title: Pa03C E96A G8 TMZ 4hr

description: Library name: G8-TMZ-4hr_S12


title: Control Subject 5

status: Public on Feb 04 2026

type: SRA

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 40 Duke Medicine Cir

country: USA

institute: Duke University

description: Library name: Subject-19

library_source: transcriptomic single cell

data_processing:
Raw base call files were analyzed using Cell Ranger v.9.0.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
CellRanger v.9.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38-2024-A human genome
Assembly: GRCh38-2024-A
Supplementary files format and content: filtered_feature_bc_matrices.tar.gz contain matrix.mtx, features.tsv, and barcodes.tsv

molecule: polyA RNA

organism: Homo sapiens

source_name: Olfactory Epithelium

extract_protocol:
After brush-biopsy specimens were collected in Hibernate-A medium containing 5 µg/mL N-acetylcysteine (NAC), cells were digested for 15 min at 37 °C in a cocktail of papain (4U/mL), DNase I (10 µg/mL), 1mM EDTA, and NAC (0.05 mg/mL), then treated for 1 min with an equal volume of Accutase. The slurry was quenched with FBS, strained through a 70 µm filter, pelleted (400 g, 5 min), washed in PBS with 2% FBS, and resuspended at 1 × 10⁶ cells/mL in Hibernate-A plus 0.2 % BSA, NAC (0.05 mg/mL) 0.05 % anti-clumping reagent for immediate scRNA-seq.
Samples were processed for scRNA-seq using Chromium Single Cell 3′ Paired-End, Dual-Index Library & Gel Bead Kit v4 GEMX kit (10X Genomics) targeting 20,000 cells, then sequenced using NovaSeqX (Illumina) flow cells.

tag: tissue

value: Olfactory Epithelium


title: Pre-clinical AD Subject 9

description: Library name: Subject-18


title: H2A-P_H2AS129A_Log_K_Rep1 (ChIP)

city: Wrocław

first: Ireneusz

middle: Bernard

last: Litwin

address: Kanonia 6/8

department: Department of Genetics and Cell Physiology

country: Poland

institute: University of Wroclaw

description: Library name: H2A-P_H2AS129A_Log_K_Rep1_IP

library_source: genomic

data_processing:
Raw sequencing data was quality controlled by Q30.
Low-quality reads and adapter sequences were cut off using Cutadapt.
Filtered reads were then mapped against the target genome (S. cerevisiae S288C assembly SacCer3) and against the spike-in genome (S. pombe assembly ASM294v2) using Bowtie2.
Unmapped reads, mitochondrial DNA and duplicates were filtered out using Samtools.
Samtools was used to count reads uniquely mapped to SacCer3 and ASM294v2 and these values were used to calculate the occupancy ratio value.
Peaks were called using MACS3.
bedGraph files were converted to bigWig format using bedGraphToBigWig utility.
Assembly: Saccharomyces cerevisiae SacCer3
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: All S. cerevisiae strains were cultured in rich YPD medium at 30°C unless indicated otherwise. The S. pombe calibration strain was cultured in YES medium at 30°C

extract_protocol:
4 × 10⁸ S. cerevisiae cells were mixed with ~1 × 10⁸ Schizosaccharomyces pombe cells expressing Rad21–6HA, fixed in 1% formaldehyde for 15 min at room temperature (RT), and quenched with 150 mM glycine for 5 min. Cells were pelleted, washed once with TBS, and resuspended in 600 µl FA lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, protease inhibitor cocktail, 1 mM PMSF). Cells were lysed by four cycles of bead beating (6,500 rpm, 30 s) and lysates were sonicated to an average DNA fragment length of ~600 bp. After centrifugation for 30 min at 15,000 rpm, cleared supernatants were transferred to new tubes and 1% of each was kept as an input sample. For immunoprecipitation, 5 µl of antibody against the S. cerevisiae protein of interest and 2 µl of anti-HA antibody recognizing Rad21–6HA were added to the lysates, and samples were incubated overnight at 4°C with rotation. The next day, DNA-protein complex es were captured with Protein G Dynabeads and sequentially washed with FA-lysis buffer, FA-500 buffer (50 mM HEPES–KOH pH 7.5, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA), LiCl wash buffer (10 mM Tris–HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA) and TE (10 mM Tris–HCl pH 7.5, 1 mM EDTA) on a rotator for 5 min each time. Beads and input samples were then resuspended in elution buffer (50 mM Tris–HCl pH 7.5, 1% SDS, 10 mM EDTA) and incubated O/N at 65°C on a thermal shaker. The next day, magnetic beads were removed, and all samples were treated with RNase A (100 µg/ml) for 1 h at 37°C, followed by a 1 h incubation at 65°C in the presence of proteinase K (1 mg/ml). DNA from H2A-S129-P, Rap1-13cMyc, Ku70-13cMyc, Tel1-12Pk, Pol2-3HA, and Rpb1 ChIP samples was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). DNA from RPA, Rad52–YFP, Rad51, Rad59–13cMyc, and Cdc13–18cMyc ChIP samples was extracted by phenol–chloroform purification and ethanol precipitation.
Sequencing libraries for H2A-S129-P, Rap1-13cMyc, Ku70-13cMyc, Tel1-12Pk, Pol2-3HA, and Rpb1 ChIP samples were prepared using the Novogene NGS DNA Library Prep Set. Libraries for RPA, Rad52–YFP, Rad51, Rad59–13cMyc, and Cdc13–18cMyc ChIP samples were generated using the xGen™ ssDNA & Low-Input DNA Library Preparation Kit (Integrated DNA Technologies) according to the manufacturer’s instructions.

treatment_protocol: The indicated S. cerevisiae strains were treated with 0.5 mM As(III) for 1 h or 2 h, or left untreated. Wild-type cells were also treated with phleomycin (2 µg/mL or 50 µg/mL). rpb1-1 mutant cells were grown at the permissive temperature (25°C) and shifted to 37°C.

tag: cell type

value: yeast

tag: genotype

tag: treatment

tag: chip antibody

value: Anti-Histone H2A (phospho S129) antibody (Abcam, ab15083)


title: Pa03C E96A B4 untreated

city: Indianapolis

first: Kelley

last: Mark

state: Indiana

institute: Herman B Wells Center for Pediatric Research

description: Library name: B4-Untr_S8

library_source: transcriptomic

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to human genes using featureCounts (from subread v2.0.1).
Raw count were subject to differential expression analysis using EdgeR
Assembly: hg38
Supplementary files format and content: raw counts file

molecule: total RNA

source_name: pancreas

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM; high glucose) supplemented with 10% fetal bovine serum (FBS) under standard culture conditions (37 °C, 5% CO₂, humidified incubator). Cells were passaged at ~70–80% confluence and seeded for RNA isolation at comparable densities to ensure equivalent growth phase at harvest

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions, including on-column DNase treatment (Qiagen RNase-Free DNase Set, Cat# 79254) where applicable. RNA integrity and concentration were assessed prior to library preparation
RNA libraries for RNA-seq were prepared using Qiagen RNeasy Mini Kit (74104) following manufacturers' protocols

value: pancreas

tag: cell line

value: pancreatic ductal adenocarcinoma


title: Pa03C E96A B4 TMZ 4hr

description: Library name: B4-TMZ-4hr_S9


title: Pre-clinical AD Subject 8

description: Library name: Subject-17


title: 12367-JF

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 12367-JF

data_processing:
CellRanger was used to map the reads (paired end) to the reference genome to generate the bam files.
Assembly: hg19
Supplementary files format and content: cellranger output format

source_name: human skin

extract_protocol:
https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf    Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE Tissue Sections
https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: human skin

value: mixed (single cell)


title: TP2

city: Hangzhou

first: Chen

last: Xue

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou

country: China

institute: Zhejiang University

description:
Library name: L01507_TM0008
MobiNova

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the MobiVision software.
Assembly: GRCh38/hg38
Supplementary files format and content: h5ad file

organism: Mus musculus

source_name: liver

extract_protocol:
Fresh liver tissue samples were cut into 1 mm3 pieces and digested in HBSS (Gibco, USA) buffer containing 0.05% collagenase IV (Invitrogen, Carlsbad, USA) and 0.002% DNase I (Invitrogen, Carlsbad, USA) at 37°C with gentle agitation for 30 minutes. The dissociated cells were filtered through 70 μm sterile cell strainers. Immune cells were then separated by density gradient centrifugation with 36% Percoll medium (Sigma-Aldrich, St. Louis, USA), and residual erythrocytes were removed using a red blood cell lysate solution (Sigma, USA). The immune cells were subsequently re-suspended in phosphate-buffered saline (PBS) to create a single-cell suspension.
The single-cell suspension was loaded onto the MobiNova®-100 chip with 3' transcriptome microspheres, droplet-generating oil, and reverse transcription reagents. RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed within the droplets formed on the chip. Following this, pooled cDNA was purified and enriched through PCR amplification to construct cDNA libraries.

value: liver

value: immune cells

value: WT

value: TPPU


title: Pa03C E96A B1 TMZ 8hr

description: Library name: B1-TMZ-8hr_S7


title: TP1

description:
Library name: L01507_TM0007
MobiNova


title: H2A-P_H2AS129A_Log_As_Rep1 (Input)

description: Library name: H2A-P_H2AS129A_Log_As_Rep1_INP

value: 0.5mM As(III)


title: H2A-P_H2AS129A_Log_As_Rep1 (ChIP)

description: Library name: H2A-P_H2AS129A_Log_As_Rep1_IP


title: Pre-clinical AD Subject 7

description: Library name: Subject-16


title: Rad51_WT_Log_As_Rep2 (ChIP)

description: Library name: Rad51_WT_Log_As_Rep2_IP

value: Anty-Rad51 antibody (Invitrogen, PA5-34905)


title: H2A-P_H2AS129A_Log_K_Rep1 (Input)

description: Library name: H2A-P_H2AS129A_Log_K_Rep1_INP


title: SP6

description:
Library name: L01507_TM0006
MobiNova

value: control


title: Pa03C E96A B1 TMZ 4hr

description: Library name: B1-TMZ-4hr_S6


title: TP3

description:
Library name: L01507_TM0009
MobiNova


title: SP5

description:
Library name: L01507_TM0005
MobiNova


title: Pa03C E96A B1 untreated

description: Library name: B1-Untr_S5


title: Clinical AD Subject 5

description: Library name: Subject-14


title: 28 DPI SSD diet 6

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description:
Library name: M48
28 DPI Read Counts.xlsx

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus musculus genome (GRCm39)
DEG determined using DESeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

source_name: Intestine

extract_protocol:
RNA was isolated utilizing the miRNAeasy Mini Kit (Qiagen #217604) in accordance with the manufacturer’s protocol. Intestinal tissue samples were homogenized in Qiazol lysis reagent using a gentleMACS Dissociator (Miltenyi Biotec, Germany) and subsequently processed through an RNAeasy spin column (from Qiagen kit) with on-column DNase treatment. The RNA concentration and purity were then assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE, USA).
standard Illumina

value: Intestine

value: 28 DPI SSD diet


title: 28 DPI SSD diet 5

description:
Library name: M47
28 DPI Read Counts.xlsx


title: SP4

description:
Library name: L01507_TM0004
MobiNova


title: Pre-clinical AD Subject 6

description: Library name: Subject-15


title: 28 DPI SSD diet 3

description:
Library name: M45
28 DPI Read Counts.xlsx


title: Pre-clinical AD Subject 5

description: Library name: Subject-12


title: Pa03C Cas9 TMZ 8hr

description: Library name: Cas9-TMZ-8hr_S4


title: Control Subject 4

description: Library name: Subject-13


title: SP3

description:
Library name: L01507_TM0003
MobiNova


title: Control Subject 3

description: Library name: Subject-11


title: Pa03C Cas9 untreated

description: Library name: Cas9-Untr_S2


title: SP1

description:
Library name: L01507_TM0001
MobiNova


title: Control Subject 2

description: Library name: Subject-10


title: Pa03C Cas9 TMZ 4hr

description: Library name: Cas9-TMZ-4hr_S3


title: SP2

description:
Library name: L01507_TM0002
MobiNova


title: Pa03C E96A G8

description: Library name: E96A_G8_S17


title: GS KO CD8+ T cells, replicate 5

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description:
Library name: Sample 10
11945-EF-10

data_processing:
Read mapping performed using STAR, gene expression quantification using featureCounts, and differential expression performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with counts for each sample
Supplementary files format and content: tab-delimited text file with gene comparisons between WT and GS KO samples

source_name: CD8+ T cells

growth_protocol: CD8+ T cells were isolated from spleens of Glul floxed CD4-Cre(-) (WT) and CD4-Cre(+) (GS KO) mice and grown in RPMI 1640 supplemented to a final concentration of 0.6 mM glutamine, 10% FBS, 10 mM HEPES, 50 μM BME, and penicillin-streptomycin (100 U/ml).

extract_protocol:
mRNA was isolated using Qiagen RNeasy kit
NEBNext® Poly(A) selection kit

treatment_protocol: Cells were activated on anti-CD3 and anti-CD28 coated plates for 48 hours, then maintained on TC treated plates in RPMI supplemented with IL-2 for an additional 3 days.

value: CD8+ T cells

value: GS knockout

value: In vitro activation, day 5


title: 28 DPI Chow Diet 6

description:
Library name: M42
28 DPI Read Counts.xlsx

value: 28 DPI Chow Diet


title: 28 DPI SSD diet 4

description:
Library name: M46
28 DPI Read Counts.xlsx


title: 28 DPI SSD diet 2

description:
Library name: M44
28 DPI Read Counts.xlsx


title: GS KO CD8+ T cells, replicate 4

description:
Library name: Sample 9
11945-EF-09


title: Pa03C E96A B1

description: Library name: E96A_B1_S15

value: pancreas


title: Control Subject 1

description: Library name: Subject-9

value: Olfactory Epithelium


title: GS KO CD8+ T cells, replicate 3

description:
Library name: Sample 8
11945-EF-08


title: 28 DPI Chow Diet 5

description:
Library name: M41
28 DPI Read Counts.xlsx


title: Pa03C Cas9

description: Library name: Cas9_4_S14

value: pancreatic ductal adenocarcinoma


title: Pre-clinical AD Subject 4

description: Library name: Subject-8


title: 28 DPI SSD diet 1

description:
Library name: M43
28 DPI Read Counts.xlsx


title: 28 DPI Chow Diet 4

description:
Library name: M40
28 DPI Read Counts.xlsx


title: Pa03C E96A B4

description: Library name: E96A_B4_S16


title: ATAC_MII-TGF1-4

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description:
Library name: ATAC_Sample16
Biological replicate 4

data_processing:
Trimmomatic was used to trim sequecning adapters and low-quality reads
STAR Aligner was used to align trimmed reads
Aligned reads were annotated and quantified against the gencode comprehensive gene annotation release 38 (GRCh38.p13) using featureCounts of subread package v2.0.0
Differential expression analysis was done using DESeq2 in R
Standard Nextflow pipeline of nf-core/atacseq v1.2.1 with default parameters was used for ATAC-seq analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include quantified reads from Subread package

growth_protocol: MCF-10A and the HRAS transformed cells were growing in 3D conditions using ultra-low attachment plates. MDA-MB-231 cells (WT and KO) were grown in mono layer cultures and maintained in DMEM medium with 10% FBS.

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell miniprep system (Promega). 600 ng of total RNA was used for the construction of sequencing libraries. For ATAC-seq, Nextera Tn5 transposase was used for the tagmentation followed by chromatin purification.
Library preparation was constructed using the TruSeq stranded total RNA Gold library preparation kit with RiboZero Gold treatment and unique dual indexes according to the manufacturer’s instructions. For ATAC-seq, Nextera Tn5 transposase was used for the tagmentation step. The generation of 50 bp paired-end reads was performed using the SP flowcell on a NovaSeq 6000

treatment_protocol: TGF-beta1 was used at 2.5 ng/ml concentration for 16 hours.

value: HRAS-transformed breast epithelial

value: TGF-beta1 2.5 ng/ml

tag: batch


title: 28 DPI Chow Diet 3

description:
Library name: M39
28 DPI Read Counts.xlsx


title: Clinical AD Subject 4

description: Library name: Subject-6


title: Pre-clinical AD Subject 3

description: Library name: Subject-7


title: GS KO CD8+ T cells, replicate 1

description:
Library name: Sample 6
11945-EF-06


title: WT CD8+ T cells, replicate 5

description:
Library name: Sample 5
11945-EF-05


title: Clinical AD Subject 2

description: Library name: Subject-4


title: Clinical AD Subject 3

description: Library name: Subject-5


title: ATAC_MII-TGF1-3

description:
Library name: ATAC_Sample15
Biological replicate 3


title: ATAC_MII-TGF1-2

description:
Library name: ATAC_Sample14
Biological replicate 2


title: WT CD8+ T cells, replicate 4

description:
Library name: Sample 4
11945-EF-04


title: GS KO CD8+ T cells, replicate 2

description:
Library name: Sample 7
11945-EF-07


title: Pre-clinical AD Subject 2

description: Library name: Subject-3


title: WT CD8+ T cells, replicate 3

description:
Library name: Sample 3
11945-EF-03


title: 28 DPI SSD Diet Hp Infection 5

description:
Library name: M35
28 DPI Read Counts.xlsx

value: 28 DPI SSD Diet Hp Infection


title: Pre-clinical AD Subject 1

description: Library name: Subject-2


title: WT CD8+ T cells, replicate 2

description:
Library name: Sample 2
11945-EF-02

value: WT


title: Clinical AD Subject 1

description: Library name: Subject-1


title: 28 DPI SSD Diet Hp Infection 6

description:
Library name: M36
28 DPI Read Counts.xlsx


title: 28 DPI Chow Diet 1

description:
Library name: M37
28 DPI Read Counts.xlsx


title: WT CD8+ T cells, replicate 1

description:
Library name: Sample 1
11945-EF-01


title: 28 DPI SSD Diet Hp Infection 4

description:
Library name: M34
28 DPI Read Counts.xlsx


title: ATAC_MII-TGF1-1

description:
Library name: ATAC_Sample13
Biological replicate 1


title: ATAC_MII-Ctrl-3

description:
Library name: ATAC_Sample11
Biological replicate 3

value: Control untreated


title: 28 DPI Chow Diet 2

description:
Library name: M38
28 DPI Read Counts.xlsx


title: NM450_114

type: genomic

city: Miaoli County

first: Shih-Sheng

last: Jiang

address: 35, Keyan Road, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: The bisulfite-converted DNA was hybridized to the Illumina HumanMethylation450/EPIC/EPIC v2.0 BeadChips according to the manufacturer’s Infinium HD protocol. Hybridization was performed at 48°C for 16 hours in a humidity-controlled chamber. Following hybridization, chips were washed using Illumina-supplied buffers to remove unbound DNA prior to extension.

scan_protocol: Arrays were scanned on the Illumina iScan System using default parameters. Images were processed using Illumina GenomeStudio Methylation Module software to extract signal intensities and compute methylation beta values. Quality control was performed using internal control probes.

data_processing: For NM450 (450K), NM850 (EPIC), and NM900 (EPICv2) samples, raw intensities were background-corrected, dye-bias-equalized, and functionally normalized using the ‘preprocessFunnorm’ function in the minfi R package. CpGs on sex chromosomes, containing SNPs (MAF ≥5%), in repetitive regions, or with poor detection p-values were removed. Three processed DNA methylation datasets were generated: NM450-114 (NM450 samples), NMC-47 (combined NM850 and NM900), and NMC-161 (combined NM450, NM850, and NM900), retaining CpGs common to the platforms within each dataset (373,275 CpGs for NM450-114; 558,115 CpGs for NMC-47; 298,801 CpGs for NMC-161). For each dataset, beta values were inverse-rank transformed to a standard normal distribution and regressed on confounders including sex, age, medical operation status, batch, top genotyping PCs, and top methylation PCs. The residuals were inverse-rank transformed again to produce the final processed DNA methylation data.

label: Cy3 and Cy5

source_name: lung

label_protocol: Genomic DNA (500 ng) underwent bisulfite treatment with the EZ DNA Methylation Kit (Zymo Research). Following conversion, samples were processed according to the Illumina Infinium HD Methylation Assay protocol, including amplification, fragmentation, and hybridization steps. Labeling was incorporated during the single-base extension step.

extract_protocol: Tissue DNA was extracted from lung tissues using the QIAamp DNA Mini Kit (Qiagen Inc, USA). Bisulfite conversion of tissue DNA was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Inc, USA) according to the manufacturer’s instructions. DNA methylation of bisulfite-converted DNA was measured using the abovementioned platform, according to Illumina’s standard procedure in Genetech Biotech Co., Ltd.

value: lung

tag: age

tag: gender

value: Male

tag: smoking status

value: Non-smoking


title: ATAC_MII-Ctrl-2

description:
Library name: ATAC_Sample10
Biological replicate 2


title: ATAC_MII-Ctrl-4

description:
Library name: ATAC_Sample12
Biological replicate 4


title: H1299_R158L-TET_RNA_rep3

city: Philadelphia

first: Steven

last: McMahon

state: PA

address: 233 S 10th St

department: Biochemistry and Molecular Biology

institute: Thomas Jefferson University

description: Library name: SM114_1299_R158L-TET_RNA_rep3

data_processing:
RNA-seq data were processed by removed adapters using TrimGalore!. Reads mapping to each gene were quanitfied using kallisto. Differential gene expression was determined using DESeq2 in R.
Assembly: hg19 (Homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos Dual Index Primers Set 1 & 2 for Illumina  according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library. Libraries were sequenced on Illumina NextSeq2000, producing 150 single-end reads

value: epithelial carcinoma

value: p53-null parental with transfected TET-inducible R158L p53

value: TET


title: 28 DPI SSD Diet Hp Infection 3

description:
Library name: M33
28 DPI Read Counts.xlsx

value: Intestine


title: H1299_R158L-TET-CPT_RNA_rep3

description: Library name: SM115_1299_R158L-TET-CPT_RNA_rep3


title: NM450_113

value: Female


title: 28 DPI SSD Diet Hp Infection 1

description:
Library name: M31
28 DPI Read Counts.xlsx


title: ATAC_MI-TGF1-4

description:
Library name: ATAC_Sample8
Biological replicate 4

value: Immortalized breast epithelial


title: NM450_112


title: 28 DPI  Chow diet Hp infection 5

description:
Library name: M30
28 DPI Read Counts.xlsx

value: 28 DPI  Chow diet Hp infection


title: H1299_R158L-TET-CPT_RNA_rep2

description: Library name: SM113_1299_R158L-TET-CPT_RNA_rep2


title: H1299_R158L-TET_RNA_rep2

description: Library name: SM112_1299_R158L-TET_RNA_rep2


title: ATAC_MII-Ctrl-1

description:
Library name: ATAC_Sample9
Biological replicate 1


title: ATAC_MI-TGF1-3

description:
Library name: ATAC_Sample7
Biological replicate 3


title: ATAC_MI-TGF1-2

description:
Library name: ATAC_Sample6
Biological replicate 2


title: 28 DPI  Chow diet Hp infection 4

description:
Library name: M29
28 DPI Read Counts.xlsx


title: 28 DPI  Chow diet Hp infection 3

description:
Library name: M28
28 DPI Read Counts.xlsx


title: H1299_R158L-TET-CPT_RNA_rep1

description: Library name: SM111_1299_R158L-TET-CPT_RNA_rep1


title: NM450_111


title: 28 DPI  Chow diet Hp infection 2

description:
Library name: M27
28 DPI Read Counts.xlsx


title: H1299_R158L-TET_RNA_rep1

description: Library name: SM110_1299_R158L-TET_RNA_rep1


title: ATAC_MI-TGF1-1

description:
Library name: ATAC_Sample5
Biological replicate 1


title: NM450_110


title: ATAC_MI-Ctrl-3

description:
Library name: ATAC_Sample3
Biological replicate 3


title: 28 DPI  Chow diet Hp infection 1

description:
Library name: M25
28 DPI Read Counts.xlsx


title: 28 DPI SSD diet Antibiotics 6

description:
Library name: M24
28 DPI Read Counts.xlsx

value: 28 DPI SSD diet Antibiotics


title: H1299_V157F-TET-CPT_RNA_rep2

description: Library name: SM107_1299_V157F-TET-CPT_RNA_rep2

value: p53-null parental with transfected TET-inducible V157F p53


title: H1299_V157F-TET-CPT_RNA_rep3

description: Library name: SM109_1299_V157F-TET-CPT_RNA_rep3


title: 28 DPI SSD diet Antibiotics 5

description:
Library name: M23
28 DPI Read Counts.xlsx


title: ATAC_MI-Ctrl-4

description:
Library name: ATAC_Sample4
Biological replicate 4


title: NM450_106


title: ATAC_MI-Ctrl-2

description:
Library name: ATAC_Sample2
Biological replicate 2


title: H1299_V157F-TET_RNA_rep3

description: Library name: SM108_1299_V157F-TET_RNA_rep3


title: H1299_V157F-TET_RNA_rep2

description: Library name: SM106_1299_V157F-TET_RNA_rep2


title: NM450_109


title: 28 DPI SSD diet Antibiotics 4

description:
Library name: M22
28 DPI Read Counts.xlsx


title: MDA-MB-231-WT-3

description:
Library name: RNA_Sample24
Biological replicate 3

value: Triple-negative breast cancer


title: H1299_V157F-TET-CPT_RNA_rep1

description: Library name: SM105_1299_V157F-TET-CPT_RNA_rep1


title: 28 DPI SSD diet Antibiotics 3

description:
Library name: M21
28 DPI Read Counts.xlsx


title: NM450_108


title: NM450_104


title: ATAC_MI-Ctrl-1

description:
Library name: ATAC_Sample1
Biological replicate 1


title: NM450_105


title: MDA-MB-231-WT-2

description:
Library name: RNA_Sample23
Biological replicate 2


title: H1299_V157F-TET_RNA_rep1

description: Library name: SM104_1299_V157F-TET_RNA_rep1


title: NM450_107


title: 28 DPI SSD diet Antibiotics 2

description:
Library name: M20
28 DPI Read Counts.xlsx


title: NM450_103


title: NM450_102


title: MDA-MB-231-WT-1

description:
Library name: RNA_Sample22
Biological replicate 1


title: H1299_WT-TET-CPT_RNA_rep3

description: Library name: SM100_1299_WT-TET-CPT_RNA_rep3

value: p53-null parental with transfected TET-inducible WT p53


title: 28 DPI SSD diet Antibiotics 1

description:
Library name: M19
28 DPI Read Counts.xlsx


title: SLUG-KO-3

description:
Library name: RNA_Sample21
Biological replicate 3

value: SLUG Knockout


title: 28 DPI Chow Diet Antibiotics 6

description:
Library name: M18
28 DPI Read Counts.xlsx

value: 28 DPI Chow Diet Antibiotics


title: NM450_101


title: H1299_WT-TET-CPT_RNA_rep2

description: Library name: SM96_1299_WT-TET-CPT_RNA_rep2


title: SLUG-KO-2

description:
Library name: RNA_Sample20
Biological replicate 2


title: H1299_WT-TET-CPT_RNA_rep1

description: Library name: SM92_1299_WT-TET-CPT_RNA_rep1


title: 28 DPI Chow Diet Antibiotics 5

description:
Library name: M17
28 DPI Read Counts.xlsx


title: NM450_100


title: H1299_WT-TET_RNA_rep2

description: Library name: SM84_1299_WT-TET_RNA_rep2


title: 28 DPI Chow Diet Antibiotics 4

description:
Library name: M16
28 DPI Read Counts.xlsx


title: SLUG-KO-1

description:
Library name: RNA_Sample19
Biological replicate 1


title: NM450_099


title: 28 DPI Chow Diet Antibiotics 3

description:
Library name: M15
28 DPI Read Counts.xlsx


title: 28 DPI Chow Diet Antibiotics 2

description:
Library name: M14
28 DPI Read Counts.xlsx


title: H1299_WT-TET_RNA_rep3

description: Library name: SM88_1299_WT-TET_RNA_rep3


title: H1299_WT-TET_RNA_rep1

description: Library name: SM80_1299_WT-TET_RNA_rep1


title: MII-TGFb-3

description:
Library name: RNA_Sample18
Biological replicate 3

value: HRAS-transformed breast epithelial

value: WT

value: TGF-beta1 2.5 ng/ml


title: MII-TGFb-1

description:
Library name: RNA_Sample16
Biological replicate 1


title: MII-TGFb-2

description:
Library name: RNA_Sample17
Biological replicate 2


title: NM450_098

value: lung

value: Male

value: Non-smoking


title: NM450_096


title: 28 DPI SSD Diet Hp Infection Antibiotics 6

description:
Library name: M12
28 DPI Read Counts.xlsx


title: MII-Ctrl-3

description:
Library name: RNA_Sample15
Biological replicate 3

value: Control untreated


title: H1299_R158L_TET_CPT_Rep2_p53_ChIP

description: Library name: SM306_R158L_TET_CPT_Rep2_p53_ChIP

data_processing:
ChIP-seq data were processed by removing adapters using TrimGalore! Reads were aligned to hg19 using BWA-mem. Aligned reads were filtered with MAPQ > 10 and PCR duplicates removed. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (Homo sapiens)
Supplementary files format and content: bigwig files for ChIP-seq data
Supplementary files format and content: narrowpeak files for ChIP-seq data

extract_protocol:
Cells were harvested and crosslinked with 1% formaldehyde, quenched with 125mM glycine, and washed twice with 1X PBS. The fixed cell pellet was lysed in ChIP lysis buffer 1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% Igepal CA-630; 0.25% Triton X-100), rocked for 10 minutes, and then spun down at 2000xRCF for 5 minutes. The supernatant was aspirated, and the pellet was lysed with ChIP lysis buffer 2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA), rocked for 5 minutes, and then spun down at 2000xRCF for 5 minutes. The supernatant was aspirated, and the nuclei pellet was lysed with ChIP lysis buffer 3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine).
Barcoded ChIP-seq libraries were produced using NEBNext UltraII DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 2000, producing 150bp single-end reads

value: epithelial carcinoma

value: p53-null parental with transfected TET-inducible R158L p53


title: H1299_R158L_TET_Rep1_p53_ChIP

description: Library name: SM303_R158L_TET_Rep1_p53_ChIP

value: TET


title: 28 DPI Chow Diet Antibiotics 1

description:
Library name: M13
28 DPI Read Counts.xlsx

value: Intestine


title: NM450_095

value: Female


title: NM450_094


title: MII-Ctrl-2

description:
Library name: RNA_Sample14
Biological replicate 2


title: H1299_R158L_TET_input

description: Library name: SM307_R158L_TET_input


title: MII-Ctrl-1

description:
Library name: RNA_Sample13
Biological replicate 1


title: NM450_097


title: 28 DPI SSD Diet Hp Infection Antibiotics 5

description:
Library name: M11
28 DPI Read Counts.xlsx


title: H1299_V157_TET_Input

description: Library name: SM302_V157_TET_Input

value: p53-null parental with transfected TET-inducible V157F p53


title: H1299_V157F_TET_CPT_Rep2_p53_ChIP

description: Library name: SM301_V157F_TET_CPT_Rep2_p53_ChIP


title: NM450_092


title: 28 DPI SSD Diet Hp Infection Antibiotics 4

description:
Library name: M10
28 DPI Read Counts.xlsx


title: 28 DPI SSD Diet Hp Infection Antibiotics 3

description:
Library name: M9
28 DPI Read Counts.xlsx


title: NM450_093


title: NM450_091


title: MI-TGFb-3

description:
Library name: RNA_Sample12
Biological replicate 3

value: Immortalized breast epithelial


title: 28 DPI SSD Diet Hp Infection Antibiotics 2

description:
Library name: M8
28 DPI Read Counts.xlsx


title: MI-TGFb-2

description:
Library name: RNA_Sample11
Biological replicate 2


title: NM450_090


title: H1299_V157_TET_Rep1_p53_ChIP

description: Library name: SM298_V157_TET_Rep1_p53_ChIP


title: MI-TGFb-1

description:
Library name: RNA_Sample10
Biological replicate 1


title: NM450_089


title: 28 DPI SSD Diet Hp Infection Antibiotics 1

description:
Library name: M7
28 DPI Read Counts.xlsx


title: H1299_V157_TET_CPT_Rep1_p53_ChIP

description: Library name: SM299_V157_TET_CPT_Rep1_p53_ChIP


title: NM450_088


title: MI-Ctrl-2

description:
Library name: RNA_Sample8
Biological replicate 2


title: MI-Ctrl-3

description:
Library name: RNA_Sample9
Biological replicate 3


title: H1299_WT_TET_input_p53_ChIP

description: Library name: SM297_WT_TET_input_p53_ChIP

value: p53-null parental with transfected TET-inducible WT p53


title: 28 DPI  Chow diet Hp infection Antibiotics 6

description:
Library name: M6
28 DPI Read Counts.xlsx


title: NM450_087


title: H1299_WT_TET_CPT_Rep2_p53_ChIP

description: Library name: SM296_WT_TET_CPT_Rep2_p53_ChIP


title: MI-Ctrl-1

description:
Library name: RNA_Sample7
Biological replicate 1


title: 28 DPI  Chow diet Hp infection Antibiotics 4

description:
Library name: M4
28 DPI Read Counts.xlsx


title: 28 DPI  Chow diet Hp infection Antibiotics 5

description:
Library name: M5
28 DPI Read Counts.xlsx


title: MDA-MB-231_SMAD_KD-3

description:
Library name: RNA_Sample6
Biological replicate 3

value: Triple-negative breast cancer

value: SMAD2/3/4 siRNAs


title: 28 DPI  Chow diet Hp infection Antibiotics 3

description:
Library name: M3
28 DPI Read Counts.xlsx


title: H1299_WT_TET_CPT_Rep1_p53_ChIP

description: Library name: SM294_WT_TET_CPT_Rep1_p53_ChIP


title: NM450_086


title: H1299_WT_TET_Rep1_p53_ChIP

description: Library name: SM293_WT_TET_Rep1_p53_ChIP


title: NM450_085


title: 28 DPI  Chow diet Hp infection Antibiotics 2

description:
Library name: M2
28 DPI Read Counts.xlsx


title: MDA-MB-231_SMAD_KD-2

description:
Library name: RNA_Sample5
Biological replicate 2


title: H661_input_p53_ChIP

description: Library name: SM292_H661_input_p53_ChIP

value: R158L endogenous p53 mutant

value: untreated


title: 28 DPI  Chow diet Hp infection Antibiotics 1

description:
Library name: M1
28 DPI Read Counts.xlsx


title: MDA-MB-231_SMAD_KD-1

description:
Library name: RNA_Sample4
Biological replicate 1

value: WT


title: MDA-MB-231_Csi-3

description:
Library name: RNA_Sample3
Biological replicate 3

value: Control scramble siRNA


title: H661_CPT_Rep2_p53_ChIP

description: Library name: SM291_H661_CPT_Rep2_p53_ChIP

value: lung

value: CPT


title: 14 DPI SSD diet 6

description:
Library name: E36
14 DPI Read Counts.xlsx

value: 14 DPI SSD diet


title: H661_UT_Rep2_p53_ChIP

description: Library name: SM290_H661_UT_Rep2_p53_ChIP

value: epithelial carcinoma


title: NM450_084

value: Non-smoking


title: NM450_082


title: MDA-MB-231_Csi-2

description:
Library name: RNA_Sample2
Biological replicate 2


title: NM450_080


title: H661_UT_Rep1_p53_ChIP

description: Library name: SM288_H661_UT_Rep1_p53_ChIP


title: NM450_081

value: Male


title: 14 DPI SSD diet 4

description:
Library name: E34
14 DPI Read Counts.xlsx

value: Intestine


title: H661_CPT_Rep1_p53_ChIP

description: Library name: SM289_H661_CPT_Rep1_p53_ChIP


title: MDA-MB-231_Csi-1

description:
Library name: RNA_Sample1
Biological replicate 1


title: 14 DPI SSD diet 3

description:
Library name: E33
14 DPI Read Counts.xlsx


title: H2087_input_p53_ChIP

description: Library name: SM287_H2087_input_p53_ChIP

value: epithelial-like adenocarcinoma

value: V157F endogenous p53 mutant


title: NM450_083


title: 14 DPI SSD diet 5

description:
Library name: E35
14 DPI Read Counts.xlsx


title: NM450_079

value: Female


title: 14 DPI SSD diet 1

description:
Library name: E31
14 DPI Read Counts.xlsx


title: 14 DPI SSD diet 2

description:
Library name: E32
14 DPI Read Counts.xlsx


title: Ec-eMSCs Exos-1

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

data_processing:
The sequencing data was processed using Cutadapt (version 2.7) to remove sequencing adapters, low-quality reads, short reads with more N, and reads shorter than 16 bp.
Subsequently, perl5 (version 26) was used to process reads with UMIs shorter than 12 bp and reads without UMIs, and to identify UMIs.
The bowtie software (version 1.3.0) was then employed to compare the reads against the miRBase database.
Finally, small RNA quantification was performed by comparing the mapped reads to the miRBase.
The R package edgeR is used to calculate the expression difference based on grouping information from the obtained expression UMI counts matrix, aiming to identify miRNAs that are significantly differentially expressed (either being up-regulated or down-regulated).
Assembly: miRBase v22
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: adenomyotic lesion

growth_protocol: Adenomyotic lesions and normal endometrial tissues were collected from patients with adenomyosis (AM) or leiomyomas undergoing hysterectomy at Jiangsu Province Hospital with Integration of Chinese and Western Medicine (Nanjing, China) for the primary culture of endometrial mesenchymal stem cells (eMSCs). Ectopic eMSCs (Ec-eMSCs) were isolated from ectopic lesions of AM patients, while normal eMSCs (N-eMSCs) were obtained from the eutopic endometrium of controls. Both Ec-eMSCs and N-eMSCs were cultured in DMEM/F12 (1:1) supplemented with 10% mesenchymal stem cell-qualified FBS (Viva Cell, China) and 1% Pen-Strep, then incubated in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
When eMSCs reached approximately 70% confluence, the medium was replaced with DMEM/F12 containing 10% exosome depleted FBS (Exo-FBS) (System Biosciences, USA) for 48 h. The cell culture supernatants of eMSCs were collected for microRNA (miRNA) sequencing (miRNA-seq). Exosomes derived from eMSCs (eMSCs-Exos) were isolated using the exoEasy Maxi Kit (Qiagen, USA), and their miRNA content was extracted using the miRNeasy Micro Kit (Qiagen, USA). 4 ng of total RNA was used for construction of sequencing libraries.
MicroRNA libraries for miRNA-seq were prepared using the QIAseq miRNA Library Kit (Qiagen, Germany) following the manufacturer’s standard protocol.

value: adenomyotic lesion

value: endometrial mesenchymal stem cells


title: NM450_078


title: Ec-eMSCs Exos-2


title: 14 DPI SSD + I3C diet Hp infection 6

description:
Library name: D30
14 DPI Read Counts.xlsx

value: 14 DPI SSD + I3C diet Hp infection


title: Ec-eMSCs Exos-3


title: N-eMSCs Exos-3

source_name: normal eutopic endometrium

value: normal eutopic endometrium


title: H2087_UT_Rep2_p53_ChIP

description: Library name: SM285_H2087_UT_Rep2_p53_ChIP

value: untreated


title: H2087_CPT_Rep2_p53_ChIP

description: Library name: SM286_H2087_CPT_Rep2_p53_ChIP


title: H2087_CPT_Rep1_p53_ChIP

description: Library name: SM284_H2087_CPT_Rep1_p53_ChIP


title: NM450_077


title: N-eMSCs Exos-1


title: 14 DPI SSD + I3C diet Hp infection 4

description:
Library name: D28
14 DPI Read Counts.xlsx


title: NM450_074


title: H460_input_p53_ChIP

description: Library name: SM282_H460_input_p53_ChIP

value: WT p53


title: 14 DPI SSD + I3C diet Hp infection 5

description:
Library name: D29
14 DPI Read Counts.xlsx


title: N-eMSCs Exos-2


title: H460_UT_Rep2_p53_ChIP

description: Library name: SM280_H460_UT_Rep2_p53_ChIP


title: 14 DPI SSD + I3C diet Hp infection 2

description:
Library name: D26
14 DPI Read Counts.xlsx


title: NM450_076


title: H2087_UT_Rep1_p53_ChIP

description: Library name: SM283_H2087_UT_Rep1_p53_ChIP


title: acaA-_00hr : replicate 1, 2, 3, 4

city: Ljubljana

first: Lena

last: Trnovec

address: Vecna pot 113

department: Faculty of Computer and Information Science

country: Slovenia

institute: University of Ljubljana

description:
Library name: Sample 7
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed using the Cell Ranger Count software v8.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cells were embedded using the four-layer Universal Cell Embedding transformer model, generating 1,280-dimensional representations through zero-shot embedding.
Quality control filtering and cell embedding were performed using a robust median absolute deviation (MAD)-based approach combined with Universal Cell Embedding methodology for dimensional reduction and clustering. The pipeline calculated library size, gene detection count, top 20 transcript proportion, and mitochondrial fraction for each cell. Cells were flagged as outliers if metrics deviated more than five MAD from the median, with mitochondrial content using three MAD or 20% thresholds. These were projected using UMAP and clustered with Leiden algorithm, with outliers and low-quality clusters removed from downstream analysis. AX4 cells were tagged with act15-GFP, mCerulean, and mCherry markers, while acaA⁻ cells included an additional mNeonGreen marker. Raw expression values were log-transformed with zero values excluded from analysis. For each fluorescent marker, expression intensity distributions were estimated using Gaussian kernel density estimation to identify peaks, with the first peak serving as the signal-background threshold, or the 99th percentile when peaks were undetectable. Thresholds were normalized by subtracting minimum values. Each cell received tag-specific scores calculated as log-expression minus the threshold shift, with assignment to the highest positive-scoring tag or "Unassigned" status for cells lacking positive scores.
Assembly: D. discoideum chromosomal DNA sequences—chromosomes 1 through 6, mitochondrial DNA (M), and floating contigs—were obtained from DictyBase (created: 2009-05-13 13:53). The chromosomal and mitochondrial DNA sequences correspond to the NCBI assembly “dicty_2.7.” Specific genomic regions were masked due to duplication: [3,016,085–3,768,655] on chromosome 2, [64,985–72,996] on chromosome BF, and [42,801–78,150] on chromosome R.  Additionally, four fluorescent protein genes were added as an artificial extra chromosome.
Supplementary files format and content: Filtered HDF5 feature-barcode matrices (.h5) from Cell Ranger analysis containing quality-filtered gene expression counts, cell barcodes, and gene identifiers compatible with 10x Genomics workflows
Supplementary files format and content: AnnData HDF5 files (.h5ad) containing  single-cell RNA-seq data with raw counts, cell and gene metadata, and embedding vectors following Universal Cell Embedding analysis.
Supplementary files format and content: AnnData HDF5 files (.h5ad) with filtered cells separated and annotated by assigned fluorescent protein tags (mCherry, mCerulean, act15-GFP, mNeonGreen) used to distinguish biological replicates.

organism: Dictyostelium discoideum

source_name: acaA-

growth_protocol: All strains were cultured in HL5 medium supplemented with the required antibiotics at 22°C with shaking.

extract_protocol:
Single-cell suspensions were immediately loaded into the 10x Genomics Chromium X system and processed according to the manufacturer’s recommended protocol.
Libraries were prepared using the Chromium Single Cell Gene Expression 3' v3.1 or v4 kits (10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded onto a Chromium X instrument (10x Genomics) to generate Gel Beads-in-Emulsions (GEMs). Within each GEM, full-length cDNA was synthesized, incorporating an Illumina R1 primer sequence, a cell-specific barcode, and a Unique Molecular Identifier (UMI). Following GEM disruption, cDNA from individual cells was pooled, purified using Dynabeads MyOne Silane Beads (Thermo Fisher Scientific), and amplified by PCR. The amplified products were then fragmented to optimal sizes, followed by end-repair, A-tailing, and adaptor ligation to add the Illumina R2 primer sequence. Final libraries were generated through a second round of amplification, during which paired-end constructs with P5 and P7 sequences were added.

treatment_protocol: To initiate development, 2.8 × 10⁷ cells from each fluorescently tagged AX4 and acaA⁻ strain were harvested during exponential growth. For the acaA⁻ PkaCoe strain, 8.4 × 10⁷ to 1.0 × 10⁸ cells were used. Each strain was developed separately on membrane filters as pure populations. Developing cells were then collected and dissociated into single-cell suspensions using KK2 buffer containing 20 mM EDTA. At each time point for AX4 and acaA⁻, equal numbers of cells from distinct tagged strains were pooled, washed with KK2, and immediately processed for single-cell RNA sequencing.

value: acaA-

tag: strain

tag: genetic modification_(replicate)

value: replicate 1, 2, 3, and 4

tag: developmental time

value: 0 hr

value: on Black filter


title: AX4_20hr : replicate 1, 2, 3

description:
Library name: Sample 6
10x Genomics

value: WT

value: replicate 1, 2, and 3

value: 20 hr


title: H460_CPT_Rep1_p53_ChIP

description: Library name: SM279_H460_CPT_Rep1_p53_ChIP

value: lung

value: epithelial carcinoma

value: CPT


title: AX4_16hr : replicate 1, 2, 3

description:
Library name: Sample 5
10x Genomics

value: 16 hr


title: 14 DPI SSD + I3C diet Hp infection 1

description:
Library name: D25
14 DPI Read Counts.xlsx

value: Intestine


title: NM450_072

value: Female

value: Non-smoking


title: CP18_5uM_USP18_O_E replicate 3

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

description: Library name: 54_CP18_5uM_USP18_O_E

data_processing:
The instrument run was processed by using Real Time Analysis software (RTA 3.10,30). The Illumina bcl2fastq2.20 was used to demultiplex and convert binary base calls and quality scores to fastq format.
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome hg38 and gencode v30
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: hg38
Supplementary files format and content: gene count matrix in csv format

extract_protocol:
For the mRNA library preparation, we used the Illumina TruSeq stranded mRNA ligation kit. We use between 100ng to 1ug of total RNA as the input to an mRNA capture with oligo-dT coated magnetic beads. The mRNA is fragmented, and then a random-primed cDNA synthesis is performed. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a sequencing ready library
Illumina TruSeq stranded mRNA ligation kit

value: lung cancer cell

tag: sample group


title: 14 DPI SSD + I3C diet Hp infection 3

description:
Library name: D27
14 DPI Read Counts.xlsx

value: 14 DPI SSD + I3C diet Hp infection


title: 14 DPI SSD + I3C diet 6

description:
Library name: C24
14 DPI Read Counts.xlsx

value: 14 DPI SSD + I3C diet


title: 14 DPI SSD + I3C diet 5

description:
Library name: C23
14 DPI Read Counts.xlsx


title: NM450_070


title: NM450_075


title: AX4_04hr : replicate 1, 2, 3

description:
Library name: Sample 2
10x Genomics

value: 4 hr


title: AX4_08hr : replicate 1, 2, 3

description:
Library name: Sample 3
10x Genomics

value: 8 hr


title: 14 DPI SSD + I3C diet 4

description:
Library name: C22
14 DPI Read Counts.xlsx


title: NM450_073


title: AX4_12hr : replicate 1, 2, 3

description:
Library name: Sample 4
10x Genomics

value: 12 hr


title: NM450_071


title: CP18_5uM_E_V replicate 3

description: Library name: 51_CP18_5uM_E_V


title: CP18_5uM_USP18_O_E replicate 1

description: Library name: 52_CP18_5uM_USP18_O_E


title: H460_UT_Rep1_p53_ChIP

description: Library name: SM278_H460_UT_Rep1_p53_ChIP

value: WT p53

value: untreated


title: 14 DPI SSD + I3C diet 2

description:
Library name: C20
14 DPI Read Counts.xlsx


title: NM450_067


title: 14 DPI SSD + I3C diet 1

description:
Library name: C19
14 DPI Read Counts.xlsx


title: Hs578T_KO8

city: Badalona

first: David

last: Olivares

state: Select One

address: Ctra de Can Ruti, Camí de les Escoles s/n 08916 Badalona, Barcelona

country: Spain

institute: Josep Carreras Research Instiute

description: Library name: Sample 12

data_processing:
Raw sequencing data were preprocessed using SOAPnuke software (BGI Genomics Co.). This involved removing reads with adaptor contamination, more than 5% N content, and low-quality reads (where more than 20% of the bases had a quality score below 15). The resulting "Clean Reads" were saved in FASTQ format. RNA-seq data were analyzed using the Galaxy workbench platform [33], adhering to specific recommendations [34]. Quality control and trimming of the reads were performed using MultiQC [35] and Cutadpt [36]. The reads were then mapped to the reference genome (Hg38, human genome build 38) using STAR [37]. From the mapped sequences, the number of reads per annotated gene was counted using featureCounts [38]. Subsequently, DESeq2 [39] was used to normalize the read counts and identify differentially expressed genes. Functional enrichment analysis of differentially expressed genes was performed using GSEA [40].
Assembly: Hg38, human genome build 38
Supplementary files format and content: Raw counts from featureCounts.

source_name: Breast

growth_protocol: TNBC cell lines HS578T (#ACC781, DSMZ), BT-549 (#HTB-122, ATCC), MDA-MB-231 (#CRM-HTB-26, ATCC), and HCC70 (#CRL-2315, ATCC), along with HR-positive cell lines MCF7 (#ACC115, DSMZ) and T-47D (DSMZ, #ACC739), were cultured in DMEM/F-12 with GlutaMAXTM Supplement medium (#31331093, GibcoTM) supplemented with 10% FBS, at 37ºC and 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using the NZY miRNA Isolation & RNA Clean-up Kit (MB13402, NZYtech) following the manufacturer’s protocol. The purity and concentration of the RNA from each sample were assessed using an Agilent TapeStation with an RNA ScreenTape Analysis Kit.
mRNA enrichment was subsequently performed using polyA-tail-connected magnetic beads and oligos. This was followed by double-stranded DNA synthesis and polymerase chain reaction (PCR) amplification using specific primers. The PCR products were subjected to thermal denaturation to produce single-stranded DNA, which was cyclized into a circular DNA library using bridge primers. Sequencing was conducted using the DNBSEQ platform (BGI Genomics Co.).

treatment_protocol: For CRISPR/Cas9 knockout transfection, Hs578T and BT-549 cells were co-transfected with a ribonucleoprotein (RNP) complex comprising Cas9 and guide RNA (gRNA), according to the manufacturer’s instructions (CMAX00015, InvitrogenTM). crRNA and tracrRNA (#1072534, IDT) were mixed at equimolar concentrations, heated at 95 °C for 5 min, and allowed to cool at room temperature. To assemble the RNP complex, Cas9-GFP enzyme (#10008161, IDT) was prepared at 1 μM in Opti-MEM™ Reduced Serum Medium (#31985047, Gibco™). Each gRNA was then combined with the Cas9-GFP in Cas9 PLUS™ Reagent and Opti-MEM. The RNP complex was subsequently mixed with CRISPRMAX™ transfection reagent at room temperature for 20 min. After 24 h at 37 °C, transfected cells were plated in 96-well dishes for cellular subcloning.

value: Breast

value: Breast Cancer


title: CP18_5uM_E_V replicate 1

description: Library name: 49_CP18_5uM_E_V

value: lung


title: CP18_5uM_USP18_O_E replicate 2

description: Library name: 53_CP18_5uM_USP18_O_E


title: NM450_068


title: 14 DPI SSD + I3C diet 3

description:
Library name: C21
14 DPI Read Counts.xlsx


title: NM450_065


title: AX4_00hr : replicate 1, 2, 3

description:
Library name: Sample 1
10x Genomics

value: WT

value: replicate 1, 2, and 3

value: 0 hr

value: on Black filter


title: Hs578T_KO7

description: Library name: Sample 11


title: NM450_066

value: Female


title: CP18_2_5uM_USP18_O_E replicate 3

description: Library name: 48_CP18_2_5uM_USP18_O_E


title: CP18_5uM_E_V replicate 2

description: Library name: 50_CP18_5uM_E_V


title: NM450_064

value: Non-smoking


title: NM450_069

value: Male


title: Hs578T_KO3

description: Library name: Sample 10


title: 14 DPI  Chow diet Hp infection 5

description:
Library name: B17
14 DPI Read Counts.xlsx

value: Intestine

value: 14 DPI  Chow diet Hp infection


title: CP18_2_5uM_USP18_O_E replicate 2

description: Library name: 47_CP18_2_5uM_USP18_O_E

value: lung cancer cell


title: 14 DPI  Chow diet Hp infection 6

description:
Library name: B18
14 DPI Read Counts.xlsx


title: NM450_063


title: Hs578T_CT5

description: Library name: Sample 9

value: Wildtype


title: Hs578T_CT4

description: Library name: Sample 8


title: 14 DPI  Chow diet Hp infection 4

description:
Library name: B16
14 DPI Read Counts.xlsx


title: 14 DPI  Chow diet Hp infection 3

description:
Library name: B15
14 DPI Read Counts.xlsx


title: CP18_2_5uM_USP18_O_E replicate 1

description: Library name: 46_CP18_2_5uM_USP18_O_E


title: CP18_2_5uM_E_V replicate 3

description: Library name: 45_CP18_2_5uM_E_V


title: Hs578T_CT3

description: Library name: Sample 7


title: NM450_062


title: CP18_2_5uM_E_V replicate 2

description: Library name: 44_CP18_2_5uM_E_V


title: BT549_KO11

description: Library name: Sample 6


title: NM450_061


title: 14 DPI  Chow diet Hp infection 2

description:
Library name: B14
14 DPI Read Counts.xlsx


title: BT549_KO8

description: Library name: Sample 5


title: CP18_2_5uM_E_V replicate 1

description: Library name: 43_CP18_2_5uM_E_V


title: NM450_060


title: 14 DPI  Chow diet Hp infection 1

description:
Library name: B13
14 DPI Read Counts.xlsx


title: BT549_KO3

description: Library name: Sample 4


title: 14 DPI Chow Diet 6

description:
Library name: A12
14 DPI Read Counts.xlsx

value: 14 DPI Chow Diet


title: BT549_CT4

description: Library name: Sample 3


title: CP18_1uM_USP18_O_E replicate 3

description: Library name: 42_CP18_1uM_USP18_O_E


title: CP18_1uM_USP18_O_E replicate 2

description: Library name: 41_CP18_1uM_USP18_O_E


title: NM450_059


title: NM450_058


title: 14 DPI Chow Diet 4

description:
Library name: A10
14 DPI Read Counts.xlsx


title: 14 DPI Chow Diet 5

description:
Library name: A11
14 DPI Read Counts.xlsx


title: BT549_CT3

description: Library name: Sample 2


title: 14 DPI Chow Diet 3

description:
Library name: A9
14 DPI Read Counts.xlsx


title: CP18_1uM_USP18_O_E replicate 1

description: Library name: 40_CP18_1uM_USP18_O_E


title: BT549_CT2

description: Library name: Sample 1


title: NM450_056


title: NM450_055


title: NM450_057


title: NM450_054


title: CP18_1uM_E_V replicate 1

description: Library name: 37_CP18_1uM_E_V


title: CP18_1uM_E_V replicate 2

description: Library name: 38_CP18_1uM_E_V


title: 14 DPI Chow Diet 2

description:
Library name: A8
14 DPI Read Counts.xlsx


title: 14 DPI Chow Diet 1

description:
Library name: A7
14 DPI Read Counts.xlsx


title: HCT116 E2F1 CRISPR cells, 6h timepoint, biological replicate 2

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
RNAseq raw data was processed with fastp software to remove sequencing adaptors and low quality bases.
Processed reads were aligned with human reference genome hg19 using the STAR package (v.020201) with -quatMode Genecounts option
Differential expression analysis was performed with DESeq2 R package.  The aligned data was also used for alternative splicing analysis with rMATS program (v4.0.2).
Alternatively, the cell synchronised RNA-seq data was analysed using the Galaxy web platform at the public server at usegalaxy.org. Raw data was processed with Cutadapt (Galaxy version 4.8) before aligning with human reference genome hg38 using RNA STAR (Galaxy version 2.7.11a) with per gene read counts option selected.
Differential gene expression for cell synchronised experiments was performed with DESeq2 (Galaxy version 2.11.40.8), whilst alternative splicing analysis was performed with rMATS.
Assembly: hg19 or hg38
Supplementary files format and content: tab-delimited files include raw counts for each sample.

growth_protocol: HCT116 and MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antiniotics in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was extracted using TRIzol, as per the manufacturer's instructions
RNA from MCF7 cells was subsequently enriched using the NEBNext Poly(A) mRNA magnetic isolation module as per the manufacturer's instructions. cDNA libraries were made using the NEBNext ultra directional RNA library prep kit for Illumina, as per the manufacturer's instructions. RNA from HCT116 cells was used to prepare libraries by BGI Genomics.  Briefly, mRNAs were isolated using oligo(dT)-based mRNA enrichment.  mRNA was fragmented and reverse transcribed with random primer, prior to second strand synthesis with dUTP, end repair and 3' A-tailing. This was followed by adaptor ligation and digestion of U-labelled second strand template with UDG, prior to PCR amplification. Library quality control was performed before circularisation and amplification to make DNA nanoballs.

treatment_protocol: HCT116 WT and DP1 Cr cells were grown untreated in culture. MCF7 WT and pRb Cr cells were treated with 5uM PRMT5 inhibitor (T1-44) for 72h, or with DMSO. HCT116 WT and E2F1 Cr cells were synchronised at G1/S by double thymidine block (2mM thymidine for 18h, followed by 10h release, followed by 2mM thymidine for 15h), and then released for either 0 hours (G1/S) or 6h (G2/M).

value: colorectal carcinoma

value: E2F1 KO

value: double thymidine block, 6h release


title: 14 DPI SSD Diet Hp Infection 6

description:
Library name: F6
14 DPI Read Counts.xlsx

value: 14 DPI SSD Diet Hp Infection


title: NM450_052

value: lung


title: CP18_1uM_E_V replicate 3

description: Library name: 39_CP18_1uM_E_V


title: CP14_5uM_USP18_O_E replicate 3

description: Library name: 36_CP14_5uM_USP18_O_E


title: CP14_5uM_USP18_O_E replicate 2

description: Library name: 35_CP14_5uM_USP18_O_E


title: NM450_053


title: CP14_5uM_USP18_O_E replicate 1

description: Library name: 34_CP14_5uM_USP18_O_E


title: HCT116 E2F1 CRISPR cells, 0h timepoint, biological replicate 3

value: double thymidine block, 0h release


title: NM450_051


title: 14 DPI SSD Diet Hp Infection 4

description:
Library name: F4
14 DPI Read Counts.xlsx


title: HCT116 E2F1 CRISPR cells, 0h timepoint, biological replicate 4


title: HCT116 E2F1 CRISPR cells, 6h timepoint, biological replicate 4


title: 14 DPI SSD Diet Hp Infection 5

description:
Library name: F5
14 DPI Read Counts.xlsx


title: HCT116 E2F1 CRISPR cells, 6h timepoint, biological replicate 1


title: 14 DPI SSD Diet Hp Infection 2

description:
Library name: F2
14 DPI Read Counts.xlsx


title: NM450_050


title: CP14_5uM_E_V replicate 2

description: Library name: 32_CP14_5uM_E_V


title: HCT116 E2F1 CRISPR cells, 0h timepoint, biological replicate 1


title: HCT116 E2F1 CRISPR cells, 0h timepoint, biological replicate 2


title: 14 DPI SSD Diet Hp Infection 3

description:
Library name: F3
14 DPI Read Counts.xlsx


title: 14 DPI SSD Diet Hp Infection 1

description:
Library name: F1
14 DPI Read Counts.xlsx


title: HCT116 E2F1 CRISPR cells, 6h timepoint, biological replicate 3


title: CP14_5uM_E_V replicate 3

description: Library name: 33_CP14_5uM_E_V


title: NM450_047


title: HCT116 WT cells, 6h timepoint, biological replicate 4

value: WT


title: L1_hrg1miR85mut_300mM_biol_rep5

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 5eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

description:
Library name: L1_hrg1miR85mut_300mM_biol_rep5
RNA-seq from L1 hatched larvae

data_processing:
For all of the library, normalized bigwig files were generated from the mapping results using millions of non-structural mappers as a normalization factor. This normalized coverage information was computed for 10 bp bins using the bedtools and bedops v.2.4.26 packages.
Assembly: ce11 C. elegans Sequencing Consortium WBcel235
Supplementary files format and content: normalized big wig files will be provided for each libraries

organism: Caenorhabditis elegans

source_name: Hatched L1 larvae

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
To obtain synchronized non-starved L1, we used the NemaSync C. elegans synchronizer model 5000. L1 larvae were frozen in dry ice with TRIzol Reagent (Invitrogen), and after six repetitions of freeze and thaw, RNA was extracted using the Direct-zol RNA Microprep kit (ZymoResearch, R2062). The small RNA fragments (17 to 200 nucleotides) were separated from the large RNAs (>200 nucleotides) using the Quick-RNA MicroPrep kit (ZymoResearch, R1051). The large RNA was DNAse treated using the reagent provided along with the Quick-RNA Microprep kit. Using these size separation kits, we were able to sequence both the small RNA and the mRNA coming from the same samples. An Agilent 2200 TapeStation System was used to evaluate the RIN indexes of the large RNAs (>200 nucleotides), and only samples with RNA integrity number RIN  > 8 were used for RNA-seq. For 2-cell embryo RNA extraction, precisely staged 2-cell embryos were obtained by alkaline hypochlorite treatment of synchronized gravid adult hermaphrodites, and fifty 2-cell embryos were collected using a mouth pipet. Embryos were lysed for 10min at 65˚C and 1min at 85˚C in a lysis solution containing Tris pH8 5mM final, EDTA 0.25mM final, Triton 100X 0.5%, Tween 20 0.5%, Proteinase K 0.5% and Water. The lysates were subjected to RNA purification using the Quick-RNA MicroPrep kit (ZymoResearch, R1051), and small RNAs (RNA fraction from 17 to 200 nucleotides) and mRNAs (RNA fraction >200 nucleotides) were collected separately. The RNA fraction > 200 nucleotides were used for preparing RNA-seq libraries.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. Ribosomal and mitochondrial rRNAs were depleted using a custom RNAse-H-based method to degrade rRNAs using complementary oligos as described in42.Strand-specific RNA libraries were prepared using at least 100 ng of rRNA-depleted RNAs using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S). RNA libraries were analysed on Agilent 2200 TapeStation System using high sensitivity D1000 screentapes and quantified using the Qubit Fluorometer High Sensitivity dsDNA assay kit (Thermo Fisher Scientific, Q32851). Multiplexed libraries were sequenced on a NextSeq 2000 Illumina platform.

treatment_protocol: To induce the degradation of DROSHA and PASHA in C. elegans intestine, we used the AID degron system. Mothers were treated with Auxin at L3 stages and embryos or hatched L1 were collected for the RNA-seq experiment. 250 mM auxin stock solution was prepared in ethanol and stored at 4 °C. Auxin plates or ethanol plates were prepared by the addition of auxin or only ethanol to NGM plates (final concentration: 500 µM auxin, 0.2% ethanol for auxin plates and 0.2% ethanol for ethanol plates). Plates were seeded with OP50 Escherichia coli.

value: Hatched L1 larvae

value: hrg-1(gcp100[hrg-1_mir85 seed mutated]) X

value: mothers exposed to 300mM NaCl


title: HCT116 WT cells, 6h timepoint, biological replicate 3


title: NM450_048

value: Female

value: Non-smoking


title: NM450_049


title: CP14_2_5uM_USP18_O_E replicate 3

description: Library name: 30_CP14_2_5uM_USP18_O_E


title: CP14_2_5uM_USP18_O_E replicate 2

description: Library name: 29_CP14_2_5uM_USP18_O_E


title: HCT116 WT cells, 6h timepoint, biological replicate 2


title: NM450_046


title: CP14_5uM_E_V replicate 1

description: Library name: 31_CP14_5uM_E_V


title: L1_hrg1miR85mut_300mM_biol_rep3

description:
Library name: L1_hrg1miR85mut_300mM_biol_rep3
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85mut_300mM_biol_rep4

description:
Library name: L1_hrg1miR85mut_300mM_biol_rep4
RNA-seq from L1 hatched larvae


title: CP14_2_5uM_USP18_O_E replicate 1

description: Library name: 28_CP14_2_5uM_USP18_O_E


title: HCT116 WT cells, 6h timepoint, biological replicate 1


title: CP14_2_5uM_E_V replicate 3

description: Library name: 27_CP14_2_5uM_E_V


title: CP14_2_5uM_E_V replicate 2

description: Library name: 26_CP14_2_5uM_E_V


title: NM450_044

value: Male


title: L1_hrg1miR85mut_300mM_biol_rep1

description:
Library name: L1_hrg1miR85mut_300mM_biol_rep1
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85mut_50mM_biol_rep5

description:
Library name: L1_hrg1miR85mut_50mM_biol_rep5
RNA-seq from L1 hatched larvae

value: mothers exposed to 50mM NaCl


title: NM450_042


title: HCT116 WT cells, 0h timepoint, biological replicate 4


title: HCT116 WT cells, 0h timepoint, biological replicate 3


title: CP14_2_5uM_E_V replicate 1

description: Library name: 25_CP14_2_5uM_E_V

value: lung cancer cell


title: L1_hrg1miR85mut_50mM_biol_rep4

description:
Library name: L1_hrg1miR85mut_50mM_biol_rep4
RNA-seq from L1 hatched larvae


title: NM450_045


title: NM450_041


title: HCT116 WT cells, 0h timepoint, biological replicate 2


title: CP14_1uM_USP18_O_E replicate 3

description: Library name: 24_CP14_1uM_USP18_O_E


title: L1_hrg1miR85mut_300mM_biol_rep2

description:
Library name: L1_hrg1miR85mut_300mM_biol_rep2
RNA-seq from L1 hatched larvae


title: CP14_1uM_USP18_O_E replicate 1

description: Library name: 22_CP14_1uM_USP18_O_E


title: CP14_1uM_USP18_O_E replicate 2

description: Library name: 23_CP14_1uM_USP18_O_E


title: HCT116 DP1 CRISPR clone 2, biological replicate 2

value: DP1 KO


title: NM450_039


title: NM450_038


title: L1_hrg1miR85mut_50mM_biol_rep2

description:
Library name: L1_hrg1miR85mut_50mM_biol_rep2
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85mut_50mM_biol_rep1

description:
Library name: L1_hrg1miR85mut_50mM_biol_rep1
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85mut_50mM_biol_rep3

description:
Library name: L1_hrg1miR85mut_50mM_biol_rep3
RNA-seq from L1 hatched larvae


title: NM450_040


title: HCT116 DP1 CRISPR clone 2, biological replicate 3


title: L1_hrg1miR85WT_300mM_biol_rep5

description:
Library name: L1_hrg1miR85WT_300mM_biol_rep5
RNA-seq from L1 hatched larvae

value: Wild-type


title: NM450_037


title: HCT116 WT cells, 0h timepoint, biological replicate 1

value: colorectal carcinoma


title: CP14_1uM_E_V replicate 2

description: Library name: 20_CP14_1uM_E_V


title: HCT116 DP1 CRISPR clone 1, biological replicate 3


title: CP14_1uM_E_V replicate 1

description: Library name: 19_CP14_1uM_E_V


title: HCT116 DP1 CRISPR clone 2, biological replicate 1


title: HCT116 DP1 CRISPR clone 1, biological replicate 2


title: L1_hrg1miR85WT_300mM_biol_rep3

description:
Library name: L1_hrg1miR85WT_300mM_biol_rep3
RNA-seq from L1 hatched larvae


title: NM450_036


title: CP2_5uM_USP18_O_E replicate 3

description: Library name: 18_CP2_5uM_USP18_O_E


title: CP14_1uM_E_V replicate 3

description: Library name: 21_CP14_1uM_E_V


title: HCT116 DP1 CRISPR clone 1, biological replicate 1


title: L1_hrg1miR85WT_300mM_biol_rep4

description:
Library name: L1_hrg1miR85WT_300mM_biol_rep4
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85WT_300mM_biol_rep2

description:
Library name: L1_hrg1miR85WT_300mM_biol_rep2
RNA-seq from L1 hatched larvae


title: NM450_034


title: HCT116 WT cells, biological replicate 1


title: HCT116 WT cells, biological replicate 3


title: CP2_5uM_USP18_O_E replicate 1

description: Library name: 16_CP2_5uM_USP18_O_E


title: L1_hrg1miR85WT_300mM_biol_rep1

description:
Library name: L1_hrg1miR85WT_300mM_biol_rep1
RNA-seq from L1 hatched larvae


title: NM450_032


title: NM450_033


title: Control

type: other

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Control (right tissue)

hyb_protocol: The slides were then hybridized overnight at 37°C with RNA-specific probes from the 6K RNA panel. Following stringent washes to remove unbound probes, DAPI staining was used for nuclear visualization, and cell segmentation markers CD298/Beta-2-Microglobulin (B2M), along with additional cellular markers PanCK and CD45, were applied.

scan_protocol: The prepared slides were loaded into the CosMx SMI for imaging. During imaging, branched fluorescent probes were hybridized to amplify signals, enabling the detection of 6,000 RNA targets within individual cells

data_processing: The raw images were processed and decoded using the AtoMx™ Spatial Informatics Platform (SIP), a cloud-based service that provided the data for visualization and detailed analysis.

molecule: other

source_name: Liver

label_protocol: Sample preparation was performed according to protocol MAN-10184-02 using the Human Universal Cell Characterization 6K Plex Panel (part number 121500041). Tissue sections were cut at 5 μm thickness, mounted on Superfrost Plus Micro Slides, and baked overnight at 60°C to enhance adherence. After deparaffinization, target retrieval was performed at 95–100°C for 15 minutes, followed by permeabilization with 3 μg/mL Proteinase K at 40°C for 30 minutes. Fiducial markers were applied for precise image alignment, followed by post-fixation with neutral buffered formalin and blocking with N-hydroxy succinimide (NHS)-acetate.

extract_protocol: Fontan patients with liver biopsy or explanted liver tissue in the past 20 years (2005-2025) at the Children’s Hospital of Pittsburgh and the University of Pittsburgh Medical School (UPMC) were identified, and formalin-fixed paraffin-embedded (FFPE) blocks were retrieved. Pre-perfusion normal liver allografts were used as controls. Formalin-Fixed Paraffin-Embedded (FFPE) liver tissue samples were analyzed using the CosMx™ Spatial Molecular Imager (SMI) platform from NanoString Technologies, a Bruker company (Seattle, WA), at the Center for Computational Immunogenetics of the University of Pittsburgh.

value: Liver

tag: Stage

value: Control


title: Early and late FALD

description: Early and late FALD (left tissue if for late FALD and right tissue is for early FALD)

value: Early and late FALD


title: L1_hrg1miR85WT_50mM_biol_rep5

description:
Library name: L1_hrg1miR85WT_50mM_biol_rep5
RNA-seq from L1 hatched larvae


title: CP2_5uM_USP18_O_E replicate 2

description: Library name: 17_CP2_5uM_USP18_O_E

value: lung


title: L1_hrg1miR85WT_50mM_biol_rep2

description:
Library name: L1_hrg1miR85WT_50mM_biol_rep2
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85WT_50mM_biol_rep4

description:
Library name: L1_hrg1miR85WT_50mM_biol_rep4
RNA-seq from L1 hatched larvae


title: L1_hrg1miR85WT_50mM_biol_rep3

description:
Library name: L1_hrg1miR85WT_50mM_biol_rep3
RNA-seq from L1 hatched larvae


title: NM450_030


title: NM450_028


title: NM450_031


title: CP2_5uM_E_V replicate 3

description: Library name: 15_CP2_5uM_E_V


title: HCT116 WT cells, biological replicate 2


title: CP2_5uM_E_V replicate 2

description: Library name: 14_CP2_5uM_E_V


title: acaA- PkaCoe_20hr : replicate 3

description:
Library name: Sample 30
10x Genomics

source_name: acaA- PkaCoe

value: acaA- PkaCoe

value: 20 hr

value: on Black filter


title: L1_hrg1miR85WT_50mM_biol_rep1

description:
Library name: L1_hrg1miR85WT_50mM_biol_rep1
RNA-seq from L1 hatched larvae

value: Hatched L1 larvae


title: CP2_5uM_E_V replicate 1

description: Library name: 13_CP2_5uM_E_V


title: CP2_2uM_USP18_O_E replicate 2

description: Library name: 11_CP2_2uM_USP18_O_E


title: NM450_029


title: NM450_027


title: L1_miR85CRISPRmut_300mM_biol_rep4

description:
Library name: L1_miR85CRISPRmut_300mM_biol_rep4
RNA-seq from L1 hatched larvae

value: mir-85(gcp109[mir-85 3p deletion]) II

value: mothers exposed to 300mM NaCl


title: CP2_2uM_USP18_O_E replicate 1

description: Library name: 10_CP2_2uM_USP18_O_E


title: CP2_2uM_USP18_O_E replicate 3

description: Library name: 12_CP2_2uM_USP18_O_E


title: acaA- PkaCoe_20hr : replicate 2

description:
Library name: Sample 29
10x Genomics


title: acaA- PkaCoe_20hr : replicate 1

description:
Library name: Sample 28
10x Genomics


title: L1_miR85CRISPRmut_300mM_biol_rep3

description:
Library name: L1_miR85CRISPRmut_300mM_biol_rep3
RNA-seq from L1 hatched larvae


title: NM450_025

value: Female

value: Non-smoking


title: acaA- PkaCoe_16hr : replicate 3

description:
Library name: Sample 27
10x Genomics

value: 16 hr


title: CP2_2uM_E_V replicate 1

description: Library name: 7_CP2_2uM_E_V

value: lung cancer cell


title: acaA- PkaCoe_12hr : replicate 3

description:
Library name: Sample 24
10x Genomics

value: 12 hr


title: acaA- PkaCoe_16hr : replicate 1

description:
Library name: Sample 25
10x Genomics


title: L1_miR85CRISPRmut_50mM_biol_rep3

description:
Library name: L1_miR85CRISPRmut_50mM_biol_rep3
RNA-seq from L1 hatched larvae

value: mothers exposed to 50mM NaCl


title: L1_miR85CRISPRmut_300mM_biol_rep2

description:
Library name: L1_miR85CRISPRmut_300mM_biol_rep2
RNA-seq from L1 hatched larvae


title: CP2_2uM_E_V replicate 3

description: Library name: 9_CP2_2uM_E_V


title: NM450_022


title: NM450_026


title: DMSO_USP18_O_E replicate 3

description: Library name: 6_DMSO_USP18_O_E


title: L1_miR85CRISPRmut_300mM_biol_rep1

description:
Library name: L1_miR85CRISPRmut_300mM_biol_rep1
RNA-seq from L1 hatched larvae


title: acaA- PkaCoe_16hr : replicate 2

description:
Library name: Sample 26
10x Genomics


title: L1_miR85CRISPRmut_50mM_biol_rep4

description:
Library name: L1_miR85CRISPRmut_50mM_biol_rep4
RNA-seq from L1 hatched larvae


title: CP2_2uM_E_V replicate 2

description: Library name: 8_CP2_2uM_E_V


title: NM450_024

value: Male


title: L1_miR85CRISPRmut_50mM_biol_rep2

description:
Library name: L1_miR85CRISPRmut_50mM_biol_rep2
RNA-seq from L1 hatched larvae


title: DMSO_USP18_O_E replicate 2

description: Library name: 5_DMSO_USP18_O_E


title: NM450_023


title: acaA- PkaCoe_12hr : replicate 2

description:
Library name: Sample 23
10x Genomics


title: NM450_021


title: L1_miR85CRISPRmut_50mM_biol_rep1

description:
Library name: L1_miR85CRISPRmut_50mM_biol_rep1
RNA-seq from L1 hatched larvae


title: NM450_020


title: acaA- PkaCoe_12hr : replicate 1

description:
Library name: Sample 22
10x Genomics


title: DMSO_USP18_O_E replicate 1

description: Library name: 4_DMSO_USP18_O_E


title: DMSO_E_V replicate 3

description: Library name: 3_DMSO_E_V


title: acaA- PkaCoe_08hr : replicate 3

description:
Library name: Sample 21
10x Genomics

value: 8 hr


title: NM450_019


title: L1_P0hetF1KO_300mM_biol_rep2

description:
Library name: L1_P0hetF1KO_300mM_biol_rep2
RNA-seq from L1 hatched larvae


title: NM450_017


title: L1_P0hetF1KO_300mM_biol_rep1

description:
Library name: L1_P0hetF1KO_300mM_biol_rep1
RNA-seq from L1 hatched larvae


title: acaA- PkaCoe_08hr : replicate 1

description:
Library name: Sample 19
10x Genomics


title: DMSO_E_V replicate 2

description: Library name: 2_DMSO_E_V


title: circPDE4B KD Vector_rep2

city: Boston

first: Junming

last: Hu

state: MA

address: 75 E Concord St

institute: Boston University

description: Library name: circPDE4B KD Vector_rep2

data_processing:
fastQC
STAR alignment
RSEM
QC and DE with DESeq2
Making plots
Assembly: GRCh38
Supplementary files format and content: Count matrix for smRNA output or RSEM gene results table

source_name: Neural proginator cells

growth_protocol: STEMdiff™ Neural Progenitor Medium

extract_protocol:
Qiagen RNeasy Plus Mini Kit
SMART-Seq® Total RNA kit

treatment_protocol: Lentiviral packaged sgRNA -Rfxcas13d treated for 48hrs, selection for puromycin for 4 days and harvest

value: Neural proginator cells

value: WT

value: circPDE4B KD Vector


title: circPDE4B KD Vector_rep3

description: Library name: circPDE4B KD Vector_rep3


title: acaA- PkaCoe_04hr : replicate 3

description:
Library name: Sample 18
10x Genomics

value: acaA- PkaCoe

value: 4 hr


title: acaA- PkaCoe_08hr : replicate 2

description:
Library name: Sample 20
10x Genomics

value: on Black filter


title: NM450_016

value: lung


title: NM450_018


title: L1_P0hetF1KO_50mM_biol_rep3

description:
Library name: L1_P0hetF1KO_50mM_biol_rep3
RNA-seq from L1 hatched larvae

value: Hatched L1 larvae


title: L1_P0hetF1KO_50mM_biol_rep1

description:
Library name: L1_P0hetF1KO_50mM_biol_rep1
RNA-seq from L1 hatched larvae


title: L1_P0hetF1KO_50mM_biol_rep2

description:
Library name: L1_P0hetF1KO_50mM_biol_rep2
RNA-seq from L1 hatched larvae


title: L1_P0hetF1KO_300mM_biol_rep3

description:
Library name: L1_P0hetF1KO_300mM_biol_rep3
RNA-seq from L1 hatched larvae

value: mothers exposed to 300mM NaCl


title: acaA- PkaCoe_04hr : replicate 2

description:
Library name: Sample 17
10x Genomics


title: NM450_014

value: Female


title: NM450_015

value: Non-smoking


title: DMSO_E_V replicate 1

description: Library name: 1_DMSO_E_V


title: Control Vector_rep3

description: Library name: Control Vector_rep3

value: Control Vector


title: acaA- PkaCoe_04hr : replicate 1

description:
Library name: Sample 16
10x Genomics


title: L1_P0hetF1het_300mM_biol_rep2

description:
Library name: L1_P0hetF1het_300mM_biol_rep2
RNA-seq from L1 hatched larvae


title: L1_P0hetF1het_300mM_biol_rep3

description:
Library name: L1_P0hetF1het_300mM_biol_rep3
RNA-seq from L1 hatched larvae


title: circPDE4B KD Vector_rep1

description: Library name: circPDE4B KD Vector_rep1


title: Control Vector_rep2

description: Library name: Control Vector_rep2


title: NM450_013


title: Control Vector_rep1

description: Library name: Control Vector_rep1


title: NM450_012


title: acaA- PkaCoe_00hr : replicate 3

description:
Library name: Sample 15
10x Genomics

value: 0 hr


title: L1_P0hetF1het_300mM_biol_rep1

description:
Library name: L1_P0hetF1het_300mM_biol_rep1
RNA-seq from L1 hatched larvae


title: acaA- PkaCoe_00hr : replicate 1

description:
Library name: Sample 13
10x Genomics


title: acaA- PkaCoe_00hr : replicate 2

description:
Library name: Sample 14
10x Genomics


title: NM450_011


title: INPUT

description:
Library name: Input
miR.Counts.csv
WB_PS_Input_S11_L001_cutadapt_trimmed

library_source: other

data_processing:
Cut Adapter according to SMARTer® smRNA-Seq Kit for Illumina® (Takara, #635030) manual
fastQC
miRge3
QC, norm and DE with edgeR
Make plots
Assembly: GRCh38
Supplementary files format and content: Count matrix for smRNA output or RSEM gene results table

extract_protocol:
NucleoSpin® miRNA kit (Takara, #740971.250)
SMARTer® smRNA-Seq Kit for Illumina® (Takara, #635030)


title: L1_P0hetF1het_50mM_biol_rep3

description:
Library name: L1_P0hetF1het_50mM_biol_rep3
RNA-seq from L1 hatched larvae


title: NM450_010


title: circPDE4B IP_rep5

description:
Library name: circPDE4B IP_rep5
miR.Counts.csv
WB_PS_PD-5_S10_L001_cutadapt_trimmed

value: circPDE4B IP


title: acaA-_20hr : replicate 1, 2, 3, 4

description:
Library name: Sample 12
10x Genomics

value: acaA-

value: replicate 1, 2, 3, and 4

value: 20 hr


title: L1_P0hetF1het_50mM_biol_rep2

description:
Library name: L1_P0hetF1het_50mM_biol_rep2
RNA-seq from L1 hatched larvae

value: mothers exposed to 50mM NaCl


title: acaA-_16hr : replicate 1, 2, 3, 4

description:
Library name: Sample 11
10x Genomics

value: 16 hr


title: L1_P0hetF1het_50mM_biol_rep1

description:
Library name: L1_P0hetF1het_50mM_biol_rep1
RNA-seq from L1 hatched larvae


title: NM450_009


title: circPDE4B IP_rep3

description:
Library name: circPDE4B IP_rep3
miR.Counts.csv
WB_PS_PD-3_S8_L001_cutadapt_trimmed

value: Neural proginator cells

value: WT


title: circPDE4B IP_rep4

description:
Library name: circPDE4B IP_rep4
miR.Counts.csv
WB_PS_PD-4_S9_L001_cutadapt_trimmed


title: L1_miR85(n4117)_300mM_biol_rep1

description:
Library name: L1_miR85(n4117)_300mM_biol_rep1
RNA-seq from L1 hatched larvae


title: NM450_008


title: acaA-_04hr : replicate 1, 2, 3, 4

description:
Library name: Sample 8
10x Genomics

value: 4 hr


title: acaA-_12hr : replicate 1, 2, 3, 4

description:
Library name: Sample 10
10x Genomics

value: 12 hr

value: on Black filter


title: acaA-_08hr : replicate 1, 2, 3, 4

description:
Library name: Sample 9
10x Genomics

value: 8 hr


title: L1_miR85(n4117)_300mM_biol_rep2

description:
Library name: L1_miR85(n4117)_300mM_biol_rep2
RNA-seq from L1 hatched larvae

value: Hatched L1 larvae

value: mothers exposed to 300mM NaCl


title: L1_miR85(n4117)_50mM_biol_rep2

description:
Library name: L1_miR85(n4117)_50mM_biol_rep2
RNA-seq from L1 hatched larvae


title: NM450_006

value: lung

value: Female

value: Non-smoking


title: L1_miR85(n4117)_50mM_biol_rep1

description:
Library name: L1_miR85(n4117)_50mM_biol_rep1
RNA-seq from L1 hatched larvae


title: NM450_004

value: Male


title: circPDE4B IP_rep2

description:
Library name: circPDE4B IP_rep2
miR.Counts.csv
WB_PS_PD-2_S7_L001_cutadapt_trimmed

value: circPDE4B IP


title: NM450_007


title: circPDE4B IP_rep1

description:
Library name: circPDE4B IP_rep1
miR.Counts.csv
WB_PS_PD-1_S6_L001_cutadapt_trimmed


title: NM450_005


title: prime edited, CCAOBAP1-WT clone 9, rep1

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

description: Library name: Mut_1

data_processing:
Reads were quality-controlled and filtered for adapter contamination, uncertain nucleotides (N>10%) and low quality nucleotides (Base quality <5 in 50%) as by the Novogene pipeline
Clean reads were mapped using HISAT2 and mapped reads were converted to counts using FeatureCounts applying the GrCh38 genome annotation file
Assembly: GRCh38 (hg38)
Supplementary files format and content: Matrix table (tab-delimited .txt format) with raw gene counts for every gene in every sample, ENSEMBL gene_id and gene_name annotations

source_name: bile duct tumor

growth_protocol: Broutier et al. Nat Med 2017. Organoids were cultured according previous protocol.

extract_protocol:
CCAOs grown in BME domes were washed three times with PBS, lysed with QIAzol Lysing Reagent, and processed using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions
Library construction was performed at the Novogene sequencing facilities, Cambridge, UK.  In short, purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution.The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

value: bile duct tumor

value: CCAOBAP1 Edit-Mut

value: organoid

value: Prime edited BAP1


title: NM450_003


title: prime edited, CCAOBAP1-WT clone 9, rep3

description: Library name: Mut_3


title: Scrambled control IP_rep5

description:
Library name: Control IP_rep5
miR.Counts.csv
WB_PS_Sc-5_S5_L001_cutadapt_trimmed

value: Neural proginator cells

value: Scrambled control IP


title: prime edited, CCAOBAP1-WT clone 9, rep2

description: Library name: Mut_2


title: L1_WT_300mM_biol_rep1

description:
Library name: L1_WT_300mM_biol_rep1
RNA-seq from L1 hatched larvae

value: Wild-type


title: Non-edited, CCAOBAP1-WT clone 9, rep2

description: Library name: Control_2

value: CCAOBAP1 Edit-NC

value: BAP1 WT

value: Non-Edited


title: Scrambled control IP_rep4

description:
Library name: Control IP_rep4
miR.Counts.csv
WB_PS_Sc-4_S4_L001_cutadapt_trimmed

value: WT


title: L1_WT_50mM_biol_rep2

description:
Library name: L1_WT_50mM_biol_rep2
RNA-seq from L1 hatched larvae

value: Hatched L1 larvae

value: mothers exposed to 50mM NaCl


title: NM450_001

value: lung

value: Female


title: Scrambled control IP_rep1

description:
Library name: Control IP_rep1
miR.Counts.csv
WB_PS_Sc-1_S1_L001_cutadapt_trimmed


title: L1_WT_300mM_biol_rep2

description:
Library name: L1_WT_300mM_biol_rep2
RNA-seq from L1 hatched larvae

value: mothers exposed to 300mM NaCl


title: Non-edited, CCAOBAP1-WT clone 9, rep1

description: Library name: Control_1


title: Scrambled control IP_rep3

description:
Library name: Control IP_rep3
miR.Counts.csv
WB_PS_Sc-3_S3_L001_cutadapt_trimmed


title: Non-edited, CCAOBAP1-WT clone 9, rep3

description: Library name: Control_3


title: Scrambled control IP_rep2

description:
Library name: Control IP_rep2
miR.Counts.csv
WB_PS_Sc-2_S2_L001_cutadapt_trimmed


title: Flox_Bex_rep2

status: Public on Feb 03 2026

first: Hang

last: Zeng

address: 79# Qingchun road

institute: Zhejiang university

description: Library name: Flox_Bex_2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Assembly: genome assembly
Supplementary files format and content: Excel file includes TPM values for each Sample

source_name: hepatocyte

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: hepatocyte


title: LKO_Con_rep1

description: Library name: LKO_Con_1


title: LKO_Con_rep2

description: Library name: LKO_Con_2


title: Flox_Con_rep2

description: Library name: Flox_Con_2


title: NM450_002

value: Non-smoking


title: 5xFAD_vehicle_2wk_rep3

city: Atlanta

first: Timothy

middle: R

last: Sampson

state: Georgia

address: 615 Michael St

institute: Emory University

description: Library name: 21173FL-12-01-08

data_processing:
Sequencing quality control was performed using FastQC (version 0.11.9) and reads were pseudoaligned to the mouse reference genome (GRCm39) using Kallisto (version 0.44.0)
Assembly: GRCm39
Supplementary files format and content: Kallisto abundance.h5 files

source_name: Brain

extract_protocol:
Brains were perfused with PBS then homogenized using a Wheaton dounce tissue grinder (with 0.114 ±0.025mm pestle clearance) in culture media comprised of HBBS with 1.5% HEPES, and 0.5% glucose. Cells were then transferred to a 35% isotonic percoll gradient solution and spun 20 minutes at 700 x g to remove the myelin layer. Transcription (Actinomycin D, Sigma #A1410) and translation (Anisomycin, Sigma #A9789) inhibitors were added to every solution throughout both procedures to prevent transcriptional changes that could impact downstream results. The remaining cells were washed several times in HBBS culture media before undergoing magnetic activated cell sorting according to the manufacturers (Miltenyi Biotec) guidelines. Samples were resuspended in PB buffer (0.5% BSA in PBS pH 7.2) with CD11b MicroBeads (Miltenyi Biotec # 130-093-634) and incubated for 15 minutes at 4° C protected from light. Cells were then washed and resuspended in PB buffer before being placed on an LS column (Miltenyi Biotec #130-042-401). Magnetic separation was repeated on a second LS column to maximize purity. After separation, cells were resuspended in Trizol and stored at -80° C for later use.
RNA was extracted from isolated brain myeloid cells using the Qiagen RNeasy Kit (#74106) according to the manufacturer’s guidelines. Bulk RNA-sequencing libraries were created for each sample using the Takara SMART-Seq mRNA HT LP kit (#634792) according to the manufacturer’s protocol and recommendations.

treatment_protocol: 2-month-old female 5xFAD mice underwent intragastric gavage with either vehicle control (50% glycerol with 5% sodium bicarbonate) or 10^8 cfu of E. coli 3x per week for either 2 weeks or 1 month.

value: Brain

value: CD11b+ brain myeloid cells

value: 2 week vehicle control

tag: Sex

value: male


title: L1_WT_50mM_biol_rep1

description:
Library name: L1_WT_50mM_biol_rep1
RNA-seq from L1 hatched larvae


title: 5xFAD_vehicle_2wk_rep1

description: Library name: 21173FL-12-01-06


title: LKO_Bex_rep2

description: Library name: LKO_Bex_2


title: LKO_Con_rep3

description: Library name: LKO_Con_3


title: LKO_Bex_rep1

description: Library name: LKO_Bex_1


title: Flox_Bex_rep3

description: Library name: Flox_Bex_3


title: Flox_Bex_rep1

description: Library name: Flox_Bex_1


title: 5xFAD_vehicle_2wk_rep2

description: Library name: 21173FL-12-01-07


title: 5xFAD_E. coli_2wk_rep3

description: Library name: 21173FL-12-01-05

value: 2 week E. coli enrichment

tag: bacterial strain

value: Escherichia coli str. K12 MC4100


title: 5xFAD_E. coli_1mo_rep2

description: Library name: 21173FL-06-01-02

treatment_protocol: 2-month-old female 5xFAD mice underwent intragastric gavage with either vehicle control (50% glycerol with 5% sodium bicarbonate) or 10^8 cfu of E. coli 3x per week for 1 month.

tag: tissue

value: 1 month E. coli enrichment

value: female


title: Flox_Con_rep3

description: Library name: Flox_Con_3

tag: cell type


title: 5xFAD_E. coli_1mo_rep3

description: Library name: 21173FL-06-01-08

tag: genotype


title: LKO_Bex_rep3

description: Library name: LKO_Bex_3


title: 5xFAD_E. coli_2wk_rep1

description: Library name: 21173FL-12-01-03

tag: treatment


title: 5xFAD_E. coli_2wk_rep2

description: Library name: 21173FL-12-01-04


title: 5xFAD_vehicle_1mo_rep3

description: Library name: 21173FL-06-01-07

value: 1 month vehicle control


title: 5xFAD_vehicle_1mo_rep1

description: Library name: 21173FL-06-01-05


title: Conventionally raised, rep 2

description:
Library name: 21173FL-04-14-01-01
10x Genomics

data_processing:
Reads were aligned to the mouse reference genome (GRCm39) using the Cell Ranger pipeline (version 4.0.10, 10x Genomics).
Assembly: GRCm39
Supplementary files format and content: Unfiltered matrix.h5 files from Cell Ranger pipeline

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
Brains were perfused with PBS then the hippocampus was dissected and flash frozen in liquid nitrogen. Nuclei were isolated using an extraction protocol outlined in PMID: 28846090. Frozen tissue was placed in homogenization buffer (consisting of 0.26M sucrose, 0.03M KCl, 0.01M MgCl2, 0.02M Tricine-KOH pH 7.8, 0.001M DTT, 0.5mM Spermidine, 0.05mM Spermine, 0.3% NP40, and protease inhibitor) and homogenized using both pestle A (0.0030-0.0050 in. clearance) and pestle B (0.0005-0.0025 in. clearance) of a KIMBLE dounce tissue grinder (Sigma D8938). Density gradient centrifugation was performed using iodixanol and the nuclei band was captured at the 30%-40% iodixanol interface. Nuclei were washed in RSB buffer (0.01M Tris-HCL pH 7.5, 0.01M NaCl, 0.003M MgCl2, and 0.1% Tween-20) then samples were combined such that each treatment group was represented by two samples, each containing roughly equal numbers of cells from two mice within a single treatment group.
After nuclei isolation, samples immediately underwent cell capture using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics # PN-1000268) according to the manufacturer’s guidelines. Approximately 1,600 cells were loaded onto a Chromium Next GEM Chip and run using a Chromium Controller and library preparation steps were performed according to the manufacturer’s guidelines.

treatment_protocol: Mice were either A) conventionally raised mice with an intact microbiome, B) born and raised in a germ-free environment, or C) ex-germ free mice that were mono-colonized with Escherichia coli for 2 or 4 weeks.

value: Hippocampus

value: Nuclei

value: Conventionally raised


title: 5xFAD_vehicle_1mo_rep2

description: Library name: 21173FL-06-01-06


title: 5xFAD_E. coli_1mo_rep1

description: Library name: 21173FL-06-01-01


title: Flox_Con_rep1

description: Library name: Flox_Con_1


city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

description: Library name: ROS1-_delta_CXXC-Flag_ros1-4_line3_Repeat_2

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : westar.v0, Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Plants were grown at 22 °C under a 16 h light/8 h dark photoperiod. Shoots and roots of two-week-old plants and stems of four-week-old plants were collected for the indicated genotypes.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp reads, Annoroad Gene Technology).

value: shoot

value: ROS1-_delta_CXXC-Flag_ros1-4 line3

tag: chip antibody

value: Flag


title: Conventionally raised, rep 1

description:
Library name: 21173FL-04-03-01-01
10x Genomics


description: Library name: ROS1-_delta_CXXC-Flag_ros1-4_line1_Repeat_1

value: ROS1-_delta_CXXC-Flag_ros1-4 line1


description: Library name: ROS1-_delta_CXXC-Flag_ros1-4_line3_Repeat_1


title: Germ-free, rep1

description:
Library name: 21173FL-04-09-01-01
10x Genomics

value: Germ-free


title: Germ-free, rep2

description:
Library name: 21173FL-04-10-01-01
10x Genomics


description: Library name: ROS1-N_delta_294-Flag_ros1-4_line2_Repeat_1

value: ROS1-N_delta_294-Flag_ros1-4 line2


title: E. coli mono-colonized 2wk, rep 2

description:
Library name: 21173FL-04-15-01-01
10x Genomics

value: 2 week E. coli mono-colonization


title: E. coli mono-colonized 2wk, rep 1

description:
Library name: 21173FL-04-08-01-01
10x Genomics


description: Library name: ROS1-N_delta_294C_delta_146-Flag_ros1-4_line1_Repeat_1


title: E. coli mono-colonized 4wk, rep 2

description:
Library name: 21173FL-04-07-01-01
10x Genomics

value: 4 week E. coli mono-colonization


description: Library name: ROS1-N_delta_294-Flag_ros1-4_line2_Repeat_2


title: ROS1-Flag_knock-in_Repeat_1

description: Library name: ROS1-Flag_knock-in_Repeat_1

value: ROS1-Flag knock-in


description: Library name: ROS1-_delta_CXXC-Flag_ros1-4_line1_Repeat_2


description: Library name: ROS1-N_delta_294C_delta_146-Flag_ros1-4_line1_Repeat_2


description: Library name: ROS1-N_delta_294-Flag_ros1-4_line1_Repeat_1

value: ROS1-N_delta_294-Flag_ros1-4 line1


title: E. coli mono-colonized 4wk, rep 1

description:
Library name: 21173FL-04-01-01-01
10x Genomics

value: Escherichia coli str. K12 MC4100


title: DML3-Flag/dml3-2_line2_Repeat_1

description: Library name: DML3-Flag/dml3-2_line2_Repeat_1

value: DML3-Flag/dml3-2 line2


title: DME-Flag/dme_Repeat_2

description: Library name: DME-Flag/dme_Repeat_2

value: DME-Flag/dme


description: Library name: ROS1-C_delta_146-Flag_ros1-4_line2_Repeat_2

value: ROS1-C_delta_146-Flag_ros1-4 line2


description: Library name: ROS1-C_delta_146-Flag_ros1-4_line1_Repeat_2

value: ROS1-C_delta_146-Flag_ros1-4 line1


title: DML2-Flag/dml2-2_line2_Repeat_1

description: Library name: DML2-Flag/dml2-2_line2_Repeat_1

value: DML2-Flag/dml2-2 line2


description: Library name: ROS1-C_delta_146-Flag_ros1-4_line2_Repeat_1


title: Arabidopsis_shoot_drdd_Repeat_2

description: Library name: Arabidopsis_shoot_drdd_Repeat_2

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-f BAMPE -B --nomodel --shift -100 --extsize 200 -q 0.01”
Assembly: Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak
Supplementary files format and content: \

extract_protocol:
The extracted nuclei were incubated with Tn5 transposase and tagmentation buffer according to the manufacturer’s instructions (Vazyme, TD501-01). After tagmentation, DNA was purified using the MinElute PCR Purification Kit (QIAGEN, 28004). PCR amplification of the library was performed for 10 cycles under the following conditions: 72 °C for 5 min, 98 °C for 30 s, followed by thermocycling at 98 °C for 10 s, 60 °C for 30 s, and 72 °C for 40 s, with a final extension at 72 °C for 5 min.
After PCR amplification, the libraries were purified using VAHTS DNA Clean Beads (Vazyme, N411) and sequenced on an Illumina NovaSeq X Plus platform.

value: drdd