title: Primary T cells, HIV-1 WT infection, donor 2, 96 h, replicate 1

description:
Library name: 22
22_R1.DeDup.sorted
Samples_18_22_26_vs_17_21_25_APA_BBstats.txt

value: HIV-1 WT infection, 96 h


title: Abd_5

status: Public on Dec 10 2025

type: SRA

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Abd_5
RNA-seq

library_source: transcriptomic

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: subcutaneous adipose tissues

extract_protocol:
RNA was extracted with Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen #74804)
Library prepration and sequencing was performed by GENEWIZ

tag: tissue

value: subcutaneous adipose tissues

tag: Sex

value: F

tag: depot

value: Abd

tag: age

tag: bmi


title: EGME75_16

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description: Library name: Library_16

data_processing:
Libraries were sequenced in single-end configuration on the IonProton sequencer.
Initial quality control was performed using FASTQC (Andrews, 2010). Two samples with extremely low read counts were identified as outliers and excluded from downstream analysis.
Small RNA expression levels were then profiled using sRNAbench (Aparicio-Puerta et al., 2022) in genome mode. Reads were mapped against the rat genome (Rnor_6_0) and compared to miRBase Release 22.1 (Kozomara et al., 2019). Default sRNAbench parametersl were applied: the bowtie seed alignment, seed length 20, minimum read count 2, minimum read length 15, allowed 1 mismatch, and 10 multiple mappings. After expression profiling, multi-map adjusted read counts for small RNAs (miRNAs, tRNAs, ncRNAs, cDNA) from sRNAbench ".grouped" files were parsed using a custom Python script.
Differential expression of small RNAs across dosage groups was determined using DESeq2 (Love et al., 2014) with default filtering.
Assembly: Rnor_6_0
Supplementary files format and content: mature_sense_counts.csv: miRNA read counts
Supplementary files format and content: Rnor_6_0_RNAcentral_sense_counts.csv: piRNA read counts
Supplementary files format and content: Rnor_6_0_genomic_tRNA_sense_counts.csv: tRNA read counts
Supplementary files format and content: Rnor_6_0_ncRNA_sense_counts.csv: other small noncoding RNA read counts

molecule: total RNA

organism: Rattus norvegicus

source_name: spermatozoa

growth_protocol: Spermatozoa obtained from the cauda epididymis of 11-12 week-old male Fischer rats.

extract_protocol:
Total RNA was extracted using the ThermoFisher miRvana kit per manufacturer's instructions, including Dnase treatment, as described in our publication.
10 ng RNA from each sample was used to construct the library using the Ion total RNA seq kit v2 (ThermoFisher)

treatment_protocol: Daily oral gavage with 0, 50, 60, or 75 mg/kg/d EGME for 5 days, followed by 5 weeks of no exposure.

value: spermatozoa

tag: genotype

value: wild-type

tag: treatment

value: 75 mg/kg/d EGME

tag: batch


title: EGME75_15

description: Library name: Library_15


title: Primary T cells, mock infected, donor 2, 96 h, replicate 1

city: Rochester

first: Eric

middle: John

last: Wagner

state: NY

address: 575 Elmwood Avenue

department: Biochemistry and Biophysics

institute: University of Rochester Medical Center

description:
Library name: 21
21_R1.DeDup.sorted
Samples_18_22_26_vs_17_21_25_APA_BBstats.txt

data_processing:
Fastp was used to remove the Illumina adapters (using -a option), trim low-quality bases in the start of the read (using -f 4) and to discard reads that are shorter than forty bases (using -l 40).
The quality trimmed reads were then aligned to the reference genome (GRCh38, version 33 downloaded from GENCODE portal), using bowtie2 version 2.3.5.1 in single end mode. Umitools were used to discard de-duplicated reads
Assembly: GRCh38, version 33
Supplementary files format and content: PolyA-miner was then run to generate counts for each polyA site in all the samples which are provided in the processed data files.

source_name: Peripheral blood T lymphocytes

growth_protocol: A549 and HEK293T cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 29.2 mg/ml L-glutamine, and 5 μg/ml plasmocin at 37°C with 5% CO₂. Primary human T cells were isolated from peripheral blood mononuclear cells from healthy donors and cultured in RPMI-1640 medium containing 10% FBS, 4 μg/ml PHA-L, and 20 IU/ml IL-2.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacturer’s protocol. Following phase separation with chloroform, RNA was precipitated with isopropanol, washed with 75% ethanol, and dissolved in RNase-free water.
First, 2 µg total RNA was mixed with 1 µl of 100 µM 3’ Illumina_4N_21T_VN primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNTTTTTTTTTTTTTTTTTTTTTVN-3’), 2 µl of 5 mM AzNTP (Baseclick, #BCT–25 to −28)/dNTP mixture, at a ratio of 1 to 5, and the total volume was raised to 13 µL by the addition of H2O. The mixture was heated at 65°C/5 min and snap-cooled on ice for 3 min. Reverse transcription was performed using SuperScript III (ThermoFisher, #18080093). In brief, 7 µl master mix containing 4 µl 5× Superscript First Strand buffer, 1 µl of 0.1 M DTT, 1 µl RNaseOUT (ThermoFisher, #10777019), and 1 µl SuperScript III were mixed with the RNA sample. Heating was performed in a thermocycler sequentially as follows: 25°C/10 min, 50°C/40 min, and 75°C/15 min, followed by RNase H (ThermoFisher, #AM2293) treatment using 1U per reaction for 37°C/30 min and then 80°C/10 min. The resulting cDNA was purified using Sera-Mag Speedbeads (Cytiva, #65152105050250). Speedbeads working solution was made by washing 1 ml bead slurry twice in 1×TE buffer and then resuspending beads in 50 ml of 1×TE buffer containing 9 g PEG-8000, 1 M NaCl, and 0.05% Tween-20. Speedbeads, 1.8× reaction volume, was mixed with cDNA followed by a 5 min incubation at room temperature. The beads were then pelleted using a magnetic bead collector, and the supernatant was discarded. Two washes with 80% ethanol were performed while the beads were pelleted on the magnet. The beads were then dried, and the cDNA was eluted by resuspending the beads in 22 µl of 50 mM HEPES pH 7.2 for 2 min at room temperature. Then, 20 µl cDNA was mixed with 11 µl Click Mix (2.5 M NaCl, 30% EtOH in H2O) and 4 µl of 5 µM UMI-click-adapter (5’-Hexynyl-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’, HPLC purified). To activate the reaction, 4 µl of 50 mM vitamin C and 1 µl of Click Catalyst (4 mM CuSO4 in H2O and 20 mM THPTA [Baseclick, #BCMI-006] in H2O) were pre-mixed before being added into the cDNA solution for 60 min incubation at room temperature in the dark. Clicked cDNA was then purified in the same manner as post-RT purification but eluted in 22 µl of 10 mM Tris pH7.4. Half of the eluted cDNA was subjected to PCR amplification with indexing primers i5 (5’-AATGATACGGCGACCACCGAGATCTACAC[Index]ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’) and i7 (5’-CAAGCAGAAGACGGCATACGAGAT[Index]GTGACTGGAGTTCAGACGTGTGCTCTTCCGAT*C-3’). Both primers have a phosphorothioate bond added at the 3’ end (denoted as *) to increase stability. The PCR reaction was conducted in a 50 µl volume, including 25 µl 2× OneTaq Master Mix (NEB, #M0482), 2 µl each of 5 µM i5 and i7, and cDNA in H2O. A total of 13 amplification cycles were conducted on 2 µg input RNA. The program was run at 94°C/4 min; 53°C/30 sec; 68°C/10 min; 15× [94°C/30 sec, 53°C/30 sec; 68°C/2 min]; 68°C/5 min; hold at 4°C. The library was then purified and size-selected with Speedbeads. In brief, 45 µl beads (0.9× volume of PCR reaction) were mixed with the reaction to remove larger fragments. Supernatant was collected and mixed with 10 µl beads (0.2× volume of PCR reaction) to remove smaller fragments and primer dimers. Two washes with 100% ethanol were then performed while the beads were on the magnet. Beads were dried before being resuspended in 12 µl of 10 mM Tris pH7.4. The library was then collected and subjected to quality control on Agilent 2200 TapeStation and analysis by Illumina NovaSeq 6000 at the Genomics Research Center at the University of Rochester.

treatment_protocol: Cells were infected with HIV-1 WT, HIV-1 N74D, or HIV-1 A77V viral particles, or mock treated, for the indicated time points. Infection was performed at the desired MOI and incubated for 40–48 h for A549 cells or 96 h for primary T cells. CPSF6 knockout A549 clones were generated using CRISPR-Cas9 RNP electroporation followed by clonal selection via limiting dilution.

value: Peripheral blood T lymphocytes

tag: cell type

value: primary T cells

value: mock infected, 96 h


title: C57BL/6 Cholangiocytes, 10 days DDC + 15 Days of Recovery (chow), Replicate 3

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: R15-M12
D10-R15-M12

data_processing:
MAP-RSeq v3.1.4 was utilized to pre-process, align, and quantify the counts and FPKM of the sequencing libraries against the mm10 genome.
Assembly: mm10
Supplementary files format and content: merged_FPKM_by_gene_annotated.tsv, tab separated file of gene annotations (row) and sample FPKM (column)

organism: Mus musculus

source_name: liver

growth_protocol: All protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of Mayo Clinic in Rochester, MN, USA. Mice were maintained on a 12-hour light/dark cycle with ample amount of food and water provided.

extract_protocol:
Wildtype male liver tissue were dissociated (#130-096-730, Miltenyi Biotech, Germany). CD326 (EpCAM) Microbeads (#130-105-958, Miltenyi Biotec, Germany) were used to isolate the cholangiocytes by immunomagnetic separation using MACS columns. To increase the purity of the cholangiocyte population, the positively selected cell population was separated over a second column. Direct-zol RNA MicroPrep Kit (#R2060, ZYMO, CA, USA) was used to isolate total RNA from the CD326+ cells.
cDNA libraries were prepared and sequenced by the Genome Analysis Core (Mayo Clinic, Rochester, MN, USA) using Illumina Stranded mRNA Prep following manufacturer recommendations.

treatment_protocol: Wildtype male mice, between 14-16 weeks of age, were fed the chow diet (control group), DDC diet for 10 days (DDC group), or DDC diet for 10 days and then transferred to a chow diet for 15 days (R15 group).

value: liver

value: cholangiocytes

value: wildtype

value: male

value: 10 days DDC diet + 15 days chow diet


title: Thi_4

description:
Library name: Thi_4
RNA-seq

value: M

value: Thi


title: C57BL/6 Cholangiocytes, 10 days DDC + 15 Days of Recovery (chow), Replicate 2

description:
Library name: R15-M11
D10-R15-M11


title: Primary T cells, HIV-1 N74D infection, donor 1, 96 h, replicate 1

description:
Library name: 19
19_R1.DeDup.sorted
Samples_19_23_27_vs_17_21_25_APA_BBstats.txt

value: HIV-1 N74D infection, 96 h


title: Primary T cells, HIV-1 WT infection, donor 1, 96 h, replicate 1

description:
Library name: 18
18_R1.DeDup.sorted
Samples_18_22_26_vs_17_21_25_APA_BBstats.txt

value: HIV-1 WT infection, 96 h


title: EGME75_08

description: Library name: Library_08


title: C57BL/6 Cholangiocytes, 10 days DDC, Replicate 4

description:
Library name: DDC-M8
D10-R0-M8

value: 10 days DDC diet


title: EGME60_38

description: Library name: Library_38

value: 60 mg/kg/d EGME


title: C57BL/6 Cholangiocytes, 10 days DDC + 15 Days of Recovery (chow), Replicate 1

description:
Library name: R15-M10
D10-R15-M10


title: Abd_3

description:
Library name: Abd_3
RNA-seq

value: subcutaneous adipose tissues

value: F

value: Abd


title: C57BL/6 Cholangiocytes, 10 days DDC, Replicate 3

description:
Library name: DDC-M7
D10-R0-M7


title: EGME60_30

description: Library name: Library_30

value: spermatozoa

value: wild-type


title: Primary T cells, mock infected, donor 1, 96 h, replicate 1

description:
Library name: 17
17_R1.DeDup.sorted
Samples_18_22_26_vs_17_21_25_APA_BBstats.txt

value: Peripheral blood T lymphocytes

value: primary T cells

value: mock infected, 96 h


title: Thi_2

description:
Library name: Thi_2
RNA-seq


title: C57BL/6 Cholangiocytes, 10 days DDC, Replicate 2

description:
Library name: DDC-M6
D10-R0-M6

value: liver

value: cholangiocytes

value: wildtype


title: EGME75_23

description: Library name: Library_23

value: 75 mg/kg/d EGME


title: Glu_2

description:
Library name: Glu_2
RNA-seq

value: Glu


title: C57BL/6 Cholangiocytes, 10 days DDC, Replicate 1

description:
Library name: DDC-M5
D10-R0-M5

value: male


title: EGME60_29

description: Library name: Library_29


title: A549 CPSF6-KO clone C8 cells, mock infected, replicate 2

description:
Library name: 15
15_R1.DeDup.sorted
Samples_7_15_vs_1_9_APA_BBstats.txt

source_name: A549 cells CPSF6-KO

tag: cell line

value: A549 cells CPSF6-KO

value: Human lung carcinoma cell line

value: CPSF6 KO lines


title: Abd_4

description:
Library name: Abd_4
RNA-seq

value: subcutaneous adipose tissues

value: M


title: EGME60_21

description: Library name: Library_21

value: 60 mg/kg/d EGME


title: C57BL/6 Cholangiocytes, Control, Replicate 4

description:
Library name: CONTROL-M4
BL-D0-M4

value: chow diet


title: EGME60_22

description: Library name: Library_22

value: spermatozoa

value: wild-type


title: Thi_3

description:
Library name: Thi_3
RNA-seq

value: F

value: Thi


title: A549 CPSF6-KO clone B7 cells, mock infected, replicate 2

description:
Library name: 14
14_R1.DeDup.sorted
Samples_6_14_vs_1_9_APA_BBstats.txt


title: Primary T cells, HIV-1 A77V infection, donor 1, 96 h, replicate 1

description:
Library name: 20
20_R1.DeDup.sorted
Samples_20_24_28_vs_17_21_25_APA_BBstats.txt

value: Peripheral blood T lymphocytes

value: primary T cells

value: HIV-1 A77V infection, 96 h


title: EGME75_07

description: Library name: Library_07

value: 75 mg/kg/d EGME


title: A549 CPSF6-KO clone B4 cells, mock infected, replicate 2

description:
Library name: 13
13_R1.DeDup.sorted
Samples_5_13_vs_1_9_APA_BBstats.txt


title: EGME60_14

description: Library name: Library_14


title: C57BL/6 Cholangiocytes, Control, Replicate 2

description:
Library name: CONTROL-M2
BL-D0-M2

value: liver

value: cholangiocytes

value: wildtype


title: C57BL/6 Cholangiocytes, Control, Replicate 3

description:
Library name: CONTROL-M3
BL-D0-M3

value: male


title: EGME60_13

description: Library name: Library_13


title: Abd_2

description:
Library name: Abd_2
RNA-seq

value: Abd


title: C57BL/6 Cholangiocytes, Control, Replicate 1

description:
Library name: CONTROL-M1
BL-D0-M1


title: Abd_1

description:
Library name: Abd_1
RNA-seq

value: subcutaneous adipose tissues


title: A549 cells, HIV-1 N74D infection for 48 h, replicate 2

description:
Library name: 11
11_R1.DeDup.sorted
Samples_3_11_vs_1_9_APA_BBstats.txt

value: Human lung carcinoma cell line

value: WT

value: HIV-1 N74D infection, 48 hpi


title: Glu_1

description:
Library name: Glu_1
RNA-seq

value: Glu


title: A549 CPSF6-KO clone D5 cells, mock infected, replicate 2

description:
Library name: 16
16_R1.DeDup.sorted
Samples_8_16_vs_1_9_APA_BBstats.txt

value: A549 cells CPSF6-KO

value: CPSF6 KO lines


title: A549 cells, HIV-1 A77V infection for 48 h, replicate 2

description:
Library name: 12
12_R1.DeDup.sorted
Samples_4_12_vs_1_9_APA_BBstats.txt

value: HIV-1 A77V infection, 48 hpi


title: EGME60_06

description: Library name: Library_06

value: spermatozoa

value: wild-type

value: 60 mg/kg/d EGME


title: C11_PAME_2

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.28.1
Assembly: UCSC hg38
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

source_name: colon cancer TNM4

growth_protocol: Cells were cultured with DMEM/F12 medium with 5%FBS and 1% Pennicilin/Streptomycin

extract_protocol:
Total RNA extraction using TRIzol
Illumina TruSeq HT stranded mRNA

treatment_protocol: Cells were treated with Staurosporine (1μM)or DMSO for 6 hours, washed withPBS and treated for 5 days with DIDS(100μM) and Q-VD-Oph (10μM). Cells were replated and harvested at 7 days for RNA extraction.

value: colon cancer TNM4

value: clone C11 from CC14 primary culture

value: STS / DIDS/ Q-VD-Oph


title: A549 cells, HIV-1 WT infection for 48 h, replicate 2

description:
Library name: 10
10_R1.DeDup.sorted
Samples_2_10_vs_1_9_APA_BBstats.txt

value: HIV-1 WT infection, 40 hpi


title: EGME60_05

description: Library name: Library_05


title: KOD7-2

city: Chicago

first: Chen

last: Han

state: IL

address: 801 S. Paulina St.

department: Center for Wound healing and Tissue Regeneration

institute: University of Illinois Chicago

description:
Library name: Sample 12
10x Genomics

library_source: transcriptomic single cell

data_processing:
GEM generation, barcoding, post-GEM-RT cleanup, cDNA amplification, and cDNA library construction were performed using Single-cell 3′ v3 chemistry (10X Genomics, Pleasanton, California). Libraries were then sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA). Dead cell removal, cell counting and viability testing, GEM generation, barcoding, post-GEM-RT cleanup, cDNA amplification, library preparation, quality control, and sequencing were all performed by Novogene (Novogene America). Transcripts were mapped to the mouse reference genome (GRCm38/mm10) using Cell Ranger Version 7.0.0.
Before downstream analyses, low-quality cells were removed and data integration was performed using the RPCA method. Quality control metrics included keeping genes present in at least 10 cells and cells with at least 200 genes, while removing cells with either a mitochondrial gene expression greater than 10% or a multiplet likelihood score greater than 0.25. Post-quality control, 72,876 cells remained for downstream bioinformatic analyses. All data quality control and downstream analyses were done by us using R version 4.4.1 with Bioconductor v3.20.
Assembly: GRCm38/mm10
Supplementary files format and content: includes .RDS files for our integrated single-cell RNA seurat object and for the fibroblast subcluster seurat object
Supplementary files format and content: Includes .xlsx files for the FindAllMarkerGenes output used for cell type identification and fibroblast subcluster analysis in this manuscript
Supplementary files format and content: Includes .csv files for generated by our sc-RNA sequencing analysis of DEGs in Mfap5+/+ and Mfap5-/- mouse fibroblasts in this manuscript

source_name: Skin

extract_protocol:
Wound tissues were collected from male and female Mfap5+/+ or Mfap5-/- mice (n=4-5 animals for each sex and each experimental group) on days 0 (D0), 3 (D3), and 7 (D7) post-wounding. A total of 48-60 mice were used for single-cell RNA-sequencing. Collected wound tissues were pooled separately based on sex, experimental group, and time post-wounding. Tissue collected from D0 was considered NS. After collection and pooling, tissues were micro-dissected, minced, and incubated at 37°C in a dispase (Worthington Biochemical Corporation, Lakewood, NJ, Catalog # 9001-92-7)/liberase (Roche, Basel, Switzerland, Catalog # 5401135001) solution supplemented with DNAse I (Sigma-Aldrich, Catalog # D5025) and penicillin-streptomycin (Gibco, Waltham, MA, Catalog # 15-140-122) for 60 min with constant rotation. The final concentrations for each solution component were 3.6 mg/mL dispase, 30 µg/mL liberase, 100 µg/mL DNAse I, and 100 Units/mL-100 µg/mL penicillin-streptomycin. Post-incubation, cell suspensions were passed through a 40 µM cell strainer (ThermoFisher Scientific, Waltham, MA). Single-cell suspensions were treated with 1x RBC lysis buffer (Biolegend, San Diego, California, Catalog # 420301), washed, and resuspended in cold PBS before debris removal using the Debris Removal Solution (Miltenyi Biotec, North Rhine-Westphalia, Germany, Catalog # 130-109-398) according to the manufacturer’s protocol. All cells were then frozen in a mixture of 70% DMEM (Corning Inc, Corning, NY), 30% Fetal Bovine Serum (FBS) (GeminiBio, Sacremento, CA), and 10% DMSO (Sigma-Aldrich) before being sent to Novogene (Novogene America, Sacramento, CA). Thawed cell suspensions underwent dead cell removal, and only samples with >100,000 cells, >70% viability, and minimal to no cell clumps were used for single-cell RNA sequencing. GEM generation, barcoding, post-GEM-RT cleanup, cDNA amplification, and cDNA library construction were performed using Single-cell 3′ v3 chemistry (10X Genomics, Pleasanton, California). Libraries were then sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA). Dead cell removal, cell counting and viability testing, GEM generation, barcoding, post-GEM-RT cleanup, cDNA amplification, library preparation, quality control, and sequencing were all performed by Novogene (Novogene America). Transcripts were mapped to the mouse reference genome (GRCm38/mm10) using Cell Ranger Version 7.0.0.
cDNA library construction was performed using Single-cell 3′ v3 chemistry (10X Genomics, Pleasanton, California).
scRNA-seq

value: Skin

value: All

value: 8-10 weeks

value: Female

tag: strain

value: Mfap5-/- (KO)

value: D7 post-wounding


title: C11_PAME_1

value: WT


title: KOD7-1

description:
Library name: Sample 11
10x Genomics

value: Male


title: EGME50_36

description: Library name: Library_36

value: 50 mg/kg/d EGME


title: C11_CTRL_3

value: DMSO


title: A549 CPSF6-KO clone D5 cells, mock infected, replicate 1

description:
Library name: 8
8_R1.DeDup.sorted
Samples_8_16_vs_1_9_APA_BBstats.txt

value: A549 cells CPSF6-KO

value: Human lung carcinoma cell line

value: CPSF6 KO lines


title: WTD7-2

description:
Library name: Sample 10
10x Genomics

value: Mfap5+/+ (WT)


title: EGME50_35

description: Library name: Library_35

value: spermatozoa

value: wild-type


title: C11_CTRL_2

value: colon cancer TNM4

value: clone C11 from CC14 primary culture


title: EGME50_28

description: Library name: Library_28


title: WTD7-1

description:
Library name: Sample 9
10x Genomics

value: Skin

value: All


title: A549 CPSF6-KO clone C8 cells, mock infected, replicate 1

description:
Library name: 7
7_R1.DeDup.sorted
Samples_7_15_vs_1_9_APA_BBstats.txt


title: C11_PAME_3

value: STS / DIDS/ Q-VD-Oph


title: A549 CPSF6-KO clone B7 cells, mock infected, replicate 1

description:
Library name: 6
6_R1.DeDup.sorted
Samples_6_14_vs_1_9_APA_BBstats.txt


title: KOD3-2

description:
Library name: Sample 8
10x Genomics

value: 8-10 weeks

value: Female

value: Mfap5-/- (KO)

value: D3 post-wounding


title: C11_CTRL_1

value: WT


title: E3KO_3R

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.4
Assembly: UCSC hg38
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

treatment_protocol: No treatmment

value: colon cancer cell primary culture CC14 clone E8

value: KO


title: KOD3-1

description:
Library name: Sample 7
10x Genomics

value: Male


title: EGME50_20

description: Library name: Library_20

value: 50 mg/kg/d EGME


title: EGME50_27

description: Library name: Library_27


title: A549 cells, HIV-1 A77V infection for 48 h, replicate 1

description:
Library name: 4
4_R1.DeDup.sorted
Samples_4_12_vs_1_9_APA_BBstats.txt

value: Human lung carcinoma cell line

value: HIV-1 A77V infection, 48 hpi


title: EGME50_19

description: Library name: Library_19

value: spermatozoa

value: wild-type


title: WTD3-1

description:
Library name: Sample 5
10x Genomics

value: Mfap5+/+ (WT)


title: E3KO_2R

value: colon cancer TNM4

value: colon cancer cell primary culture CC14 clone E7


title: E3CTR_3R

value: colon cancer cell primary culture CC14 clone E5


title: A549 cells, mock infected, replicate 2

description:
Library name: 9
9_R1.DeDup.sorted
Samples_2_10_vs_1_9_APA_BBstats.txt

value: mock infected


title: KOD0-2

description:
Library name: Sample 4
10x Genomics

value: Skin

value: All

value: 8-10 weeks

value: D0 (Normal Skin - uninjured)


title: A549 cells, HIV-1 WT infection for 40 h, replicate 1

description:
Library name: 2
2_R1.DeDup.sorted
Samples_2_10_vs_1_9_APA_BBstats.txt

value: WT

value: HIV-1 WT infection, 40 hpi


title: A549 cells, HIV-1 N74D infection for 48 h, replicate 1

description:
Library name: 3
3_R1.DeDup.sorted
Samples_3_11_vs_1_9_APA_BBstats.txt

value: HIV-1 N74D infection, 48 hpi


title: EGME50_11

description: Library name: Library_11

value: 50 mg/kg/d EGME


title: E3CTR_2R

value: colon cancer cell primary culture CC14 clone E4


title: EGME50_12

description: Library name: Library_12


title: EGME50_04

description: Library name: Library_04


title: KOD0-1

description:
Library name: Sample 3
10x Genomics

value: Female

value: Mfap5-/- (KO)


title: E3CTR_1R

value: colon cancer cell primary culture CC14 clone E3


title: EGME50_03

description: Library name: Library_03

value: spermatozoa

value: wild-type


title: SH_R3

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.0
Assembly: UCSC hg38
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

source_name: colon

treatment_protocol: 50'000 cells were infected with empty or shATP11c containing pLKO.1 lentivector and selected using 5 ug/ml puromycin for 2 days.

value: colon

value: cc14 colon cancer cells primary culture clone E3

tag: Stage

tag: sample


title: E3KO_1R

value: colon cancer TNM4

value: colon cancer cell primary culture CC14 clone E6

value: KO


title: WTD0-2

description:
Library name: Sample 2
10x Genomics

value: Skin

value: All

value: 8-10 weeks

value: Mfap5+/+ (WT)


title: A549 cells, mock infected, replicate 1

description:
Library name: 1
1_R1.DeDup.sorted
Samples_2_10_vs_1_9_APA_BBstats.txt

value: Human lung carcinoma cell line

value: WT

value: mock infected


title: OlaparibSM08502_897

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

description:
Library name: SM_Ola_897
Human tumors grown in a mouse

data_processing:
RNA-sequencing data was analyzed by the Bioinformatics and Biostatistics Shared Resource of the University of Colorado Cancer Center (RRID:SCR_021983) using the nf-core/rnasplicing Nextflow pipeline version 1.0.3 26. The pipeline uses the STAR aligner to map sequence reads to the genome, in this case, human (GRCh38) and mouse (GRCm39) combined. The gene annotations used were from Ensembl release 104 (http://may2021.archive.ensembl.org/). Gene expression was quantified using Salmon and converted to a table with the tximport R package in the pipeline. Ensembl IDs in the raw-counts table were converted to gene names, and the counts of genes with multiple IDs were aggregated. Counts were normalized to counts per million (CPM) and genes with a mean count <1 CPM were excluded from differential gene expression analysis, which was performed using the limma R package (version 3.46.0) 27 with the voom function in R version 4.0.2 (https://www.R-project.org/). P-values were adjusted for multiple testing using the Benjamini-Hochberg method 28. Principal Component Analysis was performed with the prcomp function in R 4.0.2.  Splicing changes were analyzed using rMATS 29 and the DEXSeq R package 30 as part of the nf-core/rnasplicing pipeline.  Differential splicing events between treatments detected in rMATS using both junction counts and exon body counts (JCEC) with a false discovery rate (FDR) of 0.05 or less were counted for each of the five categories (skipped exon, retained intron, mutually exclusive exons, as well as alternative 5’ and 3’ splice sites). Pathway analyses were performed with the clusterProfiler R package (version 3.18.1) 31 using the msigdbr (version 7.5.1) database.
Assembly: GRCh38
Supplementary files format and content: Format: Excel File; Content: Counts per million

source_name: Tumor

growth_protocol: 5 million HGSC cancer cells were injected I.P. Tumors were allowed to established for 4-weeks.

extract_protocol:
RNA-easy column with Dnase digest
Qiagen Fast-select (Cat. #334375) and KAPA BioSystems mRNA HyperPrep Kit (Cat. #KK8581)

treatment_protocol: Tumor bearing mice were treated with vehicle, olaparib, SM08502, or in combination for 28 days. Tumors were weighed after 28 days and processed for RNA extraction.

value: Tumor

value: HGSC PDX Model

value: Mixed Cell (Tumor)


title: OlaparibSM08502_891

description:
Library name: SM_Ola_891
Human tumors grown in a mouse


title: WTD3-2

description:
Library name: Sample 6
10x Genomics

value: Female

value: D3 post-wounding


title: A549 CPSF6-KO clone B4 cells, mock infected, replicate 1

description:
Library name: 5
5_R1.DeDup.sorted
Samples_5_13_vs_1_9_APA_BBstats.txt

value: A549 cells CPSF6-KO

value: CPSF6 KO lines


title: SH_R2

value: colon

value: cc14 colon cancer cells primary culture clone E3


title: WTF-3

description:
Library name: Sample 12
Column Name in Raw_count.txt: WTF0_3

data_processing:
Clean data was obtained by using in-house perl scripts (Novogene America) to remove reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 (v2.0.5) was used to index and map reads to the mouse reference genome. The reference genome and gene model annotation files were downloaded from the genome website directly.
The mapped reads were assembled with StringTie (v1.3.3b).
Read numbers mapped to each gene were then counted in R with FeatureCounts (v1.5.0-p3) and an FPKM of each gene was calculated.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized FKPM values for each sample
Supplementary files format and content: Includes csv files of DESeq2 output for this manuscript's analysis.

growth_protocol: Cells were grown in DMEM (4.5 g/L glucose)/10% FBS/1x Pen-strep in a 6-well plate until 80-90% confluent.

extract_protocol:
Once cells reached 80-90% confluency, RNA was harvested using Trizol and purified with an RNA Clean & Concentrator-25 kit. 1 ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for by Novogene (Novogene America).

value: Fibroblasts

value: Baseline/Unijured


title: OlaparibSM08502_880

description:
Library name: SM_Ola_880
Human tumors grown in a mouse


title: EGME0_34

description: Library name: Library_34

value: spermatozoa

value: wild-type

value: water (vehicle control)


title: SH_R1


title: WTD0-1

description:
Library name: Sample 1
10x Genomics

value: Skin

value: All

value: 8-10 weeks

value: Male

value: Mfap5+/+ (WT)

value: D0 (Normal Skin - uninjured)


title: EGME0_33

description: Library name: Library_33


title: OlaparibSM08502_879

description:
Library name: SM_Ola_879
Human tumors grown in a mouse

value: Tumor

value: HGSC PDX Model

value: Mixed Cell (Tumor)


title: WTF-2

description:
Library name: Sample 11
Column Name in Raw_count.txt: WTF0_2

value: Female

value: WT


title: WTF-1

description:
Library name: Sample 10
Column Name in Raw_count.txt: WTF0_1


title: EGME0_26

description: Library name: Library_26


title: SM08502_940

description:
Library name: SM08502_940
Human tumors grown in a mouse


title: EGME0_25

description: Library name: Library_25


title: CTR_R2

value: colon

value: cc14 colon cancer cells primary culture clone E3

value: control


title: WTM-3

description:
Library name: Sample 9
Column Name in Raw_count.txt: WTM0_3

value: Fibroblasts

value: Baseline/Unijured


title: SM08502_895

description:
Library name: SM08502_895
Human tumors grown in a mouse


title: EGME0_18

description: Library name: Library_18

value: spermatozoa

value: wild-type

value: water (vehicle control)


title: CTR_R1


title: WTM-2

description:
Library name: Sample 8
Column Name in Raw_count.txt: WTM0_2

value: Skin


title: SM08502_877

description:
Library name: SM08502_877
Human tumors grown in a mouse


title: EGME0_17

description: Library name: Library_17


title: WTM-1

description:
Library name: Sample 7
Column Name in Raw_count.txt: WTM0_1

value: Male


title: EGME0_10

description: Library name: Library_10


title: new_929_3

treatment_protocol: No treatment


title: EGME0_09

description: Library name: Library_09


title: Olaparib_899

description:
Library name: Olaparib_899
Human tumors grown in a mouse


title: new_929_2


title: CTR_R3


title: SM08502_863

description:
Library name: SM08502_863
Human tumors grown in a mouse


title: KOF-3

description:
Library name: Sample 6
Column Name in Raw_count.txt: KOF0_3

value: KO


title: KOF-2

description:
Library name: Sample 5
Column Name in Raw_count.txt: KOF0_2


title: EGME0_01

description: Library name: Library_01


title: new_P3E3_2


title: Olaparib_890

description:
Library name: Olaparib_890
Human tumors grown in a mouse


title: new_929_1


title: EGME0_02

description: Library name: Library_02


title: new_P3E3_3


title: TG NM 3

city: Seoul

first: Eun-Jin

last: Bae

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

description:
Library name: Sample 9
TG_treated 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped and counted busing Bowtie2 (parameter- Quality limit: 0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy FFPE kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  QuantSeq library prep kit following manufacturer's protocols.

value: Brain

value: Oligodendrocyte

value: TG


title: new_P3E3_1


title: KOM-3

description:
Library name: Sample 3
Column Name in Raw_count.txt: KOM0_3


title: KOM-2

description:
Library name: Sample 2
Column Name in Raw_count.txt: KOM0_2


title: KOF-1

description:
Library name: Sample 4
Column Name in Raw_count.txt: KOF0_1


title: Olaparib_875

description:
Library name: Olaparib_875
Human tumors grown in a mouse

value: Tumor

value: HGSC PDX Model

value: Mixed Cell (Tumor)


title: Control_896

description:
Library name: Control_896
Human tumors grown in a mouse


title: TG NM 2

description:
Library name: Sample 8
TG_treated 2


title: Olaparib_797

description:
Library name: Olaparib_797
Human tumors grown in a mouse


title: cl29_3

value: colon

value: CC36 colon cancer cells primary culture clone 29


title: KOM-1

description:
Library name: Sample 1
Column Name in Raw_count.txt: KOM0_1


title: Control_894

description:
Library name: Control_894
Human tumors grown in a mouse


title: TG NM 1

description:
Library name: Sample 7
TG_treated 1


title: cl29_2


title: PCLS from mouse fed DDC diet for 3 weeks

city: Trieste

first: Davide

last: Selvestrel

address: Padriciano 99

country: Italy

institute: International Centre for Genetic Engeneering and Biotechnology (ICGEB)

description:
Library name: DDC_sn_PCLS
Singleron

data_processing:
Illumina-compatible NGS libraries generated were sequenced on an Illumina NovaSeq 6000 instrument using a paired-end 150bp approach. The reads were demultiplexed on Illumina’s BaseCloud, and fastq files were used to initiate data analysis.
All the sampleswere mapped and expression levels summarized using Celescope pipeline version 2.3.0.
Assembly: Human samples were mapped against the GRCh38.v1.8.0 version of the Homo sapiens genome, while mouse sample was mapped against the Mus musculus GRCm39.v1.8.0 reference genome.
Supplementary files format and content: DDC_sn_PCLS.Rda - Rda file containing mouse snRNAseq data as Seurat object
Supplementary files format and content: Human_sn_PCLS.Rda - Rda file containing human snRNAseq  data as Seurat object. Human_sc_PCLS.Rda - Rda file containing human scRNAseq  data as Seurat object

source_name: PCLS in EM for 96 h

growth_protocol: Human and mouse PCLS were cultured ex vivo

extract_protocol:
The single nuclei suspension from liver tissue was obtained using GEXSCOPE® Single Nucleus RNA Library Kit V2 (Singleron Biotechnologies). Briefly, on ice the tissue was immersed in 1ml of cold nucleus separation solution and cut into small pieces. Further homogenization was achieved by performing 10 strokes with a loose pestle (pestle A) and a tight pestle (Pestle B) (KIMBLE® KONTES® Dounce Tissue Grinder, cat. nr. 885300-0002).  The sample was then incubated on ice for 15 minutes where the state of nuclei extraction was monitored every 5 minutes under a light microscope. Following extraction, the nuclei suspension was filtered using a 30-µm sterile strainer (Miltenyi, cat. nr.130-098-458). The nuclei suspension was centrifuged at 200xg for 2 minutes at 4°C, and the supernatant was centrifuged at 500xg for 5 minutes at 4°C. The resulting pellet containing nuclei was resuspended in 0.25 ml of cold nuclei suspension buffer. The quality of the nuclei was assessed by Trypan Blue staining (0.4% w/v, Gibco) under a light microscope. The nuclei were counted using acridine/propidium iodide with a Luna FX7 automated cell counter (Logos Biosystems, Villeneuve d’Ascq, France).
A total of 45 000 nuclei were loaded onto a microfluidic chip (Singleron GEXSCOPE® Single Nucleus RNA Library Kit V2) for a minimal capture of 10 000 nuclei. Briefly, barcoded beads containing a unique Cell Barcode were loaded into the chip, and nuclei were lysed. After nuclei lysis, polyadenylated RNA was captured onto the Barcode Beads by the poly (dT) sequence. Barcode Beads with captured mRNA molecules were collected and subjected to reverse transcription reaction. The cDNA was then amplified and QC. For scRNA-seq, six human PCLS cultured for 144 hours were collected and dissociated for 3 minutes with TriplE. The digestion was stopped, and the cells were washed three times with PBS. A suspension of 3.5 × 10⁵ cells/mL was prepared in PBS, and the cells underwent library preparation. The scRNA-seq libraries were constructed using the GEXSCOPE® Single Cell RNA Library Kit (Singleron Biotechnology) following the manufacturer's protocol for a minimal capture of 10.000 cells.

value: PCLS in EM for 96 h

value: Liver cells

value: WT

value: DDC diet (3 weeks)


title: TG 3

description:
Library name: Sample 6
TG placebo 3

value: Placebo


title: Control_860

description:
Library name: Control_860
Human tumors grown in a mouse


title: cl29_1


title: EC_WT_ALL_G18

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

description:
Library name: M4108
rawcounts_paper2025_EC-male.txt

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 109
Assembly: mm39
Supplementary files format and content: .csv files including annotation raw counts (output of featureCounts) for each sample

source_name: murine endothelial cell

growth_protocol: Murine vascular smooth muscle cell culture Primary culture of murine VSMC were obtained from knock-out (KO) and wild-type (WT) mice, accord-ing to Ray et al. {5492} and as described before {5759, 6174, 7287}. Thoracic and abdominal aorta was excised in 0.9% sterile NaCl, cleared from blood as well as surrounding tissue and rinsed several times. Subsequently the aorta was transferred to DMEM-Medium (+10% fetal calf serum, FCS), reduced me-chanically to small pieces and digested in collagenase 2 (in DMEM, 4-6 h at 37°C, 5% CO2). Thereafter cells were gently dispersed and rinsed with medium. After 5 min centrifugation at 300xg at room tem-perature the cell pellet was resuspended in 5 ml fresh medium and centrifuged a second time. Finally, the cells were seeded in plastic dishes in DMEM, containing 10% serum and incubated for 5 days at 37°C, 5 % CO2. The VSMC purity achieved by our protocol was previously tested {5759, 6174, 7287}. VSMC were cultivated in DMEM media (low-glucose media powder diluted in H2O, with 2 g/L NaHCO3, pH 7.4) supplemented with 10% FCS and 10 ng/ml bFGF. Before all experiments, the cells were syn-chronized by incubation in serum and supplement-free DMEM media for 24 h. The latter was also used for further incubations with obesity-associated stressors (see below). All experiments were performed on cells that underwent up to 7 passages. Murine endothelial cell culture Heart and lungs were removed from the thorax and placed in a 60 mm Petri dish with Krebs-buffer (NaCl 6.9 g/l, KCl 0.35 g/l, CaCl2 0.26 g/l, MgSO4 0.296 g/l, NaH2PO4 0.144 g/l). Hearts were carefully separated from the lungs, perfused and transferred to a separate 60 mm Petri dish with 6 ml enzyme solution (35 ml DMEM + 0.1 U/ml collagenase B + 0.8 U/ml Dispase + 20 µg/ml DNase). The organ was cut into small pieces, placed in the incubator at 37°C / 5% CO2 for 60 minutes with intermediate mixing. Subsequently the material was placed on 70 µm filter, rinsed with 8 ml medium and centrifuged for 5 minutes at 300 g and 20°C. Cells were then suspended in 1 ml 150 mM NH4Cl + 10 mM KHCO3 + 0.1 mM EDTA at pH 7.3. After 30 seconds 9 ml medium were added and the entire solution centrifuged for 5 minutes at 300 g and 20°C. Cells were then suspended in 90 µl MCS buffer (0.5 % BSA + 2 mM EDTA in PBS, pH 7.2), 20 µl CD45 beads (Miltenyi Biotec), incubated for 15 minutes at 4°C and after the addition of 1 ml MCS buffer centrifuged for 5 min at 300 g and 20°C. Size M column was placed on the magnet, rinsed with 1 ml MCS buffer followed by the addition of the cell pellet in 500 µl MCS buffer. Columns were washed three times with 500 µl MCS buffer and the flow-through collected (CD45- cells). After centrifugation for 5 min at 300 g and 20°C the pellet was resuspended in 90 µl MCS buffer, 20 µl CD31 beads added and the whole was incubated for 15 minutes at 4°C. After addition of 1 ml MCS buffer and centrifugation for 5 minutes at 300 g and 20°C the cell pellet (resuspended in 500 µl MCS buffer) was added to a M-size column placed on a magnet. Columns were washed 3 times with 500 µl MCS buffer. Thereafter columns were removed from the magnet, placed on a new 15 ml tube, 2 ml MCS buffer added and the cells pressed out with the plunger squeeze (CD45-/CD31+ cells). After centrifugation for 5 min at 350 g and 20°C the cell pellet was dissolved in 1 ml of medium, placed on a fibronectin-coated 35 mm Petri dish in 1 ml of fresh DMEM medium and incubated at 5% CO2 and 37°C. After reaching 80-90% conflu-ence cells were washed with EDTA, detached with 0.5 ml of trypsin (3-5 min in the incubator) followed by stopping with 1.2 ml DMEM medium. After centrifugation for 5 min at 350 g and 20°C the cell pellet was dissolved in 90 µl of MCS buffer and 20 µl of CD31 beads were added for a second round of clean-up (see above).

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. To remove eventual DNA contamination traces, RNA samples were cleaned-up with NEB Monarch Total RNA mini prep kit (#T2010S), following the procedure for "TRIZOL extracted samples.
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were exposed to for 24h  to 20 mM glucose + 100 µM free fatty acids (HG+FFA) or 30 nM angiotensin II + 300 nM epinephrine (AII+NA) or all four stressors together (ALL).

tag: samplegroupe

value: male

value: murine endothelial cell

value: C57BL/6 mice

tag: animalid

tag: cell genotype

value: ALL


title: EC_WT_HG+FFS_G18

description:
Library name: M4106
rawcounts_paper2025_EC-male.txt

value: HG+FFS


title: TG 1

description:
Library name: Sample 4
TG placebo 1

value: Brain

value: Oligodendrocyte


title: TG 2

description:
Library name: Sample 5
TG placebo 2

value: TG


title: cl28_3

value: CC36 colon cancer cells primary culture clone 28


title: cl28_2


title: WT 3

description:
Library name: Sample 3
WT placebo 3


title: siSHMT2-2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

description: Library name: Sample5

data_processing:
After obtaining the raw RNA-seq reads, the quality of raw reads was checked using FastQC software (version 0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw paired-end reads were subjected to trimming and quality control using fastp (version 0.23.4) with default parameters (Chen, Zhou et al. 2018). The quality filtered reads were then aligned separately to the reference genome via HISAT2 software (version 2.2.1) (Kim, Paggi et al. 2019). Transcriptome changes were analyzed by DESeq2 package (version 1.42.1) and curated by manual and automated methods (Love, Huber et al. 2014). We finally selected differentially expressed genes (DEGs) with criteria fold change > 2 and adjusted p-value < 0.01. Gene function and pathway enrichment of GO and KEGG were performed using clusterProfiler package (version 4.10.1) (Wu, Hu et al. 2021).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The HT-1376 cells were cultured at 37 °C with 5% CO2 in Leibovitz’s L-15 with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
we took 1.5 μg of qualified total RNA for RNA-seq library preparation, VAHTS mRNA capture beads 2.0 (N403, Vazyme, Nanjing, China) was used to capture and purify total RNA
VAHTS Universal V8 RNA seq Library Prep Kit for Illumina (NR605, Vazyme) was used to prepare RNA-seq chain specific libraries through fragmentation, first strand synthesis, second strand synthesis, end repair, linker ligation, amplification, purification, and other steps. Finally, we used Qubit 4.0 (ThermoFisher, Waltham, Massachusetts, USA) for library concentration quantification and stored the libraries at -80 ℃ in a refrigerator.

value: bladder cancer cells

value: SHMT2  knockdown


title: siSHMT2-1

description: Library name: Sample4


title: cl28_1

value: colon


title: EC_WT_ALL_G17

description:
Library name: M4104
rawcounts_paper2025_EC-male.txt


title: EC_WT_Control_G18

description:
Library name: M4105
rawcounts_paper2025_EC-male.txt

value: Control


title: WT 1

description:
Library name: Sample 1
WT placebo 1


title: WT 2

description:
Library name: Sample 2
WT placebo 2


title: cl27_3

value: CC36 colon cancer cells primary culture clone 27


title: cl27_2


title: EC_WT_AII+NA_G17

description:
Library name: M4103
rawcounts_paper2025_EC-male.txt

value: WT

value: AII+NA


title: siNC-3

description: Library name: Sample3


title: cl27_1


title: 991T

city: Tokyo

first: Yu-Yu

last: Liu

address: 5-1-1 Tsukiji, Chūō district

country: Japan

institute: National Cancer Center Research Institute

description:
Library name: RCC991TA
Column name in GEOrsem_expected_count.csv: RCC991TA

data_processing:
The sequencing data were subjected to quality control filtering, trimming, and adapter removal using fastp (v0.24.0) with default parameters.
The filtered paired-end reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b), and gene-level read counts were quantified using RNA-Seq by Expectation-Maximization (v1.3.1).
Genes with FDR < 0.05 and log Fold-change > 1 or < -1 were considered as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: csv file includes rsem expected count for each sample
Supplementary files format and content: Tab delimited files including rsem results for each sample

source_name: Clear cell renal cell carcinoma

extract_protocol:
For samples processed at Macrogen, total RNA was extracted using QIAzol Lysis reagent (QIAGEN). For samples processed at BGI, total RNA was extracted using TRIzol Reagent (Invitrogen).
For samples processed at Macrogen, libraries were constructed from the total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). For samples processed at BGI, libraries were prepared using the DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

value: Clear cell renal cell carcinoma


title: siNC-2

description: Library name: Sample2


title: EC_WT_HG+FFS_G17

description:
Library name: M4102
rawcounts_paper2025_EC-male.txt

value: male


title: Control_881

description:
Library name: Control_881
Human tumors grown in a mouse

value: Tumor

value: HGSC PDX Model

value: Mixed Cell (Tumor)


title: siNC-1

description: Library name: Sample1


title: EC_WT_AII+NA_G18

description:
Library name: M4107
rawcounts_paper2025_EC-male.txt

value: murine endothelial cell

value: C57BL/6 mice


title: siSHMT2-3

description: Library name: Sample6


title: cl26_3

value: CC36 colon cancer cells primary culture clone 26


title: EC_WT_Control_G17

description:
Library name: M4101
rawcounts_paper2025_EC-male.txt


title: 870T

description:
Library name: RCC870TA
Column name in GEOrsem_expected_count.csv: RCC870TA

source_name: TFE3-rearranged/TFEB-altered renal cell carcinoma


title: HAECs, AdCEBPB, Flag, rep2

city: Hangzhou

first: Cong

last: Qiu

state: Zhejiang

address: No.866 Yuhangtang Road

institute: Zhejiang University

library_source: genomic

data_processing:
Reads obtained from the sequencing machines were filtered by Cutadapt (v1.12).
We aligned reads of all samples to the research species reference genome using bowtie2 (v2.2.9).
bigWig files were generated using the deeptools (v3.5.1)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Human aortic endothelial cells

extract_protocol:
The CUT&Tag was performed by Hyperactive Universal CUT&Tag Assay Kit for Illumina kit (Vazyme Biotech, TD904) according to the manufacturer's protocol
The libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illunina (Vazyme Biotech, TD904-01) according to the manufacturer's protocol.

value: Human aortic endothelial cells

value: CEBPB overexpression

tag: cut&tag antibody

value: Flag-tag (Abmart, M20008)


title: 73T

description:
Library name: RCC73T
Column name in GEOrsem_expected_count.csv: RCC73T

tag: tissue


title: EC_WT_ALL_G16

description:
Library name: M3108
rawcounts_paper2025_EC-male.txt

tag: Sex

value: ALL


title: 692T

description:
Library name: RCC692TA
Column name in GEOrsem_expected_count.csv: RCC692TA


title: cl26_1

value: colon


title: cl26_2


title: HAECs, AdCEBPB, Flag, rep1


title: EC_WT_AII+NA_G16

description:
Library name: M3107
rawcounts_paper2025_EC-male.txt


title: HAECs, AdControl, Flag, rep2


title: cl24_3

value: CC36 colon cancer cells primary culture clone 24


title: EC_WT_HG+FFS_G16

description:
Library name: M3106
rawcounts_paper2025_EC-male.txt

value: HG+FFS


title: HAECs, AdControl, Flag, rep1

value: WT


title: EC_WT_Control_G16

description:
Library name: M3105
rawcounts_paper2025_EC-male.txt

value: Control


title: 48T

description:
Library name: RCC48TA
Column name in GEOrsem_expected_count.csv: RCC48TA

value: Clear cell renal cell carcinoma


title: 255T

description:
Library name: RCC255TA
Column name in GEOrsem_expected_count.csv: RCC255TA


title: cl24_2


title: 24T

description:
Library name: RCC24TA
Column name in GEOrsem_expected_count.csv: RCC24TA


title: cl24_1


title: EC_WT_ALL_G15

description:
Library name: M3104
rawcounts_paper2025_EC-male.txt

value: male


title: HAECs, AdCEBPB, IgG, rep2

value: Mouse IgG (Abmart, B30010)


title: 167T

description:
Library name: RCC167TA
Column name in GEOrsem_expected_count.csv: RCC167TA


title: HAECs, AdCEBPB, IgG, rep1


title: cl20_3

value: CC36 colon cancer cells primary culture clone 20


title: EC_WT_HG+FFS_G15

description:
Library name: M3102
rawcounts_paper2025_EC-male.txt


title: NSC34_TX_6, NSC34 ,Treatment-co-culture

city: Richmond

first: Michael

last: McClure

state: VA

address: 601 W. Main St.

institute: Virginia Commonwealth University

description:
Library name: NSC_TX_6
Column name in NSC34_all_counts.txt: NSC34_TX_6

data_processing:
Oxford Nanopore MinKNOW software
Assembly: GRCm38
Supplementary files format and content: Tab deliminated raw count file(s).

source_name: Motor Neuron

extract_protocol:
Standard Trizol total RNA extraction.
Standard minION library prep.

value: Motor Neuron

value: Treatment, Co-culture


title: cl20_2


title: EC_WT_Control_G15

description:
Library name: M3101
rawcounts_paper2025_EC-male.txt

value: murine endothelial cell

value: C57BL/6 mice


title: 163T

description:
Library name: RCC163TA
Column name in GEOrsem_expected_count.csv: RCC163TA


title: NSC34_TX_5, NSC34 ,Treatment-co-culture

description:
Library name: NSC_TX_5
Column name in NSC34_all_counts.txt: NSC34_TX_5


title: EC_WT_ALL_G14

description:
Library name: M2116
rawcounts_paper2025_EC-male.txt


title: 110T

description:
Library name: RCC110TA
Column name in GEOrsem_expected_count.csv: RCC110TA


title: cl20_1


title: cl16_3

value: CC36 colon cancer cells primary culture clone 16


title: NSC34_TX_3, NSC34 ,Treatment-co-culture

description:
Library name: NSC_TX_3
Column name in NSC34_all_counts.txt: NSC34_TX_3


title: EC_WT_AII+NA_G14

description:
Library name: M2115
rawcounts_paper2025_EC-male.txt

value: AII+NA


title: 937T

description:
Library name: 937T_23000733A
Column name in GEOrsem_expected_count.csv: 937T_23000733A

source_name: Chromophobe renal cell carcinoma

value: Chromophobe renal cell carcinoma


title: cl16_2


title: 936T

description:
Library name: 936T_23000732A
Column name in GEOrsem_expected_count.csv: 936T_23000732A


title: 933T

description:
Library name: 933T_23000731A
Column name in GEOrsem_expected_count.csv: 933T_23000731A


title: EC_WT_HG+FFS_G14

description:
Library name: M2114
rawcounts_paper2025_EC-male.txt


title: NSC34_TX_2, NSC34 ,Treatment-co-culture

description:
Library name: NSC_TX_2
Column name in NSC34_all_counts.txt: NSC34_TX_2


title: NSC34_TX_1, NSC34 ,Treatment-co-culture

description:
Library name: NSC_TX_1
Column name in NSC34_all_counts.txt: NSC34_TX_1


title: 930T

description:
Library name: 930T_23000730A
Column name in GEOrsem_expected_count.csv: 930T_23000730A


title: cl16_1


title: EC_WT_ALL_G13

description:
Library name: M2112
rawcounts_paper2025_EC-male.txt

value: ALL


title: cl15_3

value: colon

value: CC36 colon cancer cells primary culture clone 15


title: NSC34_C_6, NSC34 ,Control-No co-culture

description:
Library name: NSC_C_6
Column name in NSC34_all_counts.txt: NSC34_C_6

value: Control, No Co-culture


title: 929T

description:
Library name: 929T_23000729A
Column name in GEOrsem_expected_count.csv: 929T_23000729A


title: EC_WT_AII+NA_G13

description:
Library name: M2111
rawcounts_paper2025_EC-male.txt

value: WT


title: NSC34_C_5, NSC34 ,Control-No co-culture

description:
Library name: NSC_C_5
Column name in NSC34_all_counts.txt: NSC34_C_5


title: 928T

description:
Library name: 928T_23000728A
Column name in GEOrsem_expected_count.csv: 928T_23000728A


title: cl15_2


title: cl15_1


title: NSC34_TX_4, NSC34 ,Treatment-co-culture

description:
Library name: NSC_TX_4
Column name in NSC34_all_counts.txt: NSC34_TX_4


title: EC_WT_HG+FFS_G13

description:
Library name: M2110
rawcounts_paper2025_EC-male.txt

value: HG+FFS


title: 926T

description:
Library name: 926T_23000727A
Column name in GEOrsem_expected_count.csv: 926T_23000727A


title: NSC34_C_4, NSC34 ,Control-No co-culture

description:
Library name: NSC_C_4
Column name in NSC34_all_counts.txt: NSC34_C_4


title: EC_WT_Control_G13

description:
Library name: M2109
rawcounts_paper2025_EC-male.txt

value: Control


title: NSC34_C_2, NSC34 ,Control-No co-culture

description:
Library name: NSC_C_2
Column name in NSC34_all_counts.txt: NSC34_C_2


title: cl13_2

value: CC36 colon cancer cells primary culture clone 13


title: 921T

description:
Library name: 921T_23000725A
Column name in GEOrsem_expected_count.csv: 921T_23000725A


title: EC_WT_ALL_G12

description:
Library name: M2108
rawcounts_paper2025_EC-male.txt

value: male


title: 924T

description:
Library name: 924T_23000726A
Column name in GEOrsem_expected_count.csv: 924T_23000726A

source_name: Fumarate hydratase deficient renal cell carcinoma


title: cl13_3


title: EC_WT_Control_G14

description:
Library name: M2113
rawcounts_paper2025_EC-male.txt


title: cl13_1


title: NSC34_C_3, NSC34 ,Control-No co-culture

description:
Library name: NSC_C_3
Column name in NSC34_all_counts.txt: NSC34_C_3


title: 918T

description:
Library name: 918T_23000724A
Column name in GEOrsem_expected_count.csv: 918T_23000724A

value: Clear cell renal cell carcinoma


title: 900T

description:
Library name: 900T_23000723A
Column name in GEOrsem_expected_count.csv: 900T_23000723A


title: C2C12_TX_6, C2C12 ,Treatment-co-culture

description:
Library name: C2C12_TX_6
Column name in C2C12_all_counts.txt: C2C12_TX_6

source_name: Myoblast Cells

value: Myoblast Cells

value: Myoblast


title: EC_WT_HG+FFS_G12

description:
Library name: M2106
rawcounts_paper2025_EC-male.txt

value: murine endothelial cell


title: EC_WT_AII+NA_G12

description:
Library name: M2107
rawcounts_paper2025_EC-male.txt

value: C57BL/6 mice


title: EC_WT_Control_G12

description:
Library name: M2105
rawcounts_paper2025_EC-male.txt


title: C2C12_TX_5, C2C12 ,Treatment-co-culture

description:
Library name: C2C12_TX_5
Column name in C2C12_all_counts.txt: C2C12_TX_5

value: Treatment, Co-culture


title: cl12_1

value: CC36 colon cancer cells primary culture clone 12


title: 895T

description:
Library name: 895T_23000722A
Column name in GEOrsem_expected_count.csv: 895T_23000722A


title: C2C12_TX_4, C2C12 ,Treatment-co-culture

description:
Library name: C2C12_TX_4
Column name in C2C12_all_counts.txt: C2C12_TX_4


title: 890T

description:
Library name: 890T_23000721A
Column name in GEOrsem_expected_count.csv: 890T_23000721A


title: cl07_3

value: CC36 colon cancer cells primary culture clone 7


title: C2C12_TX_3, C2C12 ,Treatment-co-culture

description:
Library name: C2C12_TX_3
Column name in C2C12_all_counts.txt: C2C12_TX_3


title: EC_WT_AII+NA_G11

description:
Library name: M2103
rawcounts_paper2025_EC-male.txt

value: AII+NA


title: EC_WT_ALL_G11

description:
Library name: M2104
rawcounts_paper2025_EC-male.txt

value: ALL


title: 883T

description:
Library name: 883T_23000720A
Column name in GEOrsem_expected_count.csv: 883T_23000720A


title: EC_WT_HG+FFS_G11

description:
Library name: M2102
rawcounts_paper2025_EC-male.txt


title: EC_WT_Control_G11

description:
Library name: M2101
rawcounts_paper2025_EC-male.txt


title: C2C12_TX_1, C2C12 ,Treatment-co-culture

description:
Library name: C2C12_TX_1
Column name in C2C12_all_counts.txt: C2C12_TX_1


title: cl12_3

value: colon


title: cl07_2


title: cl07_1


title: NSC34_C_1, NSC34 ,Control-No co-culture

description:
Library name: NSC_C_1
Column name in NSC34_all_counts.txt: NSC34_C_1

value: Motor Neuron

value: Control, No Co-culture


title: C2C12_C_6, C2C12 ,Control-No co-culture

description:
Library name: C2C12_C_6
Column name in C2C12_all_counts.txt: C2C12_C_6

value: WT


title: cl12_2


title: EC_WT_AII+NA_G10

description:
Library name: M1115
rawcounts_paper2025_EC-male.txt


title: cl06_3

value: CC36 colon cancer cells primary culture clone 6


title: C2C12_C_5, C2C12 ,Control-No co-culture

description:
Library name: C2C12_C_5
Column name in C2C12_all_counts.txt: C2C12_C_5


title: 873T

description:
Library name: 873T_23000717A
Column name in GEOrsem_expected_count.csv: 873T_23000717A


title: EC_WT_ALL_G10

description:
Library name: M1116
rawcounts_paper2025_EC-male.txt


title: cl06_2


title: cl06_1


title: 848T

description:
Library name: 848TA
Column name in GEOrsem_expected_count.csv: 848TA


title: cl05_3

value: CC36 colon cancer cells primary culture clone 5


title: EC_WT_ALL_G9

description:
Library name: M1112
rawcounts_paper2025_EC-male.txt

value: male


title: C2C12_C_3, C2C12 ,Control-No co-culture

description:
Library name: C2C12_C_3
Column name in C2C12_all_counts.txt: C2C12_C_3


title: cl05_2


title: 843T

description:
Library name: 843TA
Column name in GEOrsem_expected_count.csv: 843TA

value: Clear cell renal cell carcinoma


title: 877T

description:
Library name: 877T_23000718A
Column name in GEOrsem_expected_count.csv: 877T_23000718A


title: EC_WT_AII+NA_G9

description:
Library name: M1111
rawcounts_paper2025_EC-male.txt


title: C2C12_TX_2, C2C12 ,Treatment-co-culture

description:
Library name: C2C12_TX_2
Column name in C2C12_all_counts.txt: C2C12_TX_2

value: Myoblast Cells


title: C2C12_C_2, C2C12 ,Control-No co-culture

description:
Library name: C2C12_C_2
Column name in C2C12_all_counts.txt: C2C12_C_2

value: Myoblast


title: 882T

description:
Library name: 882T_23000719A
Column name in GEOrsem_expected_count.csv: 882T_23000719A


title: C2C12_C_1, C2C12 ,Control-No co-culture

description:
Library name: C2C12_C_1
Column name in C2C12_all_counts.txt: C2C12_C_1


title: EC_WT_HG+FFS_G9

description:
Library name: M1110
rawcounts_paper2025_EC-male.txt

value: murine endothelial cell

value: HG+FFS


title: EC_WT_Control_G9

description:
Library name: M1109
rawcounts_paper2025_EC-male.txt

value: C57BL/6 mice

value: Control


title: cl03_2

value: CC36 colon cancer cells primary culture clone 3


title: 838T

description:
Library name: 838TA
Column name in GEOrsem_expected_count.csv: 838TA


title: 841T

description:
Library name: 841T_23000715A
Column name in GEOrsem_expected_count.csv: 841T_23000715A


title: 857T

description:
Library name: 857TA
Column name in GEOrsem_expected_count.csv: 857TA


title: cl03_3


title: 842T

description:
Library name: 842TA
Column name in GEOrsem_expected_count.csv: 842TA


title: C2C12_C_4, C2C12 ,Control-No co-culture

description:
Library name: C2C12_C_4
Column name in C2C12_all_counts.txt: C2C12_C_4


title: RORB_2

first: Qiangsong

last: Tong

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description:
Library name: Sample 4
Genomic DNA immunoprecipitated by RORB antibody replicate 2

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to reference genome of homo sapiens using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for reads distribution analysis. The MACS2 software (Version 2.1.1) was used for peak calling. The bedtools (Version 2.25.0) was used for peaks annotation and peak distribution analysis.
Assembly: hg38
Supplementary files format and content: Read densities were visualized by preparing normalized BigWig files using HOMER.

growth_protocol: Human neuroblastoma cell line SK-N-BE(2) was grown in DMEM/F12 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on HiSeq X Ten sequencer (Illumina).

treatment_protocol: Cells were fixed in 1% formaldehyde for 10 min at room temperature, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction.

value: neuroblastoma cells


title: cl05_1


title: VSMC_KOsmc_ALL_G8

description:
Library name: M7116
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

source_name: murine vascular smooth muscle cell

value: murine vascular smooth muscle cell

value: EGFR-KOsmc

value: ALL


title: 836T

description:
Library name: 836TA
Column name in GEOrsem_expected_count.csv: 836TA


title: 818T

description:
Library name: 818TA
Column name in GEOrsem_expected_count.csv: 818TA


title: cl02_3

value: colon

value: CC36 colon cancer cells primary culture clone 2


title: EC_WT_HG+FFS_G10

description:
Library name: M1114
rawcounts_paper2025_EC-male.txt

value: WT


title: VSMC_KOsmc_HG+FFS_G8

description:
Library name: M7114
rawcounts_paper2025_SMC-mono-KOsmc-male.txt


title: Input_1

description:
Library name: Sample 1
Input genomic DNA replicate 1


title: cl02_2


title: 811T

description:
Library name: 811TA
Column name in GEOrsem_expected_count.csv: 811TA


title: VSMC_KOsmc_Control_G8

description:
Library name: M7113
rawcounts_paper2025_SMC-mono-KOsmc-male.txt


title: 801T

description:
Library name: 801TA
Column name in GEOrsem_expected_count.csv: 801TA


title: RORB_RNA-seq_2

description:
Library name: Sample 4
Gene expression after stable transfection of RORB replicate 2

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 quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were stably transfected with empty vector or RORB construct.

value: SK-N-BE(2) cells stably transfected with RORB


title: VSMC_KOsmc_ALL_G7

description:
Library name: M7112
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: male


title: RORB_RNA-seq_1

description:
Library name: Sample 3
Gene expression after stable transfection of RORB replicate 1


title: cl02_1


title: 800T

description:
Library name: 800TA
Column name in GEOrsem_expected_count.csv: 800TA

value: Clear cell renal cell carcinoma


title: RORB_1

description:
Library name: Sample 3
Genomic DNA immunoprecipitated by RORB antibody replicate 1


title: cl01_3

value: CC36 colon cancer cells primary culture clone 1


title: 794T

description:
Library name: 794TA
Column name in GEOrsem_expected_count.csv: 794TA


title: cl03_1


title: Input_2

description:
Library name: Sample 2
Input genomic DNA replicate 2


title: Mock_RNA-seq_2

description:
Library name: Sample 2
Gene expression after stable transfection of empty vector replicate 2

value: SK-N-BE(2) cells stably transfected with empty vector


title: cl01_2


title: VSMC_KOsmc_AII+NA_G8

description:
Library name: M7115
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: AII+NA


title: Mock_RNA-seq_1

description:
Library name: Sample 1
Gene expression after stable transfection of empty vector replicate 1


title: VSMC_KOsmc_AII+NA_G7

description:
Library name: M7111
rawcounts_paper2025_SMC-mono-KOsmc-male.txt


title: VSMC_KOsmc_HG+FFS_G7

description:
Library name: M7110
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: HG+FFS


title: cl01_1


title: 792T

description:
Library name: 792TA
Column name in GEOrsem_expected_count.csv: 792TA


title: 788T

description:
Library name: 788TA
Column name in GEOrsem_expected_count.csv: 788TA

source_name: Papillary renal cell carcinoma

value: Papillary renal cell carcinoma


title: VSMC_KOsmc_ALL_G6

description:
Library name: M7108
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: C57BL/6 mice


title: Mouse Tumor, B16F10, rep2, scRNAseq, mMo.DT4.2

first: Sonia

middle: M

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

description:
Library name: mMo.DT4.2
10x Chromium Next GEM Single Cell 3′ Platform

data_processing:
Raw sequencing reads were demultiplexed and mapped to the GRCm38 genome using CellRanger v6.1. Data processing and analysis were performed in R v4.2 and Python v3.6, with Seurat v4.3 used for data integration and visualization. Cell type identification followed methods detailed in [Li, X. et al. Coordinated chemokine expression defines macrophage subsets across tissues. Nat Immunol (2024)], wherein IMs and recMacs were distinguished based on characteristic marker genes and clustering profiles.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: SeuratObject in rds format contains all 3 samples and different assays of mRNA expression matrices; The meta data in rds format for every cell, includes the sample source and cell types.

source_name: Pulmonary metastases of B16 melanoma

extract_protocol:
To differentiate intravascular and extravascular leukocytes, mice were injected intravenously with APC-Cy7-conjugated anti-CD45 antibody 5 minutes before harvest. Lung single cell suspensions were enriched using CD11b Miltenyi beads. Extravascular monocyte-macrophage populations, CD64+CD11b+ cells, were sorted using the FACS Aria Fusion (BD Biosciences).
Approximately 30,000 cells per sample were loaded on the Chromium Next GEM Single Cell 3′ Platform (10x Genomics) and sequenced on an Illumina NextSeq 500/550 with an average depth of approximately 50,000 reads per cell.

value: Mononuclear Phagocytes

value: Pulmonary metastases of B16 melanoma

value: 6-8 weeks old


title: Mouse Tumor, B16F10, rep3, scRNAseq, mMo.DT4.3

description:
Library name: mMo.DT4.3
10x Chromium Next GEM Single Cell 3′ Platform


title: Mouse Tumor, B16F10, rep1, scRNAseq, mMo.DT4.1

description:
Library name: mMo.DT4.1
10x Chromium Next GEM Single Cell 3′ Platform


title: VSMC_KOsmc_AII+NA_G6

description:
Library name: M7107
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: murine vascular smooth muscle cell

value: EGFR-KOsmc


title: P3E3z_1

value: colon

value: cc14 colon cancer cells primary culture clone E3


title: 780T

description:
Library name: 780TA
Column name in GEOrsem_expected_count.csv: 780TA


title: VSMC_KOsmc_Control_G6

description:
Library name: M7105
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: Control


title: 779T

description:
Library name: 779TA
Column name in GEOrsem_expected_count.csv: 779TA


title: P2D12_3

value: cc14 colon cancer cells primary culture clone D12


title: heart, diabetic, Visium replicate 3

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
Library name: Db5
10X Visium (FFPE)

data_processing:
The 10X Space Ranger pipeline v 2.0.1 was used for FASTQ generation, library QC, gene quantification, and alignment of Visium sequencing data with the tissue images. Data analysis was performed using R (v.4.3.3) and the Seurat (v5) package.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected _tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors _json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires _image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of
Supplementary files format and content: tissue positions_list.cv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: heart

extract_protocol:
Using aseptic, RNA-preserving conditions, control Db/db and T2D db/db mouse hearts were gravity-fed perfusion fixed under deep isoflurane anesthesia (3%) by ~15 seconds of a PBS flush, followed by ~15 seconds of 4% paraformaldehyde (PFA), and finished with 4% PFA with 60 mM KCl until cardiac arrest in diastole. Tissues were fixed for 24 hours in 4% PFA at 4°C and stored in 70% ethanol until paraffin embedding.
Paraffin-embedded tissue blocks were sliced in 5 µm sections and transferred to the 6.5 mm x 6.5 mm capture areas on Visium slides according to the 10X Genomics demonstrated protocol (CG000408). Prior to imaging, FFPE tissue mounted on Visium slides were deparaffinized, decrosslinked, and immunofluorescent stained according to the demonstrated protocol from 10X Genomics (CG000410). Multichannel fluorescence images of the whole-heart sections and fiducial frame were captured on a Nikon Ti2-E inverted microscope with a Nikon D-LEDI multiline LED engine and a Hamamatsu ORCA Fusion sCMOS camera. After imaging, sample tissue was prepared using the demonstrated protocol from 10X Genomics (CG000407). Prior to gene expression library construction, quantitative PCR was performed on the eluted probe DNA to determine the appropriate PCR cycle number needed per sample. Following qPCR, probe DNA from the samples were PCR amplified with Dual Index TS Set A (3000511) adapters to make Illumina-compatible libraries for sequencing. Libraries were pooled and sequenced with a target of 25,000 reads/cell using an Illumina NextSeq P2 flow cell.

value: heart

value: db/db

value: male


title: VSMC_KOsmc_AII+NA_G5

description:
Library name: M7103
rawcounts_paper2025_SMC-mono-KOsmc-male.txt


title: P2D12_2


title: heart, diabetic, Visium replicate 2

description:
Library name: Db4
10X Visium (FFPE)


title: 777T

description:
Library name: 777TA
Column name in GEOrsem_expected_count.csv: 777TA

value: Clear cell renal cell carcinoma


title: heart, diabetic, Visium replicate 1

description:
Library name: Db1
10X Visium (FFPE)


title: 776T

description:
Library name: 776TA
Column name in GEOrsem_expected_count.csv: 776TA

value: Fumarate hydratase deficient renal cell carcinoma


title: 775T

description:
Library name: 775TA
Column name in GEOrsem_expected_count.csv: 775TA

value: Chromophobe renal cell carcinoma


title: P2D12_1


title: P3E3z_3


title: 787T

description:
Library name: 787TA
Column name in GEOrsem_expected_count.csv: 787TA

source_name: Hybrid oncocytic chromophobe tumor

value: Hybrid oncocytic chromophobe tumor


title: VSMC_KOsmc_HG+FFS_G5

description:
Library name: M7102
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: C57BL/6 mice

value: HG+FFS


title: VSMC_KOsmc_Control_G5

description:
Library name: M7101
rawcounts_paper2025_SMC-mono-KOsmc-male.txt


title: VSMC_WT_ALL_G4

description:
Library name: M5116
rawcounts_paper2025_SMC-mono-WT-male.txt

value: WT

value: ALL


title: P3E3z_2

source_name: colon


title: heart, control, Visium replicate 2

description:
Library name: Het2
10X Visium (FFPE)

value: Db/db


title: VSMC_KOsmc_HG+FFS_G6

description:
Library name: M7106
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: murine vascular smooth muscle cell

value: EGFR-KOsmc


title: heart, control, Visium replicate 3

description:
Library name: Het4
10X Visium (FFPE)


title: 773T

description:
Library name: 773TA
Column name in GEOrsem_expected_count.csv: 773TA


title: P2B2z_1

value: colon

value: cc14 colon cancer cells primary culture clone B2


title: heart, control, Visium replicate 1

description:
Library name: Het1
10X Visium (FFPE)


title: VSMC_KOsmc_Control_G7

description:
Library name: M7109
rawcounts_paper2025_SMC-mono-KOsmc-male.txt

value: Control


title: 771T

description:
Library name: 771TA
Column name in GEOrsem_expected_count.csv: 771TA


title: VSMC_WT_HG+FFS_G4

description:
Library name: M5114
rawcounts_paper2025_SMC-mono-WT-male.txt


title: P2A7_3

value: cc14 colon cancer cells primary culture clone A7


title: HUVEC, siPAK2-siCXCL10, 3.1

city: Montreal

first: Jean-Philippe

last: Gratton

address: 2900 Bd Edouard-Montpetit

country: Canada

institute: Université de Montréal

description:
Library name: siPAK2-siCXCL10 3.1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2.sicxcl10_3.1

data_processing:
Tumors: Quality control of raw reads was assessed with FASTQC (v0.11.8), combined with MultiQC version 1.3. Reads were aligned to the GRCm38 genome using STAR (v2.5.1b), and raw counts were calculated with featureCounts (v1.6). DESeq2 (v1.24.0) was used to normalize gene readcounts.
HUVEC: Raw read quality was assessed with MultiQC (v1.11). Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic (v0.35) and aligned to the reference human genome version GRCh38 (gene annotation from Gencode v37, based on Ensembl 103) using STAR (v2.7.1a). Gene expressions were obtained from STAR both as readcounts and TPM values as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in FPKM and TPM values. DESeq2 (v1.30.1) was then used to normalize gene readcounts.
Assembly: GRCm38 and GRCh38
Supplementary files format and content: Excel file includes Deseq readcounts normalized to library for each Sample

source_name: HUVEC

growth_protocol:
Lewis lung carcinoma (LLC) were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 ug/ml streptomycin. 1.5 x10^6 LLC cells were injected subcutaneously into the flank of 6- to 8-weeks old mice. The tumors grew for 18 days, after which tumors were harvested.
Human umbilical vein ECs (HUVECs) were cultured in M199 media supplemented with 20% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 0.05 mg/mL ECGS.

extract_protocol:
Total mRNA from tumors and HUVEC experiments was extracted using TRIzol Reagent, according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5 mg/21 days Tamoxifen slow-release pellets

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: PAK2 and CXCL10 downregulated

value: RNAseq HUVEC 2


title: 770T

description:
Library name: 770TA
Column name in GEOrsem_expected_count.csv: 770TA

source_name: Unclassified type of renal cell carcinoma


title: P2B2z_3


title: 774T

description:
Library name: 774TA
Column name in GEOrsem_expected_count.csv: 774TA

value: Papillary renal cell carcinoma


title: HUVEC, siPAK2-siCXCL10, 2.1

description:
Library name: siPAK2-siCXCL10 2.1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2.sicxcl10_2.1


title: P2A7_1


title: 768T

description:
Library name: 768TA
Column name in GEOrsem_expected_count.csv: 768TA

value: Clear cell renal cell carcinoma


title: VSMC_WT_Control_G4

description:
Library name: M5113
rawcounts_paper2025_SMC-mono-WT-male.txt

value: male

value: C57BL/6 mice


title: VSMC_WT_AII+NA_G3

description:
Library name: M5111
rawcounts_paper2025_SMC-mono-WT-male.txt

value: WT

value: AII+NA


title: HUVEC, siCXCL10, 3.1

description:
Library name: siCXCL10 3.1
Column name in counts_normalized_relative_to_library_size.xlsx: sicxcl10_3.1

value: CXCL10 downregulated


title: HUVEC, siPAK2-siCXCL10, 1.1

description:
Library name: siPAK2-siCXCL10 1.1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2.sicxcl10_1.1


title: 767T

description:
Library name: 767TA
Column name in GEOrsem_expected_count.csv: 767TA


title: 766T

description:
Library name: 766TA
Column name in GEOrsem_expected_count.csv: 766TA


title: VSMC_WT_HG+FFS_G3

description:
Library name: M5110
rawcounts_paper2025_SMC-mono-WT-male.txt

value: murine vascular smooth muscle cell

value: HG+FFS


title: P2D8z_3

value: colon

value: cc14 colon cancer cells primary culture clone D8


title: P2D8z_2


title: 762T

description:
Library name: 762TA
Column name in GEOrsem_expected_count.csv: 762TA


title: HUVEC, siCXCL10, 2.1

description:
Library name: siCXCL10 2.1
Column name in counts_normalized_relative_to_library_size.xlsx: sicxcl10_2.1


title: VSMC_WT_AII+NA_G4

description:
Library name: M5115
rawcounts_paper2025_SMC-mono-WT-male.txt


title: P2D8z_1


title: VSMC_WT_Control_G3

description:
Library name: M5109
rawcounts_paper2025_SMC-mono-WT-male.txt

value: Control


title: 761T

description:
Library name: 761TA
Column name in GEOrsem_expected_count.csv: 761TA


title: HUVEC, siCXCL10, 1.1

description:
Library name: siCXCL10 1.1
Column name in counts_normalized_relative_to_library_size.xlsx: sicxcl10_1.1


title: P2A7_2

value: cc14 colon cancer cells primary culture clone A7


title: heart, control, Visium replicate 4

description:
Library name: Het5
10X Visium (FFPE)

value: heart

value: Db/db


title: VSMC_WT_ALL_G2

description:
Library name: M5108
rawcounts_paper2025_SMC-mono-WT-male.txt

value: ALL


title: HUVEC, siPAK2, 3.1

description:
Library name: siPAK2 3.1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2_3.1

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: PAK2 downregulated

value: RNAseq HUVEC 2


title: VSMC_WT_ALL_G3

description:
Library name: M5112
rawcounts_paper2025_SMC-mono-WT-male.txt

value: male

value: C57BL/6 mice


title: P1F3z_2

value: cc14 colon cancer cells primary culture clone F3


title: 754T

description:
Library name: 754TA
Column name in GEOrsem_expected_count.csv: 754TA

value: TFE3-rearranged/TFEB-altered renal cell carcinoma


title: VSMC_WT_AII+NA_G2

description:
Library name: M5107
rawcounts_paper2025_SMC-mono-WT-male.txt

value: murine vascular smooth muscle cell

value: WT

value: AII+NA


title: 753T

description:
Library name: 753TA
Column name in GEOrsem_expected_count.csv: 753TA

value: Clear cell renal cell carcinoma


title: HUVEC, siPAK2, 2.1

description:
Library name: siPAK2 2.1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2_2.1


title: P1F3z_1

value: colon


title: HUVEC, siPAK2, 1.1

description:
Library name: siPAK2 1.1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2_1.1


title: P2B2z_2

value: cc14 colon cancer cells primary culture clone B2


title: 744T

description:
Library name: 744TA
Column name in GEOrsem_expected_count.csv: 744TA


title: VSMC_WT_Control_G2

description:
Library name: M5105
rawcounts_paper2025_SMC-mono-WT-male.txt

value: Control


title: VSMC_WT_HG+FFS_G2

description:
Library name: M5106
rawcounts_paper2025_SMC-mono-WT-male.txt

value: HG+FFS


title: P1E6z_2

value: cc14 colon cancer cells primary culture clone E6


title: 742T

description:
Library name: 742TA
Column name in GEOrsem_expected_count.csv: 742TA


title: VSMC_WT_AII+NA_G1

description:
Library name: M5103
rawcounts_paper2025_SMC-mono-WT-male.txt


title: P1E6z_1


title: VSMC_WT_ALL_G1

description:
Library name: M5104
rawcounts_paper2025_SMC-mono-WT-male.txt

value: ALL


title: P1F3z_3


title: HUVEC, siCT, 3.1

description:
Library name: siCT 3.1
Column name in counts_normalized_relative_to_library_size.xlsx: sict_3.1

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: CT


title: 737T

description:
Library name: 737TA
Column name in GEOrsem_expected_count.csv: 737TA


title: VSMC_WT_HG+FFS_G1

description:
Library name: M5102
rawcounts_paper2025_SMC-mono-WT-male.txt

value: male


title: HUVEC, siCT, 1.1

description:
Library name: siCT 1.1
Column name in counts_normalized_relative_to_library_size.xlsx: sict_1.1

value: RNAseq HUVEC 2


title: HUVEC, siCT, 2.1

description:
Library name: siCT 2.1
Column name in counts_normalized_relative_to_library_size.xlsx: sict_2.1


title: 741T

description:
Library name: 741TA
Column name in GEOrsem_expected_count.csv: 741TA


title: HUVEC, siPAK2, 3

description:
Library name: siPAK2 3
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2_3

value: PAK2 downregulated

value: RNAseq HUVEC 1


title: P1H8_2

value: cc14 colon cancer cells primary culture clone H8


title: P1H8_3


title: 732T

description:
Library name: 732TA
Column name in GEOrsem_expected_count.csv: 732TA

value: Chromophobe renal cell carcinoma


title: HUVEC, siPAK2, 2

description:
Library name: siPAK2 2
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2_2


title: 713T

description:
Library name: 713TA
Column name in GEOrsem_expected_count.csv: 713TA


title: VSMC_WT_Control_G1

description:
Library name: M5101
rawcounts_paper2025_SMC-mono-WT-male.txt

value: murine vascular smooth muscle cell

value: C57BL/6 mice

value: WT


title: P1E6z_3

value: colon


title: HUVEC, siPAK2, 1

description:
Library name: siPAK2 1
Column name in counts_normalized_relative_to_library_size.xlsx: sipak2_1


title: 712T

description:
Library name: 712TA
Column name in GEOrsem_expected_count.csv: 712TA

value: Clear cell renal cell carcinoma


title: HUVEC, siCT, 3

description:
Library name: siCT 3
Column name in counts_normalized_relative_to_library_size.xlsx: sict_3


title: mu4_13K_AD, s4

city: Toulouse

first: Aurélie

last: Mougel

address: Avenue des arènes romaines CHU Purpan 31300 Toulouse

country: France

institute: INSERM

description: Library name: 090S-504

data_processing:
nf-core/rna-seq pipeline v3.12.0
Raw reads were trimmed for adapters and low-quality sequences using trimgalore.
Contaminant rRNAs were removed with SortMeRNA.
Filtered reads were aligned to the genome using the STAR aligner.
Reads were counted with Salmon.
Assembly: mm39, annotation v107
Supplementary files format and content: counts_genes.txt includes raw counts for each sample, TPM counts and gene length
Supplementary files format and content: counts_transcripts.txt includes raw counts for each sample, TPM counts and transcripts length
Supplementary files format and content: salmon_tx2gene.tsv gives correspondence between genes and transcripts

source_name: skin

extract_protocol:
RNA was harvested using RNeasy Lipid Tissue Kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA librairies for RNA-seq were prepared using the llumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit following manufacturer's protocol.

value: skin


title: P2C10_3

extract_protocol:
Total RNA extraction using TRIzol
Illumina TruSeq HT stranded mRNA

value: cc14 colon cancer cells primary culture clone C10


title: mu4_13K_AD, s5

description: Library name: 090S-505


title: P1H8_1


title: 709T

description:
Library name: 709TA
Column name in GEOrsem_expected_count.csv: 709TA


title: HUVEC, siCT, 2

description:
Library name: siCT 2
Column name in counts_normalized_relative_to_library_size.xlsx: sict_2


title: mu4_13K_AD, s6

description: Library name: 090S-506


title: P2C10_2


title: 697T

description:
Library name: 697TA
Column name in GEOrsem_expected_count.csv: 697TA


title: mu4_13K_AD, s3

description: Library name: 090S-503


title: P2C10_1


title: 685T

description:
Library name: 685TA
Column name in GEOrsem_expected_count.csv: 685TA

value: Papillary renal cell carcinoma


title: P1F9z_2

value: cc14 colon cancer cells primary culture clone F9


title: mu4_13K_AD, s2

description: Library name: 090S-502


title: 679T

description:
Library name: 679TA
Column name in GEOrsem_expected_count.csv: 679TA


title: P1F9z_3


title: HUVEC, siCT, 1

description:
Library name: siCT 1
Column name in counts_normalized_relative_to_library_size.xlsx: sict_1

value: HUVEC

value: Human Umbilical Vein Endothelial Cells


title: mu4_13K_AD, s1

description: Library name: 090S-501


title: P1F9z_1


title: 662T

description:
Library name: 662TA
Column name in GEOrsem_expected_count.csv: 662TA


title: P5H6_3

value: cc14 colon cancer cells primary culture clone H6


title: Patient 2_ROI 027_ PanCK+

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

country: Spain

institute: IDIBELL

description:
Library name: Sample_DSP-1001660005657-A-H01
FFPE spatial transcriptomics (NanoString DSP WTA)

data_processing:
Fastq files containing sequencing of UV-cleaved probes were processed into Digital count conversion (DCC) files using the Nanostring GeoMx NGS Pipeline v2.3.3.10. The DCC files were imported into R v4.3.0 for further analysis. Using GeomxTools v3.3.0, areas of Illumination (AOI) were assessed for sequencing quality. AOIs retained for analysis if they met the following criteria: Minimum reads per AOI greater than 1000, the percentage of trimmed reads, stitched reads and aligned reads all greater than 80%, the sequencing saturation greater than 50%, the minimum count of negative control probes greater 0.5, No Template Control (NTC) counts greater than 1300, number of nuclei per AOI is greater than 100, the area per AOI is greater than 1000 µm, and greater than 5% of genes detected above limit of quantification (LOQ, mean of negative control counts + 2 standard deviation). 6 AOIs were discarded for not meeting the criteria, for a total of 78 AOIs. Genes were retained in the analysis if detected above LOQ in at least 5% of AOIs for a total of 12236 genes. Counts were normalized using the quartile 3 (Q3) method.
Assembly: GRCh38
Supplementary files format and content: Matrix of Q3-normalized counts for the 78 AOIs
Library strategy: Spatial Transcriptomics

source_name: macrophage, DGCR8-mutated, PanCK+

extract_protocol:
GeoMx™ digital spatial profiling was performed as per the supplier’s protocol using the human Whole Transcriptome Atlas probe set with read-out by next-generation sequencing (Nanostring Technologies). Briefly, 5 µm FFPE sections of a sporadic DICER1-thyroid case and a germline DGCR8- thyroid case, were processed through deparaffinization, antigen retrieval (Tris-EDTA ph9 for 20 min at 98°C), and Proteinase K digestion (1 ug/mL Proteinase K for 15 min at 37°C) prior to overnight incubation at 37°C with the human Whole Transcriptome Atlas diluted in hybridization Buffer R. The next day, slides were washed twice in 2XSSC/formamide (25 min at 37°C), blocked with Buffer W (30 min at RT) and incubated with an antibody cocktail consisting of PanCK-AF532, CD45-AF594, VIM-AF647, and SYTO13 for 1 hr in a humidity chamber. Slides were washed 3 times in 2XSSC and then scanned on the GeoMx™ DSP instrument (at 20X), after which regions-of-interest (ROIs) in each case were laid down to capture different histological components in triplicates at least. For the DICER1-case, this included a tumour core from a DICER1-mutated PDTC, the tumor’s capsule, a non-neoplastic nodular area (DICER1-wildtype benign thyroid lesion) and normal area (DICER1-wildtype). For the DGCR8-case, this included a tumour core from a DGCR8-mutated microPTC, a normal adjacent area, non-neoplastic nodular areas (DGCR8-mutated benign thyroid lesions) and normal area (DGCR8-mutated). A total of 51 ROIs were selected and were segmented further into PanCK+ and/or VIM+ areas, and Whole Transcriptome barcodes were released from these distinct populations by UV light illumination and microfluidic collection.
The UV-released barcodes from each of the 84 area-of-illuminations (AOIs) were PCR-amplified to add unique dual-index Illumina i5 and i7 indices and bead-purified twice using AMPure XP beads (Beckman Coutler, A63881). Pooled libraries were sequenced on two 75-cycle High Output flowcells on an Illumina NextSeq sequencer, generating 916M unique raw reads. FASTQ files were converted to DCC files and uploaded onto the GeoMx™ DSP for trimming, stitching, aligning, and deduplication.

value: Patient 2_macrophage_ PanCK+

tag: patient

value: Patient 2

tag: histological type

value: macrophage

value: Male

tag: label (panck/vim)

value: VIM+ (Cy5)


title: mu13K_AD, s5

description: Library name: 090S-405


title: 664T

description:
Library name: 664TA
Column name in GEOrsem_expected_count.csv: 664TA

source_name: Clear cell renal cell carcinoma


title: Patient 2_ROI 026_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G12
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: lymphocyte 3, DGCR8-mutated, VIM+

value: Patient 2_lymphocyte 3_ VIM+

value: lymphocyte

tag: genotype


title: siGATA6

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from HPAECs treated with siRNA against GATA6.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 16.0.0) (http://mbni.org/customcdf/16.0.0/entrezg.download/hugene20st_Hs_ENTREZG_16.0.0.zip).

label: biotin

source_name: human pulmonary arterial endothelial cells (HPAECs)

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: HPAECs were purchased from Lonza (Walkersville, MD) and cultured in complete endothelial growth medium (EGM)-2 (Lonza) or endothelial cell basal medium MV2 (PromoCell, Heidelberg, Germany).

extract_protocol: Forty-eight to seventy-two hours post-transfection, total RNA was prepared using TRI reagent (MRC, Inc., Cincinnati, OH) according to the manufacturer’s protocol, whole cell lysates were prepared for immunoblot analysis, or functional assays were performed.

treatment_protocol: Eighty percent confluent cultures of HPAECs were transfected with 10 nM of small interfering RNA (siRNA) directed against GATA6 (ON-TARGET plus SMART pool™, Dharmacon, Waltham, MA) and control siRNA using Invitrogen™ Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen).

value: HPAECs

tag: sirna


title: siSCR

description: Gene expression data from HPAECs treated with scrambled siRNA control.

value: siSCR


title: 657T

description:
Library name: 657TA
Column name in GEOrsem_expected_count.csv: 657TA

value: Clear cell renal cell carcinoma


title: 612T

description:
Library name: 612TA
Column name in GEOrsem_expected_count.csv: 612TA


title: mu13K_AD, s3

description: Library name: 090S-403

value: skin


title: mu13K_AD, s4

description: Library name: 090S-404


title: P5H6_1

first: Celine

last: Delucinge

institute: University of Geneva

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.0
Assembly: UCSC hg38
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

value: colon


title: Patient 2_ROI 025_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: lymphocyte 2, DGCR8-mutated, VIM+

value: Patient 2_lymphocyte 2_ VIM+


title: P5H6_2


title: P3C11_3

value: cc14 colon cancer cells primary culture clone C11


title: 590T

description:
Library name: 590TA
Column name in GEOrsem_expected_count.csv: 590TA

value: Papillary renal cell carcinoma


title: Patient 2_ROI 024_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G10
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: lymphocyte 1, DGCR8-mutated, VIM+

value: Patient 2_lymphocyte 1_ VIM+


title: mu13K_AD, s2

description: Library name: 090S-402


title: P3C11_2


title: 589T

description:
Library name: 589TA
Column name in GEOrsem_expected_count.csv: 589TA


title: Patient 2_ROI 023_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G09
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 3, DGCR8-mutated, VIM+

value: Patient 2_Normal thyroid 3_ VIM+

value: Normal thyroid


title: mu13K_AD, s1

description: Library name: 090S-401


title: P3C11_1


title: mu13K_AD, s6

description: Library name: 090S-406


title: mu4K_AD, s6

description: Library name: 090S-306


title: 583T

description:
Library name: 583TA
Column name in GEOrsem_expected_count.csv: 583TA