title: Donor 11, 10x ST, Tumor, Stage III, Indeterminate, In-between

value: Donor 11


title: Donor 07, 10x ST, Tumor, Stage III, Indeterminate, In-between

status: Public on Dec 03 2025

type: SRA

city: Beijing

first: Zemin

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description: Fresh frozen Spatial Transcriptome sequencing

library_source: transcriptomic

data_processing:
*library strategy:  Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome for gene expression count using Space Ranger's default settings
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5: H5 format that can compress gene expression data
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution of tissue image
Supplementary files format and content: tissue_positions_list.csv: spatial barcodes and their coordinates

molecule: total RNA

organism: Homo sapiens

source_name: Gastric cancer tumor

extract_protocol:
Fresh tissues were immediately embedded in OCT once leaving the Tissue Storage Solution and cryosectioned at ten μm thickness.
Spatial Transcriptomics sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagents accoridng to manufacturer's protocol

tag: tissue

value: Gastric cancer tumor

tag: subject id

value: Donor 07

tag: Stage

value: Stage III

tag: subtype

value: Indeterminate

tag: sampling location

value: In-between


title: Distal phalange of forelimb digit 1, embryos at E16, a pool of 20 individuals

city: Shenyang

first: Wanyi

last: Dang

state: Liaoning

address: 120 Dongling Rd, Shenyang, China

institute: Shenyang Agricultural University

description:
SEF1
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

data_processing:
Reads from mRNA-seq data were aligned to NCBI mouse genome (GRCm39) using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts and TMM counts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TMM values for each Sample

organism: Mus musculus

source_name: Distal phalange of forelimb digit 1

growth_protocol: Pregnant mice were raised in a clean environment at 22 to 24℃ and 45% to 55% relative humidity, with an adequate supply of food and water and a 12 h light and 12 h dark cycle (7 pm - 7 am).

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and  RNeasy Micro kit (Qiagen, Hilden, Germany), with RNase-Free DNase set to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Phalanges of digit 1 and 2 from 20 embryos at E16 and 10 embryos at E17 obtained by using a precise mating time from mice were used to extract RNA.

value: Distal phalange of forelimb digit 1

tag: developmental stage

value: embryos at E16


title: TCF4 OE rep1

city: BOSTON

first: Min

last: Chen

state: Massachusetts

address: 300 Longwood Ave

department: Department of Cardiology

country: USA

institute: Boston Children's Hospital

data_processing:
We used TopHat v2.0.1274 to map the RNA-Seq raw reads in FASTQ format to the hg19 human reference genome with the following parameters settings: --mate-std-dev 200 -p 8 -r 200. Using UCSC KnownGenes as reference genes, the BAM file generated by TopHat was subjected to the Cuffdiff function in Cufflink suite v2.2.175 to calculate read counts and gene expression (fragments per kilobases per million, or FPKM). To identify differentially expressed genes between different RNA-Seq samples based on read counts, we used the normalizeQuantiles, estimateCommonDisp and estimateTagwiseDisp functions in the R package edgeR v3.14.0 to normalize the read counts, estimate common dispersion and estimate moderated tag-wise dispersion, respectively. The edgeR then defined differential genes based on a negative binomial test using a cutoff of differential FDR value smaller than 0.05 and FPKM value larger than 1 in at least one sample.
Assembly: hg19
Supplementary files format and content: TCF4_KD_OE_diff.xls

source_name: umbilical vein

extract_protocol: not provided

value: umbilical vein

tag: cell line

value: HUVEC

tag: cell type

value: endothelial


title: AI-M2-rep1

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v4.0.0
Initial quality control was done to keep cells with nGenes between 300 to 7500, nUMI between 500 to 75000 and pMito < 15%.
Multiplets were identified and removed using DoubletFinder V2.0 assuming a 1% doublet formation rate per 1000 cells.
Secondary QC was conducted based on assessing the pairwise distribution of nGenes, nUMI and pMito for each major cell type.
Assembly: mm10
Supplementary files format and content: QC filtered(initial QC, multiplet filtering, and secondary QC) Seurat object with relevant metadata and UMAP coordinates in R object format

source_name: Dorsal skin

extract_protocol:
On day 3 post-wounding, mice were sacrificed, and wounds were excised by cutting a 2 mm perimeter around the injured area. For  comparison, distal intact back skin was also excised as a representation of normal unwounded skin. Prior to digestion, the fat tissue layer was gently scraped, and tissues were cut into small pieces using a scalpel. Tissues were transferred into C-tubes and agitated at 37° for 90 minutes in complete RPMI media containing 0.25mg/ml Liberase TL (Roche) and 0.1mg/ml DNase 1 (Sigma). Tissues were disintegrated further using the gentleMACS dissociator m_muscle_01 protocol (Miltenyi). The single cell suspension was passed through a 100μm cell strainer and rinsed with PBS containing 3% FBS and 5mM EDTA. Cells were washed two more times with PBS+ 3% FBS and passed through a 40μm cell strainer. To isolate live single cells, 3μm DAPI was added to the suspension and incubated for 10 minutes in the dark. Live single cells were sorted using a BD Influx cell system.
For single-cell RNA experiments, isolated cells were resuspended in 0.04% BSA in PBS at a concentration of 800 to 1000 cells/μl. Single-cell  experiments were performed using Chromium Next GEM Automated Single Cell 3ʹ cDNA Kit v3.1 on the 10X Genomics Chromium Connect platform (10XGenomics). The 10X Chromium Connect is an integrated system that allows for the automated generation of single-cell libraries from cells with minimum user interference. Firstly, the supplied Gel Bead kits, Library kits, Next GEM Chip G kits and the Single index plate required for GEM generation, cDNA amplification and library construction were loaded onto the machine according to the manufacturer’s instructions. Next, 10μl of each sample (targeted recovery of 5000 cells per sample) was added into the supplied 96-well skirted plate (maximum capacity of 8 samples per run) and carefully placed into the machine. Single-cell libraries were then generated using the system’s automated workflow. A total of 23 libraries from young and aged intact skin and wounds were created and sequenced on the NovaSeq 6000 Illumina platform to an average of 100 000 reads per cell.

value: Dorsal skin

value: Skin resident  cells

tag: age

value: Aged (22-24 months)

tag: strain

tag: genotype

value: WT

tag: treatment

value: Intact


title: 8th  fraction of C series slicing [5W_HD]

type: RNA

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: sample for Transcriptome Tomography

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 GE 028005 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the one color scan setting for 8x60k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using per chip: normalize to 75th percentile.

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf08

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were grown in pathogen-free conditions.

extract_protocol: RNA was prepared using the Mag-max-96 for Microarrays Total RNA Isolation Kit (Ambion) following the manufacturer's recommendations of the spin column protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Huntington disease model R6/2

value: brain

tag: gender

value: male

value: 5 weeks post-natal age

tag: section

value: coronal plane

tag: mouse id


title: Donor 03, 10x ST, Tumor, Stage III, Intestinal, Edge

value: Gastric cancer tumor

value: Donor 03

value: Stage III

value: Intestinal

value: Edge


title: TCF4 OE rep2

value: umbilical vein

value: HUVEC


title: Control (OE) rep2

value: endothelial


title: AI-M6-rep1

description: 10X Genomics

value: Dorsal skin

value: Skin resident  cells


title: 7th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf07


title: Donor 03, 10x ST, Tumor, Stage III, Intestinal, In-between

value: In-between


title: Control (OE) rep1


title: AI-M4-rep1

description: 10X Genomics

value: Aged (22-24 months)

value: WT

value: Intact


title: TCF4 KD rep2


title: Donor 02, 10x ST, Tumor, Stage III, Indeterminate, In-between

value: Donor 02

value: Indeterminate


title: Donor 02, 10x ST, Tumor, Stage III, Indeterminate, Core

value: Core


title: BMDM Fer1 3

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

data_processing:
Primary data analysis was conducted using the rnaseq pipeline from the nf-core suite (v3.7)
sequencing reads were aligned to the GRCh38 (v103) human reference genome using STAR (v2.7.10a)
Gene quantification was conducted using Salmon (v1.5.2)
The pipeline was executed with default parameters.
Downstream differential expression analysis was performed using DESeq2 (v1.36.0), with default parameters.
To enhance the accuracy of fold-change estimation, we included mouse ID as a batch effect in the design matrix.
For some comparisons (Fer1 vs. Ctrl and 4-OH vs. Ctrl), the original p-values inferred by DESeq2 revealed significant deviation from the expected uniform null distribution, suggesting low sensitivity.
To correct for this, we recomputed the raw p-values using fdrtool (v1.2.17)to increase the power of the differential expression procedure while maintaining efficient control for false discovery.
Subsequently, the Benjamini-Hochberg procedure was applied to correct the p-values for multiple tests.
Assembly: GRCm38
Supplementary files format and content: counts.tsv is tab separated values contains the gene counts as quanitifed by salmon for all samples
Supplementary files format and content: DEA_table contain a merged table containing all DESeq2 results, CPM values as computed by edgeR::cpm method and additional information for each gene and contrast.

source_name: Bone marrow

growth_protocol: Macrophages were grown in DMEM medium supplied with 10%FBS

extract_protocol:
Macherey-Nagel RNA Extraction Kit
Lexogen QuantSeq kit

treatment_protocol: Incubation with non-ferroptotic or ferroptotic supernatants for 24h

value: Bone marrow

value: Macrophages

value: wildtype

value: Non-ferroptotic stimuli


title: AI-M4-rep2

description: 10X Genomics


title: Donor 01, 10x ST, Tumor, Stage I, Intestinal, Edge

value: Gastric cancer tumor

value: Donor 01

value: Stage I

value: Intestinal

value: Edge


title: exosome derived from  hUC-MSCs without treatment 3

city: Dalian

first: zhao

last: wang

state: Liao Ning

address: 222 Zhongshan Road, Xigang District, Dalian City

department: Dermatology Department

institute: The first affiliated hospital of  Dalian medical university

description:
Library name: Sample 6
NC_3

data_processing:
Differentially significant miRNA refers to the summary of up-regulated miRNA and down-regulated miRNA between samples or the same sample after different treatments. The input data of miRNA differential expression analysis were normalized data (norm value), and the p value calculation model based on normal distribution was used for p value calculation. When there were biological replicates, t-test (two-tailed, heteroscedasticity) was used to analyze the difference between two groups of samples, and ANOVA was used to analyze the difference between multiple groups. Fisher's exact test and chi-square (2* 2) were used to analyze the difference between two groups when there were no biological replicates, and chi-square (N*N) was used to analyze the difference between multiple groups (the difference algorithm was based on our own experimental protocol declaration at the time of writing).
Assembly: ACGT101-miR (v4.2) was used for miRNA Data analysis to obtain differentially expressed mirnas.
Supplementary files format and content: The Raw image data obtained by sequencing were obtained by base calling to obtain sequence files stored in FASTQ format, called Raw Data or Raw reads.

source_name: human umbilical cord

growth_protocol: Hucmscs were cultured in a serum-free stem cell culture system at 37 ° C with 5%CO2

extract_protocol:
The supernatant of the two groups of cultured cells was collected and the exosomes were extracted by ultracentrifugation for sequencing
The experimental procedures were performed according to the standard procedures provided by Illumina, including library preparation and sequencing experiments, sRNA sequencing library preparation using TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) kit. After library preparation, the constructed libraries were sequenced using Illumina Hiseq 2000 with a single end 50bp read length (SE50).

treatment_protocol: Human umbilical cord mesenchymal stem cells from the treatment group were cultured in medium containing 5mM lithium chloride for 6 days

value: human umbilical cord

value: mesenchymal stem cells

value: 6 days after Lithium chloride pretreatment


title: BMDM Tam 3

value: Ferroptotic stimuli


title: Donor 01, 10x ST, Tumor, Stage I, Intestinal, In-between

value: In-between


title: 4th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf04

value: Huntington disease model R6/2

value: brain

value: male

value: 5 weeks post-natal age

value: coronal plane


title: 1st  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf01


title: exosome derived from  hUC-MSCs without treatment 1

description:
Library name: Sample 4
NC_1


title: Control (KD) rep2

value: umbilical vein

value: HUVEC

value: endothelial


title: 3rd  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf03


title: 2nd  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf02


title: 6th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf06


title: 5th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf05


title: exosome derived from LiCl pretreated hUC-MSCs 3

description:
Library name: Sample 3
Li_3


title: BMDM Fer1 2

value: Bone marrow

value: Macrophages

value: wildtype

value: Non-ferroptotic stimuli


title: RNA_U87_DMOG_rep_1

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on IlluminaNovaseq 6000 or NovoSeq XPlus as indicated  (Illumina).

value: DMOG [1mM] 16h


title: BMDM Tam Fer1 3


title: exosome derived from LiCl pretreated hUC-MSCs 2

description:
Library name: Sample 2
Li_2

value: human umbilical cord

value: mesenchymal stem cells


title: BMDM Tam Fer1 2


title: TCF4 KD rep1


title: exosome derived from LiCl pretreated hUC-MSCs 1

description:
Library name: Sample 1
Li_1

value: 6 days after Lithium chloride pretreatment


title: BMDM Tam 2

value: Ferroptotic stimuli


title: exosome derived from  hUC-MSCs without treatment 2

description:
Library name: Sample 5
NC_2


title: RNA_U87_DMOG_rep_2


title: BMDM ctrl 3


title: siSpp1_rep1

city: Boston

first: I-Hsiu

last: Lee

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

description:
Library name: R1
TMM_normalized_cpm_offset.csv

data_processing:
Salmon v1.10.0, with the GRCm39 reference genome, was used to estimate transcript-level quantification from the sequencing reads for each sample.
The transcript-level quantifications were summarized into a gene-level count matrix with tximport v1.36.1.
The normalized count matrix was obtained with edgeR v4.6.3.
Assembly: GRCm39
Supplementary files format and content: csv file includes TMM-normalized CPM values with offset that corrects for potential differential isoform usage

source_name: bone marrow-derived macrophages

growth_protocol: Femurs from C57BL/6 mice were flushed and filtered to isolate bone marrow cells. These cells were cultured in DMEM enriched with 10% (v/v) heat-inactivated FBS supplemented with 30 ng/mL of M-CSF. After 5 days of culture, bone-marrow derived macrophages were polarized by adding 10 ng/mL of IL-4 and IL-13 to the medium for 24 hours.

extract_protocol:
Total RNA was extracted from bone marrow-derived macrophages using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
RNA concentration and integrity were measured using the RiboGreen assay (Thermo Fisher Scientific) and the Agilent TapeStation 4200, respectively. Next, polyadenylated mRNAs were captured using oligo-dT-conjugated magnetic beads (Watchmaker Genomics), followed by immediate fragmentation to 300-400 bp. Stranded libraries were then made by adding dUTP into the second strand with the Watchmaker mRNA Library Prep kit (Watchmaker Genomics) and X-Gen stubby adapters (Integrated DNA Technologies). Libraries were enriched and indexed using 10 cycles of amplification with the Equinox Master Mix (Watchmaker Genomics) and PCR primers which included dual 8 bp index sequences to allow for multiplexing (Integrated DNA Technologies). All library preparation volumes were miniaturized to 1/5 reaction volume, followed by removal of excess PCR reagents through magnetic bead-based cleanup using Aline PCRClean Dx paramagnetic beads. The resulting libraries were validated and quantified with the Agilent TapeStation 4200 and by real-time qPCR and subsequently sequenced on an Illumina NovaSeq X Plus using paired-end, 150 bp reads.

treatment_protocol: Bone marrow-derived macrophages were treated with either vehicle (lipofectamine RNAiMAX transfection reagent, Thermo Fisher Scientific) or siSpp1 complexed with lipofectamine RNAiMAX transfection reagent for 24 hours.

value: bone marrow-derived macrophages

value: macrophages


title: siSpp1_rep4

description:
Library name: R4
TMM_normalized_cpm_offset.csv


title: BMDM medium ctrl 2

value: Fresh medium


title: Control (KD) rep1


title: RNA_RCC4_pool_E2_ko_rep_2

value: EPAS1 enhancer 2 knockout


title: BMDM ctrl 2


title: normal diet14

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

description: Library name: sample29

data_processing:
Total RNA qualification
Assembly: hg19,mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver cancer tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver cancer tissue

value: normal diet


title: normal diet15

description: Library name: sample30


title: Vehicle_rep4

description:
Library name: L4
TMM_normalized_cpm_offset.csv

value: vehicle


title: RNA_RCC4_pool_E2_ko_rep_1

description:
NovaSeq XPlus
RNA_RCC4_pool_TPM.txt


title: Vehicle_rep3

description:
Library name: L3
TMM_normalized_cpm_offset.csv


title: RNA_U87_ctrl_rep_1

value: control


title: normal diet13

description: Library name: sample28


title: siSpp1_rep3

description:
Library name: R3
TMM_normalized_cpm_offset.csv


title: RNA_U87_ctrl_rep_2


title: RNA_RCC4_pool_nt_rep_2

description:
NovaSeq XPlus
RNA_RCC4_pool_TPM.txt

value: non-targeting control


title: BMDM Fer1 1

value: Bone marrow

value: Macrophages


title: siSpp1_rep2

description:
Library name: R2
TMM_normalized_cpm_offset.csv


title: Vehicle_rep2

description:
Library name: L2
TMM_normalized_cpm_offset.csv


title: normal diet12

description: Library name: sample27


title: Vehicle_rep1

description:
Library name: L1
TMM_normalized_cpm_offset.csv


title: RNA_760_pool_E2_ko_rep_2

description:
NovaSeq XPlus
RNA_786O_pool_TPM.txt


title: BMDM Tam 1

value: wildtype


title: BMDM Tam Fer1 1

value: Non-ferroptotic stimuli


title: RNA_RCC4_pool_nt_rep_1

description:
NovaSeq XPlus
RNA_RCC4_pool_TPM.txt


title: KLPN-9

city: Los Angeles

first: Sandy Che-Eun

middle: Serena

state: California

address: 650 Charles E Young Dr S 27-300

institute: University of California, Los Angeles

description:
Library name: KLPN-9 sample
10x Genomics

data_processing:
Raw sequencing read data of both KLluc and KLPNluc samples was quantified and then separately aggregated into single-cell level count data for KLluc and KLPNluc genotypes using Cellranger software v9.0.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

molecule: polyA RNA

source_name: lung tumor

extract_protocol:
Isolated tumors were dissociated by 2.5mg/mL of liberase (Roche) in 37°C at 300 rpm for 2 hours. Samples were then washed in 1x DPBS three times prior to filtering in 40um Mini-Strainer (PluriSelect USA) three times on ice to avoid clumping. Cells were then resuspended in 1x DBPS + 0.04% BSA solution.
Single-cell 3′ gene expression libraries were constructed from fresh cells using the 10x Genomics Chromium Single Cell 3′ Gene Expression workflow

value: lung tumor

value: lung tumor cells

value: Kras-driven, Lkb1 and Pnpase mutant


title: KLPN-7

description:
Library name: KLPN-7 sample
10x Genomics


title: RNA_760_pool_E2_ko_rep_1

description:
NovaSeq XPlus
RNA_786O_pool_TPM.txt


title: RNA_760_pool_nt_rep_2

description:
NovaSeq XPlus
RNA_786O_pool_TPM.txt


title: BMDM medium ctrl 1


title: normal diet11

description: Library name: sample26


title: normal diet10

description: Library name: sample25


title: BMDM ctrl 1


title: KLPN-4

description:
Library name: KLPN-4 sample
10x Genomics


title: normal diet8

description: Library name: sample23


title: NIH3T3 cells, DOX, Rep3

city: Richmond

first: Senthil

last: Radhakrishnan

state: VA

address: 1101 E Marshall St

institute: Virginia Commonwealth University

data_processing:
Sequence reads were trimmed for adaptor sequences using Trimmomatic v 0.39
Trimmed reads were mapped to GRCm39/mm39 using STAR aligner v 2.7.9a (parameters - default)
Read count extraction at the gene level were perfomed using the FeatureCounts summarization tool from the SourceForge Subread package v 2.0.2
Assembly: GRCm39/mm39
Supplementary files format and content: comma-separated value file includes raw counts at the gene level for each Sample

source_name: embryonic

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS at 37 degree C in a humidified CO2 incubator

extract_protocol:
RNA extraction was done with RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with CFZ (200 nM), DOXORUBICIN (5 µM) either alone or in combination for 8 hr. DMSO (vehicle) treatment used as control.

value: embryonic

value: fibroblast

value: WT

value: Doxorubicin (DOX)


title: NIH3T3 cells, CFZ-DOX, Rep3

value: combination CFZ-DOX


title: NIH3T3 cells, CFZ, Rep3

value: Carfilzomib (CFZ)


title: KLPN-3

description:
Library name: KLPN-3 sample
10x Genomics


title: RNA_ccRCC_ctrl_3_rep_2

description:
NovaSeq XPlus
RNA_PTC_ccRCC_TPM.txt

source_name: primary ccRCC cells

value: primary ccRCC cells


title: normal diet7

description: Library name: sample22

value: liver cancer tissue

value: normal diet


title: RNA_ccRCC_ctrl_3_rep_1

value: control


title: KLPN-2

description:
Library name: KLPN-2 sample
10x Genomics


title: KLPN-1

description:
Library name: KLPN-1 sample
10x Genomics


title: normal diet5

description: Library name: sample20


title: RNA_ccRCC_ctrl_2_rep_2


title: NIH3T3 cells, CFZ-DOX, Rep2


title: NIH3T3 cells, DMSO, Rep3

value: DMSO


title: KL-FVB-3

description:
Library name: KL-FVB-3 sample
10x Genomics

value: Kras-driven, Lkb1 mutant


title: normal diet4

description: Library name: sample19


title: normal diet9

description: Library name: sample24


title: RNA_ccRCC_ctrl_2_rep_1


title: RNA_760_pool_nt_rep_1

description:
NovaSeq XPlus
RNA_786O_pool_TPM.txt

value: non-targeting control


title: NIH3T3 cells, DOX, Rep2


title: KL-FVB-1

description:
Library name: KL-FVB-1 sample
10x Genomics


title: NIH3T3 cells, CFZ, Rep2


title: RNA_ccRCC_ctrl_1_rep_1


title: KL-FVB-2

description:
Library name: KL-FVB-2 sample
10x Genomics


title: RNA_ccRCC_ctrl_1_rep_2


title: normal diet3

description: Library name: sample18


title: RNA_PTC_ctrl_3_rep_2

source_name: primary tubule cells

value: primary tubule cells


title: KL-2

description:
Library name: KL-2 sample
10x Genomics

value: lung tumor


title: RNA_PTC_ctrl_2_rep_2


title: high red meat diet 14

description: Library name: sample14

value: high red meat diet


title: normal diet2

description: Library name: sample17


title: NIH3T3 cells, CFZ, Rep1


title: NIH3T3 cells, DMSO, Rep2


title: RNA-Seq,skeletalmuscle-hiit5

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description:
Library name: UPL25-003174
Column name in gene_counts.csv: UPL25.003174_dedup.bam

data_processing:
FASTQ QC with FastQC/MultiQC; adapter/poly-X/quality trimming with fastp. UMI (6 nt) and spacer (4 nt) processed using UMI-tools/cutadapt.
Deduplicated reads aligned to Mus musculus GRCm39 with STAR; BAM processed with samtools.
Assembly: Mus musculus reference genome: GRCm39; gene annotation corresponding to GRCm39 (GTF).
Supplementary files format and content: gene_counts.csv: first column = gene identifier, subsequent columns = samples; values = raw integer counts.

source_name: gastrocnemius muscle

extract_protocol:
~20–30 mg gastrocnemius homogenized; total RNA extracted with Quick-RNA™ Miniprep Plus (Zymo). Quantity/purity by NanoDrop; integrity by Agilent TapeStation.
100 ng total RNA used for QuantSeq 3′ mRNA-Seq Library Prep Kit FWD v2 (Lexogen): oligodT priming, second-strand synthesis by random priming, bead cleanup, PCR barcoding. Libraries QC’d on TapeStation and sequenced on Illumina NovaSeq X Plus (SE75).

value: gastrocnemius muscle

tag: Sex

value: male

value: BALB/c

value: HIIT

tag: batch


title: RNA_PTC_ctrl_1_rep_1


title: normal diet1

description: Library name: sample16

tag: tissue


title: high red meat diet 11

description: Library name: sample11


title: PAC-2 cells 6h blue light, rep2

city: Eggenstein-Leopoldshafen

first: Alessandra

last: Boiti

address: Hermann-von-Helmholtz-Platz 1

institute: Karlsruhe Institute of Technology

description:
Library name: Sample 11
column name in de novo analysis files: BLZF_6h_rep2
column name in standard analysis files: BLZF_6h2

data_processing:
For standard pipeline: Raw reads quality check; mapping to refecence genome; quantitation by sample; transcript exclusion TPM>5 only; quantitation by timepoint; DEG analysis with p<.001 and |logFC|>=1; functional analysis (GO enrichment analysis 0h vs all timepoints)
For de novo pipeline: Raw reads quality check; trinity assembly with Trinity software; quantitation by sample; transcript exclusion TPM>5 only; annotation against databases (blastx, uniprot, pfam); quantitation by timepoint; DEG analysis with p<.001 and |logFC|>=1; functional analysis (GO enrichment analysis 0h vs all timepoints)
Assembly: GRCz11 for PAC-2 cells, de novo Trinity software assembly for EPA
Supplementary files format and content: Tab-delimited text file contains TPM values for each sample
Supplementary files format and content: BLZF_readcount_genename.xls contains raw counts for each sample
Supplementary files format and content: BLZF_fpkm_genename.xls file contains FPKM values for each sample

organism: Danio rerio

growth_protocol: Cells are cultured in Leibovitz L-15 medium with 15% FBS (PAC-2) or 20% FBS (EPA), 100U/ml penicillin, 100ug/ml streptomycin, and 50ug/ml gentamicin

extract_protocol:
total RNA is harvested using Trizol reagent according to manufacturer’s instruction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Cells are seeded with transparent medium (no phenol red), kept in darkness for 2 days, then exposed to blue light (468nm) for up to 6h and samples are taken before exposure (0h), and after 1h, 3h, and 6h.

value: fibroblasts

value: blue light exposure

tag: type


title: normal diet6

description: Library name: sample21


title: high red meat diet 15

description: Library name: sample15


title: NIH3T3 cells, CFZ-DOX, Rep1

value: embryonic

value: fibroblast

value: WT

value: combination CFZ-DOX


title: RNA-Seq,skeletalmuscle-hiit6

description:
Library name: UPL25-003175
Column name in gene_counts.csv: UPL25.003175_dedup.bam


title: high red meat diet 13

description: Library name: sample13

value: liver cancer tissue


title: RNA_PTC_ctrl_2_rep_1

value: control


title: RNA_PTC_ctrl_1_rep_2


title: RNA-Seq,skeletalmuscle-hiit4

description:
Library name: UPL25-003173
Column name in gene_counts.csv: UPL25.003173_dedup.bam


title: PAC-2 cells 6h blue light, rep3

description:
Library name: Sample 12
column name in de novo analysis files: BLZF_6h_rep3
column name in standard analysis files: BLZF_6h3


title: KL-1

description:
Library name: KL-1 sample
10x Genomics

value: lung tumor cells

value: Kras-driven, Lkb1 mutant


title: RNA-Seq,skeletalmuscle-hiit3

description:
Library name: UPL25-002762
Column name in gene_counts.csv: UPL25.002762_dedup.bam


title: ATAC_U_87_DMOG_rep_2

library_source: genomic

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and aligned to the GRCh38 genome using Bowtie2 version 2.3.4.1.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed according to the Omni-ATAC protocol published by Corces et al. (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396). In short, libraries were prepared using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, San Diego, CA, USA) and purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer’s protocol. Following purification, library fragments were amplified by using the NEB Next® High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, UK) and custom-made indexed Nextera PCR primers (Sigma Aldrich, St. Louis, MO, USA). Libraries were amplified for a total of 8 – 12 cycles. Library clean-up and double-sided size selection was performed using AMPure XP beads (Beckman Coulter GmbH, Krefeld, Germany) according to the manufacturer’s recommendations.
ATAC-seq library preparation was carried out using the Omni-ATAC protocol. Libraries were sequenced on IlluminaNovaseq 6000 platforms following the manufacturer's protocols.

value: DMOG [1mM]

tag: time


title: RNA_PTC_ctrl_3_rep_1

value: primary tubule cells


title: high red meat diet 10

description: Library name: sample10

value: high red meat diet


title: PAC-2 cells 6h blue light, rep1

description:
Library name: Sample 10
column name in de novo analysis files: BLZF_6h_rep1
column name in standard analysis files: BLZF_6h1


title: high red meat diet 12

description: Library name: sample12


title: NIH3T3 cells, DOX, Rep1

value: Doxorubicin (DOX)


title: KL-3

description:
Library name: KL-3 sample
10x Genomics

value: lung tumor


title: high red meat diet 9

description: Library name: sample9


title: ATAC_U_87_DMOG_rep_1


title: RNA-Seq,skeletalmuscle-hiit2

description:
Library name: UPL25-002761
Column name in gene_counts.csv: UPL25.002761_dedup.bam

value: gastrocnemius muscle

value: male

value: BALB/c


title: RNA-Seq,skeletalmuscle-hiit1

description:
Library name: UPL25-002760
Column name in gene_counts.csv: UPL25.002760_dedup.bam

value: HIIT


title: NIH3T3 cells, DMSO, Rep1

value: embryonic

value: DMSO


title: PAC-2 cells 3h blue light, rep3

description:
Library name: Sample 9
column name in de novo analysis files: BLZF_3h_rep3
column name in standard analysis files: BLZF_3h3

value: fibroblasts

value: blue light exposure


title: high red meat diet 8

description: Library name: sample8

value: liver cancer tissue


title: RNA-Seq,skeletalmuscle-lactate6

description:
Library name: UPL25-002759
Column name in gene_counts.csv: UPL25.002759_dedup.bam

value: Lactate administration


title: ATAC_U_87_ctrl_rep_2


title: PAC-2 cells 3h blue light, rep2

description:
Library name: Sample 8
column name in de novo analysis files: BLZF_3h_rep2
column name in standard analysis files: BLZF_3h2


title: high red meat diet 7

description: Library name: sample7


title: ATAC_U_87_ctrl_rep_1


title: PAC-2 cells 3h blue light, rep1

description:
Library name: Sample 7
column name in de novo analysis files: BLZF_3h_rep1
column name in standard analysis files: BLZF_3h1


title: ATAC_RCC4_i.HA_VHL_Dox_rep_2

value: Doxycycline [0.5 µg/ml]


title: ATAC_RCC4_i.HA_VHL_Dox_rep_1


title: high red meat diet 4

description: Library name: sample4


title: PAC-2 cells 1h blue light, rep3

description:
Library name: Sample 6
column name in de novo analysis files: BLZF_1h_rep3
column name in standard analysis files: BLZF_1h3


title: PAC-2 cells 1h blue light, rep2

description:
Library name: Sample 5
column name in de novo analysis files: BLZF_1h_rep2
column name in standard analysis files: BLZF_1h2


title: PAC-2 cells 1h blue light, rep1

description:
Library name: Sample 4
column name in de novo analysis files: BLZF_1h_rep1
column name in standard analysis files: BLZF_1h1


title: RNA-Seq,skeletalmuscle-lactate5

description:
Library name: UPL25-002758
Column name in gene_counts.csv: UPL25.002758_dedup.bam


title: RNA-Seq,skeletalmuscle-lactate3

description:
Library name: UPL25-002756
Column name in gene_counts.csv: UPL25.002756_dedup.bam


title: ATAC_RCC4_i.HA_VHL_control_rep_2

value: DMSO control


title: high red meat diet 5

description: Library name: sample5


title: RNA-Seq,skeletalmuscle-lactate1

description:
Library name: UPL25-002754
Column name in gene_counts.csv: UPL25.002754_dedup.bam


title: high red meat diet 2

description: Library name: sample2


title: RNA-Seq,skeletalmuscle-lactate2

description:
Library name: UPL25-002755
Column name in gene_counts.csv: UPL25.002755_dedup.bam


title: RNA-Seq,skeletalmuscle-hiitmct6

description:
Library name: UPL25-002753
Column name in gene_counts.csv: UPL25.002753_dedup.bam

value: HIIT+MCT1/2 inhibitor


title: PAC-2 cells 0h blue light, rep3

description:
Library name: Sample 3
column name in de novo analysis files: BLZF_0h_rep3
column name in standard analysis files: BLZF_0h3

value: 0h (control)


title: high red meat diet 1

description: Library name: sample1

value: high red meat diet


title: ATAC_RCC4_i.HA_VHL_control_rep_1


title: PAC-2 cells 0h blue light, rep2

description:
Library name: Sample 2
column name in de novo analysis files: BLZF_0h_rep2
column name in standard analysis files: BLZF_0h2


title: ATAC_RCC4_wt_rep_2

value: control


title: 10th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf10

value: Huntington disease model R6/2

value: brain

value: 5 weeks post-natal age

value: coronal plane


title: ATAC_RCC4_wt_rep_1


title: 1527600_Donor 7-2_IL33

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

description:
Library name: 1527600
5215.16790.1527600.S51.W111102

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include read counts for  each Sample

source_name: blood

extract_protocol:
Tissues/Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen) on the Kingfisher Flex machine (Thermofisher).
The strand-specific RNA-seq libraries were prepared from 500 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2000 (Illumina) by multiplexed single-read run with 33 cycles.

value: blood

value: mast cell

tag: donor

value: Donor 7


title: ATAC_ccRCC_ctrl_3

value: primary ccRCC cells


title: PAC-2 cells 0h blue light, rep1

description:
Library name: Sample 1
column name in de novo analysis files: BLZF_0h_rep1
column name in standard analysis files: BLZF_0h1

value: fibroblasts

value: blue light exposure


title: high red meat diet 6

description: Library name: sample6

value: liver cancer tissue


title: Microglia, control

city: Hangzhou

first: Baixiu

last: Zheng

state: Zhejiang

address: Yuhangtanglu

institute: Zhejiang University

description:
Library name: Sample2
Sample2

data_processing:
Cell Ranger software v7.0.0 was used to filter, compare, quantify, and identify recovered cells from raw data.
Assembly: Rnor_6.0
Supplementary files format and content: barcodes.tsv.gz includes all cell barcodes of the Sample
Supplementary files format and content: features.tsv.gz includes gene identifiers
Supplementary files format and content: matrix.mtx.gz includes a sparse matrix that contains gene expression information for each individual cell

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Hippocampus was mechanically homogenized and made into single-cell suspension, and then microglia were isolated by flow cytometry. Combined gel beads containing barcode information with the mixture of cells and enzymes. Wrapped them with oil surfactant drops located in the microfluidic system to form Gel Beads In Emulations (GEMs). GEMs flowed into the reservoir and were collected. The gel beads were broken, and the cDNA was used as the template for PCR amplification.
Enzymatic cleavage was performed, the fragments were flattened at the end, and base A was added to connect the adapter. The target size fragments were screened and recovered using a reagent kit for library quality inspection and quantification.

value: male


title: RNA-Seq,skeletalmuscle-hiitmct4

description:
Library name: UPL25-002751
Column name in gene_counts.csv: UPL25.002751_dedup.bam

value: gastrocnemius muscle

value: BALB/c


title: RNA-Seq,skeletalmuscle-lactate4

description:
Library name: UPL25-002757
Column name in gene_counts.csv: UPL25.002757_dedup.bam

value: Lactate administration


title: 1527599_Donor 7-1_IL33

description:
Library name: 1527599
5215.16790.1527599.S51.W111102


title: high red meat diet 3

description: Library name: sample3

value: high red meat diet


title: ATAC_ccRCC_ctrl_1

value: control


title: RNA-Seq,skeletalmuscle-hiitmct3

description:
Library name: UPL25-002750
Column name in gene_counts.csv: UPL25.002750_dedup.bam

value: HIIT+MCT1/2 inhibitor


title: RNA-Seq,skeletalmuscle-hiitmct2

description:
Library name: UPL25-002749
Column name in gene_counts.csv: UPL25.002749_dedup.bam


title: RNA-Seq,skeletalmuscle-hiitmct1

description:
Library name: UPL25-002748
Column name in gene_counts.csv: UPL25.002748_dedup.bam


title: 1527598_Donor 7-2_IL13

description:
Library name: 1527598
5215.16790.1527598.S51.W111102


title: Microglia, dexamethasone

description:
Library name: Sample1
Sample1

value: brain


title: ATAC_ccRCC_ctrl_2


title: CPT, replicate 3, scRNAseq

city: Orsay

first: Lorea

last: Iturri

address: Rue Henri Becquerel

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
Single-cell matrices were generated using Cellranger (v6.0.0)
Assembly: rnor6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain tumor

extract_protocol:
14 days post-implantation (control samples, Ctl) or 7 days post-irradiation (pMBRT, Conventional PT), tumors were harvested and processed enzymatically and mechanically to obtain single cell suspension. CD45 positive cells were isolated using MACS separator kit (Miltenyi Biotec) and processed following 5′ VDJ-seq kit (10x Genomics).
Library was performed according to manufacturer's instructions (5′ VDJ-seq kit, 10x Genomics)

value: Brain tumor

value: Fischer 344

value: Conventional PT


title: ATAC_PTC_ctrl_2

value: primary tubule cells


title: 1527597_Donor 7-1_IL13

description:
Library name: 1527597
5215.16790.1527597.S51.W111102

value: blood

value: mast cell

value: Donor 7


title: ATAC_PTC_ctrl_3


title: 1527595_Donor 7-1_IL4

description:
Library name: 1527595
5215.16790.1527595.S51.W111102


title: CPT, replicate 2, scRNAseq

description: 10x Genomics


title: RNA-Seq,skeletalmuscle-control4

description:
Library name: UPL25-002747
Column name in gene_counts.csv: UPL25.002747_dedup.bam

value: PBS injection


title: CPT, replicate 1, scRNAseq

description: 10x Genomics


title: ATAC_PTC_ctrl_1


title: RNA-Seq,skeletalmuscle-hiitmct5

description:
Library name: UPL25-002752
Column name in gene_counts.csv: UPL25.002752_dedup.bam


title: pMBRT, replicate 4, scRNAseq

description: 10x Genomics

value: pMBRT


title: RNA-Seq,skeletalmuscle-control3

description:
Library name: UPL25-002746
Column name in gene_counts.csv: UPL25.002746_dedup.bam

value: male


title: 1527594_Donor 7-2_none

description:
Library name: 1527594
5215.16790.1527594.S51.W111102

value: no cytokine


title: 1527593_Donor 7-1_none

description:
Library name: 1527593
5215.16790.1527593.S51.W111102


title: ChIP_U87_DMOG_HIF1_beta

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using  BWA-mem version 0.7.17-r1188.
Reads were sorted using samtools v.1.8.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
ChIP was performed using the ChIP-IT high sensitivity kit (Active Motif, Carlsbad, CA, USA). For immunoprecipitations, 70 μg of chromatin and 3-6 μl of antibodies were used.
Novogene NGS DNA Library Prep Set (Cat No.PT004)

value: DMOG [1mM]


title: RNA-Seq,skeletalmuscle-control2

description:
Library name: UPL25-002745
Column name in gene_counts.csv: UPL25.002745_dedup.bam

value: gastrocnemius muscle

value: BALB/c


title: pMBRT, replicate 3, scRNAseq

description: 10x Genomics


title: ChIP_U87_DMOG_H3K27ac


title: RNA-Seq,skeletalmuscle-control1

description:
Library name: UPL25-002744
Column name in gene_counts.csv: UPL25.002744_dedup.bam


title: 1527582_Donor 6-2_IL33

description:
Library name: 1527582
5215.16790.1527582.S51.W111102

value: Donor 6


title: ChIP_U87_DMOG_Input


title: pMBRT, replicate 2, scRNAseq

description: 10x Genomics


title: pMBRT, replicate 1, scRNAseq

description: 10x Genomics


title: RNA-Seq,skeletalmuscle-mct6

description:
Library name: UPL25-002743
Column name in gene_counts.csv: UPL25.002743_dedup.bam

value: MCT1/2 inhibitor


title: 1527581_Donor 6-1_IL33

description:
Library name: 1527581
5215.16790.1527581.S51.W111102


title: ChIP_ccRCC_3_ctrl_H3K27ac

value: primary ccRCC cells

value: control


title: 1527596_Donor 7-2_IL4

description:
Library name: 1527596
5215.16790.1527596.S51.W111102


title: Ctrl, replicate 4, scRNAseq

description: 10x Genomics

value: Brain tumor

value: Fischer 344

value: Non-treated


title: ChIP_ccRCC_3_ctrl_Input


title: 1527580_Donor 6-2_IL13

description:
Library name: 1527580
5215.16790.1527580.S51.W111102

value: blood


title: RNA-Seq,skeletalmuscle-mct3

description:
Library name: UPL25-002740
Column name in gene_counts.csv: UPL25.002740_dedup.bam


title: RNA-Seq,skeletalmuscle-mct5

description:
Library name: UPL25-002742
Column name in gene_counts.csv: UPL25.002742_dedup.bam


title: RNA-Seq,skeletalmuscle-mct4

description:
Library name: UPL25-002741
Column name in gene_counts.csv: UPL25.002741_dedup.bam


title: Ctrl, replicate 3, scRNAseq

description: 10x Genomics


title: ChIP_ccRCC_2_ctrl_Input


title: RNA-Seq,skeletalmuscle-mct2

description:
Library name: UPL25-002739
Column name in gene_counts.csv: UPL25.002739_dedup.bam


title: Ctrl, replicate 2, scRNAseq

description: 10x Genomics


title: ChIP_ccRCC_2_ctrl_H3K27ac


title: ChIP_ccRCC_1_ctrl_H3K27ac


title: 1527579_Donor 6-1_IL13

description:
Library name: 1527579
5215.16790.1527579.S51.W111102

value: mast cell


title: Ctrl, replicate 1, scRNAseq

description: 10x Genomics


title: 1527578_Donor 6-2_IL4

description:
Library name: 1527578
5215.16790.1527578.S51.W111102


title: RNA-seq_shTgm2_4, CALM-AF10 AML

city: Toyoake

first: Yoko

last: Kuroki

address: 1-98 Denngakugakubo Kutsukake-cho

institute: Fujita Health University

data_processing:
All data analysis were performed in Galaxy Europe website (https://usegalaxy.eu).
Assembly: mm10
Supplementary files format and content: Text file includes raw gene counts for each sample

source_name: Bone marrow

growth_protocol: Methocult 3234 methylcellulose media, murine IL-3 20 ng/ml, CSF 50 ng/ml, GM-CSF 10ng/ml, and 100 U/ml Penicillin/Streptmycin. Cells were cultured at 37C, at 5 % CO2.

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
Poly(A) mRNA was isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L). NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760L).

value: Bone marrow

value: CALM-AF10 leukemia cells

value: Tgm2 knockdown


title: 1527576_Donor 6-2_none

description:
Library name: 1527576
5215.16790.1527576.S51.W111102


title: RNA-seq_shTgm2_2, CALM-AF10 AML


title: ChIP_PTC_3_ctrl_H3K27ac

value: primary tubule cells


title: 1527564_Donor 5-2_IL33

description:
Library name: 1527564
5215.16790.1527564.S51.W111102

value: Donor 5


title: daf-16(mgDf47), starved, replicate 4

city: Durham

first: Kinsey

middle: C

last: Fisher

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

description: Library name: Daf16_R4

data_processing:
Version WS273 of the genome was used for mapping reads. Bowtie version 1.2.3 was used to map paired-end reads with the following settings: bowtie -I 0 -X 500 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset. Count data was restricted to include only protein-coding genes.
Exact tests in edgeR version 3.24.3 were used for differential expression analysis between pairs of conditions.
Only genes with counts per million (CPM) > 1 in at least four libraries across both conditions were included in differential expression analysis.
Assembly: WS273
Supplementary files format and content: csv file of raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm, bulk

growth_protocol: Seven L4 larvae were picked onto each of five-seven 10 cm plates seeded with OP50 and cultured at 20°C for 96 hours (wild type, daf-16(mgDf47), and daf-16(mgDf47); daf-2(e1370) or 120 hrs (daf-2(e1370)) (the daf-2 mutant develops slower than the other genotypes). Plates were washed with S. basal and treated with hypochlorite solution to obtain sterile, developmentally synchronized embryos.

extract_protocol:
RNA was isolated from samples with TRIzol Reagent (Invitrogen#15596026) as per manufacturer’s instructions, except 100 uL of acid-washed sand (Sigma-Aldrich #27439) was added to each sample at the beginning of the extraction protocol to aid with homogenization. RNA was eluted in nuclease-free water and stored at -80°C until further use.
Libraries were prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs # E7775) starting with 200ng of total RNA per sample as input and 11 cycles of PCR.   Individually barcoded libraries were pooled and sequenced on the NovaSeq 6000 S-Prime flowcell to obtain 50 bp paired-end reads.

treatment_protocol: 20,000 embryos were placed in 20 mL of S-complete with 1x E. coli HB101 in a 50 mL flask for the wild-type fed sample, and 20,000 embryos were placed in individual cultures of 20 mL S-basal with 0.1% EtOH in a 50 mL flask for starved samples. All flasks were incubated at 20°C and 180 rpm for 24 hours. With these conditions, it takes approximately 12 hr for emrbyos to hatch following hypochlorite treatment. Samples were then washed 3x with S-complete (fed) or S-basal with 0.1% EtOH (starved) before being pelleted and snap frozen with liquid nitrogen. Samples were stored at -80°C until RNA isolation and library preparation. At least three biological replicates were collected for each condition.

value: whole worm, bulk

value: starved


title: daf-16(mgDf47), starved, replicate 3

description: Library name: Daf16_R3


title: 1527563_Donor 5-1_IL33

description:
Library name: 1527563
5215.16790.1527563.S51.W111102


title: RNA-seq_shCtrl, CALM-AF10 AML, rep2

value: WT


title: RNA-seq_shCtrl, CALM-AF10 AML, rep1


title: ChIP_PTC_2_ctrl_H3K27ac


title: daf-16(mgDf47), starved, replicate 2

description: Library name: Daf16_R2


title: daf-16(mgDf47), starved, replicate 1

description: Library name: Daf16_R1


title: RNA-seq_Ctcf_WT, CALM-AF10 AML, rep2

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
Poly(A) mRNA was isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L). The RNA library was generated by using MGIEasy RNA Directional Library Prep Kit V2.0 (Cat. No.: 1000006386).


title: 1527561_Donor 5-1_IL13

description:
Library name: 1527561
5215.16790.1527561.S51.W111102


title: ChIP_PTC_1_ctrl_H3K27ac


title: 1527560_Donor 5-2_IL4

description:
Library name: 1527560
5215.16790.1527560.S51.W111102


title: RNA-Seq,skeletalmuscle-mct1

description:
Library name: UPL25-002738
Column name in gene_counts.csv: UPL25.002738_dedup.bam

value: gastrocnemius muscle

value: male

value: BALB/c


title: RNA-seq_Ctcf_KO, CALM-AF10 AML, rep1

value: Ctcf knockout


title: RNA-seq_Ctcf_KO, CALM-AF10 AML, rep2


title: 1527559_Donor 5-1_IL4

description:
Library name: 1527559
5215.16790.1527559.S51.W111102


title: 1527562_Donor 5-2_IL13

description:
Library name: 1527562
5215.16790.1527562.S51.W111102


title: ChIP_PTC_2_ctrl_Input

value: control


title: daf-16(mgDf47); daf-2(e1370), starved, replicate 3

description: Library name: Daf16_Daf2_R3


title: daf-16(mgDf47); daf-2(e1370), starved, replicate 4

description: Library name: Daf16_Daf2_R4


title: 1527558_Donor 5-2_none

description:
Library name: 1527558
5215.16790.1527558.S51.W111102

value: no cytokine


title: daf-16(mgDf47); daf-2(e1370), starved, replicate 2

description: Library name: Daf16_Daf2_R2


title: 1527577_Donor 6-1_IL4

description:
Library name: 1527577
5215.16790.1527577.S51.W111102

value: Donor 6


title: ChIP_PTC_1_ctrl_Input


title: sh ITGB5_3

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, poly-A & adaptor addition
Fragment selection and PCR
Library quality assessement
illumina sequencing
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: liver

growth_protocol: Huh7 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

value: liver

value: Huh7 cells

value: liver cancer cells

tag: condition

value: case

tag: knockdown


title: ChIP_PTC_3_ctrl_Input


title: KO3_IP

city: Wuhan

first: Ran

last: Liu

state: Hubei

address: 1277 Jiefang avenue

institute: Union hospital, Tongji medical college, Huazhong university of science and technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Mus musculus using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software (Version 2.1.1) was used for peak calling. The bedtools (Version 2.25.0) was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by a python script, using fisher test. The Homer (version 4.10) was used for motifs analysis.
bw files were generated using genomicRanges R package.
Assembly: GRCm38_release102
Supplementary files format and content: bw file for each sample

source_name: Liver

extract_protocol:
The tissue was fixed in 1% formaldehyde for 10 min at room temperature by a vacuum pump, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tissue was then collected and frozen in liquid nitrogen, and grinded by tissue lyser. The grinded powder was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-STAT3 antibody（Cell Signaling Technology, 9139）and named “IP”. The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: Liver

value: LIF{delta}KC

value: IRI

tag: antibody


title: daf-16(mgDf47); daf-2(e1370), starved, replicate 1

description: Library name: Daf16_Daf2_R1

tag: cell type

value: whole worm, bulk


title: 1527557_Donor 5-1_none

description:
Library name: 1527557
5215.16790.1527557.S51.W111102

value: blood

value: mast cell

value: Donor 5


title: KO3_input


title: sh ITGB5_2

tag: cell line


title: 1527546_Donor 4-2_IL33

description:
Library name: 1527546
5215.16790.1527546.S51.W111102

value: Donor 4


title: daf-2(e1370), starved, replicate 4

description: Library name: Daf2_R4

value: starved


title: sh ITGB5_1


title: KO2_IP

value: anti-STAT3 antibody（Cell Signaling Technology, 9139）


title: daf-2(e1370), starved, replicate 3

description: Library name: Daf2_R3


title: sh_control_3

value: control

value: shcontrol


title: 1527544_Donor 4-2_IL13

description:
Library name: 1527544
5215.16790.1527544.S51.W111102


title: daf-2(e1370), starved, replicate 2

description: Library name: Daf2_R2


title: ChIP_ccRCC_1_ctrl_Input

value: primary ccRCC cells


title: KO1_IP


title: RNA-seq_Ctcf_WT, CALM-AF10 AML, rep1

value: Bone marrow

value: CALM-AF10 leukemia cells

value: WT


title: sh_control_2

value: liver

value: Huh7 cells

value: liver cancer cells


title: daf-2(e1370), starved, replicate 1

description: Library name: Daf2_R1


title: sh_control_1


title: 1527543_Donor 4-1_IL13

description:
Library name: 1527543
5215.16790.1527543.S51.W111102


title: KO1_input

value: Liver

value: LIF{delta}KC

value: IRI


title: 1527542_Donor 4-2_IL4

description:
Library name: 1527542
5215.16790.1527542.S51.W111102

value: blood

value: mast cell


title: WT3_IP


title: Mtb_H37Ra, IP, ChIP

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

description: Library name: Mtb_H37Ra_IP

data_processing:
Raw sequencing fastq files were assessed for quality, adapter content and duplication rates with FastQC v0.12.1, trimmed using trimmomatic v0.38 and aligned with bowtie2 v2.3.4.1 to either the  Mycobacterium tuberculosis genome using GCF_000016145.1 versions from NCBI databasename. Binding regions were identified by peak calling for each sample separately using MACS2 v2.2.7.1 (parameters: callpeak --call-summits --nomodel --extsize 200 -B -p -pv 0.05 --fe-cutoff FEvalue). The  peaks were annotated to the position of genes using ChIPseeker v1.30.2.The motifs were analyzed using HOMER v4.11.1. The  peaks visualization on genome was through igvtools v.2.10.0.
Assembly: GCF_000016145.1
Supplementary files format and content: bigWig

organism: Mycobacterium tuberculosis H37Ra

source_name: bacterial culture

extract_protocol:
Mix the sample with a 1% formaldehyde solution and crosslink it at 24°C for 20 minutes. Then, add 2.5 M glycine to a final concentration of 125 mM and shake at room temperature for 10 minutes to stop the crosslinking process.
Spin the centrifuge at 4°C for 10 minutes, discard the liquid above, and gather the bacteria; then mix the bacteria in 20 ml of cold TBS (20 mM Tris-HCl pH7.5, 150 mM NaCl), spin the centrifuge at 4°C for 10 minutes, discard the liquid above, and gather the bacteria. Resuspend the bacteria in 2 ml of TBS buffer that has been chilled beforehand, then centrifuge at 4°C for 10 minutes, discard the supernatant, and gather the cell pellet. After that, the CHIP assay and sequencing were performed by E-GENE Tech Co., Ltd.

tag: strain

value: M.tb H37Ra

value: bacterial culture

value: anti-DasR antibody


title: 1527541_Donor 4-1_IL4

description:
Library name: 1527541
5215.16790.1527541.S51.W111102

value: Donor 4


title: Mtb_H37Ra, Input, ChIP

description: Library name: Mtb_H37Ra_Input

value: none (input)


title: WT3_input

tag: genotype


title: wild type, starved, replicate 3

description: Library name: N2Starved_R3

value: whole worm, bulk

value: Wild type (N2)

tag: treatment

value: starved


title: wild type, starved, replicate 2

description: Library name: N2Starved_R2


title: 1527540_Donor 4-2_none

description:
Library name: 1527540
5215.16790.1527540.S51.W111102

value: no cytokine


title: 1527539_Donor 4-1_none

description:
Library name: 1527539
5215.16790.1527539.S51.W111102


title: slide5b3

type: other

city: Cambridge

first: Brian

last: Rabe

state: MA

address: 250 Water St

institute: Bristol Myers Squibb

hyb_protocol: Nanostring CosMx TAP 1k universal RNA panel

data_processing: A detailed description of the data processing is available in the methods section of the paper. Cell-by-gene counts are provided per slide as <slideN>_cell_by_gene_counts.csv.gz (from CosMx exprMat_file.csv). Cell metadata are provided per slide as <slideN>_cell_metadata.csv.gz (from CosMx metadata_file.csv). Raw core instrument outputs are archived per slide in <slideN>_raw_core.tar.gz (tx_file.csv for molecule detections, polygons.csv for segmentation shapes, metadata_file.csv, and fov_positions_file.csv). Raw morphology images are omitted to manage size; all spatial coordinates needed to reconstruct cell/molecule positions are included. Seurat objects (<slideN>_seurat.RDS) are provided as supplementary processed files.

molecule: other

source_name: PDAC tumor resection

growth_protocol: Tumors were resected from patients prior to receiving treatment, then formalin fixed and paraffin embedded. 5 um sections were then collected on slides and transferred to Nanostring to be processed.

treatment_protocol: treatment naïve

value: PDAC tumor resection


title: wild type, starved, replicate 1

description: Library name: N2Starved_R1


title: 1527545_Donor 4-1_IL33

description:
Library name: 1527545
5215.16790.1527545.S51.W111102


title: KO2_input


title: slide5b2

scan_protocol: Nanostring CosMx TAP 1k universal RNA panel


title: WT2_input

value: WT


title: wild type, fed, replicate 4

description: Library name: N2Fed_R4

value: fed


title: slide5

label_protocol: Nanostring CosMx TAP 1k universal RNA panel


title: slide6


title: WT1_IP

value: Liver

value: anti-STAT3 antibody（Cell Signaling Technology, 9139）


title: wild type, fed, replicate 2

description: Library name: N2Fed_R2


title: 1527529_Donor 3-1_IL33

description:
Library name: 1527529
5215.16790.1527529.S51.W111102

value: Donor 3


title: wild type, starved, replicate 4

description: Library name: N2Starved_R4


title: WT1_input

value: IRI


title: 1527528_Donor 3-2_IL13

description:
Library name: 1527528
5215.16790.1527528.S51.W111102

value: blood

value: mast cell


title: 1527527_Donor 3-1_IL13

description:
Library name: 1527527
5215.16790.1527527.S51.W111102


title: slide4


title: slide3


title: wild type, fed, replicate 1

description: Library name: N2Fed_R1


title: 1527526_Donor 3-2_IL4

description:
Library name: 1527526
5215.16790.1527526.S51.W111102


title: WT2_IP


title: ISNE3

city: Shijiazhuang

first: pei

last: zhang

state: He

address: No. 215, Heping West Road, Xinhua District,

department: Intensive Care Unit of Department of Anesthesiology

institute: HeBei Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastx_toolkit（0.0.14）and  trim-galore (0.6.5)
The quantity and purity of the RNA were evaluated using a NanoPhotometer spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The RNA integrity was assessed using Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).
Trimmed sequence reads were mapped to OryCun2.0  using hisat2(2.2.0)
Read count extraction and normalization were performed using stringtie（2.1.2）
Assembly: OryCun2.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryctolagus cuniculus

source_name: Eighteen New Zealand white rabbit trachea

growth_protocol: After a week of acclimatization, the rabbits were randomly divided into control, septic shock model, and treatment groups

extract_protocol:
The quantity of the RNA library was determined using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and diluted to 1.5 ng/µL.
The RNA library was constructed using a NEBNext® UltraTM RNA library prep kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocols.

treatment_protocol:
all three groups underwent endotracheal intubation. A cuffed tracheal tube was placed within the trachea 0.5 cm above the annular cartilage and connected to a small animal ventilator (R500IE; RWD Life Science, San Diego, CA, USA) to maintain a respiratory rate of 70 breaths/min and a tidal volume of 8 mL/kg. The cuff pressure was 25 cmH2O and continued for 2 h
Total RNA was isolated from the tracheal tissue using TRIzol reagent (1 mL per 50 – 100 mg of tissue; Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: Mucosal epithelium

value: Posttracheal intubation

tag: treatment group

value: treatment group


title: ISNE2


title: 1527525_Donor 3-1_IL4

description:
Library name: 1527525
5215.16790.1527525.S51.W111102


title: 1527530_Donor 3-2_IL33

description:
Library name: 1527530
5215.16790.1527530.S51.W111102


title: 1527524_Donor 3-2_none

description:
Library name: 1527524
5215.16790.1527524.S51.W111102


title: MSTO 211H CBP treated_biological rep 3

city: Napoli

first: Stefania

last: Crispi

address: Via Pietro Castellino,111

department: DISBA

country: Italy

institute: CNR

hyb_protocol: Total RNA was converted in labelled ssDNA and used to hybridize microarrays. All the procedures including wash and staining of array were performed following the manufacturer's instructions. Hybridization was performed by incubation with rotation at 60 rpm for 16 hours at 45°C.

scan_protocol: Clariom S arrays were scanned using the GeneChip™ Scanner 3000 7G using GCOS

data_processing: Samples data registration and primary analisys was performed using GeneChip™ Command Console™ (GCC). After laser scanning .CEL files from array were used for data analysis. Primary data analysis was performed with the Transcriptome Analysis Console software (Thermofisher version 4.0) including the Robust Multiarray Average module for normalization. Expression cut off selected was Fold change <-2 >2 and pvalue <0.05 and transcriptional modifications were detected comparing AGS treated cells to untreated cells. Differentially expressed genes were selected applying as cut-off criteria log2-fold change ≥+/−2 and a P-value≤0.05.

label: Biotin

source_name: MSTO-211H cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Applied Biosystem protocol from 100 ng total RNA (Whole Transcript Expression Array User Guide).

growth_protocol: Cells were grown in RPMI 1640 at 37°C with 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with CBP (20 micromolar) or with vehicle (0.1% DMSO) for 24 hours. After cells were detached collected and placed in Trizol for RNA extreaction

value: mesothelioma cells


title: ISNE1


title: wild type, fed, replicate 3

description: Library name: N2Fed_R3

value: whole worm, bulk


title: MSTO 211H CBP treated_biological rep 2


title: ABE_Digenome_Control_1

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description:
Library name: RW186_ABE_Digenome_Control_1
Digenome-seq

data_processing:
ABE Digenome-seq FASTQ files were first aligned to hg38 and converted to BAM files. Processed BAMs were analyzed using the digenome-seq executable tool with the following settings: minimum number of forward reads starts at the same position of 5, minimum number of reverse reads starts at the same position of 5, minimum depth of 10 reads, cleavage ratio ≥0.20, cleavage score ≥2.5, and MAPQ ≥50 for overhangs of 5–15 bp.
Assembly: hg38
Supplementary files format and content: tsv format

source_name: Human peripheral blood

extract_protocol:
Genomic DNA extracted from primary human cells using Gentra Puregene Kit (Qiagen) according to manufacturer’s protocol.
Digenome ABE and CBE targets preformed as according to the reported protocol. Purified genomic DNA was modified by base editors for 8 h at 37C, treated with RNaseA, proteinase K, (ABE samples: endonuclease V) or (CBE samples: USER), proteinase K  and purified. DNA was fragmented using a covaris and end prepped using Kappa HyperPrep PCR Free. ABE and CBE libraries were pooled and loaded on Novaseq X plus.

treatment_protocol: Primary human cells were cultured in X-VIVO media with cytokines. Cells were harvested accordingly to extract required genomic DNA.

value: Human peripheral blood

value: Primary Human T-cells

value: CD4+ CD8+


title: 1527523_Donor 3-1_none

description:
Library name: 1527523
5215.16790.1527523.S51.W111102

value: no cytokine


title: ABE_PDCD1_Digenome_E2

description:
Library name: RW183_ABE_PDCD1_Digenome_E2
Digenome-seq


title: 1094103_Donor2-12_IL33

description:
Library name: 1094103
4147.10023.1094103.S33.W111102

value: eosinophils

value: Donor 2


title: ABE_PDCD1_Digenome_E1

description:
Library name: RW182_ABE_PDCD1_Digenome_E1
Digenome-seq


title: Huh7 RYK2, Gpnmb ECD, 8 h

first: Yue

last: Xi

address: 81 St

department: College of life sciences

institute: Wuhan University

description: core_table_gene Rykt_GB2 VS Veh2.xls

data_processing:
RNAseq analysis method for Dr.TOM II delivery
The sequencing data was filtered with SOAPnuke
The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Assembly: GRCm38 (mouse) and GRCh38 (human)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Huh7 cell line

extract_protocol:
RNAprep pure Tissue/Cell Kit (TIANGEN, DP431 and DP430)
mRNA Library Preparation (DNBSEQ) BGI-NGS-JK-RNA-001 A0

value: Huh7 cell line

value: human hepatic cell

value: RYK overexpression

value: GPNMB ECD for 8 h


title: slide2

value: PDAC tumor resection


title: IS1

value: septic shock model


title: ABE_CIITA_Digenome_E2

description:
Library name: RW181_ABE_CIITA_Digenome_E2
Digenome-seq


title: 1094102_Donor2-11_IL33

description:
Library name: 1094102
4147.10023.1094102.S33.W111102

value: blood


title: CON3

value: Mucosal epithelium

value: Posttracheal intubation

value: control


title: MSTO 211H CBP treated_biological rep 1

value: mesothelioma cells


title: 1094101_Donor2-10_IL33

description:
Library name: 1094101
4147.10023.1094101.S33.W111102


title: Huh7 RYK2, Veh, 8 h

description: core_table_gene Rykt_GB2 VS Veh2.xls

value: vehicle for 8 h


title: MSTO 211H untreated_CTRL biological rep 2


title: Huh7 RYK1, Gpnmb ECD, 8 h

description: core_table_gene Rykt_GB1 VS Veh1.xls


title: ABE_CIITA_Digenome_E1

description:
Library name: RW180_ABE_CIITA_Digenome_E1
Digenome-seq

value: Human peripheral blood

value: Primary Human T-cells


title: slide1


title: CON2


title: ABE_CD7_Digenome_E2

description:
Library name: RW179_ABE_CD7_Digenome_E2
Digenome-seq

value: CD4+ CD8+


title: Huh7 RYK1, Veh, 8 h

description: core_table_gene Rykt_GB1 VS Veh1.xls


title: 1094099_Donor2-8_IL13

description:
Library name: 1094099
4147.10023.1094099.S33.W111102

value: eosinophils


title: IS3


title: ABE_CD7_Digenome_E1

description:
Library name: RW178_ABE_CD7_Digenome_E1
Digenome-seq


title: IS2


title: CON1


title: MSTO 211H untreated_CTRL biological rep 3


title: DM3

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

country: United Kingdom

institute: Brunel University London

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with HISAT
Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values algorithm.  Subsequent values were then converted to counts per million (cpm).
Assembly: NZ_CP008706.1
Supplementary files format and content: Matrix table (tab-delimited file) with raw gene counts for every gene and every sample
Supplementary files format and content: Individual tab-delimited files with normalize counts (cpm) for every sample.

organism: Acinetobacter baumannii AB5075

source_name: Acinetobacter baumannii AB5075 (VIR-O colony morphology)

growth_protocol: A. baumannii AB5075 (3 independent replicates) was inoculated from a pure VIR-O type stock and incubated overnight (approx. 16 h) in M9 supplemented with Na-succinate 20 mM (37 C, 180 rpm).

extract_protocol:
Cultures were harvested by centrifugation (or direct resuspension for desiccated cells) in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Samples were additionally treated with RNAse-free DNAse (Invitrogen). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices. Sequencing was done on a NovaSeq 6000 giving 2x51bp reads.

treatment_protocol: Cultures were split in two and each half was washed 3 times either with distilled water or with M9-succinate 20 mM diluted 1:250 (v:v). OD600 of the cell supensions was adjusted to 1.0 and 1 ml from the water-suspended cells was withdrawn as a control comparison, washed with RNAlater and stored at -80 C until further processing. 1 ml of the OD-adjusted water- and M9-suspended cells were spotted on polystyrene Petri dishes and left to air-dry in a laminar flow hood. Once dried, the plates were placed in a chamber with Drierite until reaching a relative humidity of 8-12% and were incubated during 24 h. Finally, cells were harvested by directly resspending them in RNAlater and stored at -80 C.

value: Cells resuspended in M9-succinate and desiccated for 24 h

tag: culture conditions

value: Cells grown overnight (37 C, 180 rpm, approx. 16 h) in M9-succinate (20 mM), washed with diluted M9-succinate (1:250,v:v),  diluted to OD600 1.0 in diluted M9-succinate, dried on a Petri dish and incubated for 24 h at 8-12% relative humidity.


title: ABE_CBLB_Digenome_E2

description:
Library name: RW177_ABE_CBLB_Digenome_E2
Digenome-seq


title: 1094098_Donor2-7_IL13

description:
Library name: 1094098
4147.10023.1094098.S33.W111102

value: Donor 2


title: 1094097_Donor2-6_IL4

description:
Library name: 1094097
4147.10023.1094097.S33.W111102


title: MSTO 211H untreated_CTRL biological rep 1


title: DM1


title: 1094100_Donor2-9_IL13

description:
Library name: 1094100
4147.10023.1094100.S33.W111102


title: DW3

value: Cells resuspended in water and desiccated for 24 h

value: Cells grown overnight (37 C, 180 rpm, approx. 16 h) in M9-succinate (20 mM), washed with distilled water,  diluted to OD600 1.0 in distilled water, dried on a Petri dish and incubated for 24 h at 8-12% relative humidity.


title: ABE_CBLB_Digenome_E1

description:
Library name: RW176_ABE_CBLB_Digenome_E1
Digenome-seq


title: 3DBT4743

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

description: RMA expression value derived from Affymetrix GeneChip command console software v4.0.

hyb_protocol: Labeled samples were then hybridized with Affymetrix GeneChip miRNA 4.0 Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Samples were washed and stained with the Affymetrix GeneChip2 hybridization wash and stain kit, and then scanned with the Affymetrix GeneChip Scanner 3000 7G to generate fluorescent images, as described in the manufacturer’s protocol.

data_processing: Raw data CEL files for miRNA array analysis were generated using Affymetrix GeneChip Command Console Software v4.0.

label: biotin

source_name: 3D cultures on matrigel

label_protocol: RNA labeling was performed using the FlashTag Biotin HSR Kit (Genisphere, Hatfield, PA, USA), following the manufacturer’s protocol for poly(A) tailing.

growth_protocol: 3D organotypic cultures of the BT474 cell line grown on geltrex and 2D cultures of the BT474 cell line.

extract_protocol: Total RNA was extracted from 2D and 3D cultures using TRIzol reagent (Invitrogen), following the manufacturer's instructions.

value: Luminal B breast cancer cell line


title: 1094095_Donor2-4_IL4

description:
Library name: 1094095
4147.10023.1094095.S33.W111102


title: AM711

city: New York

first: Pietro

last: Berico

address: 550 1st Ave Smilow 305

department: Pathology

institute: NYU Langone Health

description: Library name: Sample 2

data_processing:
Space Ranger v2.1.1 was used to map and annotate transcripts. Seuratv5 was used to analyzed the data by R.
Assembly: Hg38
Supplementary files format and content: spaceranger outputs: barcodes and features in tsv.gz, matrix.mtx.gz, coordinates.csv and tissue slide images (png).
Library strategy: Spatial Transcriptomics

source_name: skin

extract_protocol:
Specimens that passed preprocessing and QC criteria were prepared for spatial transcriptomics following the 10x Genomics Visium/CytAssist protocol for FFPE tissues.
Visium Spatial Gene Expression Reagent Kit from 10x Genomics was used for permeabilization, reverse transcription, second-strand synthesis, and cDNA amplification.

value: skin

tag: tissue type

value: FFPE human sample

value: melanoma


title: ABE_B2M_Digenome_E2

description:
Library name: RW175_ABE_B2M_Digenome_E2
Digenome-seq


title: DW1


title: AM3

description: Library name: Sample 1


title: DW2


title: 1094092_Donor2-1_none

description:
Library name: 1094092
4147.10023.1094092.S33.W111102

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include read counts for  each Sample

value: blood

value: no cytokine


title: 1094093_Donor2-2_none

description:
Library name: 1094093
4147.10023.1094093.S33.W111102


title: HL+HS+S+PQ+Cd+N_rep3

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

description:
Library name: HLHSSPQCDN_3
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, Cadmium stress, and Nitrogen deficiency, replicate 3

data_processing:
Read quality control was performed using Trim Galore v0.6.10 and FastQC v0.12.1. Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Gmax_880_v6.0 whole genome using Hisat2 v2.2.1. Samtools v1.18 was used to sort the bam files which were subjected toranscript assembly and quantification using Cufflinks v2.2.1. Differential expression analysis was performed later using Cuffdiff v2.2.1, comparing control conditions with each combined stress condition.
Assembly: reference gemnome used is slycopersicum_691_SL4.0.fa gene model used is Slycopersicum_691_ITAG4.0.gene.gff3
Supplementary files format and content: processed data files are in format txt and it contains the gene names along with the fpkm values for each of the replicates.

organism: Solanum lycopersicum

source_name: leaves

growth_protocol: Moneymaker tomato seeds, purchased from a commercial nursery (Clemente Viven, Semillas Clemente S.A., Vitoria, Alava, Spain), were sown in seedling trays filled with a mixture of peat moss, perlite, and vermiculite (80:10:10) under greenhouse conditions (70% relative humidity with natural photoperiod, 200 µmol photons m−2 s−1 light intensity, and day and night temperature averaging 25.0 ± 3.0◦C and 18.0 ± 3.0◦C, respectively). After germination, seedlings were transplanted to 10-cm diameter pots filled with perlite, maintained under greenhouse conditions as described above, and watered three times a week with half-strength Hoagland solution. Temperature and relative humidity were recorded regularly with a portable USB datalogger (OM-EL-WI- N-USB, Omega, NJ, United States).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The experimental design to study wild-type tomato (Moneymaker) responses to MFSC included the following stresses: Nitrogen deficiency (N-), heat stress (HS), salinity (S), high light (HL), heavy metal as cadmium treatment (Cd), and the herbicide paraquat (PQ) were applied up to a combination of all six factors. HL, HS, S and PQ were combined in all their possible combinations of 2-, 3- and 4-factors and Cd and N- were added to 4-factor combination to generate 2 different groups of 5-factor stresses, and all of them simultaneously generate the 6-MFSC. N deficiency was applied by watering plants with a half strength Hoagland solution with 10% of N (Ca(NO₃)₂) content one week after transplanting the plants. One week after the starting of the N-deficiency stress, plants with and without N deficiency were watered with half strength Hoagland solution containing each stressor(s): S (75 mM NaCl), PQ (1 µM PQ), Cd (10 µM CdSO4), S+PQ (75 mM NaCl + 1 µM PQ), S+PQ+N- (75 mM NaCl + 1 µM PQ + 10% N), S+PQ+Cd (75 mM NaCl + 1 µM PQ + 10 µM CdSO4) and S+PQ+Cd+N- (75 mM NaCl + 1 µM PQ + 10 µM CdSO4 + 10% N). Following 15 days of stress treatments, a group of CT plants and a group of plants subjected to each of the individual and combined stresses were transferred to growth chambers and were subjected to HL (700 µmol m-2s-1) and/or HS (37ºC). The tissue sampled from tomato plants were young leaves. All experiments were repeated three times with at least 8 plants per stress treatment.

value: leaves

tag: variety

value: Moneymaker

value: wild type


title: CD3

value: Untretaed control

value: Cells grown overnight (37 C, 180 rpm, approx. 16 h) in M9-succinate (20 mM), washed with distilled water and  diluted to OD600 1.0 in distilled water (control condition).


title: 3DBT4741


title: 2DBT4742

source_name: 2D cultures


title: 3DBT4742


title: DM2


title: 2DBT4743


title: ABE_B2M_Digenome_E1

description:
Library name: RW174_ABE_B2M_Digenome_E1
Digenome-seq

value: Human peripheral blood

value: Primary Human T-cells

value: CD4+ CD8+


title: 2DBT4741


title: 1094094_Donor2-3_none

description:
Library name: 1094094
4147.10023.1094094.S33.W111102

source_name: blood

extract_protocol:
Tissues/Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen) on the Kingfisher Flex machine (Thermofisher).
The strand-specific RNA-seq libraries were prepared from 500 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2000 (Illumina) by multiplexed single-read run with 33 cycles.

value: eosinophils

value: Donor 2


title: CD2


title: HL+HS+S+PQ+Cd+N_rep2

description:
Library name: HLHSSPQCDN_2
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, Cadmium stress, and Nitrogen deficiency, replicate 2


title: 1094096_Donor2-5_IL4

description:
Library name: 1094096
4147.10023.1094096.S33.W111102


title: 1094088_Donor1-12_IL33

description:
Library name: 1094088
4147.10023.1094088.S33.W111102

value: Donor 1


title: SKMEL-5

description: Library name: Sample 26

data_processing:
Fastq were trimmed using trim galore and reads were aligned to human (gencode v44) or murine (gencode v10) transcriptome using STAR.
Counts were merged across conditions using R and normalized using edgeR.
Differential expression analysis was conducted using Deseq2.
Assembly: Hg38, mm10
Supplementary files format and content: tab-delimited text file containing raw and normalized (counts per million) couts for each sample

growth_protocol: Cells were grown in 6 well plates in 2D for 72hr in complete media supplemented with 1ug/ml of doxycyline to induce shRNA or overexpressing constructs.

extract_protocol:
Macherey-Nagel Nucleospin RNA Plus kit following manufacture instructions.
RNA libraries for RNA-seq were prepared using automated TruSeq stranded total RNA RiboZero Gold library preparation.

tag: sample group


title: CD1


title: HL+HS+S+PQ+Cd+N_rep1

description:
Library name: HLHSSPQCDN_1
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, Cadmium stress, and Nitrogen deficiency, replicate 1

tag: tissue


title: 1094087_Donor1-11_IL33

description:
Library name: 1094087
4147.10023.1094087.S33.W111102


title: VC KPS14 WT RNAseq in AKI medium replicate 3

city: Jena

first: Kai

last: Papenfort

state: Thuringia

address: Winzerlaer Straße 2

department: Faculty of Biological Sciences

institute: Friedrich-Schiller-University Jena

description: Library name: VC_KPS14_aki-vs-lb_aki_3

data_processing:
Pipeline for RNAseq analysis CLC Genomics Workbench 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics Workbench 22.0.2 (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped using CLC Genomics Workbench 22.0.2 (parameters-mismatch cost:2 insertion cost:3 deletion cost:3 lenght fraction: 0.8 similarity fraction: 0.8 strand specific:fwd)
Read count extraction and normalization were performed using CLC Genomics Workbench
Fold enrichment under virulence inducing conditions was compared to standard laboratory conditions using the CLC “Differential Expression for RNA-Seq” tool.
Assembly: NC_002505.1, NC_002506.1
Supplementary files format and content: Excel table (XLSX) with RNA read counts

organism: Vibrio cholerae

growth_protocol: V. cholerae wild-type cells were cultivated in AKI and LB media.

extract_protocol:
Total RNA was isolated with Tri-reagent (Sigma) according to the manufacturer and DNase digested (ThermoFisher scientific, #AM2238).
rRNA was depleted using rRNA-specific biotinylated probes according to Culviner et al 2020 (DOI: 10.1128/mbio.00010-20)/RNA libraries for RNAseq were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, #E7300)  following manufacturer´s protocol

value: WT


title: SKMEL-5 shHOXD13-3 RNA-seq rep3

description: Library name: Sample 24

value: skin

value: SKMEL-5 shHOXD13-3


title: 1094086_Donor1-10_IL33

first: Kaitlyn

last: Gayvert

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description:
Library name: 1094086
4147.10023.1094086.S33.W111102


title: SKMEL-5 shHOXD13-3 RNA-seq rep2

description: Library name: Sample 23

value: melanoma


title: 1094085_Donor1-9_IL13

description:
Library name: 1094085
4147.10023.1094085.S33.W111102

value: blood


title: HL+HS+S+PQ+N_rep2

description:
Library name: HLHSSPQN_2
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, and Nitrogen deficiency, replicate 2


title: HL+HS+S+PQ+N_rep1

description:
Library name: HLHSSPQN_1
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, and Nitrogen deficiency, replicate 1


title: 1094084_Donor1-8_IL13

description:
Library name: 1094084
4147.10023.1094084.S33.W111102


title: VC KPS14 WT RNAseq in AKI medium replicate 2

description: Library name: VC_KPS14_aki-vs-lb_aki_2


title: SKMEL-5 shHOXD13-3 RNA-seq rep1

description: Library name: Sample 22


title: HL+HS+S+PQ+Cd_rep3

description:
Library name: HLHSSPQCD_3
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, and Cadmium stress, replicate 3


title: 1094083_Donor1-7_IL13

description:
Library name: 1094083
4147.10023.1094083.S33.W111102


title: VC KPS14 WT RNAseq in LB medium replicate 2

description: Library name: VC_KPS14_aki-vs-lb_lb_2


title: SKMEL-147

description: Library name: Sample 27


title: HL+HS+S+PQ+Cd_rep2

description:
Library name: HLHSSPQCD_2
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, and Cadmium stress, replicate 2


title: SKMEL-5 shHOXD13-2 RNA-seq rep3

description: Library name: Sample 21

value: SKMEL-5 shHOXD13-2


title: 1094082_Donor1-6_IL4

description:
Library name: 1094082
4147.10023.1094082.S33.W111102


title: VC KPS14 WT RNAseq in LB medium replicate 1

description: Library name: VC_KPS14_aki-vs-lb_lb_1


title: 1094081_Donor1-5_IL4

description:
Library name: 1094081
4147.10023.1094081.S33.W111102


title: SKMEL-5 shHOXD13-2 RNA-seq rep1

description: Library name: Sample 19


title: SKMEL-5 shHOXD13-2 RNA-seq rep2

description: Library name: Sample 20


title: HL+HS+S+PQ+Cd_rep1

description:
Library name: HLHSSPQCD_1
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, and Cadmium stress, replicate 1

value: leaves


title: HL+HS+S+PQ_rep3

description:
Library name: HLHSSPQ_3
Combination of High light stress, Heat stress, Salinity stress, and Paraquat stress, replicate 3

value: Moneymaker


title: VC KPS995 Hfq-3xFLAG RILseq in AKI medium replicate 3

description: Library name: VC_KPS995_rilseq-aki_IP_3

data_processing:
Pipeline for Chimeric fragment (https://github.com/maltesie/ChimericFragments) from Siemers M et al 2024 (doi: 10.1093/nargab/lqae035)
Assembly: NC_002505.1, NC_002506.1
Supplementary files format and content: comma separated values (CSV) file with RNA-RNA interaction information

growth_protocol: V. cholerae wild-type and hfq::3XFLAG strains were cultivated in triplicates in AKI medium. Cells were harvested after 1h of aeration.

extract_protocol:
Melamed S. et al 2018 (DOI: 10.1038/nprot.2017.115)
Melamed S. et al 2018 (DOI: 10.1038/nprot.2017.115)/RNAtag-seq protocol from Shishkin AA et al 2015 (DOI: 10.1038/nmeth.3313)/ rRNA was depleted using rRNA-specific biotinylated probes according to Culviner et al 2020 (DOI: 10.1128/mbio.00010-20)

treatment_protocol: 80,000 μJ/cm2 of 254-nm UV irradiation


title: HL+HS+S+PQ+N_rep3

description:
Library name: HLHSSPQN_3
Combination of High light stress, Heat stress, Salinity stress, Paraquat stress, and Nitrogen deficiency, replicate 3

value: wild type


title: 1094080_Donor1-4_IL4

description:
Library name: 1094080
4147.10023.1094080.S33.W111102


title: VC KPS14 WT RNAseq in AKI medium replicate 1

description: Library name: VC_KPS14_aki-vs-lb_aki_1


title: 501mel

description: Library name: Sample 25


title: VC KPS14 WT RNAseq in LB medium replicate 3

description: Library name: VC_KPS14_aki-vs-lb_lb_3


title: SKMEL-5 shNTC RNA-seq rep3

description: Library name: Sample 18

value: SKMEL-5 shNTC


title: HL+HS+S+PQ_rep2

description:
Library name: HLHSSPQ_2
Combination of High light stress, Heat stress, Salinity stress, and Paraquat stress, replicate 2


title: VC KPS995 Hfq-3xFLAG RILseq in AKI medium replicate 1

description: Library name: VC_KPS995_rilseq-aki_IP_1


title: 1094078_Donor1-2_none

description:
Library name: 1094078
4147.10023.1094078.S33.W111102

value: no cytokine


title: SKMEL-5 shNTC RNA-seq rep1

description: Library name: Sample 16


title: SKMEL-5 shNTC RNA-seq rep2

description: Library name: Sample 17


title: VC KPS995 Hfq-3xFLAG RILseq in AKI medium replicate 2

description: Library name: VC_KPS995_rilseq-aki_IP_2


title: 1094079_Donor1-3_none

description:
Library name: 1094079
4147.10023.1094079.S33.W111102


title: HL+HS+PQ_rep3

description:
Library name: HLHSPQ_3
Combination of High light stress, Heat stress, and Paraquat stress, replicate 3


title: HL+HS+S+PQ_rep1

description:
Library name: HLHSSPQ_1
Combination of High light stress, Heat stress, Salinity stress, and Paraquat stress, replicate 1


title: VC KPS14 Hfq-3xFLAG RILseq in AKI medium replicate 3

description: Library name: VC_KPS14_rilseq-aki_IP_3


title: A375 HOXD13 RNA-seq rep3

description: Library name: Sample 15

value: A375 HOXD13


title: HL+HS+PQ_rep2

description:
Library name: HLHSPQ_2
Combination of High light stress, Heat stress, and Paraquat stress, replicate 2


title: root-LN53,treated with low nitrogen for 336 hours,biol rep 3

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

description:
Library name: LN53_low nitrogen 336h
treated with low nitrogen for 336 hours,biol rep 3

data_processing:
Raw reads were converted to high-fidelity clean data through rigorous filtering of low-quality bases and adapter sequences
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Assembly: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM valus for each sample

organism: Populus ussuriensis

source_name: root

growth_protocol: Clonally propagated Populus ussuriensis plantlets were maintained in vitro on Woody Plant Medium supplemented with 25 g/L sucrose and 6 g/L agar. Cultures were incubated under a 16 h light/8 h dark photoperiod at 23°C, with a light intensity of 46 μmol photons m⁻² s⁻¹ provided by cool white fluorescent lights. The upper three internodes were excised from 4-week-old plantlets and transferred via micro-cutting to normal nitrogen WPM(NN), which contains 10 mM NO₃⁻ and 5 mM NH₄⁺.

extract_protocol:
All samples were rapidly frozen in liquid nitrogen and subsequently stored at −80 °C for RNA-seq and RNA was isolated using cetyltrimethyl ammonium bromide reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After three weeks of rooting, the rooted plantlets were subjected to low-nitrogen (LN) treatment by transferring them to modified WPM containing 0.05 mM NO₃⁻ and 0.025 mM NH₄⁺. Root samples were collected at 0, 6, 12, 24, 48, 96, and 336 hours after LN.

value: root

value: whole root system

value: treated with low nitrogen for 336 hours

tag: batch

value: low nitrogen 336h batch


title: A375 HOXD13 RNA-seq rep2

description: Library name: Sample 14


title: VC KPS14 Hfq-3xFLAG RILseq in AKI medium replicate 2

description: Library name: VC_KPS14_rilseq-aki_IP_2


title: VC KPS14 Hfq-3xFLAG RILseq in AKI medium replicate 1

description: Library name: VC_KPS14_rilseq-aki_IP_1