C. Elegans genome (WS235) using bowtie2 and samtools was used to convert sam outputs to sorted bam files.
FeatureCounts was used to count raw reads of genes using sorted bam files and count matrix is generated.
Assembly: WS235
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: whole worm, L4 stage

growth_protocol: Worms are grown on agar plates with OP50 bacteria and kept at 20 degrees C. To synchronize large plates of worms by lifestage, adult worms after laying eggs will be gently pippeted away with M9 buffer, leaving only the eggs on the bacterial lawn.

extract_protocol:
Frozen whole worm pellets are lysed and homogenized with TRI Reagent and a Kontes pellet pestle motor before total RNA is extracted using Direct-zol RNA Miniprep Kit from Zymo Research. mRNA is enriched from total RNA samples using NEXTFLEX Poly(A) Beads 2.0. In total 24 samples were prepared for RNA-seq libraries with 500 ng mRNA as starting material.
RNA-Seq libraries are prepared using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0.

treatment_protocol: Once at the L4 life stage, worms are either exposed to normoxia (kept in incubator with normal atmospheric oxygen levels) or hypoxia (0.1% oxygen) for 16 hours in an Eppendorf Galaxy 48R incubator. After 16 hours of exposure, hypoxia-treated worms are moved back into incubator with nomal oxygen levels. After normoxia or hypoxia exposure, worms are washed off the plate using M9 buffer and allowed to settle to the bottom and the excess buffer is removed. A small aliquot of the worm pellet is transferred onto a new agar plate to lay eggs and the rest of the pellet is frozen by dipping microcentrifuge tube into liquid nitrogen. This process is repeated for each generation and all worm pellets are stored at -80 degrees C until extraction.

value: whole worm, L4 stage

value: Hypoxia


title: 0905-GFP B1

description: Library name: 0905-GFP B1


title: Cell_0090

city: Manchester


title: WT L1 24 hrs CPD Damage-seq Rep2

value: anti-CPD

value: 24 hours


title: C. Elegans, 4th generation Hypoxia, replicate 2

description: 4th expo H2

value: WT


title: Cell_0088


title: Cell_0092


title: 0905-GFP B2

description: Library name: 0905-GFP B2


title: Cell_0091


title: WT L1 48 hrs CPD Damage-seq Rep1


title: 0905-GFP V2

description: Library name: 0905-GFP V2


title: WT-1-Orn/Succ

description:
Library name: 3817-3
Ribo-zero depleted RNA-seq

value: ATCC 17978VU

value: Orn/Succ


title: 0905-GFP V3

description: Library name: 0905-GFP V3


title: C. Elegans, 4th generation Normoxia, replicate 3

description: 4th expo N3

value: Normoxia


title: C. Elegans, 4th generation Normoxia, replicate 2

description: 4th expo N2


title: C. Elegans, 4th generation Hypoxia, replicate 1

description: 4th expo H1


title: Cell_0086


title: WT L1 8 hr CPD Damage-seq Rep1


title: WT L1 5 min (6-4)PP XR-seq Rep1

description: raw files are adaptor-trimmed

value: 5 minutes


title: WT L1 24 hrs CPD Damage-seq Rep1


title: Cell_0085


title: TS603-TAZ B3

description: Library name: TS603-TAZ B3

value: glioma stem-like cells

value: TAZ 4SA


title: Cell_0087


title: WT L1 0 h CPD Damage-seq Rep2

value: whole-organism


title: WT L1 8 hr CPD Damage-seq Rep2


title: TS603-TAZ B2

description: Library name: TS603-TAZ B2

value: 500 nM belinostat for 24 hours


title: 0905-GFP V1

description: Library name: 0905-GFP V1

value: DMSO vehicle for 24 hours


title: Cell_0084


title: C. Elegans, 3rd generation Hypoxia, replicate 3

description: 3rd expo H3


title: WT L1 48 hrs (6-4)PP Damage-seq Rep2


title: TS603-TAZ B1

description: Library name: TS603-TAZ B1


title: WT L1 0 h CPD Damage-seq Rep1


title: Cell_0083


title: TS603-TAZ V3

description: Library name: TS603-TAZ V3


title: Cell_0082


title: C. Elegans, 3rd generation Hypoxia, replicate 1

description: 3rd expo H1


title: TS603-TAZ V2

description: Library name: TS603-TAZ V2


title: WT L1 48 hrs (6-4)PP Damage-seq Rep1


title: C. Elegans, 4th generation Normoxia, replicate 1

description: 4th expo N1


title: WT L1 24 hrs (6-4)PP Damage-seq Rep2


title: Cell_0081


title: Cell_0080


title: TS603-TAZ V1

description: Library name: TS603-TAZ V1


title: C. Elegans, 3rd generation Normoxia, replicate 2

description: 3rd expo N2


title: C. Elegans, 3rd generation Normoxia, replicate 3

description: 3rd expo N3


title: TS603-YAP B3

description: Library name: TS603-YAP B3

value: YAP 5SA


title: TS603-YAP B2

description: Library name: TS603-YAP B2


title: Cell_0079


title: Cell_0078


title: TS603-YAP B1

description: Library name: TS603-YAP B1


title: Cell_0076


title: WT L1 8 hrs (6-4)PP Damage-seq Rep2

value: 8 hours


title: C. Elegans, 3rd generation Normoxia, replicate 1

description: 3rd expo N1


title: C. Elegans, 3rd generation Hypoxia, replicate 2

description: 3rd expo H2


title: C. Elegans, 2nd generation Hypoxia, replicate 3

description: 2nd expo H3


title: WT L1 8 hrs (6-4)PP Damage-seq Rep1


title: C. Elegans, 2nd generation Hypoxia, replicate 2

description: 2nd expo H2


title: TS603-YAP V3

description: Library name: TS603-YAP V3


title: C. Elegans, 2nd generation Hypoxia, replicate 1

description: 2nd expo H1


title: WT L1 0 h (6-4)PP Damage-seq Rep1


title: RPE, Young control, Replicate 1

city: Seoul

first: Hyewon

last: Chung

address: 120 Neungdong-ro, Gwangjin-gu

institute: Konkuk University

description:
Library name: lib-Y-C-1-RPE
Y-C-1-RPE_1

data_processing:
Raw sequencing reads were trimmed to remove adapters and low-quality bases, then aligned to the Mus musculus reference genome (GRCm38, Ensembl) using Bowtie2 v2.3.4.1. Transcript abundance was estimated with featureCounts v1.6.0, and expression levels were reported as read counts and fragments per kilobase of transcript per million mapped reads (FPKM). Differentially expressed genes (DEGs) were identified using DESeq2 (p-value < 0.05, fold-change cutoff 1.5), z-score normalized, and subjected to hierarchical clustering based on Pearson correlation with Perseus software (v.1.6.1.1). Functional enrichment analysis of DEGs was performed with g:Profiler using Gene Ontology Biological Processes (GO-BPs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and significant terms were selected using a Benjamini–Hochberg false discovery rate (FDR) threshold of 0.05. Enriched biological processes and pathways were visualized as networks in Cytoscape with the Enrichment Map plugin.
Assembly: GRCm38
Supplementary files format and content: tab-delimited xlsx file includes raw counts (RC) and FPKM

source_name: Retinal pigment epithelium

extract_protocol:
Total RNA from retinal pigment epithelial was extracted using TRIzol reagent according to manufacturer's instructions. 0.5 ug of total RNA was used to generate sequencing libraries.
0.5 µg of total RNA was used to generate sequencing libraries with the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., 20020599, San Diego, CA, USA).

value: Retinal pigment epithelium

value: young

value: Wild type

value: Control


title: WT L1 24 hrs (6-4)PP Damage-seq Rep1

source_name: whole-organism

value: 24 hours


title: TS603-YAP V2

description: Library name: TS603-YAP V2


title: Cell_0075


title: TS603-GFP B2

description: Library name: TS603-GFP B2

value: GFP


title: WT L1 0 h (6-4)PP Damage-seq Rep2


title: C. Elegans, 1st generation Hypoxia, replicate 3

description: 1st expo H3

value: whole worm, L4 stage

value: WT

value: Hypoxia


title: C. Elegans, 2nd generation Normoxia, replicate 3

description: 2nd expo N3

value: Normoxia


title: C. Elegans, 1st generation Hypoxia, replicate 2

description: 1st expo H2


title: TS603-GFP V3

description: Library name: TS603-GFP V3

value: glioma stem-like cells


title: C. Elegans, 2nd generation Normoxia, replicate 2

description: 2nd expo N2


title: Cell_0074


title: TS603-YAP V1

description: Library name: TS603-YAP V1


title: RPE, Young control, Replicate 2

description:
Library name: lib-Y-C-2-RPE
Y-C-2-RPE_1


title: TS603-GFP B3

description: Library name: TS603-GFP B3


title: Cell_0072


title: Cell_0077


title: C. Elegans, 1st generation Hypoxia, replicate 1

description: 1st expo H1


title: C. Elegans, 2nd generation Normoxia, replicate 1

description: 2nd expo N1


title: Cell_0071


title: RPE, Young control, Replicate 3

description:
Library name: lib-Y-C-3-RPE
Y-C-3-RPE_1


title: C. Elegans, 1st generation Normoxia, replicate 3

description: 1st expo N3


title: RPE, Old control, Replicate 3

description:
Library name: lib-Cont-3-RPE
Cont-3-RPE_1

value: aged


title: RPE, Vuti, Replicate 3

description:
Library name: lib-4112-3-RPE
4112-3-RPE_1

value: Vutiglabridin


title: TS603-GFP B1

description: Library name: TS603-GFP B1

value: 500 nM belinostat for 24 hours


title: RPE, Vuti, Replicate 2

description:
Library name: lib-4112-2-RPE
4112-2-RPE_1