title: Kidney_Cisplatin_day 28_rep3

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

institute: National Institute of Health Sciences

description: Gene expression after 28days  in cisplatin-administered rat kidney

hyb_protocol: 3 ug of Cy3-labelled SPIA cDNA was fragmented at 60°C for 30 minutes using Gene Expression Hybridazation Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, 2x GE Hybridization Buffer HI-PRM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K v3 (G2519) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 028282_D_F_20140723) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Cisplatin, 6 mg/kg, day 28

label_protocol: Cyanine-3 (Cy3) labeled SPIA cDNA was prepared using theSureTag DNA labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).

extract_protocol: total RNA was prepared using the RNeasy Micro Kit  (Qiagen, GmbH, Hilden, Germany) following the manufacturer's recommendations.

value: Kidney

value: Male

tag: age


title: cell-free DNA, Preeclampsia pregnancy DNA038608

status: Public on Jan 01 2026

type: SRA

city: Ghent

first: Bram

last: Van Gaever

address: C. Heymanlsaan 10

country: Belgium

institute: Ghent University

description:
Library name: DNA038608
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

library_source: genomic

data_processing:
Demultiplexing was performed using bcl-convert on standard settings
fastq files were processed with the bismark workflow of the nf-core/methylseq pipeline https://github.com/nf-core/methylseq/
the --rrbs flag was enabled for processing.
further data processing code can be found in the following git repo:https://github.com/bravgaev/ExPECT-analysis
Assembly: hg38
Supplementary files format and content: bismark coverage file

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted using the Maxwell RSC LV ccfDNA kit (Promega) according to the manufacturer’s instructions
The cfRRBS protocol was followed as described by De Koker et al.  and adapted by Van Paemel et al. https://doi.org/10.1080/15592294.2020.1790950 the EZ DNA Lightning kit (ZymoResearch) was used.

tag: tissue

value: Blood plasma

tag: disease state

value: Preeclampsia

tag: blood tube_type

value: EDTA

tag: patient id

tag: gestational age_(weeks)

tag: sequencing batch


title: cell-free DNA, Healthy pregnancy DNA038615

description:
Library name: DNA038615
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy


title: PTEN MUT 2

city: Boston

first: David

last: Chen

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana Farber Cancer Institute

description: Library name: NU02954

library_source: transcriptomic single cell

data_processing:
Standard Python-based Scanpy workflows for quality control filtering, data normalization, detection of highly variable genes, and downstream analyses were conducted. Cells with less than 200 gene feature counts and greater than 10% mitchondrial RNA content were excluded. Genes with less than 3 cells with non-zero feature counts were excluded. Counts were normalization to a factor of 10,000 and log-scaled. Principal component analysis (PCA) of the first 50 components was conducted on the normalized data using the top 6000 variable features. Nearest neighbors distance matrix was generated using the first 50 PCA components and nearest10 cell neighbors. Cells were visualized using the UMAP non-linear dimension reduction.
Assembly: Human GRCh38
Supplementary files format and content: H5 File of Cell ID and Raw FeatureCounts

molecule: total RNA

source_name: Blood

extract_protocol:
Human samples were obtained from the Nervous System Tumor Bank at Northwestern University. In brief, patients diagnosed with GBM underwent surgery for tumor resection following standard clinical practices. After the tumor was removed, an adequate amount of tissue was sent to pathology for clinical diagnosis. During the surgery, a maximum of 60 mL of peripheral blood was collected while the patient was under anesthesia. Blood was drawn by the anesthesiologist from an arterial line, central venous line, or a peripheral IV, all of which were part of routine anesthesia care.  The peripheral blood was then centrifuged using a Ficoll gradient to separate the peripheral blood leukocytes and plasma, which were collected and frozen separately. Before analysis, the peripheral blood mononuclear cells (PBMCs) were retrieved from liquid nitrogen and thawed in a 37°C water bath. The cells were washed with phosphate-buffered saline (PBS) and subjected to the EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL, #7899), following the manufacturer’s protocol. The viable cells were then sent to the NUSeq Core at Northwestern University for scRNA-seq analysis.
The scRNA-seq library was prepared by Northwestern University NUseq facility core with NIH Grant (1S10OD025120). To ensure the quality of library, the number and viability of human GBM patients' PBMCs were stained with AO/PI Staining Solution and analyzed by Nexcelom Cellometer Auto2000 cell viability analyzer. PBMCs were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip K (10X Genomics, PN-1000127), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10X Genomics, PN-1000283) according to the manufacturer’s manual.

value: Blood

tag: cell line

value: PBMC

tag: cell type

value: Mixed


title: Kidney_Cisplatin_day 5_rep4

type: RNA

country: Japan

description: Gene expression after 5days  in cisplatin-administered rat kidney

organism: Rattus norvegicus

source_name: Cisplatin, 6 mg/kg, day 5

tag: gender


title: Kidney_Cisplatin_day 5_rep3


title: Kidney_Cisplatin_day 28_rep2


title: PTEN MUT 3

description: Library name: NU03031


title: Saseq_DF2_WT_0hr_2

city: Daejeon

first: Ki-Jun

last: Yoon

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

library_source: transcriptomic

data_processing:
Illumina Real Time Analysis (RTA3) is used for base calling and blc2fastq is used for fastq file conversion.
Cutadapt (v3.5) is used for adapter trimming.
The expression level was calculated by the RSEM (v1.3.3) and STAR (v2.7.10b) with default parameters.
do rsem-calculate-expression --star -p 8  --star-gzipped-read-file --paired-end $i"_1.fastq.gz" $i"_2.fastq.gz"
Assembly: mm10
Supplementary files format and content: tab-seperated text file include TPM and FPKM values

molecule: polyA RNA

organism: Mus musculus

source_name: DIV6 Mouse Primary Neuron

growth_protocol: Mouse primary neurons were isolated from the P0 forebrain. Neurons were cultured in Neurobasal medium supplemented with B-27, GlutaMAX, penicillin-streptomycin, and gentamycin on poly-D-lysine-coated 6-well plates.

extract_protocol:
Primary neurons were collected in TRIzol (Invitrogen) and stored at -80°C overnight. Total RNA was isolated from each sample, and further RNA cleanup was performed using the RNeasy Mini Kit (Qiagen). The Dynabeads mRNA DIRECT Purification Kit (Invitrogen) was used to isolate mRNA from the samples.
The NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs) was used, and the recommended protocol was followed to generate the library.

treatment_protocol: At DIV7, Actinomycin D was added at a 5 µM concentration, and neurons were collected at two time points (0 and 5 hours) after washing with DPBS.

value: DIV6 Mouse Primary Neuron

tag: genotype

value: WT


title: PTEN WT 5

description: Library name: NU03456


title: PTEN WT 4

description: Library name: ITA2


title: Saos2/LentiCas9 #2 + sgRosa

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description:
Library name: SB4C
sgRosa expressing control

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC hg38reference genome using tophat v2.0.11.
Transcript abundances was estimated with Salmon. Salmon outputs normalized expression values, including TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: hg38
Supplementary files format and content: .tsv tab limited text file contains raw count

source_name: bone

growth_protocol: cell were grown in 10% FBS, 1% PenStrep, in DMEM media

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone

value: osteosarcoma

value: control

tag: batch

value: single


title: Saseq_M14_cKO_5hr_2

value: Nestin-Cre Mettl14 cKO

tag: treatment

value: ActD 5hr treatment


title: Saseq_DF2_cKO_5hr_2

value: Nestin-Cre Ythdf2 cKO


title: PTEN MUT 1

description: Library name: NU02962


title: Saseq_DF2_WT_5hr_2


title: Saseq_M14_cKO_5hr_1


title: Kidney_Control_Cisplatin_rep3

description: Gene expression  in saline-administered rat kidney

source_name: Saline, day 28

value: Kidney

value: Male


title: PTEN WT 1

description: Library name: NU01427


title: cell-free DNA, Healthy pregnancy DNA038600

description:
Library name: DNA038600
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma


title: Kidney_Control_Cisplatin_rep2


title: Saseq_DF2_cKO_0hr_1


title: Kidney_Control_Cisplatin_rep1


title: Saseq_DF2_cKO_0hr_2


title: cell-free DNA, Healthy pregnancy DNA038603

description:
Library name: DNA038603
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: Saseq_M14_WT_5hr_2


title: Kidney_Cisplatin_day 28_rep4


title: Saseq_DF2_WT_5hr_1


title: cell-free DNA, Healthy pregnancy DNA038592

description:
Library name: DNA038592
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: PAXgene DNA


title: Kidney_Cisplatin_day 5_rep1


title: Kidney_I/R_day 28_rep2

description: Gene expression after 28days  in I/R operated rat kidney

source_name: I/R operation, 60 min, day 28


title: Kidney_I/R_day 3_rep3

description: Gene expression after 3days  in I/R operated rat kidney

source_name: I/R operation, 60 min, day 3


title: cell-free DNA, Healthy pregnancy DNA038595

description:
Library name: DNA038595
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA038591

description:
Library name: DNA038591
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Kidney_I/R_day 3_rep4


title: Saseq_DF2_WT_0hr_1


title: cell-free DNA, Healthy pregnancy DNA035374

description:
Library name: DNA035374
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Kidney_I/R_day 3_rep2


title: Kidney_I/R_day 3_rep1


title: Kidney_Cisplatin_day 28_rep1


title: Kidney_Control_I/R_rep4

description: Gene expression  in sham-operated rat kidney

source_name: Sham operation, day 28


title: cell-free DNA, Healthy pregnancy DNA038599

description:
Library name: DNA038599
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA035353

description:
Library name: DNA035353
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: Saseq_M14_WT_0hr_2


title: cell-free DNA, Healthy pregnancy DNA038598

description:
Library name: DNA038598
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA038597

description:
Library name: DNA038597
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Kidney_Cisplatin_day 5_rep2


title: Kidney_Control_I/R_rep3


title: Saseq_M14_WT_5hr_1


title: Saseq_M14_WT_0hr_1


title: WT LinNeg 4

city: Cleveland

first: Bailey

last: Klein

state: OH

address: 10900 Euclid Ave

institute: Case Western University

data_processing:
Trimmimg sequence reads to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Reads alignemnt to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Differential gene expression analysis using DESeq2.
Gene Set Enrichment Analysis using  the Molecular Signatures Database (MSigDB).
Assembly: GRCm38
Supplementary files format and content: NA

source_name: lineage depleted bone marrow

extract_protocol:
RNA was extraced using an RNeasy plus mini kit (Qiagen). 2ug of total RNA was used for the construction of sequecining libraries.
Enrichment of target (non-ribosomal) RNA, fragmentation, reverse transcription (i.e. cDNA synthesis), and addition of sequencing adapters and amplification

value: lineage depleted bone marrow


title: Saseq_M14_cKO_0hr_1

value: DIV6 Mouse Primary Neuron


title: Saseq_M14_cKO_0hr_2


title: cell-free DNA, Healthy pregnancy DNA038594

description:
Library name: DNA038594
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Kidney_Control_Cisplatin_rep4


title: cell-free DNA, Healthy pregnancy DNA035348

description:
Library name: DNA035348
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA035352

description:
Library name: DNA035352
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Kidney_I/R_day 28_rep4


title: WT LinNeg 1

value: WT


title: Kidney_I/R_day 28_rep1


title: cell-free DNA, Healthy pregnancy DNA035345

description:
Library name: DNA035345
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Chondrosarcoma, Patient 27

city: Fukuoka

first: Eijiro

last: Shimada

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Orthopaedic Surgery

institute: Kyushu University

description: Library name: Patient 27

data_processing:
Low-quality reads and contaminations were filtered out before data analysis. In addition, adapter sequences were removed using Cutadapt (v1.9.1).
Sequence reads were mapped to reference genome via the software Hisat2 (v2.0.1).
Gene expression calculation was performed with the FPKM (Fragment per kilo bases per million reads) based on read counts from HT-seq (v0.6.1).
Assembly: hg38
Supplementary files format and content: txt file includes raw counts and FPKM

source_name: Chondrosarcoma

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
The polyA fraction (mRNA) was isolated from total RNA, followed by its fragmentation. Then, double-stranded (ds) cDNA was reverse-transcribed from fragmented mRNA. The ds cDNA fragments were processed for adaptor ligation, size selection, and amplification to generate strand-specific cDNA libraries.

treatment_protocol: Tumor samples were collected from macroscopically tumor-rich areas immediately after surgical excision and were cryopreserved.

value: Chondrosarcoma

tag: tumor grade

value: dedifferentiated

tag: idh mutation


title: Chondrosarcoma, Patient 26

description: Library name: Patient 26

value: Grade 3


title: Chondrosarcoma, Patient 35

description: Library name: Patient 35

value: Grade 1


title: Kidney_I/R_day 28_rep3


title: Kidney_Control_I/R_rep1


title: Chondrosarcoma, Patient 37

description: Library name: Patient 37

value: Grade 2


title: Kidney_Control_I/R_rep2


title: WT LinNeg 5


title: Enchondroma, Patient 32

description: Library name: Patient 32

source_name: Enchondroma

value: Enchondroma


title: cell-free DNA, Preeclampsia pregnancy DNA035351

description:
Library name: DNA035351
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Enchondroma, Patient 30

description: Library name: Patient 30


title: Chondrosarcoma, Patient 19

description: Library name: Patient 19


title: WT LinNeg 3


title: cell-free DNA, Healthy pregnancy DNA035342

description:
Library name: DNA035342
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Chondrosarcoma, Patient 40

description: Library name: Patient 40


title: WT LinNeg 2


title: Enchondroma, Patient 16

description: Library name: Patient 16


title: Chondrosarcoma, Patient 24

description: Library name: Patient 24

value: Wt


title: Chondrosarcoma, Patient 38

description: Library name: Patient 38


title: cell-free DNA, Healthy pregnancy DNA035347

description:
Library name: DNA035347
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Chondrosarcoma, Patient 21

description: Library name: Patient 21


title: Chondrosarcoma, Patient 25

description: Library name: Patient 25


title: cell-free DNA, Preeclampsia pregnancy DNA035350

description:
Library name: DNA035350
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Chondrosarcoma, Patient 28

description: Library name: Patient 28


title: SASH LinNeg 5

value: mast cell deficiient (SASH)


title: cell-free DNA, Healthy pregnancy DNA035340

description:
Library name: DNA035340
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SASH LinNeg 2


title: Chondrosarcoma, Patient 22

description: Library name: Patient 22


title: cell-free DNA, Healthy pregnancy DNA035339

description:
Library name: DNA035339
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA035343

description:
Library name: DNA035343
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Chondrosarcoma, Patient 17

description: Library name: Patient 17


title: SASH LinNeg 4


title: Chondrosarcoma, Patient 14

description: Library name: Patient 14


title: Chondrosarcoma, Patient 8

description: Library name: Patient 8


title: cell-free DNA, Healthy pregnancy DNA035341

description:
Library name: DNA035341
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA035320

description:
Library name: DNA035320
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Chondrosarcoma, Patient 13

description: Library name: Patient 13


title: Chondrosarcoma, Patient 5

description: Library name: Patient 5


title: SASH LinNeg 1


title: WT bulk 4

source_name: bulk bone marrow

value: bulk bone marrow


title: Enchondroma, Patient 11

description: Library name: Patient 11


title: WT bulk 3


title: Chondrosarcoma, Patient 12

description: Library name: Patient 12


title: cell-free DNA, Preeclampsia pregnancy DNA035317

description:
Library name: DNA035317
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma


title: WT bulk 5


title: SASH LinNeg 3


title: Chondrosarcoma, Patient 7

description: Library name: Patient 7


title: Chondrosarcoma, Patient 15

description: Library name: Patient 15


title: cell-free DNA, Healthy pregnancy DNA035338

description:
Library name: DNA035338
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: SASH bulk 5


title: Chondrosarcoma, Patient 10

description: Library name: Patient 10


title: Chondrosarcoma, Patient 3

description: Library name: Patient 3


title: Chondrosarcoma, Patient 4

description: Library name: Patient 4


title: 9_m6A-seq_SNU2491_UZH2

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

description: Library name: Sample 9

data_processing:
Raw reads were mapped to the reference mouse (mm10) or human (hg19) genome assembly using HISAT2. HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
bigWig files were generated using makeBigwig.pl script of HOMER suite.
Assembly: mm10 or hg19
Supplementary files format and content: bigWig
Library strategy: MeRIP-Seq

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
From 2-5 million cells, total RNA was extracted using the QIAzol reagent following the manufacturer's instructions. After extraction, 200 ng of total RNA was used to perform ULI-MeRIP using 1 µg of anti-m6A antibody (Cat#E1610S, New England Biolabs) as previously described.
The m6A-modified RNA was immunoprecipitated and used as an input for library construction using the SMARTer® Stranded Total RNA-Seq Kit v2 (Cat#634411, Takara) according to the manufacturer's protocol.

treatment_protocol: Treated with drugs as described in this study.

tag: strain

value: Human pancreatic cancer cell line

tag: merip antibody


title: cell-free DNA, Preeclampsia pregnancy DNA035313

description:
Library name: DNA035313
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: cell-free DNA, Preeclampsia pregnancy DNA035314

description:
Library name: DNA035314
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: cell-free DNA, Preeclampsia pregnancy DNA035316

description:
Library name: DNA035316
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT bulk 2


title: Chondrosarcoma, Patient 6

description: Library name: Patient 6


title: WT bulk 1


title: cell-free DNA, Healthy pregnancy DNA031160

description:
Library name: DNA031160
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy


title: cell-free DNA, Healthy pregnancy DNA031159

description:
Library name: DNA031159
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SASH bulk 4


title: 38_RNA-Seq_CAKI-2_sgNEG_rep2

description: Library name: Sample 38

data_processing:
Raw reads were mapped to the reference genome assembly mm10 or hg19 using HISAT2.
Differentially expressed genes were analyzed using Cufflinks.
Assembly: mm10 or hg19
Supplementary files format and content: Excel

growth_protocol: cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

value: Human kidney cancer cell line

tag: biological replicate

value: replicate 2


title: 8_m6A-seq_SNU2491_DMSO

description: Library name: Sample 8

value: DMSO

value: anti-m6A antibody (Cat#E1610S, New England Biolabs)


title: 7_m6A-seq_PaCaDD165_UZH2

description: Library name: Sample 7


title: Chondrosarcoma, Patient 2

description: Library name: Patient 2

tag: tissue

value: Chondrosarcoma

value: IDH1 R132L


title: 40_RNA-Seq_CAKI-2_sgHNF1B-2_rep2

description: Library name: Sample 40


title: 6_m6A-seq_PaCaDD165_DMSO

description: Library name: Sample 6


title: 35_RNA-Seq_CAKI-2_UZH2_rep1

description: Library name: Sample 35

value: replicate 1


title: cell-free DNA, Healthy pregnancy DNA031155

description:
Library name: DNA031155
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: disease state


title: 37_RNA-Seq_CAKI-2_sgNEG_rep1

description: Library name: Sample 37


title: 33_RNA-Seq_CAKI-2_DMSO_rep1

description: Library name: Sample 33

value: Human lung cancer cell line


title: SASH bulk 2


title: 39_RNA-Seq_CAKI-2_sgHNF1B-2_rep1

description: Library name: Sample 39


title: SASH bulk 3


title: WT, replicate 1, scRNAseq

city: Chengdu

first: chen

last: li

address: Renmin South Road

country: China

institute: Sichuan Univercity

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Freshly collected femur and tibia from Tbc1d23ΔE15/ΔE15 or wild type mice were cuted in the middle and instantaneous centrifugated to obtained the whole bone marrow cells. The Lin- cells were isolated from whole bone marrow cells by  EasySep™ Mouse Hematopoietic Cell Isolation Kit (STEMCELL Technoligies). Lin- cells were washed and resuspended in PBS buffer without calcium and magnesium.
Library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 3' Solution v2 protocol,10x Genomics). Brifly，bone marrow Lin- 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 (GEM).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence. Unique Molecular identifiern (UMI) and 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction. During the library construction illumuna R2 primer sequence, paried-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone Marrow

value: Lin- cells

value: wildtype

tag: age


title: SASH bulk 1

value: bulk bone marrow

value: mast cell deficiient (SASH)


title: cell-free DNA, Preeclampsia pregnancy DNA031156

description:
Library name: DNA031156
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

tag: blood tube_type

tag: patient id


title: Tbc1d23ΔE15/ΔE15, replicate 1, scRNAseq

description: 10X Genomics

value: 8 weeks


title: 29_RNA-Seq_NCI-H28_sgNEG_rep1

description: Library name: Sample 29


title: 31_RNA-Seq_NCI-H28_sgHNF1B-2_rep1

description: Library name: Sample 31


title: m222_3

city: HangZhou

first: Xiaoqin

last: Liu

state: ZheJiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake University

data_processing:
For 10X scRNA-seq data, raw scRNA-seq reads were mapped to mm10 genome using Cell ranger (v 1389 5.0.1, 10x Genomics). Seurat (v 4.2.0) (Butler et al., 2018) was used for filtering, 1390 normalization, dimensionality reduction, clustering and differential gene 1391 expression analysis, following the default Seurat pipeline. Quality control 1392 criteria included exclusion of cells with fewer than 200 or more than 6000 genes, 1393 and mitochondrial gene expression exceeding 20%. After quality filtering, 1394 39,993 and 21,078 cells were remained in the FVB dataset and germ-free 1395 dataset, respectively. Data normalization was performed using NormalizedData 1396 function with default settings. The vars.to.regress parameter was used to 1397 regress out cell cycle, mitochondrial percentage, batch and gene number effect 1398 when performing data scaling with ScaleData function. Dimensionality 1399 reduction was conducted using RunPCA, with the top 50 principal components 1400 input into t-SNE analysis via RunTSNE. Clustering utilized the FindNeighbors 1401 and FindClusters functions with the original Louvain algorithm at a resolution of 1402 1. Cell type annotation was done according to established cell type markers 1403 (Table S5). Differential gene expression analysis with FindMarkers identified 1404 significantly differentially expressed genes with a minimum 10% cell expression, 1405 absolute log2 fold-change of at least 0.25, and a Bonferroni-corrected p-value 1406 < 0.05. Pathway analysis was performed using the clusterProfiler R package 1407 (Wu et al., 2021), identifying significant pathways with a FDR < 0.05. For bulk RNA-seq data, raw sequencing reads were trimmed using TrimGalore 1430 (https://github.com/FelixKrueger/TrimGalore), applying a quality threshold of 1431 q20. UMI-tools (Smith et al., 2017) generated the count matrix, starting with a 66 1432 whitelist of the top 100 barcodes from trimmed reads. Aligned read1 sequences 1433 to the mm10 genome were processed using STAR (Dobin et al., 2013), with the 1434 outFilterMultimapNmax parameter set to 1. The count matrix was obtained by 1435 using featureCounts and count tools in UMI-tools. For differential gene 1436 expression analysis, the limma package (v3.52.4) (Ritchie et al., 2015) was 1437 used, considering genes with a p-value < 0.05 and log2 fold-change > 0.25 as 1438 significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: count expression profile

source_name: Tumor cell

extract_protocol:
Lungs were harvested from Control and ATBx treated Germ-free mice at the end of point of experiment. Then lungs were dissected into single cells. Live cells were sorted by FACS to do 10X scRNA-seq; Firstly, tumor cells co-cultured with live or dead bacteria. Then tumor cell containing live or dead bacteria were sorted by FACS to do bulk RNA-seq.
For 10X scRNA-seq, 500,000 CD45+ 1166 live immune cells were isolated using flow cytometry (BD, 1167 #FACAria Fusion SORP) to prepare for the 10X single-cell RNA library. The 54 1168 cells were then pelleted at 500 g for 5 minutes at 4°C and resuspended in 50 1169 μL of PBS after supernatant removal. Next, cell viability was assessed using 1170 Trypan Blue staining, and only samples with viability exceeding 80% proceeded 1171 to library preparation, as determined through microscopy counting. Cell 1172 suspension volumes were adjusted for targeted input of 10,000 cells for library 1173 construction, following the guidelines outlined in the Chromium Next GEM 1174 Single Cell 3' Reagent Kits v3.1 instructions. In the next step, the generation 1175 and barcoding of Gel Bead-In-Emulsions (GEMs) were performed using 1176 Chromium Controller, ensuring the absence of bubbles for successful GEM 1177 formation. GEMs underwent purification and cDNA amplification, followed by 1178 the construction of the 3' gene expression library, which included fragmentation, 1179 end repair, A-tailing, adaptor ligation and index addition, with purification steps 1180 interspersed. The final library was evaluated for quality before sequencing 1181 submission by Fragment Analyzer-12/96 (GENE-QC006). For bulk RNA-seq, the protocol of low-input bulk RNA-seq library preparation was adapted and 1185 refined from the method described by Fu et al (Fu et al., 2022). In brief, tdTomato+ PyMT+ 1186 tumor cells were co-cultured with CSFE-labeled live or dead 1187 bacteria for 12 hours. The dead bacteria were heat-inactivated at 85°C for 30 minutes and cultured to confirm their non-viability. We sorted 5 × 104 1188 tumor cells, 1189 both with live and dead bacteria through FACS (BD, #FACAria Fusion SORP), across three biological replicates respectively. After centrifugation at 350 g for 1191 5 minutes at 4 °C, the supernatant was discarded. Cell lysis and RNA extraction 1192 were carried out by adding 500 μL of Trizol reagent, followed by RNA 1193 quantification using a Qubit fluorometer (Thermo Fisher Scientific) and RNA 1194 integrity analysis, with the requirement of the RNA integrity number >1.8. 1195 1196 For reverse transcription, a 9.2 μL mixture containing 0.6 μL of barcode primer 1197 (10 μM), 1 μL of dNTP (10 mM), 7.6 μL of extracted RNA was prepared on ice. 1198 The mixture was incubated at 65 °C for 5 minutes. Next, a reaction mix was 1199 prepared with 4 μL of SSIV buffer (5X), 4 μL of 5 M betaine (Sigma-Aldrich, 1200 #B0300), 1 μL of RNase Inhibitor (Takara, #2313B), 1 μL of 0.1 M dithiothreitol, 1201 0.12 μL of 1 M MgCl2 (Sigma-Aldrich, #63,020), and 0.2 μL of 100 μM template 1202 switch oligo (TSO) primer, 0.5 μL of SuperScript II reverse transcriptase 1203 (Invitrogen, #18064071), and 9.2 μL of the RNA. Reverse transcription was 1204 conducted at 50 °C for 60 minutes, at 80 °C for 10 minutes, and finally holding 1205 at 4 °C. For PCR amplification, a 30 μL PCR mix composed of 25 μL of 2X KAPA HiFi 1208 HotStart ReadyMix (KK2602), 1 μL of 10 μM ISPCR oligo and 3 μL of 10 μM 3' 1209 Anchored oligo was used. The procedure began with an initial denaturation at 1210 95°C for 3 minutes, followed by 4 cycles of 98°C for 20 seconds, 65°C for 30 1211 seconds, 72°C for 5 minutes, 8-10 cycles of 98°C for 20 seconds, 67°C for 15 seconds, and 72°C for 5 minutes with a final extension at 72°C for 5 minutes. 1213 PCR products were barcoded, pooled and purified using the DNA Clean & 1214 Concentrator-5 kit (Zymo Research, #D4014). After a double purification with 1215 0.8X AMPure XP beads (Beckman, A63881 AMPure XP), the cDNA was eluted 1216 in 21 μL of H2O and pooled. Next, the cDNA was further amplified with a 1217 biotinylated index primer and ISPCR oligo for 4-5 cycles, then sonicated into 1218 ~300 bp fragments using a COVARIS system (COVARIS, #SIAUH006). 1219 Streptavidin C1 Beads (Thermo Fisher Scientific, #5002) were used to enrich 1220 the biotinylated products. Libraries were prepared with the KAPA Hyper Prep 1221 Kits (KK8505) with end repair, A-tailing, and ligation to NEB U-shaped adapters. 1222 After cleanup and 7-8 cycles of amplification, the libraries were purification 1223 twice with 0.8X AMPure XP beads and eluted in 30 μL of H2O. Libraries quality 1224 was assessed with the Fragment Analyzer-12/96 (GENE-QC006), and 1225 sequencing was performed on a Novaseq platform to obtain 150-bp paired-end 1226 reads by Novogene.
10X scRNA-seq or bulk RNA-seq according to smart-seq-2

value: Tumor cell

value: FVB


title: 34_RNA-Seq_CAKI-2_DMSO_rep2

description: Library name: Sample 34

value: Human kidney cancer cell line


title: 28_RNA-Seq_NCI-H28_UZH2_rep2

description: Library name: Sample 28

value: replicate 2


title: 36_RNA-Seq_CAKI-2_UZH2_rep2

description: Library name: Sample 36


title: cell-free DNA, Healthy pregnancy DNA031151

description:
Library name: DNA031151
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: EDTA

tag: gestational age_(weeks)

tag: sequencing batch


title: cell-free DNA, Healthy pregnancy DNA031154

description:
Library name: DNA031154
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: 24_RNA-Seq_PACADD165_sgHNF1B-2_rep2

description: Library name: Sample 24

tag: cell line

tag: cell type

value: Human pancreatic cancer cell line


title: cell-free DNA, Healthy pregnancy DNA031152

description:
Library name: DNA031152
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: 27_RNA-Seq_NCI-H28_UZH2_rep1

description: Library name: Sample 27

value: replicate 1


title: 30_RNA-Seq_NCI-H28_sgNEG_rep2

description: Library name: Sample 30

value: Human lung cancer cell line


title: 23_RNA-Seq_PACADD165_sgHNF1B-2_rep1

description: Library name: Sample 23


title: 22_RNA-Seq_PACADD165_sgHNF1B-1_rep1

description: Library name: Sample 22


title: 20_RNA-Seq_PACADD165_sgNEG_rep2

description: Library name: Sample 20

value: sgNEG


title: con955

source_name: Lung

value: Lung


title: m222_2


title: cell-free DNA, Healthy pregnancy DNA031148

description:
Library name: DNA031148
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA031149

description:
Library name: DNA031149
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: 25_RNA-Seq_NCI-H28_DMSO_rep1

description: Library name: Sample 25

value: DMSO


title: 16_RNA-Seq_PACADD165_DMSO_rep2

description: Library name: Sample 16


title: m222_1


title: 18_RNA-Seq_PACADD165_UZH2_rep2

description: Library name: Sample 18


title: PBS


title: 21_RNA-Seq_PACADD165_sgHNF1B-1_rep1

description: Library name: Sample 21


title: cell-free DNA, Healthy pregnancy DNA031147

description:
Library name: DNA031147
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT938


title: cell-free DNA, Preeclampsia pregnancy DNA031146

description:
Library name: DNA031146
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: 32_RNA-Seq_NCI-H28_sgHNF1B-2_rep2

description: Library name: Sample 32


title: M2EV

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description: Library name: M2EV

data_processing:
STAR 2.6.1 aligned to HG38
Normalized via Log2 Counts per million with offset of 1
Log normal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Assembly: HG38
Supplementary files format and content: All processed data files are in (.xlsx) format

source_name: PB

extract_protocol:
RNA extraction from EV and cells was perform using Trizol reagent and ribosomal RNA was depleted with Ribo-Zero gold from Illumina (San Diego, CA).
RNA library for sequencing was prepared with NEB Ultra II Library Preparation kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs)

value: PB

value: Primary cell

value: M2 Macrophage-derived EVs


title: 19_RNA-Seq_PACADD165_sgNEG_rep1

description: Library name: Sample 19


title: cell-free DNA, Preeclampsia pregnancy DNA031145

description:
Library name: DNA031145
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

source_name: Blood plasma

value: Blood plasma


title: 17_RNA-Seq_PACADD165_UZH2_rep1

description: Library name: Sample 17


title: 15_RNA-Seq_PACADD165_DMSO_rep1

description: Library name: Sample 15


title: cell-free DNA, Healthy pregnancy DNA031143

description:
Library name: DNA031143
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: M1Cells

description: Library name: M1Cells

source_name: BM

value: M1 Macrophages


title: 26_RNA-Seq_NCI-H28_DMSO_rep2

description: Library name: Sample 26


title: Bacteria

value: FVB


title: M1EV

description: Library name: M1EV

value: M1 Macrophage-derived EVs


title: cell-free DNA, Healthy pregnancy DNA031140

description:
Library name: DNA031140
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy


title: woBac


title: AIR_16H_1

city: Rehovot

first: Gideon

last: Schreiber

address: Herzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome
Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Normalization and differential expression was performed using DESeq2
Assembly: hg38
Supplementary files format and content: Excel file includes the normalized counts and DESeq2 output

source_name: HeLa

growth_protocol: Cells were grown using 10% DMEM media

extract_protocol:
RNA samples were extracted using the NucleoSpin RNA extraction kit REF 740955.
Bulk MARS-Seq protocol
RNA-Seq (3')

treatment_protocol: Cells were treated for 16h or 6h with 2nM IFNβ or AIR ligend respectively

value: HeLa

value: Cervical cencer epithelial cells

tag: genotype

value: WT

value: Cell transfect for 48h with AIR followed by treated for 16h with 2nM AIR ligend


title: cell-free DNA, Preeclampsia pregnancy DNA031142

description:
Library name: DNA031142
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: cell-free DNA, Preeclampsia pregnancy DNA031144

description:
Library name: DNA031144
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: M2Cells

description: Library name: M2Cells

value: M2 Macrophages


title: withBac

value: Lung


title: AIR_6H_2

value: Cell transfect for 48h with AIR followed by treated for 6h with 2nM AIR ligend


title: cell-free DNA, Healthy pregnancy DNA031139

description:
Library name: DNA031139
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: AIR_NT_1

value: Cell transfect for 48h with AIR


title: Ovary, Uba3 cKO, rep5

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw sequencing reads were preprocessed using fastp for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include normalized gene counts for each Sample

source_name: 3-week-old whole ovary

extract_protocol:
We used PicoPure RNA isolation kit (Applied Biosystems) to extract RNA.
Library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina Novaseq.

value: whole ovary

value: C57/Bl6/N;129SvEv7 strain

value: Uba3 cKO


title: cell-free DNA, Preeclampsia pregnancy DNA031137

description:
Library name: DNA031137
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Preeclampsia


title: AIR_6H_1


title: cell-free DNA, Healthy pregnancy DNA031136

description:
Library name: DNA031136
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: ATBX956

value: FVB


title: kidney1

city: Fuzhou

first: Zhimin

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

data_processing:
The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200 – 300 base pairs (bp), together with the library building process of traditional second-generation sequencing such as sequencing junction and primers. Finally the DNA library was generated by PCR amplification.
Cell capture was performed using the official library kit (10X Genomics Chromium Single-Cell 3' kit, V3) according to manufacturer’s instructions.
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz

source_name: Kidney

growth_protocol: C57BL/6 mice (8 – 10 weeks, 22 – 26 g, male) were obtained from the pathogen-free (SPF) facility of Fujian Medical University. All animal experiments were approved by the Laboratory Animal Management and Ethics Committee of Fujian Medical University and were performed in accordance with the "China Guide for the Protection and Use of Laboratory Animals". All mice were housed in a specific pathogen-free facility with a 12-hour light/dark cycle.

extract_protocol:
Harvested cells at the required densities were combined with gel beads containing the barcoded information along with a mixture of cells and enzymes. Oil surfactant droplets in a microfluidic "double-cross" system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence. The cDNA fragment was then reverse transcribed before the sample was labeled.
10X Genomics Chromium protocol

treatment_protocol: Kidneys were placed on ice-cold Dulbecco’s phosphate buffered saline (DPBS), debrided, cut longitudinally, and coronally sectioned. The renal pelvis portion of the kidney was then excised with a sterile razor, and the remaining tissue was washed in a 6 cm Petri dish with 1×DPBS to remove residues such as blood stains. Subsequently, the tissue was sheared to a size of 5×5 mm3. The cleaned samples were then transferred to 5 mL centrifuge tubes with 1×DPBS and placed on ice to rapidly shear the tissues to 1 – 3 mm3. Next, 10 times the volume of 1×DPBS was added to the sheared tissues which were cleaned by gentle blowing with a Pap sieve five times, and collected by filtering through a 70 μm cell sieve. The collected tissues were transferred into the prepared digestive enzyme solution (collagen II 2 mg/mL, collagen IV 2 mg/mL) and incubated for 30 min at 37 ℃, 100 rpm; the dissociated solution mixed with tissues and cells was transferred into 2 – 3 times the volume of 1×DPBS, washed by blowing with a Bass pipette and passed through a 40 μm cell sieve before the filtrate was collected. The filtered cell suspension was centrifuged at 300 g for 5 min at 12 °C. The supernatant was discarded and the remaining cells were collected. Any erythrocytes remaining in the cell fractions were removed by lysis in erythrocyte lysate for 3 – 10min. Subsequently, the precipitate was resuspended in 1×DPBS using 10 times the volume of cell suspension used in the previous step, washed 1 – 2 times, centrifuged again as previously described (300 g at 12 °C for 5 min). Cell densities were adjusted to 700 – 1200 cells/μL with 1640 (+5% (v/v) fetal bovine serum (FBS)) before analysis.

value: Kidney

value: 8-10 weeks

value: control


title: AIR_NT_2

value: HeLa

value: Cervical cencer epithelial cells

value: WT


title: Ovary, Uba3 cKO, rep4


title: HeLa_NT_2

value: Cells were not treated.


title: HeLa_16H_2

value: Cells were treated for 16h with 2nM IFN-beta


title: AIR_16H_2

value: Cell transfect for 48h with AIR followed by treated for 16h with 2nM AIR ligend


title: HeLa_16H_1


title: cell-free DNA, Healthy pregnancy DNA031135

description:
Library name: DNA031135
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: EDTA


title: Ovary, Uba3 cKO, rep2

value: whole ovary


title: HeLa_6H_1

value: Cells were treated for 6h with 2nM IFN-beta


title: kidney2-STX

value: shiga toxin


title: Ovary, Uba3 cKO, rep1

value: C57/Bl6/N;129SvEv7 strain

value: Uba3 cKO


title: Ovary, Uba3 cKO, rep3


title: A549 cells, treat-2

city: 上海市

first: 欣怡

last: 夏

state: 上海

address: 杨浦区淞沪路2005号

institute: 复旦大学代谢与整合生物写研究院

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwok (parameters- mismath cost:2 inserion cost:3 deleton cost:3 Lengh fraction:0.8 similarity fration:0.8)
Read count extraction and normalization were performed usina CLC genomic benchwork
Assembly: hg 38
Supplementary files format and content: tab-delimited text file includes FPKM  values  for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lung


title: Active-Ribo-seq siCTRL-3

city: Suwon-si

first: Daeho

last: Joe

state: Gyeonggi-do

address: 2066, Seobu-ro

institute: Sungkyunkwan University

library_source: other

data_processing:
For Ribo-seq data, we first trimmed reads following manufacturer’s guide(https://immaginabiotech.com/product/laceseq-12-rxns, LACEseq bioIT guidelines). Reads were processed using Cutadapt(version 2.8) and UMI-tools(version 1.1.4). Reads were trimmed from the 3’ end of each read and only reads longer than X+9 were retrieved. UMIs were moved to the read name and first T at the start of each read were removed. The processed sequences were first mapped to the contaminants using bowtie2 with parameters “—un”, which is composed of PhiX genome (GenBank accession J02482.1), predicted tRNA genes (GtRNAdb, http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/Hsapi38-seq.html), lncRNA transcripts (Gencode, https://www.gencodegenes.org/human/), rRNA repeat units (GenBank accession U13369.1) and all sequences for ribosomal RNA of human (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute). Trimmed riboseq data and raw RNA-seq data were mapped to human genome GRCh38 using STAR (v2.7.10b) following deltaTE Support Protocol. Aligned reads were sorted by samtools(v1.10) followed by quantification using featureCounts(v2.0.0). Obtained count matrices were imported into R for further analysis. DESeq2(v1.38.3) was used for calculating differential translation genes (DTGs) requires the count matrices from Ribo-seq and RNA-seq as previously described.
Assembly: GRCh38 from GENCODE, release 43 was used for analysis
Supplementary files format and content: For both Ribo-seq and RNA-seq, comma seperated values(csv) is attached containing raw countdata.

molecule: other

source_name: HeLa TO cells

extract_protocol:
Ribosome protected fragments (RPF) was acquired using RiboLace kit (Immagina) following manufacturer's protocols. 20 ng of RPF was used for the construction of sequencing libraries.
RNA libraries for Active-Ribo-seq were prepared using LACE-seq kit following manufacturer's protocols.
Active-Ribo-seq

value: HeLa TO cells

value: Cervical carcinoma

value: Shake-off after treatment of nocodazole for 16 h


title: Active-Ribo-seq siPYGO2-2

value: PYGO2 knockdown


title: HeLa_6H_2

value: HeLa

value: Cervical cencer epithelial cells


title: Active-Ribo-seq siCTRL-1

source_name: HeLa Tet-On 3G (TO) cells

value: HeLa Tet-On 3G (TO) cells

value: WT


title: Active-Ribo-seq siPYGO2-1


title: Ovary, control, rep5

value: Control


title: Active-Ribo-seq siPYGO2-3


title: cell-free DNA, Healthy pregnancy DNA031134

description:
Library name: DNA031134
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: A549 cells, treat-3

institute: 复旦大学代谢与整合生物写研究院


title: Active-Ribo-seq siCTRL-2


title: Pediatric high grade glioma case 3

first: Jenna

last: LaBelle

address: 360 Longwood Ave

department: Pediatric Oncology

data_processing:
CLC Genomics Workbench v 11.0.1
Raw sequencing reads were quality-checked with FastQC and then aligned against GRCh37
The gene counts were estimated with Gencode gene definitions and TMM normalized.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: pediatric high grade glioma

extract_protocol:
RNA was extracted from frozen tumor tissue using mirVana miRNA Isolation Kit (combination of phenol/chloroform extraction + silica columns)
From the total RNA sample, mRNA was polyA selected using NEBNext Poly(A) mRNA Magnetic Isolation Module and subsequently, the library was constructed using NEBNext Ultra II DNA Library Prep Kit.

value: pediatric high grade glioma


title: Ovary, control, rep3

value: whole ovary


title: A549 cells, veh-2

institute: 复旦大学代谢与整合生物写研究院

value: vehicle


title: HeLa_NT_1

value: Cells were not treated.


title: Pediatric high grade glioma case 2


title: Ovary, control, rep4

value: C57/Bl6/N;129SvEv7 strain


title: Ovary, control, rep2


title: CI kidney (Cis3)

city: nantong

first: Zhaozhi

last: Wen

state: jiangsu

address: Seyuan Road 9

institute: Nantong University

description: Library name: Cis3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of GRCm38.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text flile includes raw counts for each Sample

source_name: kidney

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The poly(A) RNA was fragmented into small pieces using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, China) under 94℃ 5min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, China), which were next used to synthesise U-labeled second-stranded DNAs with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, China).

value: kidney

value: cisplatin


title: A549 cells, veh-3

institute: 复旦大学代谢与整合生物写研究院

value: Lung


title: CI kidney (Cis4)

description: Library name: Cis4


title: CI kidney (Cis1)

description: Library name: Cis1


title: A549 cells, veh-1

institute: 复旦大学代谢与整合生物写研究院


title: Pediatric high grade glioma case 1


title: H460 cells, treat-2

institute: 复旦大学代谢与整合生物写研究院

source_name: Lung; Pleural effusion

value: Lung; Pleural effusion


title: Control kidney (Ctrl2)

description: Library name: Ctrl2

value: control


title: Control kidney (Ctrl1)

description: Library name: Ctrl1


title: Control kidney (Ctrl3)

description: Library name: Ctrl3


title: A549 cells, treat-1

institute: 复旦大学代谢与整合生物写研究院


title: H460 cells, veh-3

institute: 复旦大学代谢与整合生物写研究院


title: CI kidney (Cis6)

description: Library name: Cis6


title: Oocytes, control, rep3

source_name: Fully-grown GV oocyte

value: Fully-grown GV oocyte


title: Tbx21-KO cDNT_2

city: Beijing

first: Xiaotong

last: Han

address: No,8,South Road of The Worker's Stadium,Chaoyang Dist. Beijing

institute: Beijing Chao-Yang Hospital

description:
Library name: Sample 4
T-2

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: GRCm38/mm10
Supplementary files format and content: FPKM Processed Data in CSV Format. The processed data files contain gene-level FPKM values.

source_name: T cells

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen). A total of 1.3 µg of RNA was used for constructing sequencing libraries.
RNA libraries for RNA-seq were prepared using the SMARTER mRNA-Seq Library Prep Kit, following the manufacturer's protocols.

value: T cells


title: Oocytes, Uba3 cKO, rep1

value: Uba3 cKO


title: Oocytes, Uba3 cKO, rep2


title: Oocytes, Uba3 cKO, rep3


title: Ovary, control, rep1

value: Control


title: Control kidney (Ctrl5)

description: Library name: Ctrl5

value: WT


title: H460 cells, treat-3

institute: 复旦大学代谢与整合生物写研究院


title: H460 cells, treat-1

institute: 复旦大学代谢与整合生物写研究院


title: H460 cells, veh-1

institute: 复旦大学代谢与整合生物写研究院


title: WT cDNT_2

description:
Library name: Sample 2
C-2


title: Tbx21-KO cDNT_1

description:
Library name: Sample 3
T-1


title: Oocytes, control, rep1


title: WT cDNT_1

description:
Library name: Sample 1
C-1


title: CSE treated, rep3,RNA

city: Stanford

first: Juyong

middle: Brian

last: Kim

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

description: CSE_counts.txt (CSE10_3)

data_processing:
First, the fastqs were trimmed  by cutadapt to remove adaptor sequences. For unstranded samples, reads were aligned to GRCh38 reference genome with STAR and the alignments were assigned to  GENCODE reference annotation gencode.v25 by featureCounts,
DEseq2 were used for gene-level qutification and differential genes discovery.
Assembly: hg19
Supplementary files format and content: tab-delimiteed text files include raw counts for each sample

source_name: human coronary arterysmooth muscle cell

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kits (Qiagen, #74034).
RNA integrity was determined via bioanalyzer (Agilent) using standard RNA 6000 Pico chip. The libraries of samples for unstranded sequencing were constrcuted by TruSeq RNA Library Prep Kit and sequenced. Samples for stranded sequencing underwent ribosomal depletion, strand-specific library (dUTP method) synthesis followed by deep sequencing on NovaSeq 6000 platform.

treatment_protocol: cells were treated or not treated with 10nM TCDD for 24 hours.

value: human coronary arterysmooth muscle cell

value: CSE


title: Liver tissue from WT mouse, 40 weeks old #3

city: Amsterdam

first: Joana

last: Silva

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Liver_40w_WT_3

data_processing:
Reads from all samples were adapter-trimmed using the cutadapt tool (--action=trim -m 18 --adapter=TGGAATTCTCGGGTGCCAAGG --overlap=15 --error-rate=0.1). Then, trimmed reads were mapped to the hg38 and mm10 genomes using the STAR aligner.
Mouse data was analyzed solely using Gencode vM21 annotation. For human data, gencode v34 mitochondrial annotation was supplemented with the MDP annotation, 46 MS-supported ORFs identified in Kienzle et al. and 9 MDPs (MOTS-c, Humanin, SHMOOSE, and SHLPs 1-6) from the literature. For up- & down-stream analyses, the human annotation was extended further by defining all 30-nucleotide regions immediately upstream and downstream from any ORF as independent pseudo-ORFs.
Read quantification was done with the Rsubread package in R using these annotations. Multimapped reads were counted at a fractional count. Processed data includes the quantification results, including the RPKM values which represents the number of reads per kb million mitochodrial protein-coding region mapped reads.
Assembly: For human: hg38, gencode v34, Kienzle23&literature MDP annotation ; for mouse: mm10, gencode vM21
Supplementary files format and content: htseq.tsv files are tab-seperated files that reports the ORF ribosome occupancy levels based on respective annotations in file names. Ribosome occupancy is calculated by number of reads that are mapped to given ORF regions. Multimapping reads are fractioned into multimapped regions.
Library strategy: Ribo-Seq

source_name: Liver

growth_protocol: 143B and cybrid lines were cultured and maintained in Dulbecco’s modified Eagle’s media (DMEM) High Glucose, Glutamax-supplemented media (Thermo Fisher Scientific) supplemented with 10% fetal calf serum (FCS), 100 U/ml penicillin and 100 µg/ml streptomycin (Thermo Fisher Scientific). LN751 lines were cultured and maintained in Minimal Essential Medium, MEM, supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine, 1% MEM-Vitamins, 1% Non-Essential Amino Acids, 1% Penicillin-Streptomycin and 1% Sodium Pyruvate (MEM complete) (all purchased from Invitrogen, Grand Island, NY, USA). All lines were grown in standard conditions (37ºC and 5% CO2) and were routinely tested for mycoplasma contamination.

extract_protocol:
Briefly, for cell lines we used use 4x 15cm plates at approximately 80% confluent. For tissues, use approximately 0,027cm3 of snap-frozen material, bith from mouse and human, and grind them with the mortar and pestle, using liquid nitrogen to preserve the cold. Cells/ttissues were resuspended in ice-cold lysis buffer (20mM Tris-HCl pH 7.8, 10mM KCl, 10mM MgCl2, 1% Triton X-100, 0,1% NP-40, 1mM DTT, 100µg/ml chloramphenicol and 1x EDTA-free proteinase inhibitor), homogeneized with a 25G serynge and incubated for 10 min on ice. Lysates were then centrifuged at max speed for 10 min at 4°C and the supernatants were digested with 10ul of RNase I (ThermoFisher Scientific) for 40min at 25’C and the reaction was stopped by adding 13ul of SUPERASE (ThermoFisher Scientific). Mitoribosomal protected fragments were loaded onto 10-60% sucrose gradients and centrifuged for 2h at 38000rpm and at 4ºC, using a SW41 rotor. By splitting into fractions of 750ul, fractions 4, 5 and 6 were collected and mixed with 0.2mg/ml proteinase K, 0.01M of EDTA and 0.01% SDS. Samples were incubated at 42ºC for 30min. RNA was extracted using phenol:chloroform and precipitated with EtOH, sodium acetate and glycoblue.
MitoRiboSeq library preparation was performed as previously described (Loayza-Puch et al., 2013) with some modifications. To discard undigested RNA fragments, RPFs were run in a 10% TBE-Urea polyacrylamide gel and size selected between 26 nt and 48 nt using marker RNAs. 3’ ends were dephosphorylated using T4 polynucleotide kinase (PNK) (NEB) and 1.5xMES buffer (150mM MES-NaOH, 15mM MgCl2, 15mM ß-mercaptoethanol and 450mM NaCl, pH 5.5) and incubated at 37’C for 4h. After purifying RNAs with Trizol, 3’adpaters were ligated with T4 RNA ligase I (NEB) and incubated overnight at 24’C. After size-selecting the ligated products, 5’ ends were phosporylated with T4 PNK and incubated at 37’C during 30min. 5’ adapters were then ligated with T4 RNA ligase I and incubated 37’C for 2,5 hours. The RPFs containing both adapters were then size-selected one more time. cDNA was synthesized with SuperScript III (ThermoFisher Scientific) according to manufacturer’s instructions and using the RTP primer (seq). After purification with G50 columns (Merck), cDNA was amplified using Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific) for 18 cycles, with primers containing different indexes to allow for sequencing (see table). PCR products were purified using the QIAquick PCR purification kit (Qiagen) followed by a final size selection with a E-Gel SizeSelect II 2%, (ThermoFisher Scientific). All samples were accessed with the Agilent 2100 Bioanalyzer to assure high quality and quantify the molarity and the libraries were sequenced on the Illumina HiSeq2500.

treatment_protocol: LN751 cells were subjected to the PMCi triple combination therapy for 7 days. This treatment included Buparlisib (P) as the PI3K inhibitor, Mirdametinib (M) as the MEK inhibitor, and Palbociclib (C) as the CDK4/6 inhibitor.

value: Liver


title: H460 cells, veh-2

institute: 复旦大学代谢与整合生物写研究院


title: Oocytes, control, rep2


title: Liver tissue from PolgAMut/Mut mouse, 40 weeks old #3

description: Library name: Liver_40w_PolgAMut_3

value: PolgAMut


title: CD45+, tumor, PKCd KO BM, Replicate 4

city: Chicago

first: Thomas

middle: F

last: Gajewski

state: IL

address: 5841 S Maryland Ave

department: Ben May

institute: University of Chicago

data_processing:
Demultiplexing and alignment to the mm10 transcriptome (version 3.0.0) was performed, with count matrices created using the Cell Ranger pipeline (version 3.0.2)
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Syngenic Tumor

growth_protocol: Prkcd+/+ (WT) or Prkcd-/- (KO) donor mice (CD45.2) were confirmed by genotyping and sacrificed at 6-10 weeks. Bone marrow was harvested and CD90.2 cells were depleted via MACS column separation (Miltenyl, 130-121-278) before cells were counted and resuspended in PBS for sterile intravenous injection. 24 hours before engraftment, B6.SJL-Ptprca/BoyAiTac mice (Taconic, 4007, CD45.1) sex-matched transplant recipient mice were irradiated with 5 Gy and 5.5 Gy (Cesium 137 source) with a 3-hour rest period in between. Bone marrow was injected intravenously via retro-orbital injection with a minimum of 4.0x106 cells injected per host mouse in a volume of 100ul PBS. Mice were allowed to rest of a minimum of 8 weeks before experimental use.

extract_protocol:
After 26 days of growth tumors were excised from WT or PKCd KO bone marrow engrafted animals, mechanically dissociated, and incubated with a mixture of 10 mg/ml collagenase type IV (Sigma, C5138), 1 mg/ml hydrogenase type V (Sigma, H6254), and 2,000 units/ml DNAse type IV (Sigma, D5025-150ku) for 45 minutes at 37C before being washed with PBS through a 70uM filter (Corning, 352350). Tumors were then passed through a Ficoll-Paque gradient (Cytivia Life Sciences, 17144003), and the bilayer was collected. Following the ficoll gradient, the mononuclear cells obtained from two tumors were combined into a single sample forming a single replicate for that group. Samples were then stained with Live-Dead (APC-Cy7) and CD45.2 (FITC) and Live CD45.2+ cells were sorted via fluorescence activated cell sorting (FACS) before being washed 3x in PBS. 2 WT and 2 PKCd KO samples were processed simultaneously. This entire process was repeated on a second, independent collection day, for a total n of 4 replicate samples from 8 total tumors per genotype group.
Single cell partitioning and library creation was performed by the University of Chicago Genomics core using a chromium controller from 10x genomics following the “Chromium Single Cell 3ʹ Reagent Kits v3” user guide and associated reagents. 10,000 cells per sample were targeted for encapsulation. Libraries were sequenced in PE100 format of an SP-100 flowcell of an Illumina Novaseq 6000 instrument.

treatment_protocol: B16-F10-SIY-dsRed were thawed, grown in cDMEM media (DMEM, 10% FBS, 1% NEAA, 1% Penn-Strep, 1% MOPS buffer) and passaged 2-5 times before experimentation. Cells were washed 3x with PBS before being resuspended at 2x106 cells per 100ul of PBS for B16-SIY or 1x106 cells per 100ul of PBS for MC38-SIY, with 100ul of cells injected subcutaneously into the right flank and tumors were grown for 26 days before harvesting.

value: Syngenic Tumor

value: Tumor Infiltrating Live CD45+ cells

tag: bone marrow_genotype

value: PKCd KO

value: Replicate 4

tag: endpoint

value: Day 26

tag: technical replicate_group

value: B


title: Liver tissue from PolgAMut/Mut mouse, 40 weeks old #2

description: Library name: Liver_40w_PolgAMut_2


title: Liver tissue from WT mouse, 40 weeks old #1

description: Library name: Liver_40w_WT_1


title: Liver tissue from WT mouse, 40 weeks old #2

description: Library name: Liver_40w_WT_2


title: Liver tissue from WT mouse, 25 weeks old #1

description: Library name: Liver_25w_WT_1


title: Liver tissue from PolgAMut/Mut mouse, 40 weeks old #1

description: Library name: Liver_40w_PolgAMut_1


title: Liver tissue from PolgAMut/Mut mouse, 25 weeks old #1

description: Library name: Liver_25w_PolgAMut_1


title: Liver tissue from PolgAMut/Mut mouse, 25 weeks old #2

description: Library name: Liver_25w_PolgAMut_2


title: CD45+, tumor, WT BM, Replicate 3

value: Wildtype

value: Replicate 3


title: DMSO ctrl for CSE, rep3,RNA

description: CSE_counts.txt (D10_3)

tag: treatment

value: DMSO


title: CSE treated, rep1,RNA

description: CSE_counts.txt (CSE10_1)


title: CpG/N6 72h plus 4 days L47/CpG/N6, rep2

city: Saarbrücken

first: Annemarie

last: Jungmann

address: Campus, building A 2.4

department: Genetics / Epigenetics

country: Germany

institute: Saarland University

data_processing:
data was processed with nf-core atacseq pipeline, version 1.2.1
Assembly: mm10
Supplementary files format and content: bigwig files of ATAC signal
Supplementary files format and content: bed files of called ATAC peaks

source_name: B cells prepared from spleens

extract_protocol:
Qiagen MinElute PCR purification kit
Cells were harvested and nuclei were prepared. Tagmentation reaction was performed; DNA was purified (MinElute PCR purification kit; Qiagen) and PCR was performed

value: B cells prepared from spleens

value: CpG/N6 72h plus 4 days L47/CpG/N6


title: CpG/N6 72h plus 4 days L47/CpG/N6, rep1


title: Liver tissue from WT mouse, 25 weeks old #2

description: Library name: Liver_25w_WT_2


title: CD45+, tumor, PKCd KO BM, Replicate 3


title: DMSO ctrl for CSE, rep1,RNA

description: CSE_counts.txt (D10_1)


title: CD45+, tumor, WT BM, Replicate 4


title: CSE treated, rep2,RNA

description: CSE_counts.txt (CSE10_2)


title: CpG/N6 72h plus 4 days L47/IL-4/BAFF, rep2

value: CpG/N6 72h plus 4 days L47/IL-4/BAFF


title: 92.1-parental-H3K27ac-IgG-rep2

city: Shanghai

first: Tianyu

last: Zhu

address: Zhizaoju Road

institute: Shanghai Ninth People's hospital

data_processing:
Raw Reads were filtered using the Trimmomatic software with default parameters. After data filtering, we evaluated the overall quality of both Raw Reads and Clean Reads. The evaluation results included parameters such as Q20 and Q30, which indicate the base quality scores. The quality score Q is calculated using the formula Q = -10 log10 p, where p is the probability of a base call error. Q20 indicates a base call accuracy of 99%, and Q30 indicates a base call accuracy of 99.9%. Quality scores of 20 and above indicate relatively good sequencing quality, while scores of 30 and above indicate very high sequencing quality.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Briefly, 1 × 105 cells were harvested, washed, and mixed with activated concanavalin A-coated magnetic beads (Bangs Laboratories, USA) at room temperature for 15min. The cells were incubated with primary antibody (1:50) overnight at 4◦C, washed thrice, and then incubated with secondary antibody (1:50) at room temperature for approximately 1 h. After washing, the cells were incubated in 100 μL of pA-Tn5 adapter complex (∼40 nmol/L) at room temperature for approximately 1 h. After washing, the cells were resuspended in Tagmentation buffer (50 μL) and incubated at 37℃ for 1 h. DNA was then purified and prepared for PCR.
Pooled libraries were purified using 1.1× AMPure XP beads. Paired-end Illumina sequencing was performed using a HiSeq 4000 instrument (Illumina, USA).

tag: chip antibody

value: IgG


title: Liver tissue from PolgAMut/Mut mouse, 25 weeks old #3

description: Library name: Liver_25w_PolgAMut_3


title: CpG/N6 72h plus 4 days L47/CpG/DMSO, rep2

value: CpG/N6 72h plus 4 days L47/CpG/DMSO


title: CD45+, tumor, PKCd KO BM, Replicate 2

value: Replicate 2

value: A


title: DMSO ctrl for CSE, rep2,RNA

description: CSE_counts.txt (D10_2)

value: human coronary arterysmooth muscle cell


title: Liver tissue from WT mouse, 25 weeks old #3

description: Library name: Liver_25w_WT_3

value: Liver

value: WT


title: CD45+, tumor, PKCd KO BM, Replicate 1

value: Syngenic Tumor

value: Tumor Infiltrating Live CD45+ cells

value: PKCd KO

value: Replicate 1


title: CD45+, tumor, WT BM, Replicate 2

value: Wildtype

value: Day 26


title: CpG/N6 72h plus 4 days L47/IL-4/BAFF, rep1


title: 92.1-parental-H3K27ac-IgG-rep1


title: CpG / N6, 72h, rep3

value: CpG / N6 72h


title: CD45+, tumor, WT BM, Replicate 1


title: CpG/N6 72h plus 4 days L47/CpG/DMSO, rep1

value: B cells prepared from spleens


title: CpG / N6, 72h, rep2


title: CpG / N6, 72h, rep1


title: 92.1-parental-H3K9ac-IgG-rep2


title: YAP5SA

city: Philadelphia

first: Ning

last: Li

state: Pennsylvania

address: 3800 Spruce St.

department: Biomedical Sciences

institute: UPENN

description: 10x Genomics

data_processing:
Data were processed using Cell Ranger software v7.2
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Organoids from mouse intestine

growth_protocol: Organoids were cultured in a medium consisting of 50% L-WRN conditioned medium (L-WRN CM) supplemented with N2, B27, N-acetylcysteine, and 50 ng/ml mEGF.

extract_protocol:
Organoids were digested with TrypLE for 10-30min to generate single cell suspension. Single cells run through flow cytometery to move dying cells and ensure viability above 90%.
Libraries were prepared following the manufacturer's protocol for the 10x Genomics Chromium Single Cell RNA Expression Kit v3.1. Briefly, a single-cell suspension was obtained from the sample tissue and quantified to ensure a target concentration of 1000 cells per μl with over 90% viability. Cells were loaded onto a Chromium Chip along with reagents from the kit, and barcoding was performed using the Chromium Controller. Following barcoding, cDNA was synthesized, amplified, and then purified using magnetic separation. The cDNA underwent library construction which included enzymatic fragmentation, size selection, and PCR amplification. The final library quality was assessed using a bioanalyzer before sequencing.

treatment_protocol: In Ctnnb1_CtrlwithIFNr experiment, organoids were treated with 5 ng/ml IFNr (R&D, 485-MI-100)for 1 week before profiling.

value: Organoids from mouse intestine

value: Lab generated

value: Epithelial cells

value: beta-catenin exon3 f/f


title: CpG / DMSO, 72h, rep1

value: CpG / DMSO 72h


title: CpG / DMSO, 72h, rep2


title: CpG 48h with 24h N6, rep3

value: CpG 48h with 24h N8


title: dnTcf_4125_4129, scRNAseq

description: 10x Genomics

value: Apc f/f, dnTcf4 f/f


title: 92.1-resistant-H3K9ac-IgG-rep2

value: IgG


title: 92.1-resistant-H3K27ac-IgG-rep1


title: CpG 48h with 24h DMSO, rep2

value: CpG 48h with 24h DMSO


title: CpG 48h with 24h N6, rep2

value: CpG 48h with 24h N7


title: 92.1-resistant-H3K27ac-IgG-rep2


title: 92.1-parental-H3K9ac-IgG-rep1


title: CpG, 24h, rep2

value: CpG 24h


title: 92.1-parental-H3K27ac-rep1


title: dnTcf_4115_4117, scRNAseq

description: 10x Genomics


title: naive, rep1

value: naive


title: CpG 48h with 24h DMSO, rep3


title: 92.1-resistant-H3K9ac-IgG-rep1


title: beta-catenin f/f, scRNAseq

description: 10x Genomics


title: 92.1-parental-H3K27ac-rep2


title: naive, rep2


title: Ctnnb1_CtrlwithIFNr

description: 10x Genomics

value: HBSS


title: CpG 48h with 24h DMSO, rep1


title: Apc f/f, scRNAseq

description: 10x Genomics

value: Apc f/f


title: UNDETERMINED

city: Aachen

first: Benjamin

middle: Arthur

last: Vervaet

address: Pauwelstrasse 30

institute: RWTH Uniklinik Aachen

description: Library name: IRC-08_00

data_processing:
Bbduk was used to remove Illumina-specific adapter sequences (barcodes) and contaminants (poly-A tail) using 5-13 kmers, ensure a minimum Phred-quality score of 10, and ensure a minimum read length of 20 bases.
Sequences were mapped against the Ensembl release 113 reference mouse genome (GRCm39) using STAR.
STAR (v2.7.11b) was used to count all reads for each gene and set up a read count table.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file includes all raw counts for each sample

extract_protocol:
Total mRNA was extracted from a cryo pole section of the kidney using the PureLink® RNA Mini kit from Invitrogen
Libraries for RNA were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH). Input of 500 ng of total mRNA was used.
RNASeq

value: Kidney


title: CpG, 24h, rep3


title: WT_IRd3_4

description: Library name: IRC-08 34

value: UIRI

tag: timepoint


title: CpG, 24h, rep1

value: B cells prepared from spleens


title: WT_IRd3_6

description: Library name: IRC-08 36


title: scRNAseqofimmunecells from renal cortex

city: Bonn

first: Junping

last: Yin

state: State

address: Venusberg-Campus, 1

institute: uniklinikum bonn

description: cortex

data_processing:
fastq files were analyzed using Cellranger
count matrix data was analyzed using Seurat
Assembly: mm10
Supplementary files format and content: txt

extract_protocol:
kidneys were separated into cortex, OM, IM, which were further digested using enzyme
10x gene expression profiling

value: immune cell

value: wt

value: untouched


title: Ctrl

description: 10x Genomics

value: Organoids from mouse intestine

value: Lab generated

value: Epithelial cells

value: beta-catenin exon3 f/f


title: WT_IRd3_2

description: Library name: IRC-08 32


title: CpG 48h with 24h N6, rep1

value: CpG 48h with 24h N6


title: WT_IRd3_3

description: Library name: IRC-08 33


title: WT_IRd3_5

description: Library name: IRC-08 35


title: 92.1-parental-H3K9ac-rep1


title: WT_IRd3_1

description: Library name: IRC-08 31


title: scRNAseqofimmunecells from renal OM

description: OM


title: WT_IRd7_4

description: Library name: IRC-08 22


title: scRNAseqofimmunecells from renal IM

description: IM


title: 92.1-resistant-H3K9ac-rep1


title: WT_IRd7_3

description: Library name: IRC-08 21


title: FUS-BBBO 750 kPa, 1hr, 1

city: New York

first: Elisa

middle: E

last: Konofagou

department: Biomedical Engineering

institute: Columbia University

description:
single cell RNA seq
DT008

data_processing:
cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: .zip folder containing raw feature bc matrix .zip files for each library

source_name: Brain

extract_protocol:
The neural dissociation kit (P) was used to dissociate the spinal cords into a single cell suspension. Following myelin removal using Miltenyi Biotec Myelin Removal Beads II, the samples were stained with CD31-APC and PI, and live endothelial cells were FACS sorted for single cell RNA sequencing
The 10x Genomics Chromium platform was used to generate low-depth data, which was procseed using the Cell Ranger analysis pipeline to align reads and generate feature-barcode matricies.

value: Brain

value: Endothelial cell

value: FUS-BBBO 750 kPa, 1hr, 1


title: 92.1-resistant-H3K9ac-rep2


title: WT_IRd7_2

description: Library name: IRC-08 20


title: WT_IRd7_1

description: Library name: IRC-08 19


title: WT_IRNxd7_2

description: Library name: IRC-08 15

value: UIRI+Nx


title: 92.1-parental-H3K9ac-rep2


title: Control 1

description:
single cell RNA seq
DT005

value: Control 1


title: WT_IRNxd7_1

description: Library name: IRC-08 14


title: WT_IRd7_6

description: Library name: IRC-08 24


title: FUS-BBBO 450 kPa, 1hr, 2

description:
single cell RNA seq
DT004

value: FUS-BBBO 450 kPa, 1hr, 2


title: 92.1-resistant-H3K27ac-rep1


title: Stellate Ganglion, plate 11

first: Daniele

last: Neri

address: 630 West 168th Street

institute: Columbia University Irving Medical Center

description:
Library name: LS011
columns in the processed dataset from this file start with "LS011_"

data_processing:
Reads were aligned to mouse genome, GRCm38, gencode version M13 (Ensembl 88) using STAR v2.5.3a. The aligned reads were assigned to genes using featureCounts v1.5.3. Next the bam files were sorted and indexed using Samtools v1.4.1 (http://www.htslib.org/), duplicated reads were removed and a UMI count matrix was generated using umi tools.
Assembly: GRCm38, gencode version M13 (Ensembl 88)
Supplementary files format and content: processed_dataset.csv: Comma separated value file of all the count matrices generated (one for each plate) merged together.
Supplementary files format and content: stellate_combined.rds: Seurat object with the dataset processed according to the information in the manuscript to be uploaded on R.

source_name: Stellate Ganglion

extract_protocol:
The plates were centrifuged at 200g for 2 min and snap frozen on dry ice. Each well received 7.5 μl of lysis buffer [0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (Thermo Fisher Scientific), 2 mM deoxyribonucleotides (dNTPs) (Thermo Fisher Scientific), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)]. Primer annealing was performed at 72°C for 3 min. Reverse transcription was performed by adding 7.5 μl of RT mix to each well [2 M betaine (Affymetrix), 2× Protoscript Buffer (New England Biolabs), 12 mM MgCl2 (Thermo Fisher Scientific), 10 mM dithiothreitol (Thermo Fisher Scientific), 5.3 U of Protoscript II Reverse Transcriptase (New England Biolabs), 0.53 U of SUPERaseIN (Thermo Fisher Scientific), and 2 μM Template Switching Oligo (Integrated DNA Technologies; table S6)]. Reverse transcription was performed at 42°C for 90 min, followed by 10 cycles of 50°C for 2 min, 42°C for 2 min, 70°C for 10 min, followed by a 4°C hold. Excess primers were removed by adding 2 μl of Exonuclease I (Thermo Fisher Scientific) mix to each well (1.875 U of ExoI in water) and incubating at 37°C for 30 min, 85°C for 15 min, 75°C for 30 s, and 4°C hold.
The cDNA was pooled for PCR and library construction. Pooled, 3’-end sequencing libraries were sequenced on an Illumina NextSeq 500/550 platform.

value: Stellate Ganglion

tag: Sex

value: Male

value: 6-8 weeks

tag: batch

value: Set 3


title: FUS-BBBO 750 kPa, 72hr, 2

description:
single cell RNA seq
DT007

tag: tissue

value: FUS-BBBO 750 kPa, 72hr, 2


title: 92.1-Res-rep1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low qualityreads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Assembly: hg38
Supplementary files format and content: tab-delimited files include FPKM values for each sample

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen).RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.
The total RNA samples were evaluated for integrity using agarose gel electrophoresis and quantified and further assessed for quality using a NanoDrop ND-1000. For each sample, 1~2 µg of total RNA was selected for sequencing library construction. Total RNA was first enriched for mRNA using the NEB Next® Poly(A) mRNA Magnetic Isolation Module (or rRNA was removed using the RiboZero Magnetic Gold Kit). The resulting RNA was then used to construct libraries with the KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The KAPA kit employs a dUTP-based strand-specific library construction method.

value: uveal melanoma cells

value: resistant cells


title: WT_IRd7_5

description: Library name: IRC-08 23

value: Kidney

value: UIRI


title: Control 2

description:
single cell RNA seq
DT010

value: Control 2


title: WT_IRNxd7_3

description: Library name: IRC-08 16


title: 92.1-Ctrl-rep2

value: parental


title: 92.1-resistant-H3K27ac-rep2


title: PCA34, YKL-5-124, resistant-5

city: Boston

first: Ziyue

state: Massachusetts

address: 450 Brookline Ave, D718

institute: Dana-Farber Cancer Institute

data_processing:
All sequencing, alignment, and count generation was performed by Novogene.
Alignment was performed using STAR (version 2.6.1d) with mismatch parameter set to 2 to GRCh38.
Gene counts were generated using FeatureCounts (version 1.5.0-p3) with default parameters.
The gene counts matrix was then used as input for the analysis and normalization was performed using DESeq2 (version 1.24.0) with shrinkage estimates determined by the ahsr method.
Assembly: GRCh38
Supplementary files format and content: Exel file includes raw counts for each sample

source_name: PCA34 tumor

growth_protocol: PCA-34 tumors were implanted in nude mice in pathogen-free animal facility.

extract_protocol:
Total RNA was isolated using RNeasy Plus Kit(Qiagen, # 74136).
The samples were then sent to Novogene (Sacramento, CA) for the remainder of the RNA sequencing experiment.

treatment_protocol: Mice carrying PCA-34 tumors were treated with Vehicle (5%DMSO 95% D5W) or YKL-5-124 (10mg/kg dissolved in 5%DMSO 95% D5W)

value: PCA34 tumor

value: Pancreatic cancer Patient Derived Xenograft (PDX)

value: 10mg/kg YKL-5-124 dissolved in 5%DMSO 95% D5W


title: WT_IRNxd7_4

description: Library name: IRC-08 17

value: UIRI+Nx


title: FUS-BBBO 750 kPa, 72hr, 1

description:
single cell RNA seq
DT006

value: Brain

value: Endothelial cell

value: FUS-BBBO 750 kPa, 72hr, 1


title: Stellate Ganglion, plate 4

description:
Library name: LS004
columns in the processed dataset from this file start with "LS004_"

value: Stellate Ganglion

value: Male

tag: age

value: Set 1


title: Stellate Ganglion, plate 9

description:
Library name: LS009
columns in the processed dataset from this file start with "LS009_"

value: 6-8 weeks

value: Set 3


title: FUS-BBBO 450 kPa, 72hr, 2

description:
single cell RNA seq
DT002

value: FUS-BBBO 450 kPa, 72hr, 2


title: FUS-BBBO 450 kPa, 72hr, 1

description:
single cell RNA seq
DT001

value: FUS-BBBO 450 kPa, 72hr, 1


title: FUS-BBBO 750 kPa, 1hr, 2

description:
single cell RNA seq
DT009

value: FUS-BBBO 750 kPa, 1hr, 2


title: TLR5- macrophages_1

city: Nanjing

first: REN

last: DESHAN

state: --- Select One ---

address: 12 Xuefu-Road, Pukou District  Nanjing 210061, China

institute: Nanjing university

data_processing:
The sequencing data was filtered with fastp (v0.23.4) to remove reads with sequencing adapter, those with low quality (reads with Qphred<=20 base number accounting for more than 50% of the entire read length) and those with 'N' base (where 'N' represents undetermined base information). Clean reads were obtained and stored in FASTQ format.  The clean reads were aligned to the reference genome of Mus musculus (UCSC mm39) using hisat2 (v2.2.1). Aligned reads were converted and then sorted by samtools (v1.6).  Gene counts were obtained using featureCounts (v2.0.2) on GENCODE vM32 annotations. Fragments Per Kilobase of exon per Million fragments mapped (FPKM) was selected as the gene expression value for RNA sequencing.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample
Supplementary files format and content: tab-delimited txt file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturers protocols.

value: Macrophages

tag: sorted cells

value: TLR5- macrophages


title: Stellate Ganglion, plate 10

description:
Library name: LS010
columns in the processed dataset from this file start with "LS010_"


title: FUS-BBBO 450 kPa, 1hr, 1

description:
single cell RNA seq
DT003

value: FUS-BBBO 450 kPa, 1hr, 1


title: PCA34, YKL-5-124, resistant-3

value: PCA34 tumor

value: Pancreatic cancer Patient Derived Xenograft (PDX)


title: 92.1-Res-rep2

value: uveal melanoma cells

value: resistant cells


title: PCA34, YKL-5-124, 3Day-3

value: 10mg/kg YKL-5-124 dissolved in 5%DMSO 95% D5W


title: Stellate Ganglion, plate 5

description:
Library name: LS005
columns in the processed dataset from this file start with "LS005_"

value: Set 2


title: Control_1dpc_rep2

city: Palo Alto

first: Wenjun

last: Yan

state: California

address: 1651 Page Mill Rd

department: Department of Ophthalmology, Byers Eye Institute, Mary M. and Sash A. Spencer Center for Vision Research, Stanford University School of Medicine

description: 10X Genomics, Chromium Next GEM Single Cell 3’ Kits v3.1

data_processing:
The mouse mm10 reference genome was modified to incorporate the transcript sequences for AAV2tm.Flag-HDAC4 3SA or NT (need to upload the sequence) and used for alignment of corresponding libraries respectively. For mice without AAV injection, transcripts were mapped against the HDAC4 3SA composite reference.  Cell Ranger v6.1.2 (Zheng et al., 2017) was used to build the above reference genomes and for reads alignment/counting.
Assembly: mm10
Supplementary files format and content: Count_mat_RGCs.csv is the count matrix of RGCs in the format of .csv
Supplementary files format and content: tab-separed value files and matrix files

source_name: retina

extract_protocol:
scRNA-seq libraries were generated for AAVsc.Flag-HDAC4 3SA and NT injected C57BL/6J mice, as well as non-injected mice, all mice subjected to either ONC or sham injury, two each for a total of 6 libraries. For each library, 8 retinas were collected 1 day after ONC or shame injury by a modified two-step immunopanning protocol. Briefly, retinas were dissociated into a single-cell suspension using papain and incubated on antibody-coated dishes. After depletion of macrophages with an anti-mouse macrophage antibody (Accurate Chemical, AIA31240), cells were selected with an anti-mouse Thy1.2/CD90 (Bio-Rad, MCA02R). Thy1+ cells were re-suspended in DPBS (Gibco, 14287-080) with 1% BSA (Sigma-Aldrich, A4161-5G) and processed immediately. Cell concentration and viability were determined using trypan blue (Gibco, 15250061) and a Countess FL II Automated Cell Counter (Thermo Fisher).
Cells were loaded in parallel for capture onto the Chromium System using Chromium Next GEM Single Cell 3’ Kits v3.1 (Dual Index, 10X Genomics, PN-1000269). Following capture and lysis, cDNA was synthesized and amplified for 12-14 cycles, as per manufacturer’s protocol (10X Genomics). Amplified cDNA was used to construct Illumina sequencing libraries and sequenced using Nova Seq S1 flow cells and 150 bp paired end sequencing.

value: retina

value: 6 weeks

tag: strain

value: 1day post optic nerve crush


title: 92.1-Ctrl-rep1

value: parental


title: PCA34, YKL-5-124, 3Day-1


title: PCA34, YKL-5-124, resistant-2


title: Stellate Ganglion, plate 3

description:
Library name: LS003
columns in the processed dataset from this file start with "LS003_"

value: Stellate Ganglion

value: Male

value: 6-8 weeks

value: Set 1


title: PCA34, YKL-5-124, resistant-1


title: Stellate Ganglion, plate 6

description:
Library name: LS006
columns in the processed dataset from this file start with "LS006_"