title: WT_H3_rep1

description:
Library name: WT_H3_rep1
Nuclei were isolated from axillary tissue and processed with the CUT&Tag Assay Kit (CST, 77552). Nuclei were immobilized on Concanavalin A-coated beads and incubated overnight with anti-H3K27me3 antibody (CST, 9733) or normal rabbit IgG as negative control, followed by anti-rabbit IgG secondary antibody and pAG-Tn5. Tagmentation was activated with Mg2+ at 37 °C, and tagmented DNA was amplified for 16 cycles with DNA/RNA UD Indexes (Illumina, 20026121) and sequenced on the Illumina NovaSeq 6000 platform.


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-2_S1_L003

status: Public on Aug 08 2026

type: SRA

city: 乐山

first: 瀚宇

last: 汪

state: 四川省

address: 四川省乐山市市中区滨河路778号

department: 林竹科技创新产业研究院

country: China

institute: 乐山师范学院

description:
Library name: YYX-2_S1_L003
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval posterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed with Cell Ranger 6.1.1 using the Cyrtotrachelus buqueti reference genome and gene annotation.
The gene expression matrix was generated with cellranger count. The reference was built with cellranger mkref after filtering the gene annotation file for protein-coding genes.
Downstream normalization, integration, clustering, marker identification, and visualization were performed using Seurat and Harmony.
Assembly: Cyrtotrachelus buqueti reference genome
Supplementary files format and content: HDF5 files containing filtered feature-barcode matrices for each pooled scRNA-seq sample.

molecule: polyA RNA

organism: Cyrtotrachelus buqueti

source_name: larval posterior midgut

growth_protocol: Cyrtotrachelus buqueti specimens were collected in Leshan, Sichuan, China in July 2023. Gut tissues were dissected from larvae or adults according to the indicated gut region.

extract_protocol:
Gut tissues were dissected, washed in cold PBS, minced, enzymatically dissociated, filtered through a 70 um strainer, and converted into single-cell suspensions. Cell concentration, viability, and aggregate rate were checked before library construction.
Single-cell libraries were constructed using the 10x Genomics Chromium Single Cell 3' kit (V3) according to the manufacturer's protocol. Libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end sequencing.

treatment_protocol: No treatment was applied.

tag: tissue

value: larval posterior midgut

tag: cell type

value: single-cell suspension from intestinal tissue

tag: batch

value: YYX


title: 437_R

city: Macau

first: Yang

last: Gao

address: University of Macau Research Building (N22), Avenida Avenida, University of Taipa, Macau, SAR

institute: University of Macau

description: Library name: Sample7

library_source: transcriptomic

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: mm10-2020-A
Supplementary files format and content: .gz

molecule: total RNA

organism: Mus musculus

source_name: Subcutaneous tumor

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1) the target RNA was interrupted by adding ion-interrupting reagent and random primer, and the random primer was combined with the target RNA; 2) the target RNA was reversely transcribed into cDNA by adding 1-strand reverse transcription reagent, and the hybrid chain of RNA and cDNA was formed; 3) the RNA in cDNA and RNA hybrid chain was cleaved by adding 2-strand synthetic reagent, and the double-stranded cDNA was synthesized by using the remaining RNA as the primer; 4) the double-stranded cDNA synthesis product was subjected to end-padding and a-addition; the“Y”-shaped linker was ligated; 5) the linker self-connecting fragment was removed by magnetic bead screening; 6) the library template was enriched by PCR amplification; 7) the library was recovered by magnetic beads. Reagent: VAHTS Universal V 8rna-seq Prep Library Kit for Illumina

value: Subcutaneous tumor

value: CD45+ Cell

tag: treatment

value: UM-h101 treatment


title: 449_R

description: Library name: Sample8


title: Decapitated_WT_rep3

city: Beijing

first: Hao

last: Zhu

address: No. 37 Xueyuan Road, Haidian District, Beijing, China

institute: Beihang University

description:
Library name: Decapitated_WT_rep3
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.

data_processing:
RNA-seq: Raw reads were trimmed to remove adapters and low-quality reads using Cutadapt (v.3.5).
RNA-seq: High-quality reads were aligned to the Arabidopsis TAIR10 genome using HISAT2 (v.2.0.5) with default parameters; BAM files were sorted with SAMtools (v.1.13).
RNA-seq: Gene expression was quantified with FeatureCounts (v.2.0.1); differentially expressed genes were identified with DESeq2 (v.1.32.0).
CUT&Tag: Raw reads were processed with fastp (v.0.23.1); clean reads were aligned to TAIR10 using Bowtie2 (v.2.3.5.1), filtered with SAMtools (-F 1804 -f 2 -q 30), and deduplicated with Picard (v.2.23.3).
CUT&Tag: Deduplicated replicate BAMs were merged and converted to RPKM-normalized bigWig with deepTools (v.3.5.0); H3K27me3 peaks were called with MACS2 (v.2.2.7.1, --broad --broad-cutoff 0.05) and annotated with ChIPseeker (v.1.24.0).
Assembly: TAIR10
Supplementary files format and content: Tab-delimited file of raw gene-level read counts for each RNA-seq sample.
Supplementary files format and content: bigWig files of RPKM-normalized H3K27me3 CUT&Tag signal for each sample.

organism: Arabidopsis thaliana

source_name: axillary tissues

growth_protocol: Arabidopsis thaliana Col-0 seeds were surface-sterilized, sown on 1/2 MS agar plates (1/2 MS powder, 0.7% agar, 1% sucrose, pH 5.8), stratified at 4 °C for 3 days, and grown in a chamber at 22 °C under long-day conditions (16 h light/8 h dark).

extract_protocol:
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026) following the manufacturer's protocol. For CUT&Tag, nuclei were isolated from 0.2 g of axillary tissue and processed with the CUT&Tag Assay Kit (CST, 77552).
RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775). CUT&Tag libraries were prepared by immobilizing nuclei on Concanavalin A-coated beads, incubating with anti-H3K27me3 antibody (CST, 9733) or normal rabbit IgG (negative control), followed by anti-rabbit IgG, pAG-Tn5 tagmentation, and 16 cycles of amplification with DNA/RNA UD Indexes (Illumina, 20026121).

treatment_protocol: For rac-GR24 treatment, seedlings were grown on 1/2 MS plates containing 2.5 µM rac-GR24 (PhytoTech Labs, G3324) or DMSO (mock) for 7 days. For decapitation, the main shoot below the lowest cauline node was excised when the main inflorescence reached ~1 cm; axillary tissues (axillary buds and subtending rosette leaf axil tissues) were harvested after treatment.

value: axillary tissues

tag: genotype


title: C4-2, vehicle (ethanol), 10% FBS, Day 1 (24 h), biol. rep. 3

city: Notre Dame

first: Jianneng

last: Li

state: IN

address: 271 Galvin Life Sciences, Galvin building

country: USA

institute: University of Notre Dame

description: Library name: C42_FBS_Ctrl_D1_r3

data_processing:
Quality filtering: reads processed with FastP v0.24.0 (adapter trimming and low-quality base removal)
Read alignment: STAR v2.7, aligned to GRCh38 reference genome (Gencode v45 annotation)
UMI deduplication: UMICollapse v1.1.0
Gene-level quantification: featureCounts v2.1.1 (stranded mode, Gencode v45 annotation)
Differential expression: edgePython v0.2.5 with TMM normalization; DEGs defined as adjusted P < 0.05 and |log2FC| >= 1. GSEA: GSEApy v0.12, pre-ranked by log2FC, using MSigDB Hallmark gene sets and FRIDMAN_SENESCENCE_UP.
Assembly: GRCh38 (hg38); Gencode v45 gene annotation
Supplementary files format and content: 5bDHT_CRPC_RNAseq_raw_counts.txt: tab-delimited matrix; rows = Ensembl gene IDs; columns = library names matching "library name" column; values = UMI-deduplicated raw read counts.
Supplementary files format and content: 5bDHT_CRPC_RNAseq_normalized_counts.txt: tab-delimited matrix; rows = Ensembl gene IDs; columns = library names; values = TMM-normalized log2(CPM+1) expression values.

organism: Homo sapiens

source_name: prostate

growth_protocol: C4-2 cells (LNCaP-derived CRPC line, AR-positive, AR T878A) were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 °C, 5% CO2. For low-androgen experiments, cells were adapted to 10% charcoal-stripped FBS (csFBS) for 48 h before treatment.

extract_protocol:
Total RNA was extracted using a column-based RNA extraction kit per the manufacturer's instructions. RNA quantity was assessed by spectrophotometry; quality was verified by fragment analysis before library preparation.
Stranded 3' mRNA libraries incorporating unique molecular identifiers (UMIs) were prepared and sequenced at the Genomics and Bioinformatics Core Facility, University of Notre Dame. Libraries were sequenced on an Illumina platform (single-end reads) to a depth of at least 10 million deduplicated reads per sample.

treatment_protocol: Experiment 1 (low-dose): C4-2 cells in 10% csFBS were treated with vehicle (ethanol, 0.01%), 10 nM testosterone (T), 10 nM 5beta-dihydrotestosterone (5beta-DHT), or 10 nM 3beta-etiocholanediol (3beta-ecdiol) for 24 h in biological triplicate. Experiment 2 (high-dose, BAT-like): C4-2 cells in 10% FBS were treated with vehicle, 100 nM T, or 100 nM 5beta-DHT for 1 day (24 h) or 3 days (72 h) in biological triplicate. All steroids were purchased from Steraloids and dissolved in ethanol.

value: prostate

tag: cell line

value: castration-resistant prostate cancer (CRPC) cell

value: AR T878A (endogenous)

value: Vehicle (ethanol), 10% FBS, Day 1 (24 h)


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-1_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-1_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval posterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: C4-2, vehicle (ethanol), 10% FBS, Day 1 (24 h), biol. rep. 2

description: Library name: C42_FBS_Ctrl_D1_r2


title: Decapitated_WT_rep2

description:
Library name: Decapitated_WT_rep2
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: 436_R

description: Library name: Sample6


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-9_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-9_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.

source_name: larval anterior midgut

value: larval anterior midgut

value: YCS


title: C4-2, vehicle (ethanol), 10% FBS, Day 1 (24 h), biol. rep. 1

description: Library name: C42_FBS_Ctrl_D1_r1


title: 434_R

description: Library name: Sample5


title: Decapitated_WT_rep1

description:
Library name: Decapitated_WT_rep1
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-8_S1_L007

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-8_S1_L007
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: C4-2, 3beta-ecdiol 10 nM, csFBS, 24 h, biol. rep. 3

description: Library name: C42_csFBS_3bEcdiol10nM_24h_r3

value: 3beta-Etiocholanediol 10 nM, 10% csFBS, 24 h


title: 450_R

description: Library name: Sample4

value: IgG treatment


title: 441_R

description: Library name: Sample3


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-7_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-7_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: Intact_brc1-2_rep2

description:
Library name: Intact_brc1-2_rep2
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: C4-2, 3beta-ecdiol 10 nM, csFBS, 24 h, biol. rep. 2

description: Library name: C42_csFBS_3bEcdiol10nM_24h_r2


title: 439_R

description: Library name: Sample2


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-6_S1_L007

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-6_S1_L007
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: C4-2, 3beta-ecdiol 10 nM, csFBS, 24 h, biol. rep. 1

description: Library name: C42_csFBS_3bEcdiol10nM_24h_r1


title: 0_R

description: Library name: Sample1


title: Intact_brc1-2_rep1

description:
Library name: Intact_brc1-2_rep1
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: C4-2, 5beta-DHT 10 nM, csFBS, 24 h, biol. rep. 3

description: Library name: C42_csFBS_5bDHT10nM_24h_r3

value: 5beta-Dihydrotestosterone 10 nM, 10% csFBS, 24 h


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-5_S1_L006

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-5_S1_L006
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: Intact_WT_rep3

description:
Library name: Intact_WT_rep3
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: liver, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 3

city: Wuhan

first: Zhenghong

last: Kang

state: Hubei

address: 461 Luoyu Road, Hongshan District, Wuhan City, Hubei Province

department: School of Sports Medicine

institute: Wuhan Sports University

description: Library name: Union3

data_processing:
Base calling was performed using CASAVA software. Raw sequencing data in FASTQ format were assessed for quality using FastQC.
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.36) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
High-quality clean reads were aligned to the mouse reference genome (GRCm39) using STAR aligner (version 2.7.9a) with default parameters.
Gene-level read counts were generated using featureCounts (version 2.0.1) with default parameters against the mouse reference genome annotation (GENCODE).
Additionally, transcript assembly and expression quantification were performed using StringTie (version 2.1.4), and expression levels were normalized as FPKM and TPM values.
Assembly: GRCm39
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing gene-level count matrix for all samples. Rows represent genes (annotated with Ensembl gene IDs and gene symbols), and columns represent individual samples. Values are raw read counts generated by featureCounts.

source_name: liver

growth_protocol: Eight-week-old male db/db mice were randomly assigned to four groups: sedentary control (CON), HIIT only, semaglutide only, and combined intervention (HIIT + semaglutide). HIIT was performed on a motorized treadmill, consisting of 10 bouts of 4-minute high-intensity running at 85-90% of maximal running speed interspersed with 2-minute active recovery at 50-60% of maximal speed, 5 days per week for 8 weeks. Semaglutide was administered via subcutaneous injection at a dose of 30 nmol/kg once daily for 8 weeks. The combined group received both interventions simultaneously.

extract_protocol:
Immediately after euthanasia, heart, kidney, hippocampus, liver, and soleus muscle were rapidly harvested, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted from each tissue sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's standard protocol. RNA quality and integrity were assessed using a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.
Stranded mRNA-seq libraries were constructed using poly(A) mRNA enrichment with oligo(dT) magnetic beads. Library preparation was performed following the standard protocol of the NEB Next Ultra RNA Library Prep Kit for Illumina. The constructed libraries were sequenced on the Illumina NovaSeq 6000 platform in paired-end 150 bp (PE150) mode. Library construction and sequencing services were provided by Qingke Biotechnology Co., Ltd.

value: liver

value: C57BL/KsJ db/db mice

value: HIIT Exercise AND Semaglutide injection


title: C4-2, 5beta-DHT 10 nM, csFBS, 24 h, biol. rep. 2

description: Library name: C42_csFBS_5bDHT10nM_24h_r2


title: liver, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 2

description: Library name: Union2

treatment_protocol: Eight-week-old male db/db mice were randomly assigned to four groups: sedentary control (CON), HIIT only, semaglutide only, and combined intervention (HIIT + semaglutide). HIIT was performed on a motorized treadmill, consisting of 10 bouts of 4-minute high-intensity running at 85-90% of maximal running speed interspersed with 2-minute active recovery at 50-60% of maximal speed, 5 days per week for 8 weeks. Semaglutide was administered via subcutaneous injection at a dose of 30 nmol/kg once daily for 8 weeks. The combined group received both interventions simultaneously.


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-4_S1_L005

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-4_S1_L005
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.

value: single-cell suspension from intestinal tissue


title: C4-2, testosterone 100 nM, 10% FBS, Day 1 (24 h), biol. rep. 1

description: Library name: C42_FBS_T100nM_D1_r1

value: Testosterone 100 nM, 10% FBS, Day 1 (24 h)


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-3_S1_L001

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-3_S1_L001
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: C4-2, 5beta-DHT 10 nM, csFBS, 24 h, biol. rep. 1

description: Library name: C42_csFBS_5bDHT10nM_24h_r1


title: liver, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 1

description: Library name: Union1


title: Intact_WT_rep2

description:
Library name: Intact_WT_rep2
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-2_S1_L003

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-2_S1_L003
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: Intact_WT_rep1

description:
Library name: Intact_WT_rep1
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: rac-GR24_rep3

description:
Library name: rac-GR24_rep3
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.

source_name: whole seedlings

value: whole seedlings


title: C4-2, testosterone 10 nM, csFBS, 24 h, biol. rep. 3

description: Library name: C42_csFBS_T10nM_24h_r3

value: Testosterone 10 nM, 10% csFBS, 24 h


title: liver, semaglutide,0.05 mg/kg, rep3

description: Library name: Medicine3

value: Semaglutide injection


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-10_S1_L004

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-10_S1_L004
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: C4-2, testosterone 10 nM, csFBS, 24 h, biol. rep. 2

description: Library name: C42_csFBS_T10nM_24h_r2

value: prostate


title: liver, semaglutide,0.05 mg/kg, rep2

description: Library name: Medicine2


title: rac-GR24_rep2

description:
Library name: rac-GR24_rep2
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: C4-2, testosterone 10 nM, csFBS, 24 h, biol. rep. 1

description: Library name: C42_csFBS_T10nM_24h_r1

value: castration-resistant prostate cancer (CRPC) cell


title: liver, semaglutide,0.05 mg/kg, rep1

description: Library name: Medicine1


title: C. buqueti larval anterior midgut single-cell RNA-seq: YCS-1_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YCS-1_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval anterior midguts. Tissues from eight individuals were pooled to generate one pooled biological sample. No independent biological replicate was prepared; run-level files represent technical sequencing replicates from the same pooled sample.


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY14

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY14
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.

data_processing:
Raw sequencing data were processed using the Stereo-seq Analysis Workflow (SAW) and stereopy to generate the spatial gene expression matrix.
UMIs from neighboring DNBs were aggregated to create a bin50 expression matrix. Low-quality bins were filtered using minimum cell and count thresholds.
The processed matrix was normalized and analyzed for spatial transcriptomic profiling. RCTD was used with the scRNA-seq data as a reference to infer cell-type composition of spatial bins.
Spatial gene modules were identified using Hotspot-based analysis, and the processed spatial transcriptomic object was saved as CY_A02600D6.h5ad.
Assembly: Cyrtotrachelus buqueti reference genome
Supplementary files format and content: CY_A02600D6.h5ad: processed Stereo-seq spatial transcriptomic expression matrix with spatial coordinates and associated annotations.

source_name: complete larval intestine

growth_protocol: Cyrtotrachelus buqueti larvae were collected from Leshan, Sichuan, China in July 2023. One complete larval intestine from a single individual was used for Stereo-seq spatial transcriptomics.

extract_protocol:
A clean and intact larval intestine was dissected, fixed with 4% paraformaldehyde, washed with PBS, arranged on aluminum foil, embedded in OCT, sectioned, and subjected to hematoxylin and eosin staining for quality control.
Stereo-seq library construction was performed according to the Stereo-seq workflow. The library was sequenced using the DNBSEQ platform.

treatment_protocol: No experimental treatment was applied. The sample represents a complete larval intestine spatial transcriptomic section.

value: complete larval intestine

value: spatial transcriptomic section from intestinal tissue


title: C4-2, vehicle (ethanol), csFBS, 24 h, biol. rep. 3

description: Library name: C42_csFBS_Ctrl_24h_r3

value: AR T878A (endogenous)

value: Vehicle (ethanol), 10% csFBS, 24 h


title: DMSO_rep3

description:
Library name: DMSO_rep3
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.

value: DMSO


title: rac-GR24_rep1

description:
Library name: rac-GR24_rep1
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY13

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY13
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: Postmortem Minor Salivary Gland, donor 12

status: Public on Aug 10 2026

city: Bethesda

first: Blake

middle: M

last: Warner

state: MD

address: 10 Center Drive, Room 1A01

institute: NIDCR

description: Library name: P12MSG

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a custom GRCh38.v32 human genome that was modified to include ERCCs and SIRVs, using STAR v2.7.3a in single-pass mode with the --quantMode GeneCounts parameter.
Gene counts were generated with STAR v2.7.3a built-in counting option --quantMode GeneCounts against a GRCh38.v32 genome annotation GTF which included ERCCs and SIRVs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCh38.v32
Supplementary files format and content: RawCountFile.txt, raw gene counts in tab-delimited txt format.
Supplementary files format and content: RawCountFile_filtered.txt, filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: CPM_TMM_counts.txt, TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: MSG

extract_protocol:
RNA was extracted using Rneasy Plus Minikit
Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a NextSeq 2000 sequencer (Illumina) using 55x55bp paired-end  mode.

value: MSG

tag: condition

value: SARS-CoV-2 infected


title: DMSO_rep2

description:
Library name: DMSO_rep2
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: liver, exercised,60min, rep3

description: Library name: HIIT3

value: liver

value: HIIT Exercise


title: C4-2, vehicle (ethanol), csFBS, 24 h, biol. rep. 2

description: Library name: C42_csFBS_Ctrl_24h_r2


title: liver, exercised,60min, rep2

description: Library name: HIIT2

value: C57BL/KsJ db/db mice


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY12

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY12
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: C4-2, vehicle (ethanol), csFBS, 24 h, biol. rep. 1

description: Library name: C42_csFBS_Ctrl_24h_r1


title: liver, exercised,60min, rep1

description: Library name: HIIT1


title: DMSO_rep1

description:
Library name: DMSO_rep1
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY11

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY11
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: R2_Sorted

city: Shanghai

first: Jia

last: Ji

address: 386 Bibo Rd, Pudong New District

department: Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

description:
Library name: Sorted
R2-sorted population enriched for reduced GFP/mCherry signals

library_source: genomic

data_processing:
The analysis of CRISPR screening data was performed using MAGeCK-VISPR50, including read mapping, sgRNA annotation and comparison of the conditions using the MAGeCK RRA algorithm.
Assembly: hg38
Supplementary files format and content: Processed data files include sgRNA read count tables, and MAGeCK gene enrichment analysis results in comma-separated text format (.csv).
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: embryonic kidney

growth_protocol: DMEM, 10% fetal bovine serum, 100 units/mL penicillin-streptomycin, 2 mM L-glutamine. All cells were cultured at 37°C with 5% CO2.

extract_protocol:
Genomic DNA was extracted from the finally sorted cells using QIAamp DNA Blood Midi Kit.
sgRNA sequences were amplified by PCR.

treatment_protocol: Cells transduced with a pooled CRISPR-Cas9 sgRNA library were subjected to two rounds of flow cytometry-based sorting to enrich cell populations with reduced GFP/mCherry signals.

value: embryonic kidney

value: Flp-In HEK295T

value: HEK295T stable cell line

value: sorted


title: Unsorted_Control

description:
Library name: Control
Unsorted control population

value: Flp-In HEK293T

value: HEK293T stable cell line

value: unsorted


title: JKZ243_asil1-2_RNA-seq_rep2

city: Shenzhen

first: Jian-Kang

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

department: Institute of Advanced Biotechnology, Institute of Homeostatic Medicine, and School of Medicine

institute: Southern University of Science and Technology

description: Library name: asil1-2_rep2

data_processing:
Raw reads were processed using Fastp (default settings) to remove adapters and low-quality bases. Clean reads were aligned to the TAIR10 reference genome using TopHat2 with the “--b2-very-sensitive” option. The resulting BAM files were normalized and converted to BedGraph format using deepTools for visualization in IGV. Differential expression of protein-coding genes and transposable elements (TEs) was determined using Cuffdiff (Cufflinks) with the “-u -b <genome.fa>” option. Genes or TEs with FDR < 0.05 and absolute log2 fold change (log2FC) ≥ 1 were considered differentially expressed.
Assembly: Arabidopsis thaliana (Col-0) TAIR10 reference genome
Supplementary files format and content: tab-delimited bedGraph.gz files with normalized CPM values per genomic interval
Supplementary files format and content: tab-delimited TSV file containing differentially expressed genes.

source_name: Seedling

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown under long-day conditions (16 h light/8 h dark, 22°C). Seeds were surface-sterilized, stratified for 3 days at 4°C in darkness, germinated on 1/2 Murashige and Skoog (MS) medium with 2% sucrose and 0.8% agar. Fourteen-day-old seedlings were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted from 100 mg of tissue using TRIzol reagent (Invitrogen) following manufacturer’s instructions.
Library construction was performed at the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) following Illumina protocols.

value: Seedling


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY10

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY10
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.

value: complete larval intestine

value: spatial transcriptomic section from intestinal tissue


title: liver, db/db control group, rep3

description: Library name: Control3

value: Normal rearing


title: JKZ243_asil1-2_RNA-seq_rep1

description: Library name: asil1-2_rep1


title: liver, db/db control group, rep2

description: Library name: Control2


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY9

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY9
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: HESCs, siNC, rep3

last: Qi

state: Shanghai

address: No.845 Lingshan Road, Pudong District, Shanghai

institute: Shanghai Jiao Tong University, School of Medicine,Renji Hospital

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads.
The clean reads were aligned to 9606（NCBI Taxonomy ID） genome (version: GRCh38) using the Hisat2.
We applied HTseq to calculate the counts of the genes.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary human endometrial stromal cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: primary human endometrial stromal cells

value: siNC


title: liver, db/db control group, rep1

description: Library name: Conrtol1


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY8

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY8
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: JKZ243_hpd3-2_RNA-seq_rep2

description: Library name: hpd3-2_rep2


title: HESCs, siNC, rep2


title: JKZ243_hpd3-2_RNA-seq_rep1

description: Library name: hpd3-2_rep1


title: Peritoneal macrophages from aged mouse, biological replicate 4

first: Jialiang

last: Guan

address: No. 5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: A-6

data_processing:
Raw reads were trimmed to remove adaptor sequences and low-quality bases. Cleaned reads were aligned to the mouse reference genome (mm10) using HISAT2 (v2.1.0). Gene expression was quantified using featureCounts (v2.0.6).
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample. Rows correspond to genes and columns correspond to samples.

source_name: peritoneum

growth_protocol: Young (2-3 months) and aged (18-24 months) female C57BL/6J mice were housed in a specific pathogen-free (SPF) facility. They were maintained under a 12-hour light/dark cycle with ad libitum access to standard chow and water.

extract_protocol:
Total RNA was extracted from FACS-sorted peritoneal macrophages using TRIzol reagent following the manufacturer's protocol.
RNA sequencing libraries were prepared from total RNA following a standard protocol. Briefly, mRNA was first purified from total RNA using poly-T oligo-attached magnetic beads. The enriched mRNA was then fragmented using divalent cations under elevated temperature. First-strand cDNA was synthesized from the fragmented RNA using random hexamer primers and M-MuLV Reverse Transcriptase, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-stranded cDNA fragments were subjected to end-repair, 3’ end adenylation, and ligation of hairpin loop adaptors. To select for fragments of a specific size, the library was purified with an AMPure XP system to preferentially isolate fragments of 370–420 bp. The size-selected, adaptor-ligated cDNA was then amplified by PCR using Phusion High-Fidelity DNA polymerase. The final PCR products were again purified with the AMPure XP system, and the library quality was assessed using an Agilent Bioanalyzer 2100 system before sequencing on an Illumina NovaSeq platform.

treatment_protocol: Peritoneal macrophages were collected by peritoneal lavage. For RNA sequencing, peritoneal cells were subjected to fluorescence-activated cell sorting (FACS) to isolate CD11b+ F4/80+ macrophages.

value: peritoneum

value: primary peritoneal macrophage

tag: age

value: Aged control (18-24 months)


title: HESCs, siNC, rep1


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY7

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY7
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: Non(H3K4me3)-2

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
For Cut & Tag, the sequenced reads were first trimmed using Trimmomatic and then aligned to the mouse genome (GRCm38/mm10) using bowtie2 software (version 2.4.4). All aligned reads were then sorted and indexed by SAMtools function, sort and index, respectively. The duplicated reads were removed using picard (https://broadinstitute.github.io/picard/): MarkDuplicates with –REMOVE_DUPLICATES option. To increase the number of reads for accuracy, we performed sequencing twice. The resulting two FASTQ files were merged using SAMtools function “merge”. Bigwig files were generated from sorted BAM files using deepTools function, bamCoverage.
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

source_name: Embryo

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 2-cell stage (28 hours post insemination: 28 hpi).

extract_protocol:
Embryos free of polar bodies were transferred to an ice-cold extraction buffer (25 mM HEPES-NaOH [pH 7.5], 50 mM NaCl, 3 mM MgCl2, 300 mM sucrose and 0.5% Triton X-100), and incubated for 30 sec. The embryos were lightly fixed with 0.1% formaldehyde in PBS for 2 min. Embryos were washed in an antibody buffer (20 mM HEPES-NaOH [pH7.5], 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, 2 mM EDTA and 1x Protease inhibitor cocktail) and incubated with the primary antibody (anti-H3K4me3 rabbit IgG; Active motif, 39159) overnight at 4oC. After the primary antibody reaction and washing with antibody buffer, embryos were incubated with the secondary antibody (mouse anti-rabbit IgG-HRP antibody [sc-2357, SantaCruz]) for 1.5 h at room temperature. The embryos were incubated in a wash buffer (20 mM HEPES-NaOH [pH7.5], 150 mM NaCl, 0.1% BSA, 0.5 mM Spermidine and 1x Protease inhibitor cocktail). The prepared embryos were treated with the pA-Tn5 adaptor complex for 30 min at 37oC. After the treatment, embryos were further washed with wash buffer containing BSA and the washed embryos were transferred to a tube filled with Tagmentation buffer (10 mM MgCl2 in wash buffer without BSA), followed by incubation at 37°C for 1 h on a water bath. The tagmentation reaction was stopped by adding EDTA, SDS and Proteinase K with the following incubation at 50°C for 2 h. Such samples were reverse-crosslinked by incubating at 65°C for 16 h. DNA was collected by conventional Phenol/Chloroform extraction and Ethanol precipitation. The collected DNA pellet was resuspended in 20 μl of 0.1×TE buffer and treated with RNaseA.
The above-prepared DNA was PCR-amplified using Q5 High-Fidelity Master mix (NEB) and 0.25 μM barcoded primers with the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 18 cycles of 98°C for 10 sec and 63°C for 30 sec; final extension at 72 °C for 1 min and hold at 4°C. The produced DNA library was purified using the 1.1×AMPure XP magnetic beads (Beckman Coulter) method and finally eluted in 12 μl of RNase-free water. The obtained library was quality-checked by BioAnalyzer (High sensitivity kit, Agilent Technologies).

treatment_protocol: Polar bodies were carefully removed by micro-manipulation during 24-28 hpi.

value: Embryo

value: 2-cell embryo

value: Non injection control


title: Peritoneal macrophages from aged mouse, biological replicate 3

description: Library name: A-4


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY6

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY6
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: HESCs, siLPCAT3, rep3


title: Non(H3K4me3)-1


title: Peritoneal macrophages from aged mouse, biological replicate 2

description: Library name: A-3


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY5

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY5
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: HESCs, siLPCAT3, rep2


title: Peritoneal macrophages from aged mouse, biological replicate 1

description: Library name: A-1


title: HESCs, siLPCAT3, rep1


title: sfLB1(H3K4me3)-2

value: sfLB1 (LC3-binding domain of lamin B1) mRNA injection


title: sfLB1(H3K4me3)-1


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY4

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY4
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: GFP control Female1

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

department: Anatomy and Cell Biology

institute: uiowa

description: Library name: 392

data_processing:
To quantify transcript-level abundances, we performed the quality control for RNA-seq reads and used the Salmon tool with mapping-based mode again the mouse reference transcriptome (mm10). After transcript quantification, the differential gene expression analysis between different groups was conducted with the DESeq2 package. Differential expression was defined as log 2 fc > 0.58 and FDRadjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: csv files include FPKM files for each sample

source_name: Liver

extract_protocol:
For RNA-seq, Trizol-purified RNAs were re-purified using RNeasy (QIAgen) and RNA integrity validated using NanoDrop.
Briefly, 2 μg/sample of RNA was used for sequencing using Illumina HiSeq 4000/75PE Sequencer. 23 million reads were generated for each sample.

value: Liver


title: Peritoneal macrophages from young mouse, biological replicate 4

description: Library name: Y-6

value: Young control (2-3 months)


title: Flpo control Male2

description: Library name: 436


title: NCI-H226, shControl-3 [Control3.mock]

last: Jiang

address: Xincun Rd. 389

institute: Shanghai tongji hospital

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), clean reads of BS-treated libraries were aligned to the reference genome (UCSC hg19) by meRanGh (one component of meRanTK) software
The methylation status of each C within the genome was extracted by meRanCall (one component of meRankTK) softwaremeRanCompare (one component of meRanTK) software was used to identify differentially methylated sites (DMSs).
Assembly: hg19
Supplementary files format and content: This table contains information on RNA modification sites identified in each sample

extract_protocol:
RNA was harvested using RNAios Plus (TAKARA)
RNA libraries were prepared using GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.)

value: shControl


title: CD8T_24h-H2AZ-cKO_rep1

first: Mingzhao

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Library name: CD8_24h-H2AZ-cKO2-1
24hCD8CKO2-1
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt

data_processing:
Trim Galore (v0.6.7) and Trimmomatic (v0.39) was used to remove the low quality reads (parametrs- --quality 20 --stringency 3)
Bowtie2 (v2.5.1) was used to align reads to the mouse genome
Assembly: mm10
Supplementary files format and content: tab delimited text files includes FPKM values for each sample

source_name: spleen

growth_protocol: T cells were maintained in 1640 supplemented with 10% fetal bovine serum (BI), 10mM Hepes (Gibco), 1% NEAA (Gibco), 1% penicillin/streptomycin (Gibco), 50uM β-Mercaptoethanol (Gibco) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from 1 × 10⁶ naïve or activated T cells using TRIzol reagent (Invitrogen, 15596018).
RNA-seq libraries were constructed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770L) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with or without 2 µg/ml coated anti-CD3 antibody and 2 µg/ml soluble anti-CD28 antibody.

value: spleen

value: naive CD8 T cell


title: NCI-H226, shControl-2 [Control2.mock]


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY3

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY3
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.

value: complete larval intestine


title: BMDC_SHIFT_2

city: xiamen

first: YESI

last: SHI

address: xiangan south road

institute: Xiamen University

description: Library name: SHIFT_2

data_processing:
Raw reads were filtered to remove adaptor sequences, low-quality reads, and reads containing excessive unknown bases.
Clean reads were aligned to the Mus musculus reference genome (GRCm38/mm10).
Gene expression levels were quantified as raw read counts and normalized expression values.
Differential expression analysis and pathway enrichment analyses were performed between treatment groups.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all samples.
Supplementary files format and content: Microsoft Excel file containing normalized gene expression values for all samples.

source_name: Bone marrow

growth_protocol: Mouse bone marrow-derived dendritic cells (BMDCs) were isolated from the bone marrow of C57BL/6 mice and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and recombinant GM-CSF under standard culture conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality and concentration were assessed prior to library preparation.
RNA libraries were constructed using a poly(A) enrichment strategy and prepared according to the manufacturer's standard protocol. Sequencing was performed on the DNBSEQ  platform.

treatment_protocol: BMDCs were treated with saline, protoscolex-derived antigens (PSA), F127@PSA, or SHIFT-F127@PSA prior to RNA extraction for transcriptome analysis.

value: Bone marrow

value: Bone marrow-derived dendritic cells

value: Wild type


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY1

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY1
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.

value: spatial transcriptomic section from intestinal tissue


title: NCI-H226, shControl-1 [Control1.mock]


title: BMDC_SHIFT_3

description: Library name: SHIFT_3


title: Cyrtotrachelus buqueti larval complete intestine Stereo-seq: CY2

address: 四川省乐山市市中区滨河路778号

description:
Library name: CY2
Stereo-seq spatial transcriptomic sample from one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from one individual, was not pooled, and had no biological or technical replicate. Sex was not determined; collection location was China: Sichuan, Leshan; collection date was 2023-07.


title: Peritoneal macrophages from young mouse, biological replicate 3

description: Library name: Y-4

value: peritoneum


title: Peritoneal macrophages from young mouse, biological replicate 1

description: Library name: Y-1

value: primary peritoneal macrophage


title: BMDC_SHIFT_1

description: Library name: SHIFT_1


title: Non3-3

description: Library name: Non3-3

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each Sample

extract_protocol:
For RNA-seq analyses, after the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
For RNA-seq analyses, SMART-seq library preparation was performed using SMART-Seq® mRNA HT (634795, Takara). The produced cDNA was amplified by PCR. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).

treatment_protocol: After insemination, fertilized embryos were collected at 12-14 hpi for mRNA injection. mRNAs were injected using a piezo manipulator (Prime Tech, Tsukuba, Japan).


title: Peritoneal macrophages from young mouse, biological replicate 2

description: Library name: Y-3


title: NCI-H226, shNSUN4-3 [SH3.mock]


title: BMDC_F127_3

description: Library name: F127_3


title: ATN-3

type: RNA

city: Leiden

first: Ziyang

address: Albinusdreef

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: profile 770 genes across 37 pathways

hyb_protocol: Hybridization of RNA samples with the probes occurred at 65°C for 17 hours, followed by loading onto the nCounter Prep Station in accordance with the manufacturer’s instructions.

scan_protocol: Data collection was performed by the nCounter MAX Digital Analyzer.

data_processing: Data analysis was conducted using the nSolver 4.0 Analysis Software System, including quality control (QC) based on Imaging QC, Binding Density QC, Positive Control QC, and   Limit of Detection QC. Samples that passed QC were subjected to a two-step data transformation   process (positive control normalization and housekeeping gene normalization), and normalized counts   were exported for subsequent differential gene expression (DGE) analysis.

label: not applicable

source_name: renal biopsy transport medium

label_protocol: not applicable

growth_protocol: not applicable

extract_protocol: We harvested BTM from the pathology ward. Samples were centrifuged and the sediments were lysed with 500 μl TRIzol™ Reagent (Ambion, Foster City, CA, USA) or 350 μl buffered RLT (included in RNeasy Micro Kit, QIAGEN, Hilden, Germany) + 3.5 μl 2-Mercaptoethanol (Merck Schuchardt OHG, Hohenbrunn, Germany) and homogenized.

treatment_protocol: not applicable

tag: diagnosis

value: non-rejection


title: Non3-2

description: Library name: Non3-2

value: Embryo


title: BMDC_F127_2

description: Library name: F127_2


title: NCI-H226, shNSUN4-2 [SH2.mock]


title: ATN-2

description: profile 770 genes across 37 pathways


title: Non3-1

description: Library name: Non3-1

value: 2-cell embryo


title: NCI-H226, shNSUN4-1 [SH1.mock]


title: BMDC_F127_1

description: Library name: F127_1


title: flLB1(F454A/L457A)ΔC-3

description: Library name: flLB1(F454A/L457A)ΔC-3

value: flLB1(F454A/L457A)ΔC mRNA injection


title: BMDC_PSA_3

description: Library name: PSA_3

value: PSA


title: ATN-1

description: profile 770 genes across 37 pathways


title: TCMR-4

description: profile 770 genes across 37 pathways

value: rejection


title: TCMR-3

description: profile 770 genes across 37 pathways


title: flLB1(F454A/L457A)ΔC-1

description: Library name: flLB1(F454A/L457A)ΔC-1


title: BMDC_PSA_2

description: Library name: PSA_2


title: NCI-H226, shControl-3 [Control3.m5c]


title: BMDC_PSA_1

description: Library name: PSA_1


title: NCI-H226, shControl-2 [Control2.m5c]


title: TCMR-2

description: profile 770 genes across 37 pathways


title: NCI-H226, shControl-1 [Control1.m5c]


title: Non4-3

description: Library name: Non4-3

value: Non injection control


title: BMDC_Saline_3

description: Library name: Saline_3

value: Saline


title: NCI-H226, shNSUN4-3 [SH3.m5c]


title: TCMR-1

description: profile 770 genes across 37 pathways


title: Non4-2

description: Library name: Non4-2


title: CD4T_24h-WT_rep1

description:
Library name: CD4T_24h-WT-1
0h-WT-1
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: spleen

value: naive CD4 T cell

value: WT


title: NCI-H226, shNSUN4-2 [SH2.m5c]


title: BMDC_Saline_2

description: Library name: Saline_2

value: Bone marrow


title: ABMR-5

description: profile 770 genes across 37 pathways


title: NCI-H226, shNSUN4-1 [SH1.m5c]


title: ABMR-4

description: profile 770 genes across 37 pathways


title: NCI-H226, shControl-3

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the reference genome with hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling.
edgeR (v3.16.5) was used to perform normalization and differentially expressed mRNAs were identified by p-value and fold change.
Assembly: hg19
Supplementary files format and content: This table includes RNA counts and normalized values for each sample.

value: shControl


title: ABMR-3

description: profile 770 genes across 37 pathways


title: tMut-2

description: Library name: tMut-2

value: mutant tether and anchor mRNA injection


title: BMM TGFβ 3

city: Berkeley

first: Stefan

middle: A

last: Fattinger

state: California

address: 415 Weill Hall

institute: UC Berkeley

description: Library name: Sample 18

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36. Trimmed reads were mapped to the Mus musculus GRCm38 reference genome with STAR aligner v.2.5.2b. Analysis of raw counts was performed with DESeq2
Assembly: mm10
Supplementary files format and content: csv file including raw counts of each sample

source_name: Bone marrow derived macrphage (BMMs)

growth_protocol: Bone marrow-derived macrophages (BMMs) were differentiated from bone marrow and maintained in DMEM supplemented with 10% FBS, PenStrep, Glutamin, HEPES, and M-CSF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with TRK lysis buffer (Omega Bio-Tek) and 2-mercaptoethanol followed by total RNA isolation using the E.Z.N.A Total RNA Kit I (Omega Bio-Tek)
RNA libraries for RNA-seq were prepared using an Illumina Poly(A) selection kit following manufacturer's protocols.

treatment_protocol: BMMs were left untreated, stimulated with 10ng/ml of IFNβ, IFNγ, TNF, or TGFβ for 6 hours or preexposed to 10ng/ml IFNβ for 24h before adding 10ng/ml IFNγ for 6h.

value: Bone marrow derived macrphage (BMMs)

value: B6 WT

value: TGFβ


title: BMM TGFβ 2

description: Library name: Sample 17


title: NCI-H226, shControl-2


title: tMut-1

description: Library name: tMut-1


title: NCI-H226, shControl-1


title: tWT-3

description: Library name: tWT-3

value: tether and anchor mRNA injection


title: ABMR-1

description: profile 770 genes across 37 pathways


title: BMM TGFβ 1

description: Library name: Sample 16


title: BMM TNF 3

description: Library name: Sample 15

value: TNF


title: tWT-2

description: Library name: tWT-2

value: Embryo

value: 2-cell embryo


title: NCI-H226, shNSUN4-3


title: FFPE_3

description: profile 770 genes across 37 pathways

source_name: Tumor-free tissue from nephrectomy

extract_protocol: We harvested tumor-free tissues from a tumor nephrectomy. These tissues were cut into slices of 1.5x1.5x20 mm. Pairs of tissue pieces were then placed in 15 ml phosphate-buffered saline (PBS). In addition, two larger pieces of the adjacent   tissue from the same nephrectomy were processed either as FFPE or fresh-frozen samples which were stored at -80 ℃. Before centrifuging BTM, biopsies were removed, and the resulting sediments were lysed with 500 μl TRIzol™ Reagent (Ambion, Foster City, CA, USA) or 350 μl buffered RLT (included in RNeasy Micro Kit, QIAGEN, Hilden, Germany) + 3.5 μl 2-Mercaptoethanol (Merck Schuchardt OHG, Hohenbrunn, Germany) and homogenized.

value: Tumor-free tissue from nephrectomy


title: NCI-H226, shNSUN4-2


title: BMM TNF 2

description: Library name: Sample 14


title: BMM TNF 1

description: Library name: Sample 13


title: NCI-H226, shNSUN4-1


title: frozen_2

description: profile 770 genes across 37 pathways


title: Non2-3

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
After the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
SMART-seq library preparation was performed using SMART-Seq® HT Kit (Z4438N, Takara). The produced cDNA was amplified by PCR with 13 cycles. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).


title: BMM IFNβ/γ 3

description: Library name: Sample 12

value: IFNβ/γ


title: T6

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney biopsy

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

value: kidney

value: kidney biopsy

value: 6 yo


title: FFPE_2

description: profile 770 genes across 37 pathways


title: BTM_2

description: profile 770 genes across 37 pathways


title: Non2-1

value: Non injection control


title: BMM IFNβ/γ 2

description: Library name: Sample 11


title: T7

description: 10x Genomics

value: 5 yo


title: T9

description: 10x Genomics

value: 4 yo


title: BMM IFNβ/γ 1

description: Library name: Sample 10


title: frozen_1

description: profile 770 genes across 37 pathways


title: tWT-1

description: Library name: tWT-1


title: flLB1(5A)-3

value: flLB1(5A) mRNA injection


title: T8

description: 10x Genomics

value: 7 yo


title: FFPE_1

description: profile 770 genes across 37 pathways


title: T3

description: 10x Genomics

value: 3 yo


title: BMM IFNγ 2

description: Library name: Sample 8

value: Bone marrow derived macrphage (BMMs)

value: B6 WT

value: IFNγ


title: BTM_1_24h

description: profile 770 genes across 37 pathways


title: K3

description: 10x Genomics


title: flLB1(5A)-1


title: BTM_1_4h

description: profile 770 genes across 37 pathways


title: BMM IFNβ 3

description: Library name: Sample 6

value: IFNβ


title: SJRHB031691_X3_DYE8560_VT

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
Library name: SJRHB031691_C8
2355611

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

source_name: Tumor

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

value: Tumor

value: VT

value: RMS


title: flLB1(F454A/L457A)-3

value: Embryo

value: 2-cell embryo

value: flLB1(F454A/L457A) mRNA injection


title: BTM_1_2h

description: profile 770 genes across 37 pathways

value: Tumor-free tissue from nephrectomy


title: flLB1(F454A/L457A)-2


title: T2

description: 10x Genomics

value: kidney

value: kidney biopsy

value: 6 yo


title: K2

description: 10x Genomics


title: iBUC_21pl7

city: Rehovot

first: Sharon

last: Schlesinger

address: Herzl 229

department: Animal Science

country: Israel

institute: Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem

description: Library name: SV40_FBS-2

data_processing:
Sequence reads were trimmed for adaptor and polyA using Cutadapt
Trimmed sequence reads were mapped to Bos_taurus.ARS-UCD1.2 genome using STAR
Read count extraction to fatures using HTSeq
Normalization of the counts and differential expression analysis using DESeq
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: raw_counts_wj_sv40.xlsx
Library strategy: Bulk MARS-seq

organism: Bos taurus

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in low glucose Dulbecco's Modified Eagle's Medium, containing 10% Fetal Bovine Serum (FBS), penicillin-streptomycin solution 1% , Glutamine 1%, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted via PureLink RNA Minikit
Library preparation was done by Weizmann Institute, Rehovot. Sequencing Libraries were prepared using Bulk MARS-Seq. SR reads were sequenced on 1 lane(s) of an Illumina NovaSeq Sp (100 cycles). The output was ~25 million reads per sample.

treatment_protocol: cells were immortalized by transient transfection of a plasmid carrying the SV40 large T antigen for the WJ-SV40 line

value: umbilical cord

value: Immortalized SV-40

value: mesenchymal stem cells

tag: breed

value: Holstein

value: immortalized cells, 21 days culturing


title: BMM IFNβ 2

description: Library name: Sample 5

value: Bone marrow derived macrphage (BMMs)

value: B6 WT


title: BTM_1_1h

description: profile 770 genes across 37 pathways


title: K1

description: 10x Genomics

value: 3 yo


title: BMM IFNβ 1

description: Library name: Sample 4

value: IFNβ


title: BTM_1_0.5h

description: profile 770 genes across 37 pathways


title: T1

description: 10x Genomics


title: BMM untreated 3

description: Library name: Sample 3

value: Untreated


title: Non-4

value: Embryo

value: Non injection control


title: NT2.5LV liver-preferential cell line, replicate 3

city: Los Angeles

first: Evanthia

middle: T

last: Roussos Torres

state: CA

institute: University of Southern California

description: Library name: NT2.5LV_rep3

data_processing:
Base calling and demultiplexing were performed to generate paired-end FASTQ files (Novogene).
Reads were aligned to the mouse reference genome GRCm38 (mm10) using STAR v2.7.
Gene-level read counts were quantified using featureCounts (Subread package).
Counts were filtered with filterByExpr and normalized using the edgeR TMM method; normalized expression is reported as log2 counts per million (logCPM).
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw_counts__featureCounts.tsv: tab-delimited text file of raw gene-level read counts (featureCounts); rows are Ensembl gene IDs, columns are the eight samples.
Supplementary files format and content: logCPM__edgeR_TMM__withGeneNames_corrected.tsv: tab-delimited text file of edgeR TMM-normalized log2 counts per million; columns are Ensembl gene ID, gene symbol, and the eight samples.

source_name: mammary tumor

growth_protocol: NT2.5, NT2.5LM, and NT2.5LV cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum, 100 U/mL penicillin, 100 U/mL streptomycin, 0.1% non-essential amino acids, 0.1% L-glutamine, and 10 mM HEPES, at 37 C in a humidified 5% CO2 incubator. Cells were harvested at 70-80% confluence.

extract_protocol:
Total RNA was extracted from cultured cells using a Qiagen RNA extraction kit according to the manufacturer's instructions, and RNA integrity and quantity were assessed prior to library preparation.
Messenger RNA was purified from total RNA by poly-T oligo-attached magnetic beads (poly(A) enrichment). Strand-specific paired-end libraries were prepared and sequenced as 2x150 bp reads on an Illumina NovaSeq X Plus to approximately 6 Gb of raw data per sample (Novogene).

value: mammary tumor

value: HER2-positive mammary carcinoma

value: neu-N transgenic (MMTV-neu)


title: Non-3

value: 2-cell embryo


title: T4

description: 10x Genomics

value: kidney

value: kidney biopsy

value: 1 yo


title: NT2.5LV liver-preferential cell line, replicate 2

description: Library name: NT2.5LV_rep2


title: K4

description: 10x Genomics


title: BMM untreated 1

description: Library name: Sample 1


title: Non-1


title: SJRHB013758_X1_DYE8552_VT

description:
Library name: SJRHB013758_C8
2355603

value: Tumor

value: VT

value: RMS


title: tLC3-4(LC3_short-4)

value: truncated LC3 mRNA injection


title: NT2.5LM lung-preferential cell line, replicate 2

description: Library name: NT2.5LM_rep2


title: APOE4, Male, 24M, #1

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

description:
Library name: BU-APOE-6
10x Genomics v3

data_processing:
The single cell RNA sequencing data preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite v.3.0.2. Briefly, raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering, and differential expression analyses were performed using Seurat v5.0.1 with default parameter settings unless specified otherwise.
Assembly: mm10
Supplementary files format and content: compressed tab-separated and matrix values

source_name: brain

extract_protocol:
The mice were perfused with phosphate-buffered saline (PBS, pH 7.4) after anesthetization with isoflurane, followed by a quick dissection of cortex from left hemisphere to the HBSS buffer (Gibco, 14025076). The cortices were then dissociated with papain-based the Neural Tissue Dissociation kit (Miltenyi Biotec, 130–092-628) using gentleMACS™ Dissociator (Miltenyi Biotec, 130-093-235) followed by debris removal through filtering with the 70-µm cell strainer. Cell suspensions were then subject to myelin removal (Cat# 130-096-433, Miltenyi Biotec), red cell lysis (Cat# 130-094-183; Miltenyi Biotec) and dead cell removal (Cat# 130-090-101; Miltenyi Biotec) according to the manufacturer’s instructions. Finally, cell pellets were resuspended in Ca/Mg-free PBS supplemented with 0.5% FBS. Cell numbers and viability were determined through trypan blue examination under microscope. More than 90% of the cells were identified viable for all the 24 samples.
The isolated cells were subject to single cell RNA sequencing (scRNAseq) through the chromium platform (10x Genomics) with the 39 gene expression V3 kit, using a targeted input of ∼6,000–9,000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10x-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina) targeting a depth of 25,000–50,000 reads per cell.

value: brain

tag: flow cell

tag: apoe genotype

tag: age in_months

tag: Sex

value: Male


title: T5

description: 10x Genomics

value: 3 yo


title: NT2.5LM lung-preferential cell line, replicate 1

description: Library name: NT2.5LM_rep1


title: tLC3-3(LC3_short-3)


title: S8_Mut_LPS

city: Jeddah

first: xuan

last: zhou

address: Thwal

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
Raw data quality were checked with FASTQC.
BBDuk was used to remove low-quality reads and adapters.
Reads were aligned to NCBI GRCh38.p13 with STAR (v2.5.1)
Low expression reads were filtered out using HTSFilter package.
Differential expression analysis was performed using edgeR.
Assembly: GRCh38.p13
Supplementary files format and content: fpkm.txt. Normalize reads number.

source_name: macropahge cells

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep Plus Kits (R2073) for sequencing.
NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®

treatment_protocol: 0.5 million WT iMPs (WT) and WASP-KO iMPs (Mut) were treated with/without 100 μg/ml Lipopolysaccharide (LPS) for 6 hours.

value: iPS-derived macrophages

value: macropahge cells

value: WASP knock out

value: LPS


title: tLC3-2(LC3_short-2)

value: Embryo


title: APOE2, Male, 24M, #1

description:
Library name: BU-APOE-4
10x Genomics v3


title: S7_Mut


title: NT2.5 parental cell line, replicate 3

description: Library name: NT2.5_rep3

value: mammary tumor

value: HER2-positive mammary carcinoma

value: neu-N transgenic (MMTV-neu)


title: NT2.5 parental cell line, replicate 2

description: Library name: NT2.5_rep2


title: APOE4, Male, 3M, #1

description:
Library name: BU-APOE-3
10x Genomics v3


title: iBUC_21pl8

description: Library name: SV40_FBS-3

value: umbilical cord

value: Immortalized SV-40

value: mesenchymal stem cells

value: Holstein

value: immortalized cells, 21 days culturing


title: tLC3-1(LC3_short-1)

value: 2-cell embryo

value: truncated LC3 mRNA injection


title: S6_WT_LPS

value: WT


title: APOE3, Male, 3M, #1

description:
Library name: BU-APOE-2
10x Genomics v3

value: brain

value: Male


title: LC3-4

value: LC3 mRNA injection


title: NT2.5 parental cell line, replicate 1

description: Library name: NT2.5_rep1


title: LC3-3


title: APOE2, Male, 3M, #1

description:
Library name: BU-APOE-1
10x Genomics v3


title: S4_Mut_LPS

value: iPS-derived macrophages

value: macropahge cells

value: WASP knock out


title: APOE4, Male, 24M, #2

description:
Library name: BU-APOE-24
10x Genomics v3


title: Fungal hyphae, MT-36-3

city: Kunming

first: yankun

last: Liu

state: Yunnan

address: Yunnan University

institute: Yunnan university

description:
RNA sequence for different times in infection
Vps18_36h_3

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include FPKM values for each sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The WT and mutant strains were cultured in PDA at 28 °C, 180 rpm for 7 days.

extract_protocol:
The mycelium was divided and induced with about 300 nematodes for 0、12 and 36 h, respectively.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit foilowing manufacturer's protocols.

treatment_protocol:
The mycelium was divided and induced with about 300 nematodes for 36 h
Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

value: MT

value: induced with nematodes for 36 h


title: Fungal hyphae, MT-36-2

description:
RNA sequence for different times in infection
Vps18_36h_2


title: APOE3, Male, 24M, #1

description:
Library name: BU-APOE-5
10x Genomics v3


title: LC3-2

value: Embryo


title: S3_Mut


title: APOE3, Male, 24M, #2

description:
Library name: BU-APOE-23
10x Genomics v3


title: Fungal hyphae, MT-36-1

description:
RNA sequence for different times in infection
Vps18_36h_1


title: S2_WT_LPS

value: LPS


title: Fungal hyphae, MT-12-3

description:
RNA sequence for different times in infection
Vps18_12h_3

treatment_protocol:
The mycelium was divided and induced with about 300 nematodes for 12 h
Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: induced with nematodes for 12 h


title: APOE2, Male, 24M, #2

description:
Library name: BU-APOE-22
10x Genomics v3


title: Col9, pt3, veh

city: Vienna

first: Maximilian

last: Baumgartner

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine

description:
Library name: Sample 15
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol9

data_processing:
nf-core/rnaseq: 3.14.0
Assembly: Homo_sapiens.GRCh38.115
Supplementary files format and content: Salmon derived gene count tables for large intestine (LI, colon) and small intestine (SI, ileum) organoids in .tsv files

source_name: colon

extract_protocol:
Organoid monolayers were extracted using the Qiagen RNeasy mini kit with on column DNA digestion.
Library construction was performed at the commercial company Novogene, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: colon

value: organoid

value: intestinal organoid

value: vehicle

tag: individual

value: Ileum Patient 3


title: S1_WT

value: WT


title: APOE4, Male, 3M, #2

description:
Library name: BU-APOE-21
10x Genomics v3

value: brain

value: Male


title: Fungal hyphae, MT-12-2

description:
RNA sequence for different times in infection
Vps18_12h_2


title: Col8, pt3, GW

description:
Library name: Sample 14
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol8

value: GW


title: PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 4

city: LIMOGES

first: Stéphanie

last: DURAND

address: 2 rue du Dr Marcland

department: UMR 1308 INSERM

country: France

institute: University of Limoges / INSERM

description:
Library name: Sample 12
Column name in Raw_Counts_All_Samples.txt : PT_NTn4

data_processing:
Bioinformatics analysis was conducting by the Beijing Genomics Institute according following analysis pipeline: 1) Raw data obtained from sequencing were filtered using SOAPnuke to remove reads with low quality (reads with a percentage of bases with a quality value less than 15 exceeding 20% of the total bases in the read), adapter contamination, and high content of unknown bases (N) (greater than 0.1%). More of 30 million high-quality (clean) paired reads per sample were obtained after read filtering step, with more 90% of reads with quality greater than Q30 (range: 89.85 to 96.34%). 2) HISAT2 (v2.2.1) was used for aligning clean reads to human reference genome (GRCh38.p14). (3) Gene expression quantification was performed using RSEM3 (v1.3.1) software with Bowtie2 (v2.3.4.3) used as the internal transcriptome aligner. Alignment results show a range of 78.74 to 84.96% of read uniquely mapped to reference. Finally, the average alignment of the gene set was 87.20% and a total of 18856 genes were detected.
SOAPnuke (v1.5.6) parameters : -l 15 -q 0.2 -n 0.001 -G
HISAT2 (v2.2.1) parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Bowtie2 (v2.4.5) parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 20 -N 1
RSEM (v1.3.1) parameters: -p 8 --forward-prob 0
Assembly: Homo_sapiens_NCBI_GCF_000001405.40_GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: The SW480 cell line was purchased from the American Type Culture Collection (ATCC/LGC Promochem, Molsheim, France) and cultured in RPMI 1640 GlutaMAXTM medium (Gibco™, Thermo Fisher, MA, USA) supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and 1 % of penicillin-streptomycin (Thermo Fisher) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was harvested using the Quick-RNA™ Microprep kit (Zymo Research). Only samples with a concentration of at least 50 ng/µL and an RNA Integrity Number (RIN) greater than 7 were included for further analysis.
RNA sequencing was conducted by the Beijing Genomics Institute, following the manufacturer’s protocol for Rolling-Circle and DNA Nano-Ball (DNB™) technology. Paired-end reads were generated with a length of 150 bases using the DNBSEQ platform.

treatment_protocol: The optimal elution conditions for SdFFF separation were as follows: flow injection through the accumulation wall of a 100 μL SW480 cell suspension (2.5 × 106 cells/mL) ; Flow rate: 1.0 mL/min ; Mobile phase: sterile DEP, pH 7.4 and conductivity 20 mS/m ; External multigravitational field strength: 12 ± 0.2 g (270 rpm) ; Time-dependent fraction collection: F1: 3'20” to 4'30” and F3: 6'00” to 7'50”. A third fraction was also collected, constituting the total eluted population, PT: 3'20 to 7'50, without the void volume as an internal biological control

value: colorectal cancer cell

value: Wild Type

value: SdFFF fraction:PT


title: APOE3, Male, 3M, #2

description:
Library name: BU-APOE-20
10x Genomics v3


title: Fungal hyphae, MT-12-1

description:
RNA sequence for different times in infection
Vps18_12h_1

value: Fungal hyphae

value: MT


title: Col7, pt3, CDCA

description:
Library name: Sample 13
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol7

value: CDCA


title: PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 3

description:
Library name: Sample 11
Column name in Raw_Counts_All_Samples.txt : PT_NTn3


title: Fungal hyphae, MT-0-3

description:
RNA sequence for different times in infection
Vps18_0h_3

treatment_protocol:
The mycelium was divided and induced with about 300 nematodes for 0 h
Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: induced with nematodes for 0 h


title: Col6, pt2, veh

description:
Library name: Sample 12
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol6

value: Ileum Patient 2


title: APOE4, Female, 24M, #2

description:
Library name: BU-APOE-18
10x Genomics v3

value: Female


title: Fungal hyphae, MT-0-2

description:
RNA sequence for different times in infection
Vps18_0h_2


title: PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 1

description:
Library name: Sample 9
Column name in Raw_Counts_All_Samples.txt : PT_NTn1

value: colon


title: Col5, pt2, GW

description:
Library name: Sample 11
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol5

value: organoid

value: intestinal organoid


title: Fungal hyphae, MT-0-1

description:
RNA sequence for different times in infection
Vps18_0h_1


title: Col4, pt2, CDCA

description:
Library name: Sample 10
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol4


title: F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 4

description:
Library name: Sample 8
Column name in Raw_Counts_All_Samples.txt : F3_NTn4

value: SdFFF fraction:F3


title: Fungal hyphae, WT-36-3

description:
RNA sequence for different times in infection
AO_36h_3

value: WT

value: induced with nematodes for 36 h


title: Col3, pt1, veh

description:
Library name: Sample 9
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol3

value: vehicle

value: Ileum Patient 1


title: Fungal hyphae, WT-36-2

description:
RNA sequence for different times in infection
AO_36h_2


title: APOE4, Female, 3M, #2

description:
Library name: BU-APOE-15
10x Genomics v3

value: brain


title: Col2, pt1, GW

description:
Library name: Sample 8
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol2

value: GW


title: F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 2

description:
Library name: Sample 6
Column name in Raw_Counts_All_Samples.txt : F3_NTn2

value: colorectal cancer cell

value: Wild Type


title: Fungal hyphae, WT-36-1

description:
RNA sequence for different times in infection
AO_36h_1

value: Fungal hyphae


title: Col1, pt1, CDCA

description:
Library name: Sample 7
Column name in LIorganoids_gene_salmon_estimated_counts.tsv: RNAcol1

value: CDCA


title: F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 1

description:
Library name: Sample 5
Column name in Raw_Counts_All_Samples.txt : F3_NTn1


title: APOE2, Female, 3M, #2

description:
Library name: BU-APOE-13
10x Genomics v3


title: Fungal hyphae, WT-12-3

description:
RNA sequence for different times in infection
AO_12h_3

value: induced with nematodes for 12 h


title: Ile9, pt3, veh

description:
Library name: Sample 6
Column name in SIorganoids_gene_salmon_estimated_counts.tsv: Ile9

source_name: ileum

value: ileum

value: Colon Patient 3


title: F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 4

description:
Library name: Sample 4
Column name in Raw_Counts_All_Samples.txt : F1_NTn4

value: colon

value: SdFFF fraction:F1


title: APOE4, Female, 24M, #1

description:
Library name: BU-APOE-12
10x Genomics v3

value: Female


title: Fungal hyphae, WT-12-2

description:
RNA sequence for different times in infection
AO_12h_2


title: Ile8, pt3, GW

description:
Library name: Sample 5
Column name in SIorganoids_gene_salmon_estimated_counts.tsv: Ile8

value: organoid

value: intestinal organoid


title: F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 3

description:
Library name: Sample 3
Column name in Raw_Counts_All_Samples.txt : F1_NTn3


title: Fungal hyphae, WT-12-1

description:
RNA sequence for different times in infection
AO_12h_1

value: WT


title: Ile6, pt2, veh

description:
Library name: Sample 4
Column name in SIorganoids_gene_salmon_estimated_counts.tsv: Ile6

value: vehicle

value: Colon Patient 2


title: F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 2

description:
Library name: Sample 2
Column name in Raw_Counts_All_Samples.txt : F1_NTn2


title: APOE2, Female, 24M, #1

description:
Library name: BU-APOE-10
10x Genomics v3

value: brain


title: Fungal hyphae, WT-0-3

description:
RNA sequence for different times in infection
AO_0h_3

value: induced with nematodes for 0 h


title: Ile5, pt2, GW

description:
Library name: Sample 3
Column name in SIorganoids_gene_salmon_estimated_counts.tsv: Ile5

value: GW


title: S5_WT

value: iPS-derived macrophages

value: macropahge cells


title: APOE4, Female, 3M, #1

description:
Library name: BU-APOE-9
10x Genomics v3


title: Fungal hyphae, WT-0-2

description:
RNA sequence for different times in infection
AO_0h_2

value: Fungal hyphae


title: APOE3, Female, 24M, #1

description:
Library name: BU-APOE-11
10x Genomics v3


title: LC3-1

value: Embryo

value: 2-cell embryo

value: LC3 mRNA injection


title: Ile3, pt1, veh

description:
Library name: Sample 2
Column name in SIorganoids_gene_salmon_estimated_counts.tsv: Ile3

value: ileum

value: Colon Patient 1


title: Fungal hyphae, WT-0-1

description:
RNA sequence for different times in infection
AO_0h_1


title: APOE3, Female, 3M, #1

description:
Library name: BU-APOE-8
10x Genomics v3

value: Female


title: Ile2, pt1, GW

description:
Library name: Sample 1
Column name in SIorganoids_gene_salmon_estimated_counts.tsv: Ile2

value: organoid


title: S. cereviisase BY4741_Ty1 Dex24h

city: Vancouver

first: Marjan

last: Barazandeh

state: BC

address: 6622-2405 Wesbrook Mall

department: Pharmaceutical Sciences

country: Canada

institute: University of British Columbia

description: Library name: YM9_Dextrose

data_processing:
Adapters and low-quality bases were removed from reads with Trimmomatic (v0.39).
reads were filtered for the 'AACA' tag at the 5'end and the adaptor sequence “TAGTCCCTTAAGCGGAGCCCTATAG” from the 3'end
The reads were then mapped to the S. cerevisiae R64 reference genome using BWA-MEM (version 0.7.19).
Alignments were processed using SAMtools (v1.22), bedtools (v2.31.1) and picard (v 3.4.0) to convert to BAM format, sort alignments by genomic coordinates and remove PCR duplicates
Only uniquely mapped reads were retained for Ty1 insertion site analysis
Assembly: R64 (SacCer3)
Supplementary files format and content: bed

organism: Saccharomyces cerevisiae

growth_protocol: overnight in SC-Ura +2% raffinose + 0.1% dextrose, inoculated into SC-Ura + 2% Galactose or 2% Dextrose for 24h, then grown in SC + 2% Dextrose for 24h, then SC + 2% Dextrose + 1mg/mL 5-FOA for 24h, then repeated for another 24h.

extract_protocol:
triple phenol:chloroformisoamyl alcohol extractions
genomic DNA was digested with MseI, then MseI adaptors were ligated, followed by digestion with Bgl II.  The resulting DNA was PCR amplified with indexing primers that also contained with the SSB site or the MseI adaptor sequence.  The PCR products were size selected (200-1000bp) on an 8% TBE PAGE gel and fragments were extracted using an EZNA PolyGel DNA Extraction kit from OMEGA bio-tek.

treatment_protocol: Minimal media with Raffinose, Galactose, glucose

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0

value: BY4741+pJEF2365 incubuated in SC complete + 2% dextrose for 24 hours


title: APOE2, Male, 3M, #2

description:
Library name: BU-APOE-19
10x Genomics v3

value: Male


title: PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 2

description:
Library name: Sample 10
Column name in Raw_Counts_All_Samples.txt : PT_NTn2

value: colon

value: colorectal cancer cell

value: Wild Type

value: SdFFF fraction:PT


title: APOE2, Female, 3M, #1

description:
Library name: BU-APOE-7
10x Genomics v3

value: brain


title: S. cerevisiae BY4741_Ty1_Gal24h

description: Library name: YM9_Galactose

value: BY4741+pJEF2365 induced in SC complete + 2% galactose for 24 hours