title: Lung_CD45posi_Asp_rep2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

description:
Library name: Lung_CD45posi_Asp_rep2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
For RNA-seq data analyses, read sequences (76 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz, CA, USA; December 2011) using the hisat2 (version 2.2.1) software programs. Fragments per kilobase of exon per million mapped reads for each gene were calculated using the Cufflinks software program (version 2.2.0; Trapnell Lab, University of Washington, WA, USA).
Assembly: Mouse mm10, Homo sapiens hg39
Supplementary files format and content: scRNA-seq is an h5 file that integrates tab-separated value files and matrices. RNA-seq is an FPKM numerical value file.

source_name: Lung

extract_protocol:
The lungs, trachea, and bronchus were cut into small pieces with surgical scissors and incubated with a protease mixture composed of 4 U/ml elastase, 5 U/ml dispase, 450 U/ml collagenase type III, and 200 µg/ml DNase in RPMI-1640 for 30 min at 37 °C with agitation. The digested lungs were then resuspended with a trypsin mixture consisting of TrypLE Express and 80 µg/ml DNase, incubated at 37 °C for 5 min with frequent agitation, and then washed with 10% fetal bovine serum RPMI. Cell suspensions were incubated with anti-CD16/CD32 to block Fc receptors for 15 min at 4 °C. Whole mouse lung cells were freshly prepared, and for PNEC accumulation, EpCAM+ CD45- tdTomato+ cells and EpCAM+ CD45- tdTomato- cells from PNECs reporter (Ascl1-CreERT2::Rosa26-tdTomato) mice were sorted by BD FACS Aria III. For EoL-1 cells, all cells were recovered for RNA with Trizol and RNA was recovered by the chloroform-phenol method.
Library was prepared according to the manufacter's instructions (Chromium Next GEM Single Cell 3' Reagent Kits v3.1, Dual Index). Briefly, the cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which was contains an Illumina R1 primer sequence, Unique Molecular Identifier and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. RNA-Seq was performed as previously described49. Total cellular RNA was extracted using TRIzol reagent (Invitrogen). A SMARTer Stranded Total RNA-Seq Kit v2 pico (Takara Bio Inc., Shiga, Japan) was used according to the manufacturer’s protocol for cDNA library construction. Sequencing of library fragments was performed using an Illumina NextSeq500 System.

value: Lung

tag: age

value: 13-15 weeks old

value: female


title: ATCC 17978 strain, lose pAB3(LCP), supply overexpressed TetR1, rep3,3

status: Public on Aug 16 2025

type: SRA

city: Xi'an

first: Wenbo

last: He

state: ShaanXi

address: 76 Yanta West Road

department: The First Affiliated Hospital

country: China

institute: Xi'an Jiaotong University

library_source: transcriptomic

data_processing:
To remove technical sequences and low quality sequence, pass filter data of fastq format were processed by Cutadapt (version 1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Trimmed sequence data were aligned to reference genome via software Bowtie2 (v2.2.6)
HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Assembly: ASM107767v1
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: total RNA

organism: Acinetobacter baumannii

source_name: Acinetobacter baumannii strain ATCC 17978

growth_protocol: A. baumannii ATCC 17978 derivatives were grown at 37 °C in LB media at 37 ℃, supplemented with 15μg/ml tetracycline and 2 mM isopropyl β-D-1-thiogalactopyranoside (IPTG)

extract_protocol:
Total RNA from each strain was extracted using RNAsimple Total RNA Kit (Tiangen,Cat#DP419), 1 μg total RNA was used for sequencing library preparations
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

tag: cell type

value: Acinetobacter baumannii

tag: strain

tag: genotype

value: supply TetR1


title: Lung_CD45nega_Asp_rep2

country: Japan

description:
Library name: Lung_CD45nega_Asp_rep2
10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

tag: tissue

tag: Sex


title: RPE-1, APH treated,  IgG rep3

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

library_source: genomic

data_processing:
Raw sequencing reads were first preprocessed using Ktrim software to remove sequencing adaptors and low-quality cycles. The preprocessed reads were then aligned to NCBI GRCh38 reference human genome using Bowtie2 software. PCR duplicates (i.e., reads with identical start and end positions) were identified and removed using in house programs. Reads from mitochondrial chromosome were also removed and the remaining  were kept for downstream analyses ("clean reads").
For DSMO and APH treatments, data from IgG experiments were used as controls to call peaks for Lamin A/C and B1 using MACS2 software, respectively. Peaks with adjusted p-values lower than 0.01 were considered as statistically significant. CUT&Tag signals around the peaks were visualized using deptools software.
We first stitched the peaks in the Lamin A/C or B1 that were less than 20kb in distance, and only kept those longer than 100 kb after stitching. For each kept peak after stitching, we extracted the read numbers in the CUT&Tag experiments, which were further normalized using the clean read count of the corresponding experiments. The normalized read counts were compared between DMSO and APH experiments using t-tests for Lamin A/C and B1 (each had 3 replicates), respectively. The p-values were corrected using Benjamini & Hochberg method, and peaks with adjusted p-values lower than 0.05 in both Lamin A/C and B1 were called as RESS-LAD regions. An implementation of this approach was publicly available at https://github.com/hellosunking/RESS-LADs.
Assembly: hg38
Supplementary files format and content: narrowPeak for Lamin AC and B1, empty for IgG control
Supplementary files format and content: BED format for RESS-LADs regions
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: RPE-1 cells were maintained Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin and streptomycin (Gibco).

extract_protocol:
We perform Cleavage under targets and tagging (CUT&Tag) using Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen, Cat#12598ES48) against lamin A/C and lamin B1 following to the manufacture’ s instruction. Briefly, for each sample, 105 cells were harvested after treatment with/without 0.4 μM APH for 48 hour and washed three times by PBS, resuspend  the cells with cell wash buffer gently, and incubate  with the concanavalin A coated magnetic beads previously washed by ConA bind buffer. Then concanavalin A beads coupled cells were collected and incubated with 2 μg primary antibody (mouse anti lamin A/C (Santa Cruz, Cat#sc-7292) or rabbit anti-lamin B1 (Abcam, Cat#ab16048)) and rabbit anti IgG (Thermo ) at 4 °C overnight with slow rotation. After removing primary antibodies using a magnetic stand, the secondary antibodies (goat anti-rabbit IgG (H+L) (Yeasen, Cat#34850ES60) and goat anti-mouse IgG (H+L) (Yeasen, Cat#3485ES60) were incubated with the concanavalin A beads coupled cells at room temperature for 1 h. Cells were washed three times with wash buffer to remove unbound antibodies. Then, the cells were incubated with pA/G-Transposome mix for 1 h at room temperature. To terminate tagmentation, terminate solution and proteinase K were added to the sample and incubated at 55℃ for 30 min. DNA was purified using DNA selection beads and elutes  in 21 μL ddH2O.
For library amplification, 8 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer, and amplified using 2× Ultima Amplification Mix (Yeasen). The library was then purified using DNA selection beads and washed twice with 80% ethanol and eluted in 21 μL of ddH2O. Libraries were sequenced by Berry Genomic (Beijing, China) on an Illumina NovaSeq platform for 10 G per sample and 150-bp paired-end reads were generated.

treatment_protocol: RPE-1 cells were treated with/without 0.4 μM APH for 48 hour.

tag: cell line

value: retinal pigment epithelial cells

value: TP53 KO

tag: treatment

value: APH

tag: chip antibody

value: IgG


title: RPE-1, APH treated,  IgG rep1


title: Chimeric mouse diaphragm experimental dataset, Day2, gene expression

city: Montreal

first: Qian

last: Li

state: QC

address: 845 Sherbrooke Street West

country: Canada

institute: McGill University

description:
Library name: Chimeric mouse diaphragm experimental dataset Day2 gene expression library
Single-cell RNA-seq of macrophages from bone marrow transplant samples using 10X Genomics

data_processing:
Sequencing BCL files were converted to FASTQ using cellranger mkfastq (10x Genomics).
FASTQ files were processed with cellranger count for gene expression libraries and cellranger multi for CMO demultiplexing, using the mm10 (GRCm39) reference provided by 10x Genomics.
Output feature-barcode matrices were imported into R/Python for quality control, doublet removal, and annotation.
Filtering thresholds included mitochondrial gene percentage, UMI count, and detected gene number, optimized per dataset.
CMO barcode assignments were used to annotate donor/recipient origin in the validation dataset and to trace origins in the experimental dataset.
Assembly: Mouse reference genome mm10 (GRCm39), Ensembl gene annotation (Gencode M27), 10x Genomics reference refdata-gex-mm10-2020-A.
Supplementary files format and content: Cell Ranger–generated outputs in Matrix Market format: matrix.mtx (gene-by-cell UMI counts), features.tsv (gene IDs and symbols), barcodes.tsv (cell barcodes).
Supplementary files format and content: CMO demultiplexing results are provided as barcode annotation files with donor/recipient origin labels.

molecule: polyA RNA

source_name: diaphragm

extract_protocol: Diaphragm macrophages were identified as CD45-positive (CD45.1 or CD45.2), CD11b-positive, and F4/80-positive cells, and negative for SiglecF and CD11c. For the Chimeric mouse diaphragm validation dataset, Cell Multiplexing Oligos (CMO, 10x Genomics) were applied to FACS-sorted CD45.1 and CD45.2 macrophages to distinguish donor and recipient origins. In Chimeric mouse diaphragm experimental datasets, CMOs were applied to unstained muscle cell suspensions prior to sorting to trace cells from different mice. All macrophage sorting was performed in PBS supplemented with 20% fetal bovine serum (FBS) to preserve viability and cell integrity. The Single Cell 3' mRNA and CMO barcode library preparation was conducted strictly following 10x Genomics protocol CG000388.

value: diaphragm

value: macrophage

value: bone marrow transplant


title: RPE-1, APH treated,  Lamin AC rep1

value: Santa Cruz, Cat#sc-7292


title: Lung_CD45posi_Asp_rep1

description:
Library name: Lung_CD45posi_Asp_rep1
10x Genomics


title: Lung_CD45nega_Asp_rep1

description:
Library name: Lung_CD45nega_Asp_rep1
10x Genomics


title: RPE-1, DSMO control,  Lamin B1 rep2

value: DMSO

value: Abcam, Cat#ab16048


title: Chimeric mouse diaphragm experimental dataset, Day1, gene expression

description:
Library name: Chimeric mouse diaphragm experimental dataset Day1 gene expression library
Single-cell RNA-seq of macrophages from bone marrow transplant samples using 10X Genomics


title: Lung_CD45nega_Ctrl_rep1

description:
Library name: Lung_CD45nega_Ctrl_rep1
10x Genomics


title: RPE-1, DSMO control,  Lamin B1 rep1


description:
Library name: EpCAMposi_CD45nega_Ascl1_posi_cells_rep2
10x Genomics

value: Ascl1_posi_epithelial cells


title: RPE-1, DSMO control,  Lamin B1 rep3


title: Feces, OVX+FMT, No.5

city: Kaohsiung

first: Wei

middle: Shiung

last: Lian

address: No.123, Dapi Rd., Niaosong Dist.,

department: Department of Medic al Research

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Library name: Sample25

library_source: other

data_processing:
During the quality control of the original sequence (polymerase read), only sequences with an overlap number greater than 3 can be used to generate a consensus read. When multiple subreads stack on top of each other, random sequencing errors in a single subread can be corrected by the sequences of other subreads at the same position to enhance accuracy, and the sequence quality score (Read Quality, RQ) can be calculated.
Assembly: Sequencing with high quality (RQ>20) is considered a HiFi read. To achieve more accurate species resolution, full-length microbial 16S ribosomal gene analysis employs a higher-specification HiFi read (RQ>30) to carry out a series of bioinformatics analysis processes on the microbial 16S ribosomal gene. HiFi sequences will first undergo analysis using DADA2 to create ASVs (Amplicon Sequence Variants). This procedure includes quality control of sequences, removing redundancy and chimeras, and aggregating sequences, among other tasks.
Supplementary files format and content: The resulting ASVs are then matched against databases like NCBI, GreenGenes, SILVA, eHOMD, and UNITE to obtain species information and generate a species abundance table (ASVs Table).
Library strategy: 16S rRNA-seq

molecule: other

source_name: Feces

extract_protocol:
Mice stool DNA was prepared using QIAamp® PowerFecal® DNA Kit (QIAGEN) and following the manufacturer's protocol.
The labeled DNA is mixed with the sample, following quality control, and then utilized for the construction of the SMRTbell sample library. This library sample is purified using AMPure PB beads. After purification, the DNA is repaired and connected to the junction sequence before it is sent to the instrument for sequencing.

value: Feces

value: Male

value: OVX+FMT


title: RPE-1, DSMO control,  Lamin AC rep3


title: Lung_CD45posi_Ctrl_rep1

description:
Library name: Lung_CD45posi_Ctrl_rep1
10x Genomics

value: Lung

value: 13-15 weeks old

value: female


title: Feces, OVX+FMT, No.3

description: Library name: Sample23


title: Feces, OVX+FMT, No.4

description: Library name: Sample24


title: Feces, OVX+FMT, No.2

description: Library name: Sample22


title: RPE-1, DSMO control,  Lamin AC rep2

value: retinal pigment epithelial cells


description:
Library name: EpCAMposi_CD45nega_Ascl1_nega_cells_rep2
10x Genomics

value: Ascl1_nega_epithelial cells


title: Feces, OVX+FMT, No.1

description: Library name: Sample21


title: RPE-1, DSMO control,  Lamin AC rep1

value: TP53 KO


title: RPE-1, DSMO control,  IgG rep3

value: IgG


title: Feces, OVX+PBS, No.5

description: Library name: Sample20

value: OVX+PBS


title: KLTNG75_2 cells, treated with TNG260, rep2

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

country: USA

institute: NYU Langone Health

description:
Library name: KLTNG75_2
KLTNG75_2, cells treated with TNG260 at 1.026 mM (75 mpk equivalent in vivo dose)

data_processing:
Read qualities were evaluated using FASTQC (Babraham Institute) and mapping to GRCm38 (GENCODE M25) reference genome using STAR program with default parameters.
Assembly: GRCm38, Genome Reference Consortium Mouse Build 38 Organism
Supplementary files format and content: text file contains trancripts per million for each sample
Supplementary files format and content: supplementary csv file contains differential expression for each sample

source_name: Cell line

growth_protocol: KL cells were maintained in Roswell Park Memorial Institute (RPMI)-1640 medium (Gibco #11875) supplemented with 10% FBS (Sigma #12306C) and 1% antibiotic-antimycotic (Gibco #15240062) at 37 °C, 95% humidified air, and 5% CO2 atmosphere.

extract_protocol:
Following Treatment, cell monolayers were washed with ice-cold 1X Phosphate-buffered saline (PBS), scraped, and pelleted. Total genomic RNA was extracted from these pellets using RNeasy Plus MiniKit (Qiagen #74136).
Libraries were prepared with the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 platform utilizing 50-bp paired end reads.

treatment_protocol: KL cells, cultured and grown in a monolayer to ~70% confluency, were subjected to treatment with 1.026 mM of TNG260 (Tango Therapeutics) or 1% DMSO for 7 days

value: Cell line

value: KL (KRAS G12D, STK11 null) cells

value: Murine non-small cell lung cancer cell

value: KRAS G12D, STK11 null


description:
Library name: EpCAMposi_CD45nega_Ascl1_nega_cells_rep1
10x Genomics


title: RPE-1, APH treated,  IgG rep2

value: APH


title: Lung_CD45nega_Ctrl_rep2

description:
Library name: Lung_CD45nega_Ctrl_rep2
10x Genomics


title: Feces, OVX+PBS, No.4

description: Library name: Sample19


title: RPE-1, DSMO control,  IgG rep2

value: DMSO


title: KLTNG75_1 cells, treated with TNG260, rep1

description:
Library name: KLTNG75_1
KLTNG75_1 cells, treated with TNG260 at 1.026 mM (75 mpk equivalent in vivo dose)


title: RPE-1, DSMO control,  IgG rep1


title: KO2

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

data_processing:
STAR: version 2.7.4a
RMATS: v3.1.0 (Mus_musculus.GRCm38.94.chr.gtf)
iREAD (intron_mouse_3875.bed)
Genome_build: mm10
Supplementary_files_format_and_content: RMATS output: *xlsx
Supplementary_files_format_and_content: iREAD output: *ir.txt

source_name: Primary neurons

growth_protocol: Cortices from E16.5 embryos isolated and seeding of primary neurons into poly-ornithine-coated 6-wells.

extract_protocol:
RNA isolation at DIV14 using SurePrep RNA/DNA/Protein Purification Kit (Fisher Scientific) with on-column DNaseI treatment (Roche).
Preparation of RNA libraries for sequencing using standard Illumina protocols.

treatment_protocol: Infection with lentiviral vectors coding NLS-RFP or NLS-RFP:cre and glia depletion by addition of FUdR at DIV1. Half medium change at DIV3.

value: Cortex

tag: infection


title: Feces, OVX+PBS, No.3

description: Library name: Sample18

value: Feces

value: Male


title: Feces, OVX+PBS, No.2

description: Library name: Sample17


title: Feces, OVX+PBS, No.1

description: Library name: Sample16


title: KLCon1_KL cells, DMSO treated, rep1

description:
Library name: KLCon1
KLCon1_KL cells, DMSO treated


title: Ctrl2

value: NLS-RFP


title: KO1


description:
Library name: EpCAMposi_CD45nega_Ascl1_posi_cells_rep1
10x Genomics

value: Lung

value: Ascl1_posi_epithelial cells

value: 13-15 weeks old


title: KLCon2_KL cells, DMSO treated, rep2

description:
Library name: KLCon2
KLCon2_KL cells, DMSO treated


title: Ctrl1


title: Leaves,chlorella-1_26 day,rep2

city: daegu

first: myeonghoon

last: kang

state: Daegu

country: South Korea

institute: Daegu Gyeongbuk Institute of Science and Technology (DGIST)

data_processing:
Alignment of the resulting reads to the Arabidopsis thaliana genome (TAIR10) was performed using STAR aligner.
raw counts were calculated using Htseq tools, then subsequently differentially expression analysis using DESeq2 tool in R
For FPKM value generation, we used hisat2-stringtie pipeline
Assembly: TAIR 10
Supplementary files format and content: Microsoft excel worksheet includes Raw counts and FPKM  values for each samples

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

extract_protocol:
100mg arabidopsis leaves (WT/chlorella-1; 14d,26d-old) were grinded with liquid nitrogen, then extracted RNA using qiazol lysis reagent then Total RNA was used for the construction of sequencing libraries.
RNA-seq library for sequencing construction was performed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit.

value: Arabidopsis leaves

value: chlorella knockout


title: Feces, OVX+GEX, No.3

description: Library name: Sample13

value: OVX+GEX


title: Feces, OVX+GEX, No.5

description: Library name: Sample15


title: Leaves,chlorella-1_26 day,rep3


title: Feces, OVX+GEX, No.2

description: Library name: Sample12


title: Fol4287 UV poly 1

city: Rehovot

first: Shay

last: Covo

address: po Box 12

department: Microbiology and Phytopathology

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: sample_16_S16

data_processing:
Raw data quality was assessed using FASTQC (Babraham Bioinformatics)
Ribosomal RNA gene sequences of Fusarium Fujikuroi (EF1) were downloaded from ENSEMBL Fungi Biomart (http://fungi.ensembl.org/index.html) and used to construct a reference database for FMN. Raw reads were mapped against the reference rRNA database using HISAT2. Mapped reads were discarded whereas unmapped reads were collected and remapped against the F. mangiferae MRC7560 [GCA_900044065.1] reference genome, for FMN
Reads were assembled, normalized and gene-expression level was quantified using the DESeq2 R package (version 1.3.4) data-normalization method
Assembly: GCA_900044065.1
Supplementary files format and content: Excel file contaning DEseq2 DE analysis results

organism: Fusarium oxysporum

source_name: Germinating conidia

growth_protocol: Spores of F. mangiferae strain MRC7560 and F. oxysporum strain 4287 were incubated in KNO3-based medium on an orbital shaker (250 rpm) at 25 °C for 5 days. Microconidia were obtained by filtering the culture through a nylon cell strainer (mesh size 40 µm, Corning, USA) and resuspended in sterile water. Conidia were then inoculated into potato dextrose broth (PDB; BD Sparks, USA) at 1 x 108 conidia/ml. The cultures were incubated on an orbital shaker at 25 °C for 14 h and then harvested immediately or treated as specified.

extract_protocol:
Germinating conidia / filaments were disrupted in a Minilys bead beater (Bertin Instruments, France) for 30 s at medium speed. Fractions from 3-12 and 13 -24 polysomes were combined and processed for RNA extraction using Trizol LS 3:1 ratio as the manufacturer’s instructions.Total RNA was extracted with the Qiagen (USA) RNeasy micro kit and was treated on-column with RQ1 RNase-free DNase (Promega, USA) to remove additional residues of genomic DNA. RNA quality was quantified by Agilent 2200 TapeStation machine using an RNA kit (Agilent Technologies, USA). For quantification, 1 µl RNA was quantified with a Qubit 2.0 Fluorometer and RNA BR kit (Life Technologies, USA).
cDNA libraries were prepared using 0.5 µg RNA with a QuantSeq 3ʹ mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, Austria) and were sequenced using the NextSeq 500 system (Illumina, USA) at the Center for Genomic Technologies of the Hebrew University of Jerusalem.

treatment_protocol: Spores or germlings 14 h post-inoculation were obtained by filtering 10 ml of the cultures, and suspensions with 2 x 107 conidia/ml were irradiated with 50 J/m2 UV light (254 nm, 15 W lamp, Osram, Germany); the incident fluence was measured with a radiometer (YK-35UV, Digital Instruments, USA).

value: Germinating conidia

value: Fungal asexual spore

value: WT

value: 2 h following UV irradiation at 14 hpi


title: Fol4287 CTRL poly 3

description: Library name: sample_15_S2

value: Untreated at 14 hpi


title: Fol4287 UV poly 3

description: Library name: sample_18_S4


title: Fol4287 UV poly 2

description: Library name: sample_17_S17


title: Feces, OVX+GEX, No.4

description: Library name: Sample14


title: Fol4287 CTRL poly 2

description: Library name: sample_14_S14


title: Leaves,chlorella-1_14 day,rep3


title: Feces, OVX+GEX, No.1

description: Library name: Sample11


title: Fol4287 CTRL poly 1

description: Library name: sample_13_S13


title: Leaves,chlorella-1_14 day,rep2


title: Feces, OVX, No.5

description: Library name: Sample10

value: OVX


title: Leaves,chlorella-1_14 day,rep1


title: Feces, OVX, No.4

description: Library name: Sample9


title: Leaves,Col_26 day,rep3


title: Fol4287 UV mono 2

description: Library name: sample_11_S11


title: Leaves,Col_26 day,rep1


title: Feces, OVX, No.2

description: Library name: Sample7


title: Leaves,Col_26 day,rep2


title: Feces, OVX, No.3

description: Library name: Sample8


title: Fol4287 CTRL mono 3

description: Library name: sample_9_S9


title: Feces, OVX, No.1

description: Library name: Sample6


title: Leaves,chlorella-1_26 day,rep1


title: Fol4287 CTRL mono 2

description: Library name: sample_8_S8


title: Feces, Sham, No.5

description: Library name: Sample5

value: Sham


title: Feces, Sham, No.4

description: Library name: Sample4


title: Leaves,Col_14 day,rep3


title: Fol4287 CTRL mono 1

description: Library name: sample_7_S7


title: Leaves,Col_14 day,rep1


title: Feces, Sham, No.3

description: Library name: Sample3


title: Fol4287 UV total 3

description: Library name: sample_6_S6


title: Leaves,Col_14 day,rep2


title: SPHINX31_Sample 3

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

data_processing:
Illumina Casava1.7 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (version 2.7)
Trimmed sequence reads were mapped to Rnor_6.0.102/rn6 (Rat) using Hisat2 (version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAM tools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and the TMM algorithm was used for normalization.
Assembly: rn6
Supplementary files format and content: Matrix table with FPKM values and counts for each sample

organism: Rattus norvegicus

source_name: Primary cells

growth_protocol: RCCECs were maintained in endothelial cell medium (ScienCell) supplemented with 5% fetal bovine serum (FBS), endothelial cell growth supplement, and antibiotics in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
The total RNA from primary cells was extracted using Trizol (Invitrogen) following the manufacturer's procedure. The quality and integrity of each sample were checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE). 50 μg of RNA was used as input material for the RNA sample preparations.
Paired-end libraries were synthesized by using the mRNA-seq Lib Prep Kit for Illumina (ABclonal, Wuhan, Hubei, China).

treatment_protocol: Following 24h growth, RCCECs were treated with SPHINX 31 or not.

value: Primary cells

value: Rat corpus cavernosum endothelial cells


title: Fol4287 UV total 1

description: Library name: sample_4_S4


title: Feces, Sham, No.1

description: Library name: Sample1

value: Feces

value: Male


title: Fol4287 UV total 2

description: Library name: sample_5_S5


title: Fol4287 UV mono 3

description: Library name: sample_12_S1


title: Fol4287 CTRL total 3

description: Library name: sample_3_S3


title: SK-N-SH cells, LINC02449-rs149707223_Alt-G OE, rep2

city: Guangzhou

first: 杨

last: 腾飞

address: No.1023,South Shatai Road, BaiyunDistrict

department: Medical Genetics

institute: Southern Medical University

description:
Library name: SK-N-SH-Lnc-Alt-G-2
RP11-G2

data_processing:
The raw sequencing data obtained from the Illumina platform, referred to as Raw Reads, undergoes data processing to generate high-quality sequences, known as Clean Reads. This processing involves the removal of low-quality sequences and the elimination of adapter contamination. The Clean Reads are then aligned to the hg19 reference genome using the STAR aligner with default parameters. Quantification is performed using FeatureCounts, resulting in the generation of Counts and FPKM values.
Assembly: hg19
Supplementary files format and content: FPKM
Supplementary files format and content: count

source_name: SK-N-SH

growth_protocol: SK-N-SH mesenchymal cells were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested by the phenol-chloroform method using TRIZOL (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
Using magnetic beads coated with Oligo(dT), mRNA with polyA tails is enriched and purified from RNA samples. Fragmentation Buffer is then added to the purified mRNA to fragment it. The resulting RNA fragments serve as templates for the reverse transcription process, utilizing random primers to synthesize the first strand of cDNA. Subsequently, a 2nd Strand Marking Buffer and a 2nd Strand/End Repair Enzyme Mix are introduced to synthesize the second strand of cDNA. Following this, end repair is performed, an adenine base is added, and sequencing adapters are ligated. The target fragments are then recovered through magnetic bead selection and subjected to PCR amplification, thereby completing the entire library preparation process.

treatment_protocol: SK-N-SH cells were infected with lentivirus to construct stable transfected cell lines.

value: SK-N-SH

value: neuroblastoma


title: Fol4287 UV mono 1

description: Library name: sample_10_S10


title: SPHINX31_Sample 1


title: SK-N-SH cells, LINC02449-rs149707223_Alt-G OE, rep1

description:
Library name: SK-N-SH-Lnc-Alt-G-1
RP11-G1


title: Fol4287 CTRL total 2

description: Library name: sample_2_S2


title: Fol4287 CTRL total 1

description: Library name: sample_1_S1


title: PBS_H_3

data_processing:
Raw sequencing data was preprocessed using Ktrim software to remove adapters and low quality cycles; PCR duplicates were removed using in-house programs; the clean reads were subsequently aligned to the human reference genome (GRCh38) using STAR software
FeatureCount was then used to quantify gene expressions (e.g., raw read counts); the raw read counts were analyzed using DESeq2 to mine differentially expressed genes; genes with Benjamini-Hochberg adjusted p-values lower than 0.05 and at least 1.5-fold changes in expression between PBS_N and CA_N/PBS_H were considered as differentially expressed
Assembly: NCBI GRCh38
Supplementary files format and content: Matrix for raw read counts for all genes in each sample.

growth_protocol: The human colorectal cancer cell line HCT116 is cultured in RPMI 1640 Medium, supplemented with 10% Fetal Bovine Serum (FBS), and maintained at a temperature of 37°C in a humidified incubator with an atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from tumor cells using column-based purification method (Zymo, #R2052) and analyzed for quality on an Agilent 2100 Bioanalyzer. Ribosomal RNA (rRNA) was depleted using a commercially available kit (Vazyme, #N406-01), which selectively removes rRNA and enriches the mRNA fraction.
The rRNA-depleted RNA was fragmented and used to construct a cDNA library following a protocol provided by VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme, #NRM605-01). The cDNA library was amplified using PCR and analyzed for size distribution on an Agilent 4200 TapeStation System, then subjected to a circularization process to form a concatemers of the cDNA fragments (Vazyme, #NM201-01). After quantified using a Qubit fluorometer, the circularized library was loaded onto a sequencing flow cell and sequenced on a MGISEQ-2000 sequencer (MGI) in paired-end 150 bp mode.

treatment_protocol: For co-culture of cell line and strains, 1 million cells were grown to confluence on 6-well plate, then replaced medium with 2 ml serum-free medium supplemented with the PBS or strains and incubated for 6 or 12 hours (37 °C/5% CO2). For hypoxia treatment,  1 million cells were grown to confluence on 6-well plate and move to hypoxia incubator chamber (37°C/5% CO2/95% N2).

value: colorectal cancer cell

value: Hypoxia


title: SK-N-SH cells, LINC02449-rs149707223_Ref-C OE, rep2

description:
Library name: SK-N-SH-Lnc-Ref-C-2
RP11-C2


title: SK-N-SH cells, LINC02449-rs149707223_Ref-C OE, rep1

description:
Library name: SK-N-SH-Lnc-Ref-C-1
RP11-C1


title: PBS_H_2


title: Feces, Sham, No.2

description: Library name: Sample2


title: SPHINX31_Sample 2


title: SK-N-SH cells, GV502, rep2

description:
Library name: SK-N-SH-GV502-2
control2


title: SK-N-SH cells, GV502, rep1

description:
Library name: SK-N-SH-GV502-1
control1


title: PBS_H_1


title: FMN UV poly 3

description: Library name: sample_36_S36

organism: Fusarium mangiferae


title: FMN UV poly 1

description: Library name: sample_34_S34


title: FMN UV poly 2

description: Library name: sample_35_S35


title: FMN CTRL poly 3

description: Library name: sample_33_S33


title: CA_N_1

value: C. albicans infected


title: FMN CTRL poly 2

description: Library name: sample_32_S32


title: PBS_N_3

value: Normoxia


title: NC_Sample 3

value: untreated


title: NC_Sample 2


title: NC_Sample 1


title: FMN CTRL poly 1

description: Library name: sample_31_S31

value: Germinating conidia

value: Fungal asexual spore


title: FMN UV mono 3

description: Library name: sample_30_S30

value: WT

value: 2 h following UV irradiation at 14 hpi


title: PBS_N_1


title: FMN UV mono 2

description: Library name: sample_29_S29


title: RMF stimulation, replicate 3, scRNAseq

city: Shanghai

first: Li

last: Yingze

address: Zhennan Road

institute: Tongji University

description: Singleron GEXSCOPE

data_processing:
The scRNA-seq data was used CellRanger (Version 7.0.0) for read alignment (reference genome: mm10), barcode and UMI filtering and counting processes. Data normalization, cell clustering and dimensional reduction were conducted using the python package Scanpy (Version 1.7.2) 59.
Assembly: mm10
Supplementary files format and content: barcodes, features, and matrix files

source_name: Subcutaneous tumor tissue

extract_protocol:
Single-cell suspensions (2×10^5 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The libraries were sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads, according to the manufacturer’s instructions. Briefly, Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. TruSeq Read 1 (Read 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (Read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 450bp.

value: Subcutaneous tumor tissue

value: C57BL/6 mice

value: all cells isolated from tumor tissue

value: Magnetic nanomotors via intratumoral injection with MagLMP treatment


title: RMF stimulation, replicate 2, scRNAseq

description: Singleron GEXSCOPE


title: DOPAC, replicate 2, CUT&Tag-seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: DOPAC_2

data_processing:
The raw reads were further filtered by Cutadapt (version: cutadapt-4.7).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using Bowtie2 (Version 2.5.1).
Sequence tags were aligned to the genome and then subsequently analyzed by MACS2 (version 2.2.9.1) to detect genomic regions enriched for multiple overlapping DNA fragments (peaks).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: spleen

extract_protocol:
CD8⁺ T cells were cultured after isolation and purification from spleen using magnetic bead-based separation
CUT&Tag libraries was generated and indexed using Hyperactive Universal CUT&Tag Assay Kit for Illumina and then TurePrep Index Kit for Illumina.

value: spleen

value: CD8+ T

value: lymphocyte

value: DOPAC


title: CA_N_3

value: colorectal cancer cell


title: CA_N_2


title: RMF stimulation, replicate 1, scRNAseq

description: Singleron GEXSCOPE


title: DOOAC, replicate 1, CUT&Tag-seq

description: Library name: DOPAC_1


title: FMN UV mono 1

description: Library name: sample_28_S28


title: STM ∆lsrB 2

city: Bangalore

first: Anmol

last: Singh

state: Karnataka

address: Lab SA-10, New Biological Science Building,IISc.

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Library name: Sample 8
column name in raw_counts_all_samples.xlsx: DB_2

data_processing:
The quality of the reads was assessed using FastQC v 0.11.9 before proceeding with the downstream analysis. The reads were passed through SortMeRNAv4.3.7 and were used against all eight rRNA databases provided to filter and remove rRNA reads. The trimmed reads were then passed through fastp  to remove adaptors, low-quality bases (Q<30), and short reads (< 36 bp).
Salmonella Typhimurium 14028s  reference genome and annotation were downloaded from NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/022/165/GCF_000022165.1_ASM2216v1/).  HISAT2 was used to create the reference index and the trimmed & filtered reads were mapped to the indexed genome using HISAT2. Quantification was performed with featureCount.
A total of 4728 features were assigned in the raw count file. The raw count file is made into raw counts for individual sets, and the rest of the differential analysis is done according to the sets. The library sizes are plotted for individual sets. The transcripts with low read counts (< count of at least 10 for a minimum of 2 samples) were removed. The filtered read counts were normalized by transforming to the rlog transformation function (rlog) of DESeq2 and are used for further analysis.
Assembly: GCF/000/022/165/GCF_000022165.1_ASM2216v1
Supplementary files format and content: Exel file include raw count of each sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella Typhimurium 14028s

growth_protocol: Bacteria were grown in LB media at 37℃ under 170 rpm shaking condition

extract_protocol:
RNA extraction was performed using the Qiagen RNeasy Mini kit (Cat. No. 74104) with a few modifications. The remaining half of the pellet was lysed with 700 µl of TRIzol reagent and 10 µl of β-mercaptoethanol on Tissuelyser for 1 minute at 20 Hz.  The lysate was centrifuged, and the supernatant was mixed with an equal volume of 70% ethanol. RNA was captured on a spin column and washed, and on-column DNase I treatment was performed using Qiagen RNase-Free DNase I Set as per kit recommendations. The following steps were performed as per the manufacturer’s recommendations. RNA was eluted in 50 µl of RNase-free water. Using appropriate standards, the RNA samples were quantified on the Nanodrop and Qubit flurometer. Appropriate dilutions were loaded on a high-sensitivity RNA screen tape and run on Agilent Tapestation 4200 to determine the RNA integrity number (RIN).
Briefly, 1000ng of RNA sample was used for ribodepletion by using NEBNext rRNA depletion kit Bacteria (Cat. no. NEB E7850X), which includes Probe hybridization of RNA, RNase H digestion, DNase 1 digestion according to the manufacturer’s protocol. The NEBNext  Ultra II Directional RNA Library prep kit for Illumina (Cat. no. E7760L), was used to construct double-stranded cDNA libraries from the rRNA depleted RNA, using RNA fragmentation, first strand cDNA synthesis with random primers, second strand cDNA synthesis, end repair of double stranded cDNA, adapter ligation, removal of excess adapter using sample purification beads, PCR enrichment of adapter ligated DNA and clean-up of PCR products as instructed by the manufacturer. The cleaned libraries were quantitated on Qubitflurometer and appropriate dilutions loaded on a D1000 screen tape to determine the size range of the fragments and the average library size.

value: Salmonella Typhimurium 14028s

value: lsrB knockout


title: MNM injection, replicate 3, scRNAseq

description: Singleron GEXSCOPE

value: Magnetic nanomotors treatment via intratumoral injection


title: Control, replicate 2, CUT&Tag-seq

description: Library name: Control_2

value: Control


title: Control, replicate 1, CUT&Tag-seq

description: Library name: Control_1


title: STM ∆lsrK 2

description:
Library name: Sample 6
column name in raw_counts_all_samples.xlsx: DK_2

value: lsrK knockout


title: FMN CTRL mono 3

description: Library name: sample_27_S7

value: Germinating conidia

value: Fungal asexual spore

value: Untreated at 14 hpi


title: MNM injection, replicate 1, scRNAseq

description: Singleron GEXSCOPE

value: Subcutaneous tumor tissue


title: PBS_N_2

value: Normoxia


title: FH_23_Hela_siAar20R7treat

type: RNA

hyb_protocol: Hybridized to human transcriptome array (HTA2.0; Affymetrix)

scan_protocol: not provided

data_processing: TAC and Partek (Genomic Suite v6.6)

label: biotin

source_name: HeLa

label_protocol: samples were prepared for affymetrix junctions arrays

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: After 72h RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.

treatment_protocol: HeLa cells were transfected with siRNA CTRL or with siAAR2 for 72 hours

value: HeLa


title: STM ∆lsrK 1

description:
Library name: Sample 5
column name in raw_counts_all_samples.xlsx: DK_1


title: STM ∆lsrB 1

description:
Library name: Sample 7
column name in raw_counts_all_samples.xlsx: DB_1


title: 4dpi_2

first: Mengxian

last: Zhang

address: Beijing

institute: Tsinghua University

data_processing:
The initial demultiplexing of raw sequencing reads involved the utilization of Illumina bcl2fastq software, resulting in the generation of 150-bp paired-end read files in FASTQ format.
Subsequently, alignment of these reads to the mm10 mouse reference genome was executed using the Cell Ranger (v7.2.0) tool provided by 10X Genomics
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Colonic epithelial cells and stromal cells were isolated separately. For the isolation of colonic epithelial cells, the colon was extracted, washed, longitudinally cut, and incubated in 2 mM EDTA in PBS at 4°C for 20 minutes. Colonic crypts were isolated by direct scraping using slides and enriched through centrifugation. Subsequently, the colonic crypts were digested in Collagenase I (2 mg/mL, Sigma-Aldrich) at 37°C for 30 minutes. Single cells were obtained by filtering through a 40 μm cell strainer (BD Biosciences). The cells were then centrifuged and resuspended in Advanced DMEM/F12 (Gibco, 12634010) with Propidium Iodide (PI, 5 μg/mL). PI-negative live cells were isolated by flow cytometry (MoFlo Astrios EQ).For the isolation of colonic stromal cells, colon was washed with cold PBS first and then incubated in cold PBS containing DTT (1 mM) at 250 rpm for 10 min to remove chymus. Next, colon was transferred to cold PBS containing EDTA (50 mM) and HEPES (10 mM) and colonic epithelium was removed by vigorous shaking for 2 min. The last step was repeated to fully remove the epithelium. The remaining tissue was incubated in RPMI1640 containing Collagenase IV (1000 U/mL, Sigma-Aldrich) at 37°C for 60 min. The digested tissue was minced through pipetting and the muscle tissue was removed through filtering by a 70 mm cell strainer (BD Biosciences). Stroma cells were centrifuged and resuspended in MEM (Gibco, 12571063) and live stromal cells were also isolated by flow cytometry.
To conduct single-cell RNA-sequencing, Chromium Single Cell 3ʹ Reagent Kits v3 were chosen (10x Genomics). Single live colonic epithelial cells and stromal cells were isolated from mice at the designated time point after irradiation. For each sample, epithelial cells and stromal cells were mixed at a ratio of 1:1 before loading to the Chromium controller (10x Genomics). Reverse transcription, cDNA amplification, and library preparation were completed according to the manufacturer’s recommendations. scRNA libraries were sequenced using HiSeq X Ten system (PE-150 bp, Illumina).

treatment_protocol: Mice for scRNA-seq were subjected to 10 Gy abdominal X ray irradiation

value: Colon

value: 10 Gy abdominal

tag: time post_radiation

value: 4 dpi


title: FMN UV total 3

description: Library name: sample_24_S24

value: WT

value: 2 h following UV irradiation at 14 hpi


title: FH_21_Hela_siCntr2

value: ctr


title: FH_24_Hela_siCntr3


title: FH_22_Hela_siAar20R7treat


title: 4dpi_1


title: PBS control, replicate 3, scRNAseq

description: Singleron GEXSCOPE

value: C57BL/6 mice

value: all cells isolated from tumor tissue

value: PBS treatment via intratumoral injection


title: STM ∆luxS 2

description:
Library name: Sample 4
column name in raw_counts_all_samples.xlsx: DS_2

value: Salmonella Typhimurium 14028s

value: luxS knockout


title: FMN UV total 2

description: Library name: sample_23_S23

value: Germinating conidia


title: FMN UV total 1

description: Library name: sample_22_S22

value: Fungal asexual spore


title: PBS control, replicate 2, scRNAseq

description: Singleron GEXSCOPE


title: FMN CTRL mono 2

description: Library name: sample_26_S6

value: Untreated at 14 hpi


title: 2dpi

value: 2 dpi


title: PBS control, replicate 1, scRNAseq

description: Singleron GEXSCOPE

value: Subcutaneous tumor tissue


title: non_IR_2

value: no irradiation


title: non_IR_3

value: Colon


title: FMN CTRL total 3

description: Library name: sample_21_S21


title: STM WT 2

description:
Library name: Sample 2
column name in raw_counts_all_samples.xlsx: WT_2


title: FMN CTRL total 2

description: Library name: sample_20_S20


title: MNM injection, replicate 2, scRNAseq

description: Singleron GEXSCOPE

value: Magnetic nanomotors treatment via intratumoral injection


title: FMN CTRL mono 1

description: Library name: sample_25_S5


title: STM WT 1

description:
Library name: Sample 1
column name in raw_counts_all_samples.xlsx: WT_1


title: EOL1_rep1

description:
Library name: EOL1_rep1
Illumina NextSeq 500

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
For RNA-seq data analyses, read sequences (76 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz, CA, USA; December 2011) using the hisat2 (version 2.2.1) software programs. Fragments per kilobase of exon per million mapped reads for each gene were calculated using the Cufflinks software program (version 2.2.0; Trapnell Lab, University of Washington, WA, USA).
Assembly: Mouse mm10, Homo sapiens hg39
Supplementary files format and content: scRNA-seq is an h5 file that integrates tab-separated value files and matrices. RNA-seq is an FPKM numerical value file.

extract_protocol:
The lungs, trachea, and bronchus were cut into small pieces with surgical scissors and incubated with a protease mixture composed of 4 U/ml elastase, 5 U/ml dispase, 450 U/ml collagenase type III, and 200 µg/ml DNase in RPMI-1640 for 30 min at 37 °C with agitation. The digested lungs were then resuspended with a trypsin mixture consisting of TrypLE Express and 80 µg/ml DNase, incubated at 37 °C for 5 min with frequent agitation, and then washed with 10% fetal bovine serum RPMI. Cell suspensions were incubated with anti-CD16/CD32 to block Fc receptors for 15 min at 4 °C. Whole mouse lung cells were freshly prepared, and for PNEC accumulation, EpCAM+ CD45- tdTomato+ cells and EpCAM+ CD45- tdTomato- cells from PNECs reporter (Ascl1-CreERT2::Rosa26-tdTomato) mice were sorted by BD FACS Aria III. For EoL-1 cells, all cells were recovered for RNA with Trizol and RNA was recovered by the chloroform-phenol method.
Library was prepared according to the manufacter's instructions (Chromium Next GEM Single Cell 3' Reagent Kits v3.1, Dual Index). Briefly, the cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which was contains an Illumina R1 primer sequence, Unique Molecular Identifier and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. RNA-Seq was performed as previously described49. Total cellular RNA was extracted using TRIzol reagent (Invitrogen). A SMARTer Stranded Total RNA-Seq Kit v2 pico (Takara Bio Inc., Shiga, Japan) was used according to the manufacturer’s protocol for cDNA library construction. Sequencing of library fragments was performed using an Illumina NextSeq500 System.


title: non_IR_1


title: FMN CTRL total 1

description: Library name: sample_19_S19


title: 205437190095_R08C01

status: Public on Aug 15 2025

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description: Plasma cell-free DNA

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.

label: Cy5 and Cy3

source_name: Human plasma DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol.

tag: diagnosis

value: ARDS

tag: inflammation

value: Hyper


title: 205437190095_R07C01

description: Plasma cell-free DNA


title: 205437190095_R05C01

description: Plasma cell-free DNA


title: 205437190095_R04C01

description: Plasma cell-free DNA


title: 205437190095_R02C01

description: Plasma cell-free DNA


title: 205437190095_R03C01

description: Plasma cell-free DNA


title: 205437190095_R01C01

description: Plasma cell-free DNA


title: L0, C3TD078, replicate 3

city: Cleveland

first: Justin

last: Lathia

state: OH

department: Department of Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Research

description: Library name: L0_CCF59078_9

data_processing:
The raw bulk RNA-seq paired end (R1-R2, 2*100 bp) sequencing fastq data was first subjected to the quality check analysis using FastQC (v0.11.9). Then, raw reads were quality filtered utilizing multithreaded fastp tool (v0.23.2), majorly implementing deduplication, auto-detect adapter removal, N base removal, Phred quality filtering (>=Q20 is qualified), and unqualified bases percent limit (=30) with other default parameters.
Further, quality filtered reads were subjected to the alignment employing Rsubread (v2.16.1) align function with human genome reference build GRCh38. The mapped binary alignment map (BAM) files were indexed using samtools (v1.16.1) and gene-wise read counts were summarized applying featureCounts function from Rsubread, where inbuilt hg38 annotation was used and duplicated reads were ignored.
Gene symbols were obtained using org.Hs.eg.db (v3.15.0) annotation package operating on ENTREZIDs from count table. Respectively, edgeR (v3.38.4) and limma-voom (v3.52.4) packages were employed to accomplish differential transcriptional regulation analysis in R.
Genes with the logFC (~0.5) and FDR adjusted p-value cutoff (≤0.01) were considered as differentially expressed genes (DEGs).
Assembly: hg38
Supplementary files format and content: Tab-delimited file includes raw counts for each sample.

growth_protocol: CSC models were maintained in Neurobasal Complete Medium [NBMc: Neurobasal Medium (Gibco #12349015) + 1X GlutaMax + 1X Sodium Pyruvate + 1X Pen/Strep + 1X Vitamin B27-A Supplement (Life Technology #12587010) + 10 mg/L EGF (R&D #236-EG) + 10 mg/L FGF2 (R&D #4114-TC)], 37C, 5% CO2. Cells were seeded at a denisty of 300,000 cells/well in 6-well dishes at the start of the experiment.

extract_protocol:
Qiagen RNeasy Plus Kit
Illumina® Stranded mRNA Library Prep Kit

treatment_protocol: 72 hours, 200 nM inhibitors or 0.1% v:v DMSO

value: patient-derived glioblastoma stem cells

value: WT

tag: time

value: 72 hrs


title: L0,C3TD078, replicate 2

description: Library name: L0_CCF59078_8


title: EOL1_rep2

first: Masahiro

last: Kiuchi

institute: Chiba univercity

description:
Library name: EOL1_rep2
Illumina NextSeq 500


title: L0, C16, replicate 3

description: Library name: L0_CCF587_6


title: L0, DMSO, replicate 2

description: Library name: L0_DMSO_2

value: DMSO


title: L0, DMSO, replicate 3

description: Library name: L0_DMSO_3


title: L0, C16, replicate 2

description: Library name: L0_CCF587_5


title: L0, DMSO, replicate 1

description: Library name: L0_DMSO_1


title: DI318, C16, replicate 1

description: Library name: DI318_CCF587_4


title: DI318, C3TD078, replicate 2

description: Library name: DI318_CCF59078_8


title: 205437190095_R06C01

description: Plasma cell-free DNA


title: DI318, C3TD078, replicate 1

description: Library name: DI318_CCF59078_7


title: DI318, C16, replicate 2

description: Library name: DI318_CCF587_5


title: DI318, DMSO, replicate 3

description: Library name: DI318_DMSO_3


title: MOLP8_SETD7  ChIPSeq

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

institute: Jichi  Medical  University

description: Library name: MOLP8_SETD7

data_processing:
Basecalls performed using bcl2Fastq version 2.20
ChIP-seq reads were aligned to the hg38 genome assembly using bwa version 0.7.12
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
The two main peak callers used at Active Motif are MACS(v2.1.0) and SICER(v1.1) .MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II).
Assembly: hg38
Supplementary files format and content: bigWig,narrow Peak(except for Input sample)

source_name: Hematopoietic cells

growth_protocol: We cultured KMS12BM,KMM1 cells in RPMI1640 medium supplemented with 10% fetal bovine serum.We cultured MOLP8 cells in RPMI1640 medium supplemented with 20% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with anti-SETD7/9 antibody.
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.

treatment_protocol: We fixed KMS12BM,KMM1,MOLP8 cells  in 1% formaldehyde at room temperature  for 10 min and isolated  chromatin fractions using enzymatic shearing

value: Hematopoietic cells

value: Multiple Myeloma_MOLP8


title: DI318, DMSO, replicate 2

description: Library name: DI318_DMSO_2


title: DI318, DMSO, replicate 1

description: Library name: DI318_DMSO_1


title: KMS12BM_Input

description: Library name: KMS12BM_Input

value: Multiple Myeloma_KMS12BM


title: MOLP8_Input

description: Library name: MOLP8_Input


title: HepG2.6ppdq.conc8,  rep3

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

description:
Library name: HepG2_6ppdq_3_H09
cell lysate

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2 and Limma
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: count files are provided as .txt files

source_name: liver

growth_protocol: from ms

extract_protocol:
cells were lysed in QIAGEN's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following QIAGEN's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: liver

value: Hep G2

value: hepatocyte

tag: concentration


title: L0, C3TD078, replicate 1

description: Library name: L0_CCF59078_7


title: L0, C16, replicate 1

description: Library name: L0_CCF587_4


title: KMS12BM_SETD7  ChIPSeq

description: Library name: KMS12BM_SETD7


title: HepG2.6ppdq.conc7,  rep3

description:
Library name: HepG2_6ppdq_3_G09
cell lysate


title: HepG2.6ppdq.conc3,  rep3

description:
Library name: HepG2_6ppdq_3_C09
cell lysate


title: HepG2.6ppdq.conc4,  rep3

description:
Library name: HepG2_6ppdq_3_D09
cell lysate


title: HepG2.6ppdq.conc2,  rep3

description:
Library name: HepG2_6ppdq_3_B09
cell lysate


title: HepG2.6ppdq.conc5,  rep3

description:
Library name: HepG2_6ppdq_3_E09
cell lysate


title: DI318, C16, replicate 3

description: Library name: DI318_CCF587_6


title: HepG2.6ppdq.conc1,  rep3

description:
Library name: HepG2_6ppdq_3_A09
cell lysate


title: HepG2.6ppdq.conc6,  rep2

description:
Library name: HepG2_6ppdq_2_F09
cell lysate


title: HepG2.6ppdq.conc6,  rep3

description:
Library name: HepG2_6ppdq_3_F09
cell lysate


title: HepG2.6ppdq.conc4,  rep2

description:
Library name: HepG2_6ppdq_2_D09
cell lysate


title: HepG2.6ppdq.conc5,  rep2

description:
Library name: HepG2_6ppdq_2_E09
cell lysate


title: HepG2.6ppdq.conc8,  rep1

description:
Library name: HepG2_6ppdq_1_H09
cell lysate


title: HepG2.6ppdq.conc3,  rep2

description:
Library name: HepG2_6ppdq_2_C09
cell lysate


title: HepG2.6ppdq.conc7,  rep1

description:
Library name: HepG2_6ppdq_1_G09
cell lysate


title: HepG2.6ppdq.conc1,  rep2

description:
Library name: HepG2_6ppdq_2_A09
cell lysate


title: HepG2.6ppdq.conc6,  rep1

description:
Library name: HepG2_6ppdq_1_F09
cell lysate


title: KMM1_Input

description: Library name: KMM1_Input

value: Multiple Myeloma_KMM1


title: KMM1_SETD7_ChIPSeq

description: Library name: KMM1_SETD7


title: HepG2.6ppdq.conc3,  rep1

description:
Library name: HepG2_6ppdq_1_C09
cell lysate


title: HepG2.control,  rep9

description:
Library name: HepG2_control_3_A12
cell lysate


title: HepG2.control,  rep10

description:
Library name: HepG2_control_3_B12
cell lysate


title: HepG2.control,  rep8

description:
Library name: HepG2_control_2_D11
cell lysate


title: HepG2.6ppdq.conc4,  rep1

description:
Library name: HepG2_6ppdq_1_D09
cell lysate


title: HepG2.6ppdq.conc1,  rep1

description:
Library name: HepG2_6ppdq_1_A09
cell lysate


title: HepG2.control,  rep12

description:
Library name: HepG2_control_3_D12
cell lysate


title: HepG2.6ppdq.conc2,  rep1

description:
Library name: HepG2_6ppdq_1_B09
cell lysate


title: HepG2.6ppdq.conc7,  rep2

description:
Library name: HepG2_6ppdq_2_G09
cell lysate


title: HepG2.6ppdq.conc2,  rep2

description:
Library name: HepG2_6ppdq_2_B09
cell lysate


title: HepG2.control,  rep6

description:
Library name: HepG2_control_2_B11
cell lysate


title: HepG2.control,  rep7

description:
Library name: HepG2_control_2_C11
cell lysate


title: HepG2.control,  rep4

description:
Library name: HepG2_control_1_D10
cell lysate


title: HepG2.control,  rep11

description:
Library name: HepG2_control_3_C12
cell lysate


title: HepG2.control,  rep5

description:
Library name: HepG2_control_2_A11
cell lysate


title: HepG2.control,  rep1

description:
Library name: HepG2_control_1_A10
cell lysate


title: HepG2.control,  rep2

description:
Library name: HepG2_control_1_B10
cell lysate


title: HepG2.control,  rep3

description:
Library name: HepG2_control_1_C10
cell lysate


title: 208307040083_R07C01

description: Plasma cell-free DNA

value: Control


title: Caco-2.6ppdq.conc8,  rep3

description:
Library name: Caco2_6ppdq_3_H10
cell lysate

source_name: colon

value: colon

value: epithelial


title: Caco-2.6ppdq.conc7,  rep3

description:
Library name: Caco2_6ppdq_3_G10
cell lysate


title: 208307040083_R06C01

description: Plasma cell-free DNA


title: HepG2.6ppdq.conc5,  rep1

description:
Library name: HepG2_6ppdq_1_E09
cell lysate


title: Caco-2.6ppdq.conc6,  rep3

description:
Library name: Caco2_6ppdq_3_F10
cell lysate


title: 208307040083_R05C01

description: Plasma cell-free DNA


title: 208307040083_R04C01

description: Plasma cell-free DNA


title: 208307040083_R03C01

description: Plasma cell-free DNA


title: Caco-2.6ppdq.conc3,  rep3

description:
Library name: Caco2_6ppdq_3_C10
cell lysate


title: Caco-2.6ppdq.conc5,  rep3

description:
Library name: Caco2_6ppdq_3_E10
cell lysate


title: Caco-2.6ppdq.conc4,  rep3

description:
Library name: Caco2_6ppdq_3_D10
cell lysate


title: 208307040083_R02C01

description: Plasma cell-free DNA


title: 208307040083_R01C01

description: Plasma cell-free DNA

value: Hypo


title: Caco-2.6ppdq.conc2,  rep3

description:
Library name: Caco2_6ppdq_3_B10
cell lysate


title: 208307040035_R08C01

description: Plasma cell-free DNA

value: ARDS


title: 208307040083_R08C01

description: Plasma cell-free DNA


title: 208307040035_R07C01

description: Plasma cell-free DNA

value: Hyper


title: 208307040035_R06C01

description: Plasma cell-free DNA


title: Caco-2.6ppdq.conc7,  rep2

description:
Library name: Caco2_6ppdq_2_G10
cell lysate


title: Caco-2.6ppdq.conc8,  rep2

description:
Library name: Caco2_6ppdq_2_H10
cell lysate


title: Caco-2.6ppdq.conc6,  rep2

description:
Library name: Caco2_6ppdq_2_F10
cell lysate


title: Caco-2.6ppdq.conc1,  rep3

description:
Library name: Caco2_6ppdq_3_A10
cell lysate


title: Caco-2.6ppdq.conc5,  rep2

description:
Library name: Caco2_6ppdq_2_E10
cell lysate


title: 208307040035_R04C01

description: Plasma cell-free DNA


title: Caco-2.6ppdq.conc4,  rep2

description:
Library name: Caco2_6ppdq_2_D10
cell lysate


title: 208307040035_R05C01

description: Plasma cell-free DNA


title: 208307040035_R03C01

description: Plasma cell-free DNA


title: 208307040035_R01C01

description: Plasma cell-free DNA


title: Caco-2.6ppdq.conc3,  rep2

description:
Library name: Caco2_6ppdq_2_C10
cell lysate


title: Caco-2.6ppdq.conc2,  rep2

description:
Library name: Caco2_6ppdq_2_B10
cell lysate


title: Caco-2.6ppdq.conc1,  rep2

description:
Library name: Caco2_6ppdq_2_A10
cell lysate


title: HepG2.6ppdq.conc8,  rep2

description:
Library name: HepG2_6ppdq_2_H09
cell lysate


title: 208307040022_R08C01

description: Plasma cell-free DNA


title: 208307040035_R02C01

description: Plasma cell-free DNA


title: 208307040022_R07C01

description: Plasma cell-free DNA


title: Caco-2.6ppdq.conc7,  rep1

description:
Library name: Caco2_6ppdq_1_G10
cell lysate


title: Caco-2.6ppdq.conc8,  rep1

description:
Library name: Caco2_6ppdq_1_H10
cell lysate


title: 208307040022_R06C01

description: Plasma cell-free DNA


title: Caco-2.6ppdq.conc6,  rep1

description:
Library name: Caco2_6ppdq_1_F10
cell lysate


title: Caco-2.6ppdq.conc5,  rep1

description:
Library name: Caco2_6ppdq_1_E10
cell lysate


title: 𝚫dclB_pksP_IRT_3

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
Library name: dclB_pksP_IRT_R3
50-bp single read sequencing

data_processing:
The sequencing results were analyzed with Unitas (https://doi.org/10.1186/s12864-017-4031-9) using default parameters.
A. fumigatus nuclear tRNAs were referenced from GtRNAdb, mitochondrial tRNAs were scanned from the mitochondrial genome using the 27 tRNAs predicted by tRNAscan-SE. All analyses were performed using “R” version 4.3.1 (2023-06-16) and Rstudio (2022-02-02), an integrated development environment (IDE) for R.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: A single csv file (IRT_sRNAs_processed.csv) contains the abundance of each target from each sample replicate.

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: A. fumigatus was grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium. After counting, 50-mL liquid AMM cultures were inoculated with 1x10^8 freshly harvested spores and incubated at 37°C and 200 rpm. After 16 h, 10 μg/mL of doxycycline was added to the inverted-repeat transgene strains (excluding one set of wild type for comparison), followed by 8 h of additional growth (total of 24 h).

extract_protocol:
Mycelium was collected with Miracloth (EMD Millipore Corp., USA) and rinsed with sterile MilliQ water. After being pressed tightly in between paper towels to remove moisture, the dried mycelium was transferred to a 2-mL screw-cap tube filled 1/3 full with 0.5 mm soda lime glass beads (BoSpec). 1 mL of TRIzol (Thermo Fischer Scientific, Dreieich, Germany) was added to efficiently lyse the cells using the FastPrep-24™ Homogenizer by subjecting the cells to three rounds of 30 s, 4.0 m/s homogenization (1 min break between repetitions) and 5 min of incubation at room temperature. 200 μL of chloroform was added to each sample, vigorously mixed and incubated for 3 min at room temperature before centrifuging the samples at 12,000 x g for 15 min at 4°C. The upper aqueous phase containing the RNA was carefully transferred to a clean RNase-free tube and an equal volume of pure ice-cold ethanol was added and mixing thoroughly. Purification of RNA was carried out by using the RNA Clean and Concentrator™ kit (Zymo Research GmbH, Freiburg, Germany) following the manufacturer’s instructions. To eliminate DNase contamination, total RNA was treated with DNase I, RNase-free (Thermo Fisher Scientific, Darmstadt, Germany). For every 1 μg of RNA, 1 U of the enzyme was added along with 2 μL of 10x Reaction Buffer with MgCl2 and adjusted with DEPC-treated water to make up to 20 μL final volume. Following a 1-hour incubation at 37°C, the reaction was terminated by adding 2 μL of 50 mM EDTA and further incubated 65°C for 10 min. DNase treated RNA was purified using the RNA Clean and Concentrator™ kit (Zymo Research, USA) after the manufacturer’s recommendations.
Libraries were constructed by Novogene. According to the manufacturer, 3' and 5' adaptors were ligated to 3' and 5' ends of small RNA, repsectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18-40 bp were ready for sequencing with SE50.

value: mycelium

value: CEA17 delta_akuB::KU80

value: doxycycline-induced

value: delta_dclB +pksP_IRT

tag: batch


title: 𝚫dclB_pksP_IRT_2

description:
Library name: dclB_pksP_IRT_R2
50-bp single read sequencing


title: Caco-2.6ppdq.conc4,  rep1

institute: McGill University

description:
Library name: Caco2_6ppdq_1_D10
cell lysate


title: 𝚫dclB_pksP_IRT_1

description:
Library name: dclB_pksP_IRT_R1
50-bp single read sequencing


title: Caco-2.6ppdq.conc2,  rep1

description:
Library name: Caco2_6ppdq_1_B10
cell lysate


title: Caco-2.6ppdq.conc1,  rep1

description:
Library name: Caco2_6ppdq_1_A10
cell lysate


title: 𝚫dclA_pksP_IRT_1

description:
Library name: dclA_pksP_IRT_R1
50-bp single read sequencing

value: delta_dclA +pksP_IRT


title: Caco-2.control,  rep12

description:
Library name: Caco2_control_3_D09
cell lysate


title: Caco-2.6ppdq.conc3,  rep1

description:
Library name: Caco2_6ppdq_1_C10
cell lysate


title: Wild-type_pabA_IRT_3

description:
Library name: CEA17_pabA_IRT_R3
50-bp single read sequencing

value: wild type +pabA_IRT


title: 𝚫dclA_pksP_IRT_2

description:
Library name: dclA_pksP_IRT_R2
50-bp single read sequencing


title: Caco-2.control,  rep10

description:
Library name: Caco2_control_3_B09
cell lysate


title: Wild-type_pabA_IRT_2

description:
Library name: CEA17_pabA_IRT_R2
50-bp single read sequencing


title: Caco-2.control,  rep9

description:
Library name: Caco2_control_3_A09
cell lysate


title: Caco-2.control,  rep11

description:
Library name: Caco2_control_3_C09
cell lysate


title: Wild-type_dox_3

description:
Library name: CEA17_dox_R3
50-bp single read sequencing

value: wild type


title: Caco-2.control,  rep8

description:
Library name: Caco2_control_2_D08
cell lysate


title: Wild-type_pabA_IRT_1

description:
Library name: CEA17_pabA_IRT_R1
50-bp single read sequencing


title: Caco-2.control,  rep7

description:
Library name: Caco2_control_2_C08
cell lysate


title: Wild-type_dox_2

description:
Library name: CEA17_dox_R2
50-bp single read sequencing


title: Caco-2.control,  rep6

description:
Library name: Caco2_control_2_B08
cell lysate


title: Wild-type_dox_1

description:
Library name: CEA17_dox_R1
50-bp single read sequencing


title: Caco-2.control,  rep4

description:
Library name: Caco2_control_1_D07
cell lysate


title: Caco-2.control,  rep5

description:
Library name: Caco2_control_2_A08
cell lysate


title: Wild_type_2

description:
Library name: CEA17_R2
50-bp single read sequencing

value: untreated


title: Wild_type_1

description:
Library name: CEA17_R1
50-bp single read sequencing


title: 208307040022_R05C01

description: Plasma cell-free DNA


title: 𝚫dclA_pksP_IRT_3

description:
Library name: dclA_pksP_IRT_R3
50-bp single read sequencing


title: Caco-2.control,  rep3

description:
Library name: Caco2_control_1_C07
cell lysate


title: 208307040022_R04C01

description: Plasma cell-free DNA


title: Caco-2.control,  rep2

description:
Library name: Caco2_control_1_B07
cell lysate


title: 208307040022_R02C01

description: Plasma cell-free DNA


title: 208307040022_R03C01

description: Plasma cell-free DNA


title: 208307040022_R01C01

description: Plasma cell-free DNA


title: AgD3, scRNAseq

city: Lausanne

first: Renaud

last: Du Pasquier

address: Rue Du Bugnon 46

department: Department of Clinical Neurosciences

country: Switzerland

institute: Lausanne University Hospital - CHUV

description:
Library name: Sample 8
10x Genomics

data_processing:
scRNA-seq
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina) and primary data analysis performed with the Cell Ranger Gene Expression pipeline (version 7.1.0, 10X Genomics).
Assembly: hg38
Supplementary files format and content: Comma-Separated Values files (all contig, filtered contig, consensus and clonotypes), Hierarchical Data Format version 5 files (raw and filtered features and molecule info) and Tab-separated values files (Adaptive Immune Receptor Repertoire rearrangements).

source_name: CD8+  T cells

extract_protocol:
A Chromium Next GEM Chip N (10X genomics) was loaded with the appropriate number of cells, and the sequencing libraries prepared with the Chromium Next GEM Single Cell 5’ HT Reagent Kits v2 dual index following the manufacturer’s recommendations. Briefly, an emulsion encapsulating single cells, reverse transcription reagents and cell barcoding oligonucleotides was generated. After the actual reverse transcription step, the emulsion was broken, and double stranded cDNA generated and amplified in a bulk reaction.
This cDNA was fragmented, a P7 sequencing adaptor ligated, and a 5’ gene expression library generated by PCR amplification.

value: CD8+  T cells


title: AgD2, scRNAseq

description:
Library name: Sample 7
10x Genomics


title: STM ∆luxS 1

description:
Library name: Sample 3
column name in raw_counts_all_samples.xlsx: DS_1

value: Salmonella Typhimurium 14028s

value: luxS knockout


title: AgD1, scRNAseq

description:
Library name: Sample 6
10x Genomics


title: FN coated dishes + BMM + Anti-ITGAV #4

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

description: Library name: FN1_ITGAV_4

data_processing:
Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis. Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (mm10; GRCm38.p6) using HISAT2 software.
Mapped reads were assembled using Stringtie. Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare can compare Strintie assemblies to reference annotation files and help sort out new genes from known ones
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes
Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length.
Assembly: mm10
Supplementary files format and content: txt file including raw readcounts for every gene and every sample
Supplementary files format and content: txt file including FPKM values for every gene and every sample

source_name: Bone Marrow Macrophages

growth_protocol: Tibial Bone Marrow derived Macrophages (BMMs) were obtained from 2- to 3-month-old Wild-type C57BL/6J mice as previously described. Briefly, bone marrow cells were incubated for 24 h in DMEM/F-12 medium supplemented with 15% fetal calf serum (GIBCO) and 12 ng/ml CSF-1 (R&D systems). Non-adherent primitive mononuclear phagocytes were reseeded in media containing 15% fetal calf serum and CSF-1 (120 ng/ml) for 48 hours, in order to allow their differentiation to adherent mononuclear phagocytes. The resulting adherent macrophages were passaged once into 10 µg/ml fibronectin (Sigma, F1141) pre-coated plates (overnight) or normal cell culture plates. Cells used for experiments were cultured until confluent, and then treated.

extract_protocol:
RNA was isolated using TRIzol reagent (Qiagen, #79306) according to manufacterer's instructions.
RNA samples were sent to Novogene (Sacramento, California) to construct the cDNA libraries. Messenger RNA was purified and enriched 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 dTTP. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and Bioanalyzer 2100 system (Agilent) for size distribution detection
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq X Plus on 25B Flowcell and paired-end reads were generated.

treatment_protocol: A group of samples (n=4) from each group, coated vs no coated, was incubated with IgG antibody (10 µg/ml, Biolegend, 400432) or anti-ITGAV neutralizing antibody (10 µg/ml, Biolegend, 104110 ) for 24 hours. After this incubation time samples were collected for RNA isolation.

value: Bone Marrow Macrophages

tag: dish coating

value: Fibronectin 10 µg/ml

value: anti-ITGAV neutralizing antibody


title: FN coated dishes + BMM + Anti-ITGAV #3

description: Library name: FN1_ITGAV_3


title: Ri07, scRNAseq

description:
Library name: Sample 5
10x Genomics


title: FN coated dishes + BMM + Anti-ITGAV #1

description: Library name: FN1_ITGAV_1


title: Ri06, scRNAseq

description:
Library name: Sample 4
10x Genomics


title: FN coated dishes + BMM + IgG #4

description: Library name: FN1_IgG_4

value: IgG antibody


title: Ri04, scRNAseq

description:
Library name: Sample 2
10x Genomics


title: Wild_type_3

description:
Library name: CEA17_R3
50-bp single read sequencing


title: FN coated dishes + BMM + IgG #3

description: Library name: FN1_IgG_3


title: Ri03, scRNAseq

description:
Library name: Sample 1
10x Genomics


title: FN coated dishes + BMM + IgG #2

description: Library name: FN1_IgG_2


title: BSSR1947_ERRBS

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

description: Library name: BSSR1947_ERRBS

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18)
Reads were mapped on GRCh37 with bismark and bismark_methylation_extractor (v. 0.22.1)
Assembly: GRCh37
Supplementary files format and content: Table with methylation calls per cytosine in CpG context

source_name: Breast tumor

extract_protocol:
DNA was extracted on a Thermo Kingfisher Apex using MagMAX™ DNA Multi-Sample Ultra 2.0
Libraries for ERRBS were made following the protocol of Garrett-Bakeman et al (PMID: 25742437)

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: cT1 N0 M0

tag: adi (state_decile)

tag: eeds discrimination_score


title: BCG-249_ERRBS

description: Library name: BCG-249_ERRBS

tag: tissue

tag: treatment

value: cT2 N0 M0


title: BCG-189_ERRBS

description: Library name: BCG-189_ERRBS


title: BMM + Anti-ITGAV #4

description: Library name: ITGAV_4

tag: cell type

tag: strain


title: Caco-2.control,  rep1

description:
Library name: Caco2_control_1_A07
cell lysate

value: colon

tag: cell line

value: epithelial


title: BMM + Anti-ITGAV #3

description: Library name: ITGAV_3


title: FN coated dishes + BMM + IgG #1

description: Library name: FN1_IgG_1


title: BCG-157_ERRBS

description: Library name: BCG-157_ERRBS


title: BCG-099_ERRBS

description: Library name: BCG-099_ERRBS


title: BCG-097_ERRBS

description: Library name: BCG-097_ERRBS

value: Pending


title: BMM + Anti-ITGAV #1

description: Library name: ITGAV_1


title: BMM + Anti-ITGAV #2

description: Library name: ITGAV_2


title: BCG-094_ERRBS

description: Library name: BCG-094_ERRBS


title: BCG-077_ERRBS

description: Library name: BCG-077_ERRBS

value: IB


title: BCG-072_ERRBS

description: Library name: BCG-072_ERRBS


title: FN coated dishes + BMM + Anti-ITGAV #2

description: Library name: FN1_ITGAV_2


title: DI318, C3TD078, replicate 3

description: Library name: DI318_CCF59078_9

value: patient-derived glioblastoma stem cells

tag: genotype

value: WT

tag: time

value: 72 hrs


title: BMM + IgG #1

description: Library name: IgG_1

value: Bone Marrow Macrophages


title: BMM + IgG #3

description: Library name: IgG_3

value: IgG antibody


title: Ri05, scRNAseq

description:
Library name: Sample 3
10x Genomics

value: CD8+  T cells


title: BCG-030_ERRBS

description: Library name: BCG-030_ERRBS

value: Breast tumor

value: White

value: Not Listed


title: BCG-040_ERRBS

description: Library name: BCG-040_ERRBS

value: Hispanic or Latino

value: ER-positive

value: Female


title: BCG-063_ERRBS

description: Library name: BCG-063_ERRBS

value: No

value: IA


title: hog1∆gcn2∆ #11 2mM H2O2, biol rep 2

city: Buffalo

first: David

last: Goich

state: NY

address: 955 Main St

institute: The State University of New York at Buffalo

description:
Library name: 20
column name in matrix_hog1gcn2_seq.csv: 20

data_processing:
Cutadapt/3.2 - adapter trimming and quality control (quality filter of 10, minimum read length of 1, adapter (AGATCGGAAGAG))
STAR/2.7.2b - alignment (read alignment mode)
RSEM/1.2.20 - read counting (forward probability 0.5)
Assembly: FungiDB (v63) H99 genome build
Supplementary files format and content: .csv, expected_counts from RSEM for all samples

organism: Cryptococcus neoformans

source_name: strain H99

growth_protocol: Cells grown to midlogarithmic phase in YPD media at 30 degrees Celsius.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to manufacturer instructions
The NEB Ultra RNA library prep kit with the NEB PolyA selection module was used according to manufacturer instructions

treatment_protocol: Untreated cells were harvested, and hydrogen peroxide (H2O2) was added to a  remaining cells at a concentration of 2mM for 1 hour

value: strain H99

value: 2mM H2O2


title: hog1∆gcn2∆ #11 untreated, biol rep 2

description:
Library name: 19
column name in matrix_hog1gcn2_seq.csv: 19


title: BMM + IgG #2

description: Library name: IgG_2


title: hog1∆gcn2∆ #9 untreated, biol rep 2

description:
Library name: 17
column name in matrix_hog1gcn2_seq.csv: 17


title: hog1∆gcn2∆ #9 2mM H2O2, biol rep 2

description:
Library name: 18
column name in matrix_hog1gcn2_seq.csv: 18


title: BSSR3054_ERRBS

description: Library name: BSSR3054_ERRBS

value: IIA

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: gcn2∆ 2mM H2O2, biol rep 2

description:
Library name: 16
column name in matrix_hog1gcn2_seq.csv: 16


title: BSSR2060_ERRBS

description: Library name: BSSR2060_ERRBS

tag: age

tag: race

tag: ethnicity


title: BCG-007_ERRBS

description: Library name: BCG-007_ERRBS

tag: er

tag: gender

tag: clinical stage


title: gcn2∆ untreated, biol rep 2

description:
Library name: 15
column name in matrix_hog1gcn2_seq.csv: 15

tag: tissue


title: BCG-021_ERRBS

description: Library name: BCG-021_ERRBS

tag: treatment

tag: adi (state_decile)

tag: eeds discrimination_score


title: hog1∆ 2mM H2O2, biol rep 2

description:
Library name: 14
column name in matrix_hog1gcn2_seq.csv: 14


title: hog1∆ untreated, biol rep 2

description:
Library name: 13
column name in matrix_hog1gcn2_seq.csv: 13


title: BCG-389_ERRBS

description: Library name: BCG-389_ERRBS

value: IIB


title: BMM + IgG #4

description: Library name: IgG_4

tag: cell type

tag: strain

tag: dish coating


title: BSSR1957_ERRBS

description: Library name: BSSR1957_ERRBS

tag: nseas composite_score


title: BCG-385_ERRBS

description: Library name: BCG-385_ERRBS

tag: nseas safety_score


title: WT 2mM H2O2, biol rep 2

description:
Library name: 12
column name in matrix_hog1gcn2_seq.csv: 12

tag: genotype

value: WT


title: WT untreated, biol rep 2

description:
Library name: 11
column name in matrix_hog1gcn2_seq.csv: 11


title: BCG-344_ERRBS

description: Library name: BCG-344_ERRBS

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: hog1∆gcn2∆ #11 2mM H2O2, biol rep 1

description:
Library name: 10
column name in matrix_hog1gcn2_seq.csv: 10


title: BCG-343_ERRBS

description: Library name: BCG-343_ERRBS

tag: age

tag: race


title: hog1∆gcn2∆ #11 untreated, biol rep 1

description:
Library name: 9
column name in matrix_hog1gcn2_seq.csv: 9


title: BCG-328_ERRBS

description: Library name: BCG-328_ERRBS

tag: ethnicity

tag: er


title: BCG-335_ERRBS

description: Library name: BCG-335_ERRBS

tag: gender

tag: clinical stage


title: BCG-314_ERRBS

description: Library name: BCG-314_ERRBS

tag: tissue

tag: treatment


title: hog1∆gcn2∆ #9 2mM H2O2, biol rep 1

description:
Library name: 8
column name in matrix_hog1gcn2_seq.csv: 8


title: hog1∆gcn2∆ #9 untreated, biol rep 1

description:
Library name: 7
column name in matrix_hog1gcn2_seq.csv: 7


title: BCG-270_ERRBS

description: Library name: BCG-270_ERRBS

tag: adi (state_decile)

tag: eeds discrimination_score


title: gcn2∆ untreated, biol rep 1

description:
Library name: 5
column name in matrix_hog1gcn2_seq.csv: 5


title: gcn2∆ 2mM H2O2, biol rep 1

description:
Library name: 6
column name in matrix_hog1gcn2_seq.csv: 6


title: BCG-253_ERRBS

description: Library name: BCG-253_ERRBS


title: BCG-265_ERRBS

description: Library name: BCG-265_ERRBS


title: hog1∆ 2mM H2O2, biol rep 1

description:
Library name: 4
column name in matrix_hog1gcn2_seq.csv: 4


title: BCG-222_ERRBS

description: Library name: BCG-222_ERRBS


title: hog1∆ untreated, biol rep 1

description:
Library name: 3
column name in matrix_hog1gcn2_seq.csv: 3


title: BCG-174_ERRBS

description: Library name: BCG-174_ERRBS


title: BCG-187_ERRBS

description: Library name: BCG-187_ERRBS


title: WT 2mM H2O2, biol rep 1

description:
Library name: 2
column name in matrix_hog1gcn2_seq.csv: 2


title: BCG-118_ERRBS

description: Library name: BCG-118_ERRBS


title: BCG-110_ERRBS

description: Library name: BCG-110_ERRBS


title: DMSO Biol Replicate 3

city: Salt Lake City

first: Samuel

last: Alper

state: UT

department: Neurobiology

institute: University of Utah

description: Dissected trunk tissue surrounding spinal cord injury site

data_processing:
Cutadapt, FASTQC, STAR, featureCounts
Assembly: Danio_rerio.GRCz11.94
Supplementary files format and content: fastq.gz

organism: Danio rerio

source_name: 1mm of trunk tissue including the injury site

growth_protocol: Zebrafish larvae were obtained from an incross of wild type (AB) adult fish and staged according to standardized protocols (Kimmel et al., 1995). Embryonic fish were raised in E3 media supplemented with methylene blue until 24 hours post fertilization. Embryos were raised in E3 without methylene blue after 24 hours post fertilization.

extract_protocol:
Invitrogen Recover All Total Nucleic Acid Isolation Kit for FFPE was used to extract the RNA from the tissue samples
NEBNext Ultra II Directional RNA library preparation with ribo RNA depletion.

treatment_protocol: 5 day old larvae were anesthetized in 0.016% Tricaine (Sigma), and injured by complete transection of the spinal cord at the level of the anal pore using a sharpened and sterilized FST injury tool. Larvae were allowed to recover for 6 hours in E3 before being transferred into media containing E3 with 35μM IWR-1 (Sigma) in 0.25% DMSO or 0.25% DMSO as a vehicle control. Larvae were fed rotifers starting at 1 dpi until fixation at 3 dpi (8 dpf).

tag: cell line

tag: cell type

value: AB


title: BCG-057_ERRBS

description: Library name: BCG-057_ERRBS

tag: nseas composite_score


title: DMSO Biol Replicate 1

value: 1mm of trunk tissue including the injury site


title: IWR-1 Biol Replicate 3


title: WT untreated, biol rep 1

description:
Library name: 1
column name in matrix_hog1gcn2_seq.csv: 1


title: DMSO Biol Replicate 2


title: BCG-052_ERRBS

description: Library name: BCG-052_ERRBS

tag: nseas safety_score


title: TBCF5326_ERRBS

description: Library name: TBCF5326_ERRBS


title: BCG-045_ERRBS

description: Library name: BCG-045_ERRBS


title: IWR-1 Biol Replicate 1

tag: genotype


title: lung, ILC2s, rep3

first: Hongjie

last: Chen

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
The sequencing data was filtered with SOAPnuke
Bowtie2 was applied to align the clean reads to the gene set
Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel spreadsheet file, gene expression data including read counts, FPKM and TPM

source_name: lung

extract_protocol:
Freshly collected mouse lung tissues were cut into small pieces. The tissues were digested at 37°C for 15 min in RPMI 1640 medium containing Liberase (0.1 mg/ml)/deoxyribonuclease I (20 μg/ml)/10 mM Hepes/3% heat-inactivated fetal bovine serum and then mashed through 70-μm cell strainers. The cells were stained with intended FACS antibodies and processed on the BD FACSAria Fusion
RNA was harvested using phenol/chloroform extracting method. mRNA fragmentation, cDNA synthesis, end repair, add A and adaptor ligation, PCR and circularization

value: lung

value: type 2 innate lymphoid cells

value: wild type

value: IL-33 treated in vivo


title: BSSR2083_ERRBS

description: Library name: BSSR2083_ERRBS

value: Breast tumor

value: White

tag: nseas social_cohesion_score


title: lung, ILC2s, rep2


title: lung, ILC2s, rep1


title: HCC827-siDYN-2-48h

first: 雷名

last: 吴

address: sun-yat san university

institute: 中山大学药学院

description:
Library name: Sample 12
fpkm_HCC827_DYN2
siRNA treatment processed data.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Non-small cell lung cancer cell


title: VHEKO Female 2

city: Oxford

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: OP415_pos
10x Genomics

data_processing:
Preliminary sequencing results (bcl files) and FASTQ files were generated with the DRAGEN FASTQ Generation, or the DRAGEN BCL Convert workflow optimized for Single Cell RNA Library Kit 1 library prep kit, and the Single Cell RNA Index Adaptors 1-B index adaptor kit, with 28 and 152 Read 1 and 2 cycles respectively.
Assembly: The mm10 reference genome was downloaded from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz. The transcript sequence and annotation for Vhlpjr.KO, that included the tdTomato transgene, was added manually to the FASTA reference genome file and GTF file respectively using the CellRanger (v6.1.1) mkref function.
Supplementary files format and content: FASTQ files generated for each sample were aligned to the custom reference genome by CellRanger using default parameters. After aligning, for each read pair, cell barcodes and unique molecular identifiers (UMIs) were obtained from Read 1 and read counts per feature were obtained from Read 2. Only those UMIs that could be linked to a valid cell barcode and a gene exon region were included to create the cell by gene count matrix. Reads from Vhl exon 1 were excluded from analysis to prevent ambiguous alignment to Vhlwt or Vhlpjr.KO alleles. Cells were subjected to the following filters: detected genes > 200, fraction of mitochondrially-encoded reads < 0.5, and detected genes < 3*median for each sample. The threshold for mitochondrially encoded reads was set to this value in line with published kidney scRNA-seq studies to account for the high mitochondrial content in the renal tubular epithelium (RTE) cells{Park, 2018 #492}. Cells from different samples and sequencing runs were then aggregated, which sometimes required manual renaming of duplicate cell ‘names’. Downstream analysis was conducted using the R package Seurat v4.0.3 and v5.1.0.
Supplementary files format and content: Processed data made available as Seurat R objects. Two obejcts are provided. 1) Vhl_HIF_genotypes_merged_noumap.rds; contains data from filtered, high-quality VHKO, VEKO, and VHEKO cells as well as data from ConKO and VKO cells downloaded from GSE253168 . 2)  HIF_genotypes_all_umap.rds; contains data from downsampled VHKO, VEKO, and VHEKO cells so that each genotype is represented by equal numbers of cells from male and female mice. This dataset was used for batch correction and dimension reduction.

source_name: kidney

growth_protocol: Mice were housed in individually ventilated cages on a 13 h light/ 11 h dark cycle with food and water provided ad libitum. B6.Vhltm1.1b(tdTomato)Pjr (Vhlpjr.fl) mice were commissioned from Ozgene, Australia and generated using goGermline technology. Vhltm1jae mice (Vhljae.fl) (RRID:IMSR_JAX:012933) were crossed with Tg(Pgk1-cre)1Lni (Pgk1-Cre) (RRID:IMSR_JAX:020811) to generate a constitutively inactivated Vhltm1jae allele (Vhljae.KO). Tg(Pax8-cre/ERT2)CAmat (Pax8-CreERT2) (RRID:IMSR_HAR:9175) mice were obtained via EMMA. Mice carrying conditional alleles for Hif1a (Hif1atm3Rsjo; RRID: MGI:6863863; termed Hifafl) and Epas1 (Epas1tm1.1Mcs; RRID:MGI:3710345; termed Epas1fl) were a gift from Randall Johnson and Simon Celeste respectively. These lines were generated on a B6.129 mixed background but were inter-crossed with C57B6/J animals for at least five generations prior to starting experiments.

extract_protocol:
Kidneys were bisected, the renal capsule removed, and bisected kidneys were macerated for up to 7 min on a bed of ice. Macerated kidneys were then subjected to single-cell dissociation using the Multi-Tissue Dissociation Kit 2 (Miltenyi 130-110-203). Briefly, macerated tissues were suspended in 1.45 ml Buffer X, 30 µl of Enzyme D, 15 µl of Enzyme P, 15 μl of Buffer Y, and 6 µl of Enzyme A, all prepared according to the manufacturer’s instructions. The suspension was then incubated under water at 37°C for 30 min in a shaking incubator set to 150 rpm. Dissociation was stopped by the addition of 150 µl Fetal Bovine Serum (FBS; Sigma F7524) and resuspension in 9 ml of RPMI-1460 medium (Merck R0883). The digest was filtered through a 40 µm cell strainer to remove undigested tissue and the filtrate was centrifuged (300g for 10 min at 4°C). Erythrocytes were eliminated by resuspending dissociated cells in 3 ml of 1x RBC Lysis Buffer (Miltenyi 130-094-183) prepared in deionized water, and incubating for 2 min at RT. Cells were centrifuged (300g for 5 min at 4°C) and resuspended in ice-cold D-PBS before being counted on a Thermo Scientific Countess II machine for total yield and viability.
Sorted cells were prepared into single-cell droplets using the Chromium Next GEM Single-cell kit. 20,000 live cells were loaded per sample on separate Chromium Next GEM Chip G (10X Genomics PN-1000127) channels. cDNA clean-up, amplification and adaptor ligation were performed with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics PN-1000268). cDNA yield was quantified using the High Sensitivity D1000 ScreenTape Assay (Agilent 5067-5584 and 5067-5585) to optimize the number of reaction cycles for library preparation. Single cell sequencing libraries were prepared using the Library Construction Kit (10X PN-1000190) and Dual Index Kit TT Set A (10X Genomics PN-1000215) sequence indices. Single-cell libraries were sequenced on Illumina NextSeq 2000 sequencing system with P3 200 cycle (Illumina 20040560) reagents. Libraries from up to six samples were pooled in an equimolar ratio, diluted to 650 pM in RSB buffer and mixed with 1% PhiX Control v3 DNA (Illumina FC-110-3001) for sequencing.
Libraries from up to six samples were pooled in an equimolar ratio, diluted to 650 pM in RSB buffer and mixed with 1% PhiX Control v3 DNA (Illumina FC-110-3001) for sequencing.

treatment_protocol: Vhlwt/pjr.fl;Pax8-CreERT2 (“ConKO”), Vhljae.KO/pjr.fl;Pax8-CreERT2 (“VKO”), Vhlwt/pjr.fl;Hif1afl/fl;Pax8-CreERT2 (“ConHKO”), Vhljae.KO/pjr.fl;Hif1afl/fl;Pax8-CreERT2 (“VHKO”), Vhlwt/pjr.fl;Epas1fl/fl;Pax8-CreERT2 (“ConEKO”), Vhljae.KO/pjr.fl;Epas1fl/fl;Pax8-CreERT2 (“VEKO”), Vhlwt/pjr.fl;Hif1afl/fl;Epas1fl/fl;Pax8-CreERT2 (“ConHEKO”), and  Vhljae.KO/pjr.fl;Hif1afl/fl;Epas1fl/fl;Pax8-CreERT2 (“VHEKO”) mice of both sexes were administered tamoxifen (2 mg dose daily for five consecutive days) when they were >20 g in body weight. Mice were harvested either 1-3 weeks (early) or 4-12 months (late) after recombination was induced.

value: kidney

tag: cell origin

value: FAC-sorted PAX8-restricted renal epithelial cells

tag: cellular vhl_hif1a_and_epas1_status

value: Vhl(KO/KO); Hif1a(KO/KO); Epas1(KO/KO)


title: BCG-400_ERRBS

description: Library name: BCG-400_ERRBS

tag: age

tag: race

value: Hispanic or Latino

value: ER-positive

value: Female

value: No

tag: nseas aesthetic_quality_score


title: HCC827-siDYN-1-48h

description:
Library name: Sample 11
fpkm_HCC827_DYN1
siRNA treatment processed data.xls


title: VHKO Female 2

description:
Library name: JH437_pos
10x Genomics

value: Vhl(KO/KO); Hif1a(KO/KO)


title: VHEKO Female 1

description:
Library name: OP408_pos
10x Genomics


title: VEKO Male 2

description:
Library name: JP122_pos
10x Genomics

value: Vhl(KO/KO); Epas1(KO/KO)


title: VEKO Female 1

description:
Library name: JP123_pos
10x Genomics


title: H1975-siDYN-2-48h

description:
Library name: Sample 9
fpkm_H1975_DYN2
siRNA treatment processed data.xls