title: Input_Con

city: Shijiazhuang

first: Lingdan

last: Zhao

address: No. 361 Zhongshan East Road, Chang'an District

department: Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education

country: China

institute: Hebei Medical University

description: Library name: Input_Con

data_processing:
Raw reads were trimmed for adapters and low-quality bases using Trimmomatic. Clean reads were aligned to GRCr8 with Bowtie2. Duplicate reads were removed using Picard. Peak calling was performed using MACS2 with a q-value threshold of 0.05. Peaks were annotated to nearest genes using ChIPseeker.
Assembly: GRCr8
Supplementary files format and content: bigWig, narrow Peak(except for iInput sample)

organism: Rattus norvegicus

source_name: VSMCs

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at RT, quenched with glycine, and lysed in SDS buffer. Chromatin was sheared by sonication to 200–500 bp fragments. After centrifugation, supernatants were incubated with target-specific antibody and protein A/G beads overnight at 4°C. Beads were washed sequentially with low-salt, high-salt, and LiCl buffers, then eluted with SDS buffer. Crosslinks were reversed at 65°C overnight, and DNA was purified by phenol-chloroform extraction.
ChIP-enriched DNA was end-repaired, A-tailed, and ligated to sequencing adapters. Adapter-ligated fragments were amplified by PCR (12–15 cycles) with barcoded primers. PCR products were size-selected (200–400 bp) using AMPure XP beads. Library quality was assessed by Qubit for concentration and Bioanalyzer for fragment size distribution.

value: VSMCs


title: W8, Rep1, BS

status: Public on Jun 21 2026

type: SRA

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Raw reads were trimmed for base quality and adaptor sequences using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and reads below a length of 20 bases were discarded.
The trimmed reads were aligned to the reference genomes using Bismark (v0.22.3) with the following parameters -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2.
To account for A3A failure due to double-stranded DNA, reads with three or more consecutive non-converted cytosines in the CpH context were removed using the filter_non_conversion script included in the Bismark package.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing the chromosome, start position, end position, methylation percentage, count methylated, count unmethylated

molecule: genomic DNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
To isolate gDNA, brain was thawed and digested in lysis buffer (50mM Tris, pH8.0, 100mM EDTA, 0.5% SDS) with proteinase K (Sigma-Aldrich) overnight at 55°C. Genomic DNA was isolated using Phenol:Chloroform:Isoamyl Alcohol (Fisher BP17501-400) and ethanol precipitation. DNA samples resuspended in TE were stored at 4°C.
Purified mouse gDNA (200 ng) with 1 ng each of phiX, mCpG pUC19 (Zymo), and 5hmC T4 spike-in controls were sheared to approximately 350 bp using a Covaris instrument. Sheared gDNA was taken through end prep and adaptor ligation using the NEBNext Ultra II DNA Library Prep Kit (NEB). Custom-made pyrrolo-cytosine adaptors (IDT) were substituted for kit-supplied adaptors. Adapted samples were bisulfite treated using the Premium Bisulfite Kit (Diagenode) and eluted in nuclease-free water. Post bisulfite clean-up, each sample was split into two 10 µL aliquots. One aliquot was further purified with a 1.2x left-side SPRI purification (Beckman). The SPRI-purified aliquot was denatured and APOBEC3A-treated (NEB, E1725L). After A3A deamination, the sample was purified via SPRI beads (1.2x, left-sided). Quantitative PCR was used to determine the number of cycles for the indexing PCR. Indexing PCR was performed using the unique dual index primer pairs from NEBNext Multiplex Oligos for Enzymatic-Methyl Seq (NEB). After the indexing PCR, samples were purified with two 0.8x left-sided SPRI purifications. Libraries were quantified with a Qubit HS kit (Invitrogen,Q32851) and assessed for quality with an Agilent Bioanalyzer. The resulting libraries were then pooled and sequenced on an Illumina MiSeq using 150-bp read length on a nano or micro sequencing kit (Illumina).
BS-Seq, bACE-Seq

tag: tissue

value: Cortex

tag: treatment

value: Bisulfute (BS-Seq)

tag: time

value: Week 8


title: W8, Rep1, bACE

value: Bisulfute + A3A (bACE-Seq)


title: W6, Rep3, BS

value: Week 6


title: W6, Rep2, BS


title: Con_2

description: Library name: Con_2

tag: cell line

value: VSMCs were treated with H2O for 24 h


title: W6, Rep2, bACE


title: Con_1

description: Library name: Con_1


title: Cho_3

description: Library name: Cho_3

value: VSMCs were treated with cholesterol (30 μg/ml) for 24 h


title: Cho_2

description: Library name: Cho_2


title: Piezo Gel+US spinal cord lesion core biol rep 3

city: Beijing

first: Yanchun

last: Liu

address: No. 45, Changchun Street

institute: Xuanwu Hospital

description:
Library name: P_US_3
Piezo Gel+US, T9 spinal cord contusion lesion epicenter, biological replicate 3

library_source: transcriptomic

data_processing:
Raw reads were filtered to remove adapter-containing reads, reads containing N bases, and low-quality reads using fastp v0.19.7 with parameters: -g -q 5 -u 50 -n 15 -l 150.
Clean reads were aligned to the reference genome ncbi_rattus_norvegicus_gcf_011064425_1_rrattus_csiro_v1 using HISAT2 v2.0.5 with default parameters.
Gene-level read counts were generated using featureCounts v1.5.0-p3 with default parameters.
Differential expression analysis was performed using DESeq2 v1.20.0 with thresholds of |log2FoldChange| > 1 and adjusted P value < 0.05.
Assembly: ncbi_rattus_norvegicus_gcf_011064425_1_rrattus_csiro_v1
Supplementary files format and content: gene_count.txt contains the gene-level raw count matrix for all six RNA-seq samples. Rows represent genes and columns represent samples (NC_1, NC_2, NC_3, P_US_1, P_US_2, and P_US_3). Values are unnormalized read counts used for downstream differential expression analysis.

molecule: total RNA

source_name: spinal cord lesion core

extract_protocol:
Spinal cord tissue (~5 mm3) from the lesion epicenter (T9 segment) was harvested. Total RNA was extracted using the TRIzol method, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Poly(A)+ mRNA was enriched from total RNA using Oligo(dT) magnetic beads. The purified mRNA was fragmented in NEB Fragmentation Buffer and reverse transcribed using random hexamer primers to generate first-strand cDNA. Second-strand cDNA was synthesized using dUTP instead of dTTP to preserve strand information. After end repair, A-tailing, adaptor ligation, fragment size selection, USER enzyme digestion, PCR amplification, and purification, strand-specific libraries were generated for sequencing.

treatment_protocol: Rats were subjected to a T9 spinal cord contusion injury model and assigned to Gel+US or Piezo Gel+US groups. For in vivo ultrasound stimulation, back hair over the T8–T10 region was removed 24 h before stimulation. Rats were placed in a custom restraint cage, acoustic coupling gel was applied, and a linear array ultrasonic transducer was positioned over the implantation site. Ultrasound stimulation was delivered at 100 Hz, 1.0 W/cm2, and 1.0 W for 10 min daily, with a 10-s pause every 2 min to prevent thermal injury. Periodic stimulation was continued for 4 weeks.

value: spinal cord lesion core

tag: genotype

value: wild type

value: Piezo Gel+US


title: W4, Rep3, BS

value: Week 4


title: Piezo Gel+US spinal cord lesion core biol rep 2

description:
Library name: P_US_2
Piezo Gel+US, T9 spinal cord contusion lesion epicenter, biological replicate 2


title: W4, Rep3, bACE


title: W4, Rep2, BS


title: Piezo Gel+US spinal cord lesion core biol rep 1

description:
Library name: P_US_1
Piezo Gel+US, T9 spinal cord contusion lesion epicenter, biological replicate 1


title: Gel+US spinal cord lesion core biol rep 3

description:
Library name: NC_3
Gel+US, T9 spinal cord contusion lesion epicenter, biological replicate 3

value: Gel+US


title: W4, Rep2, bACE


title: Gel+US spinal cord lesion core biol rep 2

description:
Library name: NC_2
Gel+US, T9 spinal cord contusion lesion epicenter, biological replicate 2


title: W4, Rep1, BS


title: Gel+US spinal cord lesion core biol rep 1

description:
Library name: NC_1
Gel+US, T9 spinal cord contusion lesion epicenter, biological replicate 1


title: W4, Rep1, bACE


title: Day7

type: RNA

city: Yokohama City

first: Takuya

last: Ishibashi

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description:
Non-Treated : Upper one section
aAVC-Treated:Lower two sections
*The Xenium slide contains three tissue sections.
The upper one section corresponds to the NonTreated group, and the lower two sections correspond to the aAVC-Treated group.

hyb_protocol: Tissue sections were hybridized with a probe panel targeting 479 genes under stringent conditions to minimize nonspecific binding. Following overnight hybridization at 50 °C and subsequent stringent washes, probes were ligated and amplified using the rolling circle amplification strategy.

scan_protocol: Xenium analyzer

data_processing: Xenium Analyzer and Xenium Explorer

source_name: TC1 Tumor tissues

extract_protocol: For spatial transcriptomic analyis, tumor tissues were immediately processed as freshly frozen specimens, embedded in OCT compound, and cryosectioned. Fixed frozen tumor sections were prepared at a thickness of 10 μm, mounted on xenium slides.  Xenium slides contains both Non Treated sections (Upper) and aAVC-Treated sections (Lower).

treatment_protocol: Mice were inoculated with HPV-E6 and E7 expressing lung cancer (TC-1) cells and treated with cancer vaccine,  artificial Adjuvant Vector Cells (aAVC) on day7. We collected tumor samples on day3 and day7 after aAVC treatment. As a control, tumor samples were collected from TC-1 bearing, untreated mice at the same point.

tag: tag

value: Non Treat and aAVC treated


title: W2, Rep3, BS

value: Week 2


title: Day3

description:
Non-Treated : Upper two sections
aAVC-Treated:Lower two sections
*The Xenium slide contains four tissue sections.
The upper two sections correspond to the NonTreated group, and the lower two sections correspond to the aAVC-Treated group.


title: W2, Rep3, bACE


title: W2, Rep2, BS


title: Multiome, testis, KO2, GEX

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 526 Campus Rd

department: Molecular and Cell Biology

institute: Cornell University

description:
Library name: KO2_RNA
10x Next GEM Multiome libraries

library_source: transcriptomic single cell

data_processing:
Libraries were processed using the cellranger-arc count pipeline
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz files
Supplementary files format and content: filtered_feature_bc_matrix.h5 files

source_name: testis

extract_protocol:
Single cell suspensions from wild-type and Ago413-/- testis were obtained following the method described by Ascenção et al. Testis from 2-5 mice from the same genotype were collected, the tunica albuginea was removed, and tubules were placed in 10 ml of preheated (37°C) DMEM-F12 containing 2 mg of Collagenase 1A (Sigma) for 2 minutes with manual shaking. Digestion was stopped by two washes of the tubules with DMEM-F12. Next, the tubules were incubated in 10 ml of DMEM-F12 with 5 mg of trypsin (Sigma) and 7 mg/ml of DNAse I (Sigma) at 37°C with constant shaking (150 rpm) until the length of the tubules was about 1 mm (approximately 10 minutes). Digestion was stopped by addition of 3 ml of Fetal Bovine Serum (FBS, Sigma) and 30 ml of DMEM F-12. Digested tubules were strained on a 100 μm strainer and centrifuged at 15°C for 5 minutes at 600g. Before proceeding with nuclei isolation, spermatozoa were removed from the germ cell suspension samples by negative selection Magnetic Activated Cell Sorting (MACS) using an antibody against the acrosomal protein ACRV1 coupled with anti-rabbit IgG MicroBeads (Miltenyi Biotec) and following the protocol provided by the manufacturer. Briefly, cells were labeled with anti ACRV1 antibody (1:50 concentration) by incubation of 108 cells in MACS buffer (0.5% BSA, 2mM EDTA in PBS, pH7.2) for 15 minutes. Then, the labelled cells were incubated with anti-rabbit IgG MicroBeads for 20 minutes on ice and loaded into an LS Column (Miltenyi Biotec) previously rinsed with MACS buffer. After depletion of spermatozoa by retention in the column, cells were collected from the negative fraction by centrifugation at 1500rpm for 5 minutes at 4C and proceeded with nuclei isolation using 10X Genomics Demonstrated Protocol CG000365 Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing.
Single cell RNA and ATAC sequencing libraries were prepared at the Cornell Genomics Facility using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit.Nuclei were processed on the 10X Genomics Chromium System, targeting a total of 10000 cells per sample. Quality control was evaluated using a Fragment Analyzer

value: testis

tag: Sex

value: male

tag: cell type

value: enriched germ cell suspension

tag: background strain

tag: library type

value: mRNA


title: W2, Rep2, bACE

value: Cortex


title: W2, Rep1, BS

value: Bisulfute (BS-Seq)


title: W2, Rep1, bACE

value: Bisulfute + A3A (bACE-Seq)


title: Multiome, testis, WT2, ATAC

description:
Library name: WT2_ATAC
10x Next GEM Multiome libraries

library_source: genomic single cell

value: ATAC


title: P0, Rep3, BS

value: Postnatal Day 0


title: Female_midgut_control_3

status: Public on Jun 22 2026

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
After demultiplexing, raw RNAseq reads were aligned against the Ensembl Drosophila genome reference sequence assembly (dm6) and transcript annotations obtained from Illumina iGenomes using TopHat2 (v2.0.11; Kim et al., 2013).
Gene-based read counts were then obtained using the featureCounts function from the Rsubread Bioconductor package (v.1.24.2; Liao et al., 2013, Liao et al., 2014)
Assembly: dm6
Supplementary files format and content: tab-delimited csv file includes raw counts for each sample

organism: Drosophila melanogaster

source_name: Midgut

growth_protocol: Virgin males and females for each genotype were collected and aged for 6 days at 18C. Subsequently, the animals were switched to 29C for 4 days and dissected for RNAseq.

extract_protocol:
Total RNA was extracted using the Rneasy Mini kit (Qiagen). 200ng were used for the construction of the sequencing libraries.
PolyA enrichment was performed using NEBNext® Poly(A) mRNA Magnetic Isolation module, and NGS RNASeq libraries made using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® according to manufacturer’s instructions
For each sample, a minimum of 40 million Paired End 100bp reads were generated on an Illumina HiSeq2500 with single 6bp indexing.

treatment_protocol: Adults were switch from 18C to 29C to induce the expression of the dsxRNAi.

value: Midgut

value: Female

tag: developmental stage

value: Adult 10 days after hatching

value: y[1] v[1] / w[*] ; mex1-Gal4 / + ; UAS-GFP / tub-Gal80ts

value: Temperature switch 18C (6 days) to 29C (4 days)


title: CAF population from HT15B patient_biol rep1

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

description: Library name: CAF_15B_1

data_processing:
Reads were mapped using  salmon:1.10.3 to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fa.file
Then, estimated transcript abundances from Salmon were imported into R using the tximport_1.36.1 package
Assembly: Homo_sapiens.GRCh38.cdna.all.fa.file
Supplementary files format and content: excel file with the matrix of reads counts for each gene and each sample

organism: Homo sapiens

source_name: Larynx (tumor)

growth_protocol: CAFs were cultured in DMEM-GlutaMAX supplemented with 10% heat-inactivated FBS, 1% penicillin/streptomycin (Thermo Fisher Scientific) and 0.5 nM human recombinant basic fibroblast growth factor (b-FGF, Cat#78003, STEMCELL Technologies) and then maintained in exponential growth in 5% CO2/95% air in a humidified incubator at 37°C. NFs were grown in human fibroblast expansion basal medium (Cat#M106500, Gibco) supplemented with 2% low serum growth supplement (LSGS, Cat#S00310, Thermo Fisher Scientific) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from cancer cells using the Monarch Total RNA Miniprep Kit (New England Biolabs). Ribosomal RNA (rRNA) was depleted using the RiboCop rRNA Depletion Kit (Lexogen).
The rRNA-depleted RNA was then used for library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's instructions. Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 1μg total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. RNA sequencing was performed on an AVITI platform (Element Biosciences). The RNA-seq libraries were sequenced using 76 bp paired-end reads, and samples were multiplexed to achieve 20 million reads per sample.

treatment_protocol: No treatment

value: Larynx (tumor)

value: no treatment


title: RNA-seq KO baseline 3

city: Seoul

first: Jun Young

last: Hong

address: 50, Yonsei-ro, Seodaemun-gu

department: Systems Biology

country: South Korea

institute: Yonsei University

description:
Library name: Sample 9
Column name in processed_counts.csv: KO_baseline_3

data_processing:
Paired-end sequencing was performed with NovaSeqX with 101 bp reads from each end. Reads were aligned to the mouse genome mm39 by STAR v2.7.10a and quantified using featureCounts v2.0.3. Counts per million (CPM) values were calculated using edgeR v4.0.16.
Assembly: mm39
Supplementary files format and content: a tab-delimited csv file including Ensembl ID and CPM (counts per million)

source_name: lung

extract_protocol:
RNA was purified from mouse lung tissues using QIAGEN RNeasy columns (74106) with on-column DNase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed following the Illumina TruSeq stranded mRNA Reference Guide #1000000040498 v00.

treatment_protocol: Female Balb/cJ mice or Vanin-deficient mice were anesthetized with a ketamine/xylazine mixture, and the specified number of plaque-forming units (PFU) of the influenza virus (strain A/WSN/33) in 30 μl PBS was administered intranasally dropwise.

value: lung

value: Vanin-/-

value: Control


title: Multiome, testis, KO1, ATAC

description:
Library name: KO1_ATAC
10x Next GEM Multiome libraries

value: testis

value: male

value: enriched germ cell suspension


title: Multiome, testis, KO1, GEX

description:
Library name: KO1_RNA
10x Next GEM Multiome libraries

value: mRNA


title: Multiome, testis, WT2, GEX

description:
Library name: WT2_RNA
10x Next GEM Multiome libraries


title: Female_midgut_control_2


title: Grp9, mCherry quartile sort, lower middle quartile

city: Cleveland

first: Kenneth

last: Matreyek

state: Ohio

address: 2103 Cornell Rd, Room 5104

department: Pathology

institute: Case Western Reserve University

description: Library name: Grp9, eeBxb1, mCherry bin 2

data_processing:
DNA was sequenced using a NextSeq 550 Mid output (130 million reads) 150 cycle kit (Illumina) at the Case Western Reserve University Genomics Core Facility
Reads were converted to fastq format and demultiplexed by the Case Western Reserve University Genomics Core Facility.  Paired-end reads were combined using PEAR (PMC3933873) using default statistical settings.
Each paired end read was tested for exact matches from the expected library and included as a read for the appropriate library member if applicable.  Read count relative to total number of reads in the sample was used to calculate read frequency for each expected library member.
Read frequencies for quartiles from the same fluorophore sort and the same group were used to calculate a weighted average Sort-Seq score for each fluorophore for expected library member.  Scores were averaged across groups to provide a final Sort-Seq score for each expected library member.  The Sort-Seq scores were used for further analysis in the manuscript.
Assembly: Synthetic Sequences
Supplementary files format and content: "processed_data_counts_frequencies.csv" is a comma separated values data table containing read counts and read frequencies for all observed DNA sequences (library_sequence, column 1).  Each row represents a DNA sequence of interest, and each column represents either a read count ("_counted") or a read frequency ("_freq") for each sample ("IXXXX", corresponding with IXXXX from file names as described in SAMPLES section).

organism: synthetic construct

growth_protocol: DMEM with 10% FBS, 1 % Penicillin / Streptomycin, and 2 ug/mL doxycycline.

extract_protocol:
Genomic DNA was extracted using a Dneasy Blood and Tissue Kit (Qiagen, 69506) and DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265)
Extracted genomic DNA was used as a template to produce a 1564 nucleotide amplicon spanning the genomic integration junction.  Samples were run with gel electrophoresis, the appropriate band was extracted using a Bio-Rad Freeze 'N Squeeze DNA Gel Extraction Spin Column (Bio-Rad, 7326165) and cleaned using a Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4004).  The resulting DNA was used as the template for to produce a 299 nudleotide amplicon surrounding the DNA sequence of interest using distinct indices for each quartile to be run on the same Illumina NextSeq 550 kit run.  Samples were again run with gel electrophoresis, extracted, and cleaned.  DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265).  DNA amplicons were pooled to a final concentration of 10-20ng/uL in 21uL of nuclease free water using 15-20ng of DNA from each quartile prior to running the Illumina NextSeq 550 kit.

value: Cultured Cells

value: Recombination into


title: RNA-seq WT Flu 1

description:
Library name: Sample 4
Column name in processed_counts.csv: WT_Flu_1

value: WT

value: Flu


title: P0, Rep3, bACE

value: Cortex

value: Bisulfute + A3A (bACE-Seq)

value: Postnatal Day 0


title: Multiome, testis, WT1, GEX

description:
Library name: WT1_RNA
10x Next GEM Multiome libraries


title: P0, Rep2, BS

value: Bisulfute (BS-Seq)


title: Multiome, testis, WT1, ATAC

description:
Library name: WT1_ATAC
10x Next GEM Multiome libraries

value: ATAC


title: CAF population from HT3 patient_biol rep3

description: Library name: CAF_3_3

source_name: Oral cavity (tumor)

value: Oral cavity (tumor)

value: no treatment


title: RNA-seq WT baseline 3

description:
Library name: Sample 3
Column name in processed_counts.csv: WT_baseline_3

value: lung


title: AGO413-/- testes, rep3, scRNA-seq

description:
Library name: KO3
Chromium Single Cell 3' v3.1 (Dual Index)

data_processing:
Fastq files were input to cellranger count (10x Genomics) using parameter --r1-length=28 to generate counts table and hd5 files
Ambient RNA correction performed using cellbender with parameters --projected-ambient-count-threshold 0 --fpr 0.01 (--learning-rate 0.000025 for WT3; --learning-rate 0.00005 for KO1)
Assembly: Mouse mm10
Supplementary files format and content: Raw feature matrix cellranger output and filtered cellbender output hd5 files

extract_protocol:
To prepare germ cells for FACS sorting, a single cell suspension from testes was obtained following the method described by Ascenção et al.Testes from 2-5 mice were collected, the tunica albuginea was removed, and tubules were placed in 10 ml of preheated (37°C) DMEM-F12 containing 2 mg of Collagenase 1A (Sigma) for 2 minutes with manual shaking. Digestion was stopped by two washes of the tubules with DMEM-F12. Next, the tubules were incubated in 10 ml of DMEM-F12 with 5 mg of trypsin (Sigma) and 7 mg/ml of DNAse I (Sigma) at 37°C with constant shaking (150 rpm) until the length of the tubules was about 1 mm (approximately 10 minutes). Digestion was stopped by addition of 3 mls of Fetal Bovine Serum (FBS, Sigma) and 30 ml of DMEM F-12. Digested tubules were strained on a 100 μm strainer and centrifuged for at 15°C for 5 minutes at 600g. The single cell suspension of germ cells obtained was then resuspended in FBS and preserved at 37°C until fluorescent activated cell sorting (FACS). Germ cell single cell suspension was incubated with 10 μM of Vybrant dye cycle (VDG) (Invitrogen) for 30 min at 37°C in the dark and constant rocking.  Sorting of cells was performed at Cornell Flow Cytometer Facility, using a Sony MA900 fluorescent activated cell sorter, tuned to emit at 488 nm and laser power set to 100 mW to collect for VDG positive cells. Flow cytometric profiles were obtained by representing Forward Scatter (Y axes) vs VDG fluorescence intensity (X axes), to identify different cell populations in the sample based on their DNA content and size. To enrich for spermatocytes for single cell RNA-seq, a sorting gate was set to collect all germ cell types excluding sperm.
Single cell RNA sequencing libraries were prepared at the Transcriptional Regulation and Expression Facility at Cornell using the 10X Genomics Chromium Single Cell 3′ RNA-seq v3.1 kit. Flow sorted cells were processed on the 10X Genomics Chromium System, targeting a total of 7000 cells per sample. Quality control was evaluated using an ABI DNA Fragment Analyzer

tag: strain

tag: age

value: 10-15 weeks

tag: background

tag: batch


title: P0, Rep1, BS


title: P0, Rep2, bACE


title: AGO413-/- testes, rep2, scRNA-seq

description:
Library name: KO2A
Chromium Single Cell 3' v3.1 (Dual Index)

value: testis


title: AGO413-/- testes, rep1, scRNA-seq

description:
Library name: KO1A
Chromium Single Cell 3' v3.1 (Dual Index)

value: male


title: 93VU147T, 50 ng/mL IL-1B 72hr, Replicate 2

city: St. Louis

first: Sidharth

last: Puram

state: Missouri

address: 4515 McKinley Ave

department: Otolaryngology

institute: Washington University in St. Louis

data_processing:
De-multiplexed reads were trimmed with Cutadapt (V1.10), filtered with fastQC (0.11.9) to remove low quality reads and aligned against the Homo sapiens genome (Ensembl GRCh38.p13) using STAR (2.5.4b).
Gene reads counts were quantified using FeatureCounts (v2.0.2).
Assembly: Ensembl GRCh38.p13
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

molecule: polyA RNA

growth_protocol: JHU-06 cells and 93VU147T cells were maintained in RPMI and F-12/DMEM (3:1) respectively supplemented with 10% fetal bovine serum (FBS) , 1% pen/strep/glutamine in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from cells using the Zymo Research Quick-RNA Microprep Kit.
mRNA-seq libraries were generated using 250 ng of total RNA input processed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760).
RNA-Seq with a minimun target coverage of 30 million reads per sample

treatment_protocol: Cells were treated with one of the following for 72 hours before harvesting: PBS volume control (1uL/mL), 10ng/mL TGFB1 + 10ng/mL TGFB3, 50ng/mL oncostatin M, 100ng/mL SPP1, or 50ng/mL IL-1B. Two biological replicates were performed per cell line/treatment.

value: oral cavity squamous cell carcinoma

value: normal growth medium


title: P0, Rep1, bACE


title: D18, Rep3, BS

value: Embryonic Day 18


title: 93VU147T, 100 ng/mL SPP1 72hr, Replicate 2


title: 93VU147T, 50 ng/mL OSM 72hr, Replicate 2


title: W10, Rep1, bACE

value: Week 10


title: D18, Rep3, bACE


title: Wild-type testes, rep2, scRNA-seq

description:
Library name: WT2
Chromium Single Cell 3' v3.1 (Dual Index)

value: enriched germ cell suspension


title: 93VU147T, 10 ng/mL TGFB1 + 10 ng/mL TGFB3 72hr, Replicate 2


title: 93VU147T, PBS vehicle control 72hr, Replicate 2


title: W8, Rep2, BS

value: Week 8


title: D18, Rep2, BS

value: Cortex


title: JHU-06, 50 ng/mL IL-1B 72hr, Replicate 2


title: D18, Rep2, bACE

value: Bisulfute + A3A (bACE-Seq)


title: Wild-type testes, rep1, scRNA-seq

description:
Library name: WT1
Chromium Single Cell 3' v3.1 (Dual Index)


title: RIP-seq input control for MU CAFs

first: Minghe

last: Fan

state: Beijing

address: 38 Xueyuan Road, Beijing, China

institute: Peking University Health Science Center

description:
Library name: MU_Input
Input control for RIP-seq

data_processing:
Sequencing was performed on an Illumina. Reads were aligned to mm10 using HISAT2 (v2.1.0) with strand-specific parameters.Peak calling was performed using MACS2 (v2.2.7.1). Peak annotation was performed using bedtools.Motif analysis of peaks was performed using HOMER (v4.11.1).Differential expression analysis was performed using DEGseq (v1.40.0).
Assembly: mm10 (GRCm38)
Supplementary files format and content: 1) BigWig (.bw) files: Normalized signal tracks for visualization in a genome browser (WT IP, WT Input, MU IP, MU Input). 2) NarrowPeak (.narrowPeak) files: Genomic coordinates of significant binding peaks for WT and MU samples 3) CSV (.csv) files: Statistical results of differential binding analysis (IP vs Input) for WT and MU conditions.

source_name: CAFs

extract_protocol:
Cells (10-20 million) were lysed in 500 µL of lysis buffer from the RIP-Assay Kit (MBL, #RN1001) supplemented with HALT Protease Inhibitor Mixture (Thermo Fisher Scientific, #78430), 1.5 mM DTT (Solarbio, #D107), and 200 units/mL RNase inhibitor (Solarbio, #R8061). Cell lysates were precleared with 50 µL of Dynabeads Protein A/G (Thermo Fisher Scientific, #80105G) for 1 hour at 4°C with rotation.
Immunoprecipitation was performed using anti-Flag antibody (Sigma, #F1804) coupled to Protein A/G beads.  RNA was extracted using TRIzol. Libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

value: CAFs


title: JHU-06, 10 ng/mL TGFB1 + 10 ng/mL TGFB3 72hr, Replicate 2


title: D18, Rep1, bACE


title: D18, Rep1, BS

value: Bisulfute (BS-Seq)


title: JHU-06, PBS vehicle control 72hr, Replicate 2


title: RIP-seq of Flag-Lin28b-MU CAFs

description:
Library name: MU_IP
RIP-seq with anti-Flag antibody


title: 93VU147T, 50 ng/mL IL-1B 72hr, Replicate 1


title: 93VU147T, 100 ng/mL SPP1 72hr, Replicate 1


title: RIP-seq input control for WT CAFs

description:
Library name: WT_Input
Input control for RIP-seq


title: D16, Rep3, BS

value: Embryonic Day 16


title: 93VU147T, PBS vehicle control 72hr, Replicate 1


title: D16, Rep3, bACE


title: JHU-06, 50 ng/mL IL-1B 72hr, Replicate 1


title: AoV-B62 (RNA-seq)

city: Ulsan Metropolitan City

first: Hyoung-oh

last: Jeong

address: 50, UNIST-gil, Eonyang-eup , Ulju-gun

institute: Ulsan National Institute of Science and Technology

description: Library name: AoV-B62

data_processing:
Raw sequencing data were processed using CellRanger v7.0.1 (10x Genomics), with alignment to the GRCh38 reference genome via STAR. CellBender was applied to each sample to eliminate background RNA contamination. For bulk RNA sequencing, tumor tissues from an independent cohort of 62 AoV carcinoma patients were analyzed. Transcript-level quantification was achieved using RSEM, aligned to the GRCh38 genome with GENCODE v33 annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files including raw count matrices for the scRNA-seq and bulk RNA-seq datasets.

source_name: Ampulla of vater, tumor

extract_protocol:
Fresh tumor and adjacent normal tissue specimens were obtained from patients with AoV carcinoma before treatment through Endoscopic Retrograde Cholangiopancreatography (ERCP) for scRNA sequencing. Acquired tissues are collected in MACS® Tissue Storage Solution (Miltenyi Biotec., Auburn, CA, USA) on ice and processed to the single cell dissociation immediately.
Libraries were meticulously constructed using the Chromium controller in accordance with the 10x Chromium Next GEM Single Cell 3' v3.1 protocol (10x Genomics).

value: Ampulla of vater, tumor


title: D16, Rep2, BS


title: JHU-06, 50 ng/mL OSM 72hr, Replicate 1


title: AoV-B61 (RNA-seq)

description: Library name: AoV-B61

value: female


title: JHU-06, PBS vehicle control 72hr, Replicate 1


title: D16, Rep2, bACE


title: Glioblastoma cell line U3009

city: Paris

first: Clarisse

last: Brunet

address: 12 Rue Lhomond

country: France

institute: Institut Curie

description:
Library name: P95T177
Bulk RNA-seq of glioblastoma patient-derived cell line

data_processing:
Reads were assessed for quality using FastQC and MultiQC.
Adapter sequences and low-quality bases were removed using appropriate trimming tools.
Reads were aligned to the human reference genome using STAR aligner with default parameters.
Gene-level raw read counts were generated using featureCounts.
Counts were aggregated into a gene expression matrix for downstream analysis.
Assembly: Homo sapiens GRCh38 (hg38).
Supplementary files format and content: Processed data files include a tab-delimited matrix of raw gene-level counts, with rows representing Ensembl gene IDs and columns representing samples. The file “bulk_counts_ensembl_GBM_only.txt” contains the processed expression data submitted to GEO.

source_name: brain

growth_protocol: Glioblastoma patient-derived cell lines were cultured under standard conditions in serum-free neural stem cell medium supplemented with EGF and FGF2, at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using standard column-based purification methods following the manufacturer’s instructions. RNA integrity was verified using Bioanalyzer or equivalent QC instrumentation.
Libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit according to the manufacturer’s protocol. Ribosomal RNA was depleted, RNA was fragmented, cDNA was synthesized, and sequencing adapters were ligated before PCR amplification.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: brain

value: glioblastoma cell line


title: AoV-B60 (RNA-seq)

description: Library name: AoV-B60


title: D16, Rep1, BS


title: AoV-B59 (RNA-seq)

description: Library name: AoV-B59


title: Glioblastoma cell line U3047

description:
Library name: P95T175
Bulk RNA-seq of glioblastoma patient-derived cell line


title: D16, Rep1, bACE


title: Glioblastoma cell line U3031

description:
Library name: P95T174
Bulk RNA-seq of glioblastoma patient-derived cell line


title: AoV-B58 (RNA-seq)

description: Library name: AoV-B58


title: Glioblastoma cell line U3088

description:
Library name: P95T173
Bulk RNA-seq of glioblastoma patient-derived cell line


title: Round spermatids, Ago413-/- testes, rep4, smallRNA-seq

description:
Library name: T89-RS-Null
Column name in raw counts file 3029_rawCounts.txt: MC89

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 10nt with TrimGalore.
Processed reads were collapsed to fasta format using fastq2fasta.pl from miRDeep2
Collapsed reads were processed using mapper.pl from miRDeep2
Collapsed reads were mapped using qualtifier.pl from miRDeep2
Assembly: miRBase v22.1 mmu miRNA
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Single cell suspension from testes was obtained following the method described by Ascenção et al.Testes from 2-5 mice were collected, the tunica albuginea was removed, and tubules were placed in 10 ml of preheated (37°C) DMEM-F12 containing 2 mg of Collagenase 1A (Sigma) for 2 minutes with manual shaking. Digestion was stopped by two washes of the tubules with DMEM-F12. Next, the tubules were incubated in 10 ml of DMEM-F12 with 5 mg of trypsin (Sigma) and 7 mg/ml of DNAse I (Sigma) at 37°C with constant shaking (150 rpm) until the length of the tubules was about 1 mm (approximately 10 minutes). Digestion was stopped by addition of 3 mls of Fetal Bovine Serum (FBS, Sigma) and 30 ml of DMEM F-12. Digested tubules were strained on a 100 μm strainer and centrifuged for at 15°C for 5 minutes at 600g. The single cell suspension of germ cells obtained was then resuspended in FBS and enriched fractions of pachytene spermatocytes and round spermatids were obtained using the gravity-density BSA gradient method MDR developed by Da Ros and others. After collecting the corresponding fractions, cells were pelleted and washed in cold PBS by centrifugation. Purity of each fraction was evaluated by light microscopy and immunofluorescence using the marker SYCP3 and DAPI, and only fractions containing above 70% pachytene spermatocytes and round spermatids were pooled. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a Qubit and integrity assessed on a Fragment Analyzer.
RNA-seq libraries were prepared from 100ng total RNA using the NEBNext Small RNA Library Prep Kit for Illumina (New England Biolabs).

value: testis

value: enriched round spermatids

value: 10-15 weeks


title: Glioblastoma cell line U3008

description:
Library name: P95T172
Bulk RNA-seq of glioblastoma patient-derived cell line


title: Glioblastoma cell line U3039

description:
Library name: P95T171
Bulk RNA-seq of glioblastoma patient-derived cell line


title: AoV-B57 (RNA-seq)

description: Library name: AoV-B57

value: male


title: Glioblastoma cell line U3123

description:
Library name: P95T170
Bulk RNA-seq of glioblastoma patient-derived cell line


title: Glioblastoma cell line U3065

description:
Library name: P95T169
Bulk RNA-seq of glioblastoma patient-derived cell line


title: Round spermatids, Ago413+/+ testes, rep4, smallRNA-seq

description:
Library name: T77-RS-WT
Column name in raw counts file 3029_rawCounts.txt: MC77


title: D1020 M2 58C

city: Redwood City

first: Douglas

middle: V.

last: Faget

state: CA

address: 200 Cardinal Way, Ste 300

institute: Pheast Therapeutics

description: Library name: 22067XR-06Q2-29

data_processing:
FastQC (version v0.12.1, RRID:SCR_014583) was employed to check the quality of raw reads. Trimmomatic (version v0.39, RRID:SCR_011848) was applied to cut adaptors and trim low-quality bases with default setting. STAR package (version 2.7.10b, RRID:SCR_004463) was used to align the reads via the human GRCh38.p14 (Release 113) genome reference. The package of Picard tools (version 3.0.0, RRID:SCR_006525) was applied to mark duplicates of mapping. StringTie (version 2.2.1, RRID:SCR_016323) was used to assemble the RNA-Seq alignments into potential transcripts. HTSeq (version 2.0.3) (RRID:SCR_005514) was used to count mapped reads for genomic features such as genes, exons, promoters, gene bodies, genomic bins, and chromosomal locations. DESeq2 (version 1.40.2) (RRID:SCR_015687) was employed to process the differential gene expression analysis with raw read counts of samples as input.
Assembly: human GRCh38.p14 (Release 113) genome reference
Supplementary files format and content: M2vsM0_RNAseq_Jen.xlsx has TPM counts for all samples.

source_name: Monocyte-derived macrophage

extract_protocol:
After macrophage differentiation, total RNA was isolated using Qiagen RNeasy® 96 Kit following the manufacturer's instructions. Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by AccuBlue® Broad Range RNA Quantitation assay (Biotium, California, USA).
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 430bp with an insert size of about 300bp.

value: Monocyte-derived macrophage


title: AoV-B55 (RNA-seq)

description: Library name: AoV-B55


title: D0950 M2 58C

description: Library name: 22067XR-06Q2-28


title: Round spermatids, Ago413-/- testes, rep3, smallRNA-seq

description:
Library name: T83-RS-Null
Column name in raw counts file 3029_rawCounts.txt: MC83


title: AoV-B56 (RNA-seq)

description: Library name: AoV-B56


title: AoV-B54 (RNA-seq)

description: Library name: AoV-B54


title: D4303 M0 58C

description: Library name: 22067XR-06Q2-27


title: D4303 M2 58C

description: Library name: 22067XR-06Q2-30


title: Round spermatids, Ago413+/- testes, rep4, smallRNA-seq

description:
Library name: T65-RS-Het
Column name in raw counts file 3029_rawCounts.txt: MC65


title: D1020 M0 58C

description: Library name: 22067XR-06Q2-26


title: AoV-B53 (RNA-seq)

description: Library name: AoV-B53


title: D0950 M0 58C

description: Library name: 22067XR-06Q2-25


title: Round spermatids, Ago413-/- testes, rep2, smallRNA-seq

description:
Library name: T59-RS-Null
Column name in raw counts file 3029_rawCounts.txt: MC59


title: Round spermatids, Ago413+/+ testes, rep3, smallRNA-seq

description:
Library name: T71-RS-WT
Column name in raw counts file 3029_rawCounts.txt: MC71


title: D4303 M2 58B

description: Library name: 22067XR-06Q2-24


title: AoV-B52 (RNA-seq)

description: Library name: AoV-B52


title: D4977 M2 58B

description: Library name: 22067XR-06Q2-23


title: Round spermatids, Ago413-/- testes, rep1, smallRNA-seq

description:
Library name: T53-RS-Null
Column name in raw counts file 3029_rawCounts.txt: MC53


title: D7825 M2 58B

description: Library name: 22067XR-06Q2-22


title: AoV-B51 (RNA-seq)

description: Library name: AoV-B51


title: JHU-06, 100 ng/mL SPP1 72hr, Replicate 2

value: oral cavity squamous cell carcinoma

value: normal growth medium


title: JHU-06, 50 ng/mL OSM 72hr, Replicate 2


title: Round spermatids, Ago413+/+ testes, rep2, smallRNA-seq

description:
Library name: T41-RS-WT
Column name in raw counts file 3029_rawCounts.txt: MC41


title: D1020 M2 58B

description: Library name: 22067XR-06Q2-20


title: AoV-B50 (RNA-seq)

description: Library name: AoV-B50


title: D7824 M2 58B

description: Library name: 22067XR-06Q2-21


title: D0950 M2 58B

description: Library name: 22067XR-06Q2-19


title: 93VU147T, 50 ng/mL OSM 72hr, Replicate 1


title: Round spermatids, Ago413+/+ testes, rep1, smallRNA-seq

description:
Library name: T29-RS-WT
Column name in raw counts file 3029_rawCounts.txt: MC29


title: D4303 M0 58B

description: Library name: 22067XR-06Q2-18


title: 93VU147T, 10 ng/mL TGFB1 + 10 ng/mL TGFB3 72hr, Replicate 1


title: AoV-B49 (RNA-seq)

description: Library name: AoV-B49


title: Round spermatids, Ago413+/- testes, rep3, smallRNA-seq

description:
Library name: T23-RS-Het
Column name in raw counts file 3029_rawCounts.txt: MC23


title: D4977 M0 58B

description: Library name: 22067XR-06Q2-17


title: D7825 M0 58B

description: Library name: 22067XR-06Q2-16


title: RIP-seq of Flag-Lin28b-WT CAFs

description:
Library name: WT_IP
RIP-seq with anti-Flag antibody


title: AoV-B48 (RNA-seq)

description: Library name: AoV-B48


title: JHU-06, 100 ng/mL SPP1 72hr, Replicate 1


title: D7824 M0 58B

description: Library name: 22067XR-06Q2-15


title: Round spermatids, Ago413+/- testes, rep2, smallRNA-seq

description:
Library name: T17-RS-Het
Column name in raw counts file 3029_rawCounts.txt: MC17


title: D1020 M0 58B

description: Library name: 22067XR-06Q2-14


title: AoV-B47 (RNA-seq)

description: Library name: AoV-B47


title: D0950 M0 58B

description: Library name: 22067XR-06Q2-13


title: D4303 M2 58A

description: Library name: 22067XR-06Q2-12


title: D4977 M2 58A

description: Library name: 22067XR-06Q2-11


title: Round spermatids, Ago413+/- testes, rep1, smallRNA-seq

description:
Library name: T1-RS-Het
Column name in raw counts file 3029_rawCounts.txt: MC1


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep4, smallRNA-seq

description:
Library name: T90-SP-Null
Column name in raw counts file 3029_rawCounts.txt: MC90


title: AoV-B46 (RNA-seq)

description: Library name: AoV-B46


title: D7825 M2 58A

description: Library name: 22067XR-06Q2-10


title: AoV-B45 (RNA-seq)

description: Library name: AoV-B45


title: D7824 M2 58A

description: Library name: 22067XR-06Q2-09


title: JHU-06, 10 ng/mL TGFB1 + 10 ng/mL TGFB3, Replicate 1


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep3, smallRNA-seq

description:
Library name: T84-SP-Null
Column name in raw counts file 3029_rawCounts.txt: MC84


title: D1020 M2 58A

description: Library name: 22067XR-06Q2-08


title: AoV-B44 (RNA-seq)

description: Library name: AoV-B44


title: Glioblastoma cell line U3021

description:
Library name: P95T176
Bulk RNA-seq of glioblastoma patient-derived cell line


title: D0950 M2 58A

description: Library name: 22067XR-06Q2-07


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep4, smallRNA-seq

description:
Library name: T78-SP-WT
Column name in raw counts file 3029_rawCounts.txt: MC78


title: scRNA-seq of pancreatic tumor from Fsp-Cre;Lin28bfl/fl mouse_3

description:
Library name: Lin28bKO_scRNA_3
10x Genomics

data_processing:
Libraries were sequenced on Illumina NovaSeq 6000 (paired-end 150 bp). Raw reads were demultiplexed and aligned to mouse reference genome mm10 (GRCm38) using Cell Ranger v7.1.0 with default parameters.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Cell Ranger output: barcodes.tsv.gz, genes.tsv.gz, matrix.mtx.gz (raw UMI counts).  Seurat-processed: integrated SCT-normalized matrix, cluster identity, genotype metadata.

source_name: pancreas

extract_protocol:
Fresh tumors were minced and enzymatically dissociated with collagenase IV (1 mg ml⁻¹) and DNase I (40 U ml⁻¹) in RPMI-1640 at 37 °C for 30 min; single-cell suspensions were filtered through 40 µm strainers; red blood cells were removed with ACK buffer; viability > 90 % assessed by trypan blue.
Single-cell suspensions were loaded onto a 10x Chromium Next GEM Chip G and processed with the Chromium Single Cell 3′ v3 reagent kit. Briefly, cells, gel-beads containing barcoded oligos (16-bp cell barcode + 12-bp UMI + 30-bp poly-dT), and oil were combined to form GEMs. After GEM lysis and reverse transcription, barcoded cDNA was pooled, amplified for 12 cycles, enzymatically fragmented, end-repaired, A-tailed, ligated to Illumina adapters, and size-selected to ~400 bp.

value: pancreas


title: AoV-B43 (RNA-seq)

description: Library name: AoV-B43


title: D4303 M0 58A

description: Library name: 22067XR-06Q2-06


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep3, smallRNA-seq

description:
Library name: T72-SP-WT
Column name in raw counts file 3029_rawCounts.txt: MC72


title: AoV-B42 (RNA-seq)

description: Library name: AoV-B42


title: scRNA-seq of pancreatic tumor from Fsp-Cre;Lin28bfl/fl mouse_2

description:
Library name: Lin28bKO_scRNA_2
10x Genomics


title: D4977 M0 58A

description: Library name: 22067XR-06Q2-05


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep4, smallRNA-seq

description:
Library name: T66-SP-Het
Column name in raw counts file 3029_rawCounts.txt: MC66


title: D7825 M0 58A

description: Library name: 22067XR-06Q2-04


title: scRNA-seq of pancreatic tumor from Fsp-Cre;Lin28bfl/fl mouse_1

description:
Library name: Lin28bKO_scRNA_1
10x Genomics


title: AoV-B41 (RNA-seq)

description: Library name: AoV-B41


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep2, smallRNA-seq

description:
Library name: T60-SP-Null
Column name in raw counts file 3029_rawCounts.txt: MC60


title: scRNA-seq of pancreatic tumor from WT mouse_3

description:
Library name: WT_scRNA_3
10x Genomics

value: WT


title: AoV-B40 (RNA-seq)

description: Library name: AoV-B40


title: Input_Cho

description: Library name: Input_Cho

data_processing:
Raw reads were trimmed for adapters and low-quality bases using Trimmomatic. Clean reads were aligned to GRCr8 with Bowtie2. Duplicate reads were removed using Picard. Peak calling was performed using MACS2 with a q-value threshold of 0.05. Peaks were annotated to nearest genes using ChIPseeker.
Assembly: GRCr8
Supplementary files format and content: bigWig, narrow Peak(except for iInput sample)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at RT, quenched with glycine, and lysed in SDS buffer. Chromatin was sheared by sonication to 200–500 bp fragments. After centrifugation, supernatants were incubated with target-specific antibody and protein A/G beads overnight at 4°C. Beads were washed sequentially with low-salt, high-salt, and LiCl buffers, then eluted with SDS buffer. Crosslinks were reversed at 65°C overnight, and DNA was purified by phenol-chloroform extraction.
ChIP-enriched DNA was end-repaired, A-tailed, and ligated to sequencing adapters. Adapter-ligated fragments were amplified by PCR (12–15 cycles) with barcoded primers. PCR products were size-selected (200–400 bp) using AMPure XP beads. Library quality was assessed by Qubit for concentration and Bioanalyzer for fragment size distribution.

value: VSMCs


title: D7824 M0 58A

description: Library name: 22067XR-06Q2-03


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep1, smallRNA-seq

description:
Library name: T54-SP-Null
Column name in raw counts file 3029_rawCounts.txt: MC54


title: AoV-B39 (RNA-seq)

description: Library name: AoV-B39


title: D1020 M0 58A

description: Library name: 22067XR-06Q2-02


title: scRNA-seq of pancreatic tumor from WT mouse_2

description:
Library name: WT_scRNA_2
10x Genomics


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep2, smallRNA-seq

description:
Library name: T36-SP-WT
Column name in raw counts file 3029_rawCounts.txt: MC36


title: scRNA-seq of pancreatic tumor from WT mouse_1

description:
Library name: WT_scRNA_1
10x Genomics


title: AoV-B38 (RNA-seq)

description: Library name: AoV-B38


title: D0950 M0 58A

description: Library name: 22067XR-06Q2-01


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep1, smallRNA-seq

description:
Library name: T30-SP-WT
Column name in raw counts file 3029_rawCounts.txt: MC30


title: ND_B6J_Salmonella_dsopB_Pup5_S12_R1_001

city: Aachen

first: Matthias

middle: W

last: Hornef

address: Pauwellstr 30

department: Medical Microbiology

country: Germany

institute: Uniklinik Aachen

description: Library name: S12

data_processing:
Sequence reads were trimmed for adapter/low quality reads using Cutadapt v4.9 (-j 16 -a "poly A=A{20}" --quality-cutoff 20 -m 20 -u 12)
Trimmed sequences were mapped to the reference genome GRCm39_112 using STAR v2.7.11b (genomeGenerate with --sjdbOverhang 63 on GRCm39.112; then alignment with --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts)
Read count matrix creation was performed using featureCounts function from Rsubread v2.14.2
Assembly: mm39
Supplementary files format and content: fastq files are the raw data for each sample
Supplementary files format and content: bam files are the trimmed data for each sample

source_name: Neonatal intestinal epithelial cells

growth_protocol: C57BL/6 are bred locally at University Hospital RWTH Aachen under SPF conditions.

extract_protocol:
RNA was isolated from the epithelial cell pellet or homogenized intestinal tissue using TRIzol® according to manufacturer’s recommendations. 125 ng is used for library preparation
QuantSeq 3'mRNA-Seq v2 Library Prep Kit FWD with UDIs (Lexogen)

treatment_protocol: Overnight culture of wildtype (wt) S. Typhimurium (ATCC14028) or an isogenic ΔsopB mutant strain are diluted 1:10 and incubated at 37°C until reaching the logarithmic phase (OD600: 0.5). Bacteria are diluted to obtain the appropriate inoculum in PBS. One-day-old animals were orally infected with 100 CFU wt or ΔsopB S. Typhimurium.

value: Neonatal intestinal epithelial cells

value: wildtype

value: Salmonella delta sopB infected for 1 day


title: AoV-B37 (RNA-seq)

description: Library name: AoV-B37

value: Ampulla of vater, tumor


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep3, smallRNA-seq

description:
Library name: T24-SP-Het
Column name in raw counts file 3029_rawCounts.txt: MC24


title: D4977 M2

description: Library name: 22067XR-06Q1-06


title: AoV-B36 (RNA-seq)

description: Library name: AoV-B36

value: female


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep2, smallRNA-seq

description:
Library name: T18-SP-Het
Column name in raw counts file 3029_rawCounts.txt: MC18


title: ND_B6J_Salmonella_dsopB_Pup2_S10_R1_001

description: Library name: S10


title: AoV-B35 (RNA-seq)

description: Library name: AoV-B35


title: D7825 M2

description: Library name: 22067XR-06Q1-04


title: AoV-B34 (RNA-seq)

description: Library name: AoV-B34


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep1, smallRNA-seq

description:
Library name: T2-SP-Het
Column name in raw counts file 3029_rawCounts.txt: MC2


title: ND_B6J_Salmonella_dsopB_Pup1_S9_R1_001

description: Library name: S9


title: AoV-S8-T (scRNA-seq)

description: Library name: AoV-S8-T


title: D7825 M0

description: Library name: 22067XR-06Q1-03


title: ND_B6J_Salmonella_WT_Pup4_S8_R1_001

description: Library name: S8

value: Salmonella wildtype infected for 1 day


title: AoV-B33 (RNA-seq)

description: Library name: AoV-B33


title: D7824 M2

description: Library name: 22067XR-06Q1-02


title: ND_B6J_Salmonella_WT_Pup3_S7_R1_001

description: Library name: S7


title: AoV-B32 (RNA-seq)

description: Library name: AoV-B32


title: D7824 M0

description: Library name: 22067XR-06Q1-01


title: AoV-S7-T (scRNA-seq)

description: Library name: AoV-S7-T


title: ND_B6J_Salmonella_WT_Pup2_S6_R1_001

description: Library name: S6


title: AoV-S6-N (scRNA-seq)

description: Library name: AoV-S6-N

source_name: Ampulla of vater, adjacent normal

value: Ampulla of vater, adjacent normal


title: AoV-B30 (RNA-seq)

description: Library name: AoV-B30


title: ND_B6J_Salmonella_WT_Pup1_S5_R1_001

description: Library name: S5


title: shDNAJC2_2

city: Hangzhou

first: Yunkai

last: Yang

address: Zhejiang provincial people’s hospital

institute: Zhejiang provincial people’s hospital

description:
Library name: shDNAJC2_2
Lentiviral shRNA transduction (shDNAJC2)

data_processing:
Raw sequencing reads were trimmed to remove adapters and low-quality sequences to obtain clean reads. Clean reads were aligned to human reference genome for gene expression quantification. Differential expression analysis was performed between shDNAJC2 and shCtrl groups, followed by GO, KEGG and GSEA functional enrichment analysis of differentially expressed genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from ACHN ccRCC cell pellets using TRIzol reagent, RNA integrity was assessed by Agilent 2100 Bioanalyzer to ensure RNA integrity number (RIN) > 6.8 for subsequent library construction.
mRNA was enriched from qualified total RNA, fragmented randomly, followed by first-strand and second-strand cDNA synthesis, terminal repair, adapter ligation and PCR amplification to construct paired-end RNA-seq libraries. Qualified libraries were sequenced on Illumina sequencing platform.

value: Kidney

value: ACHN

value: Clear cell renal cell carcinoma cell

value: shRNA-mediated DNAJC2 knockdown


title: AoV-S5-T (scRNA-seq)

description: Library name: AoV-S5-T


title: ND_B6J_Uninfected_Pup4_S4_R1_001

description: Library name: S4

value: no treatment


title: AoV-B29 (RNA-seq)

description: Library name: AoV-B29


title: shDNAJC2_1

description:
Library name: shDNAJC2_1
Lentiviral shRNA transduction (shDNAJC2)


title: AoV-S4-T (scRNA-seq)

description: Library name: AoV-S4-T


title: ND_B6J_Uninfected_Pup3_S3_R1_001

description: Library name: S3


title: AoV-B28 (RNA-seq)

description: Library name: AoV-B28

value: male


title: shCtrl3

description:
Library name: shCtrl3
Lentiviral shRNA transduction (shCtrl)

value: negative shRNA control

value: Lentiviral shRNA transduction (shCtrl)


title: ND_B6J_Uninfected_Pup2_S2_R1_001

description: Library name: S2


title: Round spermatids, Ago413-/- testes, rep4, RNA-seq

description:
Library name: T89-RS-Null
Column name in raw counts file 3030_rawCounts.txt: T89-RS-Null

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Assembly: Mouse mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Single cell suspension from testes was obtained following the method described by Ascenção et al.Testes from 2-5 mice were collected, the tunica albuginea was removed, and tubules were placed in 10 ml of preheated (37°C) DMEM-F12 containing 2 mg of Collagenase 1A (Sigma) for 2 minutes with manual shaking. Digestion was stopped by two washes of the tubules with DMEM-F12. Next, the tubules were incubated in 10 ml of DMEM-F12 with 5 mg of trypsin (Sigma) and 7 mg/ml of DNAse I (Sigma) at 37°C with constant shaking (150 rpm) until the length of the tubules was about 1 mm (approximately 10 minutes). Digestion was stopped by addition of 3 mls of Fetal Bovine Serum (FBS, Sigma) and 30 ml of DMEM F-12. Digested tubules were strained on a 100 μm strainer and centrifuged for at 15°C for 5 minutes at 600g. The single cell suspension of germ cells obtained was then resuspended in FBS and enriched fractions of pachytene spermatocytes and round spermatids were obtained using the gravity-density BSA gradient method MDR developed by Da Ros and others. After collecting the corresponding fractions, cells were pelleted and washed in cold PBS by centrifugation. Purity of each fraction was evaluated by light microscopy and immunofluorescence using the marker SYCP3 and DAPI, and only fractions containing above 70% pachytene spermatocytes and round spermatids were pooled. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a Qubit and integrity assessed on a Fragment Analyzer.
[Directional] RNA-seq libraries were prepared from 100-200ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

value: testis

value: enriched round spermatids

value: 10-15 weeks


title: shCtrl2

description:
Library name: shCtrl2
Lentiviral shRNA transduction (shCtrl)


title: AoV-S3-N2 (scRNA-seq, biological replicate 2)

description: Library name: AoV-S3-N2


title: AoV-B26 (RNA-seq)

description: Library name: AoV-B26


title: AoV-S3-N1 (scRNA-seq, biological replicate 1)

description: Library name: AoV-S3-N1


title: shCtrl1

description:
Library name: shCtrl1
Lentiviral shRNA transduction (shCtrl)


title: Round spermatids, Ago413-/- testes, rep3, RNA-seq

description:
Library name: T83-RS-Null
Column name in raw counts file 3030_rawCounts.txt: T83-RS-Null


title: AoV-S3-T (scRNA-seq)

description: Library name: AoV-S3-T


title: AoV-B27 (RNA-seq)

description: Library name: AoV-B27


title: AoV-S2-T (scRNA-seq)

description: Library name: AoV-S2-T


title: AoV-B25 (RNA-seq)

description: Library name: AoV-B25


title: NC5

city: 广州市

first: Bochao

address: 广州市越秀区麓苑路31号

institute: GUangzhou Blood Center

description:
Library name: sample 10
Column name in raw_counts_AllSamples.txt: NC5-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Quantification of gene expression levels using RSEM. Differential expression analysis of two conditions/groups was performed using the DESeq2. The FDR < 0.01 & Fold Change ≥2 was set as the threshold for significantly differential expression.
Assembly: GRCh38(Ensembl release 111)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: PBMC

extract_protocol:
Extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA)
Atotal amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme(NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: PBMC

tag: group

value: healthy donor

value: no


title: AoV-B24 (RNA-seq)

description: Library name: AoV-B24

value: Ampulla of vater, tumor

value: female


title: Round spermatids, Ago413-/- testes, rep2, RNA-seq

description:
Library name: T59-RS-Null
Column name in raw counts file 3030_rawCounts.txt: T59-RS-Null


title: ND_B6J_Salmonella_dsopB_Pup3_S11_R1_001

description: Library name: S11

value: Neonatal intestinal epithelial cells

value: wildtype

value: Salmonella delta sopB infected for 1 day


title: NC4

address: 广州市越秀区麓苑路31号

description:
Library name: sample 9
Column name in raw_counts_AllSamples.txt: NC4-2


title: D4977 M0

description: Library name: 22067XR-06Q1-05

value: Monocyte-derived macrophage


title: AoV-S2-N (scRNA-seq)

description: Library name: AoV-S2-N

value: Ampulla of vater, adjacent normal


title: Round spermatids, Ago413-/- testes, rep1, RNA-seq

description:
Library name: T53-RS-Null
Column name in raw counts file 3030_rawCounts.txt: T53-RS-Null


title: AoV-B23 (RNA-seq)

description: Library name: AoV-B23


title: NC3

address: 广州市越秀区麓苑路31号

description:
Library name: sample 8
Column name in raw_counts_AllSamples.txt: NC3-2


title: Round spermatids, Ago413+/- testes, rep4, RNA-seq

description:
Library name: T65-RS-Het
Column name in raw counts file 3030_rawCounts.txt: T65-RS-Het


title: AoV-S1-T (scRNA-seq)

description: Library name: AoV-S1-T


title: NC2

address: 广州市越秀区麓苑路31号

description:
Library name: sample 7
Column name in raw_counts_AllSamples.txt: NC2-2


title: AoV-B22 (RNA-seq)

description: Library name: AoV-B22


title: Round spermatids, Ago413+/- testes, rep3, RNA-seq

description:
Library name: T23-RS-Het
Column name in raw counts file 3030_rawCounts.txt: T23-RS-Het


title: AoV-S1-N (scRNA-seq)

description: Library name: AoV-S1-N


title: AoV-S6-T (scRNA-seq)

description: Library name: AoV-S6-T


title: NC1

address: 广州市越秀区麓苑路31号

description:
Library name: sample 6
Column name in raw_counts_AllSamples.txt: NC1-2


title: Round spermatids, Ago413+/- testes, rep2, RNA-seq

description:
Library name: T17-RS-Het
Column name in raw counts file 3030_rawCounts.txt: T17-RS-Het


title: HEK cells expressing R273H p53

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Library name: X273
X273_1, X273_2, and X273_3 samples were polled at the RT step

data_processing:
FASTQ file integrity and formatting were assessed using FQ lint, and initial read quality was evaluated using FastQC. Adapter trimming and quality filtering were performed using Trim Galore, which wraps Cutadapt and FastQC. Where applicable, unique molecular identifiers were extracted using UMI-tools, and ribosomal RNA reads were removed using SortMeRNA. Processed reads were aligned to the human GRCh38 reference genome and transcriptome using STAR, and resulting alignment files were sorted, indexed, and summarized using SAMtools. Ribo-seq-specific quality-control metrics, including read length distribution, metagene profiles, P-site offset estimation, and trinucleotide periodicity, were generated using Ribo-TISH (Zhang, P. et al. Genome-wide identification and differential analysis of translational initiation. Nat. Commun. 8, 1749, 2017) and Ribotricer (Choudhary, S., Li, W. & D. Smith, A. Accurate detection of short and long active ORFs using Ribo-seq data. Bioinformatics 36, 2053–2059, 2020). Library quality was further confirmed by strong trinucleotide periodicity and the expected enrichment of ribosome-protected fragments at approximately 30–34 nucleotides. Summary quality-control reports were compiled using MultiQC.
Assembly: GRCh38
Supplementary files format and content: Processed RNA-seq data are provided as differential expression tables in Excel format containing gene identifiers, baseMean, log2FC values, and statistics

source_name: stable HEK293T cells express the p53 construct

growth_protocol: HEK293 cells expressing the wt, G245S, or R273H p53 were grown to 80% confluency in 10 cm dishes as a monolayer in DMEM, supplemented with 10% v/v FBS, 100 U mL-1 penicillin, and 100 µg mL-1 streptomycin.

extract_protocol:
Cells were lysed directly on plates on ice in 500 μL ice-cold polysome lysis buffer containing 20 mM Tris, pH 7.5, 150 mM NaCl, 5 mM MgCl₂, 1% Triton X-100, freshly supplemented with 20 U/mL SUPERase-In RNase inhibitor, 24 U/mL TURBO DNase, 1 mM DTT, 100 μg/mL cycloheximide, and 1× EDTA-free protease inhibitor cocktail. Lysates were clarified by centrifugation at 20,000 × g for 2 min at 4°C and were either flash-frozen or used immediately for monosome fractionation. For monosome fractionation, lysates were supplemented with 5 mM CaCl₂ and digested with micrococcal nuclease at 3 U/μg RNA for 30 min at room temperature. Digestion was quenched by addition of EGTA to a final concentration of 6.25 mM, and samples were loaded onto sucrose gradients as previously described in Jan, Williams, and Weissman (2014). Gradients were centrifuged for 2 h at 41,000 rpm in an SW-41 rotor, and monosome fractions were collected using a BioComp gradient fractionation system coupled to a Gilson FC203B fraction collector and Triax software. RNA was extracted from collected monosome fractions using TRIzol reagent according to the manufacturer’s instructions.
Ribosome-protected fragment libraries were prepared using barcoded linkers as previously described in Hacisuleyman et al (2024). Indexed libraries were pooled and sequenced on an Illumina NextSeq 2000 Sequencing System using a P3 flow cell.

treatment_protocol: Cells were treated with cycloheximide for 2 min at 37°C and 5% CO₂, then rapidly washed and harvested. Washes were performed with ice-cold polysome gradient buffer containing 20 mM Tris, pH 7.5, 150 mM NaCl, 5 mM MgCl₂, freshly supplemented with 1 mM DTT and 100 μg/mL cycloheximide.

value: epithelial cell

value: R273H p53 transient expression

value: HEK cells were transfected with Lipo2000 to transiently express wt p53 construct 24 hr prior to collection


title: AoV-B20 (RNA-seq)

description: Library name: AoV-B20

value: male


title: OBI5

address: 广州市越秀区麓苑路31号

description:
Library name: sample 5
Column name in raw_counts_AllSamples.txt: O5

value: OBI blood donors with concurrent abnormalities


title: HEK cells expressing G245S p53

description:
Library name: X245
X245_1, X245_2, and X245_3 samples were polled at the RT step

value: stable HEK293T cells express the p53 construct

value: G245S p53 transient expression


title: AoV-B19 (RNA-seq)

description: Library name: AoV-B19


title: OBI4

address: 广州市越秀区麓苑路31号

description:
Library name: sample 4
Column name in raw_counts_AllSamples.txt: O4

value: PBMC


title: Round spermatids, Ago413+/- testes, rep1, RNA-seq

description:
Library name: T1-RS-Het
Column name in raw counts file 3030_rawCounts.txt: T1-RS-Het

value: testis

value: enriched round spermatids

value: 10-15 weeks


title: shDNAJC2_3

description:
Library name: shDNAJC2_3
Lentiviral shRNA transduction (shDNAJC2)

value: Kidney

value: ACHN

value: Clear cell renal cell carcinoma cell

value: shRNA-mediated DNAJC2 knockdown


title: HEK cells expressing wt p53

description:
Library name: WT
WT_1, WT_2, and WT_3 samples were polled at the RT step

value: wt p53 transient expression

value: HEK cells stablely express the p53 construct


title: AoV-B31 (RNA-seq)

description: Library name: AoV-B31

value: Ampulla of vater, tumor

value: female


title: OBI3

address: 广州市越秀区麓苑路31号

description:
Library name: sample 3
Column name in raw_counts_AllSamples.txt: O3

value: no


title: LNCaP, IRE1 knockout, full media, 72 hours, 2

city: Oxford

first: Dimitrios

last: Doultsinos

address: Level 6, John Radcliffe Hospital

department: Nuffield Department of Surgical Sciences

institute: University of Oxford

description: Library name: IKO_n2_S20

data_processing:
Raw data were processed using a standardized computational workflow to obtain gene-level raw counts. FASTQ files were quality-checked using FastQC to assess read quality and adapter contamination.
Assembly: High-quality reads were aligned to the human reference genome (GRCh38, Ensembl release 108) using STAR aligner (Dobin et al., 2013). Gene-level quantification was performed using HTSeq-count (Anders et al., 2015). Batch effect correction was executed using the sva package (v.3.54.0). Differential gene expression analysis was performed using the DESeq2 package (v1.40.2), with subsequent LFC shrinkage using the ‘apeglm’ estimator.
Supplementary files format and content: CSV file contains raw counts for all samples

source_name: LNCaP

growth_protocol: LNCaP WT or LNCaP IRE 1KO cells were grown in RPMI media supplemented with 10% FBS (full media) or charcoal stripped fbs (charcoal stripped media) without antibiotics in humidified atmosphere with 5% CO2 at 37 degrees Celcius

extract_protocol:
RNA was extracted using the RNeasy Plus Mini kit.
Libraries were prepared using the TruSeq Stranded Total RNA with Illumina Ribo-Zero plus rRNA Depletion workflow (https://emea.support.illumina.com/downloads/truseq-stranded-total-rna-with-ribo-zero-plus-rrna-depletion-ref-guide.html).
cDNA library QC was carried out on Tapestation and Libraries were pooled, diluted to ∼10 nM, denatured, and further diluted for paired-end sequencing (NovaSeq6000 platform, Illumina, NovaSeq 6000 S2/S4 reagent kit v1.5, 300 cycles). A test run prior to full sequencing was executed on a MiSeq system.

treatment_protocol: LNCaP WT or LNCaP IRE 1KO cells were treated with 10uM Enzalutamide or DMSO control, or 1nM R1881 or Ethanol control for 12 hours in full media without antibiotics in humidified atmosphere with 5% CO2 at 37 degrees Celcius

value: LNCaP

value: Prostate Cancer epithelial cell

value: IRE1 knockout

value: Full media 10% FBS


title: AoV-B21 (RNA-seq)

description: Library name: AoV-B21

value: male


title: AoV-B18 (RNA-seq)

description: Library name: AoV-B18


title: Round spermatids, Ago413+/+ testes, rep4, RNA-seq

description:
Library name: T77-RS-WT
Column name in raw counts file 3030_rawCounts.txt: T77-RS-WT

value: testis


title: AoV-B17 (RNA-seq)

description: Library name: AoV-B17


title: Round spermatids, Ago413+/+ testes, rep3, RNA-seq

description:
Library name: T71-RS-WT
Column name in raw counts file 3030_rawCounts.txt: T71-RS-WT; outlier sample not used for downstream analysis

value: enriched round spermatids


title: OBI2

address: 广州市越秀区麓苑路31号

description:
Library name: sample 2
Column name in raw_counts_AllSamples.txt: O2

value: PBMC

value: OBI blood donors with concurrent abnormalities


title: LNCaP, IRE1 knockout, full media, 72 hours, 1

description: Library name: IKO_n1_S19


title: Round spermatids, Ago413+/+ testes, rep2, RNA-seq

description:
Library name: T41-RS-WT
Column name in raw counts file 3030_rawCounts.txt: T41-RS-WT

value: 10-15 weeks


title: AoV-B16 (RNA-seq)

description: Library name: AoV-B16


title: OBI1

address: 广州市越秀区麓苑路31号

description:
Library name: sample 1
Column name in raw_counts_AllSamples.txt: O1


title: LNCaP, R1881, 12 hours, 3

description: Library name: R1881_n3_S18

value: WT


title: Round spermatids, Ago413+/+ testes, rep1, RNA-seq

description:
Library name: T29-RS-WT
Column name in raw counts file 3030_rawCounts.txt: T29-RS-WT


title: RNA_L1KD

first: Yu

last: Qian

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

institute: Zhejiang University

description: Library name: RNA_L1KD

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
The sequencing data were processed using Easy_Ribo for trimming for adaptor sequences, masking low-complexity or low-quality reads, and mapping to the GRCh38 whole genome.
RPKM were calculated to quantify gene expression levels, and differential expression analysis was performed using DESeq2.
All samples were analyzed in sense-strand mode.
Assembly: GRCh38 (Homo sapiens)
Supplementary files format and content: Xlsx file include the RPKM representing gene expression levels for each transcript.

source_name: Colon

growth_protocol: All RKO cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 6cm dishes.

extract_protocol:
Cells were lysed in TRIzol, followed by chloroform extraction and isopropanol precipitation, with 1/5 of the RNA used for RNA-seq and 4/5 for ribosome profiling (Ribo-seq).
The library was constructed using Small RNA Library Prep Set for Illumina (E7330S, NEB).

value: Colon

value: RKO

value: colorectal carcinoma cell


title: LNCaP, R1881, 12 hours, 2

description: Library name: R1881_n2_S17


title: AoV-B15 (RNA-seq)

description: Library name: AoV-B15

value: Ampulla of vater, tumor


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep3, RNA-seq

description:
Library name: T90-SP-Null
Column name in raw counts file 3030_rawCounts.txt: T90-SP-Null

source_name: testis


title: AoV-B14 (RNA-seq)

description: Library name: AoV-B14

value: female


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep2, RNA-seq

description:
Library name: T84-SP-Null
Column name in raw counts file 3030_rawCounts.txt: T84-SP-Null


title: RNA_CTL

description: Library name: RNA_CTL

value: CTL


title: AoV-B13 (RNA-seq)

description: Library name: AoV-B13


title: LNCaP, R1881, 12 hours, 1

description: Library name: R1881_n1_S16

value: LNCaP


title: Ribo_RPL22L1IP

description: Library name: Ribo_RPL22L1IP


title: Pachytene/diplotene spermatocytes, Ago413-/- testes, rep1, RNA-seq

description:
Library name: T54-SP-Null
Column name in raw counts file 3030_rawCounts.txt: T54-SP-Null


title: LNCaP, Ethanol, 12 hours, 3

description: Library name: EtOH_n3_S15

value: Prostate Cancer epithelial cell

value: Ethanol


title: AoV-B12 (RNA-seq)

description: Library name: AoV-B12


title: Ribo_RPL22L1

description: Library name: Ribo_RPL22L1


title: LNCaP, Ethanol, 12 hours, 2

description: Library name: EtOH_n2_S14


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep4, RNA-seq

description:
Library name: T66-SP-Het
Column name in raw counts file 3030_rawCounts.txt: T66-SP-Het; outlier sample not used for downstream analysis


title: AoV-B11 (RNA-seq)

description: Library name: AoV-B11


title: Ribo_L1KD

description: Library name: Ribo_L1KD


title: LNCaP, Ethanol, 12 hours, 1

description: Library name: EtOH_n1_S13


title: AoV-B10 (RNA-seq)

description: Library name: AoV-B10


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep2, RNA-seq

description:
Library name: T2-SP-Het
Column name in raw counts file 3030_rawCounts.txt: T2-SP-Het


title: LNCaP, DMSO, 12 hours, 1

description: Library name: DMSO_n1_S7

value: DMSO


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep3, RNA-seq

description:
Library name: T24-SP-Het
Column name in raw counts file 3030_rawCounts.txt: T24-SP-Het

value: male


title: Ribo_CTL

description: Library name: Ribo_CTL


title: AoV-B9 (RNA-seq)

description: Library name: AoV-B9


title: LNCaP, DMSO, 12 hours, 2

description: Library name: DMSO_n2_S8


title: LNCaP, IRE1 knockout, Enzalutamide, 12 hours, 3

description: Library name: LNCaP_IKO_Enza_n3_S13

value: IRE1 knockout

value: Enzalutamide


title: Pachytene/diplotene spermatocytes, Ago413+/- testes, rep1, RNA-seq

description:
Library name: T18-SP-Het
Column name in raw counts file 3030_rawCounts.txt: T18-SP-Het

value: testis


title: LNCaP, IRE1 knockout, Enzalutamide, 12 hours, 1

description: Library name: LNCaP_IKO_Enza_n1_S11


title: AoV-B8 (RNA-seq)

description: Library name: AoV-B8


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep5, RNA-seq

description:
Library name: T78-SP-WT
Column name in raw counts file 3030_rawCounts.txt: T78-SP-WT


title: LNCaP, IRE1 knockout, Enzalutamide, 12 hours, 2

description: Library name: LNCaP_IKO_Enza_n2_S12


title: LNCaP, Charcoal Stripped Media, 72 hours, 2

description: Library name: Charcoal_Strip_n2_S5

value: Charcoal Stripped media


title: AoV-B6 (RNA-seq)

description: Library name: AoV-B6


title: LNCaP, IRE1 knockout, Charcoal Stripped Media, 72 hours, 3

description: Library name: LNCaP_IKO_Charcoal_n3_S9


title: LNCaP, Charcoal Stripped Media, 72 hours, 1

description: Library name: Charcoal_Strip_n1_S4


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep4, RNA-seq

description:
Library name: T42-SP-WT
Column name in raw counts file 3030_rawCounts.txt: T42-SP-WT

value: 10-15 weeks


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep3, RNA-seq

description:
Library name: T72-SP-WT
Column name in raw counts file 3030_rawCounts.txt: T72-SP-WT; outlier sample not used for downstream analysis


title: AoV-B5 (RNA-seq)

description: Library name: AoV-B5


title: LNCaP, IRE1 knockout, Charcoal Stripped Media, 72 hours, 2

description: Library name: LNCaP_IKO_Charcoal_n2_S8


title: LNCaP, Charcoal Stripped Media, 72 hours, 3

description: Library name: Charcoal_Strip_n3_S6

value: WT


title: AoV-B7 (RNA-seq)

description: Library name: AoV-B7


title: LNCaP, full media, 72hours, 3

description: Library name: Parental_n3_S3

value: Full media 10% FBS


title: AoV-B4 (RNA-seq)

description: Library name: AoV-B4


title: LNCaP, IRE1 knockout, Charcoal Stripped Media, 72 hours, 1

description: Library name: LNCaP_IKO_Charcoal_n1_S7


title: LNCaP, full media, 72hours, 2

description: Library name: Parental_n2_S2


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep1, RNA-seq

description:
Library name: T30-SP-WT
Column name in raw counts file 3030_rawCounts.txt: T30-SP-WT


title: AoV-B3 (RNA-seq)

description: Library name: AoV-B3


title: TC1aAVC_d7-2_scRNA-seq

first: Takuya

institute: RIKEN Center for Integrative Medical Sciences

description: Library name: TC1aAVC_d7-2

data_processing:
The scRNA-seq fastq files were analyzed by Cellranger 0.7.2.
Assembly: mm10

source_name: Cancer tissue

extract_protocol:
For sc-RNA-seq analysis, CD45+ TILs were enriched by positive selection using anti-biotin beads following staining with anti-CD45 biotin. Approximately 8,000 cells were loaded onto Next GEM Chip K (10x Genomics) for partitioning into GEMs using a Chromium Controller (10x Genomics).
Single-cell RNA libraries were prepared following the Chromium Next GEM Single Cell 5’ Reagent Kits v2 protocol. The scRNA-seq libraries were sequenced on a Novaseq X Plus platform (Illumina), achieving a minimum depth of 20,000 reads per cell for the 5’ gene expression library.
Tissue sections were hybridized with a probe panel targeting 479 genes under stringent conditions to minimize nonspecific binding. Following overnight hybridization at 50 °C and subsequent stringent washes, probes were ligated and amplified using the rolling circle amplification strategy.

value: Cancer tissue

value: Tumor cells and Immune cells

value: aAVC treatment


title: LNCaP, Enzalutamide, 12 hours, 3

description: Library name: LNCaP_Enza_n3_S19


title: LNCaP, full media, 72hours, 1

description: Library name: Parental_n1_S1


title: AoV-B2 (RNA-seq)

description: Library name: AoV-B2

value: Ampulla of vater, tumor

value: female


title: LNCaP, Enzalutamide, 12 hours, 2

description: Library name: LNCaP_Enza_n2_S18

value: LNCaP


title: TC1aAVC_d7-1_scRNA-seq

description: Library name: TC1aAVC_d7-1


title: LNCaP, Enzalutamide, 12 hours, 1

description: Library name: LNCaP_Enza_n1_S17

value: Prostate Cancer epithelial cell


title: AoV-B1 (RNA-seq)

description: Library name: AoV-B1


title: TC1aAVC_d3-2_scRNA-seq

description: Library name: TC1aAVC_d3-2


title: Mus musculus female lung: SARS-CoV-2 virus challenge batch 2

city: Taipei City

first: Wye-Lup

last: Kong

address: 28, Lane 70, Academia Road Section 2, Nangang District

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

description:
Library name: XFP23-EI03_C1
FFPE Probe-based spatial transcriptomics

data_processing:
Both histological images and sequencing output for the probe-based ST datasets were processed using the “count” function of the Space Ranger software (10x Genomics) to align the reads to the transcriptome reference (refdata-gex-mm10-2020-A) and quantify gene expression for each spatial barcode.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_position_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
A 5-µm thick section was taken from each treatment group and placed within the capture area of the Gene Expression (GE) Slide (catalog no. PN-2000184) using the Visium Accessory Kit (catalog no. PN-1000194)
Visium Spatial Gene Expression Reagent Kits for FFPE was utilized along with the Mouse Transcriptome kit from 10x Genomics (USA) during library preparation, following standard manufacturer's protocol.

value: lung

value: SARS-CoV-2 virus challenge


title: 293T cells, GFP, rep3

city: Suzhou

first: Zongbing

last: Hao

address: 199 Ren-ai Road

institute: Soochow University

description: Library name: GFP-3

data_processing:
Quality analysis: FastQC (v0.10.1)
Quality control: Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Alignment: Hisat2 (v2.2.1) default parameters
Expression analysis: HTSeq (v0.6.1)
Assembly: hg38
Supplementary files format and content: Microsoft Excel file include raw counts and FPKM values for each sample

growth_protocol: 293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ºC.

extract_protocol:
Total RNA was harvested using TRIZol reagent (Vazyme). 1.0 μg of total RNA was used for library construction.
Total RNA was used for library preparation. Poly(A) mRNA was isolated using Oligo(dT) beads, followed by mRNA fragmentation using divalent cations and high temperature. Random primers were used to perform priming. First-strand cDNA and the second-strand cDNA were synthesized. Both ends of the purified double-stranded cDNA were repaired and dA-tailing was added, followed by T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers.

treatment_protocol: Cells were transfected with GFP and GFP-812 plasmids, respectively, using Lipo2000 according to manufacturer's protocols.

value: Kidney

value: 293T cell line

value: Epithelial cell

value: GFP


title: NKT-3

first: Qian

last: Wang

address: 2318 Yuhangtang Road

department: School of pharmacy

institute: Hangzhou Normal University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..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 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: 200 uM NKT for 24 h


title: TC1aAVC_d3-1_scRNA-seq

city: Yokohama City

last: Ishibashi

address: 1-7-22 Suehiro-cho, Tsurumi-ku

description: Library name: TC1aAVC_d3-1


title: Mus musculus female lung: mAb pre-treatment batch 2

description:
Library name: XFP23-EI02_B1
FFPE Probe-based spatial transcriptomics

value: mAb pre-treatment


title: 293T cells, GFP, rep2

description: Library name: GFP-2


title: NKT-2


title: Mus musculus female lung: Control batch 2

description:
Library name: XFP23-EI01_A1
FFPE Probe-based spatial transcriptomics

value: Control


title: TC1cntl_d7-2_scRNA-seq

description: Library name: TC1cntl_d7-2


title: 293T cells, GFP, rep1

description: Library name: GFP-1


title: NKT-1


title: TC1cntl_d7-1_scRNA-seq

description: Library name: TC1cntl_d7-1


title: 293T cells, GFP-812, rep3

description: Library name: GFP-812-3


title: CTL-3

value: Without special treatment


title: Mus musculus female lung: mAb pre-treatment & SARS-CoV-2 virus challenge batch 1

description:
Library name: XPF22-BB23_D1
FFPE Probe-based spatial transcriptomics


title: TC1cntl_d3-2_scRNA-seq

description: Library name: TC1cntl_d3-2

value: Cancer tissue


title: Mus musculus female lung: SARS-CoV-2 virus challenge batch 1

description:
Library name: XPF22-BB21_C1
FFPE Probe-based spatial transcriptomics


title: CTL-2


title: Mus musculus female lung: mAb pre-treatment batch 1

description:
Library name: XPF22-BB17_B1
FFPE Probe-based spatial transcriptomics


title: Mus musculus female lung: mAb pre-treatment & SARS-CoV-2 virus challenge batch 2

description:
Library name: XFP23-EI04_D1
FFPE Probe-based spatial transcriptomics


title: 293T cells, GFP-812, rep2

description: Library name: GFP-812-2


title: TC1cntl_d3-1_scRNA-seq

description: Library name: TC1cntl_d3-1

value: Tumor cells and Immune cells


title: CTL-1


title: 293T cells, GFP-812, rep1

description: Library name: GFP-812-1


title: Mus musculus female lung: Control batch 1

description:
Library name: XPF22-BB07_A1
FFPE Probe-based spatial transcriptomics


title: T Cell stromal conditioned media treated replicate 3

status: Public on Jun 20 2026

city: Atlanta

first: Rachel

last: Fitzgerald

state: GA

address: 1515 Dickey Drive

department: Chemistry

institute: Emory University

description:
Library name: Mouse3 SCM rep3
M3_S

data_processing:
Raw reads were accessed through the EIGC, in Unix, and quality checked using FastQC.
Adaptor sequences and low-quality reads were removed with Trimmomatic.
Reads were aligned to GRCm39 in Bioconductor (in R) using a ‘seed-and-vote’ algorithm (Rsubread1 package).
Count matrices were generated with “feature Counts” in Rsubread.
DESeq2 (in R) was used to generate normalized RNA-seq signal values (median of ratios method to account for sequencing depth), to identify differentially expressed genes (log2 fold change ≤ -2 or ≥ 2, adjusted p value ≤ 0.05) and to generate a PCA plot (single value decomposition).
Agglomerative clustering into 4 primary groups was performed using the hclust function.
Distances between observations were measured in Euclidean distances using complete linkage clustering.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Counts matrix values as txt files
Supplementary files format and content: DESeq2 fold change values as txt files

source_name: spleen

growth_protocol: CD3+ T Cells were isolated via negative selection from C57BL/6 mouse spleens.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini Kit following the manufacturer’s protocol (QIAGEN, # 74106) and quality control was performed using a Bioanalyzer (Agilent).
Isolated RNA samples were submitted to the Emory Integrated Genomics Core (EIGC) for library preparation and sequencing. cDNA was generated using SMART-seq v4 Ultra Low Input RNA Kit (Takara Bio) and the final sequencing library was made using the Nextera XT Kit (Illumina) following standard protocols. cDNA libraries were sequenced on a Novaseq S1 flowcell that provides >50M reads per sample.

treatment_protocol: Cells were treated for 4 hours 37°C and 5% CO2 in unconditioned media, adipocyte conditioned media or stromal cell conditioned media prior to RNA-sequencing.

value: spleen

value: T cell

value: WT

value: stromal cell conditioned media 4 hours


title: T Cell stromal conditioned media treated replicate 2

description:
Library name: Mouse2 SCM rep2
M2_S


title: T Cell stromal conditioned media treated replicate 1

description:
Library name: Mouse1 SCM rep1
M1_S


title: T Cell adipocyte conditioned media treated replicate 2

description:
Library name: Mouse2 ACM rep2
M2_A

value: adipocyte conditioned media 4 hours


title: T Cell adipocyte conditioned media treated replicate 1

description:
Library name: Mouse1 ACM rep1
M1_A


title: T Cell adipocyte conditioned media treated replicate 3

description:
Library name: Mouse3 ACM rep3
M3_A


title: T Cell unconditioned media treated replicate 1

description:
Library name: Mouse1 UCM rep1
M1_R


title: T Cell unconditioned media treated replicate 2

description:
Library name: Mouse2 UCM rep2
M2_R


title: T Cell unconditioned media treated replicate 3

description:
Library name: Mouse3 UCM rep3
M3_R


title: Pachytene/diplotene spermatocytes, Ago413+/+ testes, rep2, RNA-seq

city: Ithaca

first: Andrew

last: Grimson

address: 526 Campus Rd

institute: Cornell University

description:
Library name: T36-SP-WT
Column name in raw counts file 3030_rawCounts.txt: T36-SP-WT

value: testis

value: male

value: 10-15 weeks


title: Lgr5-GFP+ ISCs, KANSL1-KO, day4, rep1

city: Tianjin

first: Chang

last: Lu

address: 94 Weijin Road, Nankai District

institute: Nankai University

description:
Library name: B5
Column name in raw counts ALL Samples.txt: B5

data_processing:
Raw reads obtained from sequencing may contain unqualified reads, such as those with low overall quality, presence of sequencing primers, or low-quality ends. These unqualified reads are likely to affect the quality of downstream analysis and therefore must be filtered to obtain clean reads suitable for data analysis. Seqtk was used for filtering.
The pre-processed reads were aligned to the genome using the spliced mapping algorithm of Hisat2 (version 2.0.4). This algorithm allows reads that cannot be mapped in full length to be split and mapped, making it particularly suitable for eukaryotic transcriptome sequencing data (which contain intronic regions). Default parameters were used. The resulting alignments were output as BAM files.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: small intestine

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorivd) following the manufacturer’s standard protocol, and purified using the RNAClean XP Kit (Beckman Coulter) and the RNase-Free DNase Set (QIAGEN). RNA integrity was assessed using the Agilent 2100 Bioanalyzer/Agilent 4200 TapeStation (Agilent Technologies), while total RNA yield and purity were determined using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and the NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific).
The purified total RNA was subjected to mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3′ end A-tailing, adapter ligation, and enrichment to complete mRNA sequencing library construction. The library concentration was measured using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and the library fragment size distribution was assessed using the Agilent 4200 TapeStation (Agilent Technologies).

value: small intestine

value: Intestinal stem cell

value: daily tamoxifen for 4 days


title: Lgr5-GFP+ ISCs, KANSL1-KO, day4, rep3

description:
Library name: B8
Column name in raw counts ALL Samples.txt: B8


title: Lgr5-GFP+ ISCs, KANSL1-KO, day4, rep2

description:
Library name: B7
Column name in raw counts ALL Samples.txt: B7


title: Lgr5-GFP+ ISCs, KANSL1-KO, day3, rep3

description:
Library name: B4
Column name in raw counts ALL Samples.txt: B4

value: daily tamoxifen for 3 days


title: Lgr5-GFP+ ISCs, KANSL1-KO, day3, rep1

description:
Library name: B1
Column name in raw counts ALL Samples.txt: B1


title: Lgr5-GFP+ ISCs, KANSL1-WT, rep3

description:
Library name: A6
Column name in raw counts ALL Samples.txt: A6

value: corn oil


title: Lgr5-GFP+ ISCs, KANSL1-KO, day3, rep2

description:
Library name: B3
Column name in raw counts ALL Samples.txt: B3


title: Lgr5-GFP+ ISCs, KANSL1-WT, rep2

description:
Library name: A3
Column name in raw counts ALL Samples.txt: A3


title: Lgr5-GFP+ ISCs, KANSL1-WT, rep1

description:
Library name: A2
Column name in raw counts ALL Samples.txt: A2


title: ATAD3A-KI-BAPN6

city: Shanghai

first: Jie

last: Lin

state: Shanghai

address: 180 Fenglin Road Street, Xuhui District

institute: Zhongshan Hospital, Fudan University

description:
Library name: ATAD3A-KI-BAPN6
AB12

data_processing:
Raw reads were filtered to remove adaptor-contaminated and low-quality reads using Trim Galore, and read quality was assessed using FastQC.
Clean reads were aligned to the Mus musculus reference genome using HISAT2.
Gene expression levels were quantified and raw gene counts were generated for downstream analysis.
Differential expression analysis was performed using DESeq2.
Functional enrichment analysis was performed using clusterProfiler.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text file containing raw read counts for all genes in all samples.

source_name: aorta

growth_protocol: Male mice were housed individually in ventilated cages under specific pathogen-free conditions at 24°C and 60% relative humidity with a 12 h light/dark cycle and free access to food and water.

extract_protocol:
Total RNA was extracted from mouse aortic tissues using TRIzol reagent according to the manufacturer’s instructions. RNA quantity was measured by Qubit 2.0 Fluorometer, and RNA integrity was assessed by agarose gel electrophoresis and Qsep/Bioanalyzer.
For eukaryotic samples, mRNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse-transcribed to first-strand cDNA using random hexamer primers. Second-strand cDNA was synthesized, followed by end repair, A-tailing, adaptor ligation, size selection, and PCR amplification. Qualified libraries were sequenced on an Illumina platform.

treatment_protocol: Mice were randomly assigned to experimental groups prior to aortic aneurysm and dissection (AAD) induction. For the BAPN-induced model, 3-week-old male mice received β-aminopropionitrile (BAPN, Sigma-Aldrich, A3134) in drinking water at 0.5% (w/v) for 28 consecutive days. Control mice received regular drinking water under the same conditions.

value: aorta

value: BAPN


title: ATAD3A-KI-BAPN3

description:
Library name: ATAD3A-KI-BAPN3
AB9


title: ATAD3A-KI-BAPN4

description:
Library name: ATAD3A-KI-BAPN4
AB10


title: ATAD3A-KI-BAPN2

description:
Library name: ATAD3A-KI-BAPN2
AB8


title: ATAD3A-KI-BAPN1

description:
Library name: ATAD3A-KI-BAPN1
AB7


title: ATAD3A-KI-BAPN5

description:
Library name: ATAD3A-KI-BAPN5
AB11