title: Spleen,LPS_R-848_CpGODN,Rep3

city: Bareilly

first: Saravanan

last: Ramakrishnan

state: Uttar Pradesh

address: Izatnagar

department: Immunology Section

country: India

institute: Indian Veterinary Research Instittue

description: Library name: LRC3

data_processing:
All samples were sequenced using NovaSeqTM 6000 (Illumina) platform and 2×150 bp paired-end reads were generated. The quality of raw sequence reads was checked using FastQC software v.0.12.0.
The pre-processed raw reads were filtered using fastp v.0.22.0  for removal of adapters, low quality reads and unknown bases.
The clean reads were mapped to chicken reference genome (GRCg7b, GCF_016699485.2) using HISAT2 v2.2.1 software.
Read counting was performed using featureCounts v.2.0.3.
Assembly: chicken reference genome; Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.110.gtf, NCBI accession no. GCF_016699485.2
Supplementary files format and content: tab-delimited text file includes read counts of all samples

organism: Gallus gallus

source_name: Spleen

extract_protocol:
Total RNA extracted from spleen using TRIzol reagent (Invitrogen).
The sequencing libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs) following manufacturer's protocol.

value: Spleen

value: wild

value: splenic cells

value: White Leghorn

value: triple agonists


title: H3K27me3 coverage on control -treated spheroids at 3 days-post treatment, replicate 2

status: Public on Jul 30 2026

type: SRA

city: Madrid

first: Leonardo

last: Beccari

address: Nicolas Cabrera 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC)

description: Library name: Ctrl_3d_H3K27me3_rep2

library_source: genomic

data_processing:
CUT&Tag sequencing reads were processed using a custom workflow in Galaxy (https://usegalaxy.eu). Adapter trimming and quality filtering were performed with Cutadapt (Galaxy version 5.2), and reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.5.4) with the --very-sensitive option. Alignments were sorted using Picard SortSam (version 3.1.1.0), and further filtering was performed with SAMtools (version 1.8) to retain properly mapped reads. For H3K27me3 samples, genome-wide coverage tracks were generated using deepTools bamCoverage with CPM normalization (10 bp bins) and converted to BigWig files for visualization. Peaks were called per replicate using MACS3 in broad peak mode (--broad, q-value < 0.05), using paired-end mode (BAMPE) and retaining duplicates (--keep-dup all). For H3K4me3 samples, coverage tracks were generated using bedtools genomecov with scaling factors calculated using the ChIPseqSpikeInFree framework (Hongjian J et al 2020) and converted to BigWig format. Peaks were called using MACS3 in narrow peak mode (q-value < 0.05, --keep-dup all). Reproducible peaks were identified using the IDR framework.
Assembly: mm10
Supplementary files format and content: coverage files are providaded as bigwig, MACS3 callpeak results as provided as narrowPêak (H3K4me3) or .broadPeak (H3K27me3( files
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: tumoroids

extract_protocol:
CUT&Tag was performed using the Active Motif protocol (Active Motif #53160), following the manufacturer’s specifications. Briefly, spheroids per sample were dissociated using Accutase, and 500,000 cells per sample were immobilized on concanavalin A-coated magnetic beads. Cells were sequentially incubated with 2 µg of primary antibodies against H3K4me3 (Sigma 17-614) or H3K27me3 (Abcam ab6002) overnight at 4°C with gentle rocking, followed by incubation with a-rabbit (H3K4me3) or a-mouse (H3K27me3) secondary antibodies  to enhance signal detection. Bead-bound cells were then incubated with a protein A–Tn5 transposase fusion protein preloaded with sequencing adapters. After targeted tagmentation (60 min at 37°C), DNA fragments were released by proteinase K digestion and purified using column-based cleanup for library preparation.
Libraries were prepared using KAPA polymerase (Roche, KK2612) and single-index barcoded primers  as described in Buenrostro J et al 2025 . Library amplification cycles were determined by qPCR (CT + 2 for each sample). Libraries were purified using SPRI beads (CleanNA, # CNGS-0050), and quality was assessed by fluorometric quantification and fragment size analysis. Sequencing was performed on an Illumina NovaSeq X platform using 150 bp paired-end reads.

tag: tissue

value: tumoroids

tag: cell line

value: PyMT derived organoids

tag: cell type

value: breast cancer

tag: genotype

value: WT

tag: treatment

value: Ctrl

tag: batch

tag: antibody


title: Lean-12

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

country: China

institute: Nanjing Medical University

description: Library name: Lean-12

data_processing:
The raw bisulfite sequencing reads were trimmed to remove adaptors and low-quality bases by using trim_galore (v0.6.10) (parameters: -q 20 --phred33 --length 30 --stringency 3 --paired --clip_R1 10 --clip_R2 10). Next, Bismark (v0.24.2) was used to map clean reads to GRCm38/GRCh38 with single-end alignment mode (parameters: --non_directional --bowtie2 --bam --single_end). PCR duplicates were removed using deduplicate_bismark with default parameters. And only the high-quality reads (MAPQ > 10) were retained for further analysis. DNA methylation level estimation. The DNA methylation level of each cytosine site in the reference genome sequence was calculated as the percentage of reads supporting C (methylated). Unless otherwise specified, the DNA methylation level of CpG sites in a given sample or region refers to the average methylation level across that sample or region. Owing to the low number of input cells, CpG sites with read depths ≥1 were included for methylation analysis. For DNA methylation pattern profiling, the whole genome was divided into consecutive 20-kb windows, and the average methylation level within each bin was calculated. Principal component analysis (PCA) of methylation data was performed using methylKit (v1.30.0). Differentially methylated regions (DMRs) calling. Differential methylation analysis was performed using metilene (v0.2.6) with default parameters, and differentially methylated regions (DMRs) were annotated using ChIPseeker (v1.36.0).
Assembly: GRCh38,GRCm39
Supplementary files format and content: BigWig including CG sites methylation values for each sample
Library strategy: EM-seq

organism: Homo sapiens

source_name: oocyte

extract_protocol:
Collect 15 mouse oocytes/one human oocyte for cell lysis.
Whole-genome bisulfite sequencing (WGBS) was performed on mouse oocytes using 15 oocytes as input, whereas Enzymatic Methyl-seq (EM-seq) was applied to human oocytes starting from a single cell due to its high efficiency with minimal input. Library preparation and sequencing: Mouse metaphase II (MII) oocytes (n = 15 per replicate, two biological replicates per group) were used for WGBS. Briefly, cells were lysed in buffer (10 mM Tris-HCl, pH 7.4, 2% SDS), and genomic DNA was extracted and digested with proteinase K. Purified DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (ZYMO, D5008), followed by purification with Agencourt AMPure XP beads (Beckman). The converted DNA was end-repaired and dA-tailed, then ligated to Illumina sequencing adapters. Libraries were amplified for 13 cycles using Illumina universal PCR primer and indexed primers. For human samples, individual oocytes were lysed and genomic DNA were fragmented to ~ 300 bp using a DNA fragmentation device (Shanghai Jingxin, DNA Fragmentation Model 26A). Libraries were constructed using the NEBNext® Enzymatic Methyl-seq kit (NEB, E7120 L) and the Unique Dual Index Primer pairs (NEB, E7140L). Unmethylated lambda phage DNA and CpG-methylated plasmid pUC19 DNA were included as negative and positive controls. For single-oocyte libraries, amplification was performed for 18 cycles. Libraries were purified using the DNA Clean & Concentrator-5 kit (ZYMO, D4013). Finally, equimolar amounts of libraries were pooled and subjected to paired-end sequencing on an Illumina NovaSeq 6000 platform.

value: oocyte


title: Spleen,LPS_R-848_CpGODN,Rep2

description: Library name: LRC2

library_source: transcriptomic

molecule: total RNA


title: Treg (CD127-CD25+) - Donor 012 - Day 1

city: Seattle

first: Laura

last: Cooeny

state: WA

address: 1201 9th Ave

department: University of Michigan

country: USA

institute: Immune Tolerance Network

description:
Library name: lib59117_AAAFM27HV
Donor ID: 012; Study day: D1

data_processing:
Adapter and quality trimming of raw reads was performed using FastqMcf (ea-utils).
Read quality was assessed using FastQC (v0.11.3).
Alignment metrics, duplication rates, and RNA-seq QC metrics (ribosomal/intronic/UTR/coding base composition, 5'/3' bias) were computed using Picard tools (v1.134; CollectRnaSeqMetrics, MarkDuplicates) and Samtools (v1.2).
Base-calling and demultiplexing were performed automatically on BaseSpace (Illumina) to generate FASTQ files.
Reads were aligned to the reference genome using STAR (v2.4.2a); gene-level read counts were generated using HTSeq-count (v0.4.1) in 'intersection (nonempty)' mode with a minimum alignment quality of 20.
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: Comma-separated file (combined_counts_GEO_submission.csv) containing gene-level raw read counts, with Ensembl gene IDs as rows and library names (matching "library name" column in SAMPLES section) as columns.

source_name: PBMC

extract_protocol:
PBMCs were thawed and immediately immunolabeled and FACS-sorted for sequencing. Dead cells were excluded from all sorts by staining with the Fixable Viability Dye eFluor™ 780 (eBioscience). For bulk RNA-seq, 250–500 CD4+CD127loCD25+ Tregs were sorted directly into lysis buffer, and cDNA was prepared using the SMART-Seq Ultra Low Input RNA Kit for Sequencing (Takara Bio).
RNA-seq libraries were constructed using the NexteraXT DNA Library Preparation Kit (Illumina) with half the recommended volumes and reagents. Paired-end sequencing of pooled libraries was run on a NextSeq 2000 (Illumina) with 59-base reads and a target depth of 5 million reads per sample.

treatment_protocol: Healthy adult volunteers in the Phase 1a single ascending dose trial received a single dose of Placebo, 1mg, 3.5mg, 5mg, or 10mg IL-2 mutein MK-6194/PT-101 subcutaneously. PBMC samples were collected at pre-treatment baseline (-10) and on study days 1 (prior to the dose, which occurred on day 1), 8, 15, and 29 and cryopreserved. For details on the clinical trial, see Scheid, et al., Safety, pharmacokinetics, and pharmacodynamics of MK-6194, an IL-2 mutein designed to selectively activate regulatory T cells: single ascending dose and multiple ascending dose trial data, ImmunoHorizons, Volume 9, Issue 5, May 2025, vlaf005, https://doi.org/10.1093/immhor/vlaf005.

value: PBMC

value: 1mg mutein


title: H3K27me3 coverage on control -treated spheroids at 3 days-post treatment, replicate 1

description: Library name: Ctrl_3d_H3K27me3_rep1


title: Lean-11

description: Library name: Lean-11


title: H3K4me3 coverage on THC -treated spheroids at 3 days-post treatment, replicate 2

description: Library name: THC_3d_H3K4me3_rep2

value: THC


title: Spleen,LPS_R-848_CpGODN,Rep1

description: Library name: LRC1


title: Treg (CD127-CD25+) - Donor 222 - Day 29

description:
Library name: lib59116_AAAFM27HV
Donor ID: 222; Study day: D29

value: 5mg mutein


title: Lean-10

description: Library name: Lean-10


title: Spleen,R-848_CpGODN,Rep3

description: Library name: RC3

value: dual agonists


title: Treg (CD127-CD25+) - Donor 222 - Day 15

description:
Library name: lib59115_AAAFM27HV
Donor ID: 222; Study day: D15


title: H3K4me3 coverage on THC -treated spheroids at 3 days-post treatment, replicate 1

description: Library name: THC_3d_H3K4me3_rep1


title: Treg (CD127-CD25+) - Donor 222 - Day 8

description:
Library name: lib59114_AAAFM27HV
Donor ID: 222; Study day: D8


title: Lean-9

description: Library name: Lean-9


title: Spleen,R-848_CpGODN,Rep2

description: Library name: RC2


title: H3K4me3 coverage on SR2 -treated spheroids at 3 days-post treatment, replicate 2

description: Library name: SR2_3d_H3K4me3_rep2


title: Lean-8

description: Library name: Lean-8


title: Spleen,R-848_CpGODN,Rep1

description: Library name: RC1


title: Treg (CD127-CD25+) - Donor 222 - Day 1

description:
Library name: lib59113_AAAFM27HV
Donor ID: 222; Study day: D1


title: Lean-7

description: Library name: Lean-7


title: H3K4me3 coverage on SR2 -treated spheroids at 3 days-post treatment, replicate 1

description: Library name: SR2_3d_H3K4me3_rep1


title: Treg (CD127-CD25+) - Donor 116 - Day 29

description:
Library name: lib59112_AAAFM27HV
Donor ID: 116; Study day: D29

value: 10mg mutein


title: Spleen,Control,Rep3

description: Library name: C3

value: Spleen

value: vehicle


title: Spleen,Control,Rep2

description: Library name: C2

value: wild

value: splenic cells


title: Treg (CD127-CD25+) - Donor 116 - Day 15

description:
Library name: lib59111_AAAFM27HV
Donor ID: 116; Study day: D15


title: Lean-6

description: Library name: Lean-6


title: H3K4me3 coverage on control -treated spheroids at 3 days-post treatment, replicate 2

description: Library name: Ctrl_3d_H3K4me3_rep2


title: Treg (CD127-CD25+) - Donor 116 - Day 8

description:
Library name: lib59110_AAAFM27HV
Donor ID: 116; Study day: D8


title: Lean-5

description: Library name: Lean-5


title: Spleen,Control,Rep1

description: Library name: C1

value: White Leghorn


title: M2d

type: RNA

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

hyb_protocol: 347 genes were included in the analysis. Gene panel probe hybridization was run overnight for 18 hours at 50°C. Slides were washed the next day to remove unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched.

scan_protocol: Imaging processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system. Data was acquired on instrument software version 4.0.1.4 and analysis version xenium-4.0.1.0.

data_processing: Xenium Onboard Analysis: 4.0.1.0. Data processing, QC, normalization, integration, clustering and visualization using nf_xpatial v.1.0.0, and R using Seurat v.5.3.0 packages.

label: Xenium probe set

source_name: Brain

label_protocol: Xenium probe set

growth_protocol: Adult C57BL/6J mice (11-12 weeks old) were purchased from Jackson Labs and housed in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food and water. Bedding and enrichment were changed weekly by animal resources program staff.

extract_protocol: tissue preparation protocol: Mice were euthanized by live decapitation and whole brains were rapidly extracted and immediately flash frozen in 2-methyl butane on dry ice. Brains were kept at -80ºC until further processing.  Tissue sections were cut at a thickness of 10 μm and placed onto a Xenium slide followed by fixation and permeabilization.

treatment_protocol: Mice were experimentally naïve at the time of tissue harvesting.

value: Brain

tag: tissue preservation method

value: Fresh Frozen

tag: age

value: 11-12 weeks


title: 7d culture of Tbxt::GFP+ in FGF/CHIR, sorted for double negative rep3

city: Edinburgh

first: Anahi

last: Binagui-Casas

address: 5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: The University of Edinburgh

description: Library name: 7d_TBXT+_DN3

data_processing:
Data processing performed by Plasmidsaurus: FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1. Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Alignment to the appropriate reference genome using STAR aligner v2.7.* with non-canonical splice junction removal and output of unmapped reads. Coordinate sorting of BAM files using samtools v1.21. UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0. Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RustQC v0.2.1.
Assembly: GRCm39_114
Supplementary files format and content: csv file include CPM for each sample

source_name: STR-KI

growth_protocol: NMP differentiation, following Gouti et al. 2014, STR-KI mESCs were plated at a density of 5,000 cells/cm2 on 0.1% gelatin-coated plates in N2B28 medium. N2B27 medium consisted of a 1:1 mixture of Neurobasal (Thermofisher #21103049) and Advanced DMEM/F12 (Thermofisher #12634028) supplemented with 2 mM L-Glutamine, 50 µM 2-mercaptoethanol, 0.5X B27 (Thermofisher #17504001) and 0.5X N2 (Thermofisher #17502048). Cells were supplemented with 10 ng/mL FGF2 (R&D Systems #3718-FB) for 48 hours, and for 24 additional hours with both 10 ng/mL FGF2 and 5µM CHIRON99021 (Axon #1386).

extract_protocol:
Bead-based extraction approach from cells preserved in Zymo DNA/RNA Shield.
Library preparation by Plasmidsaurus: Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

treatment_protocol: Cells were sorted at different time points of the protocol and replated in FGF/CHIR or FGF alone.

value: STR-KI

value: NMP derivatives

value: Sox2::mCherry/WT, Tbxt::GFP/WT

value: NMP differentiation


title: Lean-4

description: Library name: Lean-4

value: oocyte


title: Treg (CD127-CD25+) - Donor 116 - Day 1

description:
Library name: lib59109_AAAFM27HV
Donor ID: 116; Study day: D1

value: PBMC


title: Lean-3

description: Library name: Lean-3


title: Treg (CD127-CD25+) - Donor 112 - Day 29

description:
Library name: lib59108_AAAFM27HV
Donor ID: 112; Study day: D29


title: M2c


title: 7d culture of Tbxt::GFP+ in FGF/CHIR, sorted for double negative rep2

description: Library name: 7d_TBXT+_DN2


title: M2b


title: Lean-2

description: Library name: Lean-2


title: M2a


title: Lean-1

description: Library name: Lean-1


title: Treg (CD127-CD25+) - Donor 112 - Day 8

description:
Library name: lib59106_AAAFM27HV
Donor ID: 112; Study day: D8


title: Treg (CD127-CD25+) - Donor 112 - Day 15

description:
Library name: lib59107_AAAFM27HV
Donor ID: 112; Study day: D15


title: LAM16 [scATAC-seq]

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample 16

library_source: genomic single cell

data_processing:
snATAC-seq data was processed using Cell Ranger ATAC (10x Genomics). Signac was used for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Raw cell-by-peak count Matrix and filtered cell-by-peak count matrix in HDF5 format from 10x Cell Ranger ATAC

source_name: Lung

extract_protocol:
1. Roughly chop tissue into small cubes on petri dish on ice using razor blade.
2. Weigh out 30 mg lung tissue and place in petri dish on ice. Save the remaining tissue – freeze in LN.
3. Add 1 mL lysis buffer to lung tissue in petri dish. Start timer for 10 min. Mince ~50 times with razor blade.
4. Using cut 1 mL tip, pipet tissue with lysis buffer into pre-chilled 2 mL glass dounce on ice.
5. Dounce homogenize 15X with loose pestle. Pipet tissue with lysis buffer to 200 µM filter on 50 mL conical. Transfer flow-through back to dounce.
6. Dounce 7X with tight pestle (or until no significant resistance).
7. After 7 min lysis total, transfer to 15 mL conical with 2 mL wash buffer.
8. Filter using 40 µM filter on 50 mL conical; transfer flow-through to 15 mL conical.
9. Centrifuge at 400 g for 5 min at 4 C
10. Remove super, add 1 mL chilled wash buffer (free of EDTA and protease inhibitor).
11. Centrifuge at 400 g for 5 min at 4 C. Remove super
12. Re-suspend in 200-300 µL 10X re-suspension buffer.
13. Pass through 40 µM Flowmi.
14. Determine the nuclei concentration and submit for snATAC-Seq.
snATAC-seqq libraries were prepared with 10xGenomics Chromium Nuclei Isolation Kit (without RNase Inhibitor) according to manufacturer's construction

value: Lung


title: Treg (CD127-CD25+) - Donor 023 - Day 8

description:
Library name: lib59126_AAAFM27HV
Donor ID: 023; Study day: D8

value: 1mg mutein


title: M1d


title: Treg (CD127-CD25+) - Donor 112 - Day 1

description:
Library name: lib59105_AAAFM27HV
Donor ID: 112; Study day: D1

value: 10mg mutein


title: 7d culture of Sox2::mcherry+ in FGF, sorted for Sox2::mcherry+ rep2

description: Library name: 7d_Sox2_FGF_Sox2+_2


title: Treg (CD127-CD25+) - Donor 108 - Day 29

description:
Library name: lib59104_AAAFM27HV
Donor ID: 108; Study day: D29

value: Placebo


title: M1c


title: LAM15 [scATAC-seq]

description: Library name: Sample 15


title: 7d culture of Sox2::mcherry+ in FGF, sorted for Sox2::mcherry+ rep1

description: Library name: 7d_Sox2_FGF_Sox2+_1


title: LAM14 [scATAC-seq]

description: Library name: Sample 14


title: M1b


title: H3K4me3 coverage on control -treated spheroids at 3 days-post treatment, replicate 1

description: Library name: Ctrl_3d_H3K4me3_rep1

value: tumoroids

value: PyMT derived organoids

value: breast cancer

value: WT

value: Ctrl


title: 7d culture of Sox2::mcherry+ in FGF, sorted for double negative

description: Library name: 7d_Sox2_FGF_DN


title: Treg (CD127-CD25+) - Donor 108 - Day 15

description:
Library name: lib59103_AAAFM27HV
Donor ID: 108; Study day: D15


title: 7d culture of Sox2::mcherry+ in FGF/CHIR, sorted for double negative

description: Library name: 7d_Sox2_FGFCHIR_DN


title: M1a

value: Brain

value: Fresh Frozen


title: LAM13, ATAC

description:
Library name: Sample 13_ATAC
10X Multiome
LAM13.tar.gz
Chromium X Series

data_processing:
Demultiplexed data was processed using the 10X Cell Ranger count pipeline
Further processing was done with Seurat v4.1.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format
Supplementary files format and content: 10x Cell Ranger fragments fille

extract_protocol:
Frozen tissue (30 mg) from LAM lungs was minced and lysed in buffer, then filtered. Nuclei were sorted using Sony SH800 and 150,000 nuclei were collected. Nuclei were spun and resuspended and concentrations adjusted for 10X multiome: 11,000 nuclei were loaded to target recovery of 7,000 nuclei. Fresh tissue from LAM44 was minced lysed in buffer yielding 300,000 nuclei. Nuclei were washed and resuspended. Final nuclei (11,000) were loaded for 10X.
Library was constructed by following 10X protocol: Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression User Guide (CG000338).


title: Obese-1

description: Library name: Obese-1


title: Treg (CD127-CD25+) - Donor 108 - Day 8

description:
Library name: lib59102_AAAFM27HV
Donor ID: 108; Study day: D8


title: F2d

value: 11-12 weeks


title: LAM13, GEX

description:
Library name: Sample 13_RNA
10X Multiome
LAM13.tar.gz
Chromium X Series

library_source: transcriptomic single cell


title: Treg (CD127-CD25+) - Donor 108 - Day 1

description:
Library name: lib59101_AAAFM27HV
Donor ID: 108; Study day: D1


title: 48h culture of NMPs in FGF/CHIR, sorted for Tbxt::GFP+ rep2

description: Library name: 48h_Tbxt_2

value: STR-KI

value: NMP derivatives


title: F2c


title: LAM10, ATAC

description:
Library name: Sample 10_ATAC
10X Multiome
LAM10.tar.gz
Chromium X Series


title: 48h culture of NMPs in FGF/CHIR, sorted for Tbxt::GFP+ rep1

description: Library name: 48h_Tbxt_1

value: Sox2::mCherry/WT, Tbxt::GFP/WT

value: NMP differentiation


title: Treg (CD127-CD25+) - Donor 196 - Day 29

description:
Library name: lib59099_AAAFM27HV
Donor ID: 196; Study day: D29

value: PBMC

value: 3.5mg mutein


title: F2b


title: LAM10, GEX

description:
Library name: Sample 10_RNA
10X Multiome
LAM10.tar.gz
Chromium X Series

value: Lung


title: Treg (CD127-CD25+) - Donor 196 - Day 15

description:
Library name: lib59097_AAAFM27HV
Donor ID: 196; Study day: D15


title: 7d culture of Sox2::mcherry+ in FGF/CHIR, sorted for Sox2::mcherry+

description: Library name: 7d_Sox2_FGFCHIR_Sox2+


title: F2a


title: 48h culture of NMPs in FGF/CHIR, sorted for Sox2::mcherry+ rep2

description: Library name: 48h_Sox2_2


title: DMSO rep2

first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Library name: DMSO rep2
DMSO rep2

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The human Brunello CRISPR KO pooled library was obtained from Feng Zhang (Addgene 73179, 73178). The  sequencing reads were aligned to the Brunello library using bowtie2
Reads were counted against Barcodes in R
Counts per million ( cpm) reads were calculated using the cpm() function from R package, edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample.

source_name: LNCaP

growth_protocol: Cells were cultured in RPMI+10% FBS+Pen/Strep at 37C 5% CO2

extract_protocol:
DNA was harvested using the Blood & Cell Culture DNA Midi Kit
Barcode amplification was performed with 2 rounds of amplification using Phusion-HF polymerase , each 14 cycles.  Illumina adapters were added on as part of the primers for the second round PCR.

treatment_protocol: LNCaP cells were transduced with the pooled sgRNA libraries and cultured for 25 days with 10 μM ENZ, 10 nM R1881, or DMSO vehicle control. Cells (6 × 107) were used per group. Cells were treated with puromycin to kill untransduced cells at the start of the experiement

value: LNCaP

value: DMSO


title: Treg (CD127-CD25+) - Donor 196 - Day 8

description:
Library name: lib59095_AAAFM27HV
Donor ID: 196; Study day: D8


title: 48h culture of NMPs in FGF/CHIR, sorted for Sox2::mcherry+ rep1

description: Library name: 48h_Sox2_1


title: R1881A rep2

description:
Library name: R1881A rep2
R1881A rep2


title: Treg (CD127-CD25+) - Donor 196 - Day 1

description:
Library name: lib59093_AAAFM27HV
Donor ID: 196; Study day: D1


title: F1d


title: NMPs rep3, sorted cells for Sox2::mcherry and Tbxt::GFP double positive

description: Library name: NMP3

value: NMP


title: F1c


title: Enza rep2

description:
Library name: Enza rep2
Enza rep2

value: Enzalutamide


title: Treg (CD127-CD25+) - Donor 195 - Day 29

description:
Library name: lib59091_AAAFM27HV
Donor ID: 195; Study day: D29

value: Placebo


title: NMPs rep2, sorted cells for Sox2::mcherry and Tbxt::GFP double positive

description: Library name: NMP2


title: F1b


title: F1a


title: Treg (CD127-CD25+) - Donor 195 - Day 15

description:
Library name: lib59089_AAAFM27HV
Donor ID: 195; Study day: D15


title: NMPs rep1, sorted cells for Sox2::mcherry and Tbxt::GFP double positive

description: Library name: NMP1


title: Day0 rep2

description:
Library name: Day0 rep2
Day0 rep2


title: DMSO rep1

description:
Library name: DMSO rep1
DMSO rep1


title: Treg (CD127-CD25+) - Donor 195 - Day 8

description:
Library name: lib59087_AAAFM27HV
Donor ID: 195; Study day: D8


title: pd1245_LP_25_S18

city: Chapel Hill

first: Jieun

last: Park

state: North Carolina

address: 116 Manning Drive, CB 7250, Unive7008B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

description: Library name: pd1245_LP_Rep3

data_processing:
Raw sequence quality was assessed using FastQC (v0.11.7). Adapter sequences and low-quality bases were removed using Trim Galore (v0.6.5).
Trimmed reads were aligned to the Zebrafish genome (GRCz11/danRer11) using STAR (v2.7.3a).
Genome indices were generated using a --sjdbOverhang of 49. Alignment parameters included --outFilterMultimapNmax 1 (to retain only uniquely mapped reads) and --outSAMstrandField intronMotif.
Gene quantification was performed using HTSeq (v0.11.1) against the Ensembl transcriptome (Release 100).
Assembly: GRCz11/danRer11
Supplementary files format and content: Tab-delimited text files. Column 1: Gene ID (Ensembl ID); Column 2: Unnormalized read counts generated by htseq-count.

molecule: polyA RNA

organism: Danio rerio

source_name: 20 dpf whole larvae

extract_protocol:
Total RNA was extracted by adding 300 µL of TRIzol reagent and allowing the homogenate to thaw. Following the addition of 60 µL of chloroform and vigorous vortexing, the phases were separated using Phase Lock Gel Heavy tubes (QuantaBio) centrifuged at 12,000 rcf for 15 minutes at 4°C. The aqueous phase was recovered and further purified using the RNeasy MinElute Cleanup protocol (Qiagen). Briefly, the sample was mixed with 70% ethanol and transferred to an RNeasy MinElute spin column. The membrane was washed with Buffer RPE and 80% ethanol, followed by a 5-minute centrifugal drying step with open lids to eliminate residual ethanol. RNA was eluted in 14 µL of RNase-free water.
Strand-specific RNA-seq libraries were constructed from total RNA. Poly-adenylated RNA was enriched using oligo(dT) beads and fragmented. First-strand cDNA was synthesized using random hexamer priming, followed by second-strand synthesis incorporating dUTP to preserve strand information. Libraries were sequenced on an Illumina platform.

value: 20 dpf whole larvae

value: pllp pd1245

value: Low Protein (LP)


title: R1881A rep1

description:
Library name: R1881A rep1
R1881A rep1


title: 7d culture of Tbxt::GFP+ in FGF/CHIR, sorted for double negative rep1

description: Library name: 7d_TBXT+_DN1


title: Treg (CD127-CD25+) - Donor 195 - Day 1

description:
Library name: lib59085_AAAFM27HV
Donor ID: 195; Study day: D1


title: cko3

city: Guangzhou

first: YE

last: HE

address: 1023-1063 shatai South Road, Baiyun District

institute: Southern medicial unversity

description: Library name: cko3

data_processing:
Data processing step using the Illumina NovaSeq X Plus platform with the 150 paired-end sequencing strategy. The raw data was handled by Skewer v0.2.2  and data quality was checked by FastQC v0.11.2.The read length was 2×150 bp.  Clean reads were aligned to the mouse genome (GRCm39) from Ensembl using STAR (https://github.com/alexdobin/STAR), with one mismatch allowed.
StringTie (v1.3.1c) was used to generate gene expression data and differential gene expression
Differential gene expression between matched case and control samples were performed by the R package DESeq2 (v1.16.1) with the likelihood ratio test option.
Then DEGs (with a threshold for p < 0.05) were chosen for function and signaling pathway enrichment analysis using KEGG database (https://www.genome.jp/kegg/pathway.html). For Gene Set Enrichment Analysis (GSEA), differentially expressed genes were analyzed using the Python-based GSEApy with the Enrich tool. Enrichment of mRNA, library construction, sequencing and data analysis were performed by Shanghai Xu Ran Biotechnology Co., Ltd (http://www.xurangene.com)
Assembly: Clean reads were aligned to the mouse genome (GRCm39) from Ensembl using STAR (https://github.com/alexdobin/STAR)
Supplementary files format and content: gene_sample_FPKM.csv.tar.gz

source_name: sciatic nerve

extract_protocol:
Total RNA from the sciatic nerve was extracted using the Universal RNA Extraction CZ Kit (RNC643, ONREW). RNA quantity was analyzed using Qubit 4.0 (Invitrogen) and quality examined by electrophoresis on a denaturing agarosegel. Only samples with an RNA concentration ≥10 ng/μL, and a total amount ≥ 500 ng were selected for library preparation.
Libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme)

treatment_protocol: Freshly collected sciatic nerve tissue from mice were quick forzen in liquid nitrogen.

value: sciatic nerve

value: RhoAfl/fl ChATCreERT2+


title: Enza rep1

description:
Library name: Enza rep1
Enza rep1


title: pd1245_LP_23_S17

description: Library name: pd1245_LP_Rep2


title: cko2

description: Library name: cko2


title: Treg (CD127-CD25+) - Donor 049 - Day 29

description:
Library name: lib59083_AAAFM27HV
Donor ID: 049; Study day: D29


title: pd1245_LP_21_S16

description: Library name: pd1245_LP_Rep1


title: cko1

description: Library name: cko1


title: Day0 rep1

description:
Library name: Day0 rep1
Day0 rep1


title: Treg (CD127-CD25+) - Donor 049 - Day 15

description:
Library name: lib59081_AAAFM27HV
Donor ID: 049; Study day: D15


title: pd1245_HP_19_S15

description: Library name: pd1245_HP_Rep3

value: High Protein (HP)


title: flox3

description: Library name: flox3

value: RhoAfl/fl


title: Enzalutamide SPEN KO highpoly 3

description:
Library name: Enzalutamide SPEN KO highpoly 3
Enzalutamide SPEN KO highpoly 3
SB30_S30

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The  sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V22 primary assembly annotations.
Counts per million ( cpm) reads were calculated using the cpm() function from R package, edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample.

source_name: highpoly

growth_protocol: Total RNA and poylsome associated RNA was extracted from prostate cancer cell line samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

treatment_protocol: untreated

value: highpoly

value: KO


title: Treg (CD127-CD25+) - Donor 049 - Day 8

description:
Library name: lib59079_AAAFM27HV
Donor ID: 049; Study day: D8

value: PBMC


title: flox2

description: Library name: flox2


title: Enzalutamide SPEN KO lowpoly 3

description:
Library name: Enzalutamide SPEN KO lowpoly 3
Enzalutamide SPEN KO lowpoly 3
SB29_S29

source_name: lowpoly

value: lowpoly


title: pd1245_HP_18_S14

description: Library name: pd1245_HP_Rep2


title: Treg (CD127-CD25+) - Donor 049 - Day 1

description:
Library name: lib59078_AAAFM27HV
Donor ID: 049; Study day: D1

value: 3.5mg mutein


title: Treg (CD127-CD25+) - Donor 027 - Day 29

description:
Library name: lib59076_AAAFM27HV
Donor ID: 027; Study day: D29

value: 1mg mutein


title: Enzalutamide SPEN KO 80S 3

description:
Library name: Enzalutamide SPEN KO 80S 3
Enzalutamide SPEN KO 80S 3
SB28_S28


title: pd1245_HP_17_S13

description: Library name: pd1245_HP_Rep1


title: flox1

description: Library name: flox1


title: RhoA KO+RhoA E40Q_REP3(E40Q_rep3)

city: Copenhagen

first: Jesper

middle: Bøje

last: Andersen

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Library name: Sample 9

data_processing:
Raw sequencing reads were processed using fastp to remove adaptor sequences, poly-N reads, and low-quality reads, generating high-quality clean reads
Clean reads were aligned to the Mus musculus reference genome (mm39) using HISAT2 (v2.2.1)(2) with default parameters.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file include raw counts for each sample

source_name: skin

growth_protocol: Primary mouse keratinocytes were isolated from 3-week-old mouse skin and cultured in low-calcium keratinocyte medium (MEM-based) supplemented with 8% chelex-treated fetal calf serum, insulin, EGF, transferrin, phosphoethanolamine, ethanolamine, hydrocortisone, glutamine, and penicillin/streptomycin. Cells were maintained at 34°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA were harvested using RNeasy Kit (Qiagen).
RNA samples were fragmented, and first-strand cDNA was synthesized using random hexamer primers, followed by the second-strand cDNA synthesis. Libraries were prepared through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: No treatment was used

value: skin

value: primary keratinocytes

value: keratinocyte

value: RhoA E40Q homozygous

value: same batch


title: pd1116_LP_15_S12

description: Library name: pd1116_LP_Rep3

value: 20 dpf whole larvae

value: pllp pd1116


title: Enzalutamide SPEN KO highpoly 2

description:
Library name: Enzalutamide SPEN KO highpoly 2
Enzalutamide SPEN KO highpoly 2
SB27_S27

value: Enzalutamide


title: Treg (CD127-CD25+) - Donor 027 - Day 15

description:
Library name: lib59074_AAAFM27HV
Donor ID: 027; Study day: D15


title: RhoA KO+RhoA E40Q_REP2(E40Q_rep2)

description: Library name: Sample 8


title: pd1116_LP_14_S11

description: Library name: pd1116_LP_Rep2

value: Low Protein (LP)


title: Enzalutamide SPEN KO lowpoly 2

description:
Library name: Enzalutamide SPEN KO lowpoly 2
Enzalutamide SPEN KO lowpoly 2
SB26_S26


title: Treg (CD127-CD25+) - Donor 027 - Day 8

description:
Library name: lib59072_AAAFM27HV
Donor ID: 027; Study day: D8


title: RhoA KO+RhoA E40Q_REP1(E40Q_rep1)

description: Library name: Sample 7


title: Treg (CD127-CD25+) - Donor 027 - Day 1

description:
Library name: lib59070_AAAFM27HV
Donor ID: 027; Study day: D1


title: Enzalutamide SPEN KO 80S 2

description:
Library name: Enzalutamide SPEN KO 80S 2
Enzalutamide SPEN KO 80S 2
SB25_S25


title: pd1116_LP_13_S10

description: Library name: pd1116_LP_Rep1


title: Enzalutamide SPEN KO highpoly 1

description:
Library name: Enzalutamide SPEN KO highpoly 1
Enzalutamide SPEN KO highpoly 1
SB24_S24


title: RhoA HET+RhoA E40Q_REP3(HET_rep3)

description: Library name: Sample 6

value: RhoA E40Q heterozygous


title: pd1116_HP_11_S9

description: Library name: pd1116_HP_Rep3

value: High Protein (HP)


title: Treg (CD127-CD25+) - Donor 212 - Day 29

description:
Library name: lib59068_AAAFM27HV
Donor ID: 212; Study day: D29

value: 5mg mutein


title: Enzalutamide SPEN KO lowpoly 1

description:
Library name: Enzalutamide SPEN KO lowpoly 1
Enzalutamide SPEN KO lowpoly 1
SB23_S23

value: KO


title: pd1116_HP_10_S8

description: Library name: pd1116_HP_Rep2


title: RhoA HET+RhoA E40Q_REP2(HET_rep2)

description: Library name: Sample 5


title: Treg (CD127-CD25+) - Donor 212 - Day 15

description:
Library name: lib59066_AAAFM27HV
Donor ID: 212; Study day: D15

value: PBMC


title: RhoA HET+RhoA E40Q_REP1(HET_rep1)

description: Library name: Sample 4


title: pd1116_HP_9_S7

description: Library name: pd1116_HP_Rep1


title: Enzalutamide SPEN KO 80S 1

description:
Library name: Enzalutamide SPEN KO 80S 1
Enzalutamide SPEN KO 80S 1
SB22_S22


title: Treg (CD127-CD25+) - Donor 212 - Day 8

description:
Library name: lib59064_AAAFM27HV
Donor ID: 212; Study day: D8


title: WT_REP3(Control_rep3)

description: Library name: Sample 3

value: wildtype


title: EK_LP_8_S6

description: Library name: EK_LP_Rep3

value: EK


title: Enzalutamide SPEN WT highpoly 3

description:
Library name: Enzalutamide SPEN WT highpoly 3
Enzalutamide SPEN WT highpoly 3
SB21_S21

value: highpoly

value: WT


title: Treg (CD127-CD25+) - Donor 212 - Day 1

description:
Library name: lib59062_AAAFM27HV
Donor ID: 212; Study day: D1


title: WT_REP2(Control_rep2)

description: Library name: Sample 2

value: skin

value: primary keratinocytes


title: Treg (CD127-CD25+) - Donor 183 - Day 29

description:
Library name: lib59061_AAAFM27HV
Donor ID: 183; Study day: D29

value: Placebo


title: EK_LP_7_S5

description: Library name: EK_LP_Rep2


title: Treg (CD127-CD25+) - Donor 183 - Day 15

description:
Library name: lib59059_AAAFM27HV
Donor ID: 183; Study day: D15


title: WT_REP1(Control_rep1)

description: Library name: Sample 1

value: keratinocyte

value: same batch


title: intestinal epithelial cells, 25-week-old, TrnA G5081A point mutant, 81% mutation load, male

city: Hangzhou

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

institute: Westlake University

description:
Library name: sample2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellanger software 7.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine

extract_protocol:
Mouse small intestines were excised and flushed with cold PBS. The tissues were opened longitudinally along the lumen and cut into 1 cm segments. The segments were incubated in cold PBS containing 20 mM EDTA for 1 hour on ice. Following incubation, the supernatant was discarded and replaced with fresh cold PBS. The tubes were then vortexed for 30 seconds to dissociate villi and crypts from the basement membrane. The released villi and crypts were transferred to a new tube and digested with TrypLE (Thermo Fisher Scientific, 12604013) supplemented with 10 mg/mL DNase I (Roche, 10104159001) for 10 minutes at 32°C. The digested cell suspension was sequentially filtered through 70-μm and 40-μm cell strainers. Isolated single IECs were centrifuged and resuspended in cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing 2% fetal bovine serum (FBS). For flow cytometry sorting, cell suspensions were stained on ice for 30 minutes with the following antibodies diluted in cold 2% FBS in DPBS: CD45-APC (1:100, clone 30-F11, BioLegend, 103112), CD31-PE (1:50, clone MEC13.3, BioLegend, 102507), TER-119-Brilliant Violet 510™ (1:50, clone TER-119, BioLegend, 116237), and CD326-APC/Cyanine7 (1:100, clone G8.8, BioLegend, 118217). Following incubation, cells were washed with cold 2% FBS in DPBS, resuspended in the same buffer supplemented with 0.1 μg/mL DAPI (BioLegend, 422801), and filtered through a 40-μm cell strainer. Fluorescence-activated cell sorting was performed using a BD FACSAria™ Fusion instrument, and the sorting strategy was visualized using FlowJo Software.
The scRNA-seq was performed using the 10× Chromium Next GEM Automated Single Cell 3′ Reagent Kits v3.1 (1000141) following the manufacturer’s protocol (CG000286 • Rev F). Sorted cells were loaded onto a Chromium Next GEM Automated Chip G (1000136), and single-cell gel bead-in-emulsions (GEMs) were generated using the Chromium Controller Single-Cell Instrument. Following reverse transcription and library construction, library quality was assessed using the Qubit dsDNA HS Assay Kit (Invitrogen) and the High Sensitivity DNA chip (Agilent). Sequencing was performed on the NovaSeq X Plus platform using a 2 × 150 bp paired-end read configuration.

value: small intestine

value: epithelial cells

value: intestinal epithelial cells

value: TrnA point mutant mouse


title: EK_LP_5_S4

description: Library name: EK_LP_Rep1

value: 20 dpf whole larvae

value: Low Protein (LP)


title: EK_HP_4_S3

description: Library name: EK_HP_Rep3

value: High Protein (HP)


title: Enzalutamide SPEN WT highpoly 2

description:
Library name: Enzalutamide SPEN WT highpoly 2
Enzalutamide SPEN WT highpoly 2
SB18_S18

value: Enzalutamide


title: Treg (CD127-CD25+) - Donor 183 - Day 8

description:
Library name: lib59057_AAAFM27HV
Donor ID: 183; Study day: D8

value: PBMC


title: intestinal epithelial cells, 25-week-old, wild type, male

description:
Library name: sample1
10x Genomics

value: wild type mouse


title: Enzalutamide SPEN WT lowpoly 2

description:
Library name: Enzalutamide SPEN WT lowpoly 2
Enzalutamide SPEN WT lowpoly 2
SB17_S17

value: lowpoly


title: Treg (CD127-CD25+) - Donor 183 - Day 1

description:
Library name: lib59055_AAAFM27HV
Donor ID: 183; Study day: D1


title: EK_HP_1_S1

description: Library name: EK_HP_Rep1

value: EK


title: ND5-mutant, 100-week-old, 70% mutation load, mtscATAC-seq

description:
Library name: sample8
10x Genomics

library_source: other

data_processing:
The nuclear mitochondrial DNA segments (NUMTs) were masked in the mm10 genome (PMID: 32788668 and PMID: 36792778). Raw sequencing data were aligned to the modified mm10 reference genome using CellRanger-ATAC (v 2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

extract_protocol:
Mouse small intestines were excised and flushed with cold PBS. The tissues were opened longitudinally along the lumen and cut into 1 cm segments. The segments were incubated in cold PBS containing 20 mM EDTA for 1 hour on ice. Following incubation, the supernatant was discarded and replaced with fresh cold PBS. The tubes were then vortexed for 30 seconds to dissociate villi and crypts from the basement membrane. The released villi and crypts were transferred to a new tube and digested with TrypLE (Thermo Fisher Scientific, 12604013) supplemented with 10 mg/mL DNase I (Roche, 10104159001) for 10 minutes at 32°C. The digested cell suspension was sequentially filtered through 70-μm and 40-μm cell strainers. Isolated single IECs were centrifuged and resuspended in cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing 2% fetal bovine serum (FBS). For flow cytometry sorting, cell suspensions were stained on ice for 30 minutes with the following antibodies diluted in cold 2% FBS in DPBS: CD45-APC (1:100, clone 30-F11, BioLegend, 103112), CD31-PE (1:50, clone MEC13.3, BioLegend, 102507), TER-119-Brilliant Violet 510™ (1:50, clone TER-119, BioLegend, 116237), and CD326-APC/Cyanine7 (1:100, clone G8.8, BioLegend, 118217). Following incubation, cells were washed with cold 2% FBS in DPBS, resuspended in the same buffer supplemented with 0.1 μg/mL DAPI (BioLegend, 422801), and filtered through a 40-μm cell strainer. Fluorescence-activated cell sorting was performed using a BD FACSAria™ Fusion instrument, and the sorting strategy was visualized using FlowJo Software.
The mtscATAC-seq libraries were generated using the 10× Chromium Controller and the Chromium Single Cell ATAC Library & Gel Bead Kit (1000390) following the manufacturer’s protocols (CG000496 Rev B and CG000169 Rev E), with a modified mtDNA enrichment method adapted from previous studies(40). Sorted cells were washed with cold DPBS and fixed with 1% formaldehyde (ThermoFisher Scientific, 28906) for 10 minutes at room temperature. Fixation was quenched by adding glycine to a final concentration of 0.125 M. The cells were then washed again with cold DPBS and pelleted by centrifugation at 1,000 × g for 5 minutes at 4°C. The cell pellet was lysed in lysis buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, and 1% BSA) for 3 minutes on ice, followed by addition of cold wash buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, and 1% BSA). After another centrifugation step at 1,000 × g for 5 minutes at 4°C, the supernatant was removed, and the cells were resuspended in 1× nuclei buffer (10× Genomics). Cell concentration was determined using trypan blue exclusion and adjusted for Tn5 tagmentation according to the Chromium Single Cell ATAC Reagent Kit protocol. Following tagmentation, cells were loaded onto a Chromium Next GEM Chip H (1000161), and single-cell gel bead-in-emulsions (GEMs) were generated using the Chromium Controller. Barcoded, tagmented DNA was amplified via PCR after GEM breakage and purified to construct mtscATAC libraries. Library quality and concentration were assessed using the Qubit dsDNA HS Assay Kit (Invitrogen) and the High Sensitivity DNA Kit (Agilent). Libraries were sequenced on the NovaSeq 6000 and NovaSeq X Plus platforms with a 2 × 150 bp paired-end read configuration.

value: 70% ND5 mutation load


title: Treg (CD127-CD25+) - Donor 178 - Day 29

description:
Library name: lib59053_AAAFM27HV
Donor ID: 178; Study day: D29

value: 3.5mg mutein


title: Enzalutamide SPEN WT 80S 2

description:
Library name: Enzalutamide SPEN WT 80S 2
Enzalutamide SPEN WT 80S 2
SB16_S16

value: WT


title: ND5-mutant, 3-week-old, 70% mutation load, mtscATAC-seq

description:
Library name: sample7
10x Genomics


title: Treg (CD127-CD25+) - Donor 178 - Day 15

description:
Library name: lib59051_AAAFM27HV
Donor ID: 178; Study day: D15


title: TrnA-mutant, 25-week-old, 80% mutation load, mtscATAC-seq

description:
Library name: sample6
10x Genomics

value: 80% TrnA mutation load


title: Ureteral urotheliium NO4

city: New York

first: Yi

last: Liao

state: New York

address: 423 23rd Avenue

department: Urology

institute: NYU Grossman School of Medicine

description:
Library name: 4U
counts.raw.csv: 4U

data_processing:
Demultiplexing was performed using the Illumina bcl2fastq software v2.20
Sequenced reads were mapped to the rn6 rat reference genome using STAR v2.4.5a
featureCounts (Subread package v1.4.6-p3) was used to generate the matrix of read counts for annotated genomic features
The DESeq2 package (R v3.3.0) in the R statistical programming environment was utilized to calculate differential gene statistical comparisons
Assembly: rn6
Supplementary files format and content: CSV file containing normalized matrix of read counts which includes values for all features and all samples

organism: Rattus norvegicus

source_name: Ureter

extract_protocol:
The bladder and ureteral urothelia of 6-week old female Fischer CDF rats  were then scrapped off using a drug spatula and collected in ice-cold PBS buffer after centrifugation. Total RNAs were isolated using PicoPure™ RNA Isolation Kit according to the manufacturer’s instructions. mRNAs were captured using oligo(dT) beads and used to synthesize double-stranded cDNAs. cDNA libraries were subsequently prepared with TruSeq Standard Total RNA kit (Illumina Inc, San Diego, CA), and sequencing was performed with Illumina HiSeq 4000 at the Genome Technology Center of New York University Grossman School of Medicine. Data were analyzed by the institution’s Applied Bioinformatics Lab.
mRNAs were captured using oligo(dT) beads and used to synthesize double-stranded cDNAs. cDNA libraries were subsequently prepared with TruSeq Standard Total RNA kit (Illumina Inc, San Diego, CA) according to the manufacturer’s instructions.

value: Ureter

value: Epithelial cells


title: Treg (CD127-CD25+) - Donor 178 - Day 8

description:
Library name: lib59050_AAAFM27HV
Donor ID: 178; Study day: D8


title: Wild-type, 25-week-old, mtscATAC-seq

description:
Library name: sample5
10x Genomics

value: small intestine

value: 0% mutation load


title: Treg (CD127-CD25+) - Donor 178 - Day 1

description:
Library name: lib59048_AAAFM27HV
Donor ID: 178; Study day: D1


title: Enzalutamide SPEN WT 80S 1

description:
Library name: Enzalutamide SPEN WT 80S 1
Enzalutamide SPEN WT 80S 1
SB13_S13


title: Ureteral urotheliium NO3

description:
Library name: 3U
counts.raw.csv: 3U


title: Ureteral urotheliium NO1

description:
Library name: 1U
counts.raw.csv: 1U


title: DMSO SPEN KO RNA 3

description:
Library name: DMSO SPEN KO RNA 3
DMSO SPEN KO RNA 3
SB12_S12

source_name: total RNA

value: total RNA

value: KO

value: DMSO


title: TrnA-mutant, 100-week-old, 84% mutation load, mtscATAC-seq

description:
Library name: sample4
10x Genomics

value: intestinal epithelial cells

value: 84% TrnA mutation load


title: Treg (CD127-CD25+) - Donor 022 - Day 29

description:
Library name: lib59046_AAAFM27HV
Donor ID: 022; Study day: D29

value: PBMC

value: Placebo


title: TrnA-mutant, 55-week-old, 82% mutation load, mtscATAC-seq

description:
Library name: sample2
10x Genomics

value: 82% TrnA mutation load


title: Bladder urotheliium NO5

description:
Library name: 5B
counts.raw.csv: 5B

source_name: Urinary bladder

value: Urinary bladder


title: Treg (CD127-CD25+) - Donor 022 - Day 8

description:
Library name: lib59044_AAAFM27HV
Donor ID: 022; Study day: D8


title: DMSO SPEN KO RNA 1

description:
Library name: DMSO SPEN KO RNA 1
DMSO SPEN KO RNA 1
SB10_S10


title: TrnA-mutant, 55-week-old, 73% mutation load, ATAC

description:
Library name: ATAC
10x Genomics

data_processing:
The nuclear mitochondrial DNA segments (NUMTs) were masked in the mm10 genome (PMID: 32788668 and PMID: 36792778). Raw sequencing data were aligned to the modified mm10 reference genome using cellranger-arc (v 2.0.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mouse small intestines were excised and flushed with cold PBS. The tissues were opened longitudinally along the lumen and cut into 1 cm segments. The segments were incubated in cold PBS containing 20 mM EDTA for 1 hour on ice. Following incubation, the supernatant was discarded and replaced with fresh cold PBS. The tubes were then vortexed for 30 seconds to dissociate villi and crypts from the basement membrane. The released villi and crypts were transferred to a new tube and digested with TrypLE (Thermo Fisher Scientific, 12604013) supplemented with 10 mg/mL DNase I (Roche, 10104159001) for 10 minutes at 32°C. The digested cell suspension was sequentially filtered through 70-μm and 40-μm cell strainers. Isolated single IECs were centrifuged and resuspended in cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing 2% fetal bovine serum (FBS). For flow cytometry sorting, cell suspensions were stained on ice for 30 minutes with the following antibodies diluted in cold 2% FBS in DPBS: CD45-APC (1:100, clone 30-F11, BioLegend, 103112), CD31-PE (1:50, clone MEC13.3, BioLegend, 102507), TER-119-Brilliant Violet 510™ (1:50, clone TER-119, BioLegend, 116237), and CD326-APC/Cyanine7 (1:100, clone G8.8, BioLegend, 118217). Following incubation, cells were washed with cold 2% FBS in DPBS, resuspended in the same buffer supplemented with 0.1 μg/mL DAPI (BioLegend, 422801), and filtered through a 40-μm cell strainer. Fluorescence-activated cell sorting was performed using a BD FACSAria™ Fusion instrument, and the sorting strategy was visualized using FlowJo Software.
The mtscATAC-seq libraries were generated using the 10× Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (1000283) following the manufacturer’s protocols (CG000338Rev F), with a modified mtDNA enrichment method adapted from a modified DOGMA-seq protocol in previous study (E. P. Mimitou et al). In brief, sorted cells were washed with cold DPBS and fixed with 0.1% formaldehyde (ThermoFisher Scientific, 28906) for 5 minutes at room temperature. Fixation was quenched by adding glycine to a final concentration of 0.125 M. The cells were then washed again with cold DPBS and pelleted by centrifugation at 1,000 × g for 5 minutes at 4°C. The cell pellet was lysed in lysis buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, and 1% BSA) for 3 minutes on ice, followed by addition of cold wash buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, and 1% BSA). After another centrifugation step at 1,000 × g for 5 minutes at 4°C, the supernatant was removed, and the cells were resuspended in 1× nuclei buffer (10× Genomics). Cell concentration was determined using trypan blue exclusion and adjusted for Tn5 tagmentation according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit protocol. Following tagmentation, cells were loaded onto a Chromium Next GEM Chip J (2000264), and single-cell gel bead-in-emulsions (GEMs) were generated using the Chromium Controller. After GEM breakage, the sample is divided into ATAC Library Construction and cDNA Amplification, and the amplified cDNA will be used for Gene Expression Library Construction according to 10x User guide. Library quality and concentration were assessed using the Qubit dsDNA HS Assay Kit (Invitrogen) and the High Sensitivity DNA Kit (Agilent). Libraries were sequenced on the NovaSeq X Plus platforms with a 2 × 150 bp paired-end read configuration.

value: 73% TrnA mutation load


title: TrnA-mutant, 55-week-old, 73% mutation load, GEX

description:
Library name: RNA
10x Genomics


title: Treg (CD127-CD25+) - Donor 022 - Day 1

description:
Library name: lib59043_AAAFM27HV
Donor ID: 022; Study day: D1


title: Bladder urotheliium NO3

description:
Library name: 3B
counts.raw.csv: 3B


title: Treg (CD127-CD25+) - Donor 123 - Day 29

description:
Library name: lib59041_AAAFM27HV
Donor ID: 123; Study day: D29

value: 10mg mutein


title: intestinal epithelial cells, 25-week-old, TrnA G5081A point mutant, 77% mutation load

description:
Library name: sample2
10x Genomics

value: epithelial cells

value: TrnA point mutant mouse


title: Bladder urotheliium NO1

description:
Library name: 1B
counts.raw.csv: 1B

value: WT


title: DMSO SPEN WT RNA 2

description:
Library name: DMSO SPEN WT RNA 2
DMSO SPEN WT RNA 2
SB8_S8


title: Treg (CD127-CD25+) - Donor 123 - Day 15

description:
Library name: lib59039_AAAFM27HV
Donor ID: 123; Study day: D15


title: Nox-S6

description: Library name: Nox-S6

data_processing:
All raw fastq files were aligned to the Ensembl mRatBn7.2 (Rn7) genome using CellRanger v9.0.1 with the associated Ensembl gene transfer format (gtf) file (version 113) modified to add annotation for the Xist gene. CellRanger filtered outputs were analyzed with Seurat v5.2.1 in R v4.4.0.
To filter out background contamination, cell-free ambient RNA was removed using SoupX v.1.6.2. Next, we continued quality filtering in R with Seurat v.5.2.1 by removing nuclei containing <200 genes and >5% of reads mapping to the mitochondrial genome. The counts data for each individual were then normalized, scaled by a factor of 10,000, and log-transformed. Heterotypic doublets were identified and removed using scDblFinder with the default expected doublet rate of 1% per 1,000 cells. Cell sex was assigned based on expression of Xist, where cells with Xist expression > 0 were assigned as female, and cells with Xist expression = 0 were assigned as male.
For each sample, we used Seurat to determine the 2,000 genes with highest cell-to-cell variability. We then integrated the individual datasets in Harmony, using the PCA cell embeddings with 50 principal components (PCs). Downstream analysis was performed on the integrated dataset.
Expression for each gene in the integrated dataset was scaled to a mean of 0 and variance of 1 across cells. We first performed dimensionality reduction via PCA retaining 21 PCs, followed by UMAP with the 21 previously identified PCs as input. Cells were then clustered under a graph-based approach by first identifying K-nearest neighbors in PCA space, and then clustering under a Louvain algorithm with a resolution of 0.5. After removing additional low-quality cells and clusters from outside the NAc, we repeated the dimensionality reduction and clustering steps. We annotated the resulting clusters as specific cell types based on known marker genes from previous work and the Allen Institute's Whole Mouse Brain taxonomy via the MapMyCells web interface.
Assembly: Rn7 (Ensemble gtf version 113)
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

molecule: nuclear RNA

source_name: nucleus accumbens

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
Rats were euthanized by live decapitation and whole brains were rapidly extracted and briefly flash frozen in 2-methylbutane on dry ice and stored at -80°C until further processing. 2mm-deep bilateral NAc tissue punches were collected at approximately Bregma +2.42 in a cryostat at -16°C. Punches were immediately placed in pre-chilled sample dissociation tubes (10x Genomics, 2000564) and kept at -80°C until nuclei isolation.
Nuclei were isolated using the 10x Genomics Nuclei Isolation kit (PN-1000493) according to manufacturer’s instructions. Single-nucleus libraries were generated using the Chromium GEM-X Single Cell 3' Kit v4 (10x Genomics, PN-1000691). Nuclei (44,592) were sequenced on the Illumina NovaSeq 6000 at the UAB Heflin Genomics core to an average read depth of ~23,000 reads per nuclei.

treatment_protocol: Rats underwent 7 days of heroin self-administration on an FR1 schedule followed by four days on an FR3 schedule. On day 12 rats underwent a progressive ratio test followed by self-administration on an FR3 schedule on days 13 and 14. Following the last self-administration session, animals were injected with either saline or naloxone and euthanized one hour later.

value: nucleus accumbens

tag: strain

value: Sprague-Dawley

value: Naloxone

value: Postnatal day 90-120

tag: Sex

value: pooled male and female


title: Treg (CD127-CD25+) - Donor 123 - Day 8

description:
Library name: lib59037_AAAFM27HV
Donor ID: 123; Study day: D8


title: Nox-S5

description: Library name: Nox-S5


title: RNA seq, KO, male mice-2, ~20w

city: New Haven

first: Li

last: Wen

address: 300 Cedar Street

institute: Yale Univeristy

description: Library name: 6NFcre

data_processing:
Raw fastq files were processed using fastq tool.
Sequencing reads with low-quality bases were trimmed and filtered
Cleaned reads were aligned using STAR (version 2.7.9) with the mouse reference genome gencode version GRCm38.p6 with vM25 gene annotation.
Expression quantification for aligned reads was performed using featureCounts (version 2.0.0)
The filtered read counts matrix was normalized by the transcripts per million (TPM) method.
Assembly: mm10
Supplementary files format and content: csv files

source_name: islet

extract_protocol:
RNA was harvested using RNA mini kit (Qiangen)
RNA library for RNA-seq were prepared using KARA mRNA HyperPrep kit following manufacturer's instructions.

value: islet

value: beta cell

value: Pdgfrafl/fl Pdx1-Cre+ C57BL/6

tag: background strain

value: ko

value: male


title: Nox-S4

description: Library name: Nox-S4


title: Enzalutamide SPEN KO RNA 2

description:
Library name: Enzalutamide SPEN KO RNA 2
Enzalutamide SPEN KO RNA 2
SB5_S5

value: total RNA

value: KO

value: Enzalutamide


title: Treg (CD127-CD25+) - Donor 114 - Day 29

description:
Library name: lib59034_AAAFM27HV
Donor ID: 114; Study day: D29

value: PBMC

value: 10mg mutein


title: Sal-S3

description: Library name: Sal-S3

value: Saline


title: Enzalutamide SPEN KO RNA 1

description:
Library name: Enzalutamide SPEN KO RNA 1
Enzalutamide SPEN KO RNA 1
SB4_S4


title: Treg (CD127-CD25+) - Donor 114 - Day 15

description:
Library name: lib59032_AAAFM27HV
Donor ID: 114; Study day: D15


title: RNA seq, Ctr, male mice-3, ~20w

description: Library name: 4NFflfl

value: Pdgfrafl/fl Pdx1-Cre- C57BL/6

value: control


title: Sal-S2

description: Library name: Sal-S2

value: nucleus accumbens

value: Sprague-Dawley


title: Enzalutamide SPEN WT RNA 3

description:
Library name: Enzalutamide SPEN WT RNA 3
Enzalutamide SPEN WT RNA 3
SB3_S3

value: WT


title: RNA seq, KO, male mice-1, ~20w

description: Library name: 5NFcre


title: RNA seq, Ctr, male mice-2, ~20w

description: Library name: 2NFflfl


title: Sal-S1

description: Library name: Sal-S1

value: Postnatal day 90-120

value: pooled male and female


title: Enzalutamide SPEN WT RNA 2

description:
Library name: Enzalutamide SPEN WT RNA 2
Enzalutamide SPEN WT RNA 2
SB2_S2


title: Treg (CD127-CD25+) - Donor 114 - Day 1

description:
Library name: lib59028_AAAFM27HV
Donor ID: 114; Study day: D1


title: RNA seq, Ctr, male mice -1, ~20w

description: Library name: 1NFflfl

value: islet

value: beta cell


title: LAM4 (scRNA-seq)

description: Library name: Sample 2

data_processing:
Read alignment and gene-expression quantification of human single-cell RNA-seq (scRNA-seq) data were performed using Cell Ranger version 3.0.2 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built human (hg38) reference package was used.
Assembly: GRCh38
Supplementary files format and content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format

extract_protocol:
Single-cell and single-nuclei suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol single-cell RNA-seq, single-nuclear RNA-seq
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol

value: Lung


title: Enzalutamide SPEN WT RNA 1

description:
Library name: Enzalutamide SPEN WT RNA 1
Enzalutamide SPEN WT RNA 1
SB1_S1


title: Enzalutamide SPEN WT lowpoly 3

description:
Library name: Enzalutamide SPEN WT lowpoly 3
Enzalutamide SPEN WT lowpoly 3
SB20_S20

value: lowpoly


title: Enzalutamide SPEN WT 80S 3

description:
Library name: Enzalutamide SPEN WT 80S 3
Enzalutamide SPEN WT 80S 3
SB19_S19


title: Treg (CD127-CD25+) - Donor 114 - Day 8

description:
Library name: lib59030_AAAFM27HV
Donor ID: 114; Study day: D8

data_processing:
Adapter and quality trimming of raw reads was performed using FastqMcf (ea-utils).
Read quality was assessed using FastQC (v0.11.3).
Alignment metrics, duplication rates, and RNA-seq QC metrics (ribosomal/intronic/UTR/coding base composition, 5'/3' bias) were computed using Picard tools (v1.134; CollectRnaSeqMetrics, MarkDuplicates) and Samtools (v1.2).
Base-calling and demultiplexing were performed automatically on BaseSpace (Illumina) to generate FASTQ files.
Reads were aligned to the reference genome using STAR (v2.4.2a); gene-level read counts were generated using HTSeq-count (v0.4.1) in 'intersection (nonempty)' mode with a minimum alignment quality of 20.
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: Comma-separated file (combined_counts_GEO_submission.csv) containing gene-level raw read counts, with Ensembl gene IDs as rows and library names (matching "library name" column in SAMPLES section) as columns.

extract_protocol:
PBMCs were thawed and immediately immunolabeled and FACS-sorted for sequencing. Dead cells were excluded from all sorts by staining with the Fixable Viability Dye eFluor™ 780 (eBioscience). For bulk RNA-seq, 250–500 CD4+CD127loCD25+ Tregs were sorted directly into lysis buffer, and cDNA was prepared using the SMART-Seq Ultra Low Input RNA Kit for Sequencing (Takara Bio).
RNA-seq libraries were constructed using the NexteraXT DNA Library Preparation Kit (Illumina) with half the recommended volumes and reagents. Paired-end sequencing of pooled libraries was run on a NextSeq 2000 (Illumina) with 59-base reads and a target depth of 5 million reads per sample.


title: Treg (CD127-CD25+) - Donor 030 - Day 29

description:
Library name: lib59026_AAAFM27HV
Donor ID: 030; Study day: D29

value: 1mg mutein


title: BY4741_Δsnr31Δsnr54_DMS_3

city: Nashville

first: zahrat el oula

last: hassoun

state: TN

address: 200 Robinson research

department: Biochemistry

institute: Vanderbilt University

description: Library name: BY4741_Δsnr31Δsnr54_DMS_rep3

data_processing:
Adapter trimming and quality filtering were performed using Skewer. PCR duplicates were removed using SeqKit, and reads were trimmed at both ends. Processed reads were aligned to the Saccharomyces cerevisiae RDN37 pre_rRNA reference sequence using ShapeMapper v2.3.0 with Bowtie2 in DMS mode. Mutation frequencies were calculated using ShapeMapper after quality filtering. DMS_induced mutation frequencies were obtained by subtracting untreated from DMS_treated samples, and statistical analyses were performed using three biological replicates per condition.
Assembly: Saccharomyces cerevisiae RDN37 pre_rRNA reference sequence.
Supplementary files format and content: Tab_delimited text files containing per_nucleotide mutation frequencies and sequencing coverage.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cell

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium to mid_log phase before harvesting.

extract_protocol:
RNA was purified by phenol_chloroform extraction followed by ethanol precipitation.
RNA was fragmented, size_selected by denaturing polyacrylamide gel electrophoresis, dephosphorylated with T4 polynucleotide kinase, ligated to a pre_adenylated 3′ DNA adapter using truncated T4 RNA ligase 2 (K227Q), reverse transcribed using TGIRT_III reverse transcriptase, circularized with CircLigase II, amplified by indexed PCR, size_selected by native polyacrylamide gel electrophoresis, and quantified prior to sequencing. Libraries were sequenced on an Illumina NovaSeq X platform using single_end 100_bp reads.

treatment_protocol: Purified pre_40S ribosomes or mature 40S ribosomes were treated with 1% dimethyl sulfate (DMS) at 30°C for 5 min in the presence of 800 mM HEPES (pH 7.4), 500 mM NaCl, 50 mM Mg(OAc)2, and 0.2 μM Bacillus subtilis RNase P RNA. Untreated control samples were processed in parallel without DMS. Reactions were quenched with β_mercaptoethanol/NaOAc and RNA was purified by phenol_chloroform extraction.

value: Saccharomyces cerevisiae cell


title: KA13_SF_time_OP8_Control

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: KA13_SF_OP8

data_processing:
Differential analysis for comparisons between iPAAG treated and operated untreated controls was computed using Limma (Linear modeling and empirical Bayes) Voom (Mean–variance modeling) method (limma v3.62.2) longitudinal analysis with baseline (week 2 operated joints) with TMM normalization and duplicate Correlation() (block = patient) to estimate within-patient correlation
Fastp v0.23.2 was used to trim adapters and low-quality reads, STAR version 2.7.10b was used for alignment to Equus caballus EquCab3.0, annotated with Ensembl 113 and feature counts Version 2.0.1 was used to quantify reads.
Assembly: Equus caballus EquCab3.0
Supplementary files format and content: voom_logCPM_normalized_SF.csv

organism: Equus caballus

source_name: synovial fluid

growth_protocol: Synovial fluid samples (≥ 3 mL) were obtained at baseline (pre surgery) and every two weeks throughout study duration until end term (0, 2, 4, 6, 8, 10). To obtain synovial fluid samples, horses were sedated, and joints were aseptically prepared in routine fashion as described for treatment administration. Synovial fluid samples were collected under sterile conditions during routine arthrocentesis. Approximately 3 to 7 mL of synovial fluid were placed in a 15 mL conical tube and placed on ice for transport to the laboratory for processing.

extract_protocol:
The fluid was digested with 0.3 mg/mL hyaluronidase (Sigma, St. Louis, MO, USA) by incubation in a bead bath for 15 minutes at 37 ºC. Next the sample was centrifuged at 750 x g for 10 minutes at 8 ºC. The remaining cell pellet was washed with PBS and centrifuged at 500 x g for 10 minutes at 8 ºC. The cell pellet was resuspended in about 1 to 2 mL of PBS and transferred into a 2 mL microcentrifuge tube. The sample was then centrifuged for 500 x g for 15 minutes. The supernatant was discarded, and the cells were lysed in RLT buffer (Qiagen, Germantown, MD, USA) with 1% ß-Mercaptoethanol (BME; EMD Millipore Corp, Billerica, MA, USA) and stored at -80 ºC until RNA extraction.
Library preparation was conducted on synovial fluid samples using the SMARTer® Stranded Total RNA-Seq Kit -Pico input (Takara Bio USA, Inc.)

treatment_protocol: Treatment – Horses (n=8/group) were randomly assigned to receive either intra-articular 2.5% injectable polyacrylamide hydrogel (Arthramid®, Contura Vet, Franklin, TN, USA) injection (2 mL) or phosphate buffered saline (2 mL) injection. Briefly, horses were sedated with detomidine hydrochloride 0.01 mg/kg and butorphanol tartrate 0.01 mg/kg intravenously. The previously operated middle carpal joint was aseptically prepared in routine fashion and injected intra-articularly at day 14 of the study.

value: synovial fluid

value: SF cells


title: KA14_SF_time_OP4_iPAAG

description: Library name: KA14_SF_OP4


title: placenta DNA, MARBLES, male 10

city: Davis

first: Logan

middle: Allan

last: Williams

state: CA

address: 1275 Med Sci Dr

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Library name: SW019

data_processing:
Raw sequencing files were preprocessed, aligned to hg38, and used to generate cytosine reports with Epigenerator.In short, Epigenerator provides a user-friendly means of generating cytosine reports from fastq files by applying the FASTQ_Me and CpG_Me workflows in tandem. Merged reads were trimmed of adaptors, corrected for potential methylation bias at the 5’ and 3’ ends, and aligned to hg38. The aligned reads were then deduplicated and CpG methylation was extracted with to generate cytosine reports for further analysis.
Assembly: hg38
Supplementary files format and content: cytosine reports, genome-wide CpG count matrices

source_name: Placenta

extract_protocol:
Placenta samples underwent DNA isolation via the Gentra Puregene kit (Qiagen, Hilden, Germany) by following recommended procedures and quantified with the Qubit DNA Assay Kit (ThermoFisher Scientific, Q32851).
DNA was sheared by sonication, bisulfite-converted with the EZ DNA Methylation Gold kit (Zymo, Irvine, CA, USA) and made into sequencing libraries via the xGen Methyl Seq Library Prep kit (IDT, Coralville, IA, USA). Libraries were made with indexed PCR primers and underwent 7 cycles of amplification before being pooled and sequenced for 150bp paired end reads on 4 lanes of the NovaSeq 6000 S4 (San Diego, CA, USA)  by the DNA Technologies Core at the University of California, Davis (Davis, CA, USA).

treatment_protocol: Placental samples were frozen at -80C within 4 hours of birth and stored until time of isolation.

value: Placenta

value: M

tag: project

value: MARBLES

tag: pm25mass avg_prec

tag: pm25mass avg_preg

tag: pm25tracer5 avg_prec

tag: pm25tracer5 avg_preg

tag: pm25tracer10 avg_prec

tag: pm25tracer10 avg_preg

tag: wf pm25_avg_prec

tag: wf pm25_avg_preg

tag: nonwf pm25_avg_prec

tag: nonwf pm25_avg_preg

tag: pregfire any

value: Wildfire Exposed


title: placenta DNA, MARBLES, male 9

description: Library name: SW018

tag: tissue


title: LAM3 (scRNA-seq)

description: Library name: Sample 1


title: EK_HP_3_S2

description: Library name: EK_HP_Rep2

value: 20 dpf whole larvae

tag: genotype

value: EK

tag: treatment

value: High Protein (HP)


title: plus-Exp3

city: Sevilla

first: Pablo

last: Huertas

address: Av.Americo Vespucio 24

institute: University of Sevilla

description:
Library name: Simple 6
Plus-Exp3

data_processing:
Galaxy web platform
Sequences reads were trimmed for adaptor sequence/low quality sequence using FastQC and Trimmomatic tool
HISAT2 program was employed to align cleaned RNA-seq paired end reads
Gene expression measurement of the aligned sequences was done by FeatureCounts tool.
Data was analysed with Limma tool, considering p-value<0.05 and fold change <-2 and >2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: BJhTERT

growth_protocol: BJhTERT cells were growth in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvest using RNeasy Micro Kit (Qiagen)
RNA libraries for RNA-seq were constructed with the Small RNA Sequencing Kit v3 for Illumina Platforms (NEXTflex)

treatment_protocol: Cells were irradiated or not with 0.2 Gy low dose of radiation, and 5 hours after, Evs from media were collected.

tag: cell line

value: BJhTERT

tag: cell type

value: Foreskin fibroblast

value: WT

value: No treatment


title: BY4741_Δsnr31Δsnr54_DMS_2

description: Library name: BY4741_Δsnr31Δsnr54_DMS_rep2


title: Treg (CD127-CD25+) - Donor 030 - Day 15

description:
Library name: lib59024_AAAFM27HV
Donor ID: 030; Study day: D15

source_name: PBMC

value: PBMC

tag: batch


title: Liver_TuD_11

city: Neuherberg

first: Stephan

last: Herzig

state: Bayern

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

country: Germany

institute: Helmholtz Munich

description:
Library name: MUC10172
Coumn name in Expression_Matrix.txt: MUC10172

data_processing:
The DNA libraries were sequenced on an Illumina HiSeq4000 at the sequencing core facility of Helmholtz Munich. The reads were then trimmed by BBDuk and aligned to mouse genome GRCm38 using STAR 2.5.3a. Gene read quantification was performed using Rsubread. Only genes with more than 10 reads in, at least, 5 samples were included in the analysis. Differential expression analysis was performed with DESeq2 (1.38.3)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file include read counts  for each sample

source_name: Liver

extract_protocol:
Liuver samples were homogenized in TRIzol using a TissueLyser (Qiagen, Hilden, Germany) and total RNA was then isolated from these homogenates using the miRNeasy Mini Kit (Qiagen), according to manufacturer’s recommendations,
DNA libraries were generated, from an input of 500 ng of total RNA, using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit (Lexogen), according to the manufacturer’s recommendations

value: Liver

value: TuD


title: plus-Exp2

description:
Library name: Sample 5
Plus-Exp2


title: Liver_TuD_10

description:
Library name: MUC10171
Coumn name in Expression_Matrix.txt: MUC10171


title: Ureteral urotheliium NO5

description:
Library name: 5U
counts.raw.csv: 5U

value: Ureter

value: Epithelial cells


title: Enzalutamide SPEN WT lowpoly 1

description:
Library name: Enzalutamide SPEN WT lowpoly 1
Enzalutamide SPEN WT lowpoly 1
SB14_S14

value: lowpoly

value: Enzalutamide


title: BY4741_Δsnr31Δsnr54_DMS_1

description: Library name: BY4741_Δsnr31Δsnr54_DMS_rep1

value: Saccharomyces cerevisiae cell


title: Enzalutamide SPEN WT highpoly 1

description:
Library name: Enzalutamide SPEN WT highpoly 1
Enzalutamide SPEN WT highpoly 1
SB15_S15

value: highpoly


title: plus-Exp1

description:
Library name: Sample 4
Plus-Exp1


title: Treg (CD127-CD25+) - Donor 030 - Day 8

description:
Library name: lib59022_AAAFM27HV
Donor ID: 030; Study day: D8

value: 1mg mutein


title: Treg (CD127-CD25+) - Donor 030 - Day 1

description:
Library name: lib59020_AAAFM27HV
Donor ID: 030; Study day: D-10


title: BY4741_DMS_biological replicate 3

description: Library name: BY4741_DMS_rep3


title: Liver_TuD_9

description:
Library name: MUC10170
Coumn name in Expression_Matrix.txt: MUC10170


title: minus-Exp3

description:
Library name: Sample 3
Minus-Exp3

value: Irradiation


title: SEM negative control (NC), replicate 3

city: Segrate

first: Ingrid

last: Cifola

state: Milan

address: Via F.lli Cervi, 93

department: Institute for Biomedical Technologies (ITB)

country: Italy

institute: National Research Councill (CNR)

description: Library name: SEM_NC_replicate3

data_processing:
After fastq quality control by using FastQC tool (v.0.11.8), raw reads were trimmed to 100 bases and mapped to the human reference genome (hg38) using STAR aligner (v.2.7.10a).
Gene counts were calculated by HTSeq package (v.0.11.1), using the hg38 Encode-Gencode GTF file (v43) as gene annotation file.
Differential gene expression analysis was performed by DESeq2 Bioconductor/R package (v.1.38.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample, calculated by using HTSeq package (v.0.11.1).

source_name: SEM (ACC 546)

extract_protocol:
Total RNA samples were extracted using Qiagen reagents and checked for integrity by microcapillary electrophoresis on Agilent Bioanalyzer (Agilent Technologies).
Total RNA libraries were prepared using the Universal Plus Total RNAseq library preparation kit with NuQuant®, with targeted transcript depletion with AnyDeplete (Tecan) for globin genes. The yields of final libraries were assessed by Qubit 4.0 fluorimeter, and their sizes were measured by 2100 Agilent Bioanalyzer (Agilent Technologies). Libraries were sequenced on NextSeq 2000 platform (Illumina).

treatment_protocol: For AK_8_2 knock-down (KD) by RNA interference, SEM cells were transfected with two Dicer-Substrate Short Interfering RNAs (DsiRNAs) specifically designed on the AK_8_2 back-splicing junction. A commercial non-targeting DsiRNA (Integrated DNA Technologies) was used as negative control (NC). All transfections were performed using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific), which involved a reverse transfection followed by a forward transfection 24 hours later.

value: SEM (ACC 546)

value: B-ALL

value: negative control, replicate 3


title: Liver_NC_8

description:
Library name: MUC10169
Coumn name in Expression_Matrix.txt: MUC10169

value: NC


title: BY4741_DMS_biological replicate 2

description: Library name: BY4741_DMS_rep2


title: DMSO SPEN KO RNA 2

description:
Library name: DMSO SPEN KO RNA 2
DMSO SPEN KO RNA 2
SB11_S11

value: total RNA

value: KO

value: DMSO


title: BY4741_DMS_biological replicate 1

description: Library name: BY4741_DMS_rep1


title: minus-Exp2

description:
Library name: Sample 2
Minus-Exp2

value: BJhTERT

value: Foreskin fibroblast

value: WT


title: Liver_NC_7

description:
Library name: MUC10168
Coumn name in Expression_Matrix.txt: MUC10168

value: Liver


title: minus-Exp1

description:
Library name: Sample 1
Minus-Exp1


title: BY4741_Δsnr31Δsnr54_noDMS_3

description: Library name: BY4741_Δsnr31Δsnr54_noDMS_rep3


title: LCA__GAL LCA_GAL_2

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

description:
Library name: LCA_GAL_2
dr_ciliopathy_treatments_cts.csv.gz

data_processing:
fastp fastq trimming
decoy aware salmon index
salmon quant --index  --libType A --seqBias --gcBias             --validateMappings
tximport into R (4.4)
gencode.v47.primary_assembly.annotation.gtf.gz
Assembly: GRCh38.primary_assembly.genome.fa.gz
Supplementary files format and content: counts, csv

source_name: RPE

growth_protocol: All human samples were collected under an IRB-approved protocol at NEI (protocol #11-E1- 0245). Cells isolated from donor tissue were reprogrammed using Sendai virus-mediated delivery (CytoTune, LifeTechnologies) of the four Yamanaka factors (c-MYC, KLF4, OCT4, SOX2) following the manufacturer's recommendations. For differentiation, iPSCs were seeded onto vitronectin (ThermoFisher) coated T75 flasks followed by guided protocol. Triphasic developmentally guided protocol to generate retinal pigment epithelium from induced pluripotent stem cells, Sharma et. al. 2022

extract_protocol:
RNA was isolated from RPE monolayer 5 weeks post-seeding on transwells, using RNA extraction kit, Macherey&Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected after 5 weeks of maturation on transwell inserts. Samples were either untreated or treated after 4days of seeding with Pioglitazone and 6days of seeding with Galunisetib.

value: RPE

value: iRPE

value: GAL


title: LCA__PIO LCA_PIO_2

description:
Library name: LCA_PIO_2
dr_ciliopathy_treatments_cts.csv.gz

value: PIO


title: KA12_SF_time_OP10_iPAAG

description: Library name: KA12_SF_OP10

value: synovial fluid

value: SF cells


title: SEM negative control (NC), replicate 1

description: Library name: SEM_NC_replicate1

value: SEM (ACC 546)

value: negative control, replicate 1


title: SEM negative control (NC), replicate 2

description: Library name: SEM_NC_replicate2

value: B-ALL

value: negative control, replicate 2


title: Liver_NC_6

description:
Library name: MUC10167
Coumn name in Expression_Matrix.txt: MUC10167

value: NC


title: Bladder urotheliium NO4

description:
Library name: 4B
counts.raw.csv: 4B

value: Urinary bladder

value: Epithelial cells


title: SEM knocked-down (KD) for AK_8_2 fusion-circRNA, replicate 3

description: Library name: SEM_KD_replicate3

value: knock-down (KD) for AK_8_2 f-circRNA, replicate 3


title: iCLIP2 of TSN1, replicate 3

city: Ciudad Autonoma de Buenos Aires

first: Maria

middle: Clara

last: Fontana

state: Buenos Aires

address: INTENDENTE GUIRALDES 2160, IFIBYNE

country: Argentina

institute: Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE)

description:
Library name: TSN1_rep3
UV-crosslinked RNA co-purified with GFP-tagged TSN1; single-nucleotide resolution iCLIP2

data_processing:
Quality assessment with FastQC (v0.11.5) after sequencing and after each processing step.
Adapter/linker trimming and demultiplexing with Flexbar (v3.4.0) using the reverse-complemented iCLIP2 adapter (UMI + sample barcode); quality/length filtering (reads <15 nt discarded); UMIs transferred to the FASTQ read identifier with bioawk for downstream deduplication.
Alignment to the A. thaliana TAIR10 genome (index built with TAIR10 + AtRTD3 transcriptome) using STAR (v2.7.3a): <=4% mismatches, uniquely mapped reads only, --alignEndsType Extend5pOfRead1, --alignIntronMin 11, --alignIntronMax 28000. BAM sorted/indexed with samtools; PCR duplicates removed with UMI-tools (v1.0).
Strand-specific single-nucleotide crosslink tracks generated with bedtools (v2.27.1): BAM->BED, read start shifted -1 nt to the crosslink position, exported as bigWig (per replicate and merged).
Peak calling with PureCLIP (v1.3.1) on merged replicates; transcriptome-wide binding sites defined with BindingSiteFinder (v2.4.0), requiring reproducibility in >=2 of 3 replicates (20th-percentile per-replicate crosslink threshold). Final binding sites exported as BED with reassigned PureCLIP scores.
Assembly: TAIR10 (annotation: AtRTD3 / Araport11)
Supplementary files format and content: bigWig: strand-specific, single-nucleotide-resolution TSN1 crosslink signal tracks (one plus and one minus per biological replicate, plus merged tracks).
Supplementary files format and content: BED: (i) reproducible TSN1 binding sites from BindingSiteFinder with reassigned PureCLIP score; (ii) PureCLIP called crosslink peaks (single-nucleotide).
Supplementary files format and content: TSV (tab-delimited, 1-based coordinates): (i) annotated binding-site table (chrom, start, end, bsID, score, strand, geneID, geneName, geneType, transcriptRegion), same sites as the 0-based BED; (ii) TSN1 target-gene table derived from the binding sites.
Library strategy: iCLIP

organism: Arabidopsis thaliana

source_name: whole plant, enriched in aerial tissue

growth_protocol: Seeds surface-sterilized (70% ethanol), sown on 1/2-strength Murashige-Skoog medium (Duchefa) with 0.8% agar. Seedlings grown under long-day conditions (16 h light / 8 h dark) at 20 C in Percival chambers for 14 days and harvested at ZT10. Per biological replicate, tissue from three plates was pooled (~3 g). In vivo UV crosslinking of 14-day-old seedlings at 254 nm, 2000 mJ/cm2 (UVP CL-1000), on ice; plates snap-frozen in liquid nitrogen and aerial tissue harvested and ground.

extract_protocol:
Ground tissue (0.5 g aliquots) lysed in high-detergent buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 4 mM MgCl2, 0.25% Igepal CA-630, 1% SDS, 0.25% Na-deoxycholate, 5 mM DTT, protease inhibitors, RiboLock, 1 mM PMSF); homogenized (1400 rpm, 40 C), pooled and 0.45 um filtered. On-bead Turbo DNase treatment. Immunoprecipitation with GFP-Trap agarose (Proteintech) after Sepharose pre-clear; four high-stringency and two low-stringency washes. RNA 3-ends dephosphorylated (T4 PNK); after RT/library steps, RNA released with proteinase K (PK-SDS buffer, 55 C), phenol/chloroform (pH 7.0) with Phase Lock Gel, purified on Zymo columns.
iCLIP2 library preparation: 3-linker (L3-App) ligation with high-concentration RNA ligase (NEB); reverse transcription with an L3-complementary primer (RT truncation at crosslink site gives single-nucleotide resolution); cDNA purified on MyONE Silane beads. Second adapter (LXXclip2.0, containing sample barcode + UMI) ligated overnight at 20 C and purified. PCR: 6 pre-amplification cycles (P5/P3 Solexa_s), ProNex size selection (1:2.95), then final PCR to 18 total cycles; final ProNex cleanup (1:2.4). Libraries quantified by Qubit dsDNA HS, pooled at equimolar concentration (10 nM) and sequenced on an Illumina NextSeq 1000 at the Genomics Center of the Max Planck Institute for Developmental Biology (Tuebingen), generating 50-nt single-end reads.

value: whole plant, enriched in aerial tissue

value: pTSN1::GFP:TSN1 in Col-0 (wild-type background)


title: DMSO SPEN WT RNA 3

city: Seattle

description:
Library name: DMSO SPEN WT RNA 3
DMSO SPEN WT RNA 3
SB9_S9

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The  sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V22 primary assembly annotations.
Counts per million ( cpm) reads were calculated using the cpm() function from R package, edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample.

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

value: total RNA

value: WT

value: DMSO


title: Liver_TuD_5

description:
Library name: MUC10166
Coumn name in Expression_Matrix.txt: MUC10166

value: Liver

value: TuD


title: BY4741_Δsnr31Δsnr54_noDMS_2

description: Library name: BY4741_Δsnr31Δsnr54_noDMS_rep2

value: Saccharomyces cerevisiae cell


title: SEM knocked-down (KD) for AK_8_2 fusion-circRNA, replicate 2

description: Library name: SEM_KD_replicate2

value: knock-down (KD) for AK_8_2 f-circRNA, replicate 2


title: iCLIP2 of TSN1, replicate 2

description:
Library name: TSN1_rep2
UV-crosslinked RNA co-purified with GFP-tagged TSN1; single-nucleotide resolution iCLIP2


title: BY4741_Δsnr31Δsnr54_noDMS_1

description: Library name: BY4741_Δsnr31Δsnr54_noDMS_rep1


title: iCLIP2 of TSN1, replicate 1

description:
Library name: TSN1_rep1
UV-crosslinked RNA co-purified with GFP-tagged TSN1; single-nucleotide resolution iCLIP2


title: Liver_TUD_4

description:
Library name: MUC10165
Coumn name in Expression_Matrix.txt: MUC10165


title: SEM knocked-down (KD) for AK_8_2 fusion-circRNA, replicate 1

description: Library name: SEM_KD_replicate1

value: SEM (ACC 546)

value: knock-down (KD) for AK_8_2 f-circRNA, replicate 1


title: Liver_TuD_3

description:
Library name: MUC10164
Coumn name in Expression_Matrix.txt: MUC10164


title: BY4741_noDMS_3

description: Library name: BY4741_noDMS_rep3


title: BY4741_noDMS_2

description: Library name: BY4741_noDMS_rep2


title: Liver_NC_2

description:
Library name: MUC10163
Coumn name in Expression_Matrix.txt: MUC10163


title: OE_GPX3_3

city: Fuzhou

first: Yiquan

address: Fujian Cancer Hospital

institute: Fujian meidical university

description: Library name: OE_GPX3_3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and FPKM value for each Sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: cell culture

value: OE


title: OE_GPX3_2

description: Library name: OE_GPX3_2


title: BY4741_noDMS_1

description: Library name: BY4741_noDMS_rep1


title: NDM_48h_rep2

city: Numazu

first: Takefumi

last: Onodera

address: 18-24 Miyamoto

department: Numazu

country: Japan

institute: Institute of microbial chemistry

description: Gene expression in PANC-1 cells after NDM treatment 48h

hyb_protocol: For each array, 1.65 µg of Cy3-labeled cRNA was fragmented according to the manufacturer’s one-color gene expression protocol and combined with Agilent gene expression hybridization buffer. The hybridization mixture was loaded onto the Agilent Whole Human Genome 4×44K v2 microarray slide and hybridized at 65°C for 17 h with rotating Agilent hybridization oven. After hybridization, slides were washed according to the manufacturer’s recommended one-color gene expression wash procedure and then dried prior to scanning.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10 %).

data_processing:
Feature Extraction output files were generated using Feature Extraction Software 9.5.3.1 (Agilent) with protocol GE1-v5_95 and grid 014850_D_20070820. Data were imported into GeneSpring GX, thresholded to 1.0, log2-transformed (log base 2), normalized across arrays by 75th percentile shift, and baseline-transformed to the median of all samples. Processed expression matrices were exported from GeneSpring GX.
DEG list generated in GeneSpring GX after re-normalization within the subset of samples used for this comparison.

source_name: Nutrient-deprived medium, 48h, replicate 2

label_protocol: Total RNA (200 ng per sample) was labeled using the Agilent Low Input Quick Amp Labeling Kit, One-Color (manufacturer’s protocol). Briefly, double-stranded cDNA was synthesized from total RNA using an oligo(dT)-T7 primer. Cy3-labeled cRNA was then generated by in vitro transcription with T7 RNA polymerase. Approximately 10 µg of cRNA was obtained per sample. Labeled cRNA was purified according to the kit protocol and quantified prior to hybridization.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The gene expression profile under nutrient deprivation consisted of PANC-1 samples exposed to nutrient-deprived medium (NDM) for 0, 3, 6, 12, 24, and 48 h.

tag: condition

value: NDM treatment 48h


title: Liver_NC_1

description:
Library name: MUC10161
Coumn name in Expression_Matrix.txt: MUC10161

value: NC


title: NDM_24h_rep2

description: Gene expression in PANC-1 cells after NDM treatment 24h

source_name: Nutrient-deprived medium, 24h, replicate 2

value: NDM treatment 24h


title: OE_GPX3_1

last: Xu

description: Library name: OE_GPX3_1