title: 5BB control rep12

status: Public on Aug 16 2026

type: RNA

city: Eskisehir

first: Saffet

last: Teber

address: Ali Numan Kırac Yerleskesi, Ziraat Caddesi, Odunpazarı/Eskisehir

country: Turkey

institute: Eskisehir Osmangazi University

hyb_protocol: 15 ug aRNA was hybridized at 45 C for 16 h in a GeneChip Hybridization Oven 640. Arrays were washed and stained with streptavidin-phycoerythrin on a Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console with the ExpressionStat 5.0 algorithm and default analysis settings. Expression values were generated at the probe-set level and used for downstream analyses.

label: biotin

molecule: total RNA

organism: Vitis vinifera

source_name: shoot tissue, 5BB, control

label_protocol: From 100 ng total RNA, poly(A)+ mRNA was reverse-transcribed to double-stranded cDNA and in vitro-transcribed to biotin-labelled antisense RNA (aRNA) using the GeneChip IVT Express Labeling Kit (Affymetrix), per the GeneChip Expression Analysis Technical Manual.

growth_protocol: Shoots were cultured in vitro on the rooting medium of Roubelakis-Angelakis and Zivanovic (1991) for six weeks at 25 C under a 16 h light/8 h dark photoperiod (480 umol m-2 s-1). Rooted seedlings were transferred to sand culture, irrigated every two days with one-tenth-strength Hoagland nutrient solution, and grown for ten additional weeks under the same conditions. Plant material originated from the Ankara University Kalecik Viticulture Research Station.

extract_protocol: Shoot tissue was harvested, snap-frozen in liquid nitrogen and pooled from five stressed and five control plants with comparable physiological responses. Total RNA was extracted using the Tris-LiCl protocol accoridng to Tattersall et al 2005.

treatment_protocol: Salt stress: NaCl/CaCl2 increased over four days to 120/12 mM (day 1, 30/3; day 2, 60/6; day 3, 90/9; day 4, 120/12 mM), then maintained through day 7. CaCl2 was supplied at one-tenth the NaCl concentration. Drought stress: irrigation withheld for seven days. Controls were irrigated with one-tenth-strength Hoagland solution every two days throughout.

tag: cultivar

value: Kober 5BB (V. berlandieri x V. riparia)

tag: treatment

value: control:none (irrigated with 1/10-strength Hoagland solution every two days)


title: 41B drought rep3

source_name: shoot tissue, 41B, drought

value: 41B (V. vinifera cv. Chasselas x V. berlandieri)

value: drought:irrigation withheld for 7 days


title: 5BB salinity rep3

source_name: shoot tissue, 5BB, salinity

value: salinity:NaCl/CaCl2 raised stepwise to 120/12 mM over 4 days, maintained to day 7


title: 5BB control rep9


title: 5BB control rep10


title: 5BB control rep6


title: 5BB control rep8


title: 5BB control rep11


title: 5BB control rep7


title: 5BB control rep4


title: 5BB control rep5


title: 41B control rep12

source_name: shoot tissue, 41B, control


title: 41B control rep11


title: 5BB control rep3


title: 41B control rep10


title: 41B control rep9


title: CS control rep12

source_name: shoot tissue, CS, control

value: Vitis vinifera cv. Cabernet Sauvignon


title: 41B control rep7


title: 41B salinity rep3

source_name: shoot tissue, 41B, salinity


title: 41B control rep8


title: 5BB control rep2


title: 41B control rep5


title: 41B control rep4


title: 41B control rep3


title: CS drought rep3

source_name: shoot tissue, CS, drought


title: 5BB control rep1


title: 41B control rep1


title: CS drought rep2


title: 41B drought rep2


title: CS drought rep1


title: 41B drought rep1


title: 5BB drought rep3

source_name: shoot tissue, 5BB, drought


title: 5BB drought rep1


title: 5BB salinity rep2


title: 41B salinity rep2


title: 5BB drought rep2


title: CS salinity rep2

source_name: shoot tissue, CS, salinity


title: 5BB salinity rep1


title: CS salinity rep1


title: CS control rep10


title: CS control rep9


title: CS control rep7


title: CS control rep5


title: CS control rep6


title: CS salinity rep3


title: Zebrafish F1 heart bulk RNA-seq - Pi-Fu_4

type: SRA

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

description:
Library name: Pi-Fu_4
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).

library_source: transcriptomic

data_processing:
Quality control of raw sequencing reads was assessed using FastQC v0.11.9 (Andrews, 2010) and aggregated with MultiQC v1.12 (P. Ewels et al., 2016).
Adapter trimming and quality filtering were performed using Fastp v0.23.2 (Chen et al., 2018).
Zebrafish F1 heart samples were aligned to GRCz11 using Ensembl release 111.
Reads were aligned to the reference genome using STAR v2.7.10a (Dobin et al., 2013).
Gene-level read counts were generated using featureCounts from the Subread package v2.0.3 (Liao et al., 2014).
Differential expression analysis was conducted in R v4.4.0 using DESeq2 v1.44.0 (Love et al., 2014) with a design formula of ~condition.
Log2 fold change shrinkage was applied using ashr v2.2.63. Differentially expressed genes required |log2FC| > 0.58; an additional |log2FC| > 0.58 threshold was applied for volcano plot and pathway analyses.
Genes with adjusted p-value < 0.05 (Benjamini-Hochberg correction) and |log2FC| above the species-specific threshold were considered differentially expressed.
Cross-species pathway analysis: Over-representation analysis (ORA) was performed using clusterProfiler v4.12.2 (Wu et al., 2021; Yu et al., 2012) and ReactomePA v1.48.0, with parallel execution via BiocParallel v1.38.0.
Data visualization was performed using ComplexHeatmap v2.20.0, pheatmap v1.0.12 (Kolde, 2019), ggplot2 v3.5.1 (Wickham, 2016), and ggrepel v0.9.5.
Zebrafish gene identifiers were converted to mouse orthologs using biomaRt v2.60.1 via the Ensembl December 2021 archive (Durinck et al., 2009).
Assembly: Danio rerio GRCz11, Ensembl release 111
Supplementary files format and content: Gene-level read count matrix (featureCounts).

organism: Danio rerio

source_name: heart (ventricle)

growth_protocol: Adult zebrafish maintained at max 5 fish/L, 27.5-28C, 14:10h light:dark, conductivity 650-700 uS/cm, pH 7.5, 10% daily water exchange; fed Artemia + dry food 3x/day. Approved under licenses BE46/19, BE109/2021, BE05/2025 (Canton of Bern, Switzerland).

extract_protocol:
Tissues washed in PBS and snap frozen. On the day of RNA extraction, samples were homogenized in TRI Reagent (Sigma-Aldrich) using 21G and 30G syringes (BD Microlance). Following phase separation with 1-bromo-3-chloropropane (Sigma-Aldrich), the aqueous phase was mixed with an equal volume of ethanol, and RNA was purified using the RNA Clean & Concentrator kit (Zymo Research) with on-column DNase I treatment. RNA quantity and quality were assessed using a NanoDrop and a Fragment Analyzer before library preparation and sequencing.
One ng of RNA was used to generate barcoded RNA-seq libraries using the Ovation Single Cell RNA-Seq System (NuGEN) with two rounds of library amplification, performed by the Genomics Unit at CNIC (Madrid, Spain). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60-base single reads. FastQ files were obtained using CASAVA v1.8 software (Illumina).

treatment_protocol: Hearts (ventricles) collected from adult zebrafish offspring of uninjured or injured males (crossed at 7 dpi). Bulbus arteriosus and atrium removed manually; a small incision was made in each ventricle to remove erythrocytes. Four biological replicates per condition, each pooled from four sibling fish.

tag: tissue

value: heart (ventricle)

value: paternal Injured P0


title: CS control rep1


title: CS control rep8


title: CS control rep11


title: Zebrafish F1 heart bulk RNA-seq - Pi-Fu_2

description:
Library name: Pi-Fu_2
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).


title: Zebrafish F1 heart bulk RNA-seq - Pi-Fu_7

description:
Library name: Pi-Fu_7
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).


title: Zebrafish F1 heart bulk RNA-seq - Pu-Fu_4

description:
Library name: Pu-Fu_4
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).

value: paternal Uninjured P0


title: Zebrafish F1 heart bulk RNA-seq - Pu-Fu_3

description:
Library name: Pu-Fu_3
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).


title: Zebrafish F1 heart bulk RNA-seq - Pi-Fu_1

description:
Library name: Pi-Fu_1
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).


title: Zebrafish F1 heart bulk RNA-seq - Pu-Fu_5

description:
Library name: Pu-Fu_5
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).


title: CS control rep3


title: CS control rep2


title: Human region 93

city: singapore

first: Lichang

last: Deng

address: singapore

country: Singapore

institute: NUS

description: Library name: NUH NKTL2 | 009 | CD3

library_source: other

data_processing:
All data were processed using Q3 normalization, with the limit of quantification (LOQ) threshold set at 20%.
Assembly: hg38
Supplementary files format and content: The file named processed data (DSP_gene_matrix) showed the genes expression of all ENKTL tissues, sequencing by Illumina HiSeq 3000
Library strategy: Spatial Transcriptomics

molecule: other

organism: Homo sapiens

source_name: NKTL

extract_protocol:
The slides were incubated with blocking Buffer W (200 μL/slide, NanoString) for 30 min in the humidity chamber at room temperature after hybridization.Each slide was stained with corresponding morophology markers. After immunofluorescent staining, the slides were visualized using the GeoMx® DSP instrument to select regions of interest (ROIs). To acquire representative regions, ROI selection was performed by an expert pathologist. The pathologist was blinded to the group assignment during the ROIs selection. Based on fluorescent staining, each ROI was segmented into corresponding areas of interest (AOIs) - CD68+ regions and CD3+ regions. Subsequently, each AOI was exposed to UV light and photocleaved oligos were aspirated from the solution into the wells of a collection plate.
Collected photocleaved oligos were PCR amplified with the corresponding GeoMx® Seq Code Primer Plate and Master Mix (NanoString). PCR products were pooled and cleaned with AMPure XP beads (Agilent, Santa Clara, California, USA) twice to obtain the libraries. The quality and concentration of libraries were assessed using a high sensitivity DNA Kit (Agilent) and Bioanalyzer. Subsequently, libraries were sequenced on an illumina sequencing platform (Hiseq or NovaSeq) with standard workflow specifications (dual-indexing and paired-end reads (2 × 27 bp)).

value: NKTL

tag: cell type

tag: batch


title: Human region 95

description: Library name: NUH NKTL2 | 010 | CD68


title: Human region 96

description: Library name: NUH NKTL2 | 011 | CD3


title: Human region 91

description: Library name: NUH NKTL2 | 008 | CD3


title: Zebrafish F1 heart bulk RNA-seq - Pu-Fu_1

description:
Library name: Pu-Fu_1
F1 offspring heart bulk RNA-seq; library prep/sequencing by CNIC (Ovation Single Cell RNA-Seq System, NuGEN).


title: Human region 94

description: Library name: NUH NKTL2 | 009 | CD68


title: Human region 92

description: Library name: NUH NKTL2 | 008 | CD68


title: Human region 90

description: Library name: NUH NKTL2 | 007 | CD68


title: Human region 89

description: Library name: NUH NKTL2 | 007 | CD3


title: Human region 88

description: Library name: NUH NKTL2 | 006 | CD68


title: Human region 86

description: Library name: NUH NKTL2 | 005 | CD68


title: Human region 85

description: Library name: NUH NKTL2 | 005 | CD3


title: Human region 83

description: Library name: NUH NKTL2 | 004 | CD3


title: Human region 82

description: Library name: NUH NKTL2 | 003 | CD68


title: Human region 84

description: Library name: NUH NKTL2 | 004 | CD68


title: Human region 87

description: Library name: NUH NKTL2 | 006 | CD3


title: Human region 80

description: Library name: NUH NKTL2 | 002 | CD68


title: Human region 81

description: Library name: NUH NKTL2 | 003 | CD3


title: Human region 78

description: Library name: NUH NKTL2 | 001 | CD68


title: Human region 79

description: Library name: NUH NKTL2 | 002 | CD3


title: Human region 76

description: Library name: NUH NKTL1 | 031 | CD3


title: Human region 74

description: Library name: NUH NKTL1 | 030 | CD3


title: Human region 75

description: Library name: NUH NKTL1 | 030 | CD68


title: Human region 73

description: Library name: NUH NKTL1 | 029 | CD68


title: Human region 72

description: Library name: NUH NKTL1 | 029 | CD3


title: Human region 77

description: Library name: NUH NKTL2 | 001 | CD3


title: Human region 71

description: Library name: NUH NKTL1 | 028 | CD68


title: Human region 70

description: Library name: NUH NKTL1 | 028 | CD3


title: Human region 69

description: Library name: NUH NKTL1 | 027 | CD68


title: Human region 67

description: Library name: NUH NKTL1 | 026 | CD68


title: Human region 68

description: Library name: NUH NKTL1 | 027 | CD3


title: 41B control rep6


title: Human region 66

description: Library name: NUH NKTL1 | 026 | CD3


title: Human region 65

description: Library name: NUH NKTL1 | 025 | CD68


title: Human region 63

description: Library name: NUH NKTL1 | 024 | CD68


title: Human region 62

description: Library name: NUH NKTL1 | 024 | CD3


title: Human region 61

description: Library name: NUH NKTL1 | 023 | CD68


title: 41B control rep2


title: Human region 58

description: Library name: NUH NKTL1 | 022 | CD3


title: Human region 64

description: Library name: NUH NKTL1 | 025 | CD3


title: Human region 60

description: Library name: NUH NKTL1 | 023 | CD3


title: Human region 56

description: Library name: NUH NKTL1 | 021 | CD3


title: Human region 54

description: Library name: NUH NKTL1 | 020 | CD3


title: Human region 55

description: Library name: NUH NKTL1 | 020 | CD68


title: Human region 57

description: Library name: NUH NKTL1 | 021 | CD68


title: Human region 59

description: Library name: NUH NKTL1 | 022 | CD68


title: Human region 52

description: Library name: NUH NKTL1 | 019 | CD3


title: Human region 48

description: Library name: NUH NKTL1 | 016 | CD68


title: Human region 51

description: Library name: NUH NKTL1 | 018 | CD68


title: Human region 50

description: Library name: NUH NKTL1 | 017 | CD68


title: Human region 47

description: Library name: NUH NKTL1 | 016 | CD3


title: Human region 49

description: Library name: NUH NKTL1 | 017 | CD3


title: Human region 53

description: Library name: NUH NKTL1 | 019 | CD68


title: Human region 44

description: Library name: NUH NKTL1 | 014 | CD68


title: Human region 43

description: Library name: NUH NKTL1 | 014 | CD3


title: 41B salinity rep1


title: Human region 46

description: Library name: NUH NKTL1 | 015 | CD68


title: Human region 42

description: Library name: NUH NKTL1 | 013 | CD3


title: Human region 40

description: Library name: NUH NKTL1 | 012 | CD3


title: Human region 35

description: Library name: NUH NKTL1 | 008 | CD3


title: Human region 41

description: Library name: NUH NKTL1 | 012 | CD68


title: Human region 37

description: Library name: NUH NKTL1 | 010 | CD3


title: Human region 38

description: Library name: NUH NKTL1 | 010 | CD68


title: Human region 36

description: Library name: NUH NKTL1 | 008 | CD68


title: Human region 39

description: Library name: NUH NKTL1 | 011 | CD3


title: Human region 45

description: Library name: NUH NKTL1 | 015 | CD3


title: Human region 34

description: Library name: NUH NKTL1 | 007 | CD68


title: Human region 32

description: Library name: NUH NKTL1 | 006 | CD68


title: CS control rep4


title: Human region 31

description: Library name: NUH NKTL1 | 006 | CD3


title: Human region 27

description: Library name: NUH NKTL1 | 004 | CD3


title: Human region 33

description: Library name: NUH NKTL1 | 007 | CD3


title: Human region 29

description: Library name: NUH NKTL1 | 005 | CD3


title: Human region 30

description: Library name: NUH NKTL1 | 005 | CD68


title: Human region 28

description: Library name: NUH NKTL1 | 004 | CD68


title: Human region 25

description: Library name: NUH NKTL1 | 003 | CD3


title: Human region 19

description: Library name: NUH NKTL1 | 040 | CD68


title: Human region 26

description: Library name: NUH NKTL1 | 003 | CD68


title: Human region 23

description: Library name: NUH NKTL1 | 001 | CD68


title: Human region 22

description: Library name: NUH NKTL1 | 001 | CD3


title: Human region 21

description: Library name: NUH NKTL1 | 041 | CD68


title: Human region 24

description: Library name: NUH NKTL1 | 002 | CD68


title: Human region 20

description: Library name: NUH NKTL1 | 041 | CD3


title: Human region 18

description: Library name: NUH NKTL1 | 040 | CD3


title: Human region 15

description: Library name: NUH NKTL1 | 038 | CD68


title: Human region 17

description: Library name: NUH NKTL1 | 039 | CD68


title: Human region 14

description: Library name: NUH NKTL1 | 038 | CD3


title: Human region 16

description: Library name: NUH NKTL1 | 039 | CD3


title: Human region 11

description: Library name: NUH NKTL1 | 036 | CD68


title: Human region 9

description: Library name: NUH NKTL1 | 035 | CD68


title: Human region 10

description: Library name: NUH NKTL1 | 036 | CD3


title: Human region 12

description: Library name: NUH NKTL1 | 037 | CD3


title: Human region 8

description: Library name: NUH NKTL1 | 035 | CD3


title: Human region 13

description: Library name: NUH NKTL1 | 037 | CD68


title: Human region 7

description: Library name: NUH NKTL1 | 034 | CD68


title: Human region 5

description: Library name: NUH NKTL1 | 033 | CD68


title: Human region 4

description: Library name: NUH NKTL1 | 033 | CD3


title: Human region 6

description: Library name: NUH NKTL1 | 034 | CD3


title: Human region 3

description: Library name: NUH NKTL1 | 032 | CD68


title: Human region 1

description: Library name: NUH NKTL1 | 031 | CD68


title: Human region 2

description: Library name: NUH NKTL1 | 032 | CD3


title: Suspension_2day_ATAC

city: New York

first: Teng

last: Han

state: New York

address: 417 E 68th St

country: USA

institute: MSKCC

description: Library name: S2_ATAC

library_source: genomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger ARC to generate paired gene expression and chromatin accessibility count matrices. Downstream analyses were performed using Seurat and Signac.
Assembly: mus musculus mm10
Supplementary files format and content: H5 file for scMultiome

molecule: genomic DNA

organism: Mus musculus

source_name: prostate organoid

extract_protocol:
Organoids were dissociated to obtain intact nuclei for Chromium Single Cell Multiome library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for Chromium Single Cell Multiome.

value: prostate organoid


title: Matrigel_ATAC

description: Library name: MQ_ATAC


title: Suspension_2day_GEX

description: Library name: S2_GEX

library_source: transcriptomic single cell


title: 9_TKO_COMBO_D8_Rep3

description:
Library name: 9_TKO_COMBO_D8_Rep3
9c_S35_L001

data_processing:
Raw FASTQ files were quality checked, aligned to the mouse reference genome (mm10), and gene-level read counts were generated. Normalized expression matrices were generated for downstream analyses.
Assembly: mus musculus mm10
Supplementary files format and content: Raw count

molecule: polyA RNA

extract_protocol:
Organoids were dissociated to obtain total RNA for library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for bulk RNA-seq.


title: Suspension_20day_ATAC

description: Library name: U1_ATAC


title: Suspension_20day_GEX

description: Library name: U1_GEX


title: Matrigel_GEX

description: Library name: MQ_GEX


title: 9_TKO_COMBO_D8_Rep2

description:
Library name: 9_TKO_COMBO_D8_Rep2
9b_S22_L001


title: 8_PtP_COMBO_D8_Rep3

description:
Library name: 8_PtP_COMBO_D8_Rep3
8c_S34_L001


title: 8_PtP_COMBO_D8_Rep1

description:
Library name: 8_PtP_COMBO_D8_Rep1
8a_S8_L001


title: 7_WT_COMBO_D8_Rep3

description:
Library name: 7_WT_COMBO_D8_Rep3
7c_S33_L001


title: 8_PtP_COMBO_D8_Rep2

description:
Library name: 8_PtP_COMBO_D8_Rep2
8b_S21_L001


title: 7_WT_COMBO_D8_Rep2

description:
Library name: 7_WT_COMBO_D8_Rep2
7b_S20_L001


title: 6_TKO_YAPi_NOTCHi_D8_Rep3

description:
Library name: 6_TKO_YAPi_NOTCHi_D8_Rep3
6c_S32_L001


title: 9_TKO_COMBO_D8_Rep1

description:
Library name: 9_TKO_COMBO_D8_Rep1
9a_S9_L001


title: 7_WT_COMBO_D8_Rep1

description:
Library name: 7_WT_COMBO_D8_Rep1
7a_S7_L001


title: 5_PtP_YAPi_NOTCHi_D8_Rep1

description:
Library name: 5_PtP_YAPi_NOTCHi_D8_Rep1
5a_S5_L001


title: 6_TKO_YAPi_NOTCHi_D8_Rep2

description:
Library name: 6_TKO_YAPi_NOTCHi_D8_Rep2
6b_S19_L001


title: 5_PtP_YAPi_NOTCHi_D8_Rep2

description:
Library name: 5_PtP_YAPi_NOTCHi_D8_Rep2
5b_S18_L001


title: 3_TKO_DMSO_D8_Rep3

description:
Library name: 3_TKO_DMSO_D8_Rep3
3c_S29_L001


title: 6_TKO_YAPi_NOTCHi_D8_Rep1

description:
Library name: 6_TKO_YAPi_NOTCHi_D8_Rep1
6a_S6_L001


title: 1_WT_DMSO_D8_Rep1

description:
Library name: 1_WT_DMSO_D8_Rep1
1a_S1_L001


title: 1_WT_DMSO_D8_Rep2

description:
Library name: 1_WT_DMSO_D8_Rep2
1b_S14_L001


title: 2_PtP_DMSO_D8_Rep3

description:
Library name: 2_PtP_DMSO_D8_Rep3
2c_S28_L001


title: 2_PtP_DMSO_D8_Rep2

description:
Library name: 2_PtP_DMSO_D8_Rep2
2b_S15_L001


title: NEPC-3_Rep1

description:
Library name: NEPC-3_Rep1
TKONE3-1_IGO_16181_37_S27_L004


title: 3_TKO_DMSO_D8_Rep2

description:
Library name: 3_TKO_DMSO_D8_Rep2
3b_S16_L001


title: 3_TKO_DMSO_D8_Rep1

description:
Library name: 3_TKO_DMSO_D8_Rep1
3a_S3_L001


title: NEPC-2_Rep3

description:
Library name: NEPC-2_Rep3
TKONE2-3_IGO_16181_36_S26_L004


title: 1_WT_DMSO_D8_Rep3

description:
Library name: 1_WT_DMSO_D8_Rep3
1c_S27_L001


title: NEPC-3_Rep2

description:
Library name: NEPC-3_Rep2
TKONE3-2_IGO_16181_38_S28_L004


title: 2_PtP_DMSO_D8_Rep1

description:
Library name: 2_PtP_DMSO_D8_Rep1
2a_S2_L001


title: 4_WT_YAPi_NOTCHi_D8_Rep2

description:
Library name: 4_WT_YAPi_NOTCHi_D8_Rep2
4b_S17_L001


title: NEPC-2_Rep1

description:
Library name: NEPC-2_Rep1
TKONE2-1_IGO_16181_34_S24_L004


title: NEPC-2_Rep2

description:
Library name: NEPC-2_Rep2
TKONE2-2_IGO_16181_35_S25_L004


title: NEPC-1_Rep3

description:
Library name: NEPC-1_Rep3
TKONE1-3_IGO_16181_33_S23_L004


title: NEPC-1_Rep1

description:
Library name: NEPC-1_Rep1
TKONE1-1_IGO_16181_31_S21_L004


title: NEPC-1_Rep2

description:
Library name: NEPC-1_Rep2
TKONE1-2_IGO_16181_32_S22_L004


title: PRAD_COMBO_D42_Rep2

description:
Library name: PRAD_COMBO_D42_Rep2
AD5COMBOD42-2_IGO_16181_29_S18_L004


title: PRAD_COMBO_D42_Rep1

description:
Library name: PRAD_COMBO_D42_Rep1
AD5COMBOD42-1_IGO_16181_28_S17_L004


title: PRAD_COMBO_D8_Rep3

description:
Library name: PRAD_COMBO_D8_Rep3
AD5COMBOD8-3_IGO_16181_24_S16_L004


title: PRAD_COMBO_D8_Rep1

description:
Library name: PRAD_COMBO_D8_Rep1
AD5COMBOD8-1_IGO_16181_22_S14_L004


title: PRAD_YAPi_NOTCHi_D8_Rep2

description:
Library name: PRAD_YAPi_NOTCHi_D8_Rep2
AD5IN3DA-2_IGO_16181_20_S12_L004


title: PRAD_YAPi_NOTCHi_D8_Rep3

description:
Library name: PRAD_YAPi_NOTCHi_D8_Rep3
AD5IN3DA-3_IGO_16181_21_S13_L004


title: PRAD_COMBO_D8_Rep2

description:
Library name: PRAD_COMBO_D8_Rep2
AD5COMBOD8-2_IGO_16181_23_S15_L004


title: PRAD_ARi_YAPi_D8_Rep1

description:
Library name: PRAD_ARi_YAPi_D8_Rep1
AD5CASIN3-1_IGO_16181_13_S4_L004


title: PRAD_ARi_YAPi_D8_Rep2

description:
Library name: PRAD_ARi_YAPi_D8_Rep2
AD5CASIN3-2_IGO_16181_14_S5_L004


title: PRAD_YAPi_NOTCHi_D8_Rep1

description:
Library name: PRAD_YAPi_NOTCHi_D8_Rep1
AD5IN3DA-1_IGO_16181_19_S10_L004


title: PRAD_ARi_NOTCHi_D8_Rep2

description:
Library name: PRAD_ARi_NOTCHi_D8_Rep2
AD5CASDA-2_IGO_16181_17_S8_L004


title: PRAD_ARi_NOTCHi_D8_Rep1

description:
Library name: PRAD_ARi_NOTCHi_D8_Rep1
AD5CASDA-1_IGO_16181_16_S7_L004


title: PRAD_NOTCHi_D8_Rep2

description:
Library name: PRAD_NOTCHi_D8_Rep2
AD5DA-2_IGO_16181_11_S2_L004


title: PRAD_NOTCHi_D8_Rep3

description:
Library name: PRAD_NOTCHi_D8_Rep3
AD5DA-3_IGO_16181_12_S3_L004


title: PRAD_YAPi_D8_Rep2

description:
Library name: PRAD_YAPi_D8_Rep2
AD5IN3-2_IGO_16181_8_S62_L004


title: PRAD_YAPi_D8_Rep1

description:
Library name: PRAD_YAPi_D8_Rep1
AD5IN3-1_IGO_16181_7_S112_L001


title: PRAD_ARi_D8_Rep3

description:
Library name: PRAD_ARi_D8_Rep3
AD5CAS-3_IGO_16181_6_S61_L004


title: PRAD_ARi_D8_Rep2

description:
Library name: PRAD_ARi_D8_Rep2
AD5CAS-2_IGO_16181_5_S52_L004


title: PRAD_NOTCHi_D8_Rep1

description:
Library name: PRAD_NOTCHi_D8_Rep1
AD5DA-1_IGO_16181_10_S1_L004


title: PRAD_ARi_D8_Rep1

description:
Library name: PRAD_ARi_D8_Rep1
AD5CAS-1_IGO_16181_4_S41_L004


title: TKOM_suspension_D30_Rep3

description:
Library name: TKOM_suspension_D30_Rep3
DLQU-3_IGO_14404_12_S22_L001


title: PRAD_DMSO_D8_Rep1

description:
Library name: PRAD_DMSO_D8_Rep1
AD5DMSO-1_IGO_16181_1_S11_L004


title: PRAD_DMSO_D8_Rep2

description:
Library name: PRAD_DMSO_D8_Rep2
AD5DMSO-2_IGO_16181_2_S19_L004


title: TKOM_suspension_D30_Rep2

description:
Library name: TKOM_suspension_D30_Rep2
DLQU-2_IGO_14404_11_S21_L001


title: TKOM_suspension_D30_Rep1

description:
Library name: TKOM_suspension_D30_Rep1
DLQU-1_IGO_14404_10_S20_L001


title: TKOM_Matrigel_Rep3

description:
Library name: TKOM_Matrigel_Rep3
DLQ-3_IGO_14404_9_S31_L001


title: TKOM_Matrigel_Rep1

description:
Library name: TKOM_Matrigel_Rep1
DLQ-1_IGO_14404_7_S29_L001


title: TKOM_Matrigel_Rep2

description:
Library name: TKOM_Matrigel_Rep2
DLQ-2_IGO_14404_8_S30_L001


title: RPM_NEPC_LATSi_Rep2

description: Library name: RPM_NEPC_LATSi_Rep2

library_source: genomic

data_processing:
Raw FASTQ files were aligned to the mouse reference genome (mm10). Peaks were called, and normalized signal tracks (bigWig) were generated for visualization.
Assembly: mus musculus mm10
Supplementary files format and content: Bigwig

extract_protocol:
Organoids were dissociated to obtain intact nuclei for bulk ATAC library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for ATAC-seq.


title: RPM_NEPC_LATSi_Rep1

description: Library name: RPM_NEPC_LATSi_Rep1


title: RPM_NEPC_DMSO_Rep1

description: Library name: RPM_NEPC_DMSO_Rep1


title: RPM_NEPC_DMSO_Rep2

description: Library name: RPM_NEPC_DMSO_Rep2


title: NEPC_rep2

description: Library name: NEPC_rep2


title: PRAD_sgFoxa1-2_YAPi_NOTCHi_rep2

description: Library name: PRAD_sgFoxa1-2_YAPi_NOTCHi_rep2


title: PRAD_sgFoxa1-2_YAPi_NOTCHi_rep1

description: Library name: PRAD_sgFoxa1-2_YAPi_NOTCHi_rep1


title: PRAD_sgFoxa1-1_YAPi_NOTCHi_rep2

description: Library name: PRAD_sgFoxa1-1_YAPi_NOTCHi_rep2


title: PRAD_sgFoxa1-1_YAPi_NOTCHi_rep1

description: Library name: PRAD_sgFoxa1-1_YAPi_NOTCHi_rep1


title: PRAD_sgNT_YAPi_NOTCHi_rep1

description: Library name: PRAD_sgNT_YAPi_NOTCHi_rep1


title: PRAD_sgNT_YAPi_NOTCHi_rep2

description: Library name: PRAD_sgNT_YAPi_NOTCHi_rep2


title: PRAD_sgFoxa1-2_rep2

description: Library name: PRAD_sgFoxa1-2_rep2


title: 4_WT_YAPi_NOTCHi_D8_Rep3

description:
Library name: 4_WT_YAPi_NOTCHi_D8_Rep3
4c_S30_L001


title: 5_PtP_YAPi_NOTCHi_D8_Rep3

description:
Library name: 5_PtP_YAPi_NOTCHi_D8_Rep3
5c_S31_L001


title: PRAD_sgFoxa1-1_rep1

description: Library name: PRAD_sgFoxa1-1_rep1


title: PRAD_sgFoxa1-2_rep1

description: Library name: PRAD_sgFoxa1-2_rep1


title: PRAD_sgFoxa1-1_rep2

description: Library name: PRAD_sgFoxa1-1_rep2


title: PRAD_sgNT_rep2

description: Library name: PRAD_sgNT_rep2


title: PRAD_sgNT_rep1

description: Library name: PRAD_sgNT_rep1


title: NEPC_TEAD1

description: Library name: NEPC_TEAD1

data_processing:
Raw FASTQ files were aligned to the mouse reference genome (mm10). Peaks were identified, and normalized signal tracks (bigWig) were generated for downstream analyses.
Assembly: mus musculus mm10
Supplementary files format and content: Bigwig
Library strategy: CUT&Run

extract_protocol:
Organoids were dissociated to obtain intact nuclei for CUT and RUN library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for CUT and RUN.


title: 4_WT_YAPi_NOTCHi_D8_Rep1

description:
Library name: 4_WT_YAPi_NOTCHi_D8_Rep1
4a_S4_L001


title: PRAD_TEAD1

description: Library name: PRAD_TEAD1


title: PRAD_YAP1

description: Library name: PRAD_YAP1


title: PRAD_FOXA1_2

description: Library name: PRAD_FOXA1_2


title: NEPC_FOXA1_2

description: Library name: NEPC_FOXA1_2


title: NEPC_FOXA1_1

description: Library name: NEPC_FOXA1_1


title: PRAD_FOXA1_1

description: Library name: PRAD_FOXA1_1


title: Allograft, tacrolimus+anti-Gr-1 antibody (Day 8 to Day 15), Day15

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

country: China

institute: The second xiangya hospital of central south university

description:
Library name: Sample4
SeekOne DD
One sample from murine corneal tissue 15 days post-transplantation.

data_processing:
Raw sequencing data were processed through consensus assessment of sequence and variation (CASAVA) for base calling and conversion into Sequenced Reads, which were then stored in the FASTQ format. Sequencing adapters and low-quality fragments were trimmed before alignment to the reference genome using STAR software. Subsequently, gene expression levels were quantified using the FeatureCounts software, resulting in the generation of a preliminary cell-gene expression matrix. To obtain clean data, cells with low RNA expression in the matrix were filtered out using the EmptyDrops software. The count data were then imported into the Seurat R package for quality control analysis of each sample. Cells with fewer than 500 detected genes or a proportion of mitochondrial genes exceeding 10% were excluded, and genes expressed in fewer than five cells were removed. Doublets were identified and removed using the DoubletFinder package, where the Bayesian corrected Mahalanobis distance (BCMVN) was calculated for each sample to determine the optimal “pK_value,” with the “pN_value” set to 0.25. Each sample underwent these filtering procedures individually to prepare for subsequent analyses.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Mouse Cornea

extract_protocol:
Corneas (n=4-6) were isolated and each cornea was placed in 1 ml of 0.25% trypsin. Samples were incubated at 37°C for 1 hour, with mixing every 10 minutes. After incubation, 200 μl FBS was added to the wells of a 24-well plate. The corneas were then mechanically dissociated using a 2.5 ml syringe. The resulting suspension was filtered through a 40 μm cell strainer into a flow cytometry tube. The well plate and strainer were washed with 4 ml of 2% FBS-1640 medium. The cell suspension was centrifuged at 1300 RPM for 5 minutes, and the supernatant was discarded.
Each cornea was processed independently using the SeekOne® Digital Droplet System (SeekOne® DD) to complete the workflow from labeling single-cell nucleic acids to constructing the transcriptome library.  The entire procedure followed the manufacturer’s instructions for the SeekOne Digital Droplet Single-Cell 3′ library preparation kit (SeekGene), resulting in the generation of a single-cell transcriptome library suitable for high-throughput sequencing.  All libraries underwent quality testing using the Agilent 4200 TapeStation.  Qualified libraries exhibited a primary peak fragment size between 350 and 750 bp, with no small fragments, and a library concentration of at least 1 ng/μl, as measured by the Qubit 4.0.  Subsequently, the libraries were sequenced on an Illumina NovaSeq 6000 System with paired-end 150 bp read length, aiming for an approximate coverage of 50,000 raw reads per cell.

value: Mouse Cornea

value: Corneal stromal cells, corneal endothelial cells, fibroblasts, vascular endothelial cells, vascular smooth muscle cells, T cells, monocyte and dendritic cells

tag: genotype

value: C57BL/6 and BALB/c

tag: age

value: 8-10 weeks

value: tacrolimus++anti-Gr-1 antibody

value: Wild type


title: Allograft, tacrolimus+anti-Gr-1 antibody (Day 0 to Day 7), Day15

description:
Library name: Sample3
SeekOne DD
One sample from murine corneal tissue 15 days post-transplantation.


title: Allograft, IL-19, Day15

description:
Library name: Sample1
SeekOne DD
One sample from murine corneal tissue 15 days post-transplantation.


title: Isograft, Day15, scRNAseq

description: One sample from murine corneal tissue 15 days post-transplantation.

extract_protocol:
Corneas (n=4) were isolated and each cornea was placed in 1 ml of 0.25% trypsin. Samples were incubated at 37°C for 1 hour, with mixing every 10 minutes. After incubation, 200 μl FBS was added to the wells of a 24-well plate. The corneas were then mechanically dissociated using a 2.5 ml syringe. The resulting suspension was filtered through a 40 μm cell strainer into a flow cytometry tube. The well plate and strainer were washed with 4 ml of 2% FBS-1640 medium. The cell suspension was centrifuged at 1300 RPM for 5 minutes, and the supernatant was discarded.
Each cornea was processed independently using the SeekOne® Digital Droplet System (SeekOne® DD) to complete the workflow from labeling single-cell nucleic acids to constructing the transcriptome library.  The entire procedure followed the manufacturer’s instructions for the SeekOne Digital Droplet Single-Cell 3′ library preparation kit (SeekGene), resulting in the generation of a single-cell transcriptome library suitable for high-throughput sequencing.  All libraries underwent quality testing using the Agilent 4200 TapeStation.  Qualified libraries exhibited a primary peak fragment size between 350 and 750 bp, with no small fragments, and a library concentration of at least 1 ng/μl, as measured by the Qubit 4.0.  Subsequently, the libraries were sequenced on an Illumina NovaSeq 6000 System with paired-end 150 bp read length, aiming for an approximate coverage of 50,000 raw reads per cell.

tag: strain

value: BALB/c


title: Allograft, tacrolimus, Day15, scRNAseq

value: Tacrolimus


title: Allograft, Demeclocycline, Day15

description:
Library name: Sample2
SeekOne DD
One sample from murine corneal tissue 15 days post-transplantation.

value: Demeclocycline


title: Allograft, rapamycin, Day15, scRNAseq

value: Rapamycin


title: L. interrogans sv. Hardjo str. KR95, 72h in vivo (DMC model), rep3

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: Z43

data_processing:
FastQC, Flexbar, Bowtie2 and HTSeq-count were used for read quality assessment, trimming, genome alignment and read counting, respectively.
Assembly: Reads were mapped to the strain-specific RefSeq genomes: KR40 (GCF_023158895.1), N116 (GCF_023515975.1), KR93 (GCF_028402405.1) and KR95 (GCF_026013485.1).
Supplementary files format and content: tab-delimited text file (HTSeq-count output), one file per sample, containing raw read counts per annotated gene (locus tag) in the corresponding strain-specific RefSeq genome

organism: Leptospira interrogans

source_name: Bacterial cells

growth_protocol: Bacteria were grown in T80/40/LH culture medium, at 28°C under aerobic conditions for 4 days until mid-exponential phase.

extract_protocol:
Bacterial pellets were used for total RNA isolation using TRI Reagent™ Solution (ThermoFisher). Integrity of the isolated RNA was analysed using TapeStation RNA ScreenTapes (Agilent Technologies) and only samples with RIN>7 were used.
5 µg of the purified total RNA was used as an input for ribosomal RNA depletion with Ribo-off rRNA Depletion Kit V2 (Bacteria) and library preparation with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme). Library quality was assesed using TapeStation D1000 ScreenTape (Agilent Technologies) and quantified with Qubit dsDNA BR kit (ThermoFisher).

treatment_protocol: For in vivo samples, leptospires were incubated in dialysis membrane chambers (DMCs) made from Spectra-Por dialysis tubing (8,000 Da MW cutoff). Each DMC was filled with 100 ml ML medium containing 10% bovine serum albumin and 10^6 organisms per ml. The DMCs were implanted into the sheep's peritoneal cavity. The DMCs were surgically implanted into the peritoneal cavity of sheep and recovered after 24 or 72 h of incubation.

value: Bacterial cells

value: in vivo incubation

tag: time

tag: serovar

value: Copenhageni


title: L. interrogans sv. Hardjo str. KR95, 24h in vivo (DMC model), rep3

description: Library name: Z40


title: L. interrogans sv. Hardjo str. KR95, 24h in vivo (DMC model), rep2

description: Library name: Z36


title: L. interrogans sv. Hardjo str. KR95, 72h in vivo (DMC model), rep1

description: Library name: Z41


title: L. interrogans sv. Hardjo str. KR95, 24h in vivo (DMC model), rep1

description: Library name: Z32


title: L. interrogans sv. Hardjo str. KR95, in vitro, rep3

description: Library name: Z28

value: in vitro culture


title: L. interrogans sv. Hardjo str. KR95, in vitro, rep2

description: Library name: Z24


title: L. interrogans sv. Hardjo str. KR95, in vitro, rep1

description: Library name: Z20


title: L. interrogans sv. Hardjo str. KR93, 72h in vivo (DMC model), rep3

description: Library name: Z39

value: Icterohaemorrhagiae


title: L. interrogans sv. Hardjo str. KR93, 72h in vivo (DMC model), rep2

description: Library name: Z35


title: L. interrogans sv. Hardjo str. KR93, 72h in vivo (DMC model), rep1

description: Library name: Z31


title: L. interrogans sv. Hardjo str. KR93, 24h in vivo (DMC model), rep3

description: Library name: Z27


title: L. interrogans sv. Hardjo str. KR93, 24h in vivo (DMC model), rep2

description: Library name: Z23


title: L. interrogans sv. Hardjo str. KR93, in vitro, rep2

description: Library name: Z9


title: L. interrogans sv. Hardjo str. KR93, in vitro, rep1

description: Library name: Z1


title: L. interrogans sv. Hardjo str. KR93, 24h in vivo (DMC model), rep1

description: Library name: Z19


title: L. interrogans sv. Hardjo str. N116, 72h in vivo (DMC model), rep3

description: Library name: Z38

value: Hardjo


title: L. interrogans sv. Hardjo str. N116, 72h in vivo (DMC model), rep2

description: Library name: Z34


title: L. interrogans sv. Hardjo str. N116, 24h in vivo (DMC model), rep3

description: Library name: Z26


title: L. interrogans sv. Hardjo str. N116, 24h in vivo (DMC model), rep2

description: Library name: Z22


title: L. interrogans sv. Hardjo str. N116, 24h in vivo (DMC model), rep1

description: Library name: Z18


title: L. interrogans sv. Hardjo str. N116, in vitro, rep2

description: Library name: Z10


title: L. interrogans sv. Hardjo str. KR40, 72h in vivo (DMC model), rep3

description: Library name: Z37


title: L. interrogans sv. Hardjo str. N116, in vitro, rep1

description: Library name: Z4


title: L. interrogans sv. Hardjo str. N116, in vitro, rep3

description: Library name: Z14


title: L. interrogans sv. Hardjo str. KR40, 72h in vivo (DMC model), rep1

description: Library name: Z29


title: L. interrogans sv. Hardjo str. KR40, 24h in vivo (DMC model), rep3

description: Library name: Z25


title: L. interrogans sv. Hardjo str. KR40, 24h in vivo (DMC model), rep1

description: Library name: Z17


title: L. interrogans sv. Hardjo str. KR40, 24h in vivo (DMC model), rep2

description: Library name: Z21


title: L. interrogans sv. Hardjo str. KR40, in vitro, rep2

description: Library name: Z12


title: L. interrogans sv. Hardjo str. KR40, in vitro, rep1

description: Library name: Z3


title: ROI 57 CD3

type: protein

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_03.RCC

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing:
Each RCC file represents one nCounter readout lane, and multiple samples are pooled within the same lane to generate the .RCC file. The GeoMx software then separates the readout and assigns the data back to each individual sample (ROI).
The counts file was generated from the nCounter RCC files, and the normalized values were calculated in R(4.4.1) by normalizing the raw digital counts to the total number of nuclei within each segment.

molecule: protein

source_name: human ENKTL biopsies

growth_protocol: Not applicable.

extract_protocol: Antibody incubations and Ncounter readout were performed as per standardised Nanostring GeoMX DSP protocol

treatment_protocol: Not applicable.

tag: tissue type

value: human FFPE

tag: segment

value: CD3+ tumor


title: ROI 55 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_07.RCC

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: ROI 56 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_01.RCC

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: ROI 54 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_09.RCC


title: ROI 52 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_05.RCC


title: ROI 51 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_07.RCC


title: ROI 49 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_05.RCC


title: ROI 47 CD3


title: ROI 45 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_03.RCC


title: ROI 46 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_01.RCC


title: ROI 44 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_11.RCC


title: ROI 42 CD3


title: ROI 40 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_11.RCC


title: ROI 39 CD3


title: ROI 38 CD3


title: ROI 37 CD3


title: ROI 35 CD3


title: ROI 34 CD3


title: ROI 33 CD3


title: ROI 32 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_05.RCC


title: Allograft, PBS, Day15, scRNAseq

value: Mouse Cornea

value: Corneal stromal cells, corneal endothelial cells, fibroblasts, vascular endothelial cells, vascular smooth muscle cells, T cells, monocyte and dendritic cells

value: PBS


title: ROI 31 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_11.RCC


title: L. interrogans sv. Hardjo str. KR95, 72h in vivo (DMC model), rep2

description: Library name: Z42


title: ROI 30 CD3


title: ROI 29 CD3


title: ROI 28 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_09.RCC


title: L. interrogans sv. Hardjo str. KR93, in vitro, rep3

description: Library name: Z13


title: L. interrogans sv. Hardjo str. N116, 72h in vivo (DMC model), rep1

description: Library name: Z30


title: ROI 27 CD3


title: ROI 26 CD3


title: L. interrogans sv. Hardjo str. KR40, 72h in vivo (DMC model), rep2

description: Library name: Z33


title: ROI 24 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_03.RCC


title: ROI 25 CD3


title: ROI 23 CD3


title: L. interrogans sv. Hardjo str. KR40, in vitro, rep3

description: Library name: Z16


title: ROI 22 CD3


title: ROI 41 CD3


title: ROI 21 CD3


title: ROI 20 CD3


title: ROI 19 CD3


title: ROI 18 CD3


title: ROI 58 CD3


title: ROI 53 CD3


title: ROI 17 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_09.RCC


title: ROI 16 CD3


title: ROI 15 CD3


title: ROI 14 CD3


title: ROI 13 CD3


title: ROI 12 CD3


title: ROI 11 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_01.RCC


title: ROI 10 CD3


title: ROI 48 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_03.RCC


title: ROI 50 CD3


title: ROI 6 CD3


title: ROI 8 CD3


title: ROI 9 CD3


title: ROI 5 CD3


title: ROI 7 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_07.RCC


title: ROI 4 CD3


title: ROI 3 CD3


title: ROI 2 CD3


title: ROI 1 CD3


title: ROI 57 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_04.RCC

value: CD68+ macrophage


title: ROI 58 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_12.RCC


title: TCPMOH_N4_10um

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

description: Library name: TCPMOH_N4_10um

data_processing:
Reads were aligned to the human genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than four across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the DEseq2 Package for R statistical computing.
Assembly: hg38
Supplementary files format and content: tabular files with raw counts ,as process in featureCounts

source_name: Placenta

growth_protocol: Cells were cultured between passages 25-35 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
RNeasy Mini Kit
Stranded sequencing libraries for HTR-8/SVneo cells were prepared using the TruSeq Stranded mRNA Library Prep Kit with poly A enrichment (Illumina).

treatment_protocol: Cells were cultured between passages 78–84 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator. Cells were grown to 70–90% confluence at least 24 h after plating prior to use in any experiments. Cells were seeded at a density of 400,000 cells per well in 6-well cell culture plates. Twenty-four hours later, cells were treated with RPMI 1640 complete medium with DMSO vehicle control (0.1%v/v) or complete medium plus TCPMOH dissolved in DMSO (0.1%v/v) and diluted to a final concentration of 1 or 10 µM for 24 h.  Four independent biological replicate experiments were performed.

value: Placenta

tag: cell line

value: Extravillous trophoblast

tag: exposure time

value: 24 Hours


title: TCPMOH_N4_1um

description: Library name: TCPMOH_N4_1um


title: TCPMOH_N4_Control

description: Library name: TCPMOH_N4_Control


title: ROI 56 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_02.RCC


title: TCPMOH_N3_10um

description: Library name: TCPMOH_N3_10um


title: ROI 55 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_08.RCC


title: ROI 54 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_10.RCC


title: TCPMOH_N3_1um

description: Library name: TCPMOH_N3_1um


title: ROI 43 CD3


title: ROI 52 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_06.RCC


title: TCPMOH_N3_Control

description: Library name: TCPMOH_N3_Control


title: TCPMOH_N2_10um

description: Library name: TCPMOH_N2_10um


title: ROI 51 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_08.RCC


title: ROI 53 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_10.RCC


title: ROI 50 CD68


title: TCPMOH_N2_1um

description: Library name: TCPMOH_N2_1um


title: TCPMOH_N2_Control

description: Library name: TCPMOH_N2_Control


title: TCPMOH_N1_1um

description: Library name: TCPMOH_N1_1um


title: ROI 48 CD68


title: ROI 49 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_06.RCC


title: TCPMOH_N1_10um

description: Library name: TCPMOH_N1_10um


title: ROI 47 CD68


title: TCPMOH_N1_Control

description: Library name: TCPMOH_N1_Control


title: ROI 46 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_02.RCC


title: m15_Cre_WD_5

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

description: Library name: S40

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Mus musculus genome reference (GRCm39/mm39) using STAR and per transcript reads were counted with HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow.
Assembly: GRCm39/mm39
Supplementary files format and content: rawCounts.csv.gz: csv (comma-separated values) file includes ENSEMBL id and raw read counts for each transcript, in each sample

source_name: hepatocytes

extract_protocol:
Total RNA was isolated for approximately 25 mg of liver tissue using RNeasy Mini kit (Cat# 74106) from Qiagen (Valencia, CA, USA) . RNA was quantified using Qubit RNA BR Assay kit (Cat# Q10211,ThermoScientific, Waltham, MA) in a Qubit3.0 fluorometer.
RNA was checked for quality using Agilent’s 4150 Tapestation, and concentrations from ThermoFisher’s NanoDrop readings were used. Stranded RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit followed directly by IDT’s XGen Broad Range RNA Library Prep Kit and the established protocols.  The library construction was done using 1mg of RNA. Each of the libraries was indexed during library construction in order to multiplex for sequencing. Libraries were quantified using Invitrogen’s Qubit 4 fluorometer and checked for size and quality on Agilent’s 4150 Tapestation.  Samples were normalized and pooled onto a 150 paired end run on Illumina HiSeq 2500 Platform to obtain 20M reads per sample.

treatment_protocol: Male Mlklfl/fl mice on a C57BL/6J background were injected with AAV8-TBG-Cre (hepatocyte-specific) or AAV8-TBG-Null  via tail vein at 1.5 months of age to generate hepatocyte-specific Mlkl knockout (MlklHepKO) or control mice. Beginning at 2.5 months of age, mice were fed ad libitum either a control diet (CD) or a Western diet (WD) ) for 4, 8, or 15 months.  Liver was dissected out, RNA isolated using Qiagen RNeasy mini kit and was used for RNA sequencing.

value: hepatocytes

tag: study time

value: 15 months

tag: knockout

value: KO

tag: diet

value: WD


title: ROI 45 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_04.RCC


title: OGTAC rep 2

city: Hong Kong

first: Tongyang

last: Xu

address: 8/F, Area 39, CUHK

department: School of Pharmacy

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: B2

data_processing:
Analysis of the NGS data was performed in the manufacturer’s platform (Vazyme, Cut&Tag_Tool.v2.0). Data was primarily filtered in cutadapt v1.12 and normalized by spike-in and aligned to the human reference genome (hg38) in bowtie2 v2.2.9. Visualization and peak calling were performed in Macs2 v2.2.6. Difference analysis was performed in MAnorm2-utils v1.0.0 and MAnorm2 v1.2.2.
Assembly: hg38
Supplementary files format and content: bigwig (peak files)
Library strategy: CUT&Tag

growth_protocol: DMEM, supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. Cells were cultured and maintained at 37℃ with 5% CO2

extract_protocol:
Cut&Tag was performed following the manufacturer’s protocol (Vazyme, TD904), and next generation sequencing (NGS) of the constructed library was performed by Genewiz. After treating, 10,000 cells were collected, and subsequently incubated with ConA Beads Pro in the kit, followed by incubation with c-Myc antibody (Abcam, ab32072, 1μg every 50 μL system) at 4 ℃ overnight. Next, secondary antibody was incubated for 1 hour, and then treated with Hyperactive pA/G-Transposon Pro provided in the kit. Subsequently, DNA was extracted as manufacturer's instructions.
The library was constructed using the components in the Vazyme TD904 kits, under the instructions accordingly. In short, the resuspended DNA extract beads Pro in the kit were mixed with adapters. Libraries were amplified using 11 cycles on the thermocycler. The post amplification library were quality controlled (monitored) by 1% agarose gel.

treatment_protocol: In short, 2.5 × 10^6 HEK293T-fOGT cells were seeded in 10 cm dishes overnight, and then Flag-c-Myc plasmids were transfected for 24 h. After changing medium, treat CBD or OGTAC (1 μg/mL) for another 24 h.

value: Human Embryonic Kidney 293 cells containing the SV40 Large T-antigen

value: Stably transfect FKBP12(F36V)-HA-OGT, with Flag-c-Myc-OE

value: OGTAC (O-GlcNAcylation Targeting Chimera)

tag: antibody

value: abcam, #ab32072


title: m15_Cre_WD_4

description: Library name: S39


title: ROI 44 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_12.RCC

value: human FFPE


title: m15_Cre_WD_3

description: Library name: S38


title: m15_Cre_WD_2

description: Library name: S37


title: OGTAC rep 1

description: Library name: B1

tag: treatment


title: m15_Cre_WD_1

description: Library name: S36


title: m15_Cre_CD_5

description: Library name: S35

value: CD


title: CBD control rep 2

description: Library name: A2

value: CBD (c-Myc-binding DNA complex)


title: ROI 42 CD68


title: ROI 43 CD68


title: CBD control rep 1

description: Library name: A1


title: m15_Cre_CD_3

description: Library name: S33


title: m15_Cre_CD_4

description: Library name: S34


title: m15_Cre_CD_2

description: Library name: S32


title: ROI 41 CD68


title: SH-SY5Y cells, oeMCART1, MPP+ treated, rep3

city: Shanghai

first: shiliang

last: wang

address: Dongan Road No.130

institute: Fudan university

description: Library name: oeMCART1_MPP_3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each Sample

source_name: bone marrow

growth_protocol: Human HEK293T and SH-SY5Y cells were incubated in DMEM (Thermo Fisher Scientific) containing 10% FBS (Sigma) and 1% penicillin/streptomycin (MeilunBio), under an environment of 37 °C with 5% CO2.

extract_protocol:
SH-SY5Y cells were collected and lysed with TRIzol. Total RNA was extracted from cells for library preparation.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following the manufacturer's standard protocols. Briefly, mRNA was enriched from total RNA via oligo-dT capture, reverse transcribed to cDNA, end-repaired, A-tailed, ligated with sequencing adapters, and amplified by PCR to construct strand-specific RNA-seq libraries.

treatment_protocol: For establishment of the cellular PD model, 0.5 mM 1-methyl-4-phenyl-pyridine (MPP+, MCE 36913-39-0) was added to SH-SY5Y cells for 24 h.

tag: tissue

value: bone marrow

value: human neuroblastoma cell

value: oeMCART1, MPP+ treated


title: m15_Cre_CD_1

description: Library name: S31

tag: cell type


title: m15_Null_WD_5

description: Library name: S30


title: ROI 40 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_12.RCC

value: CD68+ macrophage


title: SH-SY5Y cells, oeMCART1, MPP+ treated, rep1

description: Library name: oeMCART1_MPP_1


title: ROI 36 CD3

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_09.RCC

value: CD3+ tumor


title: m15_Null_WD_3

description: Library name: S28


title: m15_Null_WD_1

description: Library name: S26


title: SH-SY5Y cells, oeMCART1, MPP+ treated, rep2

description: Library name: oeMCART1_MPP_2


title: m15_Null_WD_2

description: Library name: S27


title: SH-SY5Y cells, oeNC, MPP+ treated, rep3

description: Library name: oeNC_MPP_3

value: oeNC, MPP+ treated


title: ROI 39 CD68


title: m15_Null_CD_5

description: Library name: S25

value: hepatocytes


title: m15_Null_CD_4

description: Library name: S24

value: 15 months


title: ROI 38 CD68


title: ROI 37 CD68


title: SH-SY5Y cells, oeNC, MPP+ treated, rep2

description: Library name: oeNC_MPP_2


title: m15_Null_CD_3

description: Library name: S23


title: m15_Null_CD_2

description: Library name: S22


title: m15_Null_CD_1

description: Library name: S21


title: ROI 36 CD68


title: SH-SY5Y cells, oeNC, MPP+ treated, rep1

description: Library name: oeNC_MPP_1


title: m8_MLKL_Hep_KO_WD_5

description: Library name: S20

value: 8 months

value: KO


title: Zebrafish testes bulk RNA-seq - Uninjured_10

description:
Library name: Uninjured_10
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.

data_processing:
Quality control of raw sequencing reads was assessed using FastQC v0.11.9 (Andrews, 2010) and aggregated with MultiQC v1.12 (P. Ewels et al., 2016).
Adapter trimming and quality filtering were performed using Fastp v0.23.2 (Chen et al., 2018).
Zebrafish testes samples were aligned to GRCz11 using Ensembl release 115.
Reads were aligned to the reference genome using STAR v2.7.10a (Dobin et al., 2013).
Gene-level read counts were generated using featureCounts from the Subread package v2.0.3 (Liao et al., 2014).
Differential expression analysis was conducted in R v4.4.0 using DESeq2 v1.44.0 (Love et al., 2014) with a design formula of ~condition.
Log2 fold change shrinkage was applied using ashr v2.2.63. Differentially expressed genes required |log2FC| > 0.58.
Genes with adjusted p-value < 0.05 (Benjamini-Hochberg correction) and |log2FC| above the species-specific threshold were considered differentially expressed.
Cross-species pathway analysis: Over-representation analysis (ORA) was performed using clusterProfiler v4.12.2 (Wu et al., 2021; Yu et al., 2012) and ReactomePA v1.48.0, with parallel execution via BiocParallel v1.38.0.
Data visualization was performed using ComplexHeatmap v2.20.0, pheatmap v1.0.12 (Kolde, 2019), ggplot2 v3.5.1 (Wickham, 2016), and ggrepel v0.9.5.
Batch correction across the two experimental batches (Experiment 1: uninjured/7 dpi/130 dpi; Experiment 2: uninjured/1 dpi) was performed using ComBat-seq from the sva package v3.52.0. Sample '130_dpi_5' was identified as a PCA outlier and excluded from downstream (but not raw-data) analyses.
Zebrafish gene identifiers were converted to mouse orthologs using the Alliance of Genome Resources Orthology file.
Assembly: Danio rerio GRCz11, Ensembl release 115
Supplementary files format and content: Gene-level read count matrix (featureCounts).

source_name: testis

extract_protocol:
Tissues washed in PBS and snap frozen. On the day of RNA extraction, samples were homogenized in TRI Reagent (Sigma-Aldrich) using 21G and 30G syringes (BD Microlance). Following phase separation with 1-bromo-3-chloropropane (Sigma-Aldrich), the aqueous phase was mixed with an equal volume of ethanol, and RNA was purified using the RNA Clean & Concentrator kit (Zymo Research) with on-column DNase I treatment. RNA quantity and quality were assessed using a NanoDrop and a Fragment Analyzer before library preparation and sequencing.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina, 20020595) in combination with TruSeq RNA UD Indexes (Illumina, 20022371) at the Next Generation Sequencing Platform, University of Bern (Switzerland). RNA quantity/quality was assessed using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit RNA BR Assay Kit (Q10211) and an Advanced Analytical Fragment Analyzer System with a Fragment Analyzer RNA Kit (Agilent, DNF-471); resulting cDNA libraries were evaluated using a Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit (Q32854) and an Agilent Fragment Analyzer with a HS NGS Fragment Kit (DNF-474). Batch 1 (Experiment 1: uninjured, 7 dpi, 130 dpi; Run 264, June 2024) used 1000 ng total RNA input and was sequenced paired-end 2x51 bp on an Illumina NovaSeq 6000 instrument using an SP Reagent Kit v1.5 (100 cycles; Illumina, 20028401). Batch 2 (Experiment 2: uninjured, 1 dpi; Run 452, November 2025) was sequenced paired-end 2x151 bp on an Illumina NovaSeq 6000 instrument using an SP Reagent Kit (300 cycles; Illumina, 20028400). Sequencing run quality was assessed using Illumina Sequencing Analysis Viewer (v2.4.7); base call files were demultiplexed and converted to FASTQ using Illumina bcl2fastq conversion software v2.20.

treatment_protocol: Testes from four sibling male zebrafish pooled per biological replicate. Five biological replicates per condition (1, 7, and 130 dpi, and uninjured controls). Processed in two experimental batches: Experiment 1 = uninjured, 7 dpi, 130 dpi; Experiment 2 = uninjured, 1 dpi; data combined after batch correction. Sample '130_dpi_5' was identified as a PCA outlier and excluded from downstream (but not raw-data) analyses.

value: testis

value: Uninjured

tag: batch


title: SH-SY5Y cells, shMCART1, MPP+ treated, rep3

description: Library name: shMCART1_MPP_3

value: shMCART1, MPP+ treated


title: ROI 35 CD68


title: Zebrafish testes bulk RNA-seq - Uninjured_9

description:
Library name: Uninjured_9
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 34 CD68


title: SH-SY5Y cells, shMCART1, MPP+ treated, rep2

description: Library name: shMCART1_MPP_2


title: ROI 33 CD68


title: Zebrafish testes bulk RNA-seq - Uninjured_8

description:
Library name: Uninjured_8
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: m8_MLKL_Hep_KO_WD_4

description: Library name: S19

value: WD


title: SH-SY5Y cells, shMCART1, MPP+ treated, rep1

description: Library name: shMCART1_MPP_1


title: m8_MLKL_Hep_KO_WD_3

description: Library name: S18


title: Zebrafish testes bulk RNA-seq - Uninjured_7

description:
Library name: Uninjured_7
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: SH-SY5Y cells, shScramble, MPP+ treated, rep3

description: Library name: shScramble_MPP_3

value: shScramble, MPP+ treated


title: ROI 32 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_06.RCC

value: human FFPE


title: m8_MLKL_Hep_KO_WD_2

description: Library name: S17


title: SH-SY5Y cells, shScramble, MPP+ treated, rep2

description: Library name: shScramble_MPP_2


title: Zebrafish testes bulk RNA-seq - Uninjured_6

description:
Library name: Uninjured_6
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 31 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_12.RCC


title: m8_MLKL_Hep_KO_WD_1

description: Library name: S16


title: Zebrafish testes bulk RNA-seq - 1_dpi_5

description:
Library name: 1_dpi_5
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.

value: 1 dpi


title: ROI 30 CD68


title: SH-SY5Y cells, shScramble, MPP+ treated, rep1

description: Library name: shScramble_MPP_1

value: bone marrow


title: Zebrafish testes bulk RNA-seq - 1_dpi_4

description:
Library name: 1_dpi_4
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: m8_MLKL_Hep_KO_CD_5

description: Library name: S15

value: CD


title: SH-SY5Y cells, oeMCART1, rep3

description: Library name: oeMCART1_3

value: human neuroblastoma cell


title: m8_MLKL_Hep_KO_CD_4

description: Library name: S14


title: SH-SY5Y cells, oeMCART1, rep2

description: Library name: oeMCART1_2


title: Zebrafish testes bulk RNA-seq - 1_dpi_3

description:
Library name: 1_dpi_3
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: m8_MLKL_Hep_KO_CD_3

description: Library name: S13


title: m8_MLKL_Hep_KO_CD_2

description: Library name: S12


title: SH-SY5Y cells, oeMCART1, rep1

description: Library name: oeMCART1_1


title: ROI 26 CD68

value: CD68+ macrophage


title: SH-SY5Y cells, oeNC, rep3

description: Library name: oeNC_3

value: oeNC


title: Zebrafish testes bulk RNA-seq - 1_dpi_1

description:
Library name: 1_dpi_1
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 25 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_04.RCC


title: Zebrafish testes bulk RNA-seq - Uninjured_5

description:
Library name: Uninjured_5
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: SH-SY5Y cells, oeNC, rep2

description: Library name: oeNC_2


title: m8_Null_WD_5

description: Library name: S10


title: Zebrafish testes bulk RNA-seq - Uninjured_4

description:
Library name: Uninjured_4
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 24 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_04.RCC


title: SH-SY5Y cells, oeNC, rep1

description: Library name: oeNC_1


title: m8_Null_WD_4

description: Library name: S9


title: Zebrafish testes bulk RNA-seq - Uninjured_3

description:
Library name: Uninjured_3
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 23 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_08.RCC


title: m8_Null_WD_3

description: Library name: S8


title: SH-SY5Y cells, shMCART1, rep3

description: Library name: shMCART1_3


title: ROI 22 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_10.RCC


title: Zebrafish testes bulk RNA-seq - Uninjured_2

description:
Library name: Uninjured_2
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: SH-SY5Y cells, shMCART1, rep2

description: Library name: shMCART1_2


title: Zebrafish testes bulk RNA-seq - Uninjured_1

description:
Library name: Uninjured_1
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: m8_Null_WD_2

description: Library name: S7


title: ROI 21 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_02.RCC


title: SH-SY5Y cells, shMCART1, rep1

description: Library name: shMCART1_1


title: m8_Null_WD_1

description: Library name: S6


title: PRAD_DMSO_D8_Rep3

description:
Library name: PRAD_DMSO_D8_Rep3
AD5DMSO-3_IGO_16181_3_S30_L004

value: prostate organoid


title: ROI 20 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_08.RCC


title: Zebrafish testes bulk RNA-seq - 130_dpi_5

description:
Library name: 130_dpi_5
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.

value: 130 dpi


title: SH-SY5Y cells, shScramble, rep3

description: Library name: shScramble_3

value: shScramble


title: ROI 19 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_06.RCC


title: m8_Null_CD_5

description: Library name: S5

value: hepatocytes

value: 8 months


title: Zebrafish testes bulk RNA-seq - 130_dpi_4

description:
Library name: 130_dpi_4
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.

value: testis


title: SH-SY5Y cells, shScramble, rep2

description: Library name: shScramble_2


title: m8_Null_CD_4

description: Library name: S4


title: ROI 18 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_04.RCC


title: Zebrafish testes bulk RNA-seq - 130_dpi_3

description:
Library name: 130_dpi_3
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: SH-SY5Y cells, shScramble, rep1

description: Library name: shScramble_1


title: m8_Null_CD_3

description: Library name: S3


title: Zebrafish testes bulk RNA-seq - 130_dpi_2

description:
Library name: 130_dpi_2
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 17 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_10.RCC


title: m8_Null_CD_2

description: Library name: S2


title: Zebrafish testes bulk RNA-seq - 130_dpi_1

description:
Library name: 130_dpi_1
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: ROI 29 CD68


title: E2-8: anterior vaginal wall, estrogen-treated, scRNA-seq

city: Taiyuan

first: Xiaochun

last: Liu

state: Shanxi

address: No.99 Longcheng Street, Xiaodian district

department: department of gynecology and obstetrics

institute: Shanxi Bethune Hospital

description:
Library name: E2-8_sc
GEXSCOPE

data_processing:
For scRNA-seq: raw sequencing data were processed using the CeleScope pipeline (v1.9.0, Singleron). Low-quality reads and adapter sequences were trimmed using Cutadapt (v1.17). Clean reads were aligned to the GRCh38 reference genome (Ensembl version 92) using STAR (v2.6.1a). Gene expression counts were generated using featureCounts (v2.0.1). For spatial transcriptomics: data were processed using Space Ranger (10x Genomics) to generate count matrices.
Quality control and clustering were performed using the Seurat R package (v5.0). Cells with fewer than 200 genes or more than the top 2% of gene counts were filtered out. Mitochondrial gene content exceeding 10% was excluded. Batch effects across patient samples were corrected using Seurat v5.0 Reciprocal PCA (RPCA) integration.
For spatial transcriptomics analysis: data were analyzed in Seurat (v5.0) using the Load10X Spatial function. Spots with fewer than 10 UMI counts were filtered out. Integration of scRNA-seq and spatial transcriptomics data was performed using the Seurat integration pipeline. Anchor points were identified with FindTransferAnchors, and cell type labels from scRNA-seq were transferred to spatial spots using TransferData.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files containing gene expression count matrices for scRNA-seq (filtered feature-barcode matrices) and spatial transcriptomics (spatial count matrices).

source_name: anterior vaginal wall

growth_protocol: Not applicable (human tissue biopsy)

extract_protocol:
Fresh vaginal anterior wall tissues were collected during transvaginal reconstructive surgery. Tissues were washed three times with HBSS, minced into small pieces, and digested with 3 mL sCelLiveTM Tissue Dissociation Solution using the Singleron PythoNTM Tissue Dissociation System at 37°C for 15 minutes. The cell suspension was filtered through a 40-μm sterile strainer. Red blood cells were lysed using GEXSCOPE® Red Blood Cell Lysis Buffer (RCLB, Singleron) at a volume ratio of 1:2 (cell pellet:RCLB) for 5-8 minutes at room temperature. The mixture was centrifuged at 300 × g at 4°C for 5 minutes, and the pellet was resuspended in PBS. For spatial transcriptomics: FFPE vaginal tissue sections were cut at 5 μm thickness and mounted onto Visium HD slides (10x Genomics).
For scRNA-seq: single-cell suspensions were adjusted to 2 × 10^5 cells/mL in PBS. Cells were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding beads were collected, and reverse transcription was performed to synthesize cDNA. cDNA was amplified by PCR, fragmented, and ligated with sequencing adapters using the GEXSCOPE® Single Cell RNA Library Kit (Singleron). For spatial transcriptomics: libraries were prepared using the Visium HD Spatial Gene Expression protocol for FFPE (10x Genomics) following manufacturer's instructions.

treatment_protocol: Estrogen-treated group: topical promestriene applied once daily for 6 weeks prior to biopsy. Untreated control group: no estrogen treatment.

value: anterior vaginal wall

value: mixed vaginal cells

value: topical vaginal estrogen


title: m8_Null_CD_1

description: Library name: S1


title: E2-7: anterior vaginal wall, estrogen-treated, scRNA-seq

description:
Library name: E2-7_sc
GEXSCOPE


title: ROI 16 CD68


title: ROI 15 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_10.RCC


title: ROI 28 CD68


title: Zebrafish testes bulk RNA-seq - 7_dpi_5

description:
Library name: 7_dpi_5
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.

value: 7 dpi


title: E2-6: anterior vaginal wall, estrogen-treated, spatial transcriptomics

description:
Library name: E2-6_st
Visium

data_processing:
For scRNA-seq: raw sequencing data were processed using the CeleScope pipeline (v1.9.0, Singleron). Low-quality reads and adapter sequences were trimmed using Cutadapt (v1.17). Clean reads were aligned to the GRCh38 reference genome (Ensembl version 92) using STAR (v2.6.1a). Gene expression counts were generated using featureCounts (v2.0.1). For spatial transcriptomics: data were processed using Space Ranger (10x Genomics) to generate count matrices.
Quality control and clustering were performed using the Seurat R package (v5.0). Cells with fewer than 200 genes or more than the top 2% of gene counts were filtered out. Mitochondrial gene content exceeding 10% was excluded. Batch effects across patient samples were corrected using Seurat v5.0 Reciprocal PCA (RPCA) integration.
For spatial transcriptomics analysis: data were analyzed in Seurat (v5.0) using the Load10X Spatial function. Spots with fewer than 10 UMI counts were filtered out. Integration of scRNA-seq and spatial transcriptomics data was performed using the Seurat integration pipeline. Anchor points were identified with FindTransferAnchors, and cell type labels from scRNA-seq were transferred to spatial spots using TransferData.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files containing gene expression count matrices for scRNA-seq (filtered feature-barcode matrices) and spatial transcriptomics (spatial count matrices).
Library strategy: Spatial Transcriptomics

value: tissue section


title: Zebrafish testes bulk RNA-seq - 1_dpi_2

description:
Library name: 1_dpi_2
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.

value: 1 dpi


title: ROI 27 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_12.RCC

value: human FFPE


title: Spiny dogfish day 35 wound

city: Stockholm

first: Jakob

last: Wikstrom

address: K2 Medicin, Solna, K2 Derm o Ven

department: Dermatology and Venereology

country: Sweden

institute: Karolinska Institutet

description:
Library name: Spiny_dogfish_wound_day35
10X Genomics

data_processing:
Sequence demultiplexing, barcode processing, alignment, and gene counting was performed using 10X Genomics software CellRanger 7.1.0
Assembly: GenBank assembly GCA_030390025.1 (ASM3039002v1)
Supplementary files format and content: 10X Genomics h5 matrix, cell barcode x gene count

molecule: nuclear RNA

organism: Squalus acanthias

source_name: wounded skin after 35 days

extract_protocol:
Six full-thickness skin biopsies (3 mm diameter) were collected using a 3 mm punch biopsy tool (Kai Medical, Solingen, Germany). In spiny dogfish, samples were taken both from the ventral region, and the two lateral dorsal regions. These biopsies generated both intact (baseline, Day 0) and wounded tissue. Follow-up sampling was conducted on days 1, 14, and 35 post-injury. At each time point, two wounds were excised using a 6 mm punch biopsy tool (Kai Medical, Solingen, Germany).
Nuclei isolation was performed on fresh frozen tissues as previously described (Slyper et al., 2020). Low-retention microcentrifuge tubes (Fisher Scientific, Hampton, NH, USA) were used throughout the procedure to minimize nuclei loss. Briefly, tissues were manually dissociated by chopping with fine spring scissors for 10 minutes, homogenized in TST solution, filtered through a 30 um MACS SmartStrainer (Miltenyi Biotec, Germany), and pelleted by centrifugation for ten minutes at 500g at 4C. The nuclei pellet was resuspended in lysis buffer to permeabilize the nuclei before pelleting by centrifugation for 10 minutes at 500g at 4C. The final nuclei pellet was resuspended in 150 ul of 10x Genomics Diluted Nuclei Buffer, and trypan blue-stained nuclei were counted by eye using INCYTO C-Chip Neubauer Improved Disposable Hemacytometers (VWR International Ltd., Radnor, PA, USA).  Up to 10,000 cells per sample were loaded per channel of the Chromium Next GEM Chip K for processing on the 10x Chromium Controller (10x Genomics, Pleasanton, CA, USA) followed by cDNA generation and library construction, as per manufacturer’s instructions (Chromium Next GEM Single Cell 5ʹ Reagent Kits v2 User Guide, Rev E). Libraries were normalized and pooled for sequencing on an Illumina NovaSeq 6000 system using an SP100 flow cell (Illumina, Inc., San Diego, CA, USA) with run parameters 26, 10, 10, 90.

value: wounded skin after 35 days

value: Wounded skin


title: m8_MLKL_Hep_KO_CD_1

description: Library name: S11

value: KO

value: CD


title: Zebrafish testes bulk RNA-seq - 7_dpi_4

description:
Library name: 7_dpi_4
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: E2-6: anterior vaginal wall, estrogen-treated, scRNA-seq

description:
Library name: E2-6_sc
GEXSCOPE


title: Spiny dogfish day 14 wound

description:
Library name: Spiny_dogfish_wound_day14
10X Genomics

source_name: wounded skin after 14 days

value: wounded skin after 14 days


title: ROI 14 CD68

value: CD68+ macrophage


title: Zebrafish testes bulk RNA-seq - 7_dpi_3

description:
Library name: 7_dpi_3
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: E2-5: anterior vaginal wall, estrogen-treated, scRNA-seq

description:
Library name: E2-5_sc
GEXSCOPE


title: ROI 13 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_04.RCC


title: Spiny dogfish day 1 wound

description:
Library name: Spiny_dogfish_wound_day1
10X Genomics

source_name: wounded skin after 1 day

value: wounded skin after 1 day


title: Zebrafish testes bulk RNA-seq - 7_dpi_2

description:
Library name: 7_dpi_2
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: E2-4: anterior vaginal wall, estrogen-treated, scRNA-seq

description:
Library name: E2-4_sc
GEXSCOPE


title: ROI 12 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_02.RCC


title: Spiny dogfish intact skin

description:
Library name: Spiny_dogfish_intact_skin_day0
10X Genomics

source_name: intact skin

value: intact skin


title: Zebrafish testes bulk RNA-seq - 7_dpi_1

description:
Library name: 7_dpi_1
Bulk RNA-seq of zebrafish testis; library prep/sequencing by NGS Platform, University of Bern.


title: E2-3: anterior vaginal wall, estrogen-treated, scRNA-seq (Lib3)

description:
Library name: E2-3_sc_Lib3
GEXSCOPE


title: ROI 11 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_02.RCC


title: Mouse testes snATAC-seq - S7_46

description:
Library name: S7_46
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.

data_processing:
Raw sequencing reads processed with Cellranger atac v2.2.0 (10x Genomics, 2019); each sample aligned independently to the GRCm39/Ensembl 115 reference.
Downstream chromatin accessibility analysis performed in R 4.5.2 using ArchR v1.0.3. Nuclei retained if TSS enrichment score >= 4 and unique fragments >= 1,000. Doublet scores computed and predicted doublets removed (ArchR::addDoubletScores/filterDoublets).
Iterative LSI performed on the 500 bp TileMatrix (ArchR::addIterativeLSI, 2 iterations, initial clustering resolution 0.2); UMAP computed from the first 30 LSI dimensions; clustering at resolution 1.0 yielded 21 clusters (C1-C21).
Gene activity scores computed from chromatin accessibility within +/-2 kb of each gene's TSS; MAGIC-style imputation weights added to smooth gene scores.
Marker genes per broad cell type identified with ArchR::getMarkerFeatures on the GeneScoreMatrix; germ cell and somatic populations annotated (Sertoli, Leydig, immune, peritubular myoid, endothelial, fibroblast, SSCs, spermatocytes I/II, round and elongated spermatids) based on canonical marker genes.
Group pseudo-bulk coverages generated per broad cell type (ArchR::addGroupCoverages); peaks called with MACS3 using ArchR default single-nucleus parameters; reproducible consensus peak set built with ArchR::addReproduciblePeakSet; peak-by-cell matrix built with ArchR::addPeakMatrix.
Differentially accessible regions (DARs) between Injured and Uninjured identified per broad cell type using ArchR::getMarkerFeatures on the PeakMatrix (binomial test, bias correction for TSS enrichment and log10(fragment count)); cell types with fewer than 50 nuclei per condition excluded. DARs annotated with nearest gene (GenomicRanges::distanceToNearest against Ensembl 115).
ORA and GSEA performed using clusterProfiler v4.18.4 and ReactomePA for GO categories (BP/CC/MF) and Reactome pathways; ORA applied to DAR nearest genes at FDR <= 0.05 and log2FC >= 0.585; GSEA applied to the full ranked gene list (1,000 permutations).
Per-cell-type DAR BED files subjected to motif enrichment analysis using MEME Suite 5.5.8 (XSTREME) against CIS-BP 2.00 (Mus musculus), JASPAR 2022 (vertebrates core), and HOCOMOCOv11 (mouse) motif databases, with random genomic background sequences as explicit negative control.
Assembly: Mus musculus GRCm39, Ensembl 115
Supplementary files format and content: Per-sample Cellranger-atac filtered peak-barcode matrix (barcodes.tsv.gz, matrix.mtx.gz).

growth_protocol: C57BL/6J mice raised to weaning (3 wpp) then housed at 4 animals/cage (bred males isolated after first breeding); SPF facility, 20-24C, 12h light/dark, 45-65% RH, food/water ad libitum. Approved under license PROEX 310_19 (Comunidad de Madrid, Spain), conforming to EU Directive 86/609/EEC.

extract_protocol:
Testicular tissue was mechanically minced and enzymatically dissociated using trypsin-EDTA (0.25%), followed by neutralization with DMEM supplemented with FBS (10%). Cell suspensions were passed through a 70 um cell strainer, subjected to red blood cell lysis (1x RBC lysis buffer), and treated with DNase I (0.1 U/uL final concentration) to remove extracellular DNA and reduce cell clumping. After an additional filtration through a 40 um cell strainer and cell counting, nuclei were isolated from 1x10^5 - 1x10^6 cells using a detergent-based lysis buffer containing Tween-20 (0.1%), NP-40 (0.1%), digitonin (0.01%), Tris-HCl (10 mM), NaCl (10 mM), MgCl2 (3 mM), and BSA (1%). Nuclei were washed in buffer containing Tris-HCl (10 mM), NaCl (10 mM), MgCl2 (3 mM), Tween-20 (0.1%), and BSA (1%), resuspended in 1x diluted 10x Genomics Nuclei Buffer, filtered through a 40 um Flowmi cell strainer, and quantified.
Nuclei were counted and evaluated for structural integrity using a Countess III Cell Counter (Thermo Fisher Scientific). An appropriate volume corresponding to a targeted recovery of 10,000 nuclei was taken for the transposition reaction. Transposed nuclei were subsequently loaded into a Chromium Next GEM Chip H (10x Genomics) and encapsulated into gel beads-in-emulsion (GEMs) using the Chromium Controller (10x Genomics). scATAC-seq libraries were constructed using the Chromium Next GEM Single Cell ATAC Kit v2 (10x Genomics) following the manufacturer's instructions. Library amplification was carried out on a SureCycler 8800 Thermal Cycler (Agilent Technologies). Average fragment size distribution was assessed using a High Sensitivity DNA Kit on a 2100 Bioanalyzer (Agilent Technologies), and library concentrations were quantified using a Qubit Fluorometer (Thermo Fisher Scientific). Libraries were pooled in equimolar ratios and loaded at a final concentration of 700 pM onto two P3 flow cells (100 cycles) on a NextSeq 2000 System (Illumina) using a paired-end configuration (50 bp Read 1, 8 bp Index 1, 16 bp Index 2, and 50 bp Read 2). Raw sequencing data were demultiplexed, and FASTQ files were generated using the cellranger-atac mkfastq pipeline (10x Genomics).

treatment_protocol: Adult mouse testes, single-nuclei ATAC-seq. Injured vs Uninjured group assignment per sample confirmed from samplesheet.csv: S1_52/S5_53/S6_51 = Injured; S2_44/S3_47/S4_45/S7_46 = Uninjured.

value: Uninjured


title: Zebrafish sperm ATAC-seq - ST_CACI_4

description:
Library name: ST_CACI_4
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.

data_processing:
Adapters trimmed using Trim Galore (Martin, 2011).
Reads aligned to the zebrafish reference genome GRCz11 (Ensembl release 115) using Bowtie2 (Langmead & Salzberg, 2012).
BAM files processed and filtered to a mapping quality threshold of Q30 using SAMtools (Danecek et al., 2021). Duplicates removed and uniquely mapped reads selected using Picard Tools (Broad Institute, 2019). Tn5 offset correction applied (+4 bp forward strand, -5 bp reverse strand).
Peaks called on deduplicated BAM files using MACS2 (FDR 0.05; Zhang et al., 2008), yielding a consensus set of 126,797 peaks.
Differential accessibility analysis performed using DiffBind with DESeq2 normalisation (Love et al., 2014; Ross-Innes et al., 2012), comparing ST_ACI 7dpi vs ST_CACI Uninjured samples, Benjamini-Hochberg correction (padj < 0.05), log2FC thresholds 0.5/1.0/2.0.
Peak annotation with ChIPseeker (Yu et al., 2015). Pathway enrichment via clusterProfiler (Wu et al., 2021; Yu et al., 2012) and ReactomePA (Yu & He, 2016).
Motif enrichment analysis on differential peaks using MEME Suite v5.5.8 (Bailey et al., 2015), specifically XSTREME (Patel & Grant, 2022) against JASPAR 2022 CORE Vertebrate, CIS-BP v1.02, and CIS-BP v2.00 motif databases.
BigWig files generated using deepTools (Ramirez et al., 2016); genomic interval operations performed with BEDTools (Quinlan & Hall, 2010).
Entire preprocessing pipeline executed via nf-core/atacseq (P. A. Ewels et al., 2020) using Nextflow (Tommaso et al., 2017) within Docker containers.
Assembly: Danio rerio GRCz11, Ensembl release 115
Supplementary files format and content: Per-replicate ATAC-seq peak calls (BED format; nf-core/atacseq MACS2 output).

source_name: sperm

extract_protocol:
See treatment protocol (nuclei lysis/transposition prep).
ATAC-seq libraries were generated following Buenrostro et al. (2015, Curr. Protoc. Mol. Biol. 109:21.29.1-21.29.9; doi:10.1002/0471142727.mb2129s109), with notable exceptions: the Illumina Tagment DNA Enzyme and Buffer Large Kit (Illumina, 20034198) was used for the transposition step, and Illumina DNA/RNA UD Indexes Set A, Tagmentation (Illumina, 20091654) were used for the PCR amplification step. Resulting libraries were evaluated using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854) and an Agilent Fragment Analyzer with a HS NGS Fragment Kit (Agilent, DNF-474); quantitative PCR library quantification used a JetSeq Library Quantification Lo-ROX kit (Bioline, BIO-68029). Equimolar-pooled libraries were sequenced 100 bp paired-end on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 SP and S1 Reagent Kits v1.5 (200 cycles; Illumina, 20040719 and 20028318). Sequencing run quality was assessed using Illumina Sequencing Analysis Viewer (v2.4.7); base call files were demultiplexed and converted to FASTQ using Illumina bcl2fastq conversion software v2.20. All steps from nuclei preparation to FASTQ generation were carried out at the Next Generation Sequencing Platform, University of Bern (targeting 30-35M reads/sample; each sample retained at least 4.6M and up to 29M reads after quality-control processing).

treatment_protocol: ATAC-seq of spermatozoa was performed following Ruth Williams' protocol (Williams & Sauka-Spengler, 2021). 100,000 spermatozoa were spun down at 500 x g for 5 min at 4C, washed with 50 uL ice-cold PBS, resuspended in 50 uL lysis buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% IGEPAL CA-630), centrifuged again, and the supernatant discarded before the transposition reaction. ST_ACI = 7 dpi (cardiac cryoinjury); ST_CACI = uninjured control.

value: sperm

value: uninjured control


title: ROI 10 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191024_P1001660004152A_P1001660004152A_06.RCC


title: E2-3: anterior vaginal wall, estrogen-treated, scRNA-seq (Lib2)

description:
Library name: E2-3_sc_Lib2
GEXSCOPE

value: anterior vaginal wall

value: mixed vaginal cells


title: Zebrafish sperm ATAC-seq - ST_CACI_3

description:
Library name: ST_CACI_3
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.


title: Mouse testes snATAC-seq - S6_51

description:
Library name: S6_51
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.

value: testis

value: Injured


title: Mouse testes snATAC-seq - S5_53

description:
Library name: S5_53
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.


title: ROI 9 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_06.RCC


title: Zebrafish sperm ATAC-seq - ST_CACI_2

description:
Library name: ST_CACI_2
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.


title: ROI 8 CD68


title: POP-8: anterior vaginal wall, untreated control, scRNA-seq

description:
Library name: POP-8_sc
GEXSCOPE


title: Mouse testes snATAC-seq - S4_45

description:
Library name: S4_45
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.


title: Zebrafish sperm ATAC-seq - ST_CACI_1

description:
Library name: ST_CACI_1
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.


title: ROI 7 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_08.RCC


title: POP-7: anterior vaginal wall, untreated control, spatial transcriptomics

description:
Library name: POP-7_st
Visium

value: tissue section


title: Mouse testes snATAC-seq - S3_47

description:
Library name: S3_47
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.


title: E2-3: anterior vaginal wall, estrogen-treated, scRNA-seq (Lib1)

description:
Library name: E2-3_sc_Lib1
GEXSCOPE

value: topical vaginal estrogen


title: POP-7: anterior vaginal wall, untreated control, scRNA-seq

description:
Library name: POP-7_sc
GEXSCOPE


title: Zebrafish sperm ATAC-seq - ST_ACI_5

description:
Library name: ST_ACI_5
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.

value: cardiac cryoinjury, 7 dpi


title: ROI 6 CD68

value: human FFPE


title: Mouse testes snATAC-seq - S2_44

description:
Library name: S2_44
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.


title: Zebrafish sperm ATAC-seq - ST_ACI_4

description:
Library name: ST_ACI_4
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.


title: POP-6: anterior vaginal wall, untreated control, scRNA-seq

description:
Library name: POP-6_sc
GEXSCOPE


title: ROI 5 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1012221234567A_P1012221234567A_06.RCC


title: Mouse testes snATAC-seq - S1_52

description:
Library name: S1_52
Single-nucleus ATAC-seq (10x Genomics Chromium); Cellranger atac v2.2.0. Sequencing run: two P3 flow cells, 100 cycles; paired-end configuration: 50 bp Read 1, 8 bp Index 1, 16 bp Index 2, 50 bp Read 2.


title: POP-5: anterior vaginal wall, untreated control, scRNA-seq

description:
Library name: POP-5_sc
GEXSCOPE


title: Mouse F1 heart bulk RNA-seq - PU_FU_23

description:
Library name: PU_FU_23
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.

data_processing:
Quality control of raw sequencing reads was assessed using FastQC v0.11.9 (Andrews, 2010) and aggregated with MultiQC v1.12 (P. Ewels et al., 2016).
Adapter trimming and quality filtering were performed using Fastp v0.23.2 (Chen et al., 2018).
Mouse samples were aligned to GRCm39.
Reads were aligned to the reference genome using STAR v2.7.10a (Dobin et al., 2013).
Gene-level read counts were generated using featureCounts from the Subread package v2.0.3 (Liao et al., 2014).
Differential expression analysis was conducted in R v4.4.0 using DESeq2 v1.44.0 (Love et al., 2014) with a design formula of ~condition.
Log2 fold change shrinkage was applied using apeglm. Differentially expressed genes required |log2FC| > 1; an additional |log2FC| > 0.58 threshold was applied for volcano plot and pathway analyses.
Genes with adjusted p-value < 0.05 (Benjamini-Hochberg correction) and |log2FC| above the species-specific threshold were considered differentially expressed.
Cross-species pathway analysis: Over-representation analysis (ORA) was performed using clusterProfiler v4.12.2 (Wu et al., 2021; Yu et al., 2012) and ReactomePA v1.48.0, with parallel execution via BiocParallel v1.38.0.
Data visualization was performed using ComplexHeatmap v2.20.0, pheatmap v1.0.12 (Kolde, 2019), ggplot2 v3.5.1 (Wickham, 2016), and ggrepel v0.9.5.
Transcript-level quantification was additionally performed using Salmon v1.9.0 (Patro et al., 2017) in star_salmon mode.
Gene Set Enrichment Analysis (GSEA) was additionally performed.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Gene-level read count matrix (featureCounts).

growth_protocol: C57BL/6J mice raised together to weaning (3 wpp) then housed at 4 animals/cage (bred males isolated after first breeding); SPF facility, 20-24C, 12h light/dark, 45-65% RH, food/water ad libitum. Approved under license PROEX 310_19 (Comunidad de Madrid, Spain), conforming to EU Directive 86/609/EEC.

extract_protocol:
Tissues washed in PBS and snap frozen. On the day of RNA extraction, samples were homogenized in TRI Reagent (Sigma-Aldrich) using 21G and 30G syringes (BD Microlance). Following phase separation with 1-bromo-3-chloropropane (Sigma-Aldrich), the aqueous phase was mixed with an equal volume of ethanol, and RNA was purified using the RNA Clean & Concentrator kit (Zymo Research) with on-column DNase I treatment. RNA quantity and quality were assessed using a NanoDrop and a Fragment Analyzer before library preparation and sequencing.
Library preparation and sequencing performed by the Genomics Unit at CNIC (Madrid, Spain).

treatment_protocol: Hearts collected at 3 wpp from adult offspring of uninjured or injured males (cardiac cryoinjury performed at P1). Samples included four control and three experimental males, and two control and three experimental females. Sample 'Injured P0_16' was identified as a PCA outlier and excluded from downstream (but not raw-data) analyses.

value: heart (ventricle)

value: paternal Uninjured P0


title: Zebrafish sperm ATAC-seq - ST_ACI_3

description:
Library name: ST_ACI_3
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.