title: Rat heart_Cap_rep5

description: Library name: Sample15-3-5

value: Heart

value: No treatment


title: P0 lens, scRNAseq

status: Public on Dec 01 2025

type: SRA

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

country: USA

institute: University of Delaware

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Eye lens

extract_protocol:
Mouse lenses were micro-dissected at embryonic day (E) 16.5 and postnatal day (P) 0 followed by dissociation with Collagenase/Dispase and TrypLE to obtain a single-cell suspension
Single cell libraries prepared using the 10X Chromium Controller

tag: tissue

value: Eye lens

tag: strain

tag: age

value: Postnatal day P0


title: TX BX_1112453_03

type: RNA

city: La Jolla

first: SUNIL

last: KURIAN

state: CA

address: 10666 N Torrey Pines Rd

institute: Scripps Health

description:
TX
_

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC.

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC.

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

label: Biotin

organism: Homo sapiens

source_name: Renal Biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

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

tag: tag

value: Well Functioning Transplant


title: Circulating monocytes from healthy donor 9 (D9_CiMos)

city: Atlanta

first: Rabindra

last: Tirouvanziam

state: GA

address: 2015 Uppergate Dr

institute: Emory University

description: Library name: E16_3D9_CiMos_S24

library_source: transcriptomic

data_processing:
Hisat2 was used to align next-generation sequencing reads to the reference genome
SAMtools was used to sort BAM files.
FeatureCounts from the  Subread package was used to generate read counts expressed per gene
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: monocyte

growth_protocol: We used Alvetex (Reprocell) 200 μm-thick inert 3D scaffolds with >90% porosity (pore sizes of 36–40 μm, with interconnects of 12–14 μm). In brief, inserts were activated with 70% ethanol, coated overnight at 37ºC with rat-tail collagen I (3 mg/mL, Sigma) and seeded with H441 cells at 2.5×105 cells per 12-well insert. Cells were first grown in submerged cultures with DMEM/F12 supplemented with 10% heat-inactivated serum, penicillin, and streptomycin. After 2 days, cells were supplemented basally with serum-free DMEM/F12 with 10% Ultroser G (Pall Life Sciences) to establish air liquid interface (ALI).  Cultures were grown for 2 weeks at ALI and supplemented basally with fresh medium every 48 hours. For transmigration experiments, the ALI cultures were placed with the apical compartment exposed to RPMI, CCL2 (0.25 ng/mL), airway supernatant (ASN) from CF patiens sputum, and CFASN with EVs removed.  Then 1e6 blood monocoytes were loaded onto the 200 µm-think basal compartment of the Alvetex scaffold, and allowed to migrate at 37ºC at 5% CO2 through the collagen and epithelial layers into the apcial compartment.  The monocytes were collected 18 hours after transmigration.  Other isolated monocytes were culutred in the transmigration media without transmigrating.  Transmigrated cells were then differentiated with M-CSF for 4 days uninterrupted in either complete media (CCL2) or complete media with CFASN (CF).  Some samples were treated with SIS17 or MSA-2 for 24 hours after differentiation and other samples were used as control.

extract_protocol:
RNA was extracted from the cells using TriPure Isolation Reagent mixed with chloroform 4:1.  After spinning, the aqueous phase is mixed 1:1 with 200 proof EtOH.  The mixture is then processed following the protocol of RNA Clean and Concentrator -5 (ZYMO Research).  RNA quality and concentration was quantified using a Bioanalyzer (Agilent technologies, Inc.) and only samples with RIN >5.0 were used for sequencing.
cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) and the final sequencing library is made using the Nextera XT kit (Illumina) with an aim of ~32 million reads per sample.

treatment_protocol: In this model, circulating monocytes are migrated through a small airway epithelium grown at air-liquid interface toward CF airway supernatant (CFASN, sputum from paitents with CF sequentially centrifuged to remove cells and bacteria), CFASN without extracellular vesicles (EVs), or CCL2, placed apically.  Specifically, we transmigrated monocytes in the model for 18 hours into CFASN, CFASN without EVs, and CCL2 followed by differentiation with M-CSF.  Some samples were cultured with immunomoldulatory drugs for 24 hours after differentiation.

tag: source

value: blood

tag: cell type

value: monocyte

tag: media condition

value: untreated

tag: treatment

value: baseline no transmigration

tag: drug treatment

value: No Drug


title: TX BX_1112259_03

description:
TX
_


title: 18-hour culture of circulating monocytes from healthy donor 9 (D9_CiMos_CF)

description: Library name: E16_3D9_CiMos_CF_S25

value: 18-hour culture no transmigration


title: Rat heart_Cap_rep2

city: Nagoya-shi

first: Yuka

last: Kono

state: Aichi

address: 2-1723, Omori, Moriyama-ku

country: Japan

institute: Kinjo Gakuin University

description: Library name: Sample12-3-2

data_processing:
RNA sequencing was  performed using a NovaSeq6000 (Illumina, Inc, San Diego, USA) sequencer at 20 million paired-end reads per sample. All reads were checked, and low-quality reads were removed using fastp (ver0.23.2).
Assembly: mRatBN7.2
Supplementary files format and content: one excel file include CPM values for each Sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was extracted from the heart tissues using ISOGEN II (Nippon Gene Co., Ltd., Tokyo, Japan). Total RNA concentration was quantified using Dw-K2800 Nucleic Acid Analyzer (Shanghai Drawell Scientific Instrument Co., Ltd., Shanghai, China).
Total RNA (800 ng) from each heart sample was converted to Illumina compatible libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.


title: Memory TFH #1 (15796X4)

city: Salt Lake City

first: Jeffrey

middle: Scott

last: Hale

state: Utah

address: 15 North Medical Drive

department: Pathology

institute: University of Utah

description: bisulfite-treated genomic DNA

library_source: genomic

data_processing:
Sequencing data quality was assessed using FastQC v0.11.4
Adapters were trimmed from the sequencing reads using Trim Galore!v0.4.4
Alignment to the mm10 reference genome was performed using Bismark v0.19.0
Deduplication was performed with deduplicate_bismark
Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome. Bisulfite conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context. Bisulfite conversion was considered sufficient when this value was less than 3%
Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads.
CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0
This analysis pipeline was developed and executed in the Seven Bridges cloud platform, and included use of the Bismark Analysis public workflow. Differentially methylated regions (DMR) among the datasets were detected using BSmooth DMR finder
Genome_build: mm10
Supplementary_files_format_and_content: BED file from Bismark Methylation Extractor pipeline

molecule: genomic DNA

source_name: Spleen

extract_protocol:
DNA was harvested from FACS sorted cells using DNeasy Blood and Tissue Kit (Qiagen). DNA inputs of 50-200ng were fragmentated by sonication (Active Motif, Q120AM).
To perform genome-wide bisulfite sequencing, DNA libraries were generated using NEBNext Ultra II DNA Library Prep kit (New England Biolabs). Briefly, DNA was end-repaired to remove overhangs and methylated adaptors were ligated to DNA. Subsequently, cleanup of the ligation reaction was performed by the AmpureXP Beads (Beckman Coulter). Bisulfite treatment of DNA was then performed using EZ DNA Methylation Gold Kit (Zymo Research). Enrichment of Adaptor-ligated bisulfite-converted DNA and index incorporation was achieved through PCR amplification. DNA libraries were purified using AmpureXP Beads (Beckman Coulter) and then sequenced on the Illumina NovaSeq 6000 following the manufacturer’s protocols (NovaSeq 2x150bp for 10X_200M Read-Pairs/Sample).

value: Mouse SMARTA CD4 T Cells

tag: infection

value: LCMV Armstrong

tag: time point

value: day75 post infection

tag: Sex

value: male


title: TX BX_1112256_03

description:
TX
_


title: cAR BX_1112196_03

description:
cAR
_

value: Clinical acute rejection


title: Rat heart_Cap_rep1

description: Library name: Sample11-3-1


title: Memory TH1 #2 (15796X7)

description: bisulfite-treated genomic DNA

value: day92 post infection

value: female


title: 18-hour transmigrated monocytes from healthy donor 9 (D9_ArMos_CF)

description: Library name: E16_3D9_ArMos_CF_S26

value: CFASN

value: 18-hour transmigration toward CFASN


title: Rat heart_HFpEF_rep5

description: Library name: Sample10-2-5

value: Heart

value: No treatment


title: 18-hour transmigrated monocytes from healthy donor 9 (D9_ArMos_CF_no_EVs)

description: Library name: E16_3D9_ArMos_CF_No_EVs_S27

value: blood

value: CFASN no EVs

value: 18-hour transmigration toward CFASN with EVs removed


title: 4-day differentiated macrophages from healthy donor 9 (D9_ArMas_CF)

description: Library name: E16_3D9_ArMas_CF_S29

source_name: macrophage

value: macrophage

value: M-CSF differentiated in CFASN media


title: 4-day differentiated macrophages from healthy donor 9 (D9_ArMas_CCL2)

description: Library name: E16_3D9_ArMas_CCL2_S28

value: M-CSF differentiated in complete media

value: No Drug


title: Rat heart_Cap_rep3

description: Library name: Sample13-3-3


title: Effector TFH #2 (15796X2)

description: bisulfite-treated genomic DNA

value: Mouse SMARTA CD4 T Cells

value: LCMV Armstrong

value: day7 post infection


title: Memory TFH #2 (15796X8)

description: bisulfite-treated genomic DNA


title: Effector TFH #1 (15105X4)

description: bisulfite-treated genomic DNA


title: Rat heart_HFpEF_rep3

description: Library name: Sample8-2-3


title: Circulating monocytes from healthy donor 5 (D5_CiMos)

description: Library name: E16_3D5_CiMos_S17

value: monocyte

value: untreated

value: baseline no transmigration


title: Effector TH1 #2 (15796X1)

description: bisulfite-treated genomic DNA

value: male


title: Memory TH1 #1 (15796X6)

description: bisulfite-treated genomic DNA

value: day75 post infection


title: TX BX_1112066_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1112068_03

description:
TX
_


title: Rat heart_HFpEF_rep2

description: Library name: Sample7-2-2

value: Heart

value: No treatment


title: 18-hour culture of circulating monocytes from healthy donor 5 (D5_CiMos_CF)

description: Library name: E16_3D5_CiMos_CF_S19

value: blood

value: CFASN

value: 18-hour culture no transmigration


title: Rat heart_HFpEF_rep4

description: Library name: Sample9-2-4


title: Effector TH1 #1 (15105X3)

description: bisulfite-treated genomic DNA

value: female


title: Rat heart_HFpEF_rep1

description: Library name: Sample6-2-1


title: 18-hour culture of circulating monocytes from healthy donor 5 (D5_CiMos_CCL2)

description: Library name: E16_3D5_CiMos_CCL2_S18


title: TX BX_1112069_03

description:
TX
_


title: Naïve CD4 T cell #2 (15105X2)

description: bisulfite-treated genomic DNA

value: not infected

value: naive


title: Rat heart_Control_rep5

description: Library name: Sample5-1-5


title: Rat heart_Control_rep4

description: Library name: Sample4-1-4


title: cAR BX_1112064_03

description:
cAR
_

value: Clinical acute rejection


title: 18-hour transmigrated monocytes from healthy donor 5 (D5_ArMos_CF)

description: Library name: E16_3D5_ArMos_CF_S21

value: 18-hour transmigration toward CFASN

value: No Drug


title: 18-hour transmigrated monocytes from healthy donor 5 (D5_ArMos_CF_no_EVs)

description: Library name: E16_3D5_ArMos_CF_No_EVs_S22

value: monocyte

value: CFASN no EVs

value: 18-hour transmigration toward CFASN with EVs removed


title: TX BX_1112057_03

description:
TX
_


title: Rat heart_Control_rep3

description: Library name: Sample3-1-3


title: zebrafish caudal fin blastema, 4 dpa, ZnO treated rep3

city: Bandung

first: Alia

middle: Putri

last: Syahbaniati

state: West Java

address: Jl. Ganesa No.10

department: Biology and Biotechnology

country: Indonesia

institute: School Of Life Sciences and Technology, Institut Teknologi Bandung

description: Library name: T3

data_processing:
Transcriptomic data were processed by trimming reads with Cutadapt, align to the reference genome using BWA, pipeline DESeq2 and quantifying gene expression levels using HTSeq
Assembly: reads were mapped to Grcz11
Supplementary files format and content: csv files of countdata

molecule: polyA RNA

organism: Danio rerio

source_name: caudal fin blastema

growth_protocol: Zebrafish were maintained in a temperature-controlled room at 28°C with a 14-h light/10-h dark cycle in 12 L tanks with an aerator and fed commercial pellets three times per day.

extract_protocol:
The total RNA were isolated from caudal fin blastema 4 days post amputation (dpa) using HiPure Total RNA Kit (Magen). The purity of RNA was quantified using a NanoDrop spectrophotometer (NanoDrop, Thermofisher) at A260/280 nm, and the RNA Integrity Number (RIN) was analysed using Agilent Bioanalyzer 2100 (Agilent) and verified to be >7.0. RNA quantification was performed using a Qubit fluorometer (Invitrogen).
mRNA was enriched from the total RNA using poly A selection module. The enriched mRNA was fragmented using enzymatic methods to match the expected insert size. The fragmented DNA was ligated with Illumina-compatible Adapter. PCR was conducted to amplify the library and to generate the full-length adaptor containig unique index sequence in each library samples. The quality and quantity of library samples were determine using Tape Station, and qPCR. The library samples were proceeded to sequencing with 300 cycle (150-PE) using Illumina NextSeq 2000. The demultiplexing and Fastq generation was performed using Illumina DRAGEN BCL Convert - 4.2.7 of NextSeq 2000 Instrument.

treatment_protocol: Male zebrafish (n=5/group, triplicate) were used to model caudal fin amputation and were divided into two groups. Each zebrafish was maintained in a 250 mL beaker glass containing 150 mL distilled water (control) and Pro-ZnO 2 mg/L for 4 days to evaluate immune response in blastema.

value: caudal fin blastema

value: ZnO treated

value: 4 days post amputation (dpa)


title: Naïve CD4 T cell #1 (15105X1)

description: bisulfite-treated genomic DNA

value: Mouse SMARTA CD4 T Cells

value: male


title: 18-hour transmigrated monocytes from healthy donor 5 (D5_ArMos_CCL2)

description: Library name: E16_3D5_ArMos_CCL2_S20

value: blood

value: 18-hour transmigration toward CCL2


title: zebrafish caudal fin blastema, 4 dpa, ZnO treated rep2

description: Library name: T2


title: TX BX_1112061_03

description:
TX
_

value: Well Functioning Transplant


title: Rat heart_Control_rep2

description: Library name: Sample2-1-2

value: Heart

value: No treatment


title: 4-day differentiated macrophages from healthy donor 5 (D5_ArMas_CF)

description: Library name: E16_3D5_ArMas_CF_S23

value: macrophage

value: CFASN

value: M-CSF differentiated in CFASN media


title: zebrafish caudal fin blastema, 4 dpa, ZnO treated rep1

description: Library name: T1


title: liver, WT, ZT10, rep1

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were trimmed with Trim Galore using the specified Nextera adaptors. Reads were aligned to mm10 using STAR (v2.7.5c). Mitochondrial and unmapped contig reads were removed.  Duplicate reads were removed. Only fragments with a size < 100 was used for ATAC-seq, to assess chromatin accessibility. For ATAC-seq, peaks were called using MACS2  with paired-end format and a q-value threshold of 0.05. DiffBind was used to quantify reads in peaks and subsequent normalization with default settings.
Duplicates were flagged by MarkDuplicates (Picard tools). Filtering steps were applied to exclude reads with low mapping quality (MAPQ<30), reads/mates that were unmapped, reads failing platform and those not classified as primary alignments and duplicates (samtools view -q 30 -F 1804 -f 2).
Peaks were called using MACS2 (BAMPE format), with broad settings and a q-value cutoff of 0.05. Input samples (IPs) were used as a control in peak calling and all IPs in one experiment were pooled. Reads in peaks were quantified and normalized via DiffBind (v3.0.15) with default settings except filter=0. Overlapping TF binding sites was performed using Intervene software.
DeepTools was used for generation of bigwig tracks with RPGC normalization. Bigwig files from replicates were merged using WiggleTools for heatmaps. SparK was used for visualization of bigwig tracks.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: liver

growth_protocol: Wild type mice: C57BL/6N. Smarca2-/- and Smarca4fl/fl mice on 129/Sv background and backcrossed with C57BL/6N mice and subsequently intercrossed. 8-10 weeks old mice were used for experiments.

extract_protocol:
For the wild type mice biological replicates was merged in the circadian setup, and the tagmentation was performed in three replicates. In the SWI/SNF perturbation models tagmentation was performed on four biological replicates. A 2mL douncer was used to homogenize 15mg of tissue. 2.5 µL of TDE1 enzyme (Illumina 20034197) and 50000 nuclei were used for transposition reactions .  DNA was size selected using AMPure beads (Beckman Coulter A63881) before sequencing.
The Illumina Nextera DNA Flex Library Prep Kit was used to prepare libraries for Illumina sequencing (Illumina, 20018705).

treatment_protocol: Smarca2-/- mice, Smarca4fl/fl mice, and Smarca2-/-;smarca4fl/fl mice were tail vein injected AAV-TBG-GFP or AAV-TBG-CRE. Ten days after injection the mice were trained to night restricted feeding for another 4 days. Mice were sacrificed by cervical dislocation at different timepoints during the day (ZT 2, 6, 10, 14, 18, and 22).

tag: genotype

value: WT

value: liver

tag: zeitgeber time_(zt)


title: Rat heart_Control_rep1

description: Library name: Sample1-1-1


title: zebrafish caudal fin blastema, 4 dpa, control rep3

description: Library name: C3

value: control


title: TX BX_1112052_03

description:
TX
_


title: Circulating monocytes from healthy donor 14 (D14_CiMos)

description: Library name: E16_2D14_CiMos_S11

value: monocyte

value: untreated

value: baseline no transmigration

value: No Drug


title: ADNR BX_1111890_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: Urethra, Normal2

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

country: China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

description:
RU847
DG1000

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was Rn6.0
Assembly: Rn6.0
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: urethra

extract_protocol:
Fresh urethra tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before 10× Genomics libtar.gzy preparation.
Single-cell RNA-seq libtar.gzies were prepared using the Chromium Single Cell 3′ Libtar.gzy & Gel Bead Kit v3 (PN-1000094, 10× Genomics) according to the manufacturer’s instructions. Final libtar.gzies were sequenced on an Illumina NovaSeq 6000.

value: urethra

value: Sprague Dawley


title: 18-hour transmigrated monocytes from healthy donor 14 (D14_ArMos_CF)

description: Library name: E16_2D14_ArMos_CF_S13

value: blood

value: 18-hour transmigration toward CFASN


title: zebrafish caudal fin blastema, 4 dpa, control rep2

description: Library name: C2

value: caudal fin blastema

value: 4 days post amputation (dpa)


title: Urethra, SUI+LIPUUrethra, S2

description:
RU841
DG1000

value: ovariectomy and urethral dilatation and LIPUS


title: TX BX_1112053_03

description:
TX
_

value: Well Functioning Transplant


title: subAR BX_1111872_03

description:
subAR
_

value: Subclinical acute rejection


title: TX BX_1111870_03

description:
TX
_


title: 18-hour transmigrated monocytes from healthy donor 14 (D14_ArMos_CF_no_EVs)

description: Library name: E16_2D14_ArMos_CF_No_EVs_S14

value: CFASN no EVs

value: 18-hour transmigration toward CFASN with EVs removed


title: Urethra, SUI2

description:
RU839
DG1000

value: WT

value: ovariectomy and urethral dilatation


title: Rat heart_Sac/Val_rep1

description: Library name: Sample16-4-1

value: Heart

value: No treatment


title: 4-day differentiated macrophages from healthy donor 14 (D14_ArMas_CF)

description: Library name: E16_2D14_ArMas_CF_S16

value: macrophage

value: CFASN

value: M-CSF differentiated in CFASN media

value: No Drug


title: zebrafish caudal fin blastema, 4 dpa, control rep1

description: Library name: C1

value: control


title: cAR BX_1111873_03

description:
cAR
_

value: Clinical acute rejection


title: Urethra, SUI1

description:
RU836
DG1000

value: urethra

value: Sprague Dawley


title: TX BX_1111867_03

description:
TX
_


title: C. botulinum ATCC 19397, time point 24h, replicate R3

city: Helsinki

first: Miia

last: Lindström

address: Agnes Sjöbergin katu 2

department: Faculty of Veterinary Medicine

country: Finland

institute: University of Helsinki

data_processing:
.gtf and .bed files produced by parsing .gff3 annotation of C. botulinum ATCC_19398
Consider only locations labeled as gene/CDS/pseudogene which source is RefSeq
Remove 31 pseudogenes that have no CBO
Concatenate the gtf file produced with the gtf file of the spike-ins
Using the concatenated file, produce the bed file needed for the prokseq-v2.0
run prokseq-v2.0 to align the paired-end reads to the genome and obtain raw read counts and TPM values
Assembly: NC_009697.1 Clostridium botulinum A str. ATCC 19397
Assembly: ERCC92 Spike-ins
Supplementary files format and content: tab-delimited text file include gene raw counts for each sample
Supplementary files format and content: tab-delimited text file include gene TPM values for each sample
Supplementary files format and content: tab-delimited text file include gene spike-in normalized values for each sample
Supplementary files format and content: tab-delimited text file include raw counts of ERCC spoike-in controls for each sample

organism: Clostridium botulinum

growth_protocol: C. botulinum strain ATCC 19397 was cultured in TPGY broth at 37 °C anaerobically.

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen) and Dnase-treated (DNA-free DNA Removal Kit, Ambion)
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep (Whole transcriptome - bacteria - NEB)

treatment_protocol: Culture aliquots were sampled every hour for further total RNA-Seq.

tag: cell line

value: wild type

tag: time

value: 24 hours (post inoculation)


title: ADNR BX_1111866_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: 4-day differentiated macrophages from healthy donor 14 (D14_ArMas_CCL2)

description: Library name: E16_2D14_ArMas_CCL2_S15

value: blood

value: M-CSF differentiated in complete media


title: subAR BX_1111869_03

description:
subAR
_

value: Subclinical acute rejection


title: TX BX_1111864_03

description:
TX
_

value: Well Functioning Transplant


title: C. botulinum ATCC 19397, time point 24h, replicate R2


title: Urethra, Normal1

description:
RU802
DG1000

value: WT


title: Urethra, SUI+LIPUUrethra, S1

description:
RU833
DG1000

value: ovariectomy and urethral dilatation and LIPUS


title: 18-hour culture of circulating monocytes from healthy donor 8 (D8_CiMos_CF)

description: Library name: E16D8_CiMos_CF_S3

value: monocyte

value: 18-hour culture no transmigration


title: C. botulinum ATCC 19397, time point 24h, replicate R1


title: Circulating monocytes from healthy donor 8 (D8_CiMos)

description: Library name: E16D8_CiMos_S5

value: untreated

value: baseline no transmigration


title: C. botulinum ATCC 19397, time point 15h, replicate R3

value: 15 hours (post inoculation)


title: Pcf11_input_2

city: Shihezi City

first: sheng

last: yue

state: Xinjiang

address: Dongcheng Street, Shihezi City

department: College of Chemistry and Chemical Engineering

institute: Shihezi University

description:
Yeast overexpression Flag-pcf11 Input,sample2(CLIP-seq）
Pcf11_input_2

data_processing:
DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by Qsep100 (BiOptic Inc.)/5300 Fragment Analyzer system (Agilent). Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2μg total RNA were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
Raw sequencing data was first filtered by fastp (version 0.23.0), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Supplementary files format and content: Tab delimed text file include all raw reads counts for each sample
Supplementary files format and content: Tab delimed text file include all raw data for each sample

organism: Saccharomyces cerevisiae

source_name: eukaryotic metagenome

growth_protocol: Genome-wide expression studies using RNA-seq analysis were performed on the WT, ΔPcf11, Pcf11-AARR, Pcf11-OE1, and Pcf11-OE2 strains grown under the same growth conditions.The yeasts were cultured in liquid medium at 30°C at 220 rpm with corresponding antibiotics when necessary.

extract_protocol:
For RNA extraction, library preparation, and sequencing, total RNAs were extracted from four strains using TRIzol Reagent (Invitrogen, cat. NO.15596026); RNA was extracted using DNase I for DNA digestion. RNA quality was determined by examining the A260/A280 ratio with a NanoDrop OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA integrity was confirmed by Qsep100 (BiOptic Inc.)/5300 Fragment Analyzer system (Agilent). Qualified RNAs were quantified using a Qubit3.0 with the Qubit TM RNA Broad Range Assay kit (Life Technologies, Q10210).
Two micrograms of total RNA were used for stranded RNA sequencing library preparation using the KC-Digital TM Stranded mRNA Library Prep Kit (Catalog No. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instructions.

treatment_protocol: Three biological replicates were conducted for each strain

value: eukaryotic metagenome


title: C. botulinum ATCC 19397, time point 15h, replicate R2


title: Pcf11_input_1

description:
Yeast overexpression Flag-pcf11 Input,sample1(CLIP-seq）
Pcf11_input_1


title: 18-hour transmigrated monocytes from healthy donor 8 (D8_ArMos_CF_no_EVs)

description: Library name: E16D8_ArMos_CF_no_EVs_S4

value: CFASN no EVs

value: 18-hour transmigration toward CFASN with EVs removed

value: No Drug


title: Circulating monocytes (CiMos) from healthy donor 13 (D13_CiMos)

description: Library name: E16D13_CiMos_S1


title: TX BX_1110968_03

description:
TX
_


title: Pcf11_IP_2

description:
Yeast overexpression Flag-pcf11 Flag,antibody sample2(CLIP-seq）
Pcf11_IP_2


title: 18-hour transmigrated monocytes from healthy donor 13 (D13_CF_ArMos)

description: Library name: E16D13_CF_ArMos_S6

value: CFASN

value: 18-hour transmigration toward CFASN


title: Pcf11_IP_1

description:
Yeast overexpression Flag-pcf11 Flag,antibody sample1(CLIP-seq）
Pcf11_IP_1


title: high_disease_5

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
The 75 bp single-end reads were aligned to the murine reference genome mm10 M16 from GENCODE using kallisto v0.44.2.
Samples with more than 50,000,000 reads were downsampled to 50 % of the original number of reads.
Downstream analysis was performed in R 4.1.0 using DESeq2 v1.32.0 for normalisation.
Assembly: mm10 M16
Supplementary files format and content: normalized_expression.txt: tab-separated files holding normalized and annotated expression values
Supplementary files format and content: raw_expression.txt: tab-separated files holding unnormalized and unfiltered expression values

source_name: Brain

extract_protocol:
RNA isolation was performed using the RNeasy Mini kit (Qiagen), following the manufacturer’s instructions.
The Smart‐seq2 protocol, as described by Picelli et al. (2014) was used for the generation of non‐strand‐specific, full transcript sequencing libraries.
75 bp single-end run  was performed on a NextSeq 500

value: Brain

value: Mircroglia

value: wt/ki

value: female

tag: health status

value: disease

tag: trem2 level

value: high

tag: condition


title: Full media, rep3

city: Nijmegen

first: Cyriel

last: Huijer

address: Houtlaan 4

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University Nijmegen

description: Library name: Full_Media_3

data_processing:
Quality control, alignment to the human reference genome (hg38), and read counting was performed by Seq2science, available at https://github.com/vanheeringen-lab/seq2science.
Assembly: GRCh38.p14
Supplementary files format and content: MCF10A_Gln_lim_counts_table.txt, counts table as produced by seq2science pipeline in a .txt file

source_name: Breast

growth_protocol: Cells were maintained in DMEM/F12 MCF10A cells (Cat# CRL-10317, ATCC) were maintained in DMEM/F12 (Cat# 11320033, Gibco) supplemented with MEGM Mammary Epithelial Cell Growth Medium SingleQuots Kit (Cat# CC-4136, Lonza) without GA-1000, along with 0.1 µg/mL cholera toxin (Cat# BML-G117, Enzo Life Sciences) and 100 U/mL penicillin-streptomycin (Cat# 15140, Gibco).

extract_protocol:
RNA was extracted using the Quick-RNA Microprep Kit (Cat# R1051, Zymo Research) according to the manufacturer’s protocol.
For RNAseq, libraries were prepared from 300 ng RNA with the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Cat# KK8502, Kapa Biosystems), spiked with ERCC ExFold RNA Spike-In Mix 2 (Cat# 4456739, Invitrogen) at a final dilution of 1:1000. RNA was fragmented for 6 min at 94 °C to obtain a desired library insert size of 200-300 bp. Library concentrations were determined using the Qubit HS kit (Cat# Q32854, Invitrogen) and the library size distribution was determined using a High Sensititivy DNA analysis (Cat# 5067-4626, Agilent) on a Bioanalyzer 2100 (Agilent). Libraries were loaded on the NextSeq 2000 system (Illumina) with an average library size between 300-400 bp.

tag: tissue

value: Breast

value: Breast epithelial cells

value: WT

value: No treatment


title: subAR BX_1110965_03

description:
subAR
_

tag: tag

value: Subclinical acute rejection


title: C. botulinum ATCC 19397, time point 12h, replicate R2

value: wild type

value: 12 hours (post inoculation)


title: TX BX_1110792_03

description:
TX
_

value: Well Functioning Transplant


title: Gln (0.28 mM), rep3

description: Library name: Gln_28_mM_3

value: Glutamine limitation, 0.28 mM


title: C. botulinum ATCC 19397, time point 12h, replicate R1


title: TX BX_1110785_03

description:
TX
_


title: low_disease_5

tag: strain

tag: age

value: low


title: mid_disease_5

tag: cell type

value: mid


title: C. botulinum ATCC 19397, time point 11h, replicate R2

value: 11 hours (post inoculation)


title: Gln (0.12 mM), rep3

description: Library name: Gln_12_mM_3

tag: treatment

value: Glutamine limitation, 0.12 mM


title: high_disease_4

value: Brain

value: Mircroglia

value: wt/ki


title: C. botulinum ATCC 19397, time point 12h, replicate R3


title: Gln (0.04 mM), rep3

description: Library name: Gln_04_mM_3

value: Glutamine limitation, 0.04 mM


title: C. botulinum ATCC 19397, time point 11h, replicate R1


title: low_disease_4

value: female

value: disease


title: ADNR BX_1110532_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: high_disease_3

value: male

value: high


title: cAR BX_1110393_03

description:
cAR
_

value: Clinical acute rejection


title: Gln (0.20 mM), rep3

description: Library name: Gln_20_mM_3

value: Breast

value: Breast epithelial cells

value: WT

value: Glutamine limitation, 0.20 mM


title: C. botulinum ATCC 19397, time point 11h, replicate R3

value: wild type


title: Gln (0.28 mM), rep2

description: Library name: Gln_28_mM_2

value: Glutamine limitation, 0.28 mM


title: TX BX_1110321_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1110320_03

description:
TX
_


title: C. botulinum ATCC 19397, time point 15h, replicate R1

value: 15 hours (post inoculation)


title: Gln (0.20 mM), rep2

description: Library name: Gln_20_mM_2


title: low_disease_3

value: Brain

value: Mircroglia

value: low


title: C. botulinum ATCC 19397, time point 10h, replicate R2

value: 10 hours (post inoculation)


title: cAR BX_1111863_03

description:
cAR
_


title: C. botulinum ATCC 19397, time point 10h, replicate R1


title: Full media, rep2

description: Library name: Full_Media_2

value: No treatment


title: C. botulinum ATCC 19397, time point 9h, replicate R3

value: 9 hours (post inoculation)


title: Gln (0.04 mM), rep2

description: Library name: Gln_04_mM_2

value: Glutamine limitation, 0.04 mM


title: Gln (0.12 mM), rep2

description: Library name: Gln_12_mM_2

value: Glutamine limitation, 0.12 mM


title: high_disease_2

value: wt/ki

value: male

value: disease

value: high


title: C. botulinum ATCC 19397, time point 9h, replicate R2


title: C. botulinum ATCC 19397, time point 10h, replicate R3


title: TX BX_1110971_03

description:
TX
_


title: TX BX_1110275_03

description:
TX
_


title: mid_disease_2

value: mid


title: mid_disease_3


title: low_disease_2


title: Full media, rep1

description: Library name: Full_Media_1

value: Breast

value: Breast epithelial cells

value: WT


title: C. botulinum ATCC 19397, time point 9h, replicate R1

value: wild type


title: mid_disease_1

value: Brain


title: TX BX_1109801_03

description:
TX
_

value: Well Functioning Transplant


title: cAR BX_1109694_03

description:
cAR
_

value: Clinical acute rejection


title: C. botulinum ATCC 19397, time point 8h, replicate R3

value: 8 hours (post inoculation)


title: Gln (0.28 mM), rep1

description: Library name: Gln_28_mM_1

value: Glutamine limitation, 0.28 mM


title: Gln (0.20 mM), rep1

description: Library name: Gln_20_mM_1

value: Glutamine limitation, 0.20 mM


title: TX BX_1110313_03

description:
TX
_


title: C. botulinum ATCC 19397, time point 8h, replicate R2


title: low_disease_1

value: Mircroglia

value: low


title: Gln (0.12 mM), rep1

description: Library name: Gln_12_mM_1

value: Glutamine limitation, 0.12 mM


title: C. botulinum ATCC 19397, time point 8h, replicate R1


title: mid_healthy_5

value: wt

value: female

value: healthy


title: TX BX_1110268_03

description:
TX
_


title: TX BX_1109293_03

description:
TX
_


title: Gln (0.04 mM), rep1

description: Library name: Gln_04_mM_1

value: Glutamine limitation, 0.04 mM


title: TX BX_1109291_03

description:
TX
_


title: low_healthy_5


title: TX BX_1109290_03

description:
TX
_


title: hiPSC-ExN full deletion bio rep 2

city: San Francisco

first: Katherine

middle: S

last: Pollard

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
RNA-Seq reads were aligned to GRCh38.112 using STAR v2.7.11b in gene annotation mode.
Alignment, RNA-Seq, and Insert Size quality control metrics were generated using Picard v3.1.1.
Sample quality was accessed using FASTQC v0.12.1 and MultiQC v1.22.2.
Assembly: hg38
Supplementary files format and content: norm_counts.csv is a csv file that includes normalized counts for each gene in each sample.
Supplementary files format and content: raw_counts.txt is a tab-delimited text file that includes raw counts for each gene in each sample.

source_name: WTC11 hIPSC-ExN

growth_protocol: The WTC11 i3N iPSC line with doxycycline-inducible Ngn2 integrated at the AAVS1 safe harbor locus was used. The WTC11 i3N iPSCs were cultured on Matrigel-coated (Corning, 354277) plates and maintained in mTeSR Plus media (STEMCELL Technologies, 100-0276), and passaged with Accutase (STEMCELL Technologies, 07920) and 10-μM ROCK inhibitor Y-27632 (STEMCELL Technologies, 72302). The cells were grown with 5% CO2 at 37℃ and verified mycoplasma-free using the MycoAlert Mycoplasma Detection Kit (Lonza, LT07-218).

extract_protocol:
RNA was extracted from two weeks old excitatory neurons differentiated from iPSCs using the RNeasy Mini Kit (Qiagen, 74104).
Approximately 4 mg of extracted total RNA was used to prepare libraries for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020594).

treatment_protocol:
The designed sgRNAs were in vitro transcribed using the Precision gRNA Synthesis Kit (Invitrogen, A29377), and Cas9-NLS protein was ordered from QB3 MacroLab at the University of California, Berkeley. We assembled the Cas9/sgRNA complex by incubating the in vitro transcribed sgRNAs and Cas9-NLS protein at 20-25℃ for 15 min and delivered the complex into WTC11 i3N iPSCs using nucleofection (Lonza, VPH-5012). After nucleofection, the cells were seeded into Matrigel-coated (Corning, 354277) wells for recovery. 3-4 days later, we sorted live cells into 96-well plates with one cell per well using fluorescence-activated cell sorting (FACS) to generate clonal cell lines. About two weeks later, the viable clones were expanded.
We differentiated the iPSCs into excitatory neurons by using a two-step differentiation protocol. First, we cultured iPSCs on Matrigel-coated plates with pre-differentiation media with doxycycline (2 µg/mL; Sigma-Aldrich, D9891) for three days and changed the media daily. Three days later, the pre-differentiated cells were dissociated with Accutase (STEMCELL Technologies, 07920) and subplated on Poly-L-Ornithine-coated (15 µg/mL; Sigma-Aldrich, P3655) plates with maturation media with doxycycline. Then, the maturation media was changed seven days later by removing half of the media from each well and adding the same amount of fresh media without doxycycline.

value: WTC11 hIPSC-ExN

value: full deletion

value: excitatory neuron differentiation


title: SCRAMBLED Day_2 Biol rep 2

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow high performance computing clusters for which quality control was performed by FastQC (0.11.9) and the reads were trimmed by fastp (0.23.2). Trimmed reads were aligned to human reference genome hg38 using STAR (2.7.10a) and assigned by the feature counting tool featureCount (2.0.1). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.36.0) in R.
Assembly: human reference genome GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

growth_protocol: JURL-MK1 cell line (mycoplasma-negative; obtained from DSMZ; authenticated by Northgene Ltd, Newcastle in 2020), was grown in RPMI 1640 (Sigma) supplemented with 10-20% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine and 1% (v/v) penicillin-streptomycin.

extract_protocol:
The cells were pelleted by centrifugation in culture media, washed and then pelleted again in phosphate buffered saline pH 7.4, and total cellular RNA extracted from a minimum of 1 x106 cells in TRIzoLTM Reagent (ThermoFisher). The concentration of the RNA was measured using the Nanodrop 2000, and the quality and RIN value was determined using the Agilent Bioanalyser RNA Nano kit (Agilent).
RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: 14.2 µg of each shRNA were transfected into 293T human embryonic kidney (HEK) cells along with 12.45 μg Pax2 and 4.5 μg VSV-G constructs. After 6, 24 and 48 hr, the media was collected and replaced with 10 mL DMEM containing 20% serum. Virus was concentrated by ultracentrifugation and stored at -80ºC until needed. JURL-MK1 cells (5 x 106) were incubated with virus particles (MOI = 1) for 48 hr, with the media replaced after 24 hr. Transduction efficiency (% GFP+ cells; nominally >90% for each experiment) was measured by flow cytometry (FACSVerse) and time course experiments +/- TKI (niltotinib; 2 nM) were carried out.

value: leukaemia cell line

tag: disease state

value: CML myeloid blast crisis

value: SCR control

value: day 2

value: 73 yrs

value: male


title: mid_healhty_4

value: Brain

value: mid


title: C. botulinum ATCC 19397, time point 7h, replicate R2

value: wild type

value: 7 hours (post inoculation)


title: hiPSC-ExN full deletion bio rep 1


title: low_healthy_4

value: Mircroglia

value: wt

value: low


title: TX BX_1108914_03

description:
TX
_

value: Well Functioning Transplant


title: C. botulinum ATCC 19397, time point 7h, replicate R1


title: hiPSC-ExN CTCF deletion bio rep 2

value: WTC11 hIPSC-ExN

value: CTCF deletion


title: mid_healhty_3

value: healthy


title: C. botulinum ATCC 19397, time point 6h, replicate R3

value: 6 hours (post inoculation)


title: TX BX_1108906_03

description:
TX
_


title: TX BX_1108911_03

description:
TX
_


title: low_healthy_3


title: C. botulinum ATCC 19397, time point 6h, replicate R2


title: hiPSC-ExN CTCF deletion bio rep 1

value: excitatory neuron differentiation


title: C. botulinum ATCC 19397, time point 7h, replicate R3


title: hiPSC-ExN WT bio rep 2

value: WT


title: mid_healhty_2


title: hiPSC-ExN WT bio rep 1


title: C. botulinum ATCC 19397, time point 5h, replicate R3

value: 5 hours (post inoculation)


title: low_healthy_2


title: C. botulinum ATCC 19397, time point 5h, replicate R2


title: mid_healhty_1


title: 783nc-1

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: prostate gland

growth_protocol: 22RV1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

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

value: prostate gland

value: prostate cancer

value: the control group of knockdown of ZNF783 by siRNA


title: C. botulinum ATCC 19397, time point 5h, replicate R1


title: 783nc-3


title: TX BX_1110674_03

description:
TX
_


title: low_healthy_1

value: Brain

value: male


title: TX BX_1108900_03

description:
TX
_


title: mouse xenograft, Dinutuximab beta, 11 (T2), replicate 4

city: Rome

first: Probiomics

state: RM

address: via Montpellier 1

country: Italy

institute: Probiomics s.r.l

description: Library name: T2_QA_4

data_processing:
Raw ONT sequencing data in POD5 format were basecalled using Dorado v7.6.8 with the high-accuracy (HAC) model v4.3.0 (400 bps) within MinKNOW (v24.11.10). Basecalled reads were subjected to quality control and reads filtering with fastpLong v0.3.0. Reads in which >40% of bases had a Phred score <15 were removed to ensure downstream data quality.
High-quality reads were aligned to both the Gencode human transcriptome (GRCh38, v38) and the Gencode mouse transcriptome (GRCm39, vM28) using minimap2 v2.30 with the map-ont preset optimized for ONT long reads. Xenomapper was used to segregate human- and mouse-derived reads in xenograft samples.
Transcript-level quantification was then performed using Salmon v1.10.3 with parameters --gcBias --numBootstraps 10 -l U to account for GC bias and provide bootstrap estimates of variance. Transcript-level abundance estimates were aggregated to gene-level raw counts with tximport v1.32.0 (doi:10.12688/f1000research.7563.1).
Batch effects were corrected using the ComBat_seq function from the sva package v3.52.0.
Assembly: Gencode human transcriptome (GRCh38, v38; Gencode mouse transcriptome (GRCm39, vM28)
Supplementary files format and content: Tab-delimited text files containing human raw counts, respectively, corrected for batch effects
Supplementary files format and content: Tab-delimited text files containing mouse raw counts, respectively, corrected for batch effects

source_name: Human Ewing Sarcoma derived cells

extract_protocol:
Frozen tumor sections collected at T1 and T2, were homogenized using TissueLyser LT (Qiagen, Benelux, B.V.) in Trizol Reagent. The PureLink RNA Mini Kit (Life technologies) was adopted to extract and purify total RNA. The concentration and purity of RNA were determined at 260/280 nm using Nano Drop One Spectrophotometer (Thermo Fisher).
Bulk long-read RNA sequencing was performed using the Oxford Nanopore Technologies (ONT; Oxford, UK) PCR-cDNA Sequencing Kit (SQK-PCB114-24). Sequencing libraries were prepared according to the manufacturer’s protocol. Briefly, 700 ng of full-length RNA per sample was used as input for complementary DNA (cDNA) synthesis and strand switching with kit-supplied oligonucleotides. Double-stranded cDNA (dscDNA) was generated by PCR amplification (10 μL cDNA/sample) using primers containing 5′ tags, which enable ligase-free attachment of rapid sequencing adapters. The resulting libraries were loaded onto R10.4.1 flow cells (FLO-PRO114M) and sequenced on P2 Solo PromethION devices using MinKNOW acquisition software (v24.11.10).

treatment_protocol: To obtain the tumors, 200 µl of cell suspension containing 5 x 106 TC71 cells were injected subcutaneously into the right flanks of female Athymic nude mice. When tumor weight reached about 100 mg, mice were randomized in the following experimental groups (eight mice for each group): CTR: Placebo: NaCl 0.9% ip, daily, 5 consecutive days (qdx5); QA: Dinutuximab beta: 15mg/kg ip, daily, qdx5; 4 mice in each group were sacrificed on day 5, 4 hours after the last dose of Dinutuximab beta (T1), and the other 4 mice on day 12, 96 hours after the second dose of Doxorubicin (T2). Tumors were removed and immediately frozen in dry-ice for further analysis.

value: Human Ewing Sarcoma derived cells

value: Dinutuximab beta


title: C. botulinum ATCC 19397, time point 4h, replicate R3

value: wild type

value: 4 hours (post inoculation)


title: mouse xenograft, Dinutuximab beta, 11 (T2), replicate 3

description: Library name: T2_QA_3


title: TX BX_1108905_03

description:
TX
_

value: Well Functioning Transplant


title: 783si-3

value: the treat group of knockdown of ZNF783 by siRNA


title: 783si-2


title: C. botulinum ATCC 19397, time point 6h, replicate R1


title: C. botulinum ATCC 19397, time point 4h, replicate R2


title: mouse xenograft, Dinutuximab beta, 11 (T2), replicate 2

description: Library name: T2_QA_2


title: C. botulinum ATCC 19397, time point 4h, replicate R1


title: TX BX_1108704_03

description:
TX
_


title: 783si-1


title: ADNR BX_1108708_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: C. botulinum ATCC 19397, time point 3h, replicate R3

value: 3 hours (post inoculation)


title: TX BX_1108705_03

description:
TX
_


title: 783nc-2


title: mouse xenograft, Dinutuximab beta, 11 (T2), replicate 1

description: Library name: T2_QA_1


title: ETSnc-3

value: the control group of knockdown of ETS1 by siRNA


title: mouse xenograft, vehicle, 11 (T2), replicate 4

description: Library name: T2_CTR_4

value: vehicle


title: C. botulinum ATCC 19397, time point 3h, replicate R2


title: TX BX_1108496_03

description:
TX
_


title: ETSnc-1


title: ETSnc-2


title: mouse xenograft, vehicle, 11 (T2), replicate 3

description: Library name: T2_CTR_3


title: mouse xenograft, vehicle, 11 (T2), replicate 2

description: Library name: T2_CTR_2


title: C. botulinum ATCC 19397, time point 2h, replicate R3

value: 2 hours (post inoculation)


title: ETS1Si-3

value: the treat group of knockdown of ETS1 by siRNA


title: C. botulinum ATCC 19397, time point 3h, replicate R1


title: mouse xenograft, vehicle, 11 (T2), replicate 1

description: Library name: T2_CTR_1


title: TX BX_1108493_03

description:
TX
_


title: C. botulinum ATCC 19397, time point 2h, replicate R2


title: TX BX_1108899_03

description:
TX
_


title: subAR BX_1107553_03

description:
subAR
_

value: Subclinical acute rejection


title: mouse xenograft, Dinutuximab beta, day 5 (T1), replicate 4

description: Library name: T1_QA_4


title: C. botulinum ATCC 19397, time point 2h, replicate R1


title: subAR BX_1107538_03

description:
subAR
_


title: TX BX_1108497_03

description:
TX
_


title: ETS1Si-2

value: prostate gland

value: prostate cancer


title: Wt-PDGFB [QN22-2482_T]

type: genomic

city: London

first: Sebastian

last: Brandner

address: Queen Square

department: Institute of Neurology

institute: University College London

hyb_protocol: Infinium Mouse Methylation BeadChip

scan_protocol: Using the sesame R package unnormalised beta values where extracted. An Markdown document is included to fully process the data a la submitted paper. Similarly, all output figures from the code are supplied for reference.

data_processing: Average Beta

source_name: Wt-PDGFB

label_protocol: Infinium Mouse Methylation BeadChip

extract_protocol: Bisulphite conversion was done with the Zymo Lightning BSC deep well Kit (Zymo, # D5033-E), following manufacturer instructions. Then, DNA underwent the DNA-restore protocol (Illumina Infinium HD FFPE Restore Protocol, #WG-901-2004), followed by wash steps with Zymo Wash Buffer and was then eluted in 10 μl of dH2O und processed for microarray use.

treatment_protocol: Maxwell 16 FFPE Tissue LEV DNA Purification Kit. Extracted DNA was cleaned with Agencourt AMPure XP beads (Beckman Coulter, # A63880) according to manufacturers protocols

tag: virus used

value: pdgfb-ires-cre

tag: idh status

value: WT

tag: trp53 status

tag: pten status

tag: atrx status

tag: rb1 status

tag: pdgfb status

value: Y


title: TX BX_1108687_03

description:
TX
_


title: cAR BX_1107552_03

description:
cAR
_

value: Clinical acute rejection


title: ADNR BX_1107541_03

description:
ADNR
_


title: mouse xenograft, Dinutuximab beta, day 5 (T1), replicate 3

description: Library name: T1_QA_3

tag: cell line

value: Human Ewing Sarcoma derived cells

value: Dinutuximab beta

tag: time point


title: TX BX_1107535_03

description:
TX
_

value: Well Functioning Transplant


title: WT + AngII/PE, mouse4

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: 366D1_661

data_processing:
Raw FASTQ files were processed using Space Ranger (v1.2.2, 10X Genomics) software to align reads, detect tissue, and quantify spot-level gene expression.
On tissue spots were manually adjusted with Loupe browser (v7.0, 10x Genomics).
The resulting filtered feature-barcode expression matrices were loaded into Seurat (v5.1.0) for downstream analysis and visualization. Furthermore, spots with less than 50 or more than 8000 genes expressed, less than 1200 or more than 30000 UMIs and more than 5% of total counts of the spot corresponding to hemoglobin genes were removed.
The four samples were normalized using Seurat's SCTransform and integrated using Harmony (v1.2) with max iterations of 20. Cluster optimization to find the optimal resolution parameter was assessed with the silhouette method and visualization of the “clustree” (v.0.5.1) package. We selected a resolution of 0.8 based on silhouette score and clustree analysis.
Gene signatures distinguishing each cluster or subpopulation were identified using Seurat’s “FindMarkers” with a false discovery rate (FDR) <0.05 and a log2 fold change threshold >0.25. Pathway activity scoring utilized canonical gene sets from MsigDB (“c2.cp”) and Single Cell Signature Explorer. Differential expression between treatment groups was performed and significance denoted by absolute average log2 fold change > 1 and adjusted p value (BH method) < 0.05. Over-representation analysis and Gene Set Enrichment analysis in GO terms and KEGG pathways found in org.Mm.eg.db (v 3.16.0) was performed with clusterProfiler (v 4.6.2) R package. To rank genes, we used a combined metric of average log2 fold chang * - log10 adjusted p value.
Assembly: GRCm39/mm39
Supplementary files format and content: DECONVOLV_SCT_Spatial_RNA2.rds; Seurat RDS object containing raw counts, normalized counts, and image files.
Library strategy: Spatial Transcriptomics

source_name: left ventricle (heart)

growth_protocol: Not applicable. Whole‑organ LV tissue harvested from in‑vivo mice.

extract_protocol:
FFPE tissue samples sectioned onto standard slides underwent deparaffinization by baking at 60°C for 2h followed by a series of xylene and ethanol treatments. Next, tissue sections were stained for H&E, imaged using the ImageXpress Pico automated cell imaging system (Molecular Devices) at 20x resolution, and then subject to coverslip removal and destaining, using 0.1N HCl for 15 min at 42°C, and decrosslinking using Visium CytAssist kit reagents (10x Genomics). After decrosslinking, tissue sections were hybridized with mouse whole transcriptome probes (10x Genomics) overnight at 50°C in a thermal cycler after which slides were washed, incubated with ligation buffer at 37°C for 1 hr, washed with 2x SSC, stained with eosin, and then inserted into the CytAssist device where the hybridized tissue sections were aligned over the Visium Gene Expression slides (10x Genomics) and processed for probe release for 30 min. In the CytAssist device, a brightfield image of the tissue section was captured. The tissue was processed using manufacture-provided RNase enzyme mix to release the probes from the tissue sections to bind to the capture oligonucleotides located on the Visium Gene Expression slides. Visium Gene Expression slides were incubated to extend the captured probes.
Whole transcriptome probes were eluted from the Visium Gene Expression Slide capture areas and subjected to a PCR pre-amplification step, SPRIselect reagent (Beckman Coulter) sample cleanup, and then probe-based library construction using dual index plate TS Set A (10x Genomics). A final SPRIselect sample cleanup was performed, post-library construction quality control assessment completed to verify library 240 bp size by Agilent Bioanalzyer trace peaks, and the resulting libraries were sent for Illumunia sequencing with NextSeq P2, PE100, using paired-end, dual indexed sequencing with the following parameters: Read 1T: 28 cycles, i7 index: 10 cycles, i5 index: 10 cycles, Read 2S: 50 cycles.

treatment_protocol: We induced cardiac fibrosis in 10-week CDCP1 knockout (KO) FVB/NJ mice (n=4) using osmotic pumps infusing angiotensin II/phenylephrine (AngII/PE) or saline. After 4 weeks, cross-sectional heart tissue slides were harvested from the 4 experimental conditions (WT_Saline, KO_Saline, WT_AngII/PE, KO_AngII/PE) for spatial transcriptome sequencing (Visium 10x Genomics).

value: left ventricle (heart)

tag: genotype

value: AngII/PE


title: IDH-wildtype, ATRX mutant (loss) [QN22-0109_T]

source_name: IDH-wildtype, ATRX mutant (loss)

value: pdgfb-ires-cre-sgATRX

value: del


title: mouse xenograft, Dinutuximab beta, day 5 (T1), replicate 2

description: Library name: T1_QA_2


title: TX BX_1107495_03

city: La Jolla

first: SUNIL

address: 10666 N Torrey Pines Rd

institute: Scripps Health

description:
TX
_

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

source_name: Renal Biopsy

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


title: IDH-wildtype, ATRX wildtype [QN22-0104_T]

source_name: IDH-wildtype, ATRX wildtype


title: mouse xenograft, Dinutuximab beta, day 5 (T1), replicate 1

description: Library name: T1_QA_1


title: Cdcp1-KO + AngII/PE, mouse3

description: Library name: 366A1_735

tag: tissue


title: Cdcp1-KO + saline, mouse2

description: Library name: 333D1_637

value: saline


title: CNS control, no tumour [QN22-0104_C]

source_name: CNS control, no tumour

value: N


title: mouse xenograft, vehicle, day 5 (T1), replicate 4

description: Library name: T1_CTR_4

value: vehicle


title: WT + saline, mouse1

description: Library name: 333A1_657


title: mouse xenograft, vehicle, day 5 (T1), replicate 3

description: Library name: T1_CTR_3


title: IDH-wildtype, ATRX wildtype [QN22-0097_T]


title: CNS control, no tumour [QN22-0097_C]


title: ADNR BX_1107530_03

description:
ADNR
_

tag: tag

value: Acute dysfunction no rejection


title: TX BX_1107042_03

description:
TX
_


title: ETS1Si-1

value: prostate gland

value: the treat group of knockdown of ETS1 by siRNA


title: mouse xenograft, vehicle, day 5 (T1), replicate 2

description: Library name: T1_CTR_2


title: H. sapiens, RNA004 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA004)

library_source: other

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

molecule: other

source_name: Hs27 human fibroblast (CRL-1634)

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: Hs27 human fibroblast (CRL-1634)


title: 2-AA treated_2_IgG

city: Boston

first: Laurence

middle: G

last: Rahme

state: MA

address: 50 Blossom Street

department: Surgery

institute: Massachusetts General Hospital

description: Library name: Sample 16

data_processing:
Sequencing reads were aligned to the M. musculus reference genome using the Burrows-Wheeler aligner
Peaks were identified using the HOMER peak caller
Differences in peaks among conditions were analyzed using the DiffBind R package
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

growth_protocol: Two million RAW 264.7 cells were treated with 2-AA (200 µM/sample) and CUT&RUN assay was performed according to the manufacturer's instructions.

extract_protocol:
Anti-H3K18la, anti-H3K18ac, anti-H3K4 tri-methyl and IgG isotype antibodies were used to pull down specific nucleosomes. DNA was extracted using EpiCypher CUTANA ChIC/CUT&RUN kit.
DNA libraries for CUT&RUN experiments were performed using the NEBNext Ultra II DNA Library Prep Kit

value: Murine macrophage cell line

value: 2-AA treated

tag: time

value: 24 hrs


title: IDH-wildtype, ATRX wildtype [QN21-3975_T]

tag: strain

value: WT

value: Y


title: mouse xenograft, vehicle, day 5 (T1), replicate 1

description: Library name: T1_CTR_1

value: Human Ewing Sarcoma derived cells


title: TX BX_1106743_03

last: KURIAN

description:
TX
_

value: Well Functioning Transplant


title: 2-AA treated_1_IgG

description: Library name: Sample 15

tag: cell type


title: H. sapiens, RNA002 chemistry

description: tRNA sequencing (RNA002)


title: IDH-wildtype, ATRX mutant (loss) [QN21-3957_T]


title: 2-AA treated_2_H3K4_Trimethylation

description: Library name: Sample 14

tag: treatment


title: TX BX_1106742_03

description:
TX
_


title: TX BX_1106512_03

description:
TX
_


title: TX BX_1106755_03

description:
TX
_


title: IDH-wildtype, ATRX mutant (loss) [QN21-3953_T]


title: TX BX_1106511_03

description:
TX
_


title: Lmna iADKO mouse parametrial WAT 2 weeks post-tamoxifen sample 5

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

description:
Library name: 975 gW RNA
Column name in DESeq2_raw_counts.csv: 975_gW_RNA

data_processing:
FastQC (v.0.12.1) was used to check the quality of the raw read data. Alignment was conducted using STAR (version 2.7.11a), using UCSC mm39 as the reference genome sequence. A second quality control was performed post-alignment using FastQC to ensure that only high-quality data were used for gene expression quantitation and differential expression analyses. Differential expression analysis was conducted using DESeq2.
Assembly: UCSC mm39
Supplementary files format and content: DESeq2_raw_counts.txt contains raw counts for each sample
Supplementary files format and content: DESeq2_rlogNormalized_counts.txt contains rlogNormalized counts for each sample

source_name: Parametrial white adipose tissue

growth_protocol: Standard mouse housing conditions, 22oC housing and 6pm-6am dark

extract_protocol:
Powdered frozen adipose tissue and used RNA STAT60 for RNA isolation
Libraries were constructed using DNBSEQ Eukaryotic Strand-specific mRNA library kit via manufacturer instructions, performed by Beijing Genomic Institute (BGI)

treatment_protocol: Tamoxifen injections 50mg/kg 5 consecutive days to all mice at 12-14 weeks of age, dissected mice 2 weeks post-tamoxifen

value: Parametrial white adipose tissue

value: White adipose tissue

value: KO

value: KO two weeks post-tamoxifen

tag: batch


title: 2-AA treated_1_H3K4_Trimethylation

description: Library name: Sample 13


title: IDH-wildtype, ATRX mutant (loss) [QN21-3956_T]

tag: virus used

value: pdgfb-ires-cre-sgATRX

value: del


title: TX BX_1106745_03

description:
TX
_


title: IDH-mutant, ATRX mutant (loss) [QN21-3952_T]

source_name: IDH-mutant, ATRX mutant (loss)

tag: idh status

value: Mut


title: 2-AA treated_1_H3K18_Lactylation

description: Library name: Sample 12


title: Lmna iADKO mouse parametrial WAT 2 weeks post-tamoxifen sample 6

description:
Library name: 727 gW RNA
Column name in DESeq2_raw_counts.csv: 727_gW_RNA


title: Lmna iADKO mouse parametrial WAT 2 weeks post-tamoxifen sample 4

description:
Library name: 724 gW RNA
Column name in DESeq2_raw_counts.csv: 724_gW_RNA


title: IDH-mutant, ATRX-wildtype (retained) [QN21-3419_T]

source_name: IDH-mutant, ATRX-wildtype (retained)

tag: trp53 status


title: Lmna iADKO mouse parametrial WAT 2 weeks post-tamoxifen sample 3

description:
Library name: 974 gW RNA
Column name in DESeq2_raw_counts.csv: 974_gW_RNA


title: IDH-mutant, ATRX mutant (loss) [QN21-3411_T]

tag: pten status


title: Lmna iADKO mouse parametrial WAT 2 weeks post-tamoxifen sample 2

description:
Library name: 748 gW RNA
Column name in DESeq2_raw_counts.csv: 748_gW_RNA


title: TX BX_1106420_03

description:
TX
_


title: 2-AA treated_1_H3K18_Acetylation

description: Library name: Sample 9


title: IDH-wildtype, ATRX mutant (loss) [QN21-2978_T]

tag: atrx status


title: Lmna iADKO mouse parametrial WAT 2 weeks post-tamoxifen sample 1

description:
Library name: 765 gW RNA
Column name in DESeq2_raw_counts.csv: 765_gW_RNA


title: IDH-wildtype, ATRX wildtype [QN21-2977_T]

tag: rb1 status


title: Untreated_1_H3K4_Trimethylation

description: Library name: Sample 8

value: No treatment


title: 2-AA treated_2_H3K18_Lactylation

description: Library name: Sample 11


title: Untreated_2_H3K4_Trimethylation

description: Library name: Sample 7


title: IDH-mutant, ATRX mutant (loss) [QN21-2975_T]

tag: pdgfb status


title: TX BX_1106240_03

description:
TX
_


title: 2-AA treated_2_H3K18_Acetylation

description: Library name: Sample 10

tag: cell line


title: IDH-mutant, ATRX-wildtype (retained) [QN21-2973_T]


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 6

description:
Library name: 707 gW RNA
Column name in DESeq2_raw_counts.csv: 707_gW_RNA

value: Control

value: Control two weeks post-tamoxifen


title: subAR BX_1106417_03

description:
subAR
_

value: Subclinical acute rejection


title: TX BX_1106737_03

description:
TX
_


title: Untreated_2_IgG

description: Library name: Sample 6

value: Murine macrophage cell line


title: Untreated_1_IgG

description: Library name: Sample 5

value: 24 hrs


title: TX BX_1106232_03

description:
TX
_


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 5

description:
Library name: 726 gW RNA
Column name in DESeq2_raw_counts.csv: 726_gW_RNA


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 7

description:
Library name: 706 gW RNA
Column name in DESeq2_raw_counts.csv: 706_gW_RNA


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 3

description:
Library name: 750 gW RNA
Column name in DESeq2_raw_counts.csv: 750_gW_RNA


title: TX BX_1105677_03

description:
TX
_


title: TX BX_1106238_03

description:
TX
_


title: IDH-wildtype, ATRX wildtype [QN21-2972_T]

value: WT


title: TX BX_1105463_03

description:
TX
_


title: IDH-mutant, ATRX mutant (loss) [QN21-2969_T]

value: Y


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 2

description:
Library name: 749 gW RNA
Column name in DESeq2_raw_counts.csv: 749_gW_RNA


title: Untreated_1_H3K18_Lactylation

description: Library name: Sample 3


title: Untreated_2_H3K18_Lactylation

description: Library name: Sample 4


title: ADNR BX_1105462_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: TX BX_1106506_03

description:
TX
_

value: Well Functioning Transplant


title: Untreated_2_H3K18_Acetylation

description: Library name: Sample 2


title: ADNR BX_1105470_03

description:
ADNR
_


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 1

description:
Library name: 747 gW RNA
Column name in DESeq2_raw_counts.csv: 747_gW_RNA

value: Parametrial white adipose tissue


title: IDH-mutant, ATRX-wildtype (retained) [QN21-2518_T]


title: IDH-mutant, ATRX-wildtype (retained) [QN21-2517_T]


title: IDH-wildtype, ATRX mutant (loss) [QN21-2514_T]


title: cKO_aging_12

city: Sacramento

first: Hyun Kyu

last: Kim

address: 2425 Stockton Blvd

department: Neurology

institute: UCDAVIS

description:
Library name: Sample 9
22-month-old aged oligodendroglial Serpina3n knockout mice

data_processing:
1. Quality Control: soapnuke
2. Read Mapping: hisat2
3. Transcript Quantification: rsem
4. Differential Expression Analysis: DESeq2
5. Visualization and Clustering: pheatmap
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.27_GRCm39.v2201
Supplementary files format and content: Format: TPM; Content: Gene expression at the transcript level.

source_name: forebrain

growth_protocol: All animals were from C57BL/6 background and maintained in 12 h light/dark cycle with water and food. Animals and procedures in this study were approved by the Institutional Animal Care and Use Committee at the University of California, Davis.

extract_protocol:
polyA_selected
Strand_specific: true, seq_length: PE150, fq_phred: Phred+33

value: forebrain

value: Olig2-Cre Serpina3n flox/flox

value: Tamoxifen


title: mvfR mutant supplemented with 2-AA in infected cells_3

description:
Library name: Sample12
Column name is gene name and row name is samples in raw counts All samples.txt:mvfR mutant with 2-AA

data_processing:
Galaxy (usegalaxy.org)
File quality was assessed using FastQC (version 0.74; Galaxy).
Poly-A tails and low-quality bases were trimmed using the Cutadapt tool (version 4.8; Galaxy).
Reads mapped to the mm39 were counted using featureCounts (Galaxy version 2.0.3) with default parameters.
Differential gene expression analysis was implemented using DeSeq2 version (1.40.2) with default parameters.
Assembly: mm39
Supplementary files format and content: tab deliminated text file includes raw counts of genes for each sample
Supplementary files format and content: excel files from Deseq2 showing the raw data of log2 fold change, p-value for the genes in each sample

source_name: RAW 264.7 cells

growth_protocol: Cells were infected with PA14, mvfR mutant or mvfR mutant supplemented with 2-AA (200 µM) at a multiplicity of infection (MOI) of 5 for 30 min at 37°C under 5% CO2. Unbound bacteria were removed by washing once with cold DMEM, followed by incubation with gentamicin (100 µg/mL) for 30 min to eliminate extracellular bacteria. Cells were then transferred to antibiotic-free DMEM and incubated for 3 h at 37°C under 5% CO2. They were then scraped, centrifuged at 500 × g, and lysed in RNA lysis buffer.

extract_protocol:
Total RNA from approximately 2 × 106 of RAW 264.7 cell line infected with PA14, mvfR mutant, or mvfR mutant with 2-AA was isolated using the RNeasy minikit (Qiagen).
RNA libraries for RNA-seq using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following manufacturer's instructions.

value: RAW 264.7 cells

value: mvfR mutant with 2-AA infected cells

value: 2-AA treatment

value: 4.5 hrs


title: Untreated_1_H3K18_Acetylation

description: Library name: Sample 1

value: No treatment


title: Lmna fl/fl control mouse parametrial WAT 2 weeks post-tamoxifen sample 4

description:
Library name: 722 gW RNA
Column name in DESeq2_raw_counts.csv: 722_gW_RNA

value: White adipose tissue

value: Control

value: Control two weeks post-tamoxifen


title: mvfR mutant supplemented with 2-AA in infected cells_2

description:
Library name: Sample11
Column name is gene name and row name is samples in raw counts All samples.txt:mvfR mutant with 2-AA

value: Murine macrophage cell line


title: IDH-mutant, ATRX-wildtype (retained) [QN21-2508_T]

value: pdgfb-ires-cre-sgATRX

value: Mut

value: del

value: WT


title: cKO_aging_10

description:
Library name: Sample 7
22-month-old aged oligodendroglial Serpina3n knockout mice


title: IDH-wildtype, ATRX wildtype [QN21-2962_T]

value: Y


title: TX BX_1105461_03

description:
TX
_

value: Well Functioning Transplant


title: mvfR mutant supplemented with 2-AA in infected cells_1

description:
Library name: Sample10
Column name is gene name and row name is samples in raw counts All samples.txt: mvfR mutant with 2-AA


title: CNS control, no tumour [QN21-2508_C]

value: N


title: ADNR BX_1105167_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: Aging_7

description:
Library name: Sample 6
22-month-old aged wild-type mice

value: forebrain

value: wild-type


title: IDH-mutant, ATRX-wildtype (retained) [QN21-2507_T]


title: subAR BX_1105153_03

description:
subAR
_

value: Subclinical acute rejection


title: Aging_6

description:
Library name: Sample 5
22-month-old aged wild-type mice


title: TX BX_1104985_03

description:
TX
_


title: TX BX_1104905_03

description:
TX
_


title: mvfR mutant infected cells_2

description:
Library name: Sample8
Column name is gene name and row name is samples in raw counts All samples.txt: mvfR mutant

value: RAW 264.7 cells

value: mvfR mutant infected cells

value: 4.5 hrs


title: mvfR mutant infected cells_1

description:
Library name: Sample7
Column name is gene name and row name is samples in raw counts All samples.txt: mvfR mutant

value: No treatment


title: IDH-mutant, ATRX mutant (loss) [QN21-2502_T]


title: subAR BX_1105152_03

description:
subAR
_


title: CNS control, no tumour [QN21-2502_C]


title: TX BX_1104897_03

description:
TX
_


title: PA14 infected cells_3

description:
Library name: Sample6
Column name is gene name and row name is samples in raw counts All samples.txt: PA14

value: PA14 infected cells


title: Ctrl_2_months_old_3

description:
Library name: Sample 2
2-month-old young wild-type mice


title: P53-PDGFB [QN17-2298_T]

value: pdgfb-ires-cre


title: Ctrl_2_months_old_4

description:
Library name: Sample 3
2-month-old young wild-type mice


title: cKO_aging_11

description:
Library name: Sample 8
22-month-old aged oligodendroglial Serpina3n knockout mice

value: Olig2-Cre Serpina3n flox/flox

value: Tamoxifen


title: PA14 infected cells_2

description:
Library name: Sample5
Column name is gene name and row name is samples in raw counts All samples.txt: PA14

value: Murine macrophage cell line


title: P53-PDGFB [QN17-2291_T]

value: WT

value: del


title: ADNR BX_1103719_03

description:
ADNR
_


title: Ctrl_2_months_old_1

description:
Library name: Sample 1
2-month-old young wild-type mice


title: PA14 infected cells_1

description:
Library name: Sample4
Column name is gene name and row name is samples in raw counts All samples.txt:PA14


title: P53-PDGFB [QN17-2106_T]

value: Y


title: mvfR mutant infected cells_3

description:
Library name: Sample9
Column name is gene name and row name is samples in raw counts All samples.txt: mvfR mutant


title: IL13-41

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description:
Library name: Sample 16
IL13-41_Read_Count

data_processing:
Reads were annotated and mapped to the human genome assembly GRCh38.p12 using Bowtie2
Differential expression (q<0.05) was determined in DESeq2  compared to vehicle control.
Assembly: GRCh38.p12
Supplementary files format and content: Processed data files are normalized read counts with corresponding Entrez Gene ID after DESeq2 analysis

source_name: primary bronchial epithelial cells differentiated at air-liquid interface in the presence of 10 ug/mL IL-13 for 10 days

growth_protocol: Primary HBEC (Lonza) were expanded and transferred to transwell inserts for differentiation at the air-liquid interface in 24-well plates each containing 500 uL of assay medium utilizing the PnuemaCult™ ALI medium kit (STEMCELL Technologies, Vancouver, CA).   Cells were cultured at 37C, 5% CO2 with media changes every 48 to 72 hours.  On day 10, 10 ug/mL interleukin-13 was added to media for cells to induce an asthmatic phenotype.  IL-13 was included in every media change after day 10 for cells to induce an asthmatic phenotype.

extract_protocol:
Total RNA was isolated from HBEC (n=4) using Trizol (Thermo Fisher Scientific) and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.0.
mRNA was poly-A selected, and libraries were prepared as previously described (Dasgupta et al., 2022.

treatment_protocol: On day 25, inserts were washed with DPBS (pH 7.0 -- 7.3) and then exposed on the apical surface for 48 hours to either 25 uL 1% dimethyl sulfoxide (DMSO) with a DPBS vehicle or BAP (1 – 40 ug/mL) in DMSO with a DPBS vehicle.


title: P53-PDGFB [QN17-2009_T]


title: Uninfected cells_3

description:
Library name: Sample3
Column name is gene name and row name is samples in raw counts All samples.txt:Uninfected

value: Untreated cells


title: TX BX_1103713_03

description:
TX
_

value: Well Functioning Transplant


title: cAR BX_1103476_03

description:
cAR
_

value: Clinical acute rejection


title: TX BX_1103475_03

description:
TX
_


title: IL13-40

description:
Library name: Sample 15
IL13-40_Read_Count

value: primary bronchial epithelial cells differentiated at air-liquid interface in the presence of 10 ug/mL IL-13 for 10 days


title: Uninfected cells_2

description:
Library name: Sample2
Column name is gene name and row name is samples in raw counts All samples.txt: Uninfected


title: Aging_5

description:
Library name: Sample 4
22-month-old aged wild-type mice

value: forebrain

value: wild-type


title: Wt-PDGFB [QN17-1999_T]


title: cAR BX_1003302_03

description:
cAR
_


title: ADNR BX_1103265_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: PTEN p53-PDGFB [QN17-18_T]

source_name: PTEN p53-PDGFB


title: P53-PDGFB [QN17-1601_T]


title: IL13-39

description:
Library name: Sample 14
IL13-39_Read_Count


title: sample S-001780500

first: Vrushali

middle: Dipak

last: Fangal

address: 181 Longwood Avenue

department: Brigham and Women's Hospital

institute: Harvard Medical School

description:
Library name: S-001780500
Column name in mouse_vitd_def_th2_matrix: S-001780500

data_processing:
Trimmed reads were aligned to the mouse reference genome (GRCm38) using the STAR aligner (v2.7.10a). Gene expression read counts were quantified using HTSeq (v0.13.5).
Assembly: GRCm38
Supplementary files format and content: The processed data files are tab-delimited text files, containing normalized expression values (log-CPM) for each gene across all samples. Gene identifiers are based on Ensembl (GRCm38).

source_name: TH2 cells

growth_protocol: WT C57BL/6 mice were used as the normal control group and fed a regular rodent chow containing Vitamin D. These mice express functional VDR. VDR-KO mice, a transgenic strain on the C57BL/6 background, lack functional VDR due to deletion of an exon in the VDR gene. These mice were fed a high-calcium, high-phosphate, and Vitamin D-containing diet to compensate for metabolic imbalances caused by the lack of VDR-mediated signaling. Both groups consisted of 6–8 week old mice housed under standard conditions in a virus- and parasite-free facility with unrestricted access to food and water.

extract_protocol:
At day 5 of polarization, cells were harvested and total RNA was isolated using the microRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA quality and concentration were evaluated using a Nanodrop 8000 spectrophotometer.
RNA-seq libraries were prepared using the TruSeq® Stranded Total RNA Library Prep Globin Kit (Illumina) following the manufacturer’s protocols.

treatment_protocol: No additional treatments were applied. The dataset focuses on comparing TH2 cells derived from VDR-KO mice versus wild-type controls under basal conditions.

value: TH2 cells

value: VDR-KO

tag: treatment/diet

value: rescue


title: CON-9

description:
Library name: Sample 12
CON-9_Read_Count

source_name: primary bronchial epithelial cells differentiated at air-liquid interface


title: IL13-38

description:
Library name: Sample 13
IL13-38_Read_Count


title: P53-PDGFB [QN17-1511_T]

value: pdgfb-ires-cre


title: CON-8

description:
Library name: Sample 11
CON-8_Read_Count

value: primary bronchial epithelial cells differentiated at air-liquid interface


title: sample S-001780499

description:
Library name: S-001780499
Column name in mouse_vitd_def_th2_matrix: S-001780499

tag: genotype


title: Vulva_P6

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

description: 1K plex

hyb_protocol: not provided

scan_protocol: CosMx SMI

data_processing:
AtoMx
Counts

source_name: Vulva

label_protocol: not provided

extract_protocol: not provided

tag: timepoint

value: Post

tag: group

value: CR


title: Vulva_P7

description: 1K plex

value: PR


title: TX BX_1003301_03

description:
TX
_

tag: tag


title: sample S-001780498

description:
Library name: S-001780498
Column name in mouse_vitd_def_th2_matrix: S-001780498


title: Wt-PDGFB [QN17-1297_T]

source_name: Wt-PDGFB

tag: strain

value: WT


title: Vulva_P9

description: 1K plex

value: NR


title: CON-7

description:
Library name: Sample 10
CON-7_Read_Count

tag: cell type


title: sample S-001780497

description:
Library name: S-001780497
Column name in mouse_vitd_def_th2_matrix: S-001780497


title: TX BX_1003266_03

description:
TX
_


title: PTEN p53-PDGFB [QN17-1104_T]

value: del

value: Y


title: TX BX_1003264_03

description:
TX
_

value: Well Functioning Transplant


title: CON-10

description:
Library name: Sample 9
CON-10_Read_Count


title: sample S-001780496

description:
Library name: S-001780496
Column name in mouse_vitd_def_th2_matrix: S-001780496


title: Uninfected cells_1

description:
Library name: Sample1
Column name is gene name and row name is samples in raw counts All samples.txt: Uninfected

value: RAW 264.7 cells

value: Murine macrophage cell line

value: Untreated cells

tag: treatment

value: No treatment

tag: time

value: 4.5 hrs


title: PTEN p53-PDGFB [QN17-1103_T]

tag: virus used


title: BAP_IL13-57

description:
Library name: Sample 8
BAP_IL13-57_Read_Count

value: primary bronchial epithelial cells differentiated at air-liquid interface in the presence of 10 ug/mL IL-13 for 10 days


title: Vulva_P17

description: 1K plex


title: sample S-001780495

description:
Library name: S-001780495
Column name in mouse_vitd_def_th2_matrix: S-001780495

value: TH2 cells

value: VDR-KO

value: rescue

tag: batch


title: Vulva_P16

description: 1K plex

value: Post


title: BAP_IL13-55

description:
Library name: Sample 7
BAP_IL13-55_Read_Count


title: sample S-001780494

description:
Library name: S-001780494
Column name in mouse_vitd_def_th2_matrix: S-001780494


title: PTEN p53-PDGFB [QN17-01_T]

value: pdgfb-ires-cre

tag: idh status

tag: trp53 status


title: Vulva_P18

description: 1K plex


title: BAP_IL13-54

description:
Library name: Sample 6
BAP_IL13-54_Read_Count


title: sample S-001780483

description:
Library name: S-001780483
Column name in mouse_vitd_def_th2_matrix: S-001780483

value: regular


title: Vulva_P19

description: 1K plex

value: Healthy


title: BAP_IL13-53

description:
Library name: Sample 5
BAP_IL13-53_Read_Count


title: Rb p53 [PNET] Ad-Cre [QN07-543_T]

source_name: Rb p53 [PNET] Ad-Cre

value: AdenoCre

value: WT

tag: pten status

tag: atrx status

value: N


title: Vulva_P20

description: 1K plex


title: Rb p53 [PNET] Ad-Cre [QN08-437_T]

value: del

tag: rb1 status

tag: pdgfb status


title: sample S-001780482

description:
Library name: S-001780482
Column name in mouse_vitd_def_th2_matrix: S-001780482

tag: treatment/diet


title: BAP40-28

description:
Library name: Sample 3
BAP40-28_Read_Count

value: primary bronchial epithelial cells differentiated at air-liquid interface


title: BAP40-29

description:
Library name: Sample 4
BAP40-29_Read_Count


title: Vulva_P10

description: 1K plex


title: Vulva_P11

description: 1K plex

value: PR


title: Rb p53 [PNET] Ad-Cre [QN06-1039_T]


title: Rb p53 PTEN [Glioma] Ad-Cre [QN05-975_T]

source_name: Rb p53 PTEN [Glioma] Ad-Cre


title: BAP40-27

description:
Library name: Sample 2
BAP40-27_Read_Count


title: Rb p53 PTEN [Glioma] Ad-Cre [QN05-957_T]


title: PTEN p53-PDGFB [QN17-1068_T]

value: Y


title: sample S-001780481

description:
Library name: S-001780481
Column name in mouse_vitd_def_th2_matrix: S-001780481

tag: genotype


title: Vulva_P14

description: 1K plex

tag: timepoint


title: 402-KO-beta

city: Rehovot

first: Mike

last: Fainzilber

address: Dept. of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
counts.txt
norm_counts.txt

data_processing:
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome build mm10 using, Tophat (v2.0.10).
Counting reads on Refseq realese mm10  genes, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: txt file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: txt file includes the normalized counts (DESeq2 Normalization)

source_name: embryonic DRG tissue

extract_protocol:
isolation of lumbar DRG tissue from E13.5 embryos
Inhouse polyA based RNA seq

tag: developmental stage

value: Embryo 13.5

value: KO-beta

tag: tissue

value: embryonic DRG tissue


title: Vulva_P15

description: 1K plex

tag: group


title: Rb p53 PTEN [Glioma] Ad-Cre [QN05-819_T]

tag: strain


title: CM-PEG-PLGA@DOX/R848-treated  RAW264.7 cells replicate 3

city: xiamen

first: Zhiyuan

last: Chen

address: Xiamen, Fujian Province, China, 361000

institute: Xiamen University

description: Library name: RAWM-3

data_processing:
Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR.
Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited gene expression matrix containing gene symbols and TPM values for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared following the standard BGI mRNA library prep protocol, which includes mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: Cells were treated with either: 1. Experimental group: CM-PEG-PLGA@DOX/R848 nanoparticles at a dose equivalent to 2μg/mL DOX. 2. Control group: Phosphate Buffered Saline (PBS). Treatment duration was 24 hours.

tag: cell line

tag: treatment

value: CM-PEG-PLGA@DOX/R848 nanoparticles


title: Rb p53 PTEN [Glioma] Ad-Cre [QN05-167_T]

tag: virus used


title: 411-KO-beta

description:
counts.txt
norm_counts.txt


title: 398-KO-beta

description:
counts.txt
norm_counts.txt


title: Vulva_P2

description: 1K plex


title: 415-WT-beta

description:
counts.txt
norm_counts.txt

value: WT-beta


title: CM-PEG-PLGA@DOX/R848-treated  RAW264.7 cells replicate 1

description: Library name: RAWM-1


title: Vulva_P3

description: 1K plex


title: Rb p53 PTEN [Glioma] Ad-Cre [QN05-163_T]


title: 410-WT-beta

description:
counts.txt
norm_counts.txt


title: Vulva_P4

description: 1K plex

value: NR


title: PBS-treated  RAW264.7 cells replicate 3

description: Library name: RAW-3

value: PBS


title: Vulva_P13

description: 1K plex

value: Post


title: 401-WT-beta

description:
counts.txt
norm_counts.txt


title: Rb p53 [PNET] Ad-Cre [QN04-4551_T]


title: PBS-treated  RAW264.7 cells replicate 2

description: Library name: RAW-2


title: PBS-treated RAW264.7 cells replicate 1

description: Library name: RAW-1


title: Streptomyces coelicolor A3(2) parB2-3xFLAG replicate 2

city: Norwich

first: Leah

last: McPhillips

address: Colney Lane

department: Molecular microbiology

institute: John Innes Centre

description: Library name: TLE06

data_processing:
All data processing was done in the Galaxy platform, in the Mac terminal and in Rstudio.
Reads were mapped to the A3(2) reference genome using Bowtie2 on the Galaxy platform.
The sequencing coverage for each nucleotide position was determined using bedtools genome-cov tool.
Reads per basepair per million (RPBPPM) was calculated in Rstudio using custom R scripts.
Assembly: Streptomyces coelicolor A3(2) reference genome (AL645882.2)
Supplementary files format and content: TLE0X_chr_RPBPPM.csv data is the RPBPPM data (in csv format) for the Streptomyces coelicolor A3(2) chromosome
Supplementary files format and content: TLE0X_SCP1_RPBPPM.csv data is the RPBPPM data (in csv format) for the Streptomyces coelicolor A3(2) SCP1 plasmid
Supplementary files format and content: TLE0X_SCP2_RPBPPM.csv data is the RPBPPM data (in csv format) for the Streptomyces coelicolor A3(2) SCP2 plasmid

organism: Streptomyces coelicolor

source_name: strain A3(2)

growth_protocol: The required volume of spores for each strain was added to a 15 mL falcon tube containing 5 mL of 0.05 M Tris[hydroxymethyl]methyl-2-aminoethanesulphonic acid (TES) buffer and incubated at 50°C for 10 minutes. Following incubation, 5 mL of 2X Germination Medium (1% sterile yeast extract, 1% sterile casamino acids, sterile 0.01 M CaCl2) was added the solution was mixed by tube inversion. The solution was then incubated at 37°C with shaking at 220 rpm for 3 hours. After incubation, samples were centrifuged at 3,000 rpm for 10 minutes at room temperature. The supernatant was discarded, and the germinated spore pellet was resuspended in 500 µL of TSB:YEME 34% S (1:1) medium and transferred to 50 mL of TSB:YEME 34% S (1:1) medium in a 200 mL conical flask with sterile springs. Cultures were incubated overnight (~15 hours) at 30°C with shaking at 220 rpm.

extract_protocol:
Cells were sonicated in lysis buffer and pellted. Supernatant was incubated with anti-FLAG antibody beads at 4°C overnight. DNA was then isolated from the beads.
Libraries were prepared for Illumina sequencing using the NEXT Ultra II library preparation kit (NEB) according to the manufacturer's protocol

treatment_protocol: Cells were fixed with a final concentration of 1% formaldehyde then quenched with 250 mM glycine.

value: strain A3(2)

tag: chip antibody

value: α-FLAG M2 agarose beads (Merck)


title: 406-KO-beta

description:
counts.txt
norm_counts.txt


title: Vulva_S16

description: 1K plex

value: Pre

value: CR


title: 79-wt-alpha3

description:
counts.txt
norm_counts.txt


title: Vulva_S18

description: 1K plex


title: Streptomyces coelicolor A3(2) parB2-3xFLAG replicate 1

description: Library name: TLE05


title: CM-PEG-PLGA@DOX/R848-treated 4T1 cells replicate 3

description: Library name: T1M-3


title: 55-wt-alpha3

description:
counts.txt
norm_counts.txt


title: CM-PEG-PLGA@DOX/R848-treated  RAW264.7 cells replicate 2

description: Library name: RAWM-2


title: CM-PEG-PLGA@DOX/R848-treated 4T1 cells replicate 2

description: Library name: T1M-2


title: 54-wt-alpha3

description:
counts.txt
norm_counts.txt


title: Streptomyces coelicolor A3(2) parB1-3xFLAG replicate 2

description: Library name: TLE04


title: Streptomyces coelicolor A3(2) parB1-3xFLAG replicate 1

description: Library name: TLE03


title: Rb p53 PTEN [Glioma] Ad-Cre [QN05-105_T]

value: AdenoCre

tag: idh status

value: WT

value: N


title: CM-PEG-PLGA@DOX/R848-treated 4T1 cells replicate 1

description: Library name: T1M-1


title: Vulva_S20

description: 1K plex


title: 45-wt-alpha3

description:
counts.txt
norm_counts.txt


title: Vulva_S12

description: 1K plex


title: Streptomyces coelicolor A3(2) wild type negative control 2

description: Library name: TLE02


title: Vulva_S19

description: 1K plex

value: PR


title: 81-ko-alpha3

description:
counts.txt
norm_counts.txt


title: 399-WT-beta

description:
counts.txt
norm_counts.txt


title: Streptomyces coelicolor A3(2) wild type negative control 1

description: Library name: TLE01


title: PBS-treated 4T1 cells replicate 2

description: Library name: T1-2


title: Vulva_S17

description: 1K plex


title: Vulva_S11

description: 1K plex


title: Vulva_S13

description: 1K plex