title: Canine MCT, LCM-dissected mast cells

city: Ghent

first: Elise

last: Callens

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

description: Library name: Canine MCT

data_processing:
Pre-processing of the raw FASTQ files was conducted. Poly-A-trimming (cutadapt -a AAAAAAAAAA -m 20) and adapter removal (filtering pattern ' ATTGCGCAATG([AGCT]{3})(AAAAAAAAAA)') was performed on read 1 sequences. File synchronization was performed to maintain consistency between the filtered read 1 sequences and their corresponding index files (I1 and I2). Filtered data was then processed using zUMIs version 2.9.790. Reads were filtered for low-quality barcodes and UMIs (4 bases < phred 20, 3 bases < phred 20, respectively) and UMI-containing reads parsed by detection of the pattern (ATTGCGCAATG) while allowing up to two mismatches. Finally, within the zUMIs pipeline, filtered reads were mapped to the canine reference genome (Cfam release 111 version 1.0) using STAR version 2.7.11b. with the additional parameter '--clip3pAdapterSeq CTGTCTCTTATACACATCT'.
Raw, unfiltered FASTQ files are provided here. For downstream processing with zUMIs, the filtered FASTQ files should be used as input, together with the corresponding index barcode file.
Assembly: Cfam release 111 version 1.0
Supplementary files format and content: CanineMCT_raw_counts_all_samples.rds, rds file, raw counts for all samples
Supplementary files format and content: CanineMCT_barcodes.txt, txt file, barcodes for all samples, necessary for zUMIs processing

organism: Canis lupus familiaris

source_name: Canine mast cell tumor FFPE tissue biopsies

extract_protocol:
A separate RNA extraction step is omitted.
The LCM-FFPEseq protocol was used for library preparation. 12 µL of lysis buffer was added to each 0.2 mL adhesive cap PCR tube, containing 5% PEG 8000 (Sigma-Aldrich), 0.1% Triton X-100 (Sigma-Aldrich), 0.125 µM LCM-FFPEseq-specific oligo-dT primer (5’-Biotin-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3’, IDT), 0.5 mM dNTPs/each (Thermo Fisher Scientific), 0.5 U µL⁻¹ Recombinant RNase Inhibitor (Takara) and 0.025 µg µL⁻¹ Proteinase K (NEB). Volumes of PEG 8000, the oligo-dT primer, and dNTPs were adjusted to the RT volume, consistent with SS3X protocol specifications. After dispensing, the PCR tubes were centrifuged and subjected to a denaturation step of 50 minutes at 52°C followed by a proteinase K–heat inactivation step of 10 minutes at 72°C, and a hold at 4°C. Immediately following denaturation, 4 µL of the RT mix was dispensed to the tubes, composed of 25 mM TrisHCl pH 8.4 (Alfa Aesar), 30 mM NaCl (Thermo Fisher Scientific), 2.5 mM MgCl₂ (Thermo Fisher Scientific), 8 mM DTT (Thermo Fisher Scientific), 1.0 mM GTP (Thermo Fisher Scientific), 0.75 µM SS3X TSO (5’-Biotin—AGAGACAGATTGCGCAATGNNNNNNNNWWrGrGrG-3’, IDT), 0.5 U µL⁻¹ Recombinant RNase inhibitor (Takara), 2 U µL⁻¹ Maxima H Minus reverse transcriptase (Thermo Fisher Scientific), and 0.05 mM Proteinase K inhibitor (Sigma-Aldrich). The tubes were briefly centrifuged after RT mix dispensing. Reverse transcription was performed at 42°C for 90 minutes, followed by ten cycles of 50°C for 2 minutes and 42°C for 2 minutes, then 5 minutes at 85°C, and a hold at 4°C. Next, a PCR pre-amplification was conducted, with the addition of 24 µL PCR mix to each tube. The PCR mix consisted of 1× SeqAmp buffer (Takara), 0.025 U µL⁻¹ SeqAmp Polymerase (Takara), 0.5 µM SS3X forward primer (5’-CTACACGACGCTCTTCCGATCT-3’, IDT) and 0.1 µM LCM-FFPEseq-specific reverse primer (5’-GTCTCGTGGGCTCGGAGATGT-3’, IDT). PCR pre-amplification was performed as follows: initial denaturation at 95°C for 1 minute, followed by 19 cycles of 98°C for 10 seconds, 65°C for 30 seconds and 68°C for 4 minutes. The final elongation step was conducted at 72°C for 10 minutes. The number of PCR cycles for pre-amplification can be adapted based on the input and should be determined for each project. Subsequently, all tubes were transferred to a 96-well plate and purified using AMPure XP beads at a 0.7× ratio. Elution was performed in 16 µL of nuclease-free H₂O. Quality and quantity of the cDNA libraries were checked with the Fragment Analyzer (Agilent) using the High Sensitivity NGS Fragment Analysis kit (1 bp – 6000 bp, Agilent), and a separate concentration measurement was performed using the Qubit™ dsDNA Quantification Assay Kit (Invitrogen) following the manufacturer’s protocols. 1 µL of cDNA was transferred to a new 96-well plate for sample index PCR. To each well of this 96-well plate, 15 µL of Sample Index PCR mix was added, comprising 1× Phusion HF Buffer (Thermo Fisher Scientific), 0.2 mM dNTPs/each (Thermo Fisher Scientific), and 0.010 U µL⁻¹ Phusion HF Polymerase (Thermo Fisher Scientific). Finally, 11 µL of 0.2 µM custom premixed Nextera S50X/N70 index primers, each containing 10-bp dual indexes, were added to achieve a final reaction volume of 27 µL per well. The plate was incubated for 30 seconds at 98°C, followed by 10 cycles of 10 seconds at 98°C, 30 seconds at 55°C, and 1 minute at 72°C. The final elongation step was conducted at 72°C for 5 minutes. Purification of the final cDNA libraries was performed using AMPure XP beads at a 0.7× ratio with elution in 27 µL nuclease-free water. A strict size selection was performed to remove adaptors from the final RNA-seq libraries. cDNA fragments shorter than 220 bp were removed using E-GEL 2% (Thermo Fisher Scientific). The ZYMOclean™ Gel DNA Recovery kit (ZYMO) was then used to purify cDNA from the agarose gel with final elution in 17 µL nuclease-free water. The concentrations of the libraries were quantified using the qPCR-based KAPA Library Quantification kit (qPCR) to enable equimolar pooling.

treatment_protocol: Cutaneous mast cell tumor (MCT) FFPE blocks were retrospectively collected from the Veterinary Hospital of Ghent University, Belgium, and MedVet Laboratory (AML), Antwerp, Belgium. Samples were obtained from dogs undergoing surgical excision as part of the standardized treatment procedure for MCTs. Ethical approval was granted under EC2018-57 (2018N11) and EC2022-008 (exemption). A total of 32 MCT samples were included, graded according to both the 1984 three-tier and 2011 two-tier grading systems by a board-certified veterinary pathologist. All samples were fixed in 10% neutral buffered formalin (Sigma-Aldrich), embedded in paraffin (VWR), and archived at room temperature. For sectioning, consecutive tissue sections were cut at 7 µm thickness and mounted on PEN membrane 1.0 glass slides (ZEISS). To enhance adhesion, slides were irradiated with ultraviolet (UV) light at 254 nm for 30 minutes, followed by poly-L-lysine treatment (1:10 dilution, Sigma-Aldrich) for 5 minutes. Blades were replaced between samples to prevent cross-contamination. Slides were incubated overnight at 56°C to further improve tissue adhesion. Slides were subjected to quick histological (Nissl) staining based on the Arcturus Histogene™ Staining kit (Thermo Fisher Scientific). Ethanol solutions for staining were prepared from ≥99.5% ethanol (VWR) and nuclease-free water. After overnight incubation, slides were immersed 30 seconds in xylene (two times), 10 seconds in 94% ethanol (one time), 10 seconds in 85% ethanol (one time), and 10 seconds in 70% ethanol (one time). Slides were then covered with Histogene™ staining solution (Thermo Fisher Scientific) for 30 seconds and dehydrated in rising ethanol concentrations (70% ethanol two times, 80% ethanol one time, 94% ethanol one time). Slides were briefly air-dried. Slides were subjected to laser capture microdissection (LCM) immediately after staining using the PALM Microbeam LCM system (ZEISS), following the manufacturer’s protocol. Mast cell–rich regions were identified based on Giemsa staining, excluding blood vessels. Approximately 300 cells were collected per area at 20× magnification with minimal laser power. Captured cells were collected into 0.2 mL ZEISS adhesive caps. The CapCheck function was used to verify the expected input, after which caps were labeled and stored at −80°C until further library preparation. The total time from staining to freezing did not exceed 1.5 hours for any sample.

value: Mast cells


title: pfos_EC5_48_rep3

status: Public on Aug 03 2026

type: SRA

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Library name: SF_99

library_source: transcriptomic

data_processing:
The  quality assessment of all RNA-Seq datasets was conducted using FastQC v0.12.1
Trimming of reads, including removal of low-quality ends and adapters, was performed using cutadapt v4.4_dev with Python 3.8.10 with default parameters.
the trimmed and adapter-clipped raw reads underwent a second round of quality checks using FastQC v0.12.1
The RNA sequencing reads were aligned to the human reference genome assembly GRCh38 using the HISAT2 algorithm and its corresponding genome indexes.
Transcript abundance was determined using the featurecounts function from the Rsubread package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample. EnsemblID on the rows and samples on the columns.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: THP-1 cells (ATCC TIB-202, USA) were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% FBS (Gibco, USA) (culture media). Cells were cultured in 75 cm2 flasks at a density < 1 × 106 cells/ml. Cells were differentiated in 12 well plates, with 500,000 cells/ well (127,000 cells/cm2), in the culture media supplemented with 50 nM of phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich, USA) for 48h

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen, Germany) according to vendor’s instructions. RNA quality was assessd by Bioanalyzer. Only high quality samples were sequenced.
Novogene NGS RNA Library Prep Set (PT042)

tag: cell line

tag: cell type

value: macrophage

tag: genotype

value: WT

tag: treatment

value: PFOS

tag: time

tag: replicate

tag: concentration

tag: concentration unit

value: nM


title: Myc_fl_fl_Lgr5_Cre_Vehicle_rep3

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

country: China

institute: Shenzhen University

description:
Library name: Myc_fl_fl_Lgr5_Cre_Vehicle_rep3
Myc_fl_fl_Lgr5_Cre_Vehicle_TAM_rep3_matrix.txt

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on DNBseq G400 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from DNBseq G400 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to generate the bam file of each sample from fastq with following parameters: -3 5 --local -x hg19 -U SE_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to identify the differentially expressed genes between groups.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include transcript count for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Intstine crypt

growth_protocol: HT29 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum. LoVo cells were maintained in F12K medium supplemented with 10% fetal bovine serum. For selection of AID clones, Cells transfected with indicated plasmids were cultured with 2 ug/ml puromycin and 5 ug/ml blasticidin.

extract_protocol:
Total RNA was extracted from  cells using Trizol reagent from Thermofisher according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Acute degradation of MYC in AID cells was induced by auxin (IAA) treatment, cells were then harvested for transcriptome analysis. For conditional knock-out of Myc in intestinal stem cells, Mycf/f ; Lgr5-CreERT2 mice were intraperitoneally injected with Tamoxifen (TAM) dissolved in corn oil (80mg/kg) daily for there consecutive days, three days post last injection mice were sacrificed and intestinal crypt was harvested for transcriptome analysis.

tag: tissue

value: Intstine crypt

value: Vehicle


title: ShortDD_08_2

city: Tsukuba

first: Shuhei

last: Suzuki

address: 1-1-1 Tennodai, Tsukuba, Ibaraki

country: Japan

institute: University of Tsukuba

description: Library name: Sample 5

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 22.0.1; Qiagen, Redwood City, CA).
Assembly: mm10
Supplementary files format and content: CSV files were generated usingCLC Genomics Workbench (Version 22.0.1; Qiagen, Redwood City, CA).

source_name: whole bladder

growth_protocol: Central nervous Bmal1 cKO mice were kept in constant darkness (DD) for 2 days or 8 weeks.

extract_protocol:
RNA was extracted from mouse samples using NucleoSpin® RNA (Takara Bio, Shiga, Japan)
Total RNA (500 ng) was subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit (New England Biolabs) according to the manufacturer's protocol. Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

value: whole bladder

tag: Sex

value: female

value: CaMKII-Cre; Bmal1fx/fx

value: ShortDD


title: L-dopa_Ctrl_2

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

country: USA

institute: Weill Cornell Medicine

description:
Library name: Sample 25
mRNA expression in mouse striatum

library_source: transcriptomic single cell

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. Genes expressed in ≤3 cells were removed. Cells were filtered using dataset-specific thresholds for detected genes, UMI counts, and mitochondrial content: LID (nFeature_RNA 300–4,000; nCount_RNA <20,000; percent.mt <5%), LID_PLX (nFeature_RNA 300–5,000; nCount_RNA <15,000; percent.mt <1%), and LID_sTREM2 (nFeature_RNA 300–6,000; nCount_RNA <35,000; percent.mt <5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.2.2 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: striatum

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: striatum

value: Male

tag: age

value: lesioned L-DOPA-treated control diet


title: L-dopa_Ctrl_1

description:
Library name: Sample 24
mRNA expression in mouse striatum


title: Guinea pig, liver, Gpig9

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: Cpor_Liver_Rep3

data_processing:
Sequencing adaptors and low-quality reads were removed using Cutadapt with the following parameters: a minimum read length of 25 bp after trimming (-m 25), a minimum sequence quality score of 30 (-q 30), and the removal of any reads containing more than one N base (--max-n 1).
Trimmed reads from each species were pseudo-aligned and quantified to their respective reference transcriptome using Salmon v.013.1, with a decoy-aware index. The pseudo-mapping process included corrections for GC content bias (--gcBias) and sequence-specific biases (--seqBias). Quantification was performed at the transcript level.
For each species, we summarised transcript-level abundance estimates generated by Salmon to the gene level using the tximport v1.24 R package, with counts corrected for effective transcript length via the lengthScaledTPM method. To enable cross-species comparisons, we retained only one-to-one orthologous genes. We then merged gene-level count matrices across species and imported them into DESeq2. We normalised the combined dataset across all samples using the median-of-ratios method implemented in DESeq2, which adjusts for library size by computing sample-specific size factors as the median of ratios of observed counts to a pseudo-reference (the geometric mean across samples for each gene). To account for technical variation introduced by different data sources, we included a batch term in the DESeq2 model (~species + data source). Finally, we applied the variance-stabilising transformation (VST) to the normalised counts, which were then used for downstream analyses.
Assembly: The reference genome and transcriptomes for naked mole-rat (HetGla1.0), Damara mole-rat (DMRv1.0), guinea pig (Cavpor3.0) and mouse (GRCm38) were downloaded from Ensembl v102
Supplementary files format and content: Vst-normalised counts across 13,929 one-to-one orthologous for each sample in the study

organism: Cavia porcellus

source_name: liver

extract_protocol:
Total RNA was extracted from 10-50 mg of tissue samples, previously flash-frozen in dry ice and kept at -80C. Briefly, frozen tissue samples were homogenised in lysis buffer (RNAEasy, Qiagen) using homogenisation beads (Precellys hard tissue homogenising tubes CK28) in a FastPrep-24 tissue homogeniser (MP Biosciences) with three 20 s pulses at a speed of 4.5 m/s. Homogenised tissue lysates were used directly for RNA extraction using a commercial RNA extraction kit (RNEasy, Qiagen).
500 ng of total RNA from each sample were used for preparation of total RNA-sequencing libraries with NEBNext UltraTM II RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, total RNA was depleted of ribosomal RNA (rRNA) with rRNA Depletion Kit v2 (New England Biolabs) and RNA sample purification beads. rRNA-depleted RNA was used for preparation of cDNA and RNA-sequencing libraries following manufacturer specifications, with 12-15 minutes of RNA fragmentation at 94C and 10 cycles of PCR amplification. RNA-sequencing libraries were quantified by quantitative PCR with Kapa Illumina library quantification kit (Roche diagnostics) in a Roche LC480 instrument. RNA-seq libraries were then pooled in equimolar concentrations and sequenced in an Illumina NovaSeq instrument by commercial supplier Novogene UK.

value: liver

value: male

tag: age (months)

tag: individual


title: ShortDD_04_3

description: Library name: Sample 3


title: Guinea pig, liver, Gpig7

description: Library name: Cpor_Liver_Rep2


title: pfos_EC5_24_rep3

description: Library name: SF_23


title: Saline_Ctrl_2

description:
Library name: Sample 22
mRNA expression in mouse striatum

value: lesioned saline-treated control diet


title: Saline_Ctrl_1

description:
Library name: Sample 21
mRNA expression in mouse striatum


title: Guinea pig, liver, Gpig8

description: Library name: Cpor_Liver_Rep1


title: pfos_EC5_24_rep2

description: Library name: SF_19


title: pfos_EC5_24_rep1

description: Library name: SF_15


title: L-dopa_C_5

description:
Library name: Sample 20
mRNA expression in mouse striatum

value: non-lesioned L-DOPA-treated


title: Guinea pig, heart, Gpig9

description: Library name: Cpor_Heart_Rep3

source_name: heart

value: heart


title: TA, ORX+DHT, biol rep3

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

description: Library name: ORX DHT rep3

data_processing:
Adaptor sequences and low-quality sequences were removed, and reads with a length below 20bp were discarded using TrimGalore (v0.6.7)
The processed reads were then mapped to the GRCm38 reference genome using HISAT2 (v2.2.1).
Read counts for each gene were obtained using featureCounts (v2.0.1).
Differentially expressed genes were identified using DESeq2 (v1.36.0) with a threshold of |log2FC| > 1 and padj < 0.1.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values file includes normalized counts for each Sample

source_name: TA muscles

extract_protocol:
Total RNA was isolated from tibialis anterior (TA) muscles using ISOGEN (Nippon Gene) according to the manufacturer’s instructions.
Directional RNA-seq libraries were prepared from 500 ng of RNA per sample using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEBNext Poly(A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos for Illumina (New England Biolabs), according to the manufacturer’s instructions.

value: TA muscles

value: ORX+DHT


title: pfos_EC20_72_rep3

description: Library name: SF_189

value: macrophage

value: WT

value: PFOS

value: nM


title: Guinea pig, heart, Gpig8

description: Library name: Cpor_Heart_Rep2


title: L-dopa_C_4

description:
Library name: Sample 19
mRNA expression in mouse striatum


title: TA, ORX+DHT, biol rep2

description: Library name: ORX DHT rep2


title: pfos_EC20_72_rep2

description: Library name: SF_185


title: TA, ORX+DHT, biol rep1

description: Library name: ORX DHT rep1


title: Guinea pig, heart, Gpig7

description: Library name: Cpor_Heart_Rep1


title: L-dopa_C_3

description:
Library name: Sample 18
mRNA expression in mouse striatum


title: pfos_EC20_72_rep1

description: Library name: SF_181


title: L-dopa_C_2

description:
Library name: Sample 17
mRNA expression in mouse striatum


title: TA, ORX, biol rep3

description: Library name: ORX rep3

value: ORX


title: RBNS, guanine, G3BP1 LCD, rep2

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason Farm

department: Pharmacology

institute: UNC Chapel Hill

description:
Library name: stG4_G3BP1_LCD_SDS_PrepB
Column name in stG4_raw_counts.txt: G3BP1_LCD_SDS_WT_PrepB

data_processing:
Raw reads were trimmed of the universal Illumina adapter sequences using cutadapt. Specifically:  cutadapt -j 10 -m 18 -a TGGAATTCTCGGGTGTCAAGG -g GAGTTCTACAGTCCGACGATC -o ${line}_primer_trim.fastq ${line}.fastq
Raw counts were generated by STAR mapping against (structural_pool.fasta, structural_pool.gtf). Specifically: #### STAR index #### STAR   --runMode genomeGenerate      --runThreadN 8   --genomeDir STAR_idx/library  --genomeFastaFiles structural_pool.fasta     --sjdbGTFfile structural_pool.gtf --genomeSAindexNbases 8  #### STAR count #### #### notice: no mismatch STAR --runThreadN 16 \         --genomeDir /STAR_idx/library \         --readFilesIn ./${line}_primer_trimmed.fastq \  --outFileNamePrefix STAR/${line} \  --sjdbGTFfile structural_pool.gtf \  --outFilterMultimapNmax 1 \  --outFilterMismatchNmax 0 \  --genomeLoad NoSharedMemory \  --outSAMtype BAM Unsorted \  --outReadsUnmapped Fastx \  --quantMode GeneCounts
Assembly: structural_pool.fasta, structural_pool.gtf
Supplementary files format and content: stG4_raw_counts.txt: All raw read counts for each sequence in the pool

organism: synthetic construct

source_name: RBNS

extract_protocol:
In vitro transcribed synthetic RNA pools were made with guanine or 7dG. RT stop: RNAs were annealed in noted cations, then incubated with water or pyridostatin (where noted) for 10 minutes. RNA was reverse transcribed (RT) by SuperScript III in first strand buffer substituted with the noted cations for 40 minutes. Unless specifcially noted, RT was performed at 40ºC. After 40 minutes, samples were heated at 100ºC for 5 minutes, then proceeded to library preparation. RBNS: RNAs were annealed in KCl (or 7dG in LiCl), and allowed to incubate with noted proteins conjugated to streptavidin binding proteins. Bound RNA was eluted from streptavidin magnetic beads and concentrated by phenol-chloroform extraction. Subsequent RT was performed with SuperScript III in first strand buffer substituted with LiCl.
RT samples were PCR amplified with Phusion DNA polymerase to attach Illumina adapters and subsequently agarose gel purified. Concentrations were assessed by the Qubit dsDNA assay, and equivalent nanograms of each sample were pooled for sequencing.

value: RBNS

tag: guanine or_7dg

value: guanine

tag: rt temperature

tag: cation (and/or_pds)_treatment

value: KCl

tag: biological replicate


title: RBNS, guanine, G3BP1 LCD, rep1

description:
Library name: stG4_G3BP1_LCD_SDS_PrepA
Column name in stG4_raw_counts.txt: G3BP1_LCD_SDS_WT_PrepA


title: L-dopa_C_1

description:
Library name: Sample 16
mRNA expression in mouse striatum

value: striatum

value: Male


title: TA, ORX, biol rep2

description: Library name: ORX rep2


title: pfos_EC20_48_rep1

description: Library name: SF_101

tag: cell line


title: RBNS, guanine, G3BP1 RRM, rep1

description:
Library name: stG4_G3BP1_RRM_SDS_PrepA
Column name in stG4_raw_counts.txt: G3BP1_RRM_SDS_WT_PrepA


title: RBNS, guanine, G3BP1 RRM, rep2

description:
Library name: stG4_G3BP1_RRM_SDS_PrepB
Column name in stG4_raw_counts.txt: G3BP1_RRM_SDS_WT_PrepB


title: TA, ORX, biol rep1

description: Library name: ORX rep1


title: Saline_C_5

description:
Library name: Sample 15
mRNA expression in mouse striatum

value: non-lesioned saline-treated


title: ATAC-seq of Runx3 KO 3

status: Public on Aug 04 2026

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample 18

library_source: genomic

data_processing:
Library construction and the quality inspection was carried out using Illumina HiSeq 4000 for sequencing
Assembly: T-bet,Runx3
Supplementary files format and content: .txt
Supplementary files format and content: .bw

molecule: genomic DNA

source_name: CD8+T cells

extract_protocol:
T-bet and Runx3 CUT&RUN:We adopted Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for genome-wide mapping of Runx3 in WT and Tbx21–/–.In brief, FACS-sorted live cells (1 × 105 cells per reaction) were bound to concanavalin A-coated magnetic beads (Bangs Laboratories) and permeabilized with 0.05% (w/v) digitonin and then incubated with anti-Runx3 antibody (Active Motif, 1 µl per reaction) or IgG overnight. After removal of unbounded antibodies with proper washing, the nuclei were incubated with protein A/G-micrococcal nuclease (MNase) fusion protein (plasmid obtained from Addgene) for 1hr at 4 °C. CaCl2 was then added to activate MNase activity and incubated on ice for 30 min. ATAC-seq:WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells cells were sorted on 4 dpi. Three biological replicates for each cell type, and 50,000 cells for each replicate were used to prepare ATACseq libraries as previously described71. Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice. The extracted nuclei were resuspended in transposition mix containing 2.5 µl Transposase (Illumina) and incubated at 37oC for 30 min. The products were purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina). DNA fragments in the range of 150-1,000 bp were recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific). RNA-seq:Total RNA was extracted from the sorted WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells on 4 dpi, and triplicates were obtained for each genotype. cDNA synthesis and amplification were performed using SMARTer Ultra Low Input RNA Kit (Clontech).
T-bet and Runx3 CUT&RUN:The reaction was quenched with stopping buffer and the DNA fragments were purified with MinElute Reaction Cleanup kit (QIAGEN) and then amplified by PCR for 10–14 cycles with barcoded Nextera primers (Illumina). ATAC-seq:The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq 4000 sequencing systems in paired end 150 bp reads at the Admera Health. RNA-seq:Libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides. Sequence data in fastq format were generated using CASAVA 1.8.2 processing pipeline from Illumina.

tag: cell type

value: CD8+T cells


title: TA, Control, biol rep3

description: Library name: Control rep3

tag: genotype

value: Control


title: pfos_EC20_24_rep3

description: Library name: SF_21

tag: treatment


title: RBNS, guanine, G3BP1 FL (SDS), rep2

description:
Library name: stG4_G3BP1_FL_SDS_PrepB
Column name in stG4_raw_counts.txt: G3BP1_FL_SDS_WT_PrepB


title: TA, Control, biol rep2

description: Library name: Control rep2


title: pfos_EC20_24_rep2

description: Library name: SF_17

tag: time


title: RBNS, guanine, G3BP1 FL (SDS), rep1

description:
Library name: stG4_G3BP1_FL_SDS_PrepA
Column name in stG4_raw_counts.txt: G3BP1_FL_SDS_WT_PrepA


title: Saline_C_2

description:
Library name: Sample 12
mRNA expression in mouse striatum


title: pfos_EC20_24_rep1

description: Library name: SF_13

tag: replicate


title: RBNS, guanine, input (SDS elution)

description:
Library name: stG4_RBNSinput_SDS Set2
Column name in stG4_raw_counts.txt: Input_SDS_WT

value: input


title: Saline_C_1

description:
Library name: Sample 11
mRNA expression in mouse striatum


title: pfos_EC5_48_rep2

description: Library name: SF_107

tag: concentration


title: WD450-well-differentiated-liposarcoma

type: RNA

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: cDNA was hybridized to HG U113A oligonucleotide arrays (Affymetrix, Inc.).

scan_protocol: Fluorescence was measured by laser confocal scanner (Agilent) and converted to signal intensity by means of Affymetrix Microarray Suite v5 software.

data_processing: CEL files were processed and normalized using gcrma methods implemented in the BioConductor package gcrma. Citation: Wu J, Gentry RIwcfJMJ (2023). gcrma: Background Adjustment Using Sequence Information. R package version 2.72.0.

label: biotin

source_name: surgical specimen

label_protocol: cDNA was synthesized in the presence of oligo(dT)24-T7 from Genset Corp. cRNA was prepared using biotinylated UTP and CTP.

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols

value: well-differentiated liposarcoma

tag: tumor site

value: retroperitoneal

tag: tumor grade

value: low

tag: treatement

value: surgery


title: RNA-Seq of Homo sapiens: HSC-1 shPLEK2#2

city: Xi'an

first: Guanfei

last: Zhang

address: No.28, Xianning west road

institute: Xi'an Jiaotong University

description: Library name: Sample 6

data_processing:
Raw sequencing data in FASTQ format were initially subjected to quality control using FastQC (v0.11.9).
Adapters and low-quality reads were subsequently filtered using Trimmomatic (v0.39) under the following parameters: ILLUMINACLIP:adapter.fa:2:30:10, SLIDINGWINDOW:4:20, LEADING:3, TRAILING:3, MINLEN:36. Specifically, reads containing adapter sequences, ambiguous bases ('N') exceeding 10% of the read length, or low-quality bases (Phred score ≤5) accounting for over 50% of the read were discarded.
The resulting high-quality clean reads were aligned to the reference genome (GRC38/mm10) using HISAT2 (v2.2.1) with the following parameters: --rna-strandness RF, --known-splicesite-infile, -k 1, --score-min L,0,-0.6. Read counting and normalization (FPKM/RPKM) were then performed using featureCounts (Subread v2.0.1) based on the alignment files.
Assembly: GRC38/mm10
Supplementary files format and content: count values for each Sample

source_name: skin

growth_protocol: SCL-1 and HSC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol kit (AG). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were generated from oligo(dT)-selected mRNA using the NEBNext Ultra workflow, with strand specificity achieved via dUTP incorporation during second-strand synthesis.

treatment_protocol: PLEK2 knockdown

tag: tissue

value: skin

value: squamous cell carcinoma cell

value: PLEK2 knockdown


title: pfos_EC10_72_rep3

description: Library name: SF_190

value: macrophage

value: WT

value: PFOS

tag: concentration unit

value: nM


title: RBNS, 7-deaza-guanine, FMRP, rep2

description:
Library name: stG4_FMRP_7dG_PrepB
Column name in stG4_raw_counts.txt: FMRP_LCD_7dG_PrepB

data_processing:
Raw reads were trimmed of the universal Illumina adapter sequences using cutadapt.
Specifically:
cutadapt -j 10 -m 18 -a TGGAATTCTCGGGTGTCAAGG -g GAGTTCTACAGTCCGACGATC -o ${line}_primer_trim.fastq ${line}.fastq
Raw counts were generated by STAR mapping against (structural_pool.fasta, structural_pool.gtf). Specifically:
#### STAR index ####
STAR   --runMode genomeGenerate      --runThreadN 8   --genomeDir STAR_idx/library  --genomeFastaFiles structural_pool.fasta     --sjdbGTFfile structural_pool.gtf --genomeSAindexNbases 8
#### STAR count ####
#### notice: no mismatch
STAR --runThreadN 16 \
--genomeDir /STAR_idx/library \
--readFilesIn ./${line}_primer_trimmed.fastq \
--outFileNamePrefix STAR/${line} \
--sjdbGTFfile structural_pool.gtf \
--outFilterMultimapNmax 1 \
--outFilterMismatchNmax 0 \
--genomeLoad NoSharedMemory \
--outSAMtype BAM Unsorted \
--outReadsUnmapped Fastx \
--quantMode GeneCounts
Assembly: structural_pool.fasta, structural_pool.gtf
Supplementary files format and content: stG4_raw_counts.txt: All raw read counts for each sequence in the pool

value: RBNS

value: LiCl


title: L-dopa_5

description:
Library name: Sample 10
mRNA expression in mouse striatum

value: striatum

tag: Sex

value: Male

tag: age

value: lesioned L-DOPA-treated


title: RNA-Seq of Homo sapiens: HSC-1 shPLEK2#1

description: Library name: Sample 5


title: pfos_EC10_72_rep2

description: Library name: SF_186


title: L-dopa_4

description:
Library name: Sample 9
mRNA expression in mouse striatum


title: RNA-Seq of Homo sapiens: HSC-1 shNC

description: Library name: Sample 4


title: RBNS, guanine, FMRP, rep2

description:
Library name: stG4_FMRP_PrepB
Column name in stG4_raw_counts.txt: FMRP_LCD_WT_PrepB

tag: guanine or_7dg

value: guanine

tag: rt temperature

value: KCl


title: pfos_EC10_72_rep1

description: Library name: SF_182


title: L-dopa_3

description:
Library name: Sample 8
mRNA expression in mouse striatum


title: pfos_EC10_48_rep3

description: Library name: SF_98


title: RNA-Seq of Homo sapiens: SCL-1 shPLEK2#2

description: Library name: Sample 3


title: RBNS, guanine, FMRP, rep1

description:
Library name: stG4_FMRP_PrepA
Column name in stG4_raw_counts.txt: FMRP_LCD_WT_PrepA

tag: cation (and/or_pds)_treatment

tag: biological replicate


title: L-dopa_2

description:
Library name: Sample 7
mRNA expression in mouse striatum


title: RNA-Seq of Homo sapiens: SCL-1 shPLEK2#1

description: Library name: Sample 2

tag: cell line

tag: cell type

value: shNC

value: control


title: pfos_EC10_48_rep2

description: Library name: SF_106

tag: genotype

tag: treatment


title: RBNS, 7-deaza-guanine, G3BP1, rep2

description:
Library name: stG4_G3BP1_7dG_PrepB
Column name in stG4_raw_counts.txt: G3BP1_FL_7dG_PrepB


title: RBNS, 7-deaza-guanine, G3BP1, rep1

description:
Library name: stG4_G3BP1_7dG_PrepA
Column name in stG4_raw_counts.txt: G3BP1_FL_7dG_PrepA


title: RNA-Seq of Homo sapiens: SCL-1 shNC

description: Library name: Sample 1


title: pfos_EC10_48_rep1

description: Library name: SF_102

tag: time

tag: replicate


title: L1210R, treated with TSA and AEBSF

city: Elche

first: Miguel

last: Saceda

state: Valencian Community

address: Unidad de Investigación del Hospital geneCami de la Almazara 11, edificio Anexo II

department: Unidad de Investigación

country: Spain

institute: Fundacion para el Fomento de la Investigacion Sanitaria y Biomédica de la Comunidad Valenciana

description:
Daunomycin-resistant cell line derived from L1210
Mouse430_2.na2

hyb_protocol: Once synthesized and purified, 15 µg of cRNA from each preparation were fragmented to prepare the hybridization mixtures. The hybridization procedures were performed by PROGENIKA SA. Quality controls for the hybridizations included the detection of spike-in controls and the assessment of 3'/5' signal ratios for housekeeping genes.

scan_protocol: After hybridization, arrays were washed, stained, and scanned following the standard Affymetrix protocols. The scanned images were processed using the Affymetrix GCOS 1.2 software to generate the corresponding CEL files for subsequent analysis.

data_processing: Prior to array comparison, data from each array were scaled to minimize discrepancies due to variables such as sample preparation, hybridization, and other technical factors. Using the Affymetrix GCOS 1.2 software, all arrays were scaled by setting the target mean intensity to an arbitrary value of 100. GCOS calculates the average intensity of the entire array by averaging the signal values of all probe sets, excluding the highest and lowest 2% of values. This mean intensity is then multiplied by a scaling factor to adjust it to the user-defined target value (in this case, 100). Scaling factors for arrays within the same experiment are expected to be similar and, as far as possible, close to 1. In this study, the scaling factors applied to each sample fell within the acceptable limits established by Affymetrix.

source_name: Leukemia PreB, treated with TSA (1 uM, 6 h) and AEBSF (100 uM, 6 h)

label_protocol: Starting from 2 µg of each sample, cDNA was synthesized using the One-Cycle cDNA Synthesis Kit (Affymetrix) following the manufacturer’s Expression Analysis Technical Manual. Subsequently, cRNA was generated from the cDNA using the Affymetrix IVT Labeling Kit according to the provided protocol. The resulting cRNA was purified with the Affymetrix GeneChip Sample Cleanup Module and recovered in a final volume of 22 µL of RNase-free water. The quantity and quality of the biotinylated cRNA were assessed by spectrophotometric measurement using a NanoDrop device and by electrophoresis on an agarose gel.

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

extract_protocol: RNA was isolated using the NZY Total RNA Isolation Kit following manufacturer's instructions.

treatment_protocol: L1210 and L1210R cells were plated at a density of 3×10⁵ cells/mL and treated with 1 µM TSA in the presence or absence of 100 µM AEBSF for 6 hours. Pancreatic cell lines were treated with 1 µM TSA for 6 hours after reaching 80% confluence.

value: TSA-induced cell death sensitive


title: pfos_EC10_24_rep3

description: Library name: SF_22

tag: concentration


title: Saline_4

description:
Library name: Sample 4
mRNA expression in mouse striatum

value: lesioned saline-treated


title: RBNS, guanine, G3BP1, rep2

description:
Library name: stG4_G3BP1_PrepB
Column name in stG4_raw_counts.txt: G3BP1_FL_WT_PrepB


title: pfos_EC10_24_rep2

description: Library name: SF_18


title: L1210R, AEBSF-treated

source_name: Leukemia PreB, AEBSF-treated (100 uM, 6 h)


title: RBNS, guanine, G3BP1, rep1

description:
Library name: stG4_G3BP1_PrepA
Column name in stG4_raw_counts.txt: G3BP1_FL_WT_PrepA


title: L1210R, TSA-treated 2

source_name: Leukemia PreB, TSA-treated (1 uM, 6 h)


title: pfos_EC10_24_rep1

description: Library name: SF_14


title: RBNS, 7-deaza-guanine, input

description:
Library name: stG4_7dG_RBNSinput
Column name in stG4_raw_counts.txt: Input_7dG

value: input


title: Saline_2

description:
Library name: Sample 2
mRNA expression in mouse striatum


title: L1210R, control 2

source_name: Leukemia PreB, untreated control


title: pfos_control_72_rep3

description: Library name: SF_192

value: DMSO


title: RBNS, guanine, input

description:
Library name: stG4_RBNSinput
Column name in stG4_raw_counts.txt: Input_WT


title: Saline_1

description:
Library name: Sample 1
mRNA expression in mouse striatum


title: L1210R, TSA-treated 1


title: RTStop, 50ºC, 7-deaza-guanine, KCl, rep2

description:
Library name: stG4_50_7dG_KCl_Rep2
Column name in stG4_raw_counts.txt: 50_7dG_KCl_Rep2

source_name: RT Stop

value: RT Stop


title: pfos_control_72_rep2

description: Library name: SF_188

value: macrophage

value: WT


title: Kaede red+CD45+ cells, draining lymph node, Yummer1.7, 21 days

city: New York City

first: Ines

last: Delclaux

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description:
Library name: LN_Kaede_scRNAseq_submission
10X genomics

data_processing:
Single-cell RNA-seq data were processed with Cell Ranger (10x Genomics) using the mouse reference genome, and downstream analyses were performed in R using the Seurat package. Cells with fewer than 200 or more than 2,500 detected features, or with >5% of reads mapping to mitochondrial genes, were excluded. LN and tumor samples were merged using the merge function. Gene expression values were normalized using the LogNormalize method (scale factor = 10,000), and the top 2,000 variable features were identified with FindVariableFeatures. The data were then scaled using ScaleData. The number of principal components (PCs) to retain was determined based on inspection of elbow plots and JackStraw plots.
To analyze CD8 T cells, we used Seurat to subset cells expressing T cell receptor–related genes (Cd3d, Cd3e, Trac, and Trbc1). Dimensionality reduction and clustering were performed on the previously computed principal components. We then further restricted the dataset to subclusters expressing Cd8a. Final dimensionality reduction and clustering were conducted using 13 PCs and a clustering resolution of 0.5, selected via hyperparameter tuning with FindNeighbors and FindClusters.
Assembly: mm9
Supplementary files format and content: Tab- separated values files and matrix files

source_name: lymph node

growth_protocol: 500K Yummer1.7 cells were implanted intradermally in flank of mice

extract_protocol:
On day 21 after implantation of 500K Yummer1.7 in Kaede-Tg mice (n=3) we photoconverted the tumors and 24 hours later brachial draining lymph node single cell suspensions (To create single cell suspensions, LNs were opened with syringes and digested with 1 mg/mL collagenase D and DNase I 80 U/mL for 10 minutes in an incubator at 37C. Suspensions were passed through a 70 M cell strainer), were enriched for CD45+ using a QuadroMACs magnetic separator (CD45-APC, APC beads; Miltenyi Biotec).
Libraries were prepared using Single Cell 3’ Reagent kits (10x Genomics) and sequenced using Illumina Novaseq 6000.

value: lymph node

value: Immune cells

value: Kaede-tg


title: L1210R, control 1


title: pfos_control_72_rep1

description: Library name: SF_184

value: nM


title: RTStop, 50ºC, guanine, NoSalt, rep2

description:
Library name: stG4_50_NoSalt_Rep2
Column name in stG4_raw_counts.txt: 50_WT_NoSalt_Rep2

value: NoSalt


title: Mouse, liver, 16_33022

description: Library name: Mmus_Liver_Rep2

value: liver

value: male

tag: age (months)

tag: individual


title: pfos_control_48_rep3

description: Library name: SF_108


title: L1210, TSA-treated

value: TSA-induced cell death resistant


title: RTStop, 50ºC, guanine, LiCl, rep2

description:
Library name: stG4_50_LiCl_Rep2
Column name in stG4_raw_counts.txt: 50_WT_LiCl_Rep2

tag: tissue

value: guanine

value: LiCl


title: Mouse, liver, 16_33019

description: Library name: Mmus_Liver_Rep1


title: L-dopa_1

description:
Library name: Sample 6
mRNA expression in mouse striatum

value: striatum

value: Male

value: lesioned L-DOPA-treated


title: L1210, control


title: Saline_5

description:
Library name: Sample 5
mRNA expression in mouse striatum

value: lesioned saline-treated


title: Mouse, heart, 16_33016

description: Library name: Mmus_Heart_Rep3

value: heart


title: pfos_control_48_rep2

description: Library name: SF_104

value: macrophage

value: DMSO

tag: concentration unit


title: RTStop, 50ºC, guanine, KCl, rep2

description:
Library name: stG4_50_KCl_Rep2
Column name in stG4_raw_counts.txt: 50_WT_KCl_Rep2

value: RT Stop

value: KCl


title: CRS-C2A21 Female Control

first: Florencia

last: Schlamp

address: 435 East 30th Street

description: Library name: CRS.C2A21_S16

data_processing:
Quality control (QC) was assessed using FastQC and MultiQC software
Low-quality base noise in the first 10 basepairs of the reads was trimmed using FASTX-Toolkit fastx_trimmer (v 0.0.13).
All the reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.6.1d)
Read count tables were generated using featureCounts (Subread, v1.6.3)
Normalization based on their library size factors using DESeq2 (v1.30.1) and differential expression analysis was performed.
Assembly: mm10
Supplementary files format and content: comma separated text file includes raw counts for all samples

source_name: ventricles

growth_protocol: All animal studies were performed in accordance with institutional guidelines.

extract_protocol:
RNA was isolated from adult mouse ventricles using Qiagen RNeasy Plus Mini Kit according to manufacturer’s protocol.
RNA-seq experiments were performed at the NYU School of Medicine Genome Technology Center. Samples were sequenced as 50 bp paired-end reads at 10 million to 20 million reads per replicate on an Illumina HiSeq2500 instrument

treatment_protocol: To induce CKD, 8-week-old male and female C57BL/6 wildtype mice (Jackson Laboratories) were fed a standard chow diet (Teklad Global 18% Protein Rodent Diet, Envigo) supplemented with 0.25% adenine (formulated by Research Diets) alternating with standard chow for 6 weeks with the goal of sustaining median BUN between 40 and 70 mg/dL  and limiting median body weight loss to 20% of baseline. This protocol is referred to as the high-dose regimen. Control animals were fed standard chow for 6 weeks.

tag: strain

value: ventricles

value: WT

value: Control

tag: Sex

value: Female


title: pfos_control_48_rep1

description: Library name: SF_100

value: nM


title: RTStop, 50ºC, 7-deaza-guanine, KCl, rep1

description:
Library name: stG4_50_7dG_KCl_Rep1
Column name in stG4_raw_counts.txt: 50_7dG_KCl_Rep1

tag: guanine or_7dg


title: Saline_3

description:
Library name: Sample 3
mRNA expression in mouse striatum

tag: age


title: Mouse, heart, 16_33022

description: Library name: Mmus_Heart_Rep2

value: male


title: Mouse, heart, 16_33015

description: Library name: Mmus_Heart_Rep1


title: RTStop, 50ºC, guanine, NoSalt, rep1

description:
Library name: stG4_50_NoSalt_Rep1
Column name in stG4_raw_counts.txt: 50_WT_NoSalt_Rep1

value: guanine

tag: rt temperature

tag: cation (and/or_pds)_treatment

value: NoSalt


title: CRS-C2A14 Female Treatment

description: Library name: CRS.C2A14_S15

value: Treated


title: pfos_control_24_rep3

description: Library name: SF_24

tag: cell line


title: CRS-C2A8 Male Control

description: Library name: CRS.C2A8_S14

value: Male


title: RTStop, 50ºC, guanine, LiCl, rep1

description:
Library name: stG4_50_LiCl_Rep1
Column name in stG4_raw_counts.txt: 50_WT_LiCl_Rep1

value: LiCl

tag: biological replicate


title: ShortDD_12_1

description: Library name: Sample 7

value: whole bladder

value: female

tag: genotype

value: CaMKII-Cre; Bmal1fx/fx

value: ShortDD


title: CRS-C3A7 Male Treatment

description: Library name: CRS.C3A7_S13

tag: treatment


title: pfos_control_24_rep2

description: Library name: SF_20

tag: cell type

value: macrophage

value: DMSO

tag: time


title: Cornea - sutured - duloxetine treated

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

description:
Library name: duloxetine_treatment
10x Genomics

data_processing:
The demultiplexingand other pre-processing steps were made using the Cell Ranger software (version 7.0.1).
Alignment, filtering, barcode counting, and UMI counting was performed using "cellranger count" with default parameters.
Downsteam analyses were mainly performed using the Python packages: Scanpy (version 1.9.6), scrublet (version 0.2.3), decoupler-py (version 1.1.1) and scvi-tools version (1.0.0).
Assembly: Mouse mm10
Supplementary files format and content: Matrix files

source_name: Cornea

extract_protocol:
Mouse corneas were dissected from harvested eyes and digested in Dispase II (2.4 IU/ml) at 4ºC overnight with an additional incubation for about 2 hours at 37 ºC with collagenase type I (Gibco, 1 mg/ml) in Eagle's Minimum Essential Medium (EMEM) containing 10% FBS. Isolated cells were pelleted by centrifugation and further digested into single cells with 0.25% trypsin in EDTA (1mM) for 20 minutes at 37ºC. During this time, cell suspension was gently pipetted intermittently to produce single cells. Then the cells were rinsed once with EMEM with 10% FBS to deactivate and remove trypsin and two times with sterile PBS containing 0.04% BSA (Ca2+/Mg2+ free). Finally, cells were resuspended in 30-40 μl PBS containing 0.04% BSA and counted to achieve a number within the range of 700 to 1200 cells/μl.
Library systhesis was performed according to the manufacturer's instructions (Chromium Single Cell 3′ & Gel Bead Kit, 10x Genomics). In short, entire corneas with scleral rims were dissociated with Dispase II. Isolated cells were pelleted by centrifugation and further digested into single cells. Cells were resuspended in PBS containing BSA. The master mix containing cells and partitioing oil were loaded onto Chromium Next Chip G to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane magnetic beads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, IIlumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: PBS and duloxetine treatment of sutured mouse corneas

value: Cornea

value: Suture and duloxetine

value: post natal day 42-56


title: pfos_control_24_rep1

description: Library name: SF_16

value: WT

tag: replicate

tag: concentration


title: RTStop, 50ºC, guanine, KCl, rep1

description:
Library name: stG4_50_KCl_Rep1
Column name in stG4_raw_counts.txt: 50_WT_KCl_Rep1

value: RT Stop

value: KCl


title: Myc_fl_fl_Lgr5_Cre_TAM_rep3

description:
Library name: Myc_fl_fl_Lgr5_Cre_TAM_rep3
Myc_fl_fl_Lgr5_Cre_Vehicle_TAM_rep3_matrix.txt

source_name: Intstine crypt

value: Intstine crypt

value: TAM


title: L-dopa_Ctrl_3

description:
Library name: Sample 26
mRNA expression in mouse striatum

source_name: striatum

value: striatum

value: lesioned L-DOPA-treated control diet


title: ShortDD_08_1

description: Library name: Sample 4

source_name: whole bladder


title: Cornea - sutured - PBS treated

description:
Library name: suture
10x Genomics

value: Suture and PBS

value: male


title: HH 30 SAN Vehicle treatment pool 4

city: Chapel Hill/ 27599

first: Michael

last: Bressan

address: 100 Mason Farm Rd

department: Cell Biology and Physiology

institute: University of North Carolina Chapel Hill

description:
Library name: SAN_veh_4
column name in Log2_exp:SAN_veh_4

data_processing:
RNA sequencing quality assurance was run using FastQC
Index construction and read mapping were performed using Kallisto
Differntial gene analysis was preformed using edgeR and limma
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: cvs file including log2 counts for expressed genes

organism: Gallus gallus

source_name: HH stage 30 SAN

extract_protocol:
RNA was extracted using a standard Trizol/chloroform protocol.
Library preparation was conducted using the Illumina Stranded Total RNA-SEQ with Ribo-Zero Kit

treatment_protocol: Isolated primary tissue was cultured in DMEM/F12 with 15% FBS, 1% penicillin-streptomycin, and 1% amphotericin B with 0.25ug/ml CN03 or 1ul dH20 (vehicle)

value: HH stage 30 SAN

value: Vehicle


title: pfos_EC5_48_rep1

description: Library name: SF_103

value: PFOS

value: nM


title: Saline_Ctrl_3

description:
Library name: Sample 23
mRNA expression in mouse striatum

value: Male

value: lesioned saline-treated control diet


title: RTStop, 40ºC, 7-deaza-guanine, KCl, rep2

description:
Library name: stG4_40_7dG_KCl_Rep2
Column name in stG4_raw_counts.txt: 40_7dG_KCl_Rep2


title: Cornea - unsutured - untreated

description:
Library name: nosuture
10x Genomics

value: Cornea

value: No suture


title: ShortDD_04_1

description: Library name: Sample 1

value: whole bladder

value: female

value: CaMKII-Cre; Bmal1fx/fx

value: ShortDD


title: ShortDD_04_2

description: Library name: Sample 2


title: HH 30 SAN Vehicle treatment pool 3

description:
Library name: SAN_veh_3
column name in Log2_exp:SAN_veh_3


title: CRS-C6A14 Female Control

description: Library name: CRS.C6A14_S11

value: ventricles

value: WT

value: Control

value: Female


title: HAdV-D37 infected A549 cells, OCT4 (Input)_biol rep 2

city: San Rafael

first: Mohamed Ismail

last: Ashrafali

state: CA

address: 770 Lindaro St

department: Biology Research

institute: BioMarin Pharmaceutical

description: Library name: A549_Ad37_OCT4, Input_2

data_processing:
ChIP-Seq data was analyzed using CLC Genomics Workbench (CLCbio, version 7.5). The human reads were aligned using the hg19 reference genome and virus reads aligned with HAdV-D37 reference genome (GenBank accession No. DQ900900).
Chip-Seq peak calling analysis was performed using MACS2
Assembly: hg19
Supplementary files format and content: bedgraph (BDG) files for ChIP and Input, Biological replicates 1 and 2

organism:
Homo sapiens
Human adenovirus sp.

growth_protocol: A549 cells, a human alveolar carcinoma cell line (ATCC), were cultured in Dulbecco’s modified Eagle medium (DMEM; GIBCO) supplemented with 10% heat-inactivated fetal bovine serum (FBS; GIBCO) and maintained at 37°C with 5% CO2. HAdV-D37 (ATCC) was grown in A549 cells, purified by CsCl gradient centrifugation, dialyzed, and stored at -80°C.

extract_protocol:
A549 cells were infected with HAdV-D37 at 5 moi for 4 hrs. Virus-infected cells were cross-linked using 1% methanol-free formaldehyde solution (Thermo Fisher Scientific) for 8 min at RT. Excess formaldehyde was quenched by addition of glycine. The cells were washed twice with cold-PBS and collected by scraping in PBS containing protease inhibitor cocktail, and centrifuged at 1600 rpm for 5 min, suspended in sonication buffer, and the chromatin extracts containing cross-linked DNA sonicated (Q700 sonicator, QSonica) to shear DNA to an average fragment size of 100-500 bp. The sheared cross-linked DNA was immunoprecipitated using an ENCODE validated antibody, anti- OCT4, 2 μg (Santa Cruz Biotechnologies, # sc-9081) for ON incubation at 4°C.
ChIP-Seq library construction was performed using the illumina TruSeq ChIP sample preparation (Illumina) and AMPure XP beads purification (Beckman Coulter). DNA size selection was performed on a 2% agarose gel and DNA library fragments in the range 175-225 bp were excised, gel purified, and PCR amplified to selectively enrich adapters containing DNA fragments. DNA quality was assessed on the Bioanalyzer High sensitivity Chip, and a sample library prepared (PE50) for next-generation sequencing using illumina HiSeq 2500 platform

value: human lung adenocarcinoma

value: HAdV-D37_5 moi

tag: chip antibody


title: CRS-C6A11 Female Treatment

description: Library name: CRS.C6A11_S10

tag: tissue

value: Treated


title: RTStop, 40ºC, guanine, NoSalt, rep2

description:
Library name: stG4_40_NoSalt_Rep2
Column name in stG4_raw_counts.txt: 40_WT_NoSalt_Rep2

value: RT Stop

value: guanine

value: NoSalt


title: RTStop, 40ºC, guanine, LiCl, rep2

description:
Library name: stG4_40_LiCl_Rep2
Column name in stG4_raw_counts.txt: 40_WT_LiCl_Rep2

value: LiCl


title: HAdV-D37 infected A549 cells, OCT4 (ChIP)_biol rep 2

description: Library name: A549_Ad37_OCT4, ChIP_2

value: OCT4 (Santa Cruz, # sc-9081)


title: HH 30 SAN Vehicle treatment pool 2

description:
Library name: SAN_veh_2
column name in Log2_exp:SAN_veh_2

value: HH stage 30 SAN

value: Vehicle


title: CRS-C6A8 Male Control

description: Library name: CRS.C6A8_S9

value: Male


title: RTStop, 40ºC, guanine, KCl, rep2

description:
Library name: stG4_40_KCl_Rep2
Column name in stG4_raw_counts.txt: 40_WT_KCl_Rep2

value: KCl


title: HAdV-D37 infected A549 cells, OCT4 (Input)_biol rep 1

description: Library name: A549_Ad37_OCT4, Input_1


title: HH 30 SAN freshly isolated treatment pool 4

description:
Library name: SAN_t0_4
column name in Log2_exp:SAN_t0_4

value: no treatment


title: CRS-C6A4 Male Treatment

description: Library name: CRS.C6A4_S8

value: ventricles


title: HH 30 SAN freshly isolated treatment pool 3

description:
Library name: SAN_t0_3
column name in Log2_exp:SAN_t0_3


title: CRS-C5A3 Male Treatment

description: Library name: CRS.C5A3_S7

value: WT


title: HAdV-D37 infected A549 cells, OCT4 (ChIP)_biol rep 1

description: Library name: A549_Ad37_OCT4, ChIP_1


title: RTStop, 40ºC, guanine, NoSalt, rep1

description:
Library name: stG4_40_NoSalt_Rep1
Column name in stG4_raw_counts.txt: 40_WT_NoSalt_Rep1


title: RTStop, 40ºC, 7-deaza-guanine, KCl, rep1

description:
Library name: stG4_40_7dG_KCl_Rep1
Column name in stG4_raw_counts.txt: 40_7dG_KCl_Rep1


title: CRS-C6A13 Female Control

description: Library name: CRS.C6A13_S6

value: Control


title: CRS-C6A12 Female Control

description: Library name: CRS.C6A12_S5

value: Female


title: ΔcraA, untreated, rep2

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: craA_r2
Column name in RNAseq_counts_matrix.txt: craA_r2

data_processing:
Reads were processed using the nf-core/rnaseq v1.3dev pipeline
Quality trimming was performed using Trimmomatic v0.39.
Reads were aligned to the reference genome CP059040 using HISAT2 v2.1.0.
Gene expression levels were quantified using featureCounts.
Raw counts were normalized using the regularized log transformation (rlog) from DESeq2.
Assembly: CP059040
Supplementary files format and content: Tab-delimited text file containing raw counts and normalized (rlog) expression values for all 18 samples. Rows are genes (Locus tags), columns are samples.

organism: Acinetobacter baumannii

growth_protocol: Strains were cultured in sterile LB. Overnight cultures were inoculated into 50 mL of LB supplemented with or without sub-inhibitory concentration of chloramphenicol to an initial OD600 of 0.05, and incubated at 37°C with 130 rpm to an OD600 of 0.5-0.7.

extract_protocol:
Cell suspensions were treated with RNAprotect Bacteria Reagent (Qiagen). Total RNA was extracted using RNeasy Mini Kit (Qiagen) with on-column DNA digestion and Turbo DNase treatment, followed by purification with RNeasy MinElute Cleanup kit.
Ribosomal RNA was removed using the Ribo-Zero kit. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand synthesis, terminal repair, A-tailing, adapter ligation, size selection, and PCR enrichment.

value: deltacraA

value: Untreated


title: ΔcraA, untreated, rep3

description:
Library name: craA_r3
Column name in RNAseq_counts_matrix.txt: craA_r3


title: RTStop, 40ºC, guanine, LiCl, rep1

description:
Library name: stG4_40_LiCl_Rep1
Column name in stG4_raw_counts.txt: 40_WT_LiCl_Rep1


title: HH 30 SAN freshly isolated treatment pool 2

description:
Library name: SAN_t0_2
column name in Log2_exp:SAN_t0_2


title: HH 30 SAN freshly isolated treatment pool 1

description:
Library name: SAN_t0_1
column name in Log2_exp:SAN_t0_1


title: pfos_EC20_48_rep3

first: Dario

last: Greco

address: Arvo ylpön Katu 34

description: Library name: SF_97

data_processing:
The  quality assessment of all RNA-Seq datasets was conducted using FastQC v0.12.1
Trimming of reads, including removal of low-quality ends and adapters, was performed using cutadapt v4.4_dev with Python 3.8.10 with default parameters.
the trimmed and adapter-clipped raw reads underwent a second round of quality checks using FastQC v0.12.1
The RNA sequencing reads were aligned to the human reference genome assembly GRCh38 using the HISAT2 algorithm and its corresponding genome indexes.
Transcript abundance was determined using the featurecounts function from the Rsubread package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample. EnsemblID on the rows and samples on the columns.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen, Germany) according to vendor’s instructions. RNA quality was assessd by Bioanalyzer. Only high quality samples were sequenced.
Novogene NGS RNA Library Prep Set (PT042)

value: macrophage

value: PFOS

tag: concentration unit

value: nM


title: CRS-C3A1 Male Control

description: Library name: CRS.C3A1_S12

tag: strain


title: ΔcraA, untreated, rep1

description:
Library name: craA_r1
Column name in RNAseq_counts_matrix.txt: craA_r1


title: pfos_EC20_48_rep2

description: Library name: SF_105


title: RTStop, 40ºC, guanine, KCl, rep1

description:
Library name: stG4_40_KCl_Rep1
Column name in stG4_raw_counts.txt: 40_WT_KCl_Rep1

value: RT Stop

value: guanine


title: CRS-C6A10 Female Treatment

description: Library name: CRS.C6A10_S4

value: Treated

tag: Sex


title: RTStop, 30ºC, 7-deaza-guanine, KCl, rep2

description:
Library name: stG4_30_7dG_KCl_Rep2
Column name in stG4_raw_counts.txt: 30_7dG_KCl_Rep2

tag: guanine or_7dg


title: HH 30 SAN CN03 treatment pool 4

description:
Library name: SAN_Cn03_4
column name in Log2_exp:SAN_Cn03_4

value: HH stage 30 SAN


title: ΔadeIJ, chloramphenicol, rep2

description:
Library name: adeIJ.abx_r2
Column name in RNAseq_counts_matrix.txt: adeIJ.abx_r2

value: deltaadeIJ

value: Chloramphenicol


title: Saline_C_4

description:
Library name: Sample 14
mRNA expression in mouse striatum

value: striatum

value: Male

tag: age

value: non-lesioned saline-treated


title: CRS-C6A9 Female Treatment

description: Library name: CRS.C6A9_S3

value: ventricles

value: WT


title: HH 30 SANCN03 treatment pool 3

description:
Library name: SAN_Cn03_3
column name in Log2_exp:SAN_Cn03_3


title: RTStop, 30ºC, guanine, NoSalt, rep2

description:
Library name: stG4_30_NoSalt_Rep2
Column name in stG4_raw_counts.txt: 30_WT_NoSalt_Rep2

tag: rt temperature

value: NoSalt


title: CRS-C6A7 Male Control

description: Library name: CRS.C6A7_S2

value: Control


title: RTStop, 30ºC, guanine, LiCl, rep2

description:
Library name: stG4_30_LiCl_Rep2
Column name in stG4_raw_counts.txt: 30_WT_LiCl_Rep2

tag: cation (and/or_pds)_treatment

value: LiCl


title: CRS-C6A2 Male Treatment

description: Library name: CRS.C6A2_S1


title: HH 30 SAN CN03 treatment pool 1

description:
Library name: SAN_Cn03_1
column name in Log2_exp:SAN_Cn03_1


title: ΔadeIJ, untreated, rep1

description:
Library name: adeIJ_r1
Column name in RNAseq_counts_matrix.txt: adeIJ_r1

tag: cell line

value: Untreated


title: 125OC

city: Pisa

first: Francesca

last: Scebba

address: Piazza martiri della libertà 33

country: Italy

institute: Scuola Superiore Sant'Anna

description: Library name: 30804-100

data_processing:
Analysis was performed using CLC Genomics Server 21.0.4 with the QIAseq miRNA Quantification workflow and standard parameters. Reads were mapped to miRBase v22 after trimming of common sequences, UMIs, and adapters, followed by filtering of reads shorter than 15 nt or longer than 55 nt. Reads were then deduplicated based on their UMIs by grouping reads with the same start position, strand, and identical UMI. Singleton UMI groups were merged into non-singleton groups when their UMI differed by a single nucleotide (SNP), with assignment to the largest matching group.
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings.
Assembly: miRBase version 22
Supplementary files format and content: excel file with total miRNa count for each miRNA and each sample

source_name: saliva

extract_protocol:
RNA was isolated from 200 μl using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5 μl total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Agilent DNA 1000 Chip)

value: saliva

tag: gender

value: female

value: ovarian cancer


title: RTStop, 30ºC, 7-deaza-guanine, KCl, rep1

description:
Library name: stG4_30_7dG_KCl_Rep1
Column name in stG4_raw_counts.txt: 30_7dG_KCl_Rep1

value: RT Stop

value: KCl

tag: biological replicate


title: ΔadeIJ, untreated, rep2

description:
Library name: adeIJ_r2
Column name in RNAseq_counts_matrix.txt: adeIJ_r2

tag: genotype

tag: treatment


title: HH 30 Atria Vehicle treatment pool 4

description:
Library name: Atria_veh_4
column name in Log2_exp:Atria_veh_4

source_name: HH stage 30 Atria

value: HH stage 30 Atria

value: Vehicle


title: 122OC

description: Library name: 30804-099


title: ΔadeAB, chloramphenicol, rep3

description:
Library name: adeAB.abx_r3
Column name in RNAseq_counts_matrix.txt: adeAB.abx_r3

value: deltaadeAB

value: Chloramphenicol


title: RTStop, 30ºC, guanine, NoSalt, rep1

description:
Library name: stG4_30_NoSalt_Rep1
Column name in stG4_raw_counts.txt: 30_WT_NoSalt_Rep1

value: guanine


title: 57BC

description: Library name: 30804-098

value: breast cancer


title: ΔadeAB, chloramphenicol, rep2

description:
Library name: adeAB.abx_r2
Column name in RNAseq_counts_matrix.txt: adeAB.abx_r2


title: HH 30 Atria Vehicle treatment pool 3

description:
Library name: Atria_veh_3
column name in Log2_exp:Atria_veh_3


title: RTStop, 30ºC, guanine, LiCl, rep1

description:
Library name: stG4_30_LiCl_Rep1
Column name in stG4_raw_counts.txt: 30_WT_LiCl_Rep1


title: HH 30 Atria Vehicle treatment pool 2

description:
Library name: Atria_veh_2
column name in Log2_exp:Atria_veh_2


title: 121OC

description: Library name: 30804-097


title: ΔadeAB, untreated, rep2

description:
Library name: adeAB_r2
Column name in RNAseq_counts_matrix.txt: adeAB_r2


title: RTStop, 30ºC, guanine, KCl, rep1

description:
Library name: stG4_30_KCl_Rep1
Column name in stG4_raw_counts.txt: 30_WT_KCl_Rep1


title: 134OC

description: Library name: 30804-096


title: HH 30 Atria freshly isolated treatment pool 4

description:
Library name: Atria_t0_4
column name in Log2_exp:Atria_t0_4

value: no treatment


title: RTStop, 7-deaza-guanine, KCl, PDS, rep3

description:
Library name: stG4_7dG_KCl_PDS_Rep3
Column name in stG4_raw_counts.txt: St_7dG_KCl_Rep3_PDS

value: KCl, PDS


title: HH 30 Atria freshly isolated treatment pool 3

description:
Library name: Atria_t0_3
column name in Log2_exp:Atria_t0_3


title: ΔadeAB, untreated, rep1

description:
Library name: adeAB_r1
Column name in RNAseq_counts_matrix.txt: adeAB_r1


title: 67OC

description: Library name: 30804-094


title: HH 30 Atria freshly isolated treatment pool 2

description:
Library name: Atria_t0_2
column name in Log2_exp:Atria_t0_2


title: RTStop, guanine, LiCl, PDS, rep3

description:
Library name: stG4_LiCl_PDS_Rep3
Column name in stG4_raw_counts.txt: St_WT_LiCl_Rep3_PDS

value: LiCl, PDS


title: WT, chloramphenicol, rep2

description:
Library name: wt.abx_r2
Column name in RNAseq_counts_matrix.txt: wt.abx_r2

value: Wild-type


title: HH 30 Atria freshly isolated treatment pool 1

description:
Library name: Atria_t0_1
column name in Log2_exp:Atria_t0_1


title: RTStop, guanine, KCl, PDS, rep3

description:
Library name: stG4_KCl_PDS_Rep3
Column name in stG4_raw_counts.txt: St_WT_KCl_Rep3_PDS


title: HH 30 Atria CN03 treatment pool 4

description:
Library name: Atria_Cn03_4
column name in Log2_exp:Atria_Cn03_4


title: WT, chloramphenicol, rep1

description:
Library name: wt.abx_r1
Column name in RNAseq_counts_matrix.txt: wt.abx_r1


title: RTStop, 7-deaza-guanine, LiCl, PDS, rep2

description:
Library name: stG4_7dG_LiCl_PDS_Rep2
Column name in stG4_raw_counts.txt: St_7dG_LiCl_Rep2_PDS


title: HH 30 Atria CN03 treatment pool 3

description:
Library name: Atria_Cn03_3
column name in Log2_exp:Atria_Cn03_3


title: WT, untreated, rep3

description:
Library name: wt_r3
Column name in RNAseq_counts_matrix.txt: wt_r3


title: 8BC1

description: Library name: 30804-093


title: 48BC1

description: Library name: 30804-092


title: WT, untreated, rep2

description:
Library name: wt_r2
Column name in RNAseq_counts_matrix.txt: wt_r2


title: RTStop, 7-deaza-guanine, KCl, PDS, rep2

description:
Library name: stG4_7dG_KCl_PDS_Rep2
Column name in stG4_raw_counts.txt: St_7dG_KCl_Rep2_PDS


title: 231HS

description: Library name: 30804-090

value: healthy


title: HH 30 Atria CN03 treatment pool 2

description:
Library name: Atria_Cn03_2
column name in Log2_exp:Atria_Cn03_2


title: WT, untreated, rep1

description:
Library name: wt_r1
Column name in RNAseq_counts_matrix.txt: wt_r1

value: Untreated


title: 5BC

description: Library name: 30804-089

value: saliva


title: RTStop, guanine, KCl, PDS, rep2

description:
Library name: stG4_KCl_PDS_Rep2
Column name in stG4_raw_counts.txt: St_WT_KCl_Rep2_PDS


title: HH 30 Atria CN03 treatment pool 1

description:
Library name: Atria_Cn03_1
column name in Log2_exp: Atria_Cn03_1


title: THP-1 cells treated with 20 μM chlorquinaldol for 8 hours replicate 3

city: Wuhan

first: Xiang

state: Hubei

address: Room 100302, Building 10, Wuhan University of Science & Technology (Huangjiahu District), No.2 West Huangjiahu Road, Hongshan District

department: College of Life Science & Health

description:
Library name: TL3
TL3

data_processing:
RNA sequencing was performed by Benagen Technology (Wuhan, China).
Paired-end reads were aligned to the reference transcriptome, and read counts were quantified using RSEM.
Gene expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Differential expression analysis was performed using DESeq2 (version 1.26.0).
Functional enrichment analysis was conducted using the clusterProfiler package (version 3.14.3).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene-level read counts for each sample.
Supplementary files format and content: Tab-delimited text file containing FPKM-normalized gene expression values for each sample.

source_name: THP-1 cells

extract_protocol:
RNA was extracted using TRIzon Reagent (CW0580S; CoWin Biosciences, Taizhou, China).
RNA libraries were constructed by enriching mRNA using oligo(dT) magnetic beads, followed by cDNA library preparation. Libraries were sequenced on the BGI DNBSEQ platform.

value: THP-1 cells

tag: cell type

value: human monocytic leukemia cell line

value: 20 μM chlorquinaldol for 8 hours


title: THP-1 cells treated with 20 μM chlorquinaldol for 8 hours replicate 2

institute: Wuhan University of Science & Technology

description:
Library name: TL2
TL2


title: THP-1 cells treated with 20 μM chlorquinaldol for 8 hours replicate 1

description:
Library name: TL1
TL1


title: RTStop, 7-deaza-guanine, KCl, PDS, rep1

description:
Library name: stG4_7dG_KCl_PDS_Rep1
Column name in stG4_raw_counts.txt: St_7dG_KCl_Rep1_PDS

value: RT Stop


title: 97BC

description: Library name: 30804-086

value: female


title: HCT116, LagTag, M.EcoGII-RNAPIISer2p_mintbody, rep2

city: Pasadena

first: Yodai

last: Takei

state: California

address: 1200 E California Blvd

institute: California Institute of Technology

description: Library name: HCT116_LagTag_Ser2p_rep2

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig

growth_protocol: E14 mouse embryonic stem cells (E14Tg2a.4) were maintained on 0.1% gelatin coated plates under the serum/LIF condition in DMEM supplemented with 15% ES-grade fetal bovine serum (FBS), 1,000 units/mL leukemia inhibitory factor (LIF), 1× non-essential amino acids, 1 mM sodium pyruvate, 55 μM 2-mercaptoethanol, and 1× Penicillin-Streptomycin-Glutamine. mESC-Gata4 cells were maintained on 0.1% gelatin coated plates under the serum/LIF/2i condition by supplementing the serum/LIF medium with 1 μM PD0325901 and 3 μM CHIR99021. The human HCT116 cells (ATCC CCL‐247) were maintained in McCoy's 5A (modified) medium supplemented with 10% FBS and 1× Penicillin-Streptomycin. All cell lines were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 50 μL of 1% formaldehyde in 1× PBS at room temperature for 5 minutes on 96-well plates.
Cells were permeabilized with 0.5% Triton-X in 1× PBS. For LagTag, additional treatment with 5% RNaseA/T1 Mix as well as NaOH denaturation were performed. These treatments were omitted in CUT&Tag experiments unless noted. Samples were incubated with primary antibodies in blocking buffer (1× PBS, 1% BSA, and 0.05% Triton-X), then with nb-Tn5 transposomes (in-house) in wash 300 buffer (20 mM HEPES pH 7.4, 300 mM NaCl, and 0.05% Triton-X) supplemented with 0.1% BSA. Tagmentation was then performed in wash 300 buffer supplemented with 10 mM MgCl2 and 0.1% BSA. The DNA fragments were extracted using 20 μL SDS release buffer (10 mM TAPS buffer pH 8.5, 0.2% SDS, and 5% thermolabile proteinase K), then neutralized with 12 μL of 10% Triton-X for PCR input. Libraries were prepared by mixing 21 μL input, 2 μL each of i5 and i7 primers (10 μM stock), and 25 μL of NEBNext High-Fidelity 2X PCR Master Mix. PCR was performed as follows: 5 min at 58°C, 5 min at 72°C, and 45 sec at 98°C followed by 13-15 cycles of 15 sec at 98°C and 10 sec at 60°C, and a final extension at 72°C for 1 min. The amplified libraries were purified using 1.3× magnetic beads.

treatment_protocol: The mESC-Gata4 differentiation to endodermal cells was induced by 1 μg/mL Dox induction and LIF withdrawal for 24 hours. For LagTag, the adenine methyltransferase fusion proteins were stabilized with 1 μM Shield-1 for 16 hours in the engineered cells.

value: colonocyte

value: 1 μM Shield-1 for 16 hours

tag: antibody

value: m6A (Invitrogen MA5-35350)


title: THP-1 cells treated with 50 μM chlorquinaldol for 8 hours replicate 3

description:
Library name: TH3
TH3

value: 50 μM chlorquinaldol for 8 hours


title: 107OC

description: Library name: 30804-085

value: ovarian cancer


title: HCT116, LagTag, M.EcoGII-RNAPIISer2p_mintbody, rep1

description: Library name: HCT116_LagTag_Ser2p_rep1


title: RTStop, guanine, KCl, PDS, rep1

description:
Library name: stG4_KCl_PDS_Rep1
Column name in stG4_raw_counts.txt: St_WT_KCl_Rep1_PDS

value: guanine


title: THP-1 cells treated with 50 μM chlorquinaldol for 8 hours replicate 2

description:
Library name: TH2
TH2


title: 104OC

description: Library name: 30804-084


title: HCT116, LagTag, M.EcoGII-LMNB1, rep2

description: Library name: HCT116_LagTag_LMNB1_rep2

value: DD-linker-M.EcoGII-LMNB1, polyclonal


title: RTStop, 7-deaza-guanine, LiCl, rep3

description:
Library name: stG4_7dG_LiCl_Rep3
Column name in stG4_raw_counts.txt: St_7dG_LiCl_Rep3

value: LiCl


title: THP-1 cells treated with 50 μM chlorquinaldol for 8 hours replicate 1

description:
Library name: TH1
TH1


title: 40BC

description: Library name: 30804-083

value: breast cancer


title: HCT116, LagTag, M.EcoGII-LMNB1, rep1

description: Library name: HCT116_LagTag_LMNB1_rep1


title: RTStop, 7-deaza-guanine, KCl, rep3

description:
Library name: stG4_7dG_KCl_Rep3
Column name in stG4_raw_counts.txt: St_7dG_KCl_Rep3

value: KCl


title: THP-1 cells treated with 1 μg/mL 3’-3’-cGAMP for 8 hours replicate 3

description:
Library name: P3
P3

value: 1 μg/mL 3’-3’-cGAMP for 8 hours


title: 36OC

description: Library name: 30804-082

value: saliva


title: RTStop, guanine, LiCl, PDS, rep1

description:
Library name: stG4_LiCl_PDS_Rep1
Column name in stG4_raw_counts.txt: St_WT_LiCl_Rep1_PDS

value: LiCl, PDS


title: HCT116, CUT&Tag, RNAPIISer2p, rep2

description: Library name: HCT116_CUTTag_Ser2p_rep2

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: RNAPIISer2p (Cell Signaling 13499S)


title: RTStop, guanine, LiCl, rep3

description:
Library name: stG4_LiCl_Rep3
Column name in stG4_raw_counts.txt: St_WT_LiCl_Rep3


title: THP-1 cells treated with 1 μg/mL 3’-3’-cGAMP for 8 hours replicate 2

description:
Library name: P2
P2

value: THP-1 cells

value: human monocytic leukemia cell line


title: 37BC

description: Library name: 30804-081

value: female


title: HCT116, CUT&Tag, RNAPIISer2p, rep1

description: Library name: HCT116_CUTTag_Ser2p_rep1

value: colonocyte


title: RTStop, guanine, KCl, rep3

description:
Library name: stG4_KCl_Rep3
Column name in stG4_raw_counts.txt: St_WT_KCl_Rep3

value: RT Stop


title: THP-1 cells treated with 1 μg/mL 3’-3’-cGAMP for 8 hours replicate 1

description:
Library name: P1
P1


title: 38BC

description: Library name: 30804-080


title: HCT116, CUT&Tag, LaminB1, rep2

description: Library name: HCT116_CUTTag_LaminB1_rep2

value: LaminB1 (Abcam ab16048)


title: RTStop, 7-deaza-guanine, LiCl, rep2

description:
Library name: stG4_7dG_LiCl_Rep2
Column name in stG4_raw_counts.txt: St_7dG_LiCl_Rep2


title: THP-1 cells untreated control replicate 3

description:
Library name: C3
C3

value: control


title: HH 30 SAN CN03 treatment pool 2

description:
Library name: SAN_Cn03_2
column name in Log2_exp:SAN_Cn03_2

value: HH stage 30 SAN


title: 32BC

description: Library name: 30804-079


title: ΔadeIJ, chloramphenicol, rep1

description:
Library name: adeIJ.abx_r1
Column name in RNAseq_counts_matrix.txt: adeIJ.abx_r1

value: deltaadeIJ

value: Chloramphenicol


title: HCT116, CUT&Tag, LaminB1, rep1

description: Library name: HCT116_CUTTag_LaminB1_rep1


title: RTStop, 7-deaza-guanine, KCl, rep2

description:
Library name: stG4_7dG_KCl_Rep2
Column name in stG4_raw_counts.txt: St_7dG_KCl_Rep2


title: RTStop, 30ºC, guanine, KCl, rep2

description:
Library name: stG4_30_KCl_Rep2
Column name in stG4_raw_counts.txt: 30_WT_KCl_Rep2

value: guanine


title: THP-1 cells untreated control replicate 2

description:
Library name: C2
C2


title: 29BC

description: Library name: 30804-078

value: breast cancer


title: RTStop, guanine, LiCl, rep2

description:
Library name: stG4_LiCl_Rep2
Column name in stG4_raw_counts.txt: St_WT_LiCl_Rep2

value: LiCl


title: E42_2_VZ

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

description: Library name: Sample 36

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Chinese_treeshrew_genome_2.0(http://www.treeshrewdb.org/)whole genome using Hisat2
Gene expression counts per sample were calculated. First ly, align RNA seq reads to the Chinese_treeshrew_genome_2.0(http://www.treeshrewdb.org/)  by using  Hista2 to generate sam files; Then, sam files were sorted by samtools to generate sorted sam files; Finally, htseq-count program was used to quantify gene reads counts for every sample.
Assembly: Chinese_treeshrew_genome_2.0
Supplementary files format and content: Tab-delimited text files were calculated gene expression read counts  for each Sample

organism: Tupaia belangeri chinensis

source_name: Fetal cortex

extract_protocol:
The fetal tree shrew brain tissues were partitioned into several sections, after that, the specimens were embedded in OCT and then gradually frozen in an ethnol /dry ice, and stored at −80°C until processing. Frozen tissue was cryosectioned at 30μm onto polyethylene naphthalate (PEN) slides (Leica Microsystems) and place immediately into microslide box on dry ice, and stored at -80°C until use.   Taking the section slides from the -80°C freezer and put them on a blotting paper for 30s, and then transfer the slides into the 95% EtOH for 30s, 75% EtOH for 30s and 50% EtOH for 30s, place the slides on a blotting paper. Add 400ul Nissl stain solution on the slide, and incubate at room temperature for 40s. Proceed through the dehydration series (50%, 75% and 95% EtOH) till the two rounds of 100% EtOH, and leave the slides in the final xylene jar for 5 min. After air-drying in the fume hood for 5 min, proceed immediately with laser capture microdissection (LCM).   Laser microdissection was performed on a Leica LMD6000 (Leica Microsystems). Microdissected tissues including CP, OSVZ, SVZ and VZ were collected directly into QIAzol buffer from the miRNeasy Mini Kit (Qiagen) in a 0.2ml tubes, vortexed, centrifuged, and frozen at −80 °C. RNA was isolated following the manufacturer’s directions for the miRNeasy Mini Kit. RNA samples were run on the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA sequencing library construction followed VAHTs mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, #NR611). The total RNA input was 0.7-1ug, mRNA (with ploy-A) binds to mRNA capture beads (with Oligo dT), mRNA is eluted from beads and then fragmented, synthesis of the 1st strand of cDNA using random primers, synthesis of the 2nd strand of cDNA after RNase H digestion. Size selection and library amplication after end repair and adapter ligation, the final RNA sequencing library length is between 320-420bp. Library quality determination analyzed by an Agilent Technologies 2100 Bioanalyzer.

value: Fetal cortex

tag: cortical layer

value: Ventricular zone

value: Embryonic 42 days


title: ΔadeAB, chloramphenicol, rep1

description:
Library name: adeAB.abx_r1
Column name in RNAseq_counts_matrix.txt: adeAB.abx_r1

value: deltaadeAB


title: THP-1 cells untreated control replicate 1

description:
Library name: C1
C1

value: THP-1 cells


title: HH 30 Atria Vehicle treatment pool 1

description:
Library name: Atria_veh_1
column name in Log2_exp:Atria_veh_1

value: HH stage 30 Atria

value: Vehicle


title: 27OC

description: Library name: 30804-077

value: saliva

value: female

value: ovarian cancer


title: E42_2_OSVZ

description: Library name: Sample 35

value: Outer sub-ventricular zone


title: RTStop, 7-deaza-guanine, LiCl, PDS, rep3

description:
Library name: stG4_7dG_LiCl_PDS_Rep3
Column name in stG4_raw_counts.txt: St_7dG_LiCl_Rep3_PDS

value: RT Stop

value: LiCl, PDS


title: 63OC

description: Library name: 30804-095


title: RTStop, guanine, KCl, rep2

description:
Library name: stG4_KCl_Rep2
Column name in stG4_raw_counts.txt: St_WT_KCl_Rep2

value: KCl


title: WT, chloramphenicol, rep3

description:
Library name: wt.abx_r3
Column name in RNAseq_counts_matrix.txt: wt.abx_r3

value: Wild-type

value: Chloramphenicol


title: B16 melanoma tumor (NOD scid), E9 + FMI.12-GFP co-injection, single-cell multiome (ATAC+GEX)

city: Los Angeles

last: Teitell

address: 675 Charles E Young Drive South

department: Pathology and Laboratory Medicine

institute: University of California Los Angeles

description:
Library name: B16-FMI-GFP-E9-tumor
10x single-cell multiome (ATAC + gene expression) with mitochondrial genotyping

data_processing:
Cell Ranger ATAC (v2.1.0) / Cell Ranger ARC (v2.0.2, multiome) were used to align reads to the mouse mm10 reference (NUMT-masked) and to call peaks, fragments, and per-cell matrices.
Mitochondrial single-cell genotyping was performed with mgatk (v0.9.0) to generate per-position, per-cell base counts (A/C/G/T), coverage, and depth tables.
Heteroplasmy and mtDNA variant statistics were computed per cell from the mgatk output.
Cell type annotation and downstream analysis were performed in R/Signac/Seurat.
Assembly: mm10 (GRCm38); chrM (16,299 bp)
Supplementary files format and content: mtscATAC-seq per sample: fragments.tsv.gz (+.tbi), filtered_peak_bc_matrix.h5, peaks.bed, singlecell.csv; mgatk: {A,C,G,T}.txt.gz and coverage.txt.gz (CSV: position,barcode,fwd,rev / position,barcode,coverage), depthTable.txt, chrM_refAllele.txt, variant_stats.tsv.gz, cell_heteroplasmic_df.tsv.gz.
Supplementary files format and content: Multiome per sample: atac_fragments.tsv.gz (+.tbi), filtered_feature_bc_matrix.h5 (Gene Expression + Peaks), per_barcode_metrics.csv; plus mgatk mtDNA files as above.

source_name: melanoma

growth_protocol: rho0 B16 melanoma and 4T1 mammary carcinoma cells were repopulated with defined homoplasmic single-nucleotide mtDNA variants by MitoPunch mitochondrial transfer to generate isogenic, mtDNA-barcoded tumor cell lines, maintained in DMEM/10% FBS at 37C, 5% CO2.

extract_protocol:
Tumors were dissociated to single-cell/nuclei suspensions; nuclei were isolated for single-cell ATAC-seq / 10x Multiome following 10x Genomics protocols.
Libraries were prepared with the 10x Genomics Chromium Single Cell ATAC kit (mtscATAC-seq samples) or the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit (NOD scid samples), per manufacturer instructions.

treatment_protocol: Barcoded tumor cells were implanted into syngeneic (B16 in C57BL/6; 4T1 in BALB/c) or immunodeficient NOD scid mice and grown in vivo; tumors were harvested for single-cell profiling.

value: melanoma

value: tumor and tumor-infiltrating cells

value: co-injected E9 and GFP-labeled FMI.12 rho0 B16 mtDNA mutants

value: tumor in NOD scid host, in vivo


title: E42_2_MZ

description: Library name: Sample 34

value: Fetal cortex

value: Marginal zone

value: Embryonic 42 days


title: RTStop, 7-deaza-guanine, LiCl, rep1

address: 120 Mason Farm

description:
Library name: stG4_7dG_LiCl_Rep1
Column name in stG4_raw_counts.txt: St_7dG_LiCl_Rep1

extract_protocol:
In vitro transcribed synthetic RNA pools were made with guanine or 7dG. RT stop: RNAs were annealed in noted cations, then incubated with water or pyridostatin (where noted) for 10 minutes. RNA was reverse transcribed (RT) by SuperScript III in first strand buffer substituted with the noted cations for 40 minutes. Unless specifcially noted, RT was performed at 40ºC. After 40 minutes, samples were heated at 100ºC for 5 minutes, then proceeded to library preparation. RBNS: RNAs were annealed in KCl (or 7dG in LiCl), and allowed to incubate with noted proteins conjugated to streptavidin binding proteins. Bound RNA was eluted from streptavidin magnetic beads and concentrated by phenol-chloroform extraction. Subsequent RT was performed with SuperScript III in first strand buffer substituted with LiCl.
RT samples were PCR amplified with Phusion DNA polymerase to attach Illumina adapters and subsequently agarose gel purified. Concentrations were assessed by the Qubit dsDNA assay, and equivalent nanograms of each sample were pooled for sequencing.

value: LiCl


title: 28BC

description: Library name: 30804-076

value: saliva

value: breast cancer


title: B16 melanoma tumor (NOD scid), FMI.12-GFP, single-cell multiome (ATAC+GEX)

description:
Library name: B16-FMI-GFP-tumor
10x single-cell multiome (ATAC + gene expression) with mitochondrial genotyping

value: GFP-labeled rho0 B16 with homoplasmic mtDNA mutant (FMI.12)


title: 24OC

description: Library name: 30804-075

value: female

value: ovarian cancer


title: E42_2_IZ

description: Library name: Sample 33

value: Intermediate zone


title: RTStop, 7-deaza-guanine, KCl, rep1

description:
Library name: stG4_7dG_KCl_Rep1
Column name in stG4_raw_counts.txt: St_7dG_KCl_Rep1

value: RT Stop

value: KCl


title: 4T1 mammary carcinoma tumor, E9 mtDNA mutant, mtscATAC-seq

description:
Library name: 4T1-E9-tumor-994
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

source_name: mammary carcinoma

value: mammary carcinoma

value: rho0 4T1 repopulated with homoplasmic mtDNA mutant (E9)

value: tumor in BALB/c host, in vivo


title: 25OC

description: Library name: 30804-074


title: 227HS

description: Library name: 30804-091

value: healthy


title: E42_2_ISVZ

description: Library name: Sample 32

value: Inner sub-ventricular zone


title: RTStop, guanine, LiCl, rep1

description:
Library name: stG4_LiCl_Rep1
Column name in stG4_raw_counts.txt: St_WT_LiCl_Rep1

value: guanine


title: 23OC

description: Library name: 30804-073


title: E42_2_CPo

description: Library name: Sample 31

value: Fetal cortex

value: Outer cortical plate


title: RTStop, guanine, KCl, rep1

description:
Library name: stG4_KCl_Rep1
Column name in stG4_raw_counts.txt: St_WT_KCl_Rep1


title: 22OC

description: Library name: 30804-072


title: 4T1 mammary carcinoma tumor, WTP (wild-type mtDNA), mtscATAC-seq

description:
Library name: 4T1WTP010226
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

value: tumor and tumor-infiltrating cells

value: rho0 4T1 repopulated with wild-type mtDNA (WTP)


title: E42_2_CPi

description: Library name: Sample 30

value: Inner cortical plate

value: Embryonic 42 days


title: brl-tM, replicate 2

city: Freising

first: Brigitte

last: Poppenberger

state: Freising

address: Liesel-Beckmann-Str. 1

institute: Technical University of Munich

description:
Library name: FCHHL23CCX2_L2_ARArldtH005819-29
Arabidopsis thaliana brl-tM triple BR receptor mutant, replicate 2.

data_processing:
Raw WGBS reads were processed using the MethylStar pipeline (v1.2.3). Reads were quality-checked with FastQC and trimmed using Trim Galore. Adapter- and quality-trimmed reads were aligned to the Arabidopsis thaliana TAIR10 reference genome using Bismark (v0.23.0) with Bowtie2. Methylation calling was performed using METHimpute (v1.18.0) to generate probabilistic estimates of cytosine methylation in CG, CHG, and CHH contexts. Strand-specific cytosine methylation profiles were converted to bigWig format using custom scripts.
DMRs were called using the jDMR-grid tool (published preliminary in Hazarika et al., 2022; available on GitHub repository: https://github.com/jlab-code/jDMRgrid/), comparing each mutant to its designated control wild-type to avoid batch effects. genome into non-sliding 100 bp regions with bins. We used all consecutive bins in the analysis. As filtering approach, we used jDMR build-in control/treatment strategy, for which both of the replicate have the same state call (replicate.consensus = 1).
Separate controls were used for the ces-D/qM and bri1-1/brl-tM mutant groups.
All coordinates are based on the TAIR10 (v57) genome build.
Assembly: TAIR10 v57
Supplementary files format and content: bigWig files: strand-specific cytosine methylation levels (CG, CHG, CHH contexts)
Supplementary files format and content: METHimpute files: CX-like reports generated from METHimpute implemented in MethylStar pipeline (CG, CHG, CHH and all contexts)

organism: Arabidopsis thaliana

source_name: 21 dag soil-grown aerial tissue

growth_protocol: Seeds were germinated on ½ MS medium (Duchefa Biochemie), transferred to soil 7–8 days after germination, and grown under long-day conditions (16 h light / 8 h dark, 80 µmol m⁻² s⁻¹, 50% humidity) in a growth cabinet (Bright Boy, CLF Plant Climatics, Wertingen, Germany) at 21 ± 2 °C.

extract_protocol:
DNA was extracted from 100 mg of aerial tissue of 3-week-old plants using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). DNA was precipitated using sodium acetate, ethanol, and glycogen, and quality-checked before submission.
DNA was bisulfite-converted and used for library preparation by BGI Genomics (Tech Solution NGS Lab, Hong Kong) using the DNBseq WGBS protocol for sequencing on the Illumina HiSeq X Ten platform.

treatment_protocol: For Hpa-infected samples, 2-week-old plants were spray-inoculated with Hyaloperonospora arabidopsidis isolate Noco2 (5 × 10⁴ conidiospores/mL). Control samples were mock-treated with water. Plants were incubated at 18 °C under high humidity (90–100%) and 16 h light / 8 h dark conditions.

value: 21 dag soil-grown aerial tissue

value: brl-tM

tag: batch


title: 20BC

description: Library name: 30804-071

tag: tissue

value: saliva

value: female

value: breast cancer


title: E42_1_VZ

description: Library name: Sample 29

value: Ventricular zone


title: B16 melanoma tumor, MB77 mtDNA mutant, mtscATAC-seq

description:
Library name: B16MB77
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

value: melanoma

value: rho0 B16 repopulated with homoplasmic mtDNA mutant (MB77)

value: subcutaneous tumor in C57BL/6 host, in vivo


title: brl-tM, replicate 1

description:
Library name: FCHHL23CCX2_L2_ARArldtH005818-26
Arabidopsis thaliana brl-tM triple BR receptor mutant, replicate 1.


title: E42_1_OSVZ

description: Library name: Sample 28

value: Outer sub-ventricular zone


title: B16 melanoma tumor, E9 mtDNA mutant, mtscATAC-seq

description:
Library name: B16E9M
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

value: rho0 B16 repopulated with homoplasmic mtDNA mutant (E9)


title: 21BC

description: Library name: 30804-070


title: RTStop, guanine, LiCl, PDS, rep2

first: Daniel

last: Dominguez

description:
Library name: stG4_LiCl_PDS_Rep2
Column name in stG4_raw_counts.txt: St_WT_LiCl_Rep2_PDS

value: RT Stop

value: guanine

value: LiCl, PDS


title: bri1-1, replicate 2

description:
Library name: FCHHL23CCX2_L2_ARArldtH005817-18
Arabidopsis thaliana bri1-1 BR receptor mutant, replicate 2.


title: 31BC

description: Library name: 30804-069


title: E42_1_MZ

description: Library name: Sample 27

value: Fetal cortex

value: Marginal zone


title: 94BC

description: Library name: 30804-088


title: B16 melanoma tumor, FMI.12 mtDNA mutant, mtscATAC-seq

description:
Library name: B16FMI
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

value: tumor and tumor-infiltrating cells

value: rho0 B16 repopulated with homoplasmic mtDNA mutant (FMI.12)


title: bri1-1, replicate 1

description:
Library name: FCHHL23CCX2_L2_ARArldtH005816-16
Arabidopsis thaliana bri1-1 BR receptor mutant, replicate 1.

value: 21 dag soil-grown aerial tissue


title: B16 melanoma tumor, WTP (wild-type mtDNA), mtscATAC-seq

description:
Library name: B16WTP
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

value: rho0 B16 repopulated with wild-type mtDNA (WTP)


title: Col-0 control (bri1-1 and brl-tm), replicate 2

description:
Library name: FCHHL23CCX2_L2_ARArldtH005811-9_1
Wild-type Arabidopsis thaliana Col-0, replicate 2. Control for bri1-1 and brl-tM mutants.