title: blood_ctrl_8 (mRNA)

city: Riga

first: Tatjana

last: Kiseļova

address: Dzirciema iela

country: Latvia

institute: Riga Stradins University

description:
Library name: Sample 22
C108

data_processing:
Data processing: STAR v2.7.8a with default parameters for paired-end sequencing data was used for full transcriptome sequences mapping and adapter clipping. The mapped .bam files from the multiple sequencing lanes of one sample were merged with Samtools v1.10. Gene expression counts matrix was produced using R statistical software v4.3.2 package featureCounts.
Assembly: GRCh38.p13
Supplementary files format and content: Raw gene expression matrix where columns represent samples and rows - gene names according to HGNC.

source_name: blood

extract_protocol:
Blood samples were collected and preserved in PAXgene Blood RNA Tubes (PreAnalytiX), according to the manufacturer's specifications. RNA extraction was performed using the PAXgene 96 Blood RNA Kit, adhering to the manufacturer’s protocol. Ribosomal RNA was removed from all samples using the MGIEasy rRNA Depletion Kit, according to the manufacturer’s protocol.
Library preparation used the MGIEasy RNA Directional Library Prep Set.

value: blood

value: control


title: FPAH 29-untreated

status: Public on Mar 28 2025

type: SRA

city: Macau

first: Ning-Yi

last: Shao

address: University of Macau

department: Faculty of Health Sciences

country: China

institute: University of Macau

description: SAMPLE 5

library_source: transcriptomic

data_processing:
Hisat2
FeatureCounts
Assembly: hg38
Supplementary files format and content: Raw reads of genome-wide genes for RNA-seq.

molecule: total RNA

organism: Homo sapiens

source_name: iPSC-ECs

growth_protocol: iPSCs were differentiated into endothelial cells using a monolayer chemically-defined methods.

extract_protocol:
RNA was extrated using the a Direct-zol RNA Kit with DNA digestion, and collected total RNA was used for RNA-seq
RNA-seq construction protocol of Illumina.

treatment_protocol: iPSC-ECs were seeded into 6 well plates and once they reached 60-70% confluency, cells were treated with and without e-cigarette extraction for 24 hours.

tag: disease state

value: FPAH

tag: treatment

value: Vehicle

tag: cell type

value: iPSC-derived endothelial cells


title: FLCNKO_young_M1

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of control FlcnLiKO male mouse, 12- weeks of age, biological rep1

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files including raw counts

organism: Mus musculus

source_name: liver

extract_protocol:
For gene expression analyses, total RNA was extracted according to the manufacturer's instructions (RNeasy Mini Kit). Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 10ng/µL.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

tag: tissue

value: liver

tag: age

tag: Sex

value: Male

tag: genotype

value: FlcnLiKO


title: Healthy 273-e-cig

description: SAMPLE 4

value: Healthy

value: e-cig extract


title: FLCNKO_young_M2

description: Transcriptome profile of control FlcnLiKO male mouse, 12- weeks of age, biological rep2


title: Primary differentiated adipocytes, 100 nM hGIP_2 Hrs, rep2

type: RNA

city: Indianapolis

first: Gabor

last: Varga

state: Indiana

address: Lilly Corporate Center

country: USA

institute: Eli Lilly

hyb_protocol: Affymetrix protocol, ThermoFisher Human Clariom S Assay platform

scan_protocol: Affymetrix protocol

data_processing:
ProbeSummarizeEngine and GC-SST-RMA
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.mps

label: biotin

source_name: Human primary differentiated adipocytes

label_protocol: Affymetrix protocol

growth_protocol: Human primary differentiated adipocytes

extract_protocol: Flash frozen (500 mg) tissues were homogenized for 1-2 min in cold room. Total mRNA was prepared using miRNeasy Mini Kit (Qiagen Cat#1038703). cDNA was synthesized from 500 ng total RNA in a 20 µL reaction using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems Cat#4368814).

treatment_protocol: Adipocytes were differentiated as previously described and subsequently treated with insulin (100 nM), GIP (100 nM), insulin + GIP, or vehicle for 2, 8, and 24 h. RNA was collected and submitted for transcriptomic analysis utilizing the ThermoFisher Human Clariom S Assay platform.

value: primary differentiated adipocytes

value: 100 nM hGIP_2 Hrs


title: Healthy 273-untreated

description: SAMPLE 3


title: CUTTAG, GAF, CBPKD, c14, repl1

city: Milan

first: Yinxiu

last: Zhan

address: via Adamello, 16

institute: European Institute of Oncology (IEO)

library_source: genomic

data_processing:
The CUT&Tag data processing was done as in (Atinbayeva et al., 2024). Briefly, we used snakePipes version 2.4.0 (Bhardwaj et al., 2019) (parameters: --trim --fastqc --properPairs –dedup --mapq 1) with specific Cut&Tag Bowtie2 alignment option  (--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700) was used. Since the Cut&Tag contains lambda phage spike-ins for reliable quantification of global effects, the libraries were mapped to a constructed hybrid genome of dm6 and lambda phage (NCBI GenBank ID: J02459.1). Macs2 was used to call Cut&Tag peaks using the following options: -g dm -q 0.05 --broad. Cut&Tag normalized signals were generated using bamCoverage from deepTools (v.2.5.7). More specifically, the relative dm6/lambda total number of reads was used as normalization factor to rescale each sample through the bamCompare option --scaleFactor.  For samples with H3 Cut&Tag, the ratio between normalizations factors (H3 vs mark-specific Cut&Tag) was passed to bamCompare’s option –scaleFactor to account for differences in starting material. The coverage heatmaps were created using plotHeatmap from deepTools (v.2.5.7). To quantify the signal under the peaks, we integrated the normalized signal in a +/-1kb around each peak. Source code for data normalisation can be found https://github.com/zhanyinx/atinbayeva_paper_2023.
Assembly: dmel6
Supplementary files format and content: spike-in and H3 normalized bigwig file
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: The flies were reared under standard conditions (25 C) and transferred to cages to collect the embryos for further experiments.

extract_protocol:
CUT&Tag experiments were performed as described in Zenk, Cardamone et al., 2023 with small adaptations. Embryos were fixed with 1% of formaldehyde. Based on the developmental stage from before cycle 9 to cycle 14, 500, 150 or 50 hand-staged embryos were used for each antibody. To extract nuclei, embryos were lysed in 50 µL of Digitonin Wash Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 150 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.05% Digitonin (Millipore, #300410)). After lysis, nuclei were spin for 5 minutes at 600 g at 4 ºC and washed with 500 µL of Digitonin Wash Buffer to remove impurities. Following, 15 μL of BioMag ConcanavalinA beads (Polysciences, #86057-3) in Binding Buffer (20 mM HEPES (pH 7.5), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) were added to the sample and incubated on a wheel for 15 min at room temperature. For each condition, the pool of nuclei was split and histone H3 or another antibody was used, to use the same starting material for normalisation purposes. Next, the supernatant was removed by using a magnetic stand and beads were resuspended in 150 µL of Antibody Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 150 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.01% Digitonin (Millipore, #300410), 2 mM EDTA (ThermoScientific, #15575020) together with the respective antibody and incubated on a rocking platform at 4 ºC overnight. The following day, samples were mildly spin down and supernatant was removed with the help of a magnetic stand. Successively, the samples were washed twice with Antibody Wash Buffer, finally resuspended in 150 µL of Antibody Buffer supplemented with the secondary antibody and incubated for 1 hour at room temperature on a rocking platform. After two washes with Antibody Wash Buffer, the samples were resuspended in Digitonin Med Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 300 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.01% Digitonin (Millipore, #300410)) supplemented with the pA/G Tn5 (1:150) and incubated for 1 hour at room temperature on a rocking platform. The samples were mildly spin down and two washes were performed before starting the tagmentation reaction by adding 150 µL of Tagmentation Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 300 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 10 mM MgCl2) and by incubating the reaction in a thermomixer for 1 hour at 37 ºC. The reaction was inhibited by adding 20 mM EDTA (final), 0.5% SDS (final) and 10 mg Proteinase K (final). The samples were incubated for 30 min at 55 ºC and another 20 min at 70 ºC. DNA purification was performed by using the ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205) following manufacturer instructions.
Libraries were prepared by supplementing the NEBNext HighFidelity 2x PCR Master Mix with 1 pg of Tn5-tagmented lambda DNA (New England Biolabs, #N3011S) spike-in as normalizer supplemented in the NEBNext HighFidelity 2x PCR Master Mix (New England Biolabs, #M0541S) for each sample. The indexing was performed using Illumina i5 and i7 (Buenrostro et al., 2015) through 15 cycles (1 x 5 min at 72 °C, 1 x 30 sec at 98°C, 13 x 10 s at 98 °C, 30 sec at 63 °C, 1 x 1 min at 72 °C, hold at 4 °C). The libraires were purified using Nucleomag NGS Clean-up and Size Select beads (Macherey-Nagel, #744970.50). Quality checks were done with Qbit DNA HS Assay (ThermoScientific, #Q32854) and Bioanalyser (Agilent, #5067-4626).  Finally, libaries were pooled and sent for next generation sequencing.

treatment_protocol: To induce RNAi mediated silencing of certain gene products, we employed the Gal4-UAS system. By crossing males of a Gal4 driver line (Bloomington #7063) to females of the fly RNAi collection TRiP1 we obtained an F1 generation depleted for E(z) (Bloomington #33695). For CBP, a homemade line was used (Ciabrelli et al., 2023). These females were crossed to siblings and produced embryos that were depleted of E(z) or CBP mRNA and protein. To enrich and collect exact stages of embryo development, the flies were allowed to lay eggs on apple juice agar plates in cages for one hour at 25 °C. Prior collection, egg laying of the flies was synchronized by changing plates for three consecutive times. After three pre-lays, the embryos were collected for one hours and aged 25 °C to reach the stage of interest.

value: embryos

value: V20 RNAi CBP attP2

tag: condition

value: CBPKD

tag: Stage

value: cycle 14 (stage 5)

tag: antibody

value: GAF


title: CTRL_old_F4

description: Transcriptome profile of control Flcnfl/fl male female, 90- weeks of age, biological rep4

value: Female

value: Flcnfl/fl


title: blood_ctrl_7 (mRNA)

description:
Library name: Sample 21
C107

value: blood

value: control


title: CTRL_old_F3

description: Transcriptome profile of control Flcnfl/fl male female, 90- weeks of age, biological rep3


title: CUTTAG, H3 cofactors normalization, E-KD, c14, repl2

value: T09, Bloomington #33695

value: EzKD


title: FLCNKO_young_M3

description: Transcriptome profile of control FlcnLiKO male mouse, 12- weeks of age, biological rep3

value: liver

value: Male


title: CUTTAG, GAF, WT, c14, repl2

value: T180, Bloomington #36303

value: WT


title: blood_ctrl_6 (mRNA)

description:
Library name: Sample 20
C106


title: CTRL_old_F2

description: Transcriptome profile of control Flcnfl/fl male female, 90- weeks of age, biological rep2


title: CUTTAG, CBP, EzKD, c14, repl1

value: CBP


title: blood_ctrl_4 (mRNA)

description:
Library name: Sample 18
C104


title: Healthy C15-untreated

description: SAMPLE 1

value: Healthy

value: Vehicle

value: iPSC-derived endothelial cells


title: CUTTAG, H3 cofactors normalization, EzKD, c14, repl1

value: embryos


title: blood_ctrl_5 (mRNA)

description:
Library name: Sample 19
C105


title: CTRL_old_F1

description: Transcriptome profile of control Flcnfl/fl male female, 90- weeks of age, biological rep1


title: CUTTAG, Zld, WT, c14, repl2

value: cycle 14 (stage 5)

value: Zld


title: Retinal organoids, vehicle, mock, 24h, rep2

city: Trondheim

first: Aleksandr

last: Ianevski

address: Høgskoleringen 1

country: Norway

institute: NTNU

description:
Library name: 24hRNA_EYE23
Retinal organoids treated with vehicle and mock-infected, 24h post-treatment, replicate 2

data_processing:
Raw sequencing data were processed to remove low-quality sequences and adapter contamination. Reads containing 25% or more adapter sequence (allowing up to 2 mismatches) were discarded. Reads shorter than 150 bp were removed, as were those with an N content of 0.1% or more. Reads with stretches of a single nucleotide exceeding 50 bp were excluded. Additionally, reads where bases with a quality score below 20 constituted 40% or more of the sequence were filtered out. The resulting high-quality reads were retained for downstream analysis, with quality scores reported using the Phred33 system.
RNA-seq reads were aligned using STAR (Spliced Transcripts Alignment to a Reference) version 2.7.11b to the reference human GRCh38 genome.
Gene-level read counts were obtained using STAR's built-in --quantModeGeneCounts function.
Gene symbols and descriptions were assigned using the biomaRt package (v 2.58).
Pathway enrichment analysis was conducted using the clusterProfiler R package (v. 4.8.3) to identify overrepresented biological pathways among differentially expressed genes. Results were visualized as bubble plots, where the x-axis represented enriched pathways, the y-axis showed experimental comparisons, bubble size indicated the gene count, and bubble color intensity reflected statistical significance.
Assembly: Human GRCh38 genome
Supplementary files format and content: Tab-delimited text file containing gene-level read counts for each sample.
Supplementary files format and content: Additional processed files include differential expression analysis results comparing treatment conditions (baricitinib vs. vehicle) and infection status (RVFV vs. mock) with log2 fold changes, p-values, and adjusted p-values.

molecule: polyA RNA

source_name: Retina

growth_protocol: A549 cells were grown in Dulbecco's Modified Eagle's medium (DMEM) supplemented with 100 U/mL penicillin and 100 μg/ml streptomycin mixture, 4.5 g/L glucose, 1 mM L-glutamine, and 10% heat-inactivated fetal bovine serum. Cells were cultured at 37ºC with 5% CO2, 95% humidity and passaged using 0.05% (v/v) Trypsin/EDTA. Retinal organoids were generated from induced pluripotent stem cells (iPSCs) and cultured for 40 days prior to treatment.

extract_protocol:
Total RNA was isolated from samples using NAxtrakit following the manufacturer's protocol at 8 hours (A549 cells) or 24 hours (retinal organoids) post-infection. The quality and quantity of extracted RNA were evaluated prior to library preparation.
mRNA was enriched from total RNA using oligo-dT beads to select for polyadenylated transcripts. The enriched mRNA was fragmented into smaller pieces, which were used for cDNA synthesis. First-strand cDNA synthesis was performed using random primers, followed by second-strand synthesis incorporating dUTP in place of dTTP. The resulting cDNA fragments were end-repaired and adenylated at the 3′ ends, after which adaptors were ligated. Libraries were then amplified via polymerase chain reaction (PCR) and assessed for quality. The amplified libraries were circularized and further amplified to produce DNA nanoballs (DNBs). Sequencing was performed on the DNBSEQ Technology platform with a paired-end read length of 150 bp (PE150), using the DNBSEQ Eukaryotic Strand-specific mRNA library.

treatment_protocol: Approximately 4 × 10^4 A549 cells were seeded in each well of 96-well plates. After 24 hours, 5 μM baricitinib or vehicle control (0.01% DMSO) was added. After 15 minutes, cells were infected with recombinant Rift Valley Fever Virus expressing Katushka (rRVFV) at MOI 0.1 or mock-infected in medium containing 1% FBS. For retinal organoids, 40-day-old organoids were transferred to ultralow attachment 96-well plates with one organoid per well. 5 μM baricitinib or vehicle was added followed by rRVFV (MOI 0.1) or mock infection 15 minutes later.

value: Retina

tag: cell line

value: Organoid

value: Wild-type

value: Vehicle + Mock

tag: time point


title: Retinal organoids, vehicle, mock, 24h, rep3

description:
Library name: 24hRNA_EYE24
Retinal organoids treated with vehicle and mock-infected, 24h post-treatment, replicate 3


title: CTRL_old_M4

description: Transcriptome profile of control Flcnfl/fl male mouse, 90- weeks of age, biological rep4

value: Flcnfl/fl


title: CUTTAG, CBP, EzKD, c14, repl2

value: T09, Bloomington #33695

value: EzKD


title: CUTTAG, H3 cofactors normalization, WT, c14, repl2


title: blood_ctrl_3 (mRNA)

description:
Library name: Sample 17
C103

value: blood

value: control


title: Healthy C15-e-cig

description: SAMPLE 2

value: e-cig extract


title: Retinal organoids, vehicle, mock, 24h, rep1

description:
Library name: 24hRNA_EYE22
Retinal organoids treated with vehicle and mock-infected, 24h post-treatment, replicate 1


title: Primary differentiated adipocytes, 100 nM hGIP_2 Hrs, rep1

value: primary differentiated adipocytes

value: 100 nM hGIP_2 Hrs


title: CUTTAG, CBP, WT, c14, repl2

value: T180, Bloomington #36303

value: WT

value: CBP


title: blood_ctrl_2 (mRNA)

description:
Library name: Sample 16
C102


title: Retinal organoids, vehicle, RVFV, 24h, rep3

description:
Library name: 24hRNA_EYE21
Retinal organoids treated with vehicle and infected with RVFV, 24h post-infection, replicate 3

value: Vehicle + RVFV


title: CTRL_old_M1

description: Transcriptome profile of control Flcnfl/fl male mouse, 90- weeks of age, biological rep1

value: liver

value: Male


title: CUTTAG, GAF, WT, c14, repl1

value: embryos

value: cycle 14 (stage 5)

value: GAF


title: CTRL_old_M2

description: Transcriptome profile of control Flcnfl/fl male mouse, 90- weeks of age, biological rep2

value: Flcnfl/fl


title: blood_ctrl_1 (mRNA)

description:
Library name: Sample 15
C101


title: Retinal organoids, vehicle, RVFV, 24h, rep1

description:
Library name: 24hRNA_EYE19
Retinal organoids treated with vehicle and infected with RVFV, 24h post-infection, replicate 1

value: Retina

value: Organoid

value: Wild-type


title: CTRL_young_F4

description: Transcriptome profile of control Flcnfl/fl female mouse, 12- weeks of age, biological rep4

value: Female


title: CUTTAG, Zld, WT, c14, repl1

value: Zld


title: blood_viral_6 (mRNA)

description:
Library name: Sample 13
BI16_B

value: blood

value: viral infection


title: Retinal organoids, vehicle, RVFV, 24h, rep2

description:
Library name: 24hRNA_EYE20
Retinal organoids treated with vehicle and infected with RVFV, 24h post-infection, replicate 2


title: CTRL_young_F3

description: Transcriptome profile of control Flcnfl/fl female mouse, 12- weeks of age, biological rep3


title: CUTTAG, H3 cofactors normalization, WT, c14, repl1

value: T180, Bloomington #36303


title: Retinal organoids, baricitinib, mock, 24h, rep2

description:
Library name: 24hRNA_EYE17
Retinal organoids treated with baricitinib and mock-infected, 24h post-treatment, replicate 2

value: Baricitinib 5μM + Mock


title: CTRL_old_M3

description: Transcriptome profile of control Flcnfl/fl male mouse, 90- weeks of age, biological rep3


title: blood_viral_3 (mRNA)

description:
Library name: Sample 10
BI13_B


title: blood_viral_5 (mRNA)

description:
Library name: Sample 12
BI15_V


title: CUTTAG, CBP, WT, c14, repl1

value: WT

value: CBP


title: Retinal organoids, baricitinib, mock, 24h, rep3

description:
Library name: 24hRNA_EYE18
Retinal organoids treated with baricitinib and mock-infected, 24h post-treatment, replicate 3


title: Retinal organoids, baricitinib, RVFV, 24h, rep3

description:
Library name: 24hRNA_EYE15
Retinal organoids treated with baricitinib and infected with RVFV, 24h post-infection, replicate 3

value: Baricitinib 5μM + RVFV


title: blood_viral_7 (mRNA)

description:
Library name: Sample 14
BI17_V


title: CTRL_young_F2

description: Transcriptome profile of control Flcnfl/fl female mouse, 12- weeks of age, biological rep2

value: liver


title: CUTTAG, H3 ATAC-seq normalization, WT, st5, repl2

description: Processed from the same pool of ATAC-seq nuclei for normalization

value: embryos


title: Retinal organoids, baricitinib, mock, 24h, rep1

description:
Library name: 24hRNA_EYE16
Retinal organoids treated with baricitinib and mock-infected, 24h post-treatment, replicate 1


title: CTRL_young_M4

description: Transcriptome profile of control Flcnfl/fl male mouse, 12- weeks of age, biological rep4

value: Male


title: Retinal organoids, baricitinib, RVFV, 24h, rep2

description:
Library name: 24hRNA_EYE14
Retinal organoids treated with baricitinib and infected with RVFV, 24h post-infection, replicate 2


title: CUTTAG, H3 ATAC-seq normalization, WT, st4, repl2

value: cycle 10-12 (stage 4)


title: blood_viral_1 (mRNA)

description:
Library name: Sample 8
BI08_V


title: blood_viral_2 (mRNA)

description:
Library name: Sample 9
BI12_V


title: CTRL_young_M3

description: Transcriptome profile of control Flcnfl/fl male mouse, 12- weeks of age, biological rep3

value: Flcnfl/fl


title: blood_viral_4 (mRNA)

description:
Library name: Sample 11
BI14_V


title: CTRL_young_F1

description: Transcriptome profile of control Flcnfl/fl female mouse, 12- weeks of age, biological rep1


title: CUTTAG, H3 ATAC-seq normalization, WT, st3, repl2

value: before cycle 9 (stage 3)


title: Retinal organoids, baricitinib, RVFV, 24h, rep1

description:
Library name: 24hRNA_EYE13
Retinal organoids treated with baricitinib and infected with RVFV, 24h post-infection, replicate 1

value: Retina

value: Organoid


title: CTRL_young_M2

description: Transcriptome profile of control Flcnfl/fl male mouse, 12- weeks of age, biological rep2


title: A549 cells, vehicle, mock, 8h, rep3

description:
Library name: 8hRNA_ACE12
A549 cells treated with vehicle and mock-infected, 8h post-treatment, replicate 3

source_name: Lung

value: Lung

value: Epithelial

value: Wild-type

value: Vehicle + Mock


title: CUTTAG, H3 ATAC-seq normalization, WT, st5, repl1

value: T180, Bloomington #36303

value: cycle 14 (stage 5)


title: blood_bacterial_7 (mRNA)

description:
Library name: Sample 7
BI07_V

value: blood

value: bacterial infection


title: blood_bacterial_6 (mRNA)

description:
Library name: Sample 6
BI06_V


title: CUTTAG, H3 ATAC-seq normalization, WT, st4, repl1

value: WT


title: A549 cells, vehicle, mock, 8h, rep2

description:
Library name: 8hRNA_ACE11
A549 cells treated with vehicle and mock-infected, 8h post-treatment, replicate 2


title: A549 cells, vehicle, mock, 8h, rep1

description:
Library name: 8hRNA_ACE10
A549 cells treated with vehicle and mock-infected, 8h post-treatment, replicate 1


title: blood_bacterial_5 (mRNA)

description:
Library name: Sample 5
BI05_BS


title: CUTTAG, H3 ATAC-seq normalization, WT, st3, repl1


title: thyroid RetSat ko 5

city: Berlin

first: Michael

last: Schupp

address: Hessische Str. 3-4

department: Institute of Pharmacology

country: Germany

institute: Charite Universitätsmedizin Berlin

data_processing:
Sequence reads were trimmed with the trimmomatic tool and default parameters
Trimmed sequences were mapped to GRCm39/mm39 using the STAR method (v2.7.6)
read count extraction was performed using featureCounts v2.0.1
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: total thyroid

growth_protocol: standard mouse colony

extract_protocol:
RNA was harvested using the RNeasy kit from Qiagen, following the manufacturer`s protocol
samples were further treated with the DNase I Set from Zymo Research,following the manufacturer`s protocol
Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit and Module (New England Biolabs, USA) following manufacturer`s protocol

treatment_protocol: Mice were fed  high-fat diet for 12 weeks starting at an age of 8 weeks.

value: total thyroid

tag: strain

value: RetSat flox/flox TPO-Cre (+)

value: high fat-diet feeding


title: blood_bacterial_4 (mRNA)

description:
Library name: Sample 4
BI04_B


title: thyroid RetSat ko 4

value: Male


title: CUTTAG, H3K27ac, WT, c10-12, repl2

value: embryos

value: cycle 10-12 (stage 4)


title: A549 cells, vehicle, RVFV, 8h, rep3

description:
Library name: 8hRNA_ACE9
A549 cells treated with vehicle and infected with RVFV, 8h post-infection, replicate 3

value: Vehicle + RVFV


title: blood_bacterial_3 (mRNA)

description:
Library name: Sample 3
BI03_B


title: thyroid RetSat ko 3


title: CUTTAG, H3K27me3, WT, c10-12, repl2


title: blood_bacterial_2 (mRNA)

description:
Library name: Sample 2
BI02_B


title: A549 cells, vehicle, RVFV, 8h, rep2

description:
Library name: 8hRNA_ACE8
A549 cells treated with vehicle and infected with RVFV, 8h post-infection, replicate 2


title: CUTTAG, H3, WT, c10-12, repl2


title: CUTTAG, H3K27ac, WT, c10-12, repl1


title: A549 cells, vehicle, RVFV, 8h, rep1

description:
Library name: 8hRNA_ACE7
A549 cells treated with vehicle and infected with RVFV, 8h post-infection, replicate 1


title: blood_bacterial_1 (mRNA)

description:
Library name: Sample 1
BI01_B


title: thyroid RetSat ko 1


title: CTRL_young_M1

description: Transcriptome profile of control Flcnfl/fl male mouse, 12- weeks of age, biological rep1

value: liver

value: Flcnfl/fl


title: A549 cells, baricitinib, mock, 8h, rep3

description:
Library name: 8hRNA_ACE6
A549 cells treated with baricitinib and mock-infected, 8h post-treatment, replicate 3

value: Lung

value: Epithelial

value: Baricitinib 5μM + Mock


title: control thyroid5

value: RetSat flox/flox TPO-Cre (-)


title: iWAT-wt6

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description: 2x150 Paired-End

data_processing:
Sequencing was performed on the Illumina NovaSeq platform using a 2x150 Paired-End configuration
Raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the reference genome (mm10) using the STAR aligner v.2.5.2b.
Unique gene hit counts and transcripts per million were calculated by using feature Counts from the Subread package v.1.5.2.
Assembly: mm10
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: TPM_values.csv

source_name: inguinal adipose tissue

growth_protocol: Mice were housed at 23˚C or 30˚C in ventilated cages under a 12 h – 12 h light/dark cycle. Mice were fed a standard diet (Lab Diet 5008) with free access to food and water unless specified.

extract_protocol:
Total RNA were extracted using TRIZOL (FIsher Scientific) and Rneasy mini (QIAGEN) with DNase (Qiagen) treatment on column.
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. ERCC RNA Spike-In Mix (ThermoFisher) was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAGEN FastSelect rRNA HMR Kit (Qiagen). RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Mice were housed at thermoneutrality (30°C)  prior to cold tolerance at 6°C for 5 h.

value: inguinal adipose tissue

value: wild type

value: cold exposure 5h


title: CUTTAG, H3K27me3, WT, c10-12, repl1

value: T180, Bloomington #36303

value: WT


title: A549 cells, baricitinib, mock, 8h, rep2

description:
Library name: 8hRNA_ACE5
A549 cells treated with baricitinib and mock-infected, 8h post-treatment, replicate 2

value: Wild-type


title: iWAT-wt5

description: 2x150 Paired-End


title: control thyroid4

value: total thyroid

value: high fat-diet feeding


title: A549 cells, baricitinib, mock, 8h, rep1

description:
Library name: 8hRNA_ACE4
A549 cells treated with baricitinib and mock-infected, 8h post-treatment, replicate 1


title: iWAT-wt4

description: 2x150 Paired-End


title: CUTTAG, H3K27ac, WT, bfc9, repl2

value: embryos

value: before cycle 9 (stage 3)


title: CUTTAG, H3, WT, c10-12, repl1

value: cycle 10-12 (stage 4)


title: control thyroid2

value: Male


title: A549 cells, baricitinib, RVFV, 8h, rep3

description:
Library name: 8hRNA_ACE3
A549 cells treated with baricitinib and infected with RVFV, 8h post-infection, replicate 3

value: Baricitinib 5μM + RVFV


title: iWAT-wt3

description: 2x150 Paired-End


title: control thyroid3


title: thyroid RetSat ko 2

value: RetSat flox/flox TPO-Cre (+)


title: A549 cells, baricitinib, RVFV, 8h, rep1

description:
Library name: 8hRNA_ACE1
A549 cells treated with baricitinib and infected with RVFV, 8h post-infection, replicate 1

value: Lung

value: Epithelial


title: CUTTAG, H3K27me3, WT, bfc9, repl2


title: control thyroid1

value: RetSat flox/flox TPO-Cre (-)


title: CUTTAG, H3, WT, bfc9, repl2


title: WT MEFs, Meg3 ChIRP

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

description: WT MEFs Meg3 ChIRP

data_processing:
Adapter trimming was performed on raw fastq files using Trimmomatic. Surviving reads were aligned against the relevant reference genome (GRCm38) using Burrows-Wheeler Aligner BWA-MEM.  sorted, and deduplicated
Resulting BAM alignments were cleaned, sorted, and deduplicated (PCR and Optical duplicates) with PICARD tools.
Bigwig files were generated using deeptools
Peaks were called on the merged files using macs2
Peaks were classified as being unique to WT, KO or shared with the HOMER; and anno.txttated with HOMER.
Assembly: mm10
Supplementary files format and content: .anno.txt
Library strategy: ChIRP-seq

source_name: embryonic fibroblasts

growth_protocol: DMEM, 10% Fetal Bovine Serum, 2mM Glutamine, 2% Penicillin Streptomicin, cells were cultured in 37C at 5% CO2

extract_protocol:
Cells were crosslinked with 1% glutaraldehyde for 10 minutes,then  quenched with glycine. After lysis chromatin was sonicated using Qsonica sonicator
library was constructed by NOVOGENE

value: Mouse embryonic fibroblasts


title: A549 cells, baricitinib, RVFV, 8h, rep2

description:
Library name: 8hRNA_ACE2
A549 cells treated with baricitinib and infected with RVFV, 8h post-infection, replicate 2


title: iWAT-wt1

description: 2x150 Paired-End

value: inguinal adipose tissue

value: wild type


title: CUTTAG, H3K27ac, WT, bfc9, repl1

value: T180, Bloomington #36303


title: beta actin KO MEFs, Meg3 ChIRP

description: beta actin KO Meg3 ChIRP

value: KO


title: CUTTAG, H3K27me3, WT, bfc9, repl1

value: WT


title: urine_ctrl_7 (miRNA)

description:
Library name: Sample 21
21_C107

data_processing:
Data processing: Adapter trimming, removing short fragments (>18 nt), mapping, and miRNA quantification were carried out using miRDeep2 v0.1.2. After removing miRNAs with consistently low counts (median <10) count matrix was normalised using the TMM method as implemented in the edgeR package of R statistical software v4.3.2.
Assembly: GRCh38.p13
Supplementary files format and content: TMM normalised and log2-transformed miRNA expression matrix where columns represent samples and rows - miRNAs.

source_name: urine

extract_protocol:
Urine samples were collected in Urine Collection and Preservation Tubes (Norgen Biotek), according to the manufacturer's specifications. RNA extraction was performed using the Urine Total RNA Purification Maxi Kit, adhering to the manufacturer’s protocol. Ribosomal RNA was removed from all samples using the MGIEasy rRNA Depletion Kit, according to the manufacturer’s protocol.
Library preparation was performed using the MGIEasy Small RNA Library Prep Kit.

value: urine

value: control


title: iWAT-UCP1KO6

description: 2x150 Paired-End

value: cold exposure 5h


title: urine_ctrl_8 (miRNA)

description:
Library name: Sample 22
22_C108


title: brain, Plexin-B2_cKO, rep1, scRNAseq

city: New York

first: Mary

middle: Elizabeth

last: Ughetta

state: NY

address: 1 Gustave L. Levy Pl

institute: Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger software V7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: mice brain

extract_protocol:
Plexin-B2 knockout was induced by administrating Tamoxifen (100 mg/kg) 3 days before intracranial injection of KR158 GBM cells and every other day until 8 weeks. After 8 weeks, mice were euthanized and the brain tissues containing KR158 tumor were harvested on ice. Brain tissue pieces were taken from approximately 1 mm anterior to 1 mm posterior from the injection site and minced with scalpel blades and dissociated into single cell with papain digestion. Debris from the brain tissues were removed by Percoll centrifugation and red blood cells (RBCs) were lysed with RBC lysis solution on ice for 10 minutes. Cells were washed and resuspended in FACS buffer containing 0.2% BSA and 20 μg/ml DNase and submitted for single cell sequencing with the 10X Genomics system at the Mount Sinai Genomics core facility.
GEM formation, cDNA amplification and library preparation was performed according to the manufacture’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268; Chromium Next GEM Chip G Single Cell Kit, 48 rxns PN-1000120). Barcoding libraries was performed per User guide, CG000315 from 10x Genomics (Dual Index Kit TT Set A, 96 rxns PN-1000215).

value: mice brain

value: mouse brain cells

value: Cx3cr1 CreER/+ Plxnb2fl/fl


title: CUTTAG, H3, WT, bfc9, repl1

value: embryos

value: before cycle 9 (stage 3)


title: urine_ctrl_6 (miRNA)

description:
Library name: Sample 20
20_C106


title: KR158 brain, WT, rep1, scRNAseq

description: 10x Genomics

value: Cx3cr1 CreER/+ Plxnb2 fl/+


title: urine_ctrl_5 (miRNA)

description:
Library name: Sample 19
19_C105


title: iWAT-UCP1KO3

description: 2x150 Paired-End


title: CUTTAG, H3K27me3, EZKD, c14, repl2

value: T09, Bloomington #33695

value: EzKD

value: cycle 14 (stage 5)


title: urine_ctrl_4 (miRNA)

description:
Library name: Sample 18
18_C104


title: Ryk_KO_14_1 (#10105)

city: San Diego

first: Zhe

last: Shen

state: California

address: 9500 Gilman Dr. MC 0123, La Jolla

institute: Devision of Biological Science, UCSD

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using 10X cellranger count.
R (version 4.1.2) package Seurat for cell type and DEG analysis, monocle3 for pesudotime analysis and cellchat for the interaction of ligand-receptor analysis.  http://biit.cs.ut.ee/gprofiler/gost for gene ontology analysis.
Assembly: GRCm38/mm10
Supplementary files format and content: The processed data files contain an aggregate for all samples.
Supplementary files format and content: counts.mtx.gz: Raw Counts Matrix post cellranger alignment and quality control.
Supplementary files format and content: features.csv.gz: Features (gene symbols) corresponding to Matrix rows after quality control.
Supplementary files format and content: sample_barcodes.csv.gz: Sample barcodes corresponding to Matrix columns after quality control.
Supplementary files format and content: meta_data.csv.gz: Metadata containing sample specific information for each cell after quality control.

source_name: Spinal cord

extract_protocol:
Mice were anesthetized and were performed a trans-cardiac perfusion with fresh ice-cold carbogen-bubbled cutting solution (212 mM sucrose, 1.25 mM NaH2PO4, 26 mM NaHCO3, 10 mM Glucose, 3 mM KCl, 7 mM MgSO4, 0.5 mM CaCl2). After decapitation, the spinal cords were immediately extracted and placed in fresh ice-cold cutting solution bubbled with a carbogen gas (95% O2 and 5% CO2). And were quickly transferred to the vibratome and sectioned into 300 μm slice. The slices were incubated in ACSF (125 mM NaCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 10 mM Glucose, 2.5 mM KCl, 1.3 mM MgSO4, 2 mM CaCl2) continuously aerated with carbogen gas. Spinal cords were cut into small pieces < 1 mm in each dimension by a knife and collected to a 60 mm Petri dish leaving only enough ACSF to cover the tissues. The tissues were digested by pronase solution (1 mg/mL pronase, 45 μM ActD, 100 μg/mL DNase I in ice-cold carbogen-bubbled ACSF) at room temperature for 60 min with gentle agitation. After digestion, the tissues were exchanged into trituration buffer (1% FBS, 3 μm ActD, 100 μg/mL DNase I in ice-cold carbogen-bubbled ACSF) and triturated very gently through fire polished salinized Pasteur pipettes with the opening of 600 μm and 300 μm diameter. The supernatant was collected and centrifuged at 300 rcf for 3 min at 4 ℃. The cell pellet was resuspended in wash buffer (0.1% BSA, 3 μm ActD, 100 μg/mL DNase I in ice-cold carbogen-bubbled ACSF) and filtered by 30 μm cell strainer. The dead cells were removed by MACS Dead Cell Removal Kit by manufactory’s instruction. The final single cell suspensions were rinsed in cold DPBS solution (0.1% BSA, 3 μm ActD, 100 μg/mL DNase I in ice-cold DPBS). The cell concentration and cell viability were determined by Cell Counter with AOPI staining. In our experiment, the cell viability of all samples was at least 80%. All steps were performed on ice or at 4 ℃ except the pronase digestion step. The wide-bore pipette tips were used to resuspend the cell pellet in all steps.
Reverse transcription, cDNA amplification and library construction were performed according to the manufacturer’s instructions and used for sequencing.

value: Spinal cord

value: 8-10 weeks old

value: 14 days after SCI


title: iWAT-UCP1KO2

description: 2x150 Paired-End

value: inguinal adipose tissue


title: iWAT-wt2

description: 2x150 Paired-End

value: wild type


title: Ryk_KO_14_2 (#10104)


title: urine_ctrl_3 (miRNA)

description:
Library name: Sample 17
17_C103

value: urine


title: iWAT-UCP1KO1

description: 2x150 Paired-End


title: urine_ctrl_2 (miRNA)

description:
Library name: Sample 16
16_C102

value: control


title: iWAT-UCP1KO5

description: 2x150 Paired-End

value: cold exposure 5h


title: CUTTAG, H3K27ac, CBPKD, c14, repl2

value: V20 RNAi CBP attP2

value: CBPKD


title: CUTTAG, H3, EZKD, c14, repl2


title: Ryk_WT_14_1 (#10114)


title: CUTTAG, H3, CBPKD, c14, repl2


title: iWAT-DKO5

description: 2x150 Paired-End

value: DKO


title: iWAT-UCP1KO4

description: 2x150 Paired-End


title: urine_ctrl_1 (miRNA)

description:
Library name: Sample 15
15_C101


title: Ryk_WT_7_2 (#10117)

value: 7 days after SCI


title: CUTTAG, H3K27ac, EZKD, c14, rep1

value: embryos


title: CUTTAG, H3K27ac, EZKD, c14, repl2


title: iWAT-DKO4

description: 2x150 Paired-End


title: Ryk_KO_7_2 (#10047)


title: iWAT-DKO3

description: 2x150 Paired-End


title: CUTTAG, H3, EZKD, c14, repl1


title: Ryk_KO_1_2 (#10048)

value: 1 day after SCI


title: iWAT-DKO2

description: 2x150 Paired-End


title: CUTTAG, H3K27ac, CBPKD, c14, repl1


title: urine_viral_4 (miRNA)

description:
Library name: Sample 11
11_BI12_V

value: viral infection


title: iWAT-DKO1

description: 2x150 Paired-End


title: WT_nsci_2 (#10120)

value: Sham


title: iWAT-DKO6

description: 2x150 Paired-End


title: CUTTAG, H3,CBPKD, c14, repl1

value: cycle 14 (stage 5)


title: Ryk_WT_14_2 (#10113)

value: Spinal cord


title: Ryk_KO_nsci_2 (#10119)

value: 8-10 weeks old


title: iWAT-ALNKO6

description: 2x150 Paired-End

value: ALNKO


title: urine_viral_7 (miRNA)

description:
Library name: Sample 14
14_BI17_V


title: iWAT-ALNKO5

description: 2x150 Paired-End

value: inguinal adipose tissue


title: Ryk_KO_nsci_1 (#9169)


title: CUTTAG, H3K27me3, EZKD, c14, repl1

value: T09, Bloomington #33695

value: EzKD


title: urine_viral_6 (miRNA)

description:
Library name: Sample 13
13_BI15_V

value: urine


title: urine_viral_1 (miRNA)

description:
Library name: Sample 8
08_BI06_V


title: WT_nsci_1 （#1771）


title: CUTTAG, H3, WT,  c14, repl2

value: T180, Bloomington #36303

value: WT


title: CUTTAG, H3K27me3, c14, repl2


title: Ryk_WT_1_2 (#10115)


title: urine_viral_5 (miRNA)

description:
Library name: Sample 12
12_BI14_V


title: Ryk_WT_1_1 (#3821)


title: CUTTAG, H3K27ac, WT, c14, repl1


title: Ryk_WT_7_1 (#3820)


title: CUTTAG, H3K27me3, WT, c14, repl1


title: iWAT-ALNKO2

description: 2x150 Paired-End

value: cold exposure 5h


title: urine_viral_3 (miRNA)

description:
Library name: Sample 10
10_BI11_V


title: urine_viral_2 (miRNA)

description:
Library name: Sample 9
09_BI07_V


title: CUTTAG, H3K27ac, WT, c14, repl2


title: Ryk_KO_1_1 (#3816)


title: CUTTAG, H3, WT, c14, repl1


title: iWAT-ALNKO1

description: 2x150 Paired-End


title: urine_bacterial_4 (miRNA)

description:
Library name: Sample 4
04_BI04_B

value: bacterial infection


title: iWAT-ALNKO4

description: 2x150 Paired-End


title: Ryk_KO_7_1 (#3814)

value: 7 days after SCI


title: Mouse, lung, Naïve

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

description: Fresh tissue; imaging-based spatial transcriptomics; 100-gene panel

hyb_protocol: After fixation, lung tissues were processed for paraffin embedding, and formalin-fixed paraffin-embedded (FFPE) blocks were prepared. Sections were then cut at 5um thickness onto Xenium slides in the Pathology Shared Resource at Dartmouth (RRID: SCR_023479) according to 10x Genomics protocol CG000580).  Slides were then transferred to the Genomics and Molecular Biology Shared Resource (RRID:SCR_021293) and processed following the manufacturer’s instructions for FFPE tissue sections (Protocol: CG000581) followed by probe hybridization, ligation and amplification (Protocol: CG000582).

scan_protocol: Slides were run on a Xenium Analyzer instrument running Xenium instrument software version 2.0.1.0 and On-Board Analysis software version 2.0.0.10 to produce the output data bundle used for downstream analysis. Following the Xenium run, slides were H&E stained on a Sakura Tissue-Tek Prism stainer and whole slide imaging conducted at 40x magnification using an Aperio GT450 instrument (Leica).

data_processing: Xenium spatial transcriptomics analysis was then processed and performed using Xenium Explorer 3 (10x Genomics), with cell population identification conducted using R v.4.2 64.

source_name: Mouse, lung, Naïve

extract_protocol: Lung tissues were collected, fixed with 10% neutral buffered formalin (NBF), and paraffin embedded.

treatment_protocol: Two groups of C57BL/6 mice (n = 2 per group) were used for analysis: Group 1 (Naive), which received no treatment and was expected to contain steady-state interstitial macrophages (IMs); and Group 2 (LPS), treated with lipopolysaccharide (LPS; Sigma-Aldrich) administered intranasally at 10 μg in 50 μl sterile PBS (Corning) 24 hours before collection, expected to contain stimulated IMs and recruited monocytes.

value: Naïve


title: urine_bacterial_7 (miRNA)

description:
Library name: Sample 7
07_BI16_B


title: bulkRNAseq, CBPKD, c14, repl3

data_processing:
RNA-seq data were processed using nf-core/rnaseq pipeline v 3.11.2 with default parameters.
Assembly: dmel6
Supplementary files format and content: bigwig files with RPKM normalised signal

molecule: nuclear RNA

extract_protocol:
Embryos were collected on apple juice agar plates. Embryos were submerged with halocarbon oil 27 (Sigma-Aldrich, #H8773) to allow hand-staging using a stereo-microscope. Embryos of the correct developmental stage were then transferred into 50 µl of Trizol (ThermoScientific, #15596026), dissociated with a tissue grinder and snap-frozen and stored at -80 °C until RNA extraction. The Trizol solution was defrosted and filled up to 500 µl supplemented with 1 µL of 1:1000 ERCC RNA spike-in (Ambion, #4456740). After the addition of 100 µl chloroform and mixing, the samples were spun down at 4 °C, 12.000 g for 15 min to separate the organic and aqueous phase. The aqueous phase was recovered and transferred into 300 µl of chloroform and the first step was repeated. Right after, the aqueous phase was transferred into isopropanol containing 20 µg of glycogen. The RNA was precipitated at -20 °C overnight and pelleted by centrifugation at 12.000 g for 60 min, 4 °C. The pellet was washed with 80% ethanol, air dried for 5 minutes and resuspended water. The RNA was quantified using Qubit RNA BR Assay kit (ThermoScientific, #Q10210) and integrity was assessed on agarose gels or the BioAnalyser (Agilent, #5067-4626).
Libraries were generated using the Illumina Stranded Total RNA-seq kit with Ribo-zero Plus (Illumina, #20072063) according to the manufacturer’s instructions followed by followed NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420). Libraries were pooled and sent for next generation sequencing.

value: embryos

value: V20 RNAi CBP attP2

value: CBPKD


title: urine_bacterial_3 (miRNA)

description:
Library name: Sample 3
03_BI03_B


title: Mouse, lung, LPS 24 hrs

source_name: Mouse, lung, LPS 24 hrs

value: LPS


title: bulkRNAseq, CBPKD, c14, repl2

value: cycle 14 (stage 5)


title: urine_bacterial_2 (miRNA)

description:
Library name: Sample 2
02_BI02_B


title: iWAT-ALNKO3

description: 2x150 Paired-End


title: urine_bacterial_1 (miRNA)

description:
Library name: Sample 1
01_BI01_B


title: bulkRNAseq, CBPKD, c14, repl1


title: urine_bacterial_6 (miRNA)

description:
Library name: Sample 6
06_BI13_B


title: urine_bacterial_5 (miRNA)

description:
Library name: Sample 5
05_BI05_BS


title: type_2_diabetes_patient_plasma_eexosomes_rep4

city: Hefei

first: Qianqian

last: Tao

state: Anhui

address: Meishan Road, Shushan District, Hefei City, Anhui Province

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: micro RNA level  in human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 55°C for 20 hoursin a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: peripheral blood-derived exosomes; replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVana™ PARIS™ Kit (Ambion Inc., Austin, TX) following the manufacturer's recommendations.

value: plasma

value: Type 2 diabetes patient


title: PLAXAW cj-ESCs, aneuploid, rep2

city: Seattle

first: Min

last: Yang

state: WA

address: 850 Republican St S280

department: Ob/Gyn

institute: University of Washington

description: Library name: PLAXAW cj-ESC Aneuploid 2

data_processing:
Reads were filtered using SOAPnuke v2.2.1 with the parameters "-l 15 -q 0.5 -n 0.05 -I" to remove adapter sequences, remove reads with >5% N bases, and remove reads with 50% of bases having a sequencing quality of less than 15. Resulting reads are considered "clean reads"
Clean reads were aligned to the reference sequence using Bowtie2 v2.4.5 with parameters "-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 20 -N 1" and expression of genes and transcripts were calculated using RSEM v1.3.1 with paramters "--forward-prob 0".
Assembly: GCF_011100555.1
Supplementary files format and content: CSV file containing read counts for all samples
Supplementary files format and content: CSV file containing TPM (transcripts per million) for all samples

organism: Callithrix jacchus

extract_protocol:
cj367 cells were dissociated at 80% confluency using Accutase and centrifuged to obtain cell pellet. RNA from the pellet was extracted using an Rneasy Mini Kit (Qiagen) following the manufacturer's instructions. Samples were analyzed using a NanoDrop 2000 to confirm purity of RNA.
Libraries were generated using the Optimal Dual-mode mRNA Library Prep Kit (BGI).

value: embryonic stem cell

value: female

value: naive

tag: ploidy

value: aneuploid

value: plaxaw


title: type_2_diabetes_patient_plasma_eexosomes_rep5

description: micro RNA level  in human blood

source_name: peripheral blood-derived exosomes; replicate 5


title: bulkRNAseq, EzKD, c14, repl2

value: T09, Bloomington #33695

value: EzKD


title: Mycelium, MU412 - Replicate 2_sRNA

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description:
Library name: MU412_B_sRNA
Dataset S5.xlsx
Dataset S6.xlsx
R22

data_processing:
Raw paired-end (PE)  and single-end reads from M. lusitanicus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V.0.4.3.1
Reads with a Phred quality score (q) ≤32 and/or a total length < 20 nt were removed from the analysis
Assembly: Mucor lusitanicus (CBS 277.49) v2 (https://mycocosm.jgi.doe.gov/pages/search-for-genes.jsf?organism=Mucci2)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics and functional annotation for every gene

organism: Mucor lusitanicus

source_name: Mycelium

growth_protocol: MU636 and MU412 strains were grown on solid YPG media  at 26 ºC for 24 hours

extract_protocol:
Total RNA was extracted using the mirVana kit (AM1561) and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Mycelium


title: Mycelium, MU412 - Replicate 3_sRNA

description:
Library name: MU412_C_sRNA
Dataset S5.xlsx
Dataset S6.xlsx
R33


title: Mycelium, MU412 - Replicate 1_sRNA

description:
Library name: MU412_A_sRNA
Dataset S5.xlsx
Dataset S6.xlsx
R11


title: type_2_diabetes_patient_plasma_eexosomes_rep3

description: micro RNA level  in human blood

source_name: peripheral blood-derived exosomes; replicate 3


title: Mycelium, MU636 - Replicate 3_sRNA

description:
Library name: MU636_C_sRNA
Dataset S5.xlsx
Dataset S6.xlsx
R66


title: bulkRNAseq, EzKD, c14, repl1


title: Primed cj-ESCs, euploid, rep2

description: Library name: Primed cj-ESC 2

value: primed

value: euploid


title: Mycelium, MU636 - Replicate 2_sRNA

description:
Library name: MU636_B_sRNA
Dataset S5.xlsx
Dataset S6.xlsx
R55


title: type_2_diabetes_patient_plasma_eexosomes_rep2

description: micro RNA level  in human blood

source_name: peripheral blood-derived exosomes; replicate 2


title: bulkRNAseq, WT, c14, repl3

value: embryos

value: T180, Bloomington #36303

value: WT


title: Primed cj-ESCs, euploid, rep1

description: Library name: Primed cj-ESC 1


title: Mycelium, MU636 - Replicate 1_sRNA

description:
Library name: MU636_A_sRNA
Dataset S5.xlsx
Dataset S6.xlsx
R44


title: type_2_diabetes_patient_plasma_exosomes_rep1

description: micro RNA level  in human blood

source_name: peripheral blood-derived exosomes; replicate 1


title: PLAXAW cj-ESCs, euploid, rep2

description: Library name: PLAXAW cj-ESC 2


title: healthy_donor_plasma_exosomes_rep5

description: micro RNA level  in human blood

value: healthy donor


title: Mycelium, MU412- Replicate 3

description:
Library name: MU412_C
Dataset S4.xlsx


title: bulkRNAseq, WT, c14, repl1

source_name: embryos

value: cycle 14 (stage 5)


title: bulkRNAseq, EzKD, c14, repl3


title: PLAXAW cj-ESCs, aneuploid, rep1

description: Library name: PLAXAW cj-ESC Aneuploid 1


title: PLAXA cj-ESCs, euploid, rep2

description: Library name: PLAXA cj-ESC 2

value: plaxa


title: PLAXAW cj-ESCs, euploid, rep1

description: Library name: PLAXAW cj-ESC 1


title: Mycelium, MU412 - Replicate 2

description:
Library name: MU412_B
Dataset S4.xlsx


title: ATAC-seq, WT, c10-12, repl2

data_processing:
The ATAC-seq data processing was done using snakePipes version 2.4.0 (Bhardwaj et al., 2019) (parameters: --trim --fastqc --properPairs –dedup --mapq 1) with specific ATAC-seq Bowtie2 alignment option  (--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700) was used. Since the ATAC-seq contains lambda phage spike-ins for reliable quantification of global effects, the libraries were mapped to a constructed hybrid genome of dm6 and lambda phage (NCBI GenBank ID: J02459.1). Macs2 was used to call ATAC-seq peaks using the following options: -g dm -q 0.05 --broad. ATAC-seq normalized signals were generated using bamCoverage from deepTools (v.2.5.7). More specifically, the relative dm6/lambda total number of reads was used as normalization factor to rescale each sample through the bamCompare option --scaleFactor. We used the respective H3 CUT&Tag from the same pool of nuclei to calculate the ratio between normalizations factors (H3 vs ATAC-seq) by passing to bamCompare’s option –scaleFactor to account for differences in starting material. The coverage heatmaps were created using plotHeatmap from deepTools (v.2.5.7). To quantify the signal under the peaks, we integrated the normalized signal in a +/-1kb around each peak. Source code for data normalisation can be found https://github.com/zhanyinx/atinbayeva_paper_2023.
Assembly: dmel6
Supplementary files format and content: bigwig files with the H3 and spike-in normalised signal

extract_protocol:
ATAC-seq experiments were performed as in (Ibarra et al., 2021) with small adaptations. Briefly, embryos were collected, fixed with 1% formaldehyde and hand-selected to enrich before cycle 9, cycle 10-12 and cycle 14. Based on the developmental stage, 500, 150 or 50 hand-staged embryos were used for each experiment. To extract nuclei, embryos were lysed in 50 µL of ATAC Wash Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 50 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.05% Digitonin (Millipore, #300410)). Nuclei were spin for 5 minutes at 600 g at 4 ºC and washed with 500 µL of ATAC Wash Buffer to remove impurities. For each condition, the pool of nuclei was split in two: half of the nuclei were processed for CUT&Tag against histone H3 for normalisation purposes, while the other part of nuclei was treated for ATAC-seq. Tagmentation reaction was started by resuspending nuclei in ATAC Tagmentation buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 50 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 10 mM MgCl2) supplemented with 2 µL of Tn5. The reaction was incubated in a thermomixer for 30 minutes at 37 ºC. Immediately after, samples were purified using the ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205) following manufacturer instructions.
Libraries were prepared by supplementing the NEBNext HighFidelity 2x PCR Master Mix with 1 pg of Tn5-tagmented lambda DNA (New England Biolabs, #N3011S) spike-in as normalizer supplemented in the NEBNext HighFidelity 2x PCR Master Mix (New England Biolabs, #M0541S) for each sample. The indexing was performed using Illumina i5 and i7 (Buenrostro et al., 2015) through 15 cycles (1 x 5 min at 72 °C, 1 x 30 sec at 98°C, 13 x 10 s at 98 °C, 30 sec at 63 °C, 1 x 1 min at 72 °C, hold at 4 °C). The libraires were purified using Nucleomag NGS Clean-up and Size Select beads (Macherey-Nagel, #744970.50). Quality checks were done with Qbit DNA HS Assay (ThermoScientific, #Q32854) and Bioanalyser (Agilent, #5067-4626).  Finally, libaries were pooled and sent for next generation sequencing.

value: cycle 10-12 (stage 4)


title: healthy_donor_plasma_exosomes_rep3

description: micro RNA level  in human blood

value: plasma


title: PLAXA cj-ESCs, euploid, rep1

description: Library name: PLAXA cj-ESC 1

value: embryonic stem cell

value: female


title: Mycelium, MU412 - Replicate 1

description:
Library name: MU412_A
Dataset S4.xlsx


title: Mycelium, MU636 - Replicate 3

description:
Library name: MU636_C
Dataset S4.xlsx


title: healthy_donor_plasma_exosomes_rep1

description: micro RNA level  in human blood


title: WT, mesoderm, H27me3, repl2

data_processing:
The ChIP-seq data processing was done using snakePipes version 2.4.0 (Bhardwaj et al., 2019) (parameters: --trim --fastqc --properPairs –dedup --mapq 1) with specific ATAC-seq Bowtie2 alignment option  (--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700) was used. Macs2 was used to call ChIP-seq peaks using the input as control and the following options: -g dm -q 0.05 --broad. ChIP-seq normalized signals were generated using bamCoverage from deepTools (v.2.5.7) using RPKM normalization.
Assembly: dmel6
Supplementary files format and content: bigwig files

extract_protocol:
FACS sorted mesoderm nuclei were obtained from twiPEMK::SBP-His2B embryos at the 6–8 h stage of development as described in Bonn et al., 2012. Immediately after sorting, chromatin immunoprecipitation is performed for H3K27me3 (add this) as described in Sandmann et al., 2006.
Libraries were prepared using NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturers instructions.

value: mesoderm

value: twiPEMK::SBP-His2B embryos at the 6-8 h stage of development

value: 6-8 hours of development


title: ATAC-seq, WT, c14, repl2


title: LN229 glioblastoma cell line ATAC-seq rep1

city: Leuven

first: Stein

last: Aerts

address: ON6 Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

description: Library name: GBM__b9a290__L1

data_processing:
The quality of raw reads was evaluated using FastQC (0.11.9) and any adapters were trimmed using the fastq-mcf command from ea-utils (1.1.2.779).
Reads were mapped to hg38 genome using bowtie2 (2.4.4) and duplicates were removed using picard (2.27.1).
Peaks were called using MACS3 (3.0.0b1) with BAMPE format and arguments --gsize hs --qvalue 0.05 --nomodel --keep-dup all --call-summits
Aggregate genome coverage was generated with the bamCoverage command of deepTools (3.5.0) with arguments --normalizeUsing CPM --binSize 1.
Assembly: hg38
Supplementary files format and content: Bigwig files of each sample to illustrate the genome coverage (generated by the bamCoverage command of deepTools)
Supplementary files format and content: NarrowPeak files of each sample that represent the peaks called by MACS3

source_name: glioblastoma cell lines

growth_protocol: A-172 cells were cultured in DMEM (ThermoFisher 11965-092) medium supplemented with 10% FBS (ThermoFisher 17479-633), and 1% penicillin/streptomycin (Life Technologies 15140122). MO59J cells were cultured in DMEM/F12 (ThermoFisher 11320-033) medium supplemented with 10% FBS, 1% penicillin/streptomycin and 0.05 mM non-essential amino acids (ThermoFisher 11140-068). LN229 cells were cultured in DMEM (ThermoFisher 11965-092) medium supplemented with 5% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were treated with Trypsin-EDTA 0.05% and washed with DPBS (ThermoFisher 14190-169). Cell viability and concentration were assessed by the LUNA-FL Dual Fluorescence Cell Counter. Per cell line, 80,000 cells were used to perform ATAC-seq. After centrifugation at 500 g for 5 min at 4°C, the supernatant was replaced with 50 µl ice cold ATAC-seq lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, 1% BSA and 0.01% Digitonin) and the cells were mixed by pipetting. After incubation for 5 min on ice, 1 ml of wash buffer (20 mM Tris-HCl, 20 mM NaCl, 6 mM MgCl2, 0.1% Tween-20, and 1% BSA) was added to the lysed cells and mixed gently by inverting 3 times. After centrifugation at 500 g for 5 min at 4°C, supernatant was removed and the nuclei were resuspended in 50 µl ATAC mix (10 mM Tris-HCl, 10% dimethylformamide, 5 mM MgCl2, 1x DPBS, 0.1% Tween-20, 0.01% Digitonin and 3.75 ng/µl Tn5 enzyme) and incubated for 1 hour at 37°C.
Transposed DNA was purified using a QIAGEN MinElute purification column and eluted in 15 µl elution buffer (Qiagen). The ATAC-seq library was completed by amplifying the transposed DNA in a total volume of 50 µl PCR mix (15 µl purified DNA, 25 µl NEBNext High Fidelity PCR Master Mix (NEB), 2.5 µl FWD and 2.5 µl REV primer) with the following program: 72°C for 5 min, 98°C for 30 s, followed by 10 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min). The final libraries were subjected to 0.4x-1.2x doublesided Ampure purification and eluted in 20 µl elution buffer (Qiagen).

value: glioblastoma cell lines

tag: batch


title: ATAC-seq, WT, c10-12, repl1


title: LN229 glioblastoma cell line ATAC-seq rep2

description: Library name: GBM__b9a290__L2


title: bulkRNAseq, WT, c14, repl2


title: WT, mesoderm, input, repl2


title: ATAC-seq, WT, c14, repl1


title: ATAC-seq, WT, bfc9, repl2

value: before cycle 9 (stage 3)


title: Mycelium, MU636 - Replicate 1

description:
Library name: MU636_A
Dataset S4.xlsx

value: Mycelium


title: M059J glioblastoma cell line ATAC-seq rep2

description: Library name: GBM__51bd12__L2


title: PBS treated rep4

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

institute: WuHan University

data_processing:
Raw data with adapter sequences or low-quality sequences were filtered using SOAPnuke developed by BGI with the following parameters: ”-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --polyX 50 --minReadLen 150”. Filtering steps included removing reads matching over 25.0% of adapter sequences, reads shorter than 150 bp, reads with over 0.1% N content, reads with polyX lengths exceeding 50 bp, and reads with over 40.0% of bases having a quality value below 20. Clean reads were obtained with the quality value system set to Phred+33.
The high quality clean reads were aligned to the reference genome with STAR software (v2.7.11b)
Raw read counts were extracted from the second column of the STAR output file 'ReadsPerGene.out.tab', which contained the unstranded RNA-seq read counts.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: KPC Subcutaneous tumor

extract_protocol:
Total RNA samples were obtained and mRNAs with poly(A) tails were enriched using oligo(dT) beads. The mRNA was then fragmented, and first- and second-strand cDNA were synthesized using random primers.
The cDNA underwent end-repair, 3' adenylation, and adaptor ligation, followed by PCR amplification and purification. Library quality was assessed, circularized, and amplified to form DNA nanoballs (DNBs). Sequencing was performed on the DNBSEQ platform using DNBSEQ Technology.

value: KPC Subcutaneous tumor

value: PBS


title: WT, mesoderm, input, repl1

value: embryos


title: M059J glioblastoma cell line ATAC-seq rep1

description: Library name: GBM__51bd12__L1


title: PBS treated rep5


title: ATAC-seq, WT, bfc9, repl1

value: T180, Bloomington #36303

value: WT


title: WT, mesoderm, H27me3, repl1


title: PBS treated rep3


title: A172 glioblastoma cell line ATAC-seq rep2

description: Library name: GBM__8a59ff__L2


title: WT_shield_PGCs_RNA_rep2

city: Beijing

first: Xiaotong

last: Wu

address: Haidian

institute: Tsinghua University

data_processing:
RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low-quality reads.
The filtered data were then mapped to the zebrafish reference genome (danRer11) by STAR (version: STAR_2.5.3a_modified).
The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1).
Assembly: danRer11
Supplementary files format and content: tab-delimited ext file includes FPKM values for each samples

organism: Danio rerio

source_name: embryo

growth_protocol: The wild-type Tuebingen (Tu) and India strains were used throughout the experiments. The transgenic line Tg(kop:EGFP-nanos 3’UTR) (citation) was described before. Unless stated, all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.

extract_protocol:
Total RNA of oocytes were purified using RNeasy Mini kit (QIAGEN, 74104) as recommended protocols. Total RNA (5 μg) was DNase I (Fermentas, EN0521) treated at 37°C for 1 h. Poly-A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit (Invitrogen 61006).
RNA-seq was carried out with the SMART-seq2 protocol, as previously described, and subjected to paired-end sequencing on the Nextseq 500 (Illumina) platform according to the manufacturer’s instructions. Notably, SMART-seq2 of low-input RNA-seq relies on poly(A)-based amplification.

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 214 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.

value: embryo

value: germ cell

value: PGCs

value: Wile type


title: PBS treated rep2


title: A172 glioblastoma cell line ATAC-seq rep1

description: Library name: GBM__8a59ff__L1


title: PBS treated rep1


title: WT_bud_PGCs_RNA_rep2

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 210 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.


title: control group 4

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

description: miRNA expression data from adults

hyb_protocol: Standard GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: ). Array scanning was performed following  GeneChip Command ConsoleTM v6.1 user guide (Applied Biosystems™ , P/N 702569). Expression data were extracted from CEL files by Trascriptome Analysis Console v4.0.

data_processing: Data normalization and summarization was performed using TAC software, with batch correction including scan date, plate barcode, and clusters identified in exploratory analysis . TAC analysis type: Expression (Gene); Summarization Method: RMA+DABG (Human Only). Annotation: miRNA-4 0-st-vl.annotations.20160922.csv . Statistical analysis after Log2 transformation was performerd for stroke vs control group using Mann-whitney test

source_name: platelet‐depleted plasma

label_protocol: 100ng total RNA was labeled using standard GeneChip buffers and reagents (Affymetrix). Microarrays analyzes were performed only with 24-h acute ischemic stroke vs control samples. In total 10 samples were analyzed. However, 1 samples in stroke group was excluded as it did not pass the pre-specified treshold for quality control. Microarray data were generated by human transcriptome array 2.0 ST (Affymetrix Inc, Santa Clara, CA, USA).  FlashTag™ Biotin HSR RNA Labeling Kits (Applied Biosystems™, P/N 901910) were used  to prepare target for GeneChip™ miRNA 4.0 Arrays. 100 ng  of total RNA sample was adjusted to 8 uL of volume and used for poly (A) tailing reaction according to the manufacturer instructions. FlashTag™ Biotin HSR Ligation was then performed with the use of T4 DNA Ligase at room temperature for 30 minutes. All the reaction mix were used to hybridize miRNA 4.0 GeneChip™ arrays at 48°C and 60 RPM rotation for 16 hours in the Hybridization Oven 645 (Affymetrix, Santa Clara, CA, USA). Wash and stain of arrays were performed with Fluidics Station 450 using the fluidics script appropriate for the Fluidics Station 450 (Protocol FS450_0002 according to Affymetrix instruction for 100 format array).

extract_protocol: Concentrations of miRNAs were determined by research team of Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, University of Catanzaro, Italy

treatment_protocol: Venous blood samples were collected from the control group and patients with IS on ASA therapy (a) 24 hours after onset of acute IS, (b) 7-days following index hospitalization. Briefly, blood was collected in 10-mL citrated blood collection tubes (S‐Monovette, Sarstedt) via antecubital vein puncture using a 19‐gauge needle, without a tourniquet. The first 2 mL were discarded to avoid pre‐activation of platelets. Right after blood collection, platelet‐depleted plasma was prepared by double centrifugation as previously described. Supernatant platelet‐depleted plasma was transferred into 1.5 mL low‐protein binding Eppendorfs (Thermo Fisher Scientific) tubes, and stored in −80°C until analyzed.

tag: group

value: control

tag: scane date

tag: patient information

value: The control group consisted of 35 age- and gender-matched patients on acetylsalicylic acid  (ASA) therapy without history of stroke and/or transient ischemic attack (TIA) with established stable coronary artery disease (CAD) and concomitant cardiovascular risk factors.


title: control group 5

description: miRNA expression data from adults


title: WT_bud_PGCs_RNA_rep1

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 208 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.


title: control group 3

description: miRNA expression data from adults


title: U2OS, TDP43-mNLS-Clover not_aggregated (sorted), rep2

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

institute: Vlaams Instituut voor Biotechnologie

description:
Library name: NoAggregates_Rep2
Stranded RNA-seq

data_processing:
bases2fastq version 2.0 was used to generate fastq files from raw AVITI basecalls
Raw, paired FASTQ files were first filtered using fastp v0.23.2.
Filtered FASTQ files were mapped to, and quantified against the hg38 genome using STAR v.2.7.11a.
All junctions were identified per sample using regtools v1.0.0 with the junctions command the following arguments: -a 6 -m 30 -M 500000 -s RF.
Following junction identification, junctions were quantified using the leafcutter_cluster_regtools.py script from leafcutter
Assembly: hg38
Supplementary files format and content: All_Samples_Counts.csv: Comma separated file with raw strand specific counts per sample.
Supplementary files format and content: Leafcutter_Junction_Counts.txt.gz: Gzip compressed space delimitted file containing counts per junction for each sample

source_name: U2OS TDP-43-mNLS-Clover (DOX-induced)

growth_protocol: standard cell culture conditions were used (DMEM + 10% FBS)

extract_protocol:
The Innuprep 2.0 Total RNA extraction kit was used following the manufacturers guidelines.
Illumina stranded mRNA Library prep kit, following manufacturers guidelines

treatment_protocol: Cell transfection with recombinant TDP-43 LCD fibril seeds was performed with lipofectamine-3000 (Invitrogen) according to the manufacturer's instructions.

value: U2OS TDP-43-mNLS-Clover (DOX-induced)

tag: treatment

value: no fibril seeds


title: Exosomes treated rep5

value: Exosomes


title: pigu_homo_shield_PGCs_RNA_rep2

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 206 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.

tag: cell type


title: Exosomes treated rep4

tag: tissue


title: U2OS, TDP43-mNLS-Clover not_aggregated (sorted), rep1

description:
Library name: NoAggregates_Rep1
Stranded RNA-seq


title: U2OS, TDP43-mNLS-Clover aggregated (sorted), rep3

description:
Library name: Aggregates_Rep3
Stranded RNA-seq

value: 50nM fibril seeds (TDP-43 LCD)


title: control group 2

description: miRNA expression data from adults


title: U2OS, TDP43-mNLS-Clover aggregated (sorted), rep2

description:
Library name: Aggregates_Rep2
Stranded RNA-seq


title: control group 1

description: miRNA expression data from adults


title: Exosomes treated rep3


title: Exosomes treated rep2


title: patients with IS on ASA therapy 7.1

description: miRNA expression data from adults

value: stroke

value: patients with the diagnosis of the acute IS based on clinical features according to the World Health Organisation definition and supported by brain imaging (CT or MRI).  Patients with IS were on ASA therapy 24 hours after onset of acute IS


title: pigu_homo_bud_PGCs_RNA_rep2

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 202 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.


title: pigu_homo_bud_PGCs_RNA_rep1

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.


title: U2OS, TDP43-mNLS-Clover aggregated (sorted), rep1

description:
Library name: Aggregates_Rep1
Stranded RNA-seq


title: Exosomes treated rep1

value: KPC Subcutaneous tumor


title: patients with IS on ASA therapy 5.1

description: miRNA expression data from adults


title: CF, no S4U labeling, rep1

status: Public on Mar 27 2025

city: Düsseldorf

first: Julia

last: Hesse

address: Universitätsstr. 1

department: Molecular Cardiology

institute: Heinrich Heine University Düsseldorf

description:
Library name: NegCtr_1
alkylated RNA

data_processing:
Demultiplexing was performed using bcl2fastq2 as part of a snakemake-based pipeline (https://github.com/WestGermanGenomeCenter/bcl2fastq2_Pipeline).
Sequence quality was checked using FastQC, MultiQC and the SLAM-DUNK software (doi: 10.1186/s12859-019-2849-7) utilizing its utrrates function.
T>C conversions, which result from the incorporation of guanine at alkylated S4U nucleotides during NGS library preparation, were detected and quantified with one minor addition. Briefly, the previously added UMI were moved from the reads sequence into the read header using umi-tools (https://umi-tools.readthedocs.io/en/latest/) extract function, discarding all reads without complete UMI and TATA-spacer sequence before mapping.
After the mapping step of SLAM-DUNK (using mm39 as the reference genome), mapped reads were deduplicated with umi-tools dedup.
Assembly: mm39
Supplementary files format and content: tsv files including reads CPM and T>C conversion rates

source_name: cardiac fibroblasts

growth_protocol: Cardiac fibroblasts were isolated from  adult healthy male C57Bl/6J wildtype mice using Langendorff-based perfusion of the heart with collagenase and grown until confluency.

extract_protocol:
RNA was extracted using TRIsure (Meridian Bioscience) and alkylated by iodoacetamide according to the SLAMseq Explorer and Kinetics Kit protocol (Lexogen). At least 500 pg of alkylated RNA samples were used as input for library construction.
The QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen) was used to prepare NGS libraries with the optional UMI added for duplicate removal in later stages of the analysis.

treatment_protocol: Isolated cardiac fibroblasts were cultured for 12 h in cell culture medium with the uridine analog 4-Thiouridine (S4U, 0,1 mM) to allow S4U incorporation into newly synthesized RNA transcripts. As negative control, cells were incubated in parallel without addition of S4U.

value: cardiac fibroblasts

value: no S4U labeling


title: CF, no S4U labeling, rep2

description:
Library name: NegCtr_2
alkylated RNA


title: CF, 12h S4U labeling, rep2

description:
Library name: 12h_S4U_2
alkylated RNA

value: S4U labeling


title: CF, 12h S4U labeling, rep1

description:
Library name: 12h_S4U_1
alkylated RNA


title: CF, 12h S4U labeling, rep3

description:
Library name: 12h_S4U_3
alkylated RNA


title: SP torpid 4

city: Tromsoe

first: Shona

last: Wood

address: Hansine Hansens veg 18

institute: UiT

description: Short photoperiod 8-12 weeks torpid

data_processing:
Mapping was performed using STARaligner and the standard settings (Dobin et al. 2013). Reads were mapped to the golden hamster genome (BCM_Maur_2.0, ref.seq: GCF_017639785.1) and the annotation was provided by NCBI (GCF_017639785.1_BCM_Maur_2.0_genomic.gtf). The mapping rate was 88%. Feature counts was used to count the mapped reads to genes, using these parameters: featureCounts -p -t exon -g gene_id, on average 70% of alignments were assigned to an annotated feature.
Assembly: BCM_Maur_2.0, ref.seq: GCF_017639785.1
Supplementary files format and content: Txt files containing the raw counts for each sample

organism: Mesocricetus auratus

source_name: Laser captured ependymal region (tancyte enriched)

extract_protocol:
The RNA was extracted from the microdissected tissue using the Qiagen all prep DNA/RNA micro kit (80284) following the supplied instructions. The RNA integrity numbers were determined by TapeStation high sensitivity RNA analysis (5067-5579, 5067-5581, 5067-5580, Agilent) and all used samples had a RNA integrity numbers (RIN) between 7 to 9.
RNA-seq library construction was performed by BGI using their standard RNAseq protocol and Illumina high seq 4000. Quality control checks and barcode removal according to BGI protocol.

treatment_protocol: Three months old male golden hamsters (Mesocricetus auratus) were housed under long photoperiod (LP, 14 hr of light/24 hrs) and an ambient temperature of 22°C. Animals had ad libitum access to food and water throughout the experiment and received nesting material and a wooden stick in their home cage. Three weeks prior to the experiment, isoflurane anesthesia was given, and an iButton (Maxim) was implanted in the abdominal cavity to record body temperature. At the start of the experiment, one group were kept on LP at 22°C and were sampled immediately prior to the photoperiodic switch and at the end of the experiment (LP). The remaining animals were transferred to short photoperiod (SP, 10 hr of light/24 hrs) and an ambient temperature of 8°C to initiate hibernation. Animals were sampled 4 weeks after transfer to SP (pre-hibernation), after 8-12 weeks of SP prior to intiating T-A cycling (late pre-hibernation), or after three T-A cycles either when interbout euthermic (IBE) or torpid. The average IBE duration in this experiment was approximately 24 hours, animals were sampled late in their interbout euthermia phase (23 hours). Torpid animals were sampled at their mid-point of torpor, which in this experiment was 13 hours. After approximately 20 weeks of SP exposure, animals spontaneously stopped hibernating and were sampled at least 2 weeks after the last torpor bout (refractory).   Animals were anesthetised with 4% isoflurane and cervical dislocation was performed. The brains (6 per group) were covered with pre-cooled OCT, snap frozen in chilled isopentane over dry ice and 95% ethanol and sectioned on the cryostat (-20 ⁰C; (CM3050 S, Leica Biosystems)) at 20 µm. The brains were cut in series to cover the whole medio-basal hypothalamic region on two slides.  For LASER capture microdissection (LCMD) each animal had 6-8 membrane slides (415190-9081-000, Carl Zeiss) of 8 sections. Slides were stored at -80 ⁰C until further use. Immediately before LCMD the membrane slides were stained using cresyl violet as described previously (Melum et al. 2024). When ready, the slides were transferred to the laser micro dissector (PALM MicroBeam system, Zeiss) with the PALMRobo software (V4.8, Zeiss) and microdissection was completed within 45 minutes to minimize RNA degradation. LCMD was carried out at 10x, with the following settings: Cut energy = 42-49; Cut focus = 84; LPC Energy = 58; LPC focus =84, to capture the tanycytes on the transfer film of the microdissection caps (415190-9211-000, Carl Zeiss). The dorsal ventral extent of the area was determined by two times the PT width for each animal to correct for size differences. The width of the LCMD-sample was strived to be two to three cell bodies. When done, the tube was closed and snap frozen on dry ice and stored at -80 ⁰C.

tag: age

value: 6 months

value: male

value: short photoperiod 8 degrees


title: SP torpid 5

description: Short photoperiod 8-12 weeks torpid

value: Laser captured ependymal region (tancyte enriched)

tag: Sex


title: SP torpid 6

description: Short photoperiod 8-12 weeks torpid


title: SP torpid 2

description: Short photoperiod 8-12 weeks torpid


title: SP torpid 3

description: Short photoperiod 8-12 weeks torpid


title: patients with IS on ASA therapy 4.1

description: miRNA expression data from adults


title: SP torpid 1

description: Short photoperiod 8-12 weeks torpid


title: SP refractory 3

description: Short photoperiod refractory animal reproductive

value: 8 months


title: patients with IS on ASA therapy 6.1

description: miRNA expression data from adults


title: SP refractory 1


title: SP pre-hib 4

description: Short photoperiod for 4 weeks pre-hibernation

value: 4 months


title: SP refractory 4


title: SP pre-hib 6


title: SP refractory 2


title: SP pre-hib 3


title: SP pre-hib 2


title: SP late pre-hib 6

description: Short photoperiod 8-12 weeks late pre-hibernation


title: SP late pre-hib 5


title: SP pre-hib 1


title: SP late pre-hib 3


title: Sp pre-hib 5


title: SP late pre-hib 2


title: SP refractory 5


title: SP late pre-hib 1


title: LP2 4

description: Long photoperiod reproductive

value: long photoperiod 22 degrees


title: LP2 2

description: Long photoperiod reproductive


title: LP 2 3

description: Long photoperiod reproductive


title: IBE 6

description: Short photoperiod 8-12 weeks Interbout euthermia


title: LP2 6

description: Long photoperiod reproductive


title: LP2 1

description: Long photoperiod reproductive


title: IBE 5


title: IBE 3


title: WT_shield_PGCs_RNA_rep1

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 212 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.

value: embryo

value: germ cell

value: PGCs

tag: genotype

value: Wile type


title: IBE 2


title: HOMO mKO muscle, AAV, 21 dpi, sample 4

city: Madrid

first: Roberto

last: Silva-Rojas

address: Calle de Melchor Fernández Almagro 3

institute: Spanish Nacional Center for Cardiovascular Research

data_processing:
Sequencing reads were pre-processed by a pipeline that used FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to asses read quality, and Cutadapt80 to remove adaptor remains from Illumina and to discard reads that were shorter than 30 bp.
The resulting reads were mapped against reference transcriptome GRCm38.99 and quantified with RSEM81, using Bowtie as aligner. The expected expression counts calculated with RSEM were processed with a pipeline that used Limma package82, from Bioconductor, for normalization and differential expression testing, taking only into account those genes expressed with at least 1 count per million (CPM) in at least three samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: Tibialis anterior

growth_protocol: Mice were euthanized by euthanized CO2 inhalation, tibialis anterior dissected and frozen in liquid nitrogen.

extract_protocol:
Muscles were mechanically lysed using CK28 beads (Bertin Technologies) and RNA extracted using TRI reagent (Sigma) following manufacturer´s instructions.
NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: Muscles were injected with saline buffer or AAV virus encoding GFP-TEV protease fusion protein 3, 7 or 21 days prior to dissection.

value: Tibialis anterior

value: HOMO mKO

value: AAV

tag: timepoint

value: 21 dpi


title: IBE 1


title: HOMO mKO muscle, AAV, 21 dpi, sample 3


title: LP2 5

description: Long photoperiod reproductive


title: HOMO mKO muscle, AAV, 21 dpi, sample 2


title: HOMO mKO muscle, NaCl, 21 dpi, sample 4

value: Saline


title: WT muscle, AAV, 21 dpi, sample 4

value: WT


title: pigu_homo_shield_PGCs_RNA_rep1

treatment_protocol:
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 204 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.
GFP-nanos1-3’UTR mRNA was injected into WT and pigu-/- zygotes, respectively, to label PGCs. Then, the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS-containing embryos was adjusted to 200 µl, and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP-labeled PGCs were manually picked under fluorescence microscope with mouth pipette.


title: HOMO mKO muscle, NaCl, 21 dpi, sample 3


title: HOMO mKO muscle, AAV, 21 dpi, sample 1


title: HOMO mKO muscle, NaCl, 21 dpi, sample 1


title: HOMO mKO muscle, NaCl, 21 dpi, sample 2


title: WT muscle, AAV, 21 dpi, sample 1


title: WT muscle, AAV, 21 dpi, sample 3


title: IBE 4

value: 6 months


title: WT muscle, NaCl, 21 dpi, sample 4


title: WT muscle, NaCl, 21 dpi, sample 1


title: WT muscle, NaCl, 21 dpi, sample 2


title: WT muscle, NaCl, 21 dpi, sample 3


title: HET mKo muscle, AAV, 7 dpi, sample 2

value: HET mKO

value: 7 dpi


title: HET mKo muscle, AAV, 7 dpi, sample 3


title: HET mKo muscle, AAV, 7 dpi, sample 4


title: HET mKo muscle, NaCl, 7 dpi, sample 4


title: HET mKo muscle, NaCl, 7 dpi, sample 3


title: HOMO mKo muscle, AAV, 7 dpi, sample 5


title: HET mKo muscle, NaCl, 7 dpi, sample 1


title: WT muscle, AAV, 21 dpi, sample 2


title: HOMO mKo muscle, AAV, 7 dpi, sample 4


title: HOMO mKo muscle, NaCl, 7 dpi, sample 3


title: HOMO mKo muscle, NaCl, 7 dpi, sample 4


title: HOMO mKo muscle, AAV, 7 dpi, sample 1


title: HOMO mKo muscle, AAV, 7 dpi, sample 2


title: HOMO mKo muscle, NaCl, 7 dpi, sample 2


title: WT muscle, AAV, 7 dpi, sample 4


title: HOMO mKo muscle, NaCl, 7 dpi, sample 1


title: WT muscle, AAV, 7 dpi, sample 2


title: WT muscle, NaCl, 7 dpi, sample 2


title: WT muscle, NaCl, 7 dpi, sample 1


title: HOMO mKO muscle, AAV, 3 dpi, sample 3

value: 3 dpi


title: WT muscle, NaCl, 7 dpi, sample 3


title: HOMO mKO muscle, AAV, 3 dpi, sample 1


title: HOMO mKo muscle, AAV, 7 dpi, sample 3


title: HOMO mKO muscle, NaCl, 3 dpi, sample 4


title: HOMO mKO muscle, AAV, 3 dpi, sample 2


title: HET mKo muscle, NaCl, 7 dpi, sample 2


title: HOMO mKO muscle, NaCl, 3 dpi, sample 2


title: HOMO mKO muscle, NaCl, 3 dpi, sample 1


title: WT muscle, AAV, 3 dpi, sample 5


title: WT muscle, AAV, 3 dpi, sample 3


title: WT muscle, AAV, 3 dpi, sample 1


title: WT muscle, AAV, 3 dpi, sample 2


title: WT muscle, AAV, 3 dpi, sample 4


title: HOMO mKO muscle, AAV, 3 dpi, sample 4


title: WT muscle, NaCl, 3 dpi, sample 1


title: WT muscle, NaCl, 3 dpi, sample 2