title: FLOX_ZT12_b

description: Library name: sample_11

source_name: CD36f/f mice, sampling at ZT12, biol rep 2


title: LC053_IV

status: Public on Jun 15 2026

type: RNA

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

hyb_protocol: Amplification and labelling efficiency were controlled on the NanoDrop. The cRNA quality was assessed by measuring the RNA absorbance ratio 260nm/280nm. The specific activity of labeled cRNA (pmol Cy3 per ug cRNA) was defined to be 6 or above according to the Agilent recommendations.

scan_protocol: Standard Illumina Protocol

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

molecule: total RNA

organism: Homo sapiens

source_name: Gut epithelium, NP, Descendens

label_protocol: mRNA amplification, labelling, and hybridization were done following the manufacturer’s instructions (Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling). In short, 50 ng RNA was amplified and labelled with Cy3 using the Low Input Quick Amp Labeling Kit, one-color (product number 5190-2331), and the labelled cRNA was purified using the Qiagen RNeasy Mini Kit.

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

tag: tissue

value: gut epithelium

tag: status

value: Non-progressor

tag: segment

value: Descendens

tag: inflammation

value: Chronic active

tag: neoplasia


title: HSAEC_IRIS_1

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description:
Library name: Sample 80
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 1

library_source: transcriptomic

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

source_name: HSAEC

extract_protocol:
Total RNA was extracted using TriPure™ Isolation Reagent (Sigma-Aldrich), following the manufacturer's instructions with phenol-chloroform extraction.
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

tag: cell line

value: HSAEC

tag: cell type

value: Lung epithelial

tag: genotype

value: WT

tag: treatment

value: Ionizing radiation-induced senescence (8 days 10 Gy)


title: 22Rv1_RNAseq_siNHSL1_R3

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Cancer Biology

institute: University of Southern California

description:
Library name: 22Rv1 RNAseq siNHSL1 R3
RNA-seq

data_processing:
RNA-seq reads were aligned to the human reference genome hg38 using in-house RNA-seq analysis pipeline, which is adapted from NCI Genomic Data Commons bioinformatic pipieline (https://gdc.cancer.gov/). Reads were first trimmed using Trimgalore (https://github.com/FelixKrueger/TrimGalore) to filter out low quality reads and the adapter sequences. The trimmed reads were then aligned to human reference genome version 38 (hg38) with the annotation GENCODE V29 using STAR (PMID: 23104886) to generate bam files. Htseq was used to quantify the reads counts for each gene, with the bam files as the input.
Assembly: hg38
Supplementary files format and content: .tsv

molecule: polyA RNA

source_name: Prostate

growth_protocol: 22Rv1 (CRL-2505) and RWPE-1 (CRL-11609) cells were obtained from the American Type Culture Collection (ATCC). RC-77N/E and RC77T/E cells were received from Johng Sik Rhim. Cells were cultured according to the suggested protocols at 37°C with 5% CO2. 22Rv1 cells were cultured in RPMI 1640 (Corning, #10-040-CV) supplemented with 10% FBS (Avantor Seradigm, #89510-188) and 1% penicillin/streptomycin. RWPE-1, RC-77N/E, and RC77T/E cells were cultured in the Keratinocyte Serum Free Medium kit (Thermo Fisher Scientific, #17005-042).

extract_protocol:
For RNA-seq, extraction was done using the Direct-zol RNA MiniPrep Kit (Zymo Research), with phenol. RNA was extracted in 3 replicates for each condition.
RNA-seq library: Libraries were prepared by polyA capture, and reverse transcription of cDNA. A 150 bp paired-end sequencing strategy was used to sequence the samples.

value: Prostate

value: prostate cells


title: HSAEC_ETIS_4

description:
Library name: Sample 79
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 20 µM)


title: LC053_III

source_name: Gut epithelium, NP, Transversum

value: Transversum


title: 22Rv1_RNAseq_siNHSL1_R2

description:
Library name: 22Rv1 RNAseq siNHSL1 R2
RNA-seq


title: FLOX_ZT8_c

city: Chongqing

first: Mengyue

last: Chen

state: Chongqing

address: No. 1, Medical College Road, Yuzhong District, Chongqing City

department: Department of Infectious Diseases

country: China

institute: the Second Affiliated Hospital，Chongqing medical university

description: Library name: sample_9

data_processing:
Compare the quality-controlled raw data, which is referred to as “clean data” (reads), with the reference genome to obtain mapped data (reads) for subsequent transcript assembly, expression quantification, and other purposes. Conduct a quality assessment of the alignment results from this transcriptome sequencing, focusing on sequencing saturation, gene coverage, the distribution of reads across different regions of the reference genome, and the distribution of reads across different chromosomes. Software used: HiSat2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
The abundance of transcripts reflects the level of gene expression. The higher the abundance of transcripts, the higher the level of gene expression. In RNA-Seq analysis, the level of gene expression is calculated by counting the number of sequences (clean reads) that are localized to specific regions of the genome. The expression levels of genes and transcripts are quantitatively analyzed using software RSEM to facilitate subsequent analysis of differences in gene/transcript expression between different samples. By combining sequence functional information, the regulatory mechanisms of genes can be elucidated. Software used: RSEM (http://deweylab.github.io/RSEM/).
After obtaining the read counts for the genes, perform an analysis of gene expression differences between samples (≥ 2) to identify genes with differential expression between samples. Subsequently, study the functions of the differentially expressed genes. The software used for differential expression analysis is DESeq2 (with biological replicates) or DEGseq (without biological replicates, used by default). The default screening criteria for significantly differentially expressed genes are: FDR < 0.05 and |log2FC| ≥ 1. When a gene meets both of these conditions, it is considered a differentially expressed gene (DEG). The software used is DEGseq (https://www.rdocumentation.org/packages/DEGseq/versions/1.26.0); DESeq2 (http://bioconductor.org/packages/stats/bioc/DESeq2/).
Using the GO (Gene Ontology) database, genes can be categorized based on the biological processes (Biological Process, BP) they are involved in, the cellular components (Cellular Component, CC) they comprise, and the molecular functions (Molecular Function, MF) they perform. Differentially expressed genes can be annotated with GO terms. Using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database, genes can be classified based on the pathways or functions they participate in. Differentially expressed genes can also be annotated with KEGG terms. Software used: Diamond (https://github.com/bbuchfink/diamond).
Assembly: mm10
Supplementary files format and content: gene.TPM.matrix.annot.xlsx

organism: Mus musculus

source_name: CD36f/f mice, sampling at ZT8, biol rep 3

extract_protocol:
Take a suitable amount of tissue, the liquid nitrogen is fully milled and transferred to a 1.5ml centrifuge with 1ml Trizol pre-cooled. The vibration causes it to fully crack. Place it at room temperature for 5 minutes, which may be extended appropriately if difficult to extract tissue. 4C, 13000g centrifuge for 5 minutes, draw the upper liquid into another centrifuge tube, according to 0.2 ml chloroform / 1 ml trizol amount of pre-cooled chloroform, that is, 200 ul, vibrate mix and leave at room temperature for 5 minutes. 4C, 13000g centrifuge for 15 minutes, draw the upper aqueous phase (the tip of the gun does not contact the intermediate protein layer) to another centrifuge (400 ul), add an equal volume of pre-cooled isopropanol, and leave at room temperature for 10 minutes.After centrifuging 13,000 g at 4 ° C for 10 minutes, discard the liquid, there will be a small white precipitation on the bottom of the tube (perhaps not visible to the naked eye when the amount of RNA is very small). Add 1ml pre-cooled 75% ethanol to float the precipitation.At 4 ° C, 12,000 g centrifuged for 5 minutes, purified (suck purified with 1000 sets of 10uL gunheads and discarded), centrifuged the centrifuge tube for a few seconds, dumped the residue suspended on the wall of the tube, sucked out the residues with 10ul gunheads, and left it at room temperature for 3-5min. Note not to be too dry, otherwise the RNA is insoluble and may cause degradation.Add 20-50 ul (the amount added depends on the amount of RNA extracted) of sterilized 0.1% DEPC water to dissolve.
Total RNA is extracted from the tissue sample, and the concentration and purity of the extracted RNA are analyzed using the Nanodrop2000. The integrity of the RNA is assessed through agarose gel electrophoresis, and the RIN value is determined using the Agilent5300. For a single library construction, the total RNA required is 1 μg, with a concentration ≥ 30 ng/μL and an RQN > 6.5, with an OD260/280 range of 1.8 to 2.2. In eukaryotic organisms, mRNA has a polyA tail structure. Using magnetic beads coated with Oligo(dT) and polyA, A-T base pairing can be achieved, allowing mRNA to be isolated from total RNA for transcriptome analysis. The Illumina platform is designed for sequencing short sequence fragments; the enriched mRNA obtained is a complete RNA sequence with an average length of several kilobases.It needs to be subjected to random disruption. By incorporating a fragmentation buffer and selecting suitable conditions, mRNA can be randomly broken into small fragments of approximately 300 bp. Under the action of reverse transcriptase, using random primers, mRNA serves as a template to reverse-synthesize a single strand of cDNA. Subsequently, double-strand synthesis (dUTP replacing dTTP; this strand is subsequently degraded by the UDG enzyme; ultimately, the first strand representing the original RNA direction is amplified and sequenced) is performed, resulting in a stable double-stranded structure. The double-stranded cDNA structure has sticky ends; EndRepairMix is added to fill these with blunt ends, followed by the addition of an A base at the 3’ end for connecting Y-shaped adapters. UDG enzyme is used to degrade the second-strand cDNA containing dUTI, leaving only the first-strand cDNA, which is then amplified by PCR. The product after connecting the adapter is purified and fragmented, and the purified fragment is used for PCR amplification to obtain the final library. Sequencing is performed on the Nova seq X plus platform.

value: renal cortical


title: LC093_D1

source_name: Gut epithelium, P, Sigmoideum

value: Progressor

value: Sigmoideum

value: LGD


title: FLOX_ZT8_b

description: Library name: sample_8

source_name: CD36f/f mice, sampling at ZT8, biol rep 2


title: 22Rv1_RNAseq_siNHSL1_R1

description:
Library name: 22Rv1 RNAseq siNHSL1 R1
RNA-seq


title: 22Rv1_CTCF_cPCE_del_R2

description:
Library name: 22Rv1 CTCF cPCE del R2
ChIP-seq

library_source: genomic

data_processing:
ChIP-seq data were processed following ENCODE3 guidelines (PMID: 22955616). Briefly, BWA (PMID: 19451168) was used to align the raw sequencing reads to the human reference genome (hg38). Library complexity was computed to determine the PCR bottleneck coefficients, non-redundant fraction, normalized strand cross-correlation coefficient, and relative strand cross-correlation coefficient. PCR duplicates and unaligned reads were removed using Picard (https://github.com/broadinstitute/picard) and samtools (PMID: 19505943). Uniquely mapped reads were used to call peaks using MACS2 (PMID: 18798982) (narrowPeak format).
Assembly: hg38
Supplementary files format and content: .bw

molecule: genomic DNA

extract_protocol:
For ChIP-seq, cells were grown to 70%-90% confluence and cross-linked with 1% formaldehyde for 10 minutes and quenched with 125nM glycine for 5 minutes at RT. Nuclei were lysed in nuclei lysis buffer, and performed snap-freeze using liquid nitrogen. Chromain was sonicated to an approximate length of 200 bp - 500 bp using bioruptor sonicator.
ChIP-seq library: Libraries were prepared using the KAPA Hyper Prep Kit from KAPA Biosystems. End-Repair and A-Tailing Buffers, DNA ligase, and ligation buffer were used. Ampure beads were used for post-ligation clean up, and KAPA HiFi HotStart Ready Mix and Nextflex Primer Mix were used for amplification of adapter modified DNA fragments.

tag: batch

value: CTCF


title: HUVEC_IRIS_2

description:
Library name: Sample 92
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 2

source_name: HUVEC

value: HUVEC

value: Venal endothelial

value: Ionizing radiation-induced senescence (8 days 7.5 Gy)


title: HSAEC_ETIS_2

description:
Library name: Sample 77
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 2


title: 22Rv1_RNAseq_siHEBP2_R3

description:
Library name: 22Rv1 RNAseq siHEBP2 R3
RNA-seq


title: LC078_IV

value: gut epithelium

value: Non-progressor

value: Descendens

value: Chronic


title: FLOX_ZT8_a

description: Library name: sample_7

source_name: CD36f/f mice, sampling at ZT8, biol rep 1


title: 22Rv1_CTCF_NTC_R1

description:
Library name: 22Rv1 CTCF NTC R1
ChIP-seq


title: LC078_II

source_name: Gut epithelium, NP, Ascendens

value: Ascendens


title: HSAEC_ETIS_1

description:
Library name: Sample 76
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 1

value: HSAEC

value: Lung epithelial

value: WT


title: 22Rv1_RNAseq_siHEBP2_R2

description:
Library name: 22Rv1 RNAseq siHEBP2 R2
RNA-seq

value: Prostate

value: prostate cells


title: LC046_II


title: FLOX_ZT4_c

description: Library name: sample_6

source_name: CD36f/f mice, sampling at ZT4, biol rep 3

value: renal cortical


title: HSAEC_P_4

description:
Library name: Sample 75
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: 22Rv1_RNAseq_siHEBP2_R1

description:
Library name: 22Rv1 RNAseq siHEBP2 R1
RNA-seq


title: FLOX_ZT4_b

description: Library name: sample_5

source_name: CD36f/f mice, sampling at ZT4, biol rep 2


title: FLOX_ZT20_b

description: Library name: sample_18

source_name: CD36f/f mice, sampling at ZT20, biol rep 2


title: LC076_V

source_name: Gut epithelium, NP, Sigmoideum

value: Sigmoideum


title: LC076_IV


title: HSAEC_P_3

description:
Library name: Sample 74
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: 22Rv1_RNAseq_siNTControl_R3

description:
Library name: 22Rv1 RNAseq siNTControl R3
RNA-seq


title: FLOX_ZT4_a

description: Library name: sample_4

source_name: CD36f/f mice, sampling at ZT4, biol rep 1


title: HSAEC_P_2

description:
Library name: Sample 73
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: 22Rv1_RNAseq_siNTControl_R2

description:
Library name: 22Rv1 RNAseq siNTControl R2
RNA-seq


title: FLOX_ZT0_c

description: Library name: sample_3

source_name: CD36f/f mice, sampling at ZT0, biol rep 3


title: LC076_II


title: LC054_VI

source_name: Gut epithelium, NP, Rectum

value: Rectum


title: LC067_VI


title: 22Rv1_RNAseq_siNTControl_R1

description:
Library name: 22Rv1 RNAseq siNTControl R1
RNA-seq


title: HSAEC_P_1

description:
Library name: Sample 72
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: FLOX_ZT0_b

description: Library name: sample_2

source_name: CD36f/f mice, sampling at ZT0, biol rep 2


title: LC067_V


title: HeMn_IRIS_4

description:
Library name: Sample 71
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 4

source_name: HeMn

value: HeMn

value: Skin melanocytes


title: 22Rv1_RNAseq_resPCE_del_R3

description:
Library name: 22Rv1 RNAseq resPCE del R3
RNA-seq

source_name: Prostate


title: FLOX_ZT0_a

description: Library name: sample_1

source_name: CD36f/f mice, sampling at ZT0, biol rep 1


title: LC054_II


title: HeMn_IRIS_3

description:
Library name: Sample 70
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 3

value: Ionizing radiation-induced senescence (8 days 7.5 Gy)


title: 22Rv1_H3K27ac_cPCE_del_R1

description:
Library name: 22Rv1 H3K27ac cPCE del R1
ChIP-seq


title: 22Rv1_RNAseq_resPCE_del_R2

description:
Library name: 22Rv1 RNAseq resPCE del R2
RNA-seq


title: RNAseq_Low_2

city: Tianjin

first: Xiaoxi

last: Xu

address: No. 154, Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

description:
Library name: sample4
Low glucose (2.5 mM), biological repeat 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution.
Assembly: mm10
Supplementary files format and content: RNAseq_gene_count.xlsx

extract_protocol:
RNA extraction using the Qiagen RNeasy kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing,adapter ligation, size selection, amplification, and purification.

value: low glucose (2.5 mM) 2h


title: AS061_IV

value: gut epithelium

value: Non-progressor


title: 22Rv1_RNAseq_resPCE_del_R1

description:
Library name: 22Rv1 RNAseq resPCE del R1
RNA-seq


title: RNAseq_Low_1

description:
Library name: sample3
Low glucose (2.5 mM), biological repeat 1


title: HeMn_IRIS_2

description:
Library name: Sample 69
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 2


title: AS041_III

source_name: Gut epithelium, P, Descendens

value: Progressor

value: Descendens


title: HeMn_IRIS_1

description:
Library name: Sample 68
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 1


title: AS041_I

source_name: Gut epithelium, P, Ascendens

value: Ascendens


title: RNAseq_High_2

description:
Library name: sample2
High glucose (25 mM) 2h, biological repeat 2

value: High glucose (25 mM) 2h


title: 22Rv1_RNAseq_rPCE_del_R3

description:
Library name: 22Rv1 RNAseq rPCE del R3
RNA-seq


title: 22Rv1_RNAseq_rPCE_del_R2

description:
Library name: 22Rv1 RNAseq rPCE del R2
RNA-seq


title: HeMn_ETIS_4

description:
Library name: Sample 67
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 4

value: WT

value: Etoposide-induced senescence (8 days 25 µM)


title: RNAseq_High_1

description:
Library name: sample1
High glucose (25 mM) 2h, biological repeat 1


title: HeMn_ETIS_3

description:
Library name: Sample 66
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 3


title: 22Rv1_RNAseq_rPCE_del_R1

description:
Library name: 22Rv1 RNAseq rPCE del R1
RNA-seq

value: Prostate

value: prostate cells


title: FLOX_ZT12_a

description: Library name: sample_10

source_name: CD36f/f mice, sampling at ZT12, biol rep 1

value: renal cortical


title: LC093_III

source_name: Gut epithelium, P, Transversum

value: Transversum

value: Chronic active


title: DysfA6 mouse rep 2 (4 month old, female)

city: Chicago

first: GaHyun

last: Lee

address: 303 E Superior

institute: Northwestern University

description: Library name: DysfA6 2

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation was conducted on the CellRanger software v8.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/8.0)
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Quadriceps, abdominal, paraspinal muscle

extract_protocol:
Quadriceps, abdominal, and paraspinal muscles were freshly harvested from 4-month-old female Dysf and DysfA6 (n=2 each, 4 mice total), washed in sterile-filtered DPBS with calcium and magnesium (MT21030CV; Thermo Fisher Scientific), combined and weighed. The tissues were minced in 6 mg/mL of collagenase type II (LS004177; Worthington) solution in 1:5 weight to volume ratio and enzymatically digested at 37°C for 1.5 hours with shaking.  The digested tissues were then filtered through 70µm nylon filter and washed with calcium and magnesium-free DPBS (14190144; Thermo Fisher Scientific).  Debris was removed from the samples using Debris Removal Solution (130-109-398; Miltenyi Biotec) following the manufacturer’s instructions. Subsequent cell pellet was resuspended in 1X TheraPEAK ACK lysing buffer (BP10-548E; Lonza) to remove the red blood cells, filtered through 40µm nylon filter, and resuspended in 1% BSA/DPBS solution.  The final cell suspension was diluted 1:10, mixed 1:1 with ViaStain AOPI Staining Solution (CS2-0106-5ML; Revvity) and counted on Nexcelom Cellometer Auto2000 to ensure viability > 70%.
Mononuclear cells isolated as described above were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method for cell number and viability.  29,000 cells were loaded into the Chromium iX Controller (PN-1000328, 10X Genomics) on a Chromium GEM-X Single cell 3’ Chip Kit v4 (PN-1000215; 10X Genomics), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol.  The cDNA and library were generated using the GEM-X Single cell 3’ Kit v4 (PN-1000691; 10X Genomics) and Dual Index Kit TT Set A (PN-1000215; 10X Genomics) according to the manufacturer’s manual.  Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (5067-4626; Agilent Technologies) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina Novaseq X Plus sequencer with 100 cycle kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.  The single cell library preparation and sequencing was done at Northwestern University NUseq facility core with the support of NIH Grant (1S10OD025120).

value: Isolated mononuclear cells

tag: age

value: 4 month old

tag: Sex

value: female


title: 22Rv1_RNAseq_cPCE_del_R3

description:
Library name: 22Rv1 RNAseq cPCE del R3
RNA-seq


title: HeMn_ETIS_2

description:
Library name: Sample 65
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 2

value: HeMn

value: Skin melanocytes


title: LC093_II

value: gut epithelium


title: DysfA6 mouse rep 1 (4 month old, female)

description: Library name: DysfA6 1

value: Quadriceps, abdominal, paraspinal muscle


title: LC093_IV

value: Progressor

value: Descendens


title: LC093_I

source_name: Gut epithelium, P, NA


title: HeMn_ETIS_1

description:
Library name: Sample 64
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 1


title: 22Rv1_RNAseq_cPCE_del_R2

description:
Library name: 22Rv1 RNAseq cPCE del R2
RNA-seq


title: Dysf mouse rep 2 (4 month old, female)

description: Library name: Dysf 2

value: Dysf


title: HSAEC_ETIS_3

description:
Library name: Sample 78
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 3

source_name: HSAEC

value: HSAEC

value: Lung epithelial

value: WT

value: Etoposide-induced senescence (8 days 20 µM)


title: 22Rv1_RNAseq_cPCE_del_R1

description:
Library name: 22Rv1 RNAseq cPCE del R1
RNA-seq

value: Prostate

value: prostate cells


title: HeMn_P_4

description:
Library name: Sample 63
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: LC093_D2

source_name: Gut epithelium, P, Sigmoideum

value: Sigmoideum

value: LGD


title: Dysf mouse rep 1 (4 month old, female)

description: Library name: Dysf 1

value: Isolated mononuclear cells

value: 4 month old

value: female


title: DysfA6 mouse rep 2 (6 month old, female)

description: Library name: DysfA6 2

data_processing:
Sequenced raw reads were processed through FASTQC (v0.11.5), trimmed with trimmomatic (v0.36), and aligned to the mouse reference genome (mm10) using STAR (v2.5.2).  Raw read counts were quantified with HTSeq.
Assembly: mm10
Supplementary files format and content: Aligned counts

source_name: Quadriceps

extract_protocol:
Quadriceps muscles were removed from Dysf and DysfA6 female mice (n=2 each, 4 mice total) and longitudinally cut along the orientation of the myofibers into smaller pieces and digested in in 6 mg/mL of collagenase type II (LS004177; Worthington) solution in 1:5 weight to volume ratio and enzymatically digested at 37°C for 2.5 hours with shaking.  Digested tissues were filtered through 70µm nylon filter to enrich for myofibers.  Remaining tissues on the filter were washed with DPBS with calcium and magnesium (MT21030CV; Thermo Fisher Scientific).  The suspension was then filtered through 100µm nylon filter.  Filtered isolated myofibers were pelleted and flash frozen in liquid nitrogen until RNA isolation.  RNA was isolated using TRIzol Reagent (15596018; Thermo Fisher Scientific) followed by Aurum Total RNA Mini Kit (7326820; Bio-Rad).  Briefly, the frozen myofiber pellet was treated with 1mL of TRIzol Reagent (15596018; Thermo Fisher Scientific) and combined with 200µL of chloroform.  The aqueous phase was combined with equal volume of 70% ethanol and used as starting material for RNA isolation using the Aurum Total RNA Mini Kit following manufacturer’s instructions.
RNA quality and quantity were assessed by Bioanalyzer RNA pico chip and Qubit RNA HS assay kit, respectively. Then, 25ng of RNA was used as input for library construction using Illumina stranded mRNA prep kit (Illumina 20040534) according to manufacturers’ protocol.  The multiplexed libraries were sequenced on Novaseq X Plus using single end 50nt mode.

value: Quadriceps

value: Myofiber


title: LC067_II

source_name: Gut epithelium, NP, Ascendens

value: gut epithelium

value: Non-progressor

value: Ascendens


title: [ATAC-Seq] shYT#2_3

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

description: Library name: Sample 8

data_processing:
For the ATAC-Seq analysis the nextflow pipeline (https://nf-co.re/atacseq/2.1.2/) was used.
Assembly: mm10
Supplementary files format and content: bigWig files for each sample

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols. Cells were then incubated with Fc receptor blocking reagent (Miltenyi) for 10 minutes on ice. Tumor cells were labeled with anti-EpCAM-APC antibody (eBioscience, #17-5791-82; 1:100) for 30 minutes on ice. After washing, cells were incubated with anti-APC microbeads (Miltenyi) for an additional 30 minutes. Labeled cells were then loaded onto LS columns (Miltenyi) and processed according to the manufacturer’s instructions. Positively labeled EpCAM⁺ cells were eluted and further processed for downstream applications.
A total of 5 × 10^4 cells were pelleted in a pre-wetted 1.5 mL low-binding tube by centrifugation at 500 × g for 5 minutes at 4°C using a fixed-angle rotor. Cells were resuspended in 50 µL ice-cold ATAC-Resuspension Buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% (v/v) NP-40, 0.1% (v/v) Tween-20, and 0.01% (w/v) digitonin. The suspension was pipetted up and down three times and incubated on ice for 3 minutes to lyse the cells. To remove the lysis reagents, 1 mL ice-cold RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and the tube was gently inverted three times. Nuclei were pelleted by centrifugation at 500 × g for 10 minutes at 4°C, and the supernatant was carefully removed. Nuclei were resuspended in 50 µL of transposition reaction mix containing: 25 µL 2× TD buffer (Illumina), 2.5 µL Tn5 transposase (to reach 100 nM final concentration), 16.5 µL 1× PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, 5 µL nuclease-free water. The mix was pipetted up and down six times to ensure homogeneous suspension. Samples were incubated at 37°C for 30 minutes at 1000 rpm using a thermomixer. Following transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit (Zymo Research) according to the manufacturer's instructions and amplified by PCR.

value: shYT


title: scRNA-seq of HNSCC-infiltrating T cells; 12A

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

description: Library name: 12A_GEX

data_processing:
The resulting fastq files were processed using cellranger multi (version 7.1.0).
Supplementary files format and content: Cellranger output files:  sample_id_filtered_feature_bc_matrix.h5, sample_id_clonotypes.csv, sample_id_filtered_contig_annotations.csv, sample_id_vdj_contig_info.pb

source_name: tumor tissue

extract_protocol:
Fresh pre- and post-treatment tumor biopsies were digested using the Human Tumor Dissociation Kit and the gentleMACS Dissociator (Miltenyi Biotec) per manufacturer recommendations. Single cell tumor suspensions were washed with RPMI-1640, passed through a 70-m filter, stained with TruStain FcX (Biolegend), primarily-conjugated anti-human CD3 antibody (clone SK7, Biolegend) and the viability marker Sytox Blue (Thermo) and viable CD3-positive cells were isolated using fluorescent activated cell sorting (FACSAria III, BD Biosciences).
Cells were mixed with barcoded gelbeads and 5′ GEM Kit v2 reagents (10X Genomics), and single-cell capture was performed. Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the manufacturer’s recommendations. Each fragmented DNA library was loaded into a sequencing lane on a NovaSeq or HiSeq system (Illumina) and was sequenced with pair-end reads of 75 bp.

value: tumor tissue

value: T cells

value: mixed

value: treatment-naïve


title: HeMn_P_2

description:
Library name: Sample 61
Cells were cultured for 8 days in DMSO-containing media - replicate 2

value: HeMn

value: Skin melanocytes

value: WT


title: 22Rv1_RNAseq_NTC_R2

description:
Library name: 22Rv1 RNAseq NTC R2
RNA-seq

value: Prostate

value: prostate cells


title: DysfA6 mouse rep 1 (6 month old, female)

description: Library name: DysfA6 1

value: 4 month old


title: 22Rv1_RNAseq_NTC_R1

description:
Library name: 22Rv1 RNAseq NTC R1
RNA-seq


title: 22Rv1_RNAseq_NTC_R3

description:
Library name: 22Rv1 RNAseq NTC R3
RNA-seq


title: HeMn_P_1

description:
Library name: Sample 60
Cells were cultured for 8 days in DMSO-containing media - replicate 1

value: Control proliferating cells


title: LC052_VI

source_name: Gut epithelium, P, Rectum

value: Progressor

value: Rectum

value: Other neoplasia


title: HeMn_P_3

description:
Library name: Sample 62
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: LC053_II

value: gut epithelium

value: Non-progressor


title: Dysf mouse rep 2 (6 month old, female)

description: Library name: Dysf 2

value: Quadriceps

value: Myofiber

value: Dysf

value: female


title: HEKn_IRIS_4

description:
Library name: Sample 59
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 4

source_name: HEKn

value: HEKn

value: Skin keratinocytes

value: Ionizing radiation-induced senescence (8 days 10 Gy)


title: LC052_IV

value: Descendens


title: 22Rv1_ATAC_rPCE_del_R2

description:
Library name: 22Rv1 ATAC rPCE del R2
ATAC-seq

data_processing:
ATAC-seq data were processed following ENCODE3 guidelines (PMID: 22955616). Briefly, raw sequencing reads were trimmed to remove adapter sequences using the Cutadapt (https://cutadapt.readthedocs.io/) program. Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (PMID: 22388286). PCR duplicates, low-quality alignments, and mitochondrial reads were removed using Picard (https://github.com/broadinstitute/picard) and samtools (PMID: 19505943). Library complexity was assessed by calculating the non-redundant fraction, PCR bottleneck coefficients, and strand cross-correlation metrics. Uniquely mapped, properly paired reads were used to call accessible chromatin peaks using MACS2 (PMID: 18798982) (narrowPeak format).
Assembly: hg38
Supplementary files format and content: .bw

extract_protocol:
For ATAC-seq, cells with over 90% viability were harvested. Cells were lysed on ice to obtain intact nuclei.
ATAC-seq library: Libraries were made using Zymo ATAC-seq kit (Zymo Research, D5458) following manufacturer's instructions. Briefly, Zymo's Tn5 Transposase was used to tagment the genomic DNA, and the tagmented DNA fragments were amplified with Zymo's PCR mix during library preparation.

value: Prostate


title: Dysf mouse rep 1 (6 month old, female)

description: Library name: Dysf 1


title: HEKn_IRIS_3

description:
Library name: Sample 58
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 3

value: WT


title: 22Rv1_ATAC_rPCE_del_R1

description:
Library name: 22Rv1 ATAC rPCE del R1
ATAC-seq

value: prostate cells


title: LC052_III

value: Transversum


title: HEKn_IRIS_2

description:
Library name: Sample 57
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 2


title: 22Rv1_ATAC_cPCE_del_R2

description:
Library name: 22Rv1 ATAC cPCE del R2
ATAC-seq


title: Double-Ko-3

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

description: Library name: Double-Ko-3

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

source_name: lung

extract_protocol:
Total RNA was extracted from the sorted WT, Tle3–/–, Klf2–/–, or Tle3–/–Klf2–/– cells on 14 dpi, and triplicates were obtained for each genotype. cDNA synthesis and amplification were performed using SMARTer Ultra Low Input RNA Kit (Clontech).
Libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides. Sequence data in fastq format were generated using CASAVA 1.8.2 processing pipeline from Illumina.

value: lung

value: Tissue resident memory cells

value: mice intranasal infection with WSN-GP33


title: AS101_V

source_name: Gut epithelium, NP, Rectum

value: gut epithelium

value: Rectum


title: 22Rv1_ATAC_cPCE_del_R1

description:
Library name: 22Rv1 ATAC cPCE del R1
ATAC-seq

source_name: Prostate


title: Double-Ko-1

description: Library name: Double-Ko-1


title: HEKn_IRIS_1

description:
Library name: Sample 56
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 1


title: Double-Ko-2

description: Library name: Double-Ko-2


title: HEKn_ETIS_4

description:
Library name: Sample 55
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 25 µM)


title: LC003_IV

source_name: Gut epithelium, NP, Descendens

value: Non-progressor

value: Chronic


title: 22Rv1_ATAC_NTC_R2

description:
Library name: 22Rv1 ATAC NTC R2
ATAC-seq


title: klf2-Ko-3

description: Library name: klf2-Ko-3


title: LC003_II

value: Ascendens


title: AS101_III


title: HEKn_ETIS_3

description:
Library name: Sample 54
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 3

value: HEKn


title: 22Rv1_ATAC_NTC_R1

description:
Library name: 22Rv1 ATAC NTC R1
ATAC-seq


title: klf2-Ko-2

description: Library name: klf2-Ko-2


title: HEKn_ETIS_2

description:
Library name: Sample 53
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 2

value: Skin keratinocytes


title: Spike-reactive memory T cells, Post Dose 2 Timepoint 5, TCR

city: Toronto

first: Tania

middle: H

last: Watts

state: Ontario

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

description:
Library name: PostDose3_Tcells_TCR
TCR sequencing

data_processing:
CITE-seq: FASTQ paired-end reads were processed using the cellranger count command from 10x Genomics’ Cell Ranger (v.8.0.1) and aligned against the human reference refdata-gex-GRCh38-2024-A. TCR-seq: FASTQ paired-end reads were processed using cellranger vdj command from 10x Genomics’ Cell Ranger (v8.0.1) and aligned to the VDJ reference- vdj_GRCh38_alts_ensembl-7.1.0
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: CITE-seq GEX and HTO: CellRanger output filtered tab-separated values files and matrix files (libraries for CITE-seq GEX and HTO are combined in the tsv and matrix files). Files can be found in Supplementary Files.
Supplementary files format and content: TCR-seq: CellRanger output files containing filtered assembled contigs and filtered contig annotations.
Supplementary files format and content: Feature reference csv files contain feature reference information, see Supplementary Files.
Library strategy: TCR-Seq

source_name: blood

extract_protocol:
Sorted Spike-reactive memory T cells were sequenced in two batches by Timepoint. Single cells were encapsulated in Gel-Beads-in emulsions (GEMs) using a 10X Genomics Chromium X with the Chromium GEM-X Single Cell 5' Kit v3.
CITE-seq gene expression libraries (Single Cell 5' R2-only v3, 10X Genomics) and TCR V(D)J libraries (Single Cell V(D)J R2-only v3, 10X Genomics) were prepared as recommended by the 10X Genomics user guides.

treatment_protocol: PBMCs from healthy controls (n=3), anti-TNF treated IBD patients (n=5) and anti-IL-12/23 treated IBD patients (n=4) were stimulated with ancestral Spike peptide pools (PepMix, JPT) for 18 hours, then hashtagged, pooled and Spike-reactive memory T cells were sorted for based on the dual expression of activation induced markers. This was done at two timepoints, Timepoint 3 (2-4 weeks post dose 2) and Timepoint 5 (2-4 weeks post dose 3), independently.

value: blood

value: PBMCs

value: T cells

value: mixed samples (immunized)

tag: library type

value: TCR


title: AS101_I


title: HEKn_ETIS_1

description:
Library name: Sample 52
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 1

value: WT


title: klf2-Ko-1

description: Library name: klf2-Ko-1

value: lung


title: Spike-reactive memory T cells, Post Dose 2 Timepoint 5, HTO

description:
Library name: PostDose3_Tcells_HTO
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
CITE-seq: FASTQ paired-end reads were processed using the cellranger count command from 10x Genomics’ Cell Ranger (v.8.0.1) and aligned against the human reference refdata-gex-GRCh38-2024-A. TCR-seq: FASTQ paired-end reads were processed using cellranger vdj command from 10x Genomics’ Cell Ranger (v8.0.1) and aligned to the VDJ reference- vdj_GRCh38_alts_ensembl-7.1.0
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: CITE-seq GEX and HTO: CellRanger output filtered tab-separated values files and matrix files (libraries for CITE-seq GEX and HTO are combined in the tsv and matrix files). Files can be found in Supplementary Files.
Supplementary files format and content: TCR-seq: CellRanger output files containing filtered assembled contigs and filtered contig annotations.
Supplementary files format and content: Feature reference csv files contain feature reference information, see Supplementary Files.
Library strategy: CITE-seq

molecule: protein

tag: hto

value: TotalSeq_C_0251_anti-human_Hashtag_1 (healthy control #1), TotalSeq_C_0252_anti-human_Hashtag_2 (healthy control #2), TotalSeq_C_0253_anti-human_Hashtag_3 (healthy control #3), TotalSeq_C_0254_anti-human_Hashtag_4 (anti-IL-12/23 treated IBD patient #1), TotalSeq_C_0255_anti-human_Hashtag_5 (anti-IL-12/23 treated IBD patient #2), TotalSeq_C_0256_anti-human_Hashtag_6 (anti-IL-12/23 treated IBD patient #3), TotalSeq_C_0257_anti-human_Hashtag_7 (anti-IL-12/23 treated IBD patient #4), TotalSeq_C_0258_anti-human_Hashtag_8 (anti-TNF treated IBD patient #1), TotalSeq_C_0259_anti-human_Hashtag_9 (anti-TNF treated IBD patient #2), TotalSeq_C_0260_anti-human-Hashtag_10 (anti-TNF treated IBD patient #4), TotalSeq_C_0296_anti-human_Hashtag_11 (anti-TNF treated IBD patient #5)

value: HTO


title: Tle3-Ko-3

description: Library name: Tle3-Ko-3

value: Tissue resident memory cells

value: mice intranasal infection with WSN-GP33


title: HEKn_P_4

description:
Library name: Sample 51
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: Spike-reactive memory T cells, Post Dose 2 Timepoint 5, GEX

description:
Library name: PostDose3_Tcells_mRNA
polyA RNA

value: mRNA


title: [ATAC-Seq] shYT#2_2

description: Library name: Sample 7

value: shYT


title: AS098_V

value: gut epithelium

value: Non-progressor

value: Rectum

value: Chronic active


title: AS098_II

source_name: Gut epithelium, NP, Transversum

value: Transversum


title: Tle3-Ko-2

description: Library name: Tle3-Ko-2


title: Spike-reactive memory T cells, Post Dose 2 Timepoint 3, TCR

description:
Library name: PostDose2_Tcells_TCR
TCR sequencing

value: blood

value: PBMCs

value: T cells


title: HEKn_P_3

description:
Library name: Sample 50
Cells were cultured for 8 days in DMSO-containing media - replicate 3

value: HEKn

value: Skin keratinocytes

value: WT


title: AS098_I

value: Ascendens


title: Tle3-Ko-1

description: Library name: Tle3-Ko-1

value: lung

value: Tissue resident memory cells


title: HEKn_P_2

description:
Library name: Sample 49
Cells were cultured for 8 days in DMSO-containing media - replicate 2

value: Control proliferating cells


title: Spike-reactive memory T cells, Post Dose 2 Timepoint 3, HTO

description:
Library name: PostDose2_Tcells_HTO
Hashtag-derived oligonucleotide (HTO)

value: mixed samples (immunized)

value: TotalSeq_C_0251_anti-human_Hashtag_1 (healthy control #1), TotalSeq_C_0252_anti-human_Hashtag_2 (healthy control #2), TotalSeq_C_0253_anti-human_Hashtag_3 (healthy control #3), TotalSeq_C_0254_anti-human_Hashtag_4 (anti-IL-12/23 treated IBD patient #1), TotalSeq_C_0255_anti-human_Hashtag_5 (anti-IL-12/23 treated IBD patient #2), TotalSeq_C_0256_anti-human_Hashtag_6 (anti-IL-12/23 treated IBD patient #3), TotalSeq_C_0257_anti-human_Hashtag_7 (anti-IL-12/23 treated IBD patient #4), TotalSeq_C_0258_anti-human_Hashtag_8 (anti-TNF treated IBD patient #1), TotalSeq_C_0259_anti-human_Hashtag_9 (anti-TNF treated IBD patient #2), TotalSeq_C_0260_anti-human-Hashtag_10 (anti-TNF treated IBD patient #3), TotalSeq_C_0296_anti-human_Hashtag_11 (anti-TNF treated IBD patient #5)

value: HTO


title: WT3

description: Library name: WT3

value: mice intranasal infection with WSN-GP33


title: Liver, High-fat diet, rep2

status: Public on Jun 16 2026

city: Santa Cruz

first: Andrew

middle: David

last: Holmes

state: California

address: 1156 High Street

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

description: Library name: LIVER_HF_2

data_processing:
Sequences were trimmed with  "cutadapt --no-indels -O 15 -m 2 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" ,"cutadapt -u 7" , and then "cutadapt -u -1" to remove the adapter, the UMI, and the TPRT base (the UMI was not used for removing duplicates)  Only reads >65 bases were used for most analyses
Data was mapped and counted using TRAX, which uses an all-best mapping approach and uses Deseq2 for normalization and detection of differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for calculated by tRAX, with mitochondrial tRNA counts appended

source_name: Liver

growth_protocol: Mice were group-housed (maximum of 5 per cage) with a 12-hour light-dark cycle (lights off at 6 pm) and free access to food and water ad libitum.

extract_protocol:
Samples were vortexed for 5 minutes to ensure complete breakdown of the sperm, followed by centrifugation at 12,000 RCF for 4 minutes. The aqueous phase was then removed and transferred to a low-binding RNase/DNase-free microcentrifuge tube, followed by the addition of 20 µg of glycoblue (Invitrogen) and 1 volume of Isopropanol. The RNA was then precipitated for 30 minutes or greater at -20°C, followed by centrifugation at 18,000 RCF for 30 minutes at 4°C, and one wash with 70% cold ethanol followed by centrifugation at 12,000 RCF for 10 minutes at 4°C. Finally, the RNA was reconstituted in nuclease-free water.
Library was constructed using Ottr-seq protocol.  Input RNA was PNK treated and labelled at the 3’ end by incubation in buffer containing ddATP for 90 minutes in 30˚C, followed by an addition of ddGTP and another incubation at 30˚C for 30 minutes. The reaction was stopped by incubating at 65°C for 5 minutes, followed by the addition of 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (NEB, cat# M0371S) at 37°C for 15 minutes, then stopped by the addition of 5 mM EGTA, and incubated at 65°C for 5 minutes. Samples were then incubated in templated cDNA synthesis buffer, adaptors, and dNTPs at 37˚C for 20 minutes, followed by heat inactivation at 65˚C for 5 minutes and RNase A/H treatment. cDNA was size selected on a 10% PAGE urea gel to minimize adaptor dimers. Size selected cDNA was PCR amplified for 12 cycles with Q5 high fidelity polymerase (NEB, cat# M0491S). The final PCR product was cleaned up with AMPure XP beads (Beckman, cat # A63881) and finally separated by 6% TBE gel to remove adaptor dimers. The desired product was excised from the gel and eluted in 400ul elution buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) overnight at -20, followed by isopropanol precipitation and resuspension in 9µl nuclease-free H2O.

treatment_protocol: Animals were raised on one of four diets – a low protein diet (LP; 10% of protein rather than 18%, remaining mass made up with sucrose, BioServ, cat# S3156), control for low protein diet (C; BioServ AIN-93g, cat# F3156), a high fat diet (HF; 60% of fat calories rather than 16%, BioServ, cat# S3282) , or control for high-fat diet  (C_HF; 7.2% fat calories, BioServ, cat# S4031)

value: Liver

value: High-fat diet


title: HEKn_P_1

description:
Library name: Sample 48
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: Spike-reactive memory T cells, Post Dose 2 Timepoint 3, GEX

description:
Library name: PostDose2_Tcells_mRNA
polyA RNA

value: mRNA


title: LC026_VI

value: gut epithelium

value: Progressor

value: Rectum


title: LC026_V

value: Sigmoideum


title: WT2

description: Library name: WT2


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 4B

description: Library name: 4B_TCR

data_processing:
The resulting fastq files were processed using cellranger multi (version 8.1.0).
Supplementary files format and content: Cellranger output files:  sample_id_filtered_feature_bc_matrix.h5, sample_id_clonotypes.csv, sample_id_filtered_contig_annotations.csv, sample_id_vdj_contig_info.pb

source_name: peripheral blood

extract_protocol:
CD8+ peripheral blood T cells were isolated from fresh PBMC using the EasySep Human CD8+ T cell Isolation Kit (Stemcell Technologies) per manufacturer recommendations. 3x105 cells suspended in PRMI-1640-based media supplemented with 10% fetal bovine serum (FBS), 5 mM glutamine and 25 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) were plated in a 12 well tissue culture plate and cultured for 4 days in the presence or absence of Human T-Activator CD3/28 Dynabeads (Thermo Fisher) used per manufacturer recommendations. After culture, cells were harvested, magnetic stimulation beads were removed, and cells were subjected to capture for single cell RNA- and TCR-sequencing.
Cells were mixed with barcoded gelbeads and 5′ GEM Kit v2 reagents (10X Genomics), and single-cell capture was performed. Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the manufacturer’s recommendations. Each fragmented DNA library was loaded into a sequencing lane on a NovaSeq X Plus (Illumina) and was sequenced with pair-end reads of 75 bp.

value: peripheral blood

value: CD8+ T cells

value: mixed

value: aCD3/aCD28 TCR stimulation


title: WT1

description: Library name: WT1

value: lung

value: Tissue resident memory cells

value: WT


title: HCAEC_IRIS_4

description:
Library name: Sample 47
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 4

source_name: HCAEC

value: HCAEC

value: Arterial endothelial

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: HCAEC_IRIS_3

description:
Library name: Sample 46
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 3


title: Surface-KO

description: Library name: Surface-KO

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

extract_protocol:
Lungs were cut into pieces and digested for 30 min with 1mg/ml type I collagenase and 0.1mg/ml DNase Ⅰ in DMEM at 37 °C. After enzymatic incubations, lungs were further dissociated over a 70-μ m nylon cell strainer (Falcon). For isolation of lymphocytes, single-cell suspensions were then separated using a 44/67% Percoll density gradient. Red blood cells were lysed with ACK buffer (140 mM NH4Cl and 17 mM Tris-base, pH 7.4).The cells were washed in PBS and resuspended in PBS supplemented with 2% w/v FBS.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

value: mice intranasal infection with WSN-GP33


title: LC026_IV

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

source_name: Gut epithelium, P, Descendens

value: Descendens


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 4A

description: Library name: 4A_TCR

value: treatment-naïve


title: LC026_III_D1

source_name: Gut epithelium, P, Transversum

value: gut epithelium

value: Transversum

value: Chronic


title: HCAEC_IRIS_1

description:
Library name: Sample 45
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 1

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 3B

description: Library name: 3B_TCR


title: LC026_II_D1

source_name: Gut epithelium, P, Ascendens

value: Progressor

value: Ascendens

value: LGD


title: GEM-KO

description: Library name: GEM-KO


title: HCAEC_DIS_4

description:
Library name: Sample 44
Cells were cultured for 8 days in 250 nM doxorubicin-containing media - replicate 4

value: Doxorubicin-induced senescence (8 days 250 nM)


title: Pw Retina Sample (ATAC)

city: Berkeley

first: Dario

last: Tommasini

address: 242 Stanley Hall

institute: UC Berkeley

description:
Library name: Pw_Retina_ATAC
Single-nucleus ATAC-seq library from multiome assay

data_processing:
Joint alignment, quantification, and cell calling were performed using CellRanger-ARC (10X Genomics).
Assembly: Species-specific reference genomes for Ambystoma mexicanum and Pleurodeles waltl
Supplementary files format and content: For each sample, paired single-nucleus RNA-seq and single-nucleus ATAC-seq feature-barcode matrices are provided containing synchronized transcriptomic profiles and open-chromatin fragments per individual nucleus.

organism: Pleurodeles waltl

source_name: Retina

growth_protocol: N/A (Wild-type adult animals: 5 axolotls aged 4–8 months, 5 Iberian ribbed newts aged 6 months)

extract_protocol:
Salamander retinas were dissected in cold amphibian PBS (PBS + 25% volume water) and snap-frozen by submerging in an isopentane bath cooled on liquid nitrogen. Nuclei were isolated according to the described protocol (PMID: 39240519) using 30 seconds of lysis incubation. Isolated nuclei were resuspended in 1X Diluted Nuclei Buffer (10X Genomics; PN-2000207).
8000–16000 nuclei were loaded per reaction. Single-nucleus transcriptomes and chromatin accessibility profiles were generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10X Genomics cat. PN-1000285) following 10X Genomics protocol CG000338 Rev F. Libraries were sequenced at the Novogene Sequencing Core (Sacramento, CA & Beaverton, OR) on the NovaSeq X Plus instrument (Illumina).

value: Retina

value: Nuclei

value: Wild-type


title: TRM-2

description: Library name: TRM-2

data_processing:
CLC Genomics Workbench v 11.0.1
Seguence reads were trimmed for adaptor sequence/low-quality sequence using CLc genomicbenchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: bigwig, narrowpeak( except for input sample)

source_name: mice intranasal infection with WSN-GP33

extract_protocol:
The reaction was quenched with stopping buffer and the DNA fragments were purified with MinElute Reaction Cleanup kit (QIAGEN) and then amplified by PCR for 10–14 cycles with barcoded Nextera primers (Illumina).
Libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides. Sequence data in fastq format were generated using CASAVA 1.8.2 processing pipeline from Illumina.

value: lung

value: Tissue resident memory cells

value: WT


title: HCAEC_DIS_3

description:
Library name: Sample 43
Cells were cultured for 8 days in 250 nM doxorubicin-containing media - replicate 3

extract_protocol:
Total RNA was extracted using TriPure™ Isolation Reagent (Sigma-Aldrich), following the manufacturer's instructions with phenol-chloroform extraction.
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

value: HCAEC

value: Arterial endothelial


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 3A

description: Library name: 3A_TCR

value: peripheral blood

value: CD8+ T cells

value: mixed


title: LC026_II

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

value: gut epithelium


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 2B

description: Library name: 2B_TCR

value: aCD3/aCD28 TCR stimulation


title: TRM-1

description: Library name: TRM-1

value: mice intranasal infection with WSN-GP33


title: HCAEC_DIS_2

description:
Library name: Sample 42
Cells were cultured for 8 days in 250 nM doxorubicin-containing media - replicate 2


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 2A

description: Library name: 2A_TCR

value: treatment-naïve


title: Tle3-Ko-3

description: Library name: Tle3-Ko-3

extract_protocol:
WT or Tle3–/– cells were sorted on 14 dpi. Three biological replicates for each cell type, and 50,000 cells for each replicate were used to prepare ATACseq libraries as previously described. Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice. The extracted nuclei were resuspended in transposition mix containing 2.5 µl Transposase (Illumina) and incubated at 37oC for 30 min. The products were purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina). DNA fragments in the range of 150-1,000 bp were recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific).
The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq 4000 sequencing systems in paired end 150 bp reads at the Admera Health.


title: LC003_VI

value: Non-progressor

value: Rectum


title: HCAEC_DIS_1

description:
Library name: Sample 41
Cells were cultured for 8 days in 250 nM doxorubicin-containing media - replicate 1

value: Doxorubicin-induced senescence (8 days 250 nM)


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 1B

description: Library name: 1B_TCR


title: LC003_V

source_name: Gut epithelium, NP, Sigmoideum

value: Sigmoideum

value: Chronic active


title: Tle3-Ko-2

description: Library name: Tle3-Ko-2

value: lung


title: HCAEC_P_4

description:
Library name: Sample 40
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: LC043_IV

value: Descendens

value: Chronic


title: Tle3-Ko-1

description: Library name: Tle3-Ko-1

value: Tissue resident memory cells


title: scVDJ-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 1A

description: Library name: 1A_TCR

value: peripheral blood


title: LC043_II

source_name: Gut epithelium, NP, Ascendens

value: Ascendens


title: HCAEC_P_3

description:
Library name: Sample 39
Cells were cultured for 8 days in DMSO-containing media - replicate 3

value: HCAEC

value: Arterial endothelial

value: WT


title: LC040_VI

value: gut epithelium


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 4B

description: Library name: 4B_GEX

value: CD8+ T cells

value: mixed

value: aCD3/aCD28 TCR stimulation


title: WT3

description: Library name: WT3

value: mice intranasal infection with WSN-GP33


title: WT2

description: Library name: WT2


title: HCAEC_P_2

description:
Library name: Sample 38
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 4A

description: Library name: 4A_GEX

value: treatment-naïve


title: LC040_IV

value: Non-progressor

value: Chronic active


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 3B

description: Library name: 3B_GEX


title: HCAEC_P_1

description:
Library name: Sample 37
Cells were cultured for 8 days in DMSO-containing media - replicate 1

value: Control proliferating cells


title: LC040_II


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 3A

description: Library name: 3A_GEX


title: BMMSC_IRIS_4

description:
Library name: Sample 36
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 4

source_name: BMMSC

value: BMMSC

value: Bone marrow mesenchymal stem cells

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: TREND,SLC43A2sg,3

first: Honglin

last: Tang

address: 866 Yuhangtang Road

institute: Zhejiang  University

description:
Library name: Sample6
Column name in TPM.matrix_All_Samples.txt:SLC_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Tumor

extract_protocol:
etinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor

value: tumor-infiltrating lymphocytes

value: Lymphocytes

value: SLC43A2 knockdown

value: Tail vein injection


title: TREND,SLC43A2sg,2

description:
Library name: Sample5
Column name in TPM.matrix_All_Samples.txt:SLC_2


title: Liver, Low-protein diet, rep2

description: Library name: LIVER_LP_2

value: Liver

value: Low-protein diet


title: LC037_VI

source_name: Gut epithelium, NP, Rectum

value: gut epithelium

value: Rectum


title: C57BL/6J mouse liver,resmetirom-treated MASH,12 weeks,replicate 2

city: nanjing

first: xin

last: Qian

address: No. 24 Tongjia Lane, Gulou District, Nanjing, Jiangsu Province, P.R.China

institute: China Pharmaceutical University

description: Library name: RE8

data_processing:
Raw paired-end reads were trimmed and quality controlled by fastp with default parameters to remove adapter sequences, low-quality reads, reads with high N content, and reads shorter than 20 bp after trimming, generating clean reads.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes gene expression matrix for all samples.

source_name: liver tissue

growth_protocol: C57BL/6J mice were housed under standard laboratory conditions with free access to food and water. Mice were maintained under a 12 h light/12 h dark cycle before and during the experiment.

extract_protocol:
Total RNA was extracted from mouse liver tissues using TRIzol Reagent according to the manufacturer's instructions. RNA quality was assessed using an Agilent 5300 Bioanalyzer, and RNA concentration was quantified using a NanoDrop ND-2000 spectrophotometer. Only high-quality RNA samples were used for library construction.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer's instructions. Briefly, mRNA was enriched from total RNA using oligo(dT) beads, fragmented, reverse-transcribed into cDNA, end-repaired, adapter-ligated, size-selected, PCR-amplified, and purified. The qualified libraries were sequenced on the Illumina NovaSeq X Plus platform using paired-end 150 bp sequencing.

treatment_protocol: C57BL/6J mice were divided into four groups: normal control group, high-fat diet-induced MASH model group, Eleutheroside E-treated MASH group, and resmetirom-treated MASH group. After 8 weeks of model establishment, mice in the Eleutheroside E-treated group were orally administered Eleutheroside E at 100 mg/kg for 4 weeks, and mice in the resmetirom-treated group were orally administered resmetirom at 3 mg/kg for 4 weeks. Mice in the normal control group and MASH model group were orally administered 0.5% CMC-Na as vehicle control for 4 weeks. At the end of treatment, liver tissues were collected for RNA extraction, library construction, and high-throughput RNA sequencing.

value: liver tissue

value: high-fat diet-induced MASH + resmetirom


title: LC037_IV

source_name: Gut epithelium, NP, Descendens

value: Non-progressor

value: Descendens


title: BMMSC_IRIS_2

description:
Library name: Sample 34
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 2

value: WT


title: BMMSC_IRIS_1

description:
Library name: Sample 33
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 1

value: BMMSC


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 1B

description: Library name: 1B_GEX

value: peripheral blood

value: CD8+ T cells

value: mixed

value: aCD3/aCD28 TCR stimulation


title: AS041_L1d

source_name: Gut epithelium, P, Rectum

value: Progressor


title: BMMSC_ETIS_4

description:
Library name: Sample 32
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 4

value: Bone marrow mesenchymal stem cells

value: Etoposide-induced senescence (8 days 50 µM)


title: AS041_L1b

value: AdenoCa


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 1A

description: Library name: 1A_GEX

value: treatment-naïve


title: TREND,Mocksg,2

description:
Library name: Sample2
Column name in TPM.matrix_All_Samples.txt:Con_2

value: Tumor

value: tumor-infiltrating lymphocytes

value: Lymphocytes

value: Mock

value: Tail vein injection


title: PolyA-RNA_FKT_BamMut 38h-heat-shock, bam, rep 2

city: Risskov

first: Thomas

middle: Høgsbro

last: Grønbæk

address: Broloftet 5, 4.tv

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Library name: Sample_46

data_processing:
RNA and sRNAseq: RNA reads were demultiplexed and trimmed for standard illumina adapter sequences including 4 random nucleotides from each end.
cutntag: Paired-end illumina reads were adapter-trimmed using Trim Galore for standard illumina adapters.
Assembly: dm6, r6.63
Supplementary files format and content: SLX-19644_totalRNA_RNAseq_GeTMM_TE_sense.xlsx, R17585_TOsK_MZ-piwiaub_dKD_TE_GeTMM_sense.xlsx, R18168_GeTMM_gene.xlsx,  R18168_GeTMM_TE_sense.xlsx, SLX-17461_GeTMM_gene.xlsx. All xlsx file with RNAseq reads mapping to TE consensus sequences in sense orientation or to whole transcriptiome. Mapped to the Drosophila transcriptome using STAR, allowing 2 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: R16775_1kb_tiles_RNA_mappers_sum-PlusMinus.xlsx. xlsx file, Small RNAseq mapping to 1kb tiles. Not accounting for orientation (summed). Reads were mapped to the Drosophila genome using Bowtie allowing 0 MM and only uniquely mapping reads. Read coverage was quantified over non-overlapping 1 kb genomic windows using bedtools and normalized to 10 million uniquely mapping reads.
Supplementary files format and content: CutnTag_avg_GeTMM_TE_consensus_unistrand.xlsx. Xlsx file, cutntag reads mapping to TE consensus sequence unistrand. Mapped to the Drosophila transcriptome using Bowtie, allowing 0 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: CutnTag_bam_Table_for_heatmap_log2CPMadd1_single_TE_insertions.xlsx. Xlsx table of cutntag reads mapping to 50bp windows 500bp +/- to all identified single TE insertions in log2 counts per million (CPM). Reads were mapped to in-house ONT long-read assembled D. melanogaster genome from MTD-GAL4; white-sh fly cross using Bowtie2 with concordant-only alignment. The resulting alignments were coordinate-sorted and duplicate marking was done using samtools. Finally reads were filtered for only paired alignments with MAPQ ≥ 30 and no duplicates. Bigwig tracks (all mappers and unique mappers) were generated per sample using deeptools bamCoverage (bin size 10 bp, CPM normalization). Bigwig tracks were intersected with TE insertion coordinates (CutnTag_single_TE_insertions_table.xlsx) from long read DNA sequencing and Cut&Tag data for info on how these were called).
Supplementary files format and content: CutnTag_single_TE_insertions_table.xlsx. Xlsx file of single TE insertions and genome coordinates. TE annotation in long-read genome assembly was done using EDTA v. 2.2 with Drosophila consensus TE library supplied as the reference. TE annotation with CUT&Tag data was done using ngs_te_mapper2 v. 1.0.2. Briefly, the reads from CUT&Tag experiments were used to search for TE insertions by means of finding reads spanning TE consensus sequence and flanking long-read genome assembly sequence at candidate insertion sites. To call an insertion, we required the detection of reads spanning the TE and the flanking genome at both ends of the TE. Insertions identified this way were then pooled for the same fly line and then we analyzed only TE insertions present – but not necessarily homozygous – across every experimental cross in our CUT&Tag analyses.

organism: Drosophila melanogaster

source_name: bam mutant ovarian cysts

growth_protocol: D. melanogaster strains were crossed and reared for experiments at 25°C and 70% humidity with 12:12 hrs light/dark cycle in vials containing standard medium. Before dissection, the flies were fed extra yeast and kept with 3-5 males to support ovary development. The day before dissection, the flies were transferred to a fresh vial to provide the females ample space for egg-laying, preventing egg accumulation in the ovaries.

extract_protocol:
Bulk ovary RNA and small-RNA: 6-8 Ovary pairs from 3-4 days old females were dissected into ice-cold Phosphate-buffered saline (PBS) for bam mutant flies. Bam mutant and heat-shock bam ovarian cysts: 30 ovarian cysts were collected for each sample to compensate for their significantly smaller size.  RNA isolation for RNAseq and small-RNAseq: Samples were subjected to homogenization in TRIzolTM using handheld elecrtric pestle. After 5 minutes incubation Chloroform was added and samples were shaken vigorously and incubated for 3 minutes at RT, then centrifuged at 12,000g and 4°C for 15 minutes. The aqueous phase was transferred to a clean tube and the RNA was subsequently purified first using isopropanol and pelleting the RNA then 75% ethanol. The RNA was resuspended in Rnase-free water and concentrations were measured by spectrophotometry. The samples were stored at -70°C if not immediately used for RNA or small-RNA sequencing library preparation.  Cut&tag: approximately 150 whole ovaries were dissected into Drosophila Ringers buffer for 512C nurse cell nuclei FACS sorting. the ovaries were digested in 5mg/mL collagenase for 15 minutes at RT with continous shaking and intermittent pipetting. Cell suspension was collected by centrifugation 3min at 500rcf and rinced buffort adding nuclear isolation buffer. We disrupted cells with 10 strokes in a Dounce homogenizer with the B pestle and the homogenate was filtered twice through 100µM Nitex mesh. The filtered homogenate was placed on a sucrose step gradient of 2.2 M, 1.6 M, and 0.8 M sucrose and centrifuged for 20 min at 20,000 x g. After centrifugation the sucrose gradient was removed and the pellet was resuspended in nuclear isolation buffer. Hoechst was added to the homogenate at a concentration of 0.5 mg/ml. Nuclei were stored on ice until FACS. Approximately 400 ovaries from Vasa-GFP, bam-/- ovarian cysts, were dissected into Schneider’s insect medium supplemented with 10% fetal bovine serum. GSC-like cells were collected based GFP positive staining. Vasa-GFP, bam –/– ovaries were dissociated in 0,5% trypsin–0,05% EDTA and 5 mg/mL collagenase for 15 min at room temperature, with continuous shaking and intermittent pipetting. Ovarian cell suspension is then filtered through a 70µM Nitex mesh to remove aggregates or debris. The filter was rinsed with S-FBS and cells were collected by centrifugation 5min at 400g, 4ºC. Cells were stored on ice and GFP-positive germline cells were elected from the suspension via fluorescence-activated cell sorting (FACS).
RNAseq: RNA Sample of 2 µg were DNaseI treated and purified using the RNA clean & ConcentratorTM-5 kit (ZYMO #R1013). mRNA were isolated by polyA-RNA enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S). For total RNAseq, Ribosomal RNA was removed by hybridisation to standard 50nt DNA oligos covering relevant regions in the rRNA precursor and mitochrondrial genome in ratio 1µg RNA : 4µg oligomix and subsequent digestion using thermostable RNAse H (NEB #M0523S). Libraries were cloned using the NEBNextTM Ultra II directional RNA library prep kit for illumina (NEB # E7760) following the instructions. libraries were amplified by PCR using Q5 high-fidelity DNA polymerase with unique dual barcoded primers. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads. Samples were multiplexed in equal amounts and sequenced by VBCF NGS facility on an illumina NovaSeq X flowcell single- or paried-end or an illumina HiSeq 4000 flowcell paired-end or at the CRUK facility in cambridge on an illumina NovaSeq 6000 flowcell singleRead.  Small-RNA: Argonaute bound small RNAs were isolated using the Trans-kingdom, rapid, affordable Purification of RISCs (TRAPR) isolation technique specified in the punlication: Grentzinger et al. 2020. “A Universal Method for the Rapid Isolation of All Known Classes of Functional Silencing Small RNAs.” Nucleic Acids Research 48 (14): e79. sRNA libraries were generated based on protocol from:  Jayaprakash et al. 2011. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39 (21): e141. In brief, 3’ linker ligation was performed by adding uniquely barcoded 3’RNA linkers to the samples. Ligation was performed O/N using T4 RNA ligase 2, truncated K227Q (NEB #M0242). The samples were then multiplexed into sub-multiplexes of individually barcoded samples (biological replicates together), and purified using ZYMO RNA clean and concentrator-5 kit (ZYMO #R1013).  Then the samples were recovered and size selected for 52-63 nt reads (18-29nt RNAs + 3’linker) using PAGE purification. To follow exact size selection on the gel, fluorescently labeled oligos migrating similar to 40 and 60-nucleotide single-stranded RNA was added to samples prior to gel electrophoresis. PAGE purification was performed using ZYMO small-RNATM PAGE Recovery Kit (ZYMO #R1070). 5’ RNA linkers were added to samples, and ligation was performed O/N using T4 RNA ligase (NEB #M0204). The samples were subjected to SPRI purification. The sRNA libraries were then reverse transcribed using Superscript II (InvitrogenTM #18064014) following the manufacturer's instructions using the illumina_RvnTxn primer. Libraries were amplified by PCR using Q5 High-Fidelity DNA Polymerases (NEB #M0491) and unique dual-barcoded primers. Samples were then inspected and purified from a 2% low-melt agarose gel using the Zymoclean gel DNA recovery kit (ZYMO #D4001). Concentrations were measured using QubitTM DNA HS kit (InvitrogenTM Q32851) and sub-multiplexes were multiplexed in equal amounts and sequenced by VBCF NGS facility on a NovaSeqX XP flowcell singleRead.  Cut&tag: Library preparation were conduced on freshly FACS-isolated cells or nuclei in duplicates following the published protocol with minor modifications Kaya-Okur et al. 2019. “CUT&Tag for Efficient Epigenomic Profiling of Small Samples and Single Cells.” Nature Communications 10 (1): 1930. Around 40,000 GSCs sorted-cells (40,000 2C cells) and 500-800 512C sorted-nuclei  (128,000-200,000 2c nuclei) were used for each CUT&Tag reaction. The cells or nuclei were bound to 10µL of concanavalin A-coated beads (Polysciences,  86057-10) by incubation 15min at room temperature . The unbound supernatant was removed and bead-bound cells/nuclei were resuspended in Wash Buffer (WB150 : 20 mM HEPES pH 7.9; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and 0,1% BSA with the appropriate primary antibody (listed in the Reagent Table). Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Secondary antibodies were then added (1:100 dilution in WB150) and incubate for 1h at room temperature. Protein A–Tn5 transposase (gift from the Joan Barau laboratory), pre-loaded with MEDS adaptors (see Oligonucleotide Table), was added at a 1:200 dilution in WB150 with adapted 0,01% Digitonin (WB300). Following an incubation of 1h at room temperature, cells/nuclei and beads were washed with WB300 and mixed in a tagmentation buffer (10 mM MgCl2 in WB300). The tagmentation was performed 1h at 37ºC and stoped by adding 10µL a Digest solution ( 90mM EDTA, 1,2% SDS, 3mg/mL Proteinase K) and incubate 1h at 55ºC. DNA was extracted using the DNA Clean & Concentrator kit and libraries were amplified by Q5 high-fidelity DNA polymerase with unique dual barcoded primers for 10-15 amplification cycles. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads and DNA quality was assessed using the 5200 Fragment Analyzer system. Pooled  libraries  were  sequenced by the VBCF NGS facility on an Illumina NextSeq 2000 sequencing device.

treatment_protocol: For heat-shock bam experiments: Heat-shock treatment was performed on 3-4 day old females as described in (Samuels et al. 2024). The treatment involved 1 hour at 37°C followed by 2 hours at 34°C. The 'hours after HS' is defined as starting immediately after this 3-hour treatment.

value: bam mutant ovarian cysts

value: Bulk ovarian cysts


title: TREND,Mocksg,3

description:
Library name: Sample3
Column name in TPM.matrix_All_Samples.txt:Con_3


title: TREND,Mocksg,1

description:
Library name: Sample1
Column name in TPM.matrix_All_Samples.txt:Con_1


title: BMMSC_ETIS_2

description:
Library name: Sample 30
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 2

value: BMMSC

value: WT


title: AS041_II

value: gut epithelium

value: Transversum


title: Blastocyst (mouse), miR-21-5p agomir 50 nM, rep4 (pool of 5 embryos)

city: Wuhan

first: Yuehan

last: Li

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

description:
Library name: Blastocyst_miR21_agomir_rep4
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 4; miR-21-5p agomir 50 nM treatment

data_processing:
Adapters and low-quality bases were removed with fastp (v0.18.0); QC by FastQC/MultiQC.
Clean reads were aligned to the mouse reference genome GRCm39 (mm39) using HISAT2 (v2.1.0).
Gene expression quantification was performed using StringTie (v1.3.1) and RSEM to calculate FPKM values.
Differential expression between miR-21-5p agomir and blank control groups was assessed with DESeq2 (v1.36.0) using the raw count matrix; p-values were adjusted by the Benjamini–Hochberg method, and genes with FDR < 0.05 and |log2FC| > 1 were considered differentially expressed.
Assembly: Mus musculus GRCm39 (mm39); annotation Gencode M28.
Supplementary files format and content: "genes_expression.xls" is the  gene-level matrix combining normalized expression, raw counts, and annotations.  id: Ensembl gene ID (mm39 / Gencode M28).  FPKM columns: Control_1_fpkm, Control_2_fpkm, Control_3_fpkm, Control_4_fpkm, miR-21-5p_1_fpkm, miR-21-5p_2_fpkm, miR-21-5p_3_fpkm, miR-21-5p_4_fpkm  Raw count columns: Control_1_count, Control_2_count, Control_3_count, Control_4_count, miR-21-5p_1_count, miR-21-5p_2_count, miR-21-5p_3_count, miR-21-5p_4_count  Annotation columns: Symbol, Description, KEGG_A_class, KEGG_B_class, Pathway, K_ID, GO Component, GO Function, GO Process, TF_family.  Rows correspond to genes; columns correspond to samples listed in the Series.

source_name: embryo, blastocyst

growth_protocol: Female ICR mice (6–8 wk) were superovulated with 5 IU PMSG followed 48 h later by 5 IU hCG. At 16–18 h post-hCG, cumulus–oocyte complexes were collected from the oviductal ampullae. Sperm from 8–10 wk ICR males were capacitated in HTF for 1 h at 37 °C. IVF was performed by co-incubating COCs with capacitated sperm for 6 h. Zygotes were washed and cultured in KSOM micro-drops at 37 °C under 5% CO₂, 5% O₂, 90% N₂ until the blastocyst stage.

extract_protocol:
At the blastocyst stage, pools of 5 embryos were lysed in TRIzol (Invitrogen) and total RNA extracted per manufacturer’s instructions, using glycogen as carrier.
mRNA libraries were prepared with Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (Yeasen) following the poly(A)-selection workflow: RNA fragmentation, first/second-strand cDNA synthesis, end-repair/A-tailing, adaptor ligation, PCR amplification, and bead-based size selection. Libraries were sequenced PE150 on Illumina NovaSeq X Plus.

treatment_protocol: Embryos in the treatment group were cultured in KSOM containing miR-21-5p agomir (50 nM) from post-fertilization to blastocyst (~75 h). Blank control embryos received vehicle only (no oligo). For RNA-seq, each biological replicate comprised 5 pooled blastocysts; n = 4 replicates per condition.

value: embryo, blastocyst

value: blastocyst

value: wild-type, ICR

value: miR-21-5p agomir 50 nM


title: RNA_BamMut No-Heat-Shock, piwi_sh, rep 2

description:
Library name: Sample_6
piwiKD_2 RNA_run19644

value: w ; nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pGLKD>piwi_sh2[attP2]/ bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 2B

description: Library name: 2B_GEX

source_name: peripheral blood

value: peripheral blood

value: CD8+ T cells

value: mixed

value: aCD3/aCD28 TCR stimulation


title: AS038_V

value: Non-progressor

value: Rectum


title: Blastocyst (mouse), miR-21-5p agomir 50 nM, rep3 (pool of 5 embryos)

description:
Library name: Blastocyst_miR21_agomir_rep3
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 3; miR-21-5p agomir 50 nM treatment


title: RNA_BamMut No-Heat-Shock, piwi_sh, rep 1

description:
Library name: Sample_5
piwiKD_1 RNA_run19644

value: bam mutant ovarian cysts


title: BMMSC_P_4

description:
Library name: Sample 28
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Bone marrow mesenchymal stem cells

value: Control proliferating cells


title: BMMSC_P_3

description:
Library name: Sample 27
Cells were cultured for 8 days in DMSO-containing media - replicate 3

value: BMMSC

value: WT


title: AS044_III

value: gut epithelium

value: Descendens


title: RNA_BamMut No-Heat-Shock, rhino_sh, rep 2

description:
Library name: Sample_4
rhinoKD_2 RNA_run19644

value: Bulk ovarian cysts

value: w ; nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pGLKD>rhino_sh1[attP2]/ bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: BMMSC_P_2

description:
Library name: Sample 26
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: RNA_BamMut No-Heat-Shock, rhino_sh, rep 1

description:
Library name: Sample_3
rhinoKD_1 RNA_run19644


title: Blastocyst (mouse), blank control, rep4 (pool of 5 embryos)

description:
Library name: Blastocyst_blankCtrl_rep4
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 4; blank control

value: embryo, blastocyst

value: blastocyst

value: wild-type, ICR

value: blank control (vehicle, no oligo)


title: BMMSC_P_1

description:
Library name: Sample 25
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: Blastocyst (mouse), blank control, rep3 (pool of 5 embryos)

description:
Library name: Blastocyst_blankCtrl_rep3
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 3; blank control


title: BJ_OIS_4

description:
Library name: Sample 24
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 4

source_name: BJ

value: BJ

value: foreskin fibroblasts

value: RasV12 (MOI:3)


title: AS042_IV

source_name: Gut epithelium, P, Sigmoideum

value: Progressor

value: Sigmoideum


title: Blastocyst (mouse), blank control, rep2 (pool of 5 embryos)

description:
Library name: Blastocyst_blankCtrl_rep2
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 2; blank control


title: Liver, Control diet, rep1

description: Library name: LIVER_C_2

source_name: Liver

value: Liver

value: Control diet


title: RNA_BamMut No-Heat-Shock, white_sh, rep 1

description:
Library name: Sample_1
control_1 RNA_run19644

value: bam mutant ovarian cysts

value: w ;nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pW20>w_sh[attP2] / bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: AS042_III

source_name: Gut epithelium, P, Descendens

value: gut epithelium

value: Chronic


title: BJ_OIS_3

description:
Library name: Sample 23
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 3

value: WT


title: Blastocyst (mouse), blank control, rep1 (pool of 5 embryos)

description:
Library name: Blastocyst_blankCtrl_rep1
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 1; blank control


title: Peptidergic cells, amino acid deprived

city: Durham

first: Vincent

last: Croset

address: Department of Biosciences, South Road

country: United Kingdom

institute: Durham University

description:
Library name: HNOA
10X Genomics

data_processing:
Reads were aligned these to the FB2023_06 Drosophila melanogaster genome assembly (v6.52) using CellRanger 7.2.0 to create digital gene expression (DGE) matrices
Assembly: FB2023_06 Drosophila melanogaster genome assembly (v6.52)
Supplementary files format and content: Gene expression matrices H5 archives

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Samples were mechanically dissociated for 30s in 1ml homogenisation buffer (250 mM Sucrose, 10 mM Tris-HCl pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton-x 100, 0.5% RNasin Plus, 1X 50X protease inhibitor, 0.1 mM DTT) using a pestle motor (DWK Life Sciences, 7495400000) before being released by 25 strokes of a dounce pestle (DWK Life Sciences, 8855000021). These steps were performed on ice. The homogenate was filtered through a 40µm cell strainer (pluriSelect, 43-10040-50) to remove unlysed tissue and again using a 40µm Flowmi (BelArt, H13680-0040) into a 1.5ml Eppendorf tube. Samples were centrifuged at 1000 x g for 10 mins at 4ºC, supernatant discarded and pellet resuspended in 500µl resuspension buffer (1X PBS, 0.5% BSA, 0.5% RNasin Plus). Samples were filtered once more using 40µm Flowmi into a 5ml FACs tube and incubated with Hoechst-33342 (1:1000, Invitrogen, 11534886) for 15 minutes on ice prior to fluorescent sorting.
mRNA barcoding was performed using 10X Genomics Chromium Single Cell 3’ Reagent Kit v3 according to manufacturer's instructions.

value: Brain

value: Peptidergic

value: Amino acid deprived


title: LS7

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

description: 10 days of saline self-administration

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie
Mapped small RNA tags were used to look for known miRNA. miRBase22.0 was used as reference, and mirdeep2  and srna-tools-cli were used to obtain the potential miRNA. Custom scripts were used to obtain the miRNA counts
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: rn6
Supplementary files format and content: TPM in .xls format

organism: Rattus norvegicus

source_name: blood serum

extract_protocol:
Total RNA was extracted from prefrontal cortex and nucleus accumbens tissue samples with Trizol, according to manufacter's protocols. Exosomal RNA was extracted from blood serum using the SeraMir kit, using manufacturer's protocols.
Small RNA sequencing was performed on six biological replicate samples per treatment group, per region of interest (prefrontal cortex, nucleus accumbens, or serum). 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing

treatment_protocol: Adult male Sprague Dawley rats were aged 8 weeks on arrival. Forheroin exposure, animals were acclimited to the animal facility for 1 week then underwent jugular vein catheterization. Following 1 week of recovery, animals self-administered  heroin at a dose of 0.075mg/kg/infusion for 6 hours per day in 10 daily sessions. Saline animals underwent the same surgical procedures but self-administered saline for 10 days. Following the last self-administration session, animals were euthanized with 60 minutes and their brains were frozen in ice cold isopentane. Trunk blood was collected during decapitation. Blood was collected into sterile tubes, allowed to clot, and then spun at 2g for 10 min to collect serum. Prefrontal cortex and nucleus accumbens tissue was dissected from each animal on dry ice then RNA extraction proceeded.

value: blood serum

tag: strain

value: Sprague-Dawley

value: male

value: adult

value: saline self-administration for 10 days


title: BJ_OIS_2

first: Supriyo

last: De

address: 251 Bayview Blvd

institute: NIA-IRP, NIH

description:
Library name: Sample 22
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 2

value: BJ

value: foreskin fibroblasts

value: RasV12 (MOI:3)


title: AS042_II

city: Lørenskog

first: Hilde

last: Nilsen

address: Sykehusveien 25

institute: Akershus University Hospital

source_name: Gut epithelium, P, Transversum

value: Progressor

value: Transversum


title: BJ_OIS_1

city: Baltimore

description:
Library name: Sample 21
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 1


title: Lung 15

description:
Library name: Sample 33
Lung nuclei pooled from three Doxorubicin-treated mice, 6 days after treatment – replicate 3

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 9.0.0 (10x Genomics) with prebuilt annotation platform GRCm39-2024-A.
Assembly: GRCm39
Supplementary files format and content: filtered_feature_bc_matrix including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

source_name: Lung

extract_protocol:
Before tissue extraction, lungs were perfused by injecting PBS through the right ventricle. The extracted pieces were frozen in liquid nitrogen. For kidney samples, half of a frozen mouse kidney was minced on dry ice and homogenized in 5 ml of ice-cold homogenization buffer until no visible chunks remained. Samples from 3 mice were pooled. A 200 µl aliquot of the pooled homogenate was mixed with 400 µl of cold lysis buffer from the Minute™ Single Nucleus Isolation Kit (Invent Biotechnologies) and processed according to the manufacturer's protocol. Nuclei were filtered, centrifuged, washed, and resuspended in PBS containing 1% BSA and 0.2 U/µl RNase inhibitor. Nuclei concentration was measured with Trypan Blue and adjusted to 700–1200 nuclei/µl. For lung samples, the protocol was similar, but only ~50 mg of frozen lung tissue was used for homogenization.
The single-nucleus libraries were prepared with Single Cell 3' v4 (polyA) chemistry  (10x Genomics).

value: Lung

value: Lung cells

value: Doxo

value: 3 months old


title: Peptidergic cells, sated, biol rep 1

description:
Library name: H1
10X Genomics

value: Brain

value: Sated


title: Lung 14

description:
Library name: Sample 32
Lung nuclei pooled from three Doxorubicin-treated mice, 6 days after treatment – replicate 2