title: glioma tissue from patient09

city: Xuzhou

first: Xiuping

last: Zhou

state: Jiangsu

address: Huaihaixi Road 84#

institute: Xuzhou Medical University

description:
Library name: BEFORE_RT_05
Column name in raw_counts.txt:read_count_Before_RT_05

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke [1] 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). Structure variation detection The clean reads were mapped to the reference genome using HISAT2 [2]. After that, Ericscript (v0.5.5) [3] and rMATS (V4.1.2) [4] were used to detect fusion genes and differential splicing genes (DSGs), respectively RNA identification Bowtie2[5] 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) [6]. The heatmap was drawn by pheatmap (v1.0.12) [7] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) [8] (or DEGseq （v1.48.0）[9] or PoissonDis[10])with Q value ≤ 0.05(or FDR ≤ 0.001). Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [11].
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt: format (txt file) , content (raw read counts of all samples along with average read counts of "AFTER_RT" group and "BEFORE_RT" group) .
Supplementary files format and content: FPKM_AFTER_RT_01.xlsx: format (xlsx file), content (RNA expression of sample "AFTER_RT_01" normalized by FPKM)
Supplementary files format and content: FPKM_AFTER_RT_02.xlsx: format (xlsx file), content (RNA expression of sample "AFTER_RT_02" normalized by FPKM)
Supplementary files format and content: FPKM_AFTER_RT_03.xlsx: format (xlsx file), content (RNA expression of sample "AFTER_RT_03" normalized by FPKM)
Supplementary files format and content: FPKM_AFTER_RT_04.xlsx: format (xlsx file), content (RNA expression of sample "AFTER_RT_04" normalized by FPKM)
Supplementary files format and content: FPKM_BEFORE_RT_01.xlsx: format (xlsx file), content (RNA expression of sample "BEFORE_RT_01" normalized by FPKM)
Supplementary files format and content: FPKM_BEFORE_RT_02.xlsx: format (xlsx file), content (RNA expression of sample "BEFORE_RT_02" normalized by FPKM)
Supplementary files format and content: FPKM_BEFORE_RT_03.xlsx: format (xlsx file), content (RNA expression of sample "BEFORE_RT_03" normalized by FPKM)
Supplementary files format and content: FPKM_BEFORE_RT_04.xlsx: format (xlsx file), content (RNA expression of sample "BEFORE_RT_04" normalized by FPKM)
Supplementary files format and content: FPKM_BEFORE_RT_05.xlsx: format (xlsx file), content (RNA expression of sample "BEFORE_RT_05" normalized by FPKM)

source_name: brain tissue

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction. Appropriate amount of tissue was ground into powder under liquid nitrogen, then transferred into a 2ml EP tube containing 1.5ml of TRIzol, standing for 5 minutes. For cell samples, the TRIzol was directly added to the cell sample with the amount 1 mL per 1×10^6 cells, followed by vortex mixing and standing for 5-minute. The mixture was centrifuged at 4°C at 12,000xg for 5 minutes, and the supernatant was transferred to a new EP tube for extraction. 300μl of chloroform/isoamyl alcohol (24:1) was added into the transferred supernatant and the mixture was vigorously vortexed to ensure thorough mixing. Then the mixture was centrifuged at 4°C and 12,000xg for 8 minutes. Take the clear upper aqueous layer and repeat the above process one time. After centrifugation, the final upper aqueous layer  was carefully transferred to a new 1.5ml EP tube with a 2/3 supernatant volume of isopropanol (for low amount of tissues/ cell, 2µL 5mg/mL glycogen can be added for precipitation), gently inverted to mix well, placed in a -20°C refrigerator for 2 hours. Next, the precipitation mixture was centrifuged with 17500xg at 4°C for 25 minutes. The supernatant was discarded, and the precipitation was washed with 0.9ml of 75% ethanol. The precipitation was suspended by inverting the tube up and down several times. Then the precipitation was collected by centrifuging at 17500g for 3 minutes at 4°C and discarding the supernatant. Repeat the centrifugation to remove supernatant completely and the precipitation was dried in the biosafety cabinet for 3-5 minutes. Finally, 20µL~200µL of DEPC-treated or RNase-free water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Fragment Analyzer or Agilent 2100 Bioanalyzer (Agilent, CA, USA), or Qseq-400 (Bioptic, Taiwan, China).
2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Radiation type: 6-mVz line. Radiation therapy scope: CT: delineated based on imaging findings PTV: 3mm external placement around CTV Radiotherapy dose: 2.0Gy/f * 30f

value: brain tissue

value: before radiation treatment


title: IR_RL_031

status: Public on Aug 09 2026

type: SRA

city: Rochester

first: Gagandeep

last: Kaur

address: 601 Elmwood Ave

department: Environmental Medicine

country: USA

institute: University of Rochester Medical Center

description:
Library name: IR_RL_031
10x Genomics

library_source: transcriptomic single cell

data_processing:
Samples RL_15, RL_16, and RL_17 - 10X provided cellranger mkfastq and count version 6.0.1 using standard parameters
Visium - 10X provided spaceranger mkfastq and count version 1.3.1 using standard parameters
All remaining scRNA-Seq samples - 10X provided cellranger mkfastq and count version 7.0.1 using standard parameters
Assembly: 10X provided GRCh38-2020-A transcriptome
Supplementary files format and content: scRNA-Seq - compressed filtered gene bc matrices output folder
Supplementary files format and content: Spatial Transcriptomics - whole compressed output folder excluding bams as generated by spaceranger version 1.3.1

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
We used three distinct lung sections (1”) –   parenchymal, peri-bronchial and sub-pleural regions-for each lung sample. The lung lobes were weighed and placed into Gentle MACS C-tube (Miltenyi, Gaithersburg, MD) with Liberase (Cat# 5401127001; Roche, Basel, Switzerland) enzymatic cocktail with 1% DNase. The tubes were then transferred to the gentleMACS dissociator (Miltenyi, Gaithersburg, MD) and the manufacturer’s protocol for human lung digestion was run.  The sample tubes were then transferred to the MACSmix rotator and incubated at 370C for 30 minutes with constant rotation. After incubation, the cell suspension was mixed with 5 mL of DMEM with 10% FBS and strained through a 100-micron MACS Smart Strainer. Thereafter, the suspension was centrifuged at 500g for 10 minutes at 40C, the supernatant was discarded, and 1 mL of RBC lysis buffer was added to the cell pellet to digest RBCs. The suspension was left on ice for 5 min in RBC lysis buffer and then 4 mL of ice-cold PBS with 10% FBS was added to stop the lysis. The suspension was again centrifuged at 500g for 10 minutes at 40C. The cell pellet was suspended in 5 mL PBS with 10% FBS, and cell number and viability were checked using AO/PI staining on a Nexcelom Cellometer Auto2000. This cell suspension was immediately used for C12FdG staining as described earlier [37] and submitted to the Genomics Research Core at URMC for library preparation for scRNA seq.
scRNA-seq -Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s NovaSeq 6000 at a mean sequence depth of 30,000 reads per cell. Read alignment was performed to GRCh38 genome. Spatial transriptomics - 5um sections were placed on the spatially barcoded capture areas of a 10X Genomics Visium Gene Expression Slide (10X Genomics, Pleasanton, CA). Following tissue placement, slide drying, and overnight incubation in a desiccator, the slide was deparaffinized, H&E stained, and imaged using a VS120 Slide Scanner (Olympic) at 20X magnification. Sequence ready libraries were then constructed according to the manufacturer’s instructions (10X Genomics, CG000407). Final libraries were sequenced on the NovaSeq6000 (Illumina, San Diego, CA) to obtain at least 50,000 reads per spot.

treatment_protocol: The human lung samples were procured through United Network for Organ Sharing facilitated by the International Institute for the Advancement of Medicine (IIAM). Few of the samples used for spatial transcriptomics/proteomics were obtained from commercial sources (Origene)

tag: tissue

value: Lung

tag: age

tag: Sex

value: female

tag: smoking status

value: Non Smoker

tag: disease state

value: Normal


title: Lck_GEX_Data

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: Library name: Lck-W1-GEX

data_processing:
Resulting cDNA libraries were sequenced on NextSeq 2000 (Illumina, NextSeq 1000/2000 Control Software 1.7.2.48444) with NextSeq 1000/2000 P3 XLEAP-SBS 100-cycle kit.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 109 and prepared using the mkref tool from 10x Cell Ranger v8.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from 10x Cell Ranger v8.0.1 using R2 sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm39 v109 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples and finalized results.

organism: Mus musculus

source_name: spleen

extract_protocol:
Splenocytes were collected on day 5 post LM-OVA-immunization. Samples were enriched for CD8+ cells by using Dynabeads™ Untouched™ Mouse CD8 Cells Kit (Cat#11417D, Invitrogen) according to manufacturer’s instructions. The cells were resuspended in HBSS and stained with with LIVE/DEAD near-IR dye, anti-CD8a BV421, anti-CD45.1 PE, and anti-CD45.2 APC antibodies together with TotalSeq-C Hashtag antibodies for multiplexing (BioLegend; MH1: #155861, MH2: #155863, MH3: #155865, MH5: #155869, MH6: #155871, MH7: #155873, MH8: #155875, MH9: #155877, MH10: #155879). Viable CD8α+, CD45.2+OT-I cells were FACS sorted.
Cells were loaded onto a 10X Chromium X machine (10X Genomics). The sequencing libraries were prepared using the Chromium GEM-X Single Cell 5′ Reagent Kits v3 with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10x Genomics; #PN-1000263, #PN-1000286, #PN-1000541, #PN-1000190, #PN-1000215, #PN-1000250), following the manufacturer's protocol (#CG000736 Rev A).

value: spleen

tag: cell line

value: CD8+ T cells

tag: genotype

value: WT/cLCK KO


title: glioma tissue from patient08

country: China

description:
Library name: BEFORE_RT_04
Column name in raw_counts.txt:read_count_Before_RT_04

library_source: transcriptomic

tag: treatment


title: WT-C1

city: hefei

first: Xinwei

last: Zhao

state: anhui

address: changjiang strest

institute: anhui agricultural university

description: Library name: sample1

data_processing:
RNA extracted from Arabidopsis thaliana, Illumina PE150 library construction. Raw reads demultiplexed with Bcl2fastq v2.20.0.422, quality checked by FastQC v0.10.1, trimmed via Cutadapt v1.9.1. Clean reads mapped to TAIR10.51 with HISAT2 v2.2.1. Transcripts assembled with StringTie v1.3.3b, novel transcripts annotated with Cuffcompare v2.2.1. SNV/InDel called by samtools v0.1.19 and annotated by ANNOVAR v2013.02.11. Gene counts quantified with HTSeq v0.6.1; global RNA-seq QC via RSeQC. DEGs calculated by DESeq2 v1.26.0, GO/KEGG functional enrichment conducted. Alternative splicing analyzed with rMATS v4.1.0; DEXSeq v1.18.4 for DEU.
Assembly: Arabidopsis thaliana TAIR10.51
Supplementary files format and content: all.fpkm_anno.xls

organism: Arabidopsis thaliana

source_name: Whole plant

extract_protocol:
Plant material preparation: Arabidopsis thaliana materials included wild-type Col-0, uap1-1 and uap1-2 mutant seedlings. Seeds were germinated and grown to 10-day-old seedlings under standard normal growth conditions; a subset of seedlings was treated at 4 °C for 24 h cold stress before tissue collection. Whole seedling tissues were harvested and immediately frozen in liquid nitrogen for RNA extraction. Total RNA isolation: Total RNA extraction, integrity detection and purity quantification were performed by Azenta Life Sciences (Suzhou, China) following their proprietary standard RNA extraction protocol for plant tissue. Briefly, high-quality intact total RNA was purified from frozen seedling tissues, followed by rigorous quality control to verify RNA integrity number (RIN), OD260/280 and OD260/230 ratios to exclude degraded or contaminated RNA samples.
Total RNA was isolated from Arabidopsis tissues and quality-checked for purity, concentration and integrity (RIN) via Nanodrop, agarose electrophoresis and Agilent 2100. Poly(A) mRNA was enriched with oligo(dT) beads to remove non-coding RNAs. Purified mRNA was randomly fragmented to 200–300 bp. First-strand cDNA was synthesized with random hexamers and M-MuLV reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. cDNA fragments were end-repaired, 3’-A-tailed, and ligated to Illumina barcoded PE adapters. Target-size fragments were purified by magnetic beads and amplified via 10–15 cycles of high-fidelity PCR. Libraries were quality-controlled by qPCR and Agilent 2100, then pooled and sequenced on Illumina platform with PE150 strategy.

value: Whole plant

value: Wild type (Col-0)

value: Cold (4°C for 24-h)


title: IR_RL_029

description:
Library name: IR_RL_029
10x Genomics

value: Current Smoker

value: COPD


title: glioma tissue from patient07

description:
Library name: BEFORE_RT_03
Column name in raw_counts.txt:read_count_Before_RT_03


title: run2_Sample10_KO_act_inh_Cyclosp

description: Library name: run2_Sample10

data_processing:
The libraries were sequenced in two runs: the first in paired-end mode and the second in single-end mode, on an Illumina NextSeq 2000 (NextSeq 1000/2000 Control Software v1.7.2.48444) using the NextSeq 1000/2000 P3 XLEAP-SBS 100-cycle Kit for both runs.
Reads were mapped using STAR v2.7.11b(Dobin et al., 2013) to the GRCm39 mouse reference genome obtained from Ensembl (release 109)(Howe et al., 2021).
Gene counts were quantified R v4.5.2 using the GenomicAlignments v1.44.0 and tximport 1.36.0 packages.
Downstream differential expression analysis was performed using DESeq2 v1.48.1 (14) in R v4.5.2.
Assembly: GRCm39 v109 (Ensembl)
Supplementary files format and content: Annotated (symbols) raw counts for whole bulk experiment

source_name: lymph-nodes

extract_protocol:
In total, 3 × 106 CD8+ cells were FACS-sorted from lymph nodes of mice. Non-activated controls were directly used for RNA isolation. The remaining cells were activated with 1 µM OVA peptide (SIINFEKL) alone or in combination with the following inhibitors, P38 inhibitor SB203580 (12.5µM), ERK inhibitor (328006-M Millipore) (10µM), Cyclosporin A (C3662 Sigma-Aldrich) (0.1 µM), TPCA-1 (T1452 Sigma) (10µM) for 16h 5% CO2 at 37°C.
cDNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio, #634413) and the Unique Dual Index Kit (Takara Bio, #634752) according to the manufacturer's guidelines.

treatment_protocol: WT or cLCK KO mice were treated with tamoxifen.

value: lymph-nodes

value: cLCK KO

value: OVA 1uM activation + Cyclosporin 0.1 uM

tag: batch


title: IR_RL_028_2

description:
Library name: IR_RL_028_2
10x Genomics

value: male


title: run2_Sample9_KO_act_inh_ERK

description: Library name: run2_Sample9

value: OVA 1uM activation + inhERK 10 uM


title: GFP control DAP-seq library from biological replicate 4, technical replicate B

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: Institute of Plant Biology

description:
Library name: GFP-4-B
GFP control DAP-seq library using genomic DNA from Oryza sativa roots.

library_source: genomic

data_processing:
Raw reads were trimmed using fastp (v0.23.2) and quality assessed with FastQC. Clean reads were aligned to the reference genome using Bowtie2. Signal normalization and visualization were performed using deepTools. Peaks were called using MACS2 with a q-value cutoff of 0.05. IDD7-enriched peaks relative to GFP control were identified from two independent technical replicates (Rep A and Rep B), each comprising pooled genomic DNA from three biological replicates. Peak overlap and annotation were performed using BEDTools, and motif discovery was conducted using MEME.
Assembly: Nipponbare reference genome (https://rice.uga.edu/)
Supplementary files format and content: .bed

molecule: genomic DNA

organism: Oryza sativa

source_name: root

extract_protocol:
Rice (Oryza sativa ssp. japonica cv. Nipponbare) plants inoculated with Rhizophagus irregularis were grown under a 12-h light/dark cycle at 30/28 °C. Roots were harvested at 7 weeks post-inoculation with >90% colonization. Genomic DNA was extracted using a CTAB-based protocol and treated with RNase A.
Genomic DNA was fragmented to ~250 bp using a Covaris ultrasonicator and purified with AMPure XP beads. Sequencing libraries were constructed using the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs). HaloTag–IDD7 and HaloTag–GFP (control) proteins were expressed using the TNT® SP6 Wheat Germ Cell-Free System (Promega) and incubated with the DNA library for 1 h. Bound DNA was eluted, PCR-amplified, and sequenced on an Illumina NovaSeq platform (150-bp paired-end, ~6 Gb per sample).

value: root

tag: sample group

value: GFP control DAP-seq library

value: Rhizophagus irregularis, 25 uM Pi, 7wpi


title: glioma tissue from patient06

description:
Library name: BEFORE_RT_02
Column name in raw_counts.txt:read_count_Before_RT_02

value: brain tissue

value: before radiation treatment


title: GFP control DAP-seq library from biological replicate 4, technical replicate A

description:
Library name: GFP-4-A
GFP control DAP-seq library using genomic DNA from Oryza sativa roots.


title: IR_RL_028_1

description:
Library name: IR_RL_028_1
10x Genomics

value: Lung

value: Non Smoker

value: Normal


title: glioma tissue from patient05

description:
Library name: BEFORE_RT_01
Column name in raw_counts.txt:read_count_Before_RT_01


title: run2_Sample8_KO_act_inh_IP39

description: Library name: run2_Sample8

value: CD8+ T cells

value: OVA 1uM activation + Ip38 12.5 uM inhibitor


title: IR_RL_027_2

description:
Library name: IR_RL_027_2
10x Genomics

value: Current Smoker


title: run2_Sample7_KO_act

description: Library name: run2_Sample7

value: OVA 1uM activation


title: glioma tissue from patient04

description:
Library name: AFTER_RT_04
Column name in raw_counts.txt:read_count_After_RT_04

value: after radiation treatment


title: GFP control DAP-seq library from biological replicate 3, technical replicate A

description:
Library name: GFP-3-A
GFP control DAP-seq library using genomic DNA from Oryza sativa roots.


title: GFP control DAP-seq library from biological replicate 3, technical replicate B

description:
Library name: GFP-3-B
GFP control DAP-seq library using genomic DNA from Oryza sativa roots.


title: IR_RL_027_1

description:
Library name: IR_RL_027_1
10x Genomics

value: COPD


title: run2_Sample6_KO

description: Library name: run2_Sample6

value: lymph-nodes

value: cLCK KO


title: glioma tissue from patient03

description:
Library name: AFTER_RT_03
Column name in raw_counts.txt:read_count_After_RT_03


title: IR_RL_023

description:
Library name: IR_RL_023
10x Genomics

value: male


title: GFP control DAP-seq library from biological replicate 2, technical replicate B

description:
Library name: GFP-2-B
GFP control DAP-seq library using genomic DNA from Oryza sativa roots.

value: root


title: glioma tissue from patient02

description:
Library name: AFTER_RT_02
Column name in raw_counts.txt:read_count_After_RT_02


title: run2_Sample5_WT_act_inh_Cyclosp

description: Library name: run2_Sample5

value: WT

value: OVA 1uM activation + Cyclosporin 0.1 uM


title: GFP control DAP-seq library from biological replicate 2, technical replicate A

description:
Library name: GFP-2-A
GFP control DAP-seq library using genomic DNA from Oryza sativa roots; used as control for IDD7 peak calling.

value: GFP control DAP-seq library

value: Rhizophagus irregularis, 25 uM Pi, 7wpi


title: run2_Sample4_WT_act_inh_ERK

description: Library name: run2_Sample4

value: OVA 1uM activation + inhERK 10 uM


title: IR_RL_021_2

description:
Library name: IR_RL_021_2
10x Genomics

value: Lung

value: Non Smoker


title: glioma tissue from patient01

description:
Library name: AFTER_RT_01
Column name in raw_counts.txt:read_count_After_RT_01

value: brain tissue


title: IDD7 DAP-seq library from biological replicate 4, technical replicate B

description:
Library name: IDD7-4-B
DAP-seq using IDD7 protein with genomic DNA from Oryza sativa roots; peaks called relative to GFP control; replicate A or B represents one technical replicate pooling three biological replicates.
IDD7-B_summits_500bp.bed

value: IDD7 DAP-seq library


title: IR_RL_021_1

description:
Library name: IR_RL_021_1
10x Genomics

value: Normal


title: IDD7 DAP-seq library from biological replicate 4, technical replicate A

description:
Library name: IDD7-4-A
DAP-seq using IDD7 protein with genomic DNA from Oryza sativa roots; peaks called relative to GFP control; replicate A or B represents one technical replicate pooling three biological replicates.
IDD7-A_summits_500bp.bed


title: IR_RL_018

description:
Library name: IR_RL_018
10x Genomics

value: Former Smoker


title: run2_Sample2_WT_act

description: Library name: run2_Sample2

value: CD8+ T cells

value: OVA 1uM activation


title: E. coli C600 (pL53T), SspA-6xHis ChIP

city: Hangzhou

first: Ziyi

last: Liu

address: Wusu Road 666

institute: Zhejiang A&F university

description:
Library name: C600_WT_ChIP
SspA-6xHis was enriched via Ni-NTA magnetic bead pull-down (IDA-Co beads). No antibody was used. Cross-links were reversed by proteinase K treatment at 65C for 10 min. DNA was purified using a commercial kit.

data_processing:
Raw sequencing reads were demultiplexed and converted to FASTQ format using bcl2fastq v2.20.
FASTQ files were quality-trimmed using Trimmomatic v0.39. Reads with length < 20 bp after trimming were discarded. Quality control was assessed using FastQC v0.11.9.
Trimmed paired-end reads were aligned to the Escherichia coli K-12 MG1655 reference genome (ASM584v2) using Bowtie2 v2.4.2. Only uniquely mapped reads with at most 2 mismatches were retained. PCR duplicates were removed using Picard MarkDuplicates v2.27.4.
Peaks were called using MACS2 v2.2.7.1 with the significance cutoff q-value <= 0.01. The Input sample was used as the control for background subtraction. Both narrowPeak and broadPeak outputs were generated.
BigWig files were generated using deepTools v3.5.1 (bamCoverage) with normalization to reads per million (RPM). Signal tracks were extended to 150 bp to represent fragment sizes. deepTools computeMatrix was used to generate signal profiles around gene bodies (+/- 3 kb from TSS/TES).
Motif analysis was performed using MEME-ChIP v5.5.0 on peak summit sequences (+/- 50 bp). GO enrichment and KEGG pathway analysis were performed on peak-associated genes using clusterProfiler v4.6.0 in R. Peaks were annotated to nearest genes using HOMER v4.11 annotatePeaks.
Assembly: Escherichia coli K-12 MG1655 (ASM584v2 / GCF_000005845.2)
Supplementary files format and content: bigWig files: normalized ChIP-seq coverage tracks (RPM). narrowPeak files: MACS2 peak calls with genomic coordinates and significance scores. The Input sample has no peak file.

organism: Escherichia coli

source_name: bacterium

growth_protocol: E. coli C600 strains carrying the IncX3 plasmid pL53T and pET-28a-SspA expression vector were cultured in LB broth supplemented with kanamycin (50 ug/mL) at 37C with shaking at 200 rpm.

extract_protocol:
Cells were harvested by centrifugation, washed 2-3 times with PBS, and resuspended in 1 mL PBS supplemented with 1% formaldehyde. Cross-linking was performed at 37C for 10 min, followed by quenching with 0.125 M glycine for 5 min at room temperature. Cells were collected by centrifugation at 4C (4000 x g, 5 min), washed 2-3 times with ice-cold PBS, resuspended in Wash Buffer, and lysed by sonication on ice. A 20 uL aliquot was retained as DNA Input control prior to bead incubation.
ChIP-seq libraries were prepared from purified DNA after reverse cross-linking and proteinase K treatment. SspA-6xHis was enriched via Ni-NTA magnetic agarose beads (IDA-Co) at 4C for 20-30 min. Beads were washed three times with Wash Buffer. Complexes were eluted with Elution Buffer, followed by proteinase K treatment at 65C for 10 min to reverse formaldehyde cross-links. DNA was purified using a commercial DNA purification kit. Libraries were prepared using standard Illumina library prep kits.

treatment_protocol: SspA expression was induced by adding IPTG to a final concentration of 0.5 mM when OD600 reached approximately 0.6. Induction was carried out at 16C with shaking at 200 rpm for 16 h.

value: bacterium

tag: cell type

value: E. coli C600

value: Wild type; carries pET-28a-SspA and IncX3 plasmid pL53T

value: IPTG-induced SspA expression (0.5 mM, 16C, 16h); 1% formaldehyde cross-linking; Ni-NTA magnetic bead immunoprecipitation

value: Batch 1


title: IDD7 DAP-seq library from biological replicate 3, technical replicate B

description:
Library name: IDD7-3-B
DAP-seq using IDD7 protein with genomic DNA from Oryza sativa roots; peaks called relative to GFP control; replicate A or B represents one technical replicate pooling three biological replicates.
IDD7-B_summits_500bp.bed

value: root


title: IR_RL_018_RUL_IR_LL_018_LLL

description:
Library name: IR_RL_018_RUL_IR_LL_018_LLL
10x Genomics

value: male

value: COPD


title: E. coli C600 (pL53T), SspA-6xHis, Input control

description:
Library name: C600_input
Input DNA collected before Ni-NTA magnetic bead incubation. No antibody was used; SspA-6xHis was enriched via Ni-NTA affinity pull-down. Input serves as background control for ChIP-seq peak calling.

value: IPTG-induced SspA expression (0.5 mM, 16C, 16h); 1% formaldehyde cross-linking


title: run2_Sample1_WT

description: Library name: run2_Sample1

value: lymph-nodes

value: WT


title: IDD7 DAP-seq library from biological replicate 3, technical replicate A

description:
Library name: IDD7-3-A
DAP-seq using IDD7 protein with genomic DNA from Oryza sativa roots; peaks called relative to GFP control; replicate A or B represents one technical replicate pooling three biological replicates.
IDD7-A_summits_500bp.bed

value: Rhizophagus irregularis, 25 uM Pi, 7wpi


title: IR_LL_032

description:
Library name: IR_LL_032
10x Genomics

value: Lung

value: female


title: SR9009 and LPS, mouse 3

city: Dublin

first: Paula

middle: Austra

last: Klavina

address: 123 St Stephens Green

department: School of Pharmacy and Biomolecular Sciences

country: Ireland

institute: Royal College of Surgeons in Ireland

description:
Library name: Sample 15
Column WT3_SR9_LPS in gene_count_all.txt

data_processing:
Raw data from RNA sequencing was bioinformatically processed in-house by Novogene. Briefly, this included quality control of reads where read removed if they included adaptor contamination, >10% of bases were resolved as uncertain (N), and where >50% of bases had a base quality < 5. All samples had >97% of bases with a Q Phred values greater than 20, and over 94% of bases with a Q Phred value greater than 30. With these filtered samples and reads, reads were aligned to the mouse GRCm39 reference using HISAT2 to generate gene counts.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files contain FPKM values for each sample

source_name: Bone marrow

growth_protocol: Bone marrow cells were extracted from mouse femurs and tibias and differentiated into macrophages in high glucose DMEM supplemented with 10% FBS, antibiotics and 20% supernatant from L929 cells.

extract_protocol:
RNA was harvested using the PureLink RNA Mini Kit (Thermo Fisher)
Libraries were constructed using polyA capture and reverse transcription into cDNA in-house by Novogene (Cambridge)

treatment_protocol:
Following differentiation, macrophages were grown and treated in high glucose DMEM supplemented with 10% FBS, antibiotics and 10% supernatant from L929 cells.
Bone marrow-derived macrophages were treated with 10 µM SR9009 (Merck) overnight or DMSO as a vehicle control. Following overnight incubation, macrophages were treated with 100 ng/mL LPS (Merck) for 6 hours.

value: Bone marrow

value: Primary cell

value: Bone marrow derived macrophage

value: Wild type

value: 10 µM SR9009 and 100 ng/mL LPS


title: run1_Sample15_KO_act_inh_Cyclosp

description: Library name: run1_Sample15

value: CD8+ T cells

value: cLCK KO

value: OVA 1uM activation + Cyclosporin 0.1 uM


title: IDD7 DAP-seq library from biological replicate 2, technical replicate B

description:
Library name: IDD7-2-B
DAP-seq using IDD7 protein with genomic DNA from Oryza sativa roots; peaks called relative to GFP control; replicate A or B represents one technical replicate pooling three biological replicates.
IDD7-B_summits_500bp.bed

value: root

value: IDD7 DAP-seq library


title: SR9009 and LPS, mouse 4

description:
Library name: Sample 16
Column WT4_SR9_LPS in gene_count_all.txt


title: M07E-GNE987-2

city: Suzhou

first: Fang

last: Fang

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description:
M07E-GNE987-2
M07E-counts.txt

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: M07E sample with GNE987

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


title: run1_Sample14_KO_act_inh_ERK

description: Library name: run1_Sample14

value: OVA 1uM activation + inhERK 10 uM


title: SR9009 and LPS, mouse 2

description:
Library name: Sample 14
Column WT2_SR9_LPS in gene_count_all.txt


title: IDD7 DAP-seq library from biological replicate 2, technical replicate A

description:
Library name: IDD7-2-A
DAP-seq using IDD7 protein with genomic DNA from Oryza sativa roots; peaks called relative to GFP control; replicate A or B represents one technical replicate pooling three biological replicates.
IDD7-A_summits_500bp.bed


title: SR9009 and LPS, mouse 1

description:
Library name: Sample 13
Column WT1_SR9_LPS in gene_count_all.txt


title: M07E-GNE987-1

description:
M07E-GNE987-1
M07E-counts.txt


title: Ri, root, idd7 mutant, 7wpi, sample 3

description: Library name: idd7_7wpi_3

data_processing:
High-quality RNA samples (OD260/280 = 1.69–2.15; RIN ≥ 6.7) underwent library preparation and sequencing on an Illumina NovaSeq6000 platform, generating 150 bp paired-end reads with a read depth of 6 Gb. Raw sequencing reads in FASTAQ format were subjected to adaptor trimming and quality assessment using FastQC and MultiQC, after which RNA sequences were filtered with Trimmomatic (version 0.38) to ensure data integrity. The filtered reads were subsequently mapped to the Oryza sativa reference genome IRGSP1.0 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001433935.1/) by HISAT2 (version 2.1.0)(Kim et al. 2015; Sahraeian et al. 2017). Mapped sequences were counted by featureCounts (version 2.0.0)(Liao et al. 2014). The relation log expression (RLE) gene expression normalization approach was adopted, and DESeq2 (version 1.26.0) was used for standardized differential gene analysis(Schurch et al. 2016; Love et al. 2014). The DEG threshold was a |fold-change| ≥ 2 and adjusted p value < 0.05, which was obtained by Benjamini and Hochberg's approach to control the false discovery rate (FDR)(Benjamini and Hochberg 1995).   Raw sequencing reads in FASTAQ format were subjected to adaptor trimming and quality assessment using FastQC and MultiQC, after which RNA sequences were filtered with Trimmomatic (version 0.38) to ensure data integrity. The filtered reads were subsequently mapped to the Oryza sativa reference genome IRGSP1.0 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001433935.1/) by HISAT2 (version 2.1.0)(Kim et al. 2015; Sahraeian et al. 2017). Mapped sequences were counted by featureCounts (version 2.0.0)(Liao et al. 2014). The relation log expression (RLE) gene expression normalization approach was adopted, and DESeq2 (version 1.26.0) was used for standardized differential gene analysis(Schurch et al. 2016; Love et al. 2014). The DEG threshold was a |fold-change| ≥ 2 and adjusted p value < 0.05, which was obtained by Benjamini and Hochberg's approach to control the false discovery rate (FDR)(Benjamini and Hochberg 1995)
Assembly: Oryza sativa reference genome IRGSP1.0 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001433935.1/)
Supplementary files format and content: raw count values for each Sample

extract_protocol:
Total RNA was extracted from 100 mg root tissue by using TRIzol Reagent (Invitrogen™) following the manufacturer’s instructions. A total amount of RNA (≥ 1 μg) per sample were used for transcriptome sequencing.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: idd7 mutant


title: M07E-NC-2

description:
M07E-DMSO-2
M07E-counts.txt

source_name: M07E sample with no treatment


title: run1_Sample13_KO_act_inh_IP39

description: Library name: run1_Sample13

value: lymph-nodes

value: OVA 1uM activation + Ip38 12.5 uM inhibitor


title: run1_Sample12_KO_act

description: Library name: run1_Sample12

value: OVA 1uM activation


title: SR9009, mouse 4

description:
Library name: Sample 12
Column WT4_SR9009 in gene_count_all.txt


title: Ri, root, idd7 mutant, 7wpi, sample 2

description: Library name: idd7_7wpi_2

value: Rhizophagus irregularis, 25 uM Pi, 7wpi


title: run1_Sample11_KO

description: Library name: run1_Sample11


title: M07E-NC-1

description:
M07E-DMSO-1
M07E-counts.txt

value: WT


title: CMK-GNE987-2

description:
CMK-GNE987-2
CMK-counts.txt

source_name: CMK sample with GNE987

value: CMK


title: SR9009, mouse 3

description:
Library name: Sample 11
Column WT3_SR9009 in gene_count_all.txt

value: Bone marrow

value: Primary cell


title: Ri, root, idd7 mutant, 7wpi, sample 1

description: Library name: idd7_7wpi_1


title: run1_Sample10_WT_act_inh_Cyclosp

description: Library name: run1_Sample10


title: SR9009, mouse 2

description:
Library name: Sample 10
Column WT2_SR9009 in gene_count_all.txt

value: Bone marrow derived macrophage

value: Wild type


title: Ri, root, idd7 mutant, 5wpi, sample 3

description: Library name: idd7_5wpi_3

value: Rhizophagus irregularis, 25 uM Pi, 5wpi


title: CMK-GNE987-1

description:
CMK-GNE987-1
CMK-counts.txt


title: Ri, root, idd7 mutant, 5wpi, sample 2

description: Library name: idd7_5wpi_2


title: CMK-NC-2

description:
CMK-DMSO-2
CMK-counts.txt

source_name: CMK sample with no treatment


title: run1_Sample9_WT_act_inh_ERK

description: Library name: run1_Sample9

value: CD8+ T cells


title: run1_Sample8_WT_act_inh_IP39

description: Library name: run1_Sample8


title: Ri, root, idd7 mutant, 5wpi, sample 1

description: Library name: idd7_5wpi_1


title: LPS, mouse 4

description:
Library name: Sample 8
Column WT4_LPS in gene_count_all.txt

value: 100 ng/mL LPS


title: CMK-NC-1

description:
CMK-DMSO-1
CMK-counts.txt


title: run1_Sample7_WT_act

description: Library name: run1_Sample7


title: Ri, root, Azygous, 7wpi, sample 3

description: Library name: Azy_7wpi_3

value: root

value: Azygous


title: LPS, mouse 3

description:
Library name: Sample 7
Column WT3_LPS in gene_count_all.txt


title: BMDMs,contact3

city: Shanghai

first: Chen

last: Kun

address: DonganRoad 270

institute: Shanghai Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10using CLC genomic benchwork(parameters- mismath cost:2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files includes FPKM values for all Samples

source_name: bone marrow

extract_protocol:
RNA was harvested using Trizol reagent (Invtrogen)
RNA libraries for RNA-seq were prepared using mRNA-seq library preparation kit following guides.

value: bone marrow

value: bone marrow cells

tag: protocol

value: co-cluture with mEC25 in contact

value: M-CSF induction


title: run1_Sample6_WT

description: Library name: run1_Sample6

value: lymph-nodes


title: Ri, root, Azygous, 7wpi, sample 2

description: Library name: Azy_7wpi_2

value: Rhizophagus irregularis, 25 uM Pi, 7wpi


title: BMDMs,contact2


title: LPS, mouse 1

description:
Library name: Sample 5
Column WT1_LPS in gene_count_all.txt


title: Ri, root, Azygous, 7wpi, sample 1

description: Library name: Azy_7wpi_1


title: run1_Sample4_WT_act_inh_ERK

description: Library name: run1_Sample4

value: WT

value: OVA 1uM activation + inhERK 10 uM


title: DMSO, mouse 4

description:
Library name: Sample 4
Column WT4_control in gene_count_all.txt

value: Bone marrow

value: DMSO


title: Ri, root, Azygous, 5wpi, sample 3

description: Library name: Azy_5wpi_3


title: BMDMs,traswell3

value: co-cluture with mEC25 in non-contact


title: run1_Sample3_WT_act_inh_IP39

description: Library name: run1_Sample3

value: OVA 1uM activation + Ip38 12.5 uM inhibitor


title: BMDMs,traswell2


title: DMSO, mouse 3

description:
Library name: Sample 3
Column WT3_control in gene_count_all.txt

value: Primary cell

value: Bone marrow derived macrophage

value: Wild type


title: Ri, root, Azygous, 5wpi, sample 2

description: Library name: Azy_5wpi_2

value: root

value: Rhizophagus irregularis, 25 uM Pi, 5wpi


title: run1_Sample2_WT_act

description: Library name: run1_Sample2

value: CD8+ T cells

value: OVA 1uM activation


title: DMSO, mouse 2

description:
Library name: Sample 2
Column WT2_control in gene_count_all.txt


title: Ri, root, Azygous, 5wpi, sample 1

description: Library name: Azy_5wpi_1

value: Azygous


title: run1_Sample1_WT

description: Library name: run1_Sample1


title: BMDMs,traswell1

value: bone marrow

value: bone marrow cells

value: M-CSF induction


title: DMSO, mouse 1

description:
Library name: Sample 1
Column WT1_control in gene_count_all.txt


title: C22 cells, NE treatment (10 μM), 3h, replicate 2

status: Public on Aug 08 2026

first: Junkun

last: Jiang

address: 500 Zhennan Road, Putuo District

institute: Tongji University

description:
Library name: C22_NE_2
NE-4_count

data_processing:
Raw sequencing reads were subjected to quality control and preprocessing to remove adapter contamination and low-quality reads.
Clean reads were aligned to the mouse reference genome (GRCm39/mm39).
Gene expression levels were quantified based on aligned reads to generate gene-level read counts.
Read counts were normalized and processed for downstream RNA-seq analysis.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Processed data are provided as an Excel spreadsheet (.xlsx) containing gene-level raw read counts for all RNA-seq samples.

source_name: C22 murine bronchial epithelial Club cell line

growth_protocol: The immortalized mouse lung Club cell line C22 was maintained in DMEM supplemented with 2% fetal bovine serum (FBS) and required growth supplements at 37°C in a humidified atmosphere with 5% CO₂ prior to experiments.

extract_protocol:
Total RNA was extracted from C22 cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Approximately 1 μg of total RNA was used for RNA-seq library construction.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Preparation Kit (NEB) according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq X platform.

treatment_protocol: C22 cells were treated with norepinephrine (NE, 10 μM) for 3 h before RNA extraction. Control cells were treated with vehicle for the same duration.

value: Club cell

value: wild type


title: C22 cells, vehicle control, 3h, replicate 2

description:
Library name: C22_Vehicle_2
PBS-2_count

value: C22 murine bronchial epithelial Club cell line

value: vehicle control


title: C22 cells, vehicle control, 3h, replicate 1

description:
Library name: C22_Vehicle_1
PBS-1_count


title: C22 cells, NE treatment (10 μM), 3h, replicate 1

description:
Library name: C22_NE_1
NE-3_count


title: PTPS PBS control rep 3

city: Pathum Thani

first: Philip

middle: James

last: Shaw

state: Pathum Thani

address: 113 Thailand Science Park

country: Thailand

institute: BIOTEC, NSTDA

data_processing:
The raw data were processed with fastp with default settings (Chen et al 2018) to trim adapter sequence and remove low-quality reads.
Genome fasta sequence and gtf annotation file were modified for each transgenic line to account for the genome modification using the reform tool (Khalfan and Gresham 2021).
Processed reads were aligned to custom genomes with HISAT2 in the spliced mode with maxintron=5000 (Kim et al 2019).
Read counts for each annotated gene were obtained using featureCounts (Liao et al 2014).
The read counts were analysed with a mixed-effect model of differential gene expression using limma-voom (Law et al 2016).
Assembly: Plasmodium falciparum 3D7 v3.2; PlasmoDB v55 annotation
Supplementary files format and content: Comma separated text file includes raw counts for all Samples
Supplementary files format and content: Tab delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Plasmodium falciparum

source_name: saponin-lysed parasite

growth_protocol: Plasmodium falciparum parasites were cultured in vitro in human O+ erythrocytes and buffered Roswell Park Memorial Institute 1640 medium containing Albumax I. Clonal transgenic parasites with modified target genes were created by CRISPR-Cas9 gene editing as described in Leela et al 2024.

extract_protocol:
Total RNA was extracted and purified from parasites following the Direct-zol protocol optimized for P. falciparum (Kucharski et al 2020). Parasite pellets obtained by saponin-lysis of infected red blood cells were lysed with TRIzol™ reagent (Invitrogen). The aqueous phase from the lysate obtained after the addition of chloroform was applied to a Direct-zol column (Zymo) and total RNA was purified according to the kit instructions. Total RNA samples were shipped on dry ice to Novogene AIT (Singapore) for eukaryote stranded RNA-Seq service.
RNA libraries were prepared using the TruSeq stranded protocol

treatment_protocol: Cultures were synchronized to ring stages by sorbitol treatment. Ring stage parasites were treated for 12 h with 2.5 mM glucosamine or 1x PBS.

value: saponin-lysed parasite

value: in vitro cultured parasites

value: PBS control 12 h


title: run2_Sample3_WT_act_inh_IP39

description: Library name: run2_Sample3

value: lymph-nodes

value: WT

value: OVA 1uM activation + Ip38 12.5 uM inhibitor


title: PTPS PBS control rep 2


title: PTPS PBS control rep 1


title: ciToti4

city: Beijing

first: Hua

last: Wu

address: Zhongguancun Street

institute: Tsinghua University

description:
Library name: sample7
10x Genomics

data_processing:
The raw sequences obtained from sequencing on the Illumina platform (Raw reads) are first processed by trimming the data according to the 10x transcriptome library structure. This results in the acquisition of Read1 containing barcode and UMI sequence information, and Read2 containing the target sequence. The data is then analyzed and processed using the official 10x software, CellRanger v7.1.0.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: embryo

extract_protocol:
ciTotiSCs were directly harvested from the cell culture plate. E3.5, E4.5 natural embryos and ciToti1-ciToti4 embryo models were manually picked for sequencing. E6.5-E8.5 natural embryox and ciToti7-ciToti10 embryo models were processed including extraembryonic compartments without any dissection. E10.5 natural embryos and ciToti12 embryo models were dissected to obtain cardiac tissues for further processing. All samples were dissociated into single cells suspension with cell activity > 85%
First, obtain a single-cell suspension and perform a viability test. The cell viability should be >85%, with good dispersion and low impurity content. Then, proceed with the preparation of a microfluidic channel oil-in-water droplet library and the subsequent machine operation. To ensure effective capture of individual cells, the cell concentration should generally be controlled within the range of 700-1200 cells/μL. During the library preparation process, individual Gel Beads are encapsulated with individual cells in separate oil-in-water droplets to form GEMs (Gel Bead-in-Emulsion). Each Gel Bead contains a unique barcode and UMI (Unique Molecular Identifier) sequence, along with a Poly-dT primer sequence used to initiate the reverse transcription reaction. Afterward, within the GEM reaction system, the cells are lysed to release mRNA, which then undergoes reverse transcription in the presence of the Poly-dT primer and reverse transcriptase, generating full-length cDNA. The cDNA is then amplified and used to construct the library.

value: embryo

value: embryo cells


title: MDR1 PBS control rep 3


title: MDR1 PBS control rep 2


title: MDR1 PBS control rep 1


title: ciToti2

description:
Library name: sample5
10x Genomics


title: ciToti3

description:
Library name: sample6
10x Genomics


title: ciToti1

description:
Library name: sample4
10x Genomics


title: ciTotiSCs_TAWa

description:
Library name: sample3
10x Genomics

source_name: cell colony

value: cell colony

value: Embryonic stem cells


title: DHFR-TS PBS control rep 3


title: ciTotiSCs_TAW

description:
Library name: sample2
10x Genomics


title: DHFR-TS PBS control rep 2


title: DHFR-TS PBS control rep 1


title: S. polyrhiza UY001 PS05-treated replicate 3

city: Kofu

first: Tadashi

last: Toyama

country: Japan

institute: University of Yamanashi

description:
Library name: SP_PS05_3
Column name in raw_counts_All_Samples.txt: SP_PS05_3

data_processing:
Raw read quality was assessed using FastQC v0.11.2.
Adapter sequences and low-quality bases (Phred score < 20) were trimmed using CLC Genomics Workbench 26.
Trimmed reads were mapped to the Spirodela polyrhiza strain SP162 reference genome and annotation data using CLC Genomics Workbench 26 to calculate expression levels.
Differential expression analysis was performed using the Differential Expression for RNA-Seq tool in CLC Genomics Workbench 26 with default settings.
Assembly: Spirodela polyrhiza strain SP162 (ID: 5676) [Figshare: https://doi.org/10.6084/m9.figshare.29942036]
Supplementary files format and content: tab-delimited file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

organism: Spirodela polyrhiza

source_name: whole plant

growth_protocol: Spirodela polyrhiza were grown in sterilze 0.1 × diluted Hutner’s medium under a 16h/8h light/dark cycle at 28°C for 10 days.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plant (Takara Bio, Japan).
RNA libraries were prepared using the KAPA RNA HyperPrep Kit (Roche) following the manufacturer's protocol with a 20 ng of RNA input.

treatment_protocol: Spirodela polyrhiza was inoculated in each bacterial cell suspension of Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05 for 24 h. Inoculated fronds were transferred into fresh sterilze 0.1 × diluted Hutner’s medium and grown under a 16h/8h light/dark cycle at 28°C for 10 days.

value: whole plant

value: Inoculated with PS05

tag: time

value: Day 10


title: DHFS-FPGS PBS control rep 3


title: mESC

description:
Library name: sample1
10x Genomics


title: DHFS-FPGS PBS control rep 2


title: S. polyrhiza UY001 PS05-treated replicate 2

description:
Library name: SP_PS05_2
Column name in raw_counts_All_Samples.txt: SP_PS05_2


title: E7.5_Ex utero

description:
Library name: sample19
10x Genomics

extract_protocol:
ciTotiSCs and ciTotiSCs were directly harvested from the cell culture plate. E3.5, E4.5 nEmbryos and ciToti4 sEmbryos were manually picked for sequencing. E6.5-E8.5 nEmbryo and ciToti7~ciToti10 sEmbryo samples were processed including extraembryonic compartments without any dissection. E10.5 nEmbryos and ciToti12 sEmbryo samples were dissected to obtain cardiac tissues for further processing. All samples were dissociated into single cells suspension with cell activity > 85%
First, obtain a single-cell suspension and perform a viability test. The cell viability should be >85%, with good dispersion and low impurity content. Then, proceed with the preparation of a microfluidic channel oil-in-water droplet library and the subsequent machine operation. To ensure effective capture of individual cells, the cell concentration should generally be controlled within the range of 700-1200 cells/μL. During the library preparation process, individual Gel Beads are encapsulated with individual cells in separate oil-in-water droplets to form GEMs (Gel Bead-in-Emulsion). Each Gel Bead contains a unique barcode and UMI (Unique Molecular Identifier) sequence, along with a Poly-dT primer sequence used to initiate the reverse transcription reaction. Afterward, within the GEM reaction system, the cells are lysed to release mRNA, which then undergoes reverse transcription in the presence of the Poly-dT primer and reverse transcriptase, generating full-length cDNA. The cDNA is then amplified and used to construct the library.


title: PTPS GlcN treated rep 3

value: 2.5 mM glucosamine 12 h


title: S. polyrhiza UY001 PS05-treated replicate 1

description:
Library name: SP_PS05_1
Column name in raw_counts_All_Samples.txt: SP_PS05_1


title: E6.5_Ex utero

description:
Library name: sample18
10x Genomics


title: PTPS GlcN treated rep 1


title: PTPS GlcN treated rep 2


title: S. polyrhiza UY001 PS02-treated replicate 3

description:
Library name: SP_PS02_3
Column name in raw_counts_All_Samples.txt: SP_PS02_3

value: Inoculated with PS02


title: MDR1 GlcN treated rep 3


title: MDR1 GlcN treated rep 2


title: E4.5_Ex utero

description:
Library name: sample17
10x Genomics


title: SR9009, mouse 1

description:
Library name: Sample 9
Column WT1_SR9009 in gene_count_all.txt

value: Bone marrow

value: Primary cell

value: Bone marrow derived macrophage

value: Wild type


title: S. polyrhiza UY001 PS02-treated replicate 2

description:
Library name: SP_PS02_2
Column name in raw_counts_All_Samples.txt: SP_PS02_2


title: E10.5_H_In utero

description:
Library name: sample16
10x Genomics


title: DHFR-TS GlcN treated rep 3

value: saponin-lysed parasite

value: in vitro cultured parasites


title: MDR1 GlcN treated rep 1


title: S. polyrhiza UY001 PS02-treated replicate 1

description:
Library name: SP_PS02_1
Column name in raw_counts_All_Samples.txt: SP_PS02_1


title: DHFR-TS GlcN treated rep 2


title: LPS, mouse 2

description:
Library name: Sample 6
Column WT2_LPS in gene_count_all.txt

value: 100 ng/mL LPS


title: DHFR-TS GlcN treated rep 1


title: S. polyrhiza UY001 Control replicate 3

description:
Library name: SP_control_3
Column name in raw_counts_All_Samples.txt: SP_control_3

value: Uninoculated control


title: DHFS-FPGS GlcN treated rep 3


title: E8.5_In utero

description:
Library name: sample15
10x Genomics

value: embryo


title: run1_Sample5_WT_act_inh_Cyclosp

description: Library name: run1_Sample5

value: lymph-nodes

value: CD8+ T cells

value: WT

value: OVA 1uM activation + Cyclosporin 0.1 uM


title: BMDMs,contact1

value: bone marrow

value: bone marrow cells

value: co-cluture with mEC25 in contact

value: M-CSF induction


title: S. polyrhiza UY001 Control replicate 2

description:
Library name: SP_control_2
Column name in raw_counts_All_Samples.txt: SP_control_2

value: whole plant

value: Day 10


title: DHFS-FPGS GlcN treated rep 2

value: 2.5 mM glucosamine 12 h


title: E7.5_In utero

description:
Library name: sample14
10x Genomics

value: embryo cells


title: E6.5_In utero

description:
Library name: sample13
10x Genomics


title: DHFS-FPGS GlcN treated rep 1

value: saponin-lysed parasite


title: S. polyrhiza UY001 Control replicate 1

description:
Library name: SP_control_1
Column name in raw_counts_All_Samples.txt: SP_control_1


title: HD183 vehicle-treated TAMs

city: Oeiras

first: Gonçalo

last: Trindade

address: Edifício iBET BioFarma, Av. da República

country: Portugal

institute: iBET

description:
Library name: HD183_UNT
CD45-positive macrophages sorted from a 7-day BT474-monocyte co-culture established with healthy donor HD183. Column name in processed matrices: HD183_UNT.

data_processing:
Raw sequencing reads were filtered to remove adapter-contaminated reads, reads containing more than 10% undetermined bases, and low-quality reads.
Clean paired-end reads were aligned to the human hg38 reference genome using HISAT2 v2.2.1 with default parameters.
Gene-level read counts were generated from aligned reads using featureCounts v2.1.1 with default parameters.
FPKM values were calculated from gene-level counts and gene lengths.
Differential expression analysis reported in the associated manuscript was performed using DESeq2 with a paired design accounting for donor and treatment condition.
Assembly: hg38
Supplementary files format and content: Comma-separated matrix containing raw gene-level read counts for all six samples, with Ensembl gene identifiers in rows and samples in columns (readcount.csv).
Supplementary files format and content: Comma-separated matrix containing gene-level FPKM expression values for all six samples, with Ensembl gene identifiers in rows and samples in columns (fpkm_sample.csv).

source_name: peripheral blood

growth_protocol: BT474 breast cancer cells and freshly isolated primary human monocytes were mixed at a 1:1 ratio and seeded at 5 × 10^4 total cells per well in round-bottom ultra-low attachment 96-well plates. Plates were centrifuged at 300 × g for 5 min to induce aggregate formation and maintained for 7 days at 37°C and 5% CO2, with half-medium replacement on day 3.

extract_protocol:
Sorted CD45-positive cells were collected directly into RLT buffer supplemented with β-mercaptoethanol, snap-frozen, and stored at −80°C. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat#74106) with 15-min on-column DNase digestion. RNA concentration was measured by NanoDrop and integrity was assessed using Agilent RNA ScreenTape on a TapeStation 4200. Samples with RINe ≥ 8 were used for sequencing.
Messenger RNA was enriched from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were quantified using Qubit and real-time PCR and assessed for size distribution using a bioanalyzer. Libraries were sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000 platform by Novogene.

treatment_protocol: R406 besylate was added at seeding to a final concentration of 0.2 µM and refreshed during the half-medium replacement on day 3. Vehicle-control cultures received matched DMSO (0.314%, v/v). After 7 days, aggregates were dissociated and live singlet CD45-positive cells were isolated by fluorescence-activated cell sorting.

value: peripheral blood

value: tumor-associated macrophages

value: vehicle (0.314% DMSO)


title: HD183 R406-treated TAMs

description:
Library name: HD183_R406
CD45-positive macrophages sorted from a 7-day BT474-monocyte co-culture established with healthy donor HD183. Column name in processed matrices: HD183_R406.

value: 0.2 µM R406 besylate


title: HD180 R406-treated TAMs

description:
Library name: HD180_R406
CD45-positive macrophages sorted from a 7-day BT474-monocyte co-culture established with healthy donor HD180. Column name in processed matrices: HD180_R406.


title: E3.5_In utero

description:
Library name: sample12
10x Genomics

value: embryo


title: ciToti12_H

description:
Library name: sample11
10x Genomics


title: C. buqueti adult hindgut single-cell RNA-seq: CC-6_S1_L003

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

institute: 乐山师范学院

description:
Library name: CC-6_S1_L003
Single-cell RNA sequencing sample from a pooled tissue suspension of eight adult hindguts. 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.

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.

organism: Cyrtotrachelus buqueti

source_name: adult hindgut

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.

value: adult hindgut

value: single-cell suspension from intestinal tissue

value: CC


title: HD180 vehicle-treated TAMs

description:
Library name: HD180_UNT
CD45-positive macrophages sorted from a 7-day BT474-monocyte co-culture established with healthy donor HD180. Column name in processed matrices: HD180_UNT.


title: C. buqueti adult hindgut single-cell RNA-seq: CC-5_S1_L005

address: 四川省乐山市市中区滨河路778号

description:
Library name: CC-5_S1_L005
Single-cell RNA sequencing sample from a pooled tissue suspension of eight adult hindguts. 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: HD127 R406-treated TAMs

description:
Library name: HD127_R406
CD45-positive macrophages sorted from a 7-day BT474-monocyte co-culture established with healthy donor HD127. Column name in processed matrices: HD127_R406.


title: HD127 vehicle-treated TAMs

description:
Library name: HD127_UNT
CD45-positive macrophages sorted from a 7-day BT474-monocyte co-culture established with healthy donor HD127. Column name in processed matrices: HD127_UNT.


title: C. buqueti adult hindgut single-cell RNA-seq: CC-4_S1_L004

address: 四川省乐山市市中区滨河路778号

description:
Library name: CC-4_S1_L004
Single-cell RNA sequencing sample from a pooled tissue suspension of eight adult hindguts. 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: ciToti10_2

description:
Library name: sample10
10x Genomics


title: ciToti10_1

description:
Library name: sample9
10x Genomics


title: HAND2_OE rep2

city: Urumqi

first: Ning

state: Xinjiang

address: Liyushan South Road 138#

department: The First Affiliated Hospital

institute: Xinjiang medical univerisity

description: Library name: sample7

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: cell line

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols.

value: cell line

value: Hepatic stellate cells

value: WT

value: HAND2 overexpression


title: HAND2_OE rep4

description: Library name: sample9


title: C. buqueti adult hindgut single-cell RNA-seq: CC-3_S1_L003

address: 四川省乐山市市中区滨河路778号

description:
Library name: CC-3_S1_L003
Single-cell RNA sequencing sample from a pooled tissue suspension of eight adult hindguts. 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: ciToti8_3

description:
Library name: sample8
10x Genomics


title: HAND2_OE rep3

description: Library name: sample8


title: HAND2_OE rep5

description: Library name: sample10


title: HAND2_OE rep1

description: Library name: sample6


title: C. buqueti adult hindgut single-cell RNA-seq: CC-2_S1_L002

address: 四川省乐山市市中区滨河路778号

description:
Library name: CC-2_S1_L002
Single-cell RNA sequencing sample from a pooled tissue suspension of eight adult hindguts. 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: ciToti8_2

description:
Library name: sample7
10x Genomics


title: C. buqueti adult hindgut single-cell RNA-seq: CC-1_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: CC-1_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight adult hindguts. 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: BMP5 rep5

description: Library name: sample10

value: BMP5 stimulation


title: BMP5 rep3

description: Library name: sample8


title: ciToti8_1

description:
Library name: sample6
10x Genomics


title: BMP5 rep2

description: Library name: sample7


title: ciToti7

description:
Library name: sample5
10x Genomics


title: C. buqueti larval hindgut single-cell RNA-seq: YYC-7_S1_L004

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-7_S1_L004
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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 hindgut

value: larval hindgut

value: YYC


title: C. buqueti larval hindgut single-cell RNA-seq: YYC-6_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-6_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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: C. buqueti larval hindgut single-cell RNA-seq: YYC-5_S1_L007

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-5_S1_L007
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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: Control rep5

description: Library name: sample5

value: untreated


title: Control rep3

description: Library name: sample3


title: Control rep4

description: Library name: sample4


title: XETG00181__0070929__LD_NAC

type: RNA

city: Roanoke

first: Thomas

last: Maynard

state: VA

address: 2 Riverside Circle

institute: Virginia Tech Carilion/FBRI

description: LgDel, NAC treated, n=5

hyb_protocol: Hybridization was performed using a customized 347-gene Xenium probe panel following the standard 10x Genomics Xenium protocol (Janesick et al., 2023) using standard Xenium probe kit default conditions.

scan_protocol: Imaging, decoding, quality score generation, and DAPI-based cell segmentation were performed automatically by the Xenium Analyzer instrument (10x Genomics). Data were acquired on instrument software version 3.4.1.0, with onboard analysis version 'xenium-3.3.0.1'.

data_processing: Raw Xenium Onboard Analysis (XOA) outputs (decoded transcripts, cell/nucleus segmentation, transcript counts) were generated by the Xenium Analyzer instrument software. Downstream processing was performed in R (v4.5) using Seurat (v5.1.0) and SeuratDisk. Raw outputs were imported using LoadXenium() and filtered for low-quality cells based on transcript count (nCount) and number of expressed genes (nFeature). Expression counts were log-normalized (NormalizeData()); variable features were identified using FindVariableFeatures() with the 'vst' method together with canonical cell-type markers (Zeisel et al., 2015) to annotate clusters. Dimensionality reduction was performed by PCA followed by UMAP; clustering used the Louvain algorithm (FindNeighbors(), FindClusters()) at resolution 0.1, yielding 10 transcriptionally distinct clusters. Marker gene identification used FindAllMarkers() with the Wilcoxon rank-sum test. Cell-proportion comparisons across genotype/treatment conditions used one-way ANOVA with Dunnett's post hoc test vs. WT controls. Differential expression analysis of the 347-gene probe panel across conditions was performed using edgeR (Robinson and Smyth, 2007).

label: Xenium probe set

source_name: brain

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: P6 mouse pups were fixed by perfusion with a brief saline rinse followed by  4% paraformaldehyde, then post-fixed in 4% paraformaldehyde overnight. Brains were cryoprotected in successive 10%, 20%, and 30% sucrose/PBS solutions, embedded in OCT in a consistent coronal orientation, and stored at -80°C. 12 µm coronal cryostat sections were mounted on Xenium slides and processed according to the 10x Genomics Fixed Frozen tissue preparation procedure (Janesick et al., 2023).

value: brain

tag: tissue preservation method

value: Other

value: NAC

value: LgDel heterozygote


title: XETG00181__0070929__WT_NAC

description: WT control, NAC treated, n=3

value: wild-type control


title: Control rep2

description: Library name: sample2


title: Control rep1

description: Library name: sample1


title: C. buqueti larval hindgut single-cell RNA-seq: YYC-4_S1_L007

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-4_S1_L007
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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 100 nM, 10% FBS, Day 3 (72 h), biol. rep. 2

city: Notre Dame

first: Jianneng

last: Li

state: IN

address: 271 Galvin Life Sciences, Galvin building

institute: University of Notre Dame

description: Library name: C42_FBS_5bDHT100nM_D3_r2

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.

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

value: castration-resistant prostate cancer (CRPC) cell

value: AR T878A (endogenous)

value: 5beta-Dihydrotestosterone 100 nM, 10% FBS, Day 3 (72 h)


title: C4-2, 5beta-DHT 100 nM, 10% FBS, Day 3 (72 h), biol. rep. 3

description: Library name: C42_FBS_5bDHT100nM_D3_r3


title: XETG00181__0071270__LD

description: LgDel, untreated, n=5

value: control


title: C. buqueti larval hindgut single-cell RNA-seq: YYC-3_S1_L001

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-3_S1_L001
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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, 5beta-DHT 100 nM, 10% FBS, Day 3 (72 h), biol. rep. 1

description: Library name: C42_FBS_5bDHT100nM_D3_r1


title: XETG00181__0070929__WT

description: WT control, untreated, n=1


title: C. buqueti larval hindgut single-cell RNA-seq: YYC-2_S1_L003

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-2_S1_L003
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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 100 nM, 10% FBS, Day 3 (72 h), biol. rep. 3

description: Library name: C42_FBS_T100nM_D3_r3

value: Testosterone 100 nM, 10% FBS, Day 3 (72 h)


title: C4-2, testosterone 100 nM, 10% FBS, Day 3 (72 h), biol. rep. 2

description: Library name: C42_FBS_T100nM_D3_r2


title: C4-2, testosterone 100 nM, 10% FBS, Day 3 (72 h), biol. rep. 1

description: Library name: C42_FBS_T100nM_D3_r1


title: XETG00181__0071270__WT

description: WT control, untreated, n=4


title: C4-2, vehicle (ethanol), 10% FBS, Day 3 (72 h), biol. rep. 3

description: Library name: C42_FBS_Ctrl_D3_r3

value: Vehicle (ethanol), 10% FBS, Day 3 (72 h)


title: C. buqueti larval hindgut single-cell RNA-seq: YYC-1_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYC-1_S1_L008
Single-cell RNA sequencing sample from a pooled tissue suspension of eight larval hindguts. 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 3 (72 h), biol. rep. 2

description: Library name: C42_FBS_Ctrl_D3_r2


title: BRC1-OE_IgG_rep2

first: Hao

last: Zhu

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

institute: Beihang University

description:
Library name: BRC1-OE_IgG_rep2
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.

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.

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


title: C4-2, vehicle (ethanol), 10% FBS, Day 3 (72 h), biol. rep. 1

description: Library name: C42_FBS_Ctrl_D3_r1


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-9_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-9_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.

source_name: larval posterior midgut

value: larval posterior midgut

value: YYX


title: BRC1-OE_IgG_rep1

description:
Library name: BRC1-OE_IgG_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: D4_double-KO_H4K16ac_repB

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: Sample 89

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and MultiQC. The removal of read adapters and low-quality filtering was done with trimgalore(v0.6.7).
Reads were mapped to the mm10 reference genome with STAR v2.6.1d (--outSAMtype BAM Unsorted --runMode alignReads --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --readFilesCommand zcat).
Duplicate reads were marked with picard tool (3.1.1)
Bigwig files were generated with deepTools v3.5.1 using bamCoverage (--normalizeUsing 'RPGC').
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Double-KO differentiated cells

growth_protocol: mESC were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM (Thermo Fisher Scientific, 10829018) supplemented with 15% fetal bovine serum (FBS; Thermo Fisher Scientific, A5256801), 1x antibiotic and antimycotic solution (Sigma-Aldrich, A5955), 1x glutaMAX (Thermo Fisher Scientific, 35050038), 1x non-essential amino acids (NEAA; Thermo Fisher Scientific, 11140035), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, 21985023) and leukemia inhibitory factor (LIF; made in-house). Cells were maintained at 37 °C with 5% CO2. For the multilineage differentiation, cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days.

extract_protocol:
Approximately 10 million and 40 million cells were used for histone PTMs and COMPASS subunits ChIPs, respectively.  For histone modification ChIP assays, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature (RT) before being quenched with 0.125 M glycine for another 10 minutes, while for COMPASS subunits ChIP assays cells were double crosslinked with ChIP cross-link Gold (Diagenode, C01019027) and 1% formaldehyde according to the manufactor’s instructions. Chromatin was isolated through sequential incubation with three distinct lysis buffers: LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin sonication was carried out in LB3 using an EpiShearTM sonicator (Active Motif; 4-5 minutes, 20 seconds ON and 30 seconds OFF at 25% amplitude). The sheared chromatin was then incubated O/N at 4 °C with either 5 or 10 μg of antibody for histone PTMs or COMPASS subunits respectively.
DNA libraries were prepared using the TruSeq ChIP-seq sample preparation kit. 10 ng of ChIP DNA was used as starting material.

treatment_protocol: Starting from a previously described Cre-inducible Mll2-KO mESC line, Mll1-KO mESC were generated via CRISPR editing. Two sg-RNAs were designed flanking the region to-be deleted for each line, using Benchling’s CRISPR tool (https://www.benchling.com/crispr). For each sgRNA, two oligonucleotides were synthesized , annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p, provided by Leo Kurian’s lab). mESC were transfected with CRISPR-Cas9 constructs using LipofectamineTM 3000 (Thermo Fisher Scientific, L3000001).  For the generation of Mll2-KO and double-KO mESC lines, cells were treated with (Z)-4-Hydroxytamoxifen (4-OHT; Sigma-Aldrich, H7904) at a final concentration of 800 nM for 48 hours.

value: Double-KO differentiated cells

value: Differentiated cells

value: Double-KO

value: H4K16ac antibody (Abcam, ab109463)


title: C4-2, 5beta-DHT 100 nM, 10% FBS, Day 1 (24 h), biol. rep. 3

description: Library name: C42_FBS_5bDHT100nM_D1_r3

value: 5beta-Dihydrotestosterone 100 nM, 10% FBS, Day 1 (24 h)


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-8_S1_L007

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-8_S1_L007
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: BRC1-OE_H3_rep2

description:
Library name: BRC1-OE_H3_rep2
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: D4_double-KO_H4K16ac_repA

description: Library name: Sample 88


title: C4-2, 5beta-DHT 100 nM, 10% FBS, Day 1 (24 h), biol. rep. 2

description: Library name: C42_FBS_5bDHT100nM_D1_r2


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-7_S1_L008

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-7_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: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-6_S1_L007

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-6_S1_L007
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: BRC1-OE_H3_rep1

description:
Library name: BRC1-OE_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: C4-2, 5beta-DHT 100 nM, 10% FBS, Day 1 (24 h), biol. rep. 1

description: Library name: C42_FBS_5bDHT100nM_D1_r1


title: WT_IgG_rep2

description:
Library name: WT_IgG_rep2
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: D4_WT_H4K16ac_repB

description: Library name: Sample 87

source_name: WT differentiated cells

value: WT differentiated cells

value: WT


title: D4_WT_H4K16ac_repA

description: Library name: Sample 86


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-5_S1_L006

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-5_S1_L006
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, testosterone 100 nM, 10% FBS, Day 1 (24 h), biol. rep. 3

description: Library name: C42_FBS_T100nM_D1_r3

value: prostate

value: castration-resistant prostate cancer (CRPC) cell

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


title: WT_IgG_rep1

description:
Library name: WT_IgG_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: 435_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: Sample9

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

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

value: Repeat group


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-4_S1_L005

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-4_S1_L005
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.

value: single-cell suspension from intestinal tissue


title: BMP5 rep1

description: Library name: sample6

value: cell line

value: Hepatic stellate cells

value: BMP5 stimulation


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

description: Library name: C42_FBS_T100nM_D1_r2

value: AR T878A (endogenous)


title: WT_H3_rep2

description:
Library name: WT_H3_rep2
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.

value: axillary tissues


title: C. buqueti larval posterior midgut single-cell RNA-seq: YYX-3_S1_L001

address: 四川省乐山市市中区滨河路778号

description:
Library name: YYX-3_S1_L001
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.

value: larval posterior midgut

value: YYX