title: WT heart replaced with healthy macrophages_2 (healthy 2)

description: Library name: WT_RNA2_FPKM

data_processing:
Quality control and read alignment were performed by MedGenome. Data quality control was performed via FastQC (v0.11.9). Low-quality sequence reads were excluded, and adapter sequences were trimmed using fastq-mcf (v1.05) and cutadapt (v4.7). Removal of other unwanted sequences (mitochondrial genome sequences, ribosomal RNA, transfer RNA, adapter sequences, etc.) was performed via Bowtie2 (v2.5.3). Paired-end reads were aligned to the Ensembl Mus musculus genome (GRCm39) via STAR (2.7.11b). Raw read counts were estimated from the aligned reads using HTSeq (v2.0.5). FPKM (Fragments per kilobase per million) expression values for each gene were estimated from the aligned reads using cufflinks (v2.2.1).
Assembly: GRCm39
Supplementary files format and content: Raw_Counts_HTSEQ_heart.xlsx contains the raw counts for gene expression (calculated with HTSeq) for all eight samples, with each sample corresponding to one row. The file also contains the Ensembl gene ID, gene names, and biotype as rows.
Supplementary files format and content: FPKM_heart.xlsx contains the FPKM units for gene expression for all eight samples, with each sample corresponding to one row. The file also contains the Ensembl gene ID, gene names, and biotype as rows.

source_name: whole heart

extract_protocol:
Total RNA was extracted from one minced mouse heart tissue for bulk RNA-seq
Whole heart tissue was collected from WT and YG8s800 mice at 20- and 22-weeks post-bone marrow transplantation (BMT), following conditioning with Busulfan (BU) and PLX3397. The time points corresponded to an age of 7–8 months for each group. Following two washes with cold 1x PBS, the heart tissues were dissected in cold 1x PBS using a sterile knife to facilitate efficient RNA extraction. Total RNA was extracted from the minced heart tissue of each mouse group using the Invitrogen™ PureLink™ RNA Mini Kit (#12-183-018A), following the manufacturer's instructions for RNA purification.
Library preparation and sequencing was conducted by MedGenome Inc. (Foster City, CA, USA) using the Illumina Stranded mRNA Prep kit and Novaseq 6000 sequencer (Illumina, San Diego, CA) with paired-end 100 base pair (bp) reads.

value: whole heart

value: C57BL/6J (WT)


title: WT heart replaced with healthy macrophages_1 (healthy 1)

status: Public on Jul 02 2026

type: SRA

city: Stanford

first: Natalia

last: Gomez-Ospina

address: 265 Campus Drive

country: USA

institute: Stanford

description: Library name: WT_RNA1_FPKM

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment

value: Busulfan + PLX3397 + Bone Marrow Transplant


title: 39490_NativeHepG2_FOXA1_BX_rep1-1

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: Library name: 39490_NativeHepG2_FOXA1_BX_rep1-1

library_source: genomic

data_processing:
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg38
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 cells were grown in suspension at ~0.5-1.0 x 106 cell/mL in complete IMDM with ~10% FBS and ~1% PenStrep at 5% CO2 and 37oC.

extract_protocol:
Cells were crosslinked in methanol-free formaldehyde (final 1% concentration in IMDM media) at 25 °C for 10 min. 1 mole of formaldehyde was quenched with 3 mole extra Tris (pH 8.0) at 25 °C for 5 min. Fixed cells were washed with PBS and stored at -80 oC. 25 million (M) formaldehyde crosslinked K562 were lysed by incubating with 1 mL Lysis Buffer F (20 mM Tris, pH 8.0, 85 mM KCl, 0.5% NP-40, 0.5% Triton X-100) for 20 min at 4°C, then with 1 mL RIPA Buffer M (1x PBS 1.0% NP40, 0.5% NaDeoxycholate, 0.1% SDS) for 20 min at 4°C. Nuclei (25 M) were incubated in 500 ul Benzonase Digestion Buffer (10 mM Tris, pH 8, 10 mM NaCl, 2 mM MgCl2) at a Benzonase concentration of 100 U/ml for 10 min at 25 °C. Reactions were quenched by adding 500 ul Benzonase Quench Buffer (10 mM Tris, pH 8, 800 mM NaCl, 20 mM EDTA), The quenched reactions were centrifuged at 14,000 rpm for 10 minutes to collect Benzonase-solubilized chromatin in the supernatant. Nuclei pellets were sonicated in a Bioruptor PICO model sonicator (Diagenode) for 8 cycles (30-on/ 30-off). Sonicated material was centrifuged at 13.2K rpm for 15 minutes using a Microfuge (Eppendorf 5415R). Solubilized chromatin supernatant was collected. Benzonase solubilized and sonication chromatin were collected for incubation with pAG Mag Sepharose ™ (Cytiva™) preloaded with 3 ug of antibody overnight. Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: SMC3 (ab9263, Sigma), P300 (HPA003128, Atlas), NFIA (HPA008884, Atlas), WDR5 (HPA047182, Atlas), GABPA (HPA003258, Atlas), SP1 (HPA001853, Atlas), RAD21(HPA020044, Atlas), GTFIIB (HPA061626, Atlas), P300(A300-358A, Bethyl labs), RbBP5 (A300-109A, Bethyl labs), and CTCF (07-729, Millipore). TBP (Pugh lab). The immunoprecipitated chromatin was then processed through Lambda exonuclease digestion, first adapter ligation, cross-link reversal, second adapter ligation, and PCR for final high-throughput sequencing.
Illumina or Element library prep

tag: cell line

tag: pegr id

tag: source

value: Native HepG2

tag: method

value: Benzonase ChIP-exo (v6)

tag: target

tag: antibody

tag: biological replicate

tag: resequencing replicate


title: RNAseq_SynTEF1_RGFP109_s46_rep1

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM"
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: gene-based raw counts, FPKM and TPM normalized txt files

molecule: total RNA

source_name: B-Lymphocyte

growth_protocol: RPMI + 15% FBS + anti/anti

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
Library was constructed using standard Illumina protocols

treatment_protocol: Cells were treated with indicated compounds for 24 hours

tag: cell type

value: Patient Derived B-Lymphocyte


title: Control, biological replicate 2

city: Oldenburg

first: Anna-Galina

last: Arndt

address: Carl-von-Ossietzky-Straße 9-11

department: Department für Humanmedizin

country: Germany

institute: Carl von Ossietzky Universität Oldenburg

description:
Library name: HD_2n_ctrl
Healthy donor 2, day 2 culture

data_processing:
RNA-seq was performed on an Illumina NovaSeq X Plus platform generating 150 bp paired-end reads. Raw sequencing reads were filtered to remove adapter sequences and low-quality reads using fastp. Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2, and the number of reads mapped to each gene was quantified using featureCounts.
Assembly: GRCh38 (hg38)
Supplementary files format and content: The file gene_count.xls provides raw read counts per gene for each sample.

source_name: Peripheral blood

growth_protocol: T and B cell depleted, myeloid enriched peripheral blood cells were cultured in MDSC medium consisting of basal cell culture medium supplemented with 10% FCS, non-essential amino acids, L-glutamine, HEPES, sodium pyruvate and penicillin/ streptomycin at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared from total RNA using poly(A) enrichment with poly-T oligo-attached magnetic beads according to the manufacturer's standard protocol (Novogene).

treatment_protocol: Cells were cultured for 2 days under three experimental conditions: MDSC medium alone (control), MDSC medium supplemented with 10 ng/ml GM-CSF and IL-6, or MDSC medium supplemented with 10 ng/ml GM-CSF and IL-6 and 1 nM α-MSH.

value: Peripheral blood

value: in vitro differentiated MDSCs

value: Basal medium alone


title: 39487_NativeK562_FOXA1_BX_rep1-1

description: Library name: 39487_NativeK562_FOXA1_BX_rep1-1

value: Native K562


title: 39314_NativeK562_FOXA1_BX_rep2-1

description: Library name: 39314_NativeK562_FOXA1_BX_rep2-1


title: Control, biological replicate 1

description:
Library name: HD_1n_ctrl
Healthy donor 1, day 2 culture


title: RNAseq_RGFP109_s42_rep3


title: RNAseq_RGFP109_s41_rep2


title: FRDA heart only replaced with FRDA macrophages_1 (FA sham 1)

description: Library name: FR_FR_RNA1_FPKM


title: FOLR2_neg_donor_49

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

country: United Kingdom

institute: Imperial College London

description: Library name: IGF141570

data_processing:
Alignments were generated using the nf-core/rnaseq pipeline v3.26.0 (doi:10.5281/zenodo.20072251)
Transcripts generated were adapter trimmed with Trim Galore! (v0.6.5) and mapped against the human reference genome (GRCh38.p14) using STAR (v2.7.11b) and Salmon (v.1.11.4)
Assembly: GRCh38.p14
Supplementary files format and content: salmon.merged.gene_tpm gives estimated relative abundance of transcripts in units of Transcripts Per Million (TPM) for all 12 samples as a .tsv file
Supplementary files format and content: salmon.merged.gene_counts_length_scaled gives an estimate of the number of reads mapping to each transcript that was quantified (the NumReads output of Salmon) for all 12 samples as a .tsv file

source_name: Decidua parietalis

growth_protocol: Cells were isolated directly ex vivo: no growth protocol

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Micro kit. RNA concentration and quality were assessed using an Agilent Tapestation
cDNA libraries were prepared from 200ng RNA using a NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina. Libraries were sequenced on a NextSeq 2000

treatment_protocol: Cells were isolated directly ex vivo: no treatment protocol

value: Decidua parietalis

value: FOLR2 negative macrophage

value: donor 49


title: RNAseq_RGFP109_s40_rep1


title: 38819_NativeK562_IgG_BX_rep1-1

description: Library name: 38819_NativeK562_IgG_BX_rep1-1

value: IgG


title: FRDA heart treated by replacement with healthy macrophages_3 (FA treated 3)

description: Library name: DP_FR_RNA3_FPKM


title: FOLR2_pos_donor_49

description: Library name: IGF141569

value: FOLR2 positive macrophage


title: mouse MSCs miRNAseq E1705K replicate 3

city: Los Angeles

first: Mona

last: Wu

state: California

address: 4650 Sunset Boulevard

institute: CHLA

description: Library name: miRNA6C.fq

data_processing:
data was analyzed with PartekFlow minimum read length 10, end quality level 20, trim from both ends
Assembly: mm10 -miRBase mature microRNAs version 22 deduplicated
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: cell line

growth_protocol: mouse MSCs were grown in OPTI-MEM supplemented with 10% FBS and antibiotics and grown in an incubator at 37oC 5% CO2

extract_protocol:
For miRNAseq RNA was extracted with miRneasy mini kit and 1 ug was used for library preparation.
library preparation was performed by BGI using DNBSeq Small RNA library preparation

value: cell line

value: mesenchymal stromal cell

value: female


title: RNAseq_DMSO_s39_rep3

value: DMSO


title: FOLR2_neg_donor_48

description: Library name: IGF141568

value: donor 48


title: FRDA heart treated by replacement with healthy macrophages_2 (FA treated 2)

description: Library name: DP_FR_RNA2_FPKM

value: whole heart

value: Busulfan + PLX3397 + Bone Marrow Transplant


title: mouse MSCs miRNAseq E1705K replicate 2

description: Library name: miRNA6B.fq


title: FRDA heart treated by replacement with healthy macrophages_1 (FA treated 1)

description: Library name: DP_FR_RNA1_FPKM


title: mouse MSCs miRNAseq E1705K replicate 1

description: Library name: miRNA6A.fq


title: RNAseq_DMSO_s38_rep2

value: Patient Derived B-Lymphocyte


title: FOLR2_pos_donor_48

description: Library name: IGF141567


title: RNAseq_DMSO_s37_rep1


title: 41963_WCEK562_FOXA1_BX_rep1-1

description: Library name: 41963_WCEK562_FOXA1_BX_rep1-1

value: Benzonase ChIP-exo (v6)


title: FOLR2_neg_donor_47

description: Library name: IGF141566

value: donor 47


title: COMM066_SCO5231_Ct

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

description: Library name: C66

data_processing:
Filtered reads from BGI were aligned to the reference genome (AL645882.2) using bowtie2 v2.4.2 with the options --no-mixed --no-discordant. Peaks were called using MACS3 v3.0.3, using negative control sample with SRA accession SRR39372742 (CTg_004)
Assembly: AL645882.2
Supplementary files format and content: *.narrowpeak: BED: chrom, chromStart (0-based), chromEnd, name, score (−log10(qvalue)×10), strand ("."), signalValue, pValue (−log10), qValue (−log10), peak (summit offset from chromStart, 0-based).

organism: Streptomyces coelicolor A3(2)

growth_protocol: Approximately 10^⁶ - 10^⁷ spores were inoculated in 25 ml NMMP medium and grown for 46 h.

extract_protocol:
Cultures were cross-linked with 1% formaldehyde for 10 min at 30°C, followed by quenching with glycine. Biomass was collected, washed with ice-cold TBS and lysed enzymatically before chromosomal DNA was sheared to fragments of approximately 100–500 bp using a Bioruptor Plus sonication system. FLAG-tagged protein–DNA complexes were immunoprecipitated overnight at 4°C using anti-FLAG M2 magnetic beads. A fraction of the cleared lysate was retained as input genomic DNA control. After washing, protein–DNA complexes were eluted, cross-links were reversed and DNA was purified using the DNA Clean & Concentrator-5 kit.
Out sourced to BGI, steps include: received ChIPed DNA was end repaired, then subjected to 3'-dA overhang addition, adaptor ligation, PCR amplification and size selection. Library quality control was then made and flowed by circularization. The library was amplified to make DNA nanoball (DNB) and then sequenced on DNBSEQ (DNBSEQ Technology) platform.

value: bacteria cell culture


title: mouse MSCs miRNAseq D1320A replicate 3

description: Library name: miRNA5C.fq


title: KO6 retina RNA-seq

city: Iowa City

first: Sheila

middle: A

last: Baker

state: IA

address: 51 Newton Rd

department: Biochemistry and Molecular Biology

institute: University of Iowa

description: Library name: KO6

data_processing:
Adapter trimming was performed using TrimGalore.
Reads were quantified against the mouse transcriptome (GENCODE Mus musculus GRCm38) using Salmon (v1.10.2).
Transcript-level abundances were summarized to gene-level counts using tximport.
Differential expression analysis was performed in R using DESeq2 following filtering of low-count genes.
Surrogate variable analysis (SVA) was used to estimate and adjust for latent sources of unwanted variation.
Assembly: GRCm38
Supplementary files format and content: Gene-level count matrix generated using tximport and differential expression results from DESeq2.

source_name: retina

growth_protocol: Mice were maintained under standard laboratory conditions with a 12-hour light/dark cycle and ad libitum access to food and water.

extract_protocol:
Two retinas from individual mice were pooled per sample. Total RNA was isolated from retinas dissected into RNAlater using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared by Novogene using standard Illumina-compatible protocols.

treatment_protocol: No treatment was applied.

value: retina

value: Kv8.2 KO


title: COMM061_SCO3696_Nt

description: Library name: C61


title: FOLR2_neg_donor_46

description: Library name: IGF141565

value: Decidua parietalis

value: FOLR2 negative macrophage

value: donor 46


title: KO5 retina RNA-seq

description: Library name: KO5


title: COMM060_SCO3668_Ct

description: Library name: C60


title: FOLR2_neg_donor_45

description: Library name: IGF141564

value: donor 45


title: COMM057_SCO1262_Ct

description: Library name: C57


title: KO4 retina RNA-seq

description: Library name: KO4


title: FOLR2_neg_donor_44

description: Library name: IGF141563

value: donor 44


title: KO3 retina RNA-seq

description: Library name: KO3


title: mouse MSCs miRNAseq WT replicate 3

description: Library name: miRNA4C.fq

value: cell line

value: mesenchymal stromal cell


title: COMM056_SCO1186_Ct

description: Library name: C56


title: mouse MSCs miRNAseq WT replicate 2

description: Library name: miRNA4B.fq

value: female


title: KO2 retina RNA-seq

description: Library name: KO2


title: COMM055_SCO1145_Ct

description: Library name: C55


title: FOLR2_pos_donor_46

description: Library name: IGF141559

value: FOLR2 positive macrophage


title: mouse MSCs miRNAseq WT replicate 1

description: Library name: miRNA4A.fq


title: WT3 retina RNA-seq

description: Library name: WT3

value: WT


title: COMM034_SCO4158_Ct

description: Library name: C34


title: FOLR2_pos_donor_45

description: Library name: IGF141558


title: FOLR2_pos_donor_44

description: Library name: IGF141557


title: FOLR2_pos_donor_47

description: Library name: IGF141560


title: CD34 Donnor 4 Day 5 gRNA NINJ1/2

city: Murcia

first: Lola

last: Rodríguez Ruiz

address: C/Campus universitario, 5

country: Spain

institute: University of Murcia

description: Library name: 388_S32

data_processing:
Raw FASTQ files generated after sequencing had a maximum read length of 100 bp before adapter trimming. After adapter removal, read lengths ranged from 15 to 101 bp. The number of reads per sample ranged from 8,208,497 to 15,687,432, with uniquely mapped reads above 70.38% in all samples.
Cleaned reads were mapped to the human reference genome GRCh38, Ensembl release 111, using STAR, and transcript abundance was quantified with Salmon.
Read mapping and quantification were performed using the nf-core/rnaseq pipeline v3.23.0, while differential expression analysis was carried out with the nf-core/differentialabundance pipeline v1.5.0. Both pipelines are implemented in Nextflow within the nf-core framework [3].
Following preprocessing and mapping, count matrices in TSV format were imported into R v4.5.3 using tximport. Data normalization and differential expression analysis were performed with DESeq2 . Genes were considered differentially expressed when they showed a false discovery rate below 0.05 and an absolute log2 fold change greater than 1.
Assembly: human reference genome GRCh38, Ensembl release 111, using STAR, and transcript abundance was quantified with Salmon
Supplementary files format and content: tsv, comparation between samples

source_name: cord blood

extract_protocol:
Total RNA was extracted from tail larvae or human CD34+ cells using TRIzol reagent (Invitrogen) following the manufacturer’s instructions
Total RNA from human samples was processed using the QuantSeq 3’ RNA-Seq V2 FWD kit with Unique Dual Indices, 12 nt, following the manufacturer’s recommendations. Libraries were generated from polyadenylated RNA using oligo-dT priming and included unique molecular identifiers to enable the identification of PCR duplicates. Library quality control confirmed an appropriate insert size, greater than 200 bp, and absence of adapter dimers. The libraries were sequenced on an Illumina NextSeq 2000 platform, generating single-end reads of 110 bp.

value: cord blood

value: CD34+ HSPCs


title: WT2 retina RNA-seq

description: Library name: WT2


title: COMM031_SCO3699_Ct

description: Library name: C31


title: mouse MSCs miRNAseq EV replicate 3

description: Library name: miRNA3C.fq

value: empty vector


title: mouse MSCs miRNAseq EV replicate 1

description: Library name: miRNA3A.fq


title: COMM021_SCO2243_Ct

description: Library name: C21


title: mouse MSCs miRNAseq EV replicate 2

description: Library name: miRNA3B.fq


title: RXRgKO T3 04

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 98 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: mouse neural stem cell - derived OPCs

extract_protocol:
10mln OPC cells were lysed using micro RNAeasy kit according to manufacturer instructions
RNA-Seq libraries were generated from 200ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: mouse neural stem cell - derived OPCs

tag: strain

value: C57BL6J/129svEmx mixed background

tag: age

value: 4 days in monolayer culture


title: CD34 Donnor 4 Day 3 gRNA NINJ1/2

description: Library name: 387_S31


title: WT1 retina RNA-seq

description: Library name: WT1

value: retina


title: COMM029_SCO3320_Ct

description: Library name: C29

value: bacteria cell culture


title: 38_GB_CP_5_Mono

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

institute: University of Cambridge

description: Library name: SLX22742_idtUDP0242

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39) - kmer 23
Supplementary files format and content: Raw count data in tab-delimited salmon file

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent (15596018; Invitrogen). RNA was extracted using the PureLink RNA mini kit (12183018A; Invitrogen). RNA concentration was measured using a Qubit and RNA quality was assessed on a TapeStation 4200 (Agilent) using the Agilent RNA ScreenTape kit. mRNA library preparations were performed using 55 mL of 10 ng/mL per sample (RNA integrity number, RIN ≥ 8.8)
Illumina mRNA library

tag: batch


title: HT-29 cells, Control2

city: Hefei

first: hailiang

last: hu

address: jixi road

country: China

institute: First Affiliated Hospital of Anhui Medical University

description: Library name: Sample 2

data_processing:
Using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution. For plant and fungi samples, we use NanoDropTM to identify the purity of the RNA samples.
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads
Then we map those clean reads onto reference genome, followed with novel gene prediction,  SNP & INDEL  calling and gene splicing detection
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations
Assembly: 6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
The concentration of total RNA was detected using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
The libraries were sequenced with the Illumina HiSeq 2000 sequencing platform to produce PE100 reads.

value: Colon adenocarcinoma

value: Conventional  culture


title: RXRgKO T3 03


title: COMM006_SCO3632_Ct

description: Library name: C06


title: CD34 Donnor 4 Day 5 gRNA AAVS1

description: Library name: 386_S30


title: RXRgKO T3 02


title: GM-CSF + IL-6 + 1 nM α-MSH, biological replicate 1

description:
Library name: HD_1n_MSH
Healthy donor 1, day 2 culture

value: Peripheral blood

value: in vitro differentiated MDSCs

value: GM-CSF plus IL-6 plus 1 nM α-MSH


title: mouse MSCs RNAseq E1705K replicate 2

description: Library name: 6B_

data_processing:
Data was analyzed with PartekFlow
Min read length 25, end min quality level 20, trim from both ends
Assembly: mm10-GENCODE Genes-release M25
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: mesenchymal stromal cell

extract_protocol:
For RNAseq, RNA was extracted with Rneasy mini plus kit and 1 ug was used for library preparation.
library construction was performed by BGI DNBSEQ strand specific transcriptome library

tag: Sex

value: mesenchymal stromal cell


title: NCI-H69 cells, SCRMP knockout, biol rep 3

city: suzhou

first: Jiahao

last: Guo

address: Address: 16 Baita West Road, Gusu District, Suzhou

institute: SUZHOU MUNICIPAL HOSPITAL

description:
Library name: KO_3
Column name in gene_expression.xls: KO_3

data_processing:
Raw sequencing reads were assessed for quality control.
Adapter sequences and low-quality bases were removed to obtain clean reads.
Clean reads were aligned to the human reference genome using HISAT2.
Gene expression levels were quantified using StringTie and summarized as FPKM values.
Differentially expressed genes between SCRMP knockout and negative control cells were identified using DESeq2.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: gene_expression.xls: spreadsheet containing gene-level expression values for all six RNA-seq samples.
Supplementary files format and content: Rows correspond to genes and columns correspond to sample-level expression values; sample columns include NC_1, NC_2, NC_3, KO_1, KO_2 and KO_3.

source_name: lung

growth_protocol: NCI-H69 small cell lung cancer cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified incubator with 5% CO2. Cells were routinely tested and confirmed negative for mycoplasma contamination.

extract_protocol:
Total RNA was extracted using TRIzol Reagent, followed by DNase I treatment to remove genomic DNA. RNA quality was assessed using an Agilent 2100 Bioanalyzer and NanoDrop spectrophotometer; samples with RIN > 8.0 and acceptable purity ratios were used for library construction.
Strand-specific RNA-seq libraries were prepared by BGI. Poly(A)+ mRNA was enriched using Oligo(dT) magnetic beads, fragmented, reverse-transcribed into double-stranded cDNA, end-repaired, adapter-ligated and PCR-amplified. Libraries were sequenced on the DNBSEQ-T7 platform. The raw files available for this GEO submission contain one FASTQ file per sample and are therefore listed as single-end in the sample table.

treatment_protocol: NCI-H69 cells were engineered as stable SCRMP knockout cells using a CRISPR/Cas9 system targeting the MIR7-3HG ORF/SCRMP coding sequence. Negative control cells were generated using non-targeting control sgRNA. Three biological replicates were prepared for each group.

value: lung

value: small cell lung cancer cell

value: SCRMP knockout

value: CRISPR/Cas9-mediated SCRMP knockout


title: CD34 Donnor 4 Day 3 gRNA AAVS1

description: Library name: 385_S29

value: cord blood

value: CD34+ HSPCs


title: GM-CSF + IL-6, biological replicate 3

description:
Library name: HD_3n_GI
Healthy donor 3, day 2 culture

value: GM-CSF plus IL-6


title: mouse MSCs RNAseq E1705K replicate 1

description: Library name: 6A_

value: female


title: 39492_NativeHepG2_IgG_BX_rep1-1

description: Library name: 39492_NativeHepG2_IgG_BX_rep1-1

value: Native HepG2

value: Benzonase ChIP-exo (v6)

value: IgG


title: RNAseq_SynTEF1_RGFP109_s48_rep3

value: Patient Derived B-Lymphocyte


title: NCI-H69 cells, SCRMP knockout, biol rep 2

description:
Library name: KO_2
Column name in gene_expression.xls: KO_2


title: CD34 Donnor 3 Day 5 gRNA NINJ1/2

description: Library name: 383_S28


title: RXRgKO ctrl 04

value: mouse neural stem cell - derived OPCs

value: C57BL6J/129svEmx mixed background

value: 4 days in monolayer culture


title: NCI-H69 cells, SCRMP knockout, biol rep 1

description:
Library name: KO_1
Column name in gene_expression.xls: KO_1


title: CD34 Donnor 3 Day 3 gRNA NINJ1/2

description: Library name: 382_S27


title: mouse MSCs RNAseq D1320A replicate 3

description: Library name: 5C_


title: Control, biological replicate 3

description:
Library name: HD_3n_ctrl
Healthy donor 3, day 2 culture

value: Peripheral blood

value: in vitro differentiated MDSCs

value: Basal medium alone


title: RXRgKO ctrl 03


title: mouse MSCs RNAseq D1320A replicate 2

description: Library name: 5B_

value: mesenchymal stromal cell


title: NCI-H69 cells, negative control, biol rep 3

description:
Library name: NC_3
Column name in gene_expression.xls: NC_3

value: lung

value: small cell lung cancer cell

value: control

value: negative control sgRNA


title: FRDA heart only replaced with FRDA macrophages_3 (FA sham 3)

description: Library name: FR_FR_RNA3_FPKM

value: whole heart

value: Busulfan + PLX3397 + Bone Marrow Transplant


title: mouse MSCs RNAseq D1320A replicate 1

description: Library name: 5A_

value: female


title: CD34 Donnor 3 Day 5 gRNA AAVS1

description: Library name: 381_S26

value: cord blood

value: CD34+ HSPCs


title: RXRgKO ctrl 02


title: NCI-H69 cells, negative control, biol rep 2

description:
Library name: NC_2
Column name in gene_expression.xls: NC_2


title: CD34 Donnor 3 Day 3 gRNA AAVS1

description: Library name: 380_S25


title: mouse MSCs RNAseq WT replicate 3

description: Library name: 4C_


title: NCI-H69 cells, negative control, biol rep 1

description:
Library name: NC_1
Column name in gene_expression.xls: NC_1


title: RXRgKO ctrl 01


title: mouse MSCs RNAseq E1705K replicate 3

description: Library name: 6C_


title: CD34 Donnor 2 Day 5 gRNA NINJ1/2

description: Library name: 371_S24


title: Wt T3 04


title: CD34 Donnor 2 Day 3 gRNA NINJ1/2

description: Library name: 369_S23


title: mouse MSCs RNAseq WT replicate 1

description: Library name: 4A_


title: Wt T3 03


title: Gut_E7_replicate1

city: lyon

first: valérie

last: CASTELLANI

address: 8 Avenue Rockefeller

institute: MeLiS | CNRS UMR 5284 | INSERM U1314

description:
Library name: sample 7
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, alignment, gene counting and aggregation were done using Cell Ranger sofware version 7.1 (10X Genomics).
Assembly: GRCg7b-2021
Supplementary files format and content: matrix files in h5 format (CellRanger filtered output with features (rows) and nuclei (columns))

molecule: nuclear RNA

organism: Gallus gallus

source_name: pre-Umbilic intestine

extract_protocol:
Dissected frozen gut pieces were resuspended into 600µl of cold homogenization buffer that consisted of 10mM Tris Hcl pH 7.5, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 0.03% Tween20, 0.01% BSA, 10% EZ buffer (Sigma) and 0.2U/µl Protector RNase Inhibitor (Roche). Tissues were then transferred into 2ml Dounce (Kimble) and homogenized using 8 strokes of the loose pestle followed by 10 strokes of the tight pestle to release nuclei, on ice. Homogenate was then strained through a 40μm cell strainer (Pluriselect) and centrifuged at 500xg for 5 minutes to pellet nuclei. After removing supernatant, nuclei were washed in 1ml resuspension buffer containing 10mM Tris Hcl pH 7.5, 10mM NaCl, 3mM MgCl2, 1% BSA and 0.2U/µl Protector RNase Inhibitor and centrifuged at 500xg for 5 minutes. Nuclei were then washed again in 1ml resuspension buffer followed by centrifugation at 500xg for 5 minutes. Nuclei are then resuspended in resuspension buffer, strained through a 70μm cell strainer (Pluriselect) and finally diluted in resuspension buffer to a concentration of 1200 nuclei/µl before encapsulation in 10x Chromium. All steps were carried on ice or at 4°C.
Libraries were prepared according to 10x Genomics 3’ version 3.1 chemistry & Illumina protocols

value: pre-Umbilic intestine

value: all gut

value: wild type


title: RXRgKO T3 01

value: mouse neural stem cell - derived OPCs

value: C57BL6J/129svEmx mixed background

value: 4 days in monolayer culture


title: mouse MSCs RNAseq EV replicate 3

description: Library name: 3C_

value: empty vector


title: CD34 Donnor 2 Day 5 gRNA AAVS1

description: Library name: 366_S22


title: Wt T3 02


title: Gut_E6_replicate2

description:
Library name: sample 5
10x Genomics


title: CD34 Donnor 2 Day 3 gRNA AAVS1

description: Library name: 364_S21


title: mouse MSCs RNAseq EV replicate 2

description: Library name: 3B_

value: mesenchymal stromal cell


title: CD34 Donnor 1 Day 5 gRNA NINJ1/2

description: Library name: 347_S20


title: mouse MSCs RNAseq EV replicate 1

description: Library name: 3A_


title: Wt T3 01


title: WT ctrl 04


title: Gut_E6_replicate1

description:
Library name: sample 4
10x Genomics


title: CD34 Donnor 1 Day 3 gRNA NINJ1/2

description: Library name: 345_S19


title: WT ctrl 03


title: B16-DZNep_rep3 [B16-DZNep-3_S20]

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

department: Medicine

country: Australia

institute: Monash University

data_processing:
FASTQ files were processed using Laxy (https://zenodo.org/record/3767372) which encompasses the RNAsik pipeline (https://joss.theoj.org/papers/10.21105/joss.00583). Briefly, GRCm38 reference genome was used for STAR alignment (PubmedID: 23104886)
Gene expression counts were performed using featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw gene count matrix

source_name: melanoma

extract_protocol: Total RNA from cells were extracted using Purelink RNA mini isolation kit according to the manufacturer’s instructions (Thermo Fischer Scientific) with the additional Purelink On-Column DNA purification (ThermoFisher Scientific) step

value: mouse melanoma cell line

value: DZNep


title: Gut_E5_replicate3

description:
Library name: sample 3
10x Genomics


title: Gut_E5_replicate2

description:
Library name: sample 2
10x Genomics


title: B16-DZNep_rep2 [B16-DZNep-2_S19]


title: WT ctrl 02


title: CD34 Donnor 1 Day 3 gRNA AAVS1

description: Library name: 340_S17


title: Gut_E5_replicate1

description:
Library name: sample 1
10x Genomics


title: B16-DZNep_rep1 [B16-DZNep-1_S18]


title: mouse MSCs miRNAseq D1320A replicate 2

description: Library name: miRNA5B.fq

value: cell line


title: CD34 Donnor 1 Day 5 gRNA AAVS1

description: Library name: 342_S18


title: WT ctrl 01


title: Retina, Tbx3 conditional knockout, rep03

city: Syracuse

first: Andrea

middle: Sophia

last: Viczian

address: 750 East Adams Street

department: Ophthalmology and Visual Sciences

institute: SUNY Upstate Medical University

description: Library name: Tbx3cKO_rep03

data_processing:
Partek™ Flow™ software, version 12.10.0.
Adaptor sequences were removed using the Partek module CUTADAPT 4.2. Sequences were trimmed on both ends to an end minimum quality score (Phred) of 35 using Partek™ Flow™ software.
Trimmed sequence reads were mapped to GRCm39/mm39 using STAR Aligner version 2.7.8a with Partek™ Flow™ using default settings.
Read count extraction and normalization were performed using Partek™ Flow™ software.
Assembly: GRCm39/mm39
Supplementary files format and content: csv file includes normalized read countsfor each sample

source_name: Retina

growth_protocol: All animals were kept on a C57Bl/6J background.

extract_protocol:
Total RNA was isolated from E13.5 retinal tissue using miRNAeasy Micro Kit (Qiagen). PolyA RNA was prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Strand-specific RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: Conditional deletion of Tbx3 was achieved by crossing the Tbx3∆Fl/∆Fl transgenic strain (Derbyshire  et al., 2023, PMID: 36477806) with the commercially available mice strain Dkk3-Cre (Tg(Dkk3-cre)D9Tfur; RIKEN BioResource Research Center #RBRC05427 (Sato et al., 2007, PMID: 17661397). Sibling wild type (WT) were Dkk3-Crenegative;Tbx3Fl/+ and conditional knockouts (cKO) were Dkk3-Cre+;Tbx3∆Fl/∆Fl. Timed pregnancies were performed by overnight harem breeding and weighing dams, as described (Heyne et al., 2015, PMID: 26224435). Embryonic day 13.5 (E13.5) embryos were extracted from the euthanized dam.

value: Retina

value: Tbx3 knockout

tag: developmental stage

value: Embryonic day 13.5


title: Player 2 post-soccer match

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

description: Library name: player_2_socpost

data_processing:
RNA-seq reads were demultiplexed using bcl2fastq/2.20.0 and preprocessed with fastp/0.23.4. Gene abundance was quantified with Salmon/1.5.2.
Assembly: GENCODE Release 39 based on GRCh38
Supplementary files format and content: csv text file includes the counts for each sample

source_name: muscle

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientiﬁc)
Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, #E7490 and #E7760)

tag: tissue

value: muscle


title: Player 2 pre-soccer match

description: Library name: player_2_socpre


title: Retina, Tbx3 conditional knockout, rep02

description: Library name: Tbx3cKO_rep02

tag: genotype


title: B16-F10_siEzh2_rep2 [B16.siEzh2.2_S8]

tag: treatment


title: mouse MSCs miRNAseq D1320A replicate 1

description: Library name: miRNA5A.fa

tag: cell line

value: female


title: B16-F10_siEzh2_rep3 [B16.siEzh2.3_S9]


title: Player 1 post-soccer match

description: Library name: player_1_socpost


title: Retina, Tbx3 conditional knockout, rep01

description: Library name: Tbx3cKO_rep01


title: B16-F10_siEzh2_rep1 [B16.siEzh2.1_S7]


title: Retina, wild-type, rep03

description: Library name: WT_rep03

value: Wild-type


title: Player 1 pre-soccer match

description: Library name: player_1_socpre


title: B16-F10_scr_rep3 [B16.scr.3_S6]

value: scrambled control


title: HPMEC_RA_40min_rep4

type: RNA

first: Charlotte

middle: H

last: Dean

address: Imperial College London Hammersmith Campus, Level 5 Dr Victor Phillip Dahdaleh (VPD) Building, Du Cane Rd

description: Gene expression data from HPMECs treated with RA at t = 40 min

hyb_protocol: Biotin-labeled cDNA was fragmented and hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChips according to the manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual). Arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner following the manufacturer’s standard protocols.

data_processing: The data were analyzed using the Transcriptome Analysis Console (TAC) software v4.0.2 (Thermo Scientific). Raw data were normalized and summarized using the MAS5 algorithm with global scaling to a target intensity of 500. Probe sets were mapped to the human genome reference assembly hg19. Differential expression was assessed using moderated t-statistics with empirical Bayes (ANOVA framework), applying a fold-change cutoff of ±1.5 and false discovery rate (Benjamini–Hochberg) < 0.05.

label: biotin

source_name: HPMEC, RA, 40 min

label_protocol: cRNA was synthesised using the Ovation® Pico WTA System V2 and labelled with the Encore Biotin Module, following the manufacturer’s protocols.

growth_protocol: Primary HPMECs were cultured in Endothelial Cell Growth Medium MV at 37°C in a 5% CO2 atmosphere. Cells were used between passages 3 and 7.

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

treatment_protocol: HPMECs were serum-starved for 24 hours before treatment. HPMECs were treated with either the vehicle (0.1% EtOH) or 10 μM RA, and seeded on 24-well plates pre-coated with growth factor-reduced Matrigel (5 mg/ml).

value: lung


title: HPMEC_RA_0h_rep4

description: Gene expression data from HPMECs treated with RA at t = 0 h

source_name: HPMEC, RA, 0 h


title: HPMEC_RA_4h_rep4

description: Gene expression data from HPMECs treated with RA at t = 4 h

source_name: HPMEC, RA, 4 h


title: Retina, wild-type, rep02

description: Library name: WT_rep02


title: HPMEC_EtOH_4h_rep4

description: Gene expression data from HPMECs treated with EtOH at t = 4 h

source_name: HPMEC, EtOH, 4 h


title: THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 5

city: Rochester

first: Shumin

last: Wang

state: New York

address: 601 Elmwood Avenue, Box CVRI

department: CVRI

institute: University of Rochester medical center

description: Library name: THP1TNFaDll4si05

data_processing:
Raw Illumina BCL files were demultiplexed using bcl2fastq v2.20.0. Adapter trimming and quality filtering were performed using fastp v0.23.1 (minimum read length 35 bp; sliding-window quality score >=13 at both 5′ and 3′ ends). Clean reads were aligned to the human GRCh38 reference genome using STAR v2.7.9a in two-pass mode. Non-canonical splice junctions were removed, and unmapped reads were retained in FASTQ format. Gene-level counts were generated using featureCounts from Subread v2.0.1 against the GENCODE v42 annotation with stranded, exon-based summarization. Differential expression analysis was performed in R v4.0.2 using DESeq2 v1.34.0 under the negative binomial generalized linear model framework, with Benjamini-Hochberg adjusted P values; genes with adjusted P value <0.05 were considered differentially expressed.
Assembly: human GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

growth_protocol: THP-1 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% non-essential amino acids, and 1 mM sodium pyruvate in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated from treated THP-1 cells after 24 hours using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared from total RNA using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer's protocol. All samples are of excellent quality (RIN/RQN > 7) and have sufficient RNA (> 100 ng) to proceed to mRNA Stranded Library prep.

treatment_protocol: THP-1 cells were transfected with 30µM Dll4 siRNA or control siRNA via Lipofectamine™ RNAiMAX and cultured for 24 hours in the presence of either 200ng/mL of LPS or 20ng/mL of TNF-α stimulation. Cells were harvested 24 hours after treatment for RNA extraction.

value: acute monocytic leukemia cell line

value: TNF-alpha Dll4 knockdown


title: B16-F10_scr_rep2 [B16.scr.2_S5]


title: Retina, wild-type, rep01

description: Library name: WT_rep01


title: THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 4

description: Library name: THP1TNFaDll4si04


title: B16-F10_scr_rep1 [B16.scr.1_S4]


title: HPMEC_EtOH_40min_rep4

description: Gene expression data from HPMECs treated with EtOH at t = 40 min

source_name: HPMEC, EtOH, 40 min


title: THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 3

description: Library name: THP1TNFaDll4si03


title: 4 pooled E9.5 microdissected Tbx1Cre/+; Kmt2d F/+; GFP F/+ Embryos

city: Bronx

first: Bernice

last: Morrow

address: 1301 Morris Park Ave, Price Center, Room 469

department: Genetics

institute: Albert Einstein College of Medicine

description:
Library name: Control-Kmt2d-E95
10X Genomics

data_processing:
The deumltiplexing, barcode processing, and gene counting for each sample were done using the 10X Genomics Cell Ranger Software v8.0.1.
Quality control, cell filtering, sample clustering, integration, subclustering, differential expression, and gene set enrichment analysis were performed using the R packages SoupX v1.6.2 and scDAPP v1.2.2 (https://github.com/bioinfoDZ/scDAPP).
Assembly: Mouse mm10
Supplementary files format and content: tab separated value files and matrix files

source_name: pharyngeal region and heart

extract_protocol:
Embryos were collected at E9.5 and microdissected in 1x PBS at 4 °C. Dissected tissue was maintained in DMEM (Dulbecco’s Modified Eagle Medium, GIBCO 11885084) at 4°C while genotyping was performed. Microdissections included the pharyngeal region from PA1 onwards and included the heart. Embryos were pooled by genotype and then incubated in 1 ml of 0.25% Trypsin-EDTA (GIBCO, 25200056) containing 50 U/ml of DNase I (Millipore, 260913-10MU), at room temperature for 7 min with occasional pipetting to break up the tissue. 100 uL of FBS (fetal bovine serum, ATCC, 30-2021) kept at 4°C was added to stop the reaction at a final concentration of 10%. Dissociated cells were centrifugated for 5 min at 300 × g at 4 °C and the supernatant was removed. Cells were then resuspended in 1x PBS (without Ca2+ and Mg2+, Coming, 21-031-cv) containing 10% FBS at 4 °C. These preparations were then filtered with a 100-μm cell strainer and 1 μl DAPI (1 mM) (Thermo Fisher Scientific, D3571) was added to each sample. Cells were FACS (Fluorescence Activated Cell Sorting) purified using a BD FACSAria II (BD Biosciences) system and BD FACSDiva 8.0.1 software in order to collect EGFP-positive and DAPI negative living cells in 1x PBS containing 10% FBS at 4°C. Following collection, these cells were centrifuged at 4 °C for 5 min at 300 × g. Finally, supernatant was removed and the cells were resuspended in 50 μl of 10% FBS.
Library preparation was performed using standard manufacter's instructions using the 10X  Genomics Chromium Next GEM Single Cell 3ʹ Kit v3.1 PN-1000268. Libraries were indexed using the Dual Index Kit TT Set A  PN-1000215 and standard Illumina adaptors. The sequencing primers are standard Illumina, i5 and i7.

value: pharyngeal region and heart

value: outbred SwissWebster

value: E9.5 embryos

value: Tbx1Cre/+; Kmt2d F/+; GFP F/+

value: Conditional Heterozygote


title: B16-F10_GSK126_rep3 [B16.GSK126.3_S17]

value: mouse melanoma cell line


title: THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 2

description: Library name: THP1TNFaDll4si02


title: mouse MSCs RNAseq WT replicate 2

description: Library name: 4B_

value: mesenchymal stromal cell


title: 4 pooled E9.5 microdissected Tbx1Cre/+; Kmt2d F/F; GFP F/+ Embryos

description:
Library name: Mutant-Kmt2d-cKO-E95
10X Genomics

value: Tbx1Cre/+; Kmt2d F/F; GFP F/+

value: Conditional Knockout


title: HPMEC_EtOH_0h_rep4

description: Gene expression data from HPMECs treated with EtOH at t = 0 h

source_name: HPMEC, EtOH, 0 h


title: B16-F10_GSK126_rep2 [B16.GSK126.2_S16]


title: B78 melanoma cells, 20uCi+ISV+DCP, week 3 rep3

city: MADISON

first: Rene

last: Welch

state: WI

address: 1111 Highland Avenue,

department: Department of Biostatistics and Medical Informatics

institute: University Wisconsin - Madison

description:
Library name: Sam24
Column name in raw_counts_all_samples.tsv: Sam24

data_processing:
RSEM v1.3.1
rsem_calculate_expression with parameters '--star --star-gzipped-read-file --paired-end'
Add both lanes for each sample to have only one column per sample
Keep only genes with more than 20 reads in average
f
Assembly: Grcmm39
Supplementary files format and content: tsv delimited raw count files for all samples, one sample per column

source_name: tumor

extract_protocol:
Samples homogenized w/ Qiagen Tissuelyser (2min @ 20Hz) up to four rounds, icing for 5min in between each round.
Organic extraction followed with clean up on Qiagen RNeasy Mini Kit. On-column DNase treatment. Sample eluted w/ 40uL nuclease-free water added to column

treatment_protocol: Treatment- The first day of treatment with TRT was defined as “day 1”.  20 μCi (M2h model) of 90Y-NM600 was injected into the tail vein of tumor-bearing mice to deliver an estimated 2.5 Gy mean tumor dose from TRT. Tumor-targeted external beam RT was delivered at a dose of 8 Gy (right flank only) on treatment day 1, after MOC2WT tail vein injection and before TRT treatments. Intratumoral injection of adjuvants to promote ISV were delivered to the radiated primary tumor site as that combines of cetuximab (50 µg/injection) and IL2 (75,000 U/injection) and were administrated in 100 µl of PBS daily on treatment days 6 to 10. Anti–CTLA-4 (IgG2c, clone 9D9, NeoClone) and anti–PD-L1 (IgG2b, clone 10F.9G2, BioXCell) were administered as DCP (200 µg each/injection) by intraperitoneal injection on treatment days 3, 6, and 9.  Fresh left flank tumors were collected on day 12 and sent for RNAseq.

value: tumor

value: B78 melanoma cells

tag: time

value: week 3


title: THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 1

description: Library name: THP1TNFaDll4si01


title: B16-F10_GSK126_rep1 [B16.GSK126.1.2_S3]


title: HPMEC_RA_4h_rep3


title: HPMEC_RA_40min_rep3


title: THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 5

description: Library name: THP1TNFaCtrlsi05

value: TNF-alpha WT


title: Gut_E6_replicate3

description:
Library name: sample 6
10x Genomics

value: pre-Umbilic intestine

value: all gut

value: wild type


title: B16-F10_DMSO_rep3 [B16.DMSO.3_S15]

value: DMSO


title: B78 melanoma cells, 20uCi+ISV+DCP, week 3 rep2

description:
Library name: Sam20
Column name in raw_counts_all_samples.tsv: Sam20


title: HPMEC_RA_0h_rep3

value: lung


title: B78 melanoma cells, 20uCi+ISV+DCP, week 3 rep1

description:
Library name: Sam19
Column name in raw_counts_all_samples.tsv: Sam19


title: THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 4

description: Library name: THP1TNFaCtrlsi04

value: acute monocytic leukemia cell line


title: B16-F10_DMSO_rep2 [B16.DMSO.2_S14]


title: B78 melanoma cells, ISV+DCP, week 3 rep3

description:
Library name: Sam17
Column name in raw_counts_all_samples.tsv: Sam17

value: ISV+DCP


title: HPMEC_EtOH_4h_rep3


title: THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 3

description: Library name: THP1TNFaCtrlsi03


title: B16-F10_DMSO_rep1 [B16.DMSO.1_S13]


title: HPMEC_EtOH_40min_rep3


title: B78 melanoma cells, ISV+DCP, week 3 rep2

description:
Library name: Sam16
Column name in raw_counts_all_samples.tsv: Sam16


title: HPMEC_EtOH_0h_rep3


title: THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 2

description: Library name: THP1TNFaCtrlsi02


title: B78 melanoma cells, ISV+DCP, week 3 rep1

description:
Library name: Sam14
Column name in raw_counts_all_samples.tsv: Sam14


title: THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 1

description: Library name: THP1TNFaCtrlsi01


title: Vancomycin-5

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

country: Israel

institute: Bar-Ilan University

description: Library name: 24h_v_23_S11

data_processing:
Data were processed using the RASflow package, DOI: 10.1186/s12859-020-3433-x
Trimming: Reads were trimmed using Trim Galore version: 0.6.2 and adapters removed using Cutadapt version: 3.5. Quality Phred score cutoff: 20. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected). Maximum trimming error rate: 0.1 (default). Minimum required adapter overlap (stringency): 1 bp. Minimum required sequence length before a sequence gets removed: 20 bp.
Mapping: Reads were mapped to the transcriptome (Rattus_norvegicus.GRCr8) using Salmon. The normalized values are estimated Transcripts Per Million (TPM) from Salmon and are scaled using the average transcript length over samples and then the library size by “tximport”. Any missing gene names (using rnorvegicus_gene_ensembl) are replaced with gene IDs. We filtered out sparse genes, which we defined as those with over 50% zero values. We started with 35,534 genes and removed 15,077 sparse genes, leaving us with 20,457 genes. We normalized each sample’s reads to 1M reads.
Assembly: rnorvegicus_gene_ensembl
Supplementary files format and content: Tab-delimited text files include both ENSMUSG and gene name identifiers, and normalized expression levels per gene.

organism: Rattus norvegicus

extract_protocol:
RNA was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
RNA sequencing libraries were produced by using the QuantSeq 3’ mRNA-Seq V2 Library Prep (LX-191.96). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 200nM of each library was pooled together and diluted to 2nM. 750pM was loaded onto the Flow Cell with 2% PhiX library control according to the NextSeq manufacturer’s instructions. Libraries were sequenced with the Illumina NextSeq 1000 platform with P1 kit single-end reads of 100bp.

value: pheochromocytoma

value: Vancomycin


title: Vancomycin-6

description: Library name: 24h_v_24_S12


title: B78 melanoma cells, 20uCi+DCP, week 3 rep3

description:
Library name: Sam13
Column name in raw_counts_all_samples.tsv: Sam13


title: THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 5

description: Library name: THP1LPSDll4si05

value: LPS Dll4 knockdown


title: Vancomycin-4

description: Library name: 24h_v_22_S10


title: B78 melanoma cells, 20uCi+DCP, week 3 rep2

description:
Library name: Sam12
Column name in raw_counts_all_samples.tsv: Sam12


title: THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 4

description: Library name: THP1LPSDll4si04


title: Vancomycin-3

description: Library name: 24h_v_21_S9


title: HPMEC_RA_0h_rep2

city: London

institute: Imperial College London


title: HPMEC_RA_4h_rep2


title: B78 melanoma cells, 20uCi+DCP, week 3 rep1

description:
Library name: Sam10
Column name in raw_counts_all_samples.tsv: Sam10


title: HPMEC_RA_40min_rep2

description: Gene expression data from HPMECs treated with RA at t = 40 min


title: THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 3

description: Library name: THP1LPSDll4si03


title: Vancomycin-2

description: Library name: 24h_v_20_S8


title: HPMEC_EtOH_4h_rep2


title: Vancomycin-1

description: Library name: 24h_v_19_S7


title: THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 1

description: Library name: THP1LPSDll4si01


title: B78 melanoma cells, 20uCi+ISV, week 3 rep1

description:
Library name: Sam6
Column name in raw_counts_all_samples.tsv: Sam6


title: B78 melanoma cells, 20uCi+ISV, week 3 rep2

description:
Library name: Sam7
Column name in raw_counts_all_samples.tsv: Sam7


title: THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 2

description: Library name: THP1LPSDll4si02


title: Control-6

description: Library name: 24h_c_18_S6

value: PBS


title: HPMEC_EtOH_40min_rep2


title: B78 melanoma cells, PBS control, week 3 rep3

description:
Library name: Sam5
Column name in raw_counts_all_samples.tsv: Sam5

value: PBS control


title: THP-1 cells, control siRNA, LPS, 24 h, biological replicate 5

description: Library name: THP1LPSCtrlsi05

value: LPS WT


title: Control-4

description: Library name: 24h_c_16_S4


title: THP-1 cells, control siRNA, LPS, 24 h, biological replicate 4

description: Library name: THP1LPSCtrlsi04


title: Control-5

description: Library name: 24h_c_17_S5


title: B78 melanoma cells, PBS control, week 3 rep2

description:
Library name: Sam4
Column name in raw_counts_all_samples.tsv: Sam4

value: tumor


title: B78 melanoma cells, PBS control, week 3 rep1

description:
Library name: Sam3
Column name in raw_counts_all_samples.tsv: Sam3

value: B78 melanoma cells


title: Control-3

description: Library name: 24h_c_15_S3


title: 3 pooled E9.5 microdissected Tbx1Cre/+; Kmt2d F/+; GFP F/+ Embryos

description:
Library name: Control2-Kmt2d-E95
10X Genomics

data_processing:
The deumltiplexing, barcode processing, and gene counting for each sample were done using the 10X Genomics Cell Ranger Software v8.0.1.
Quality control, cell filtering, sample clustering, integration, subclustering, differential expression, and gene set enrichment analysis were performed using the R packages SoupX v1.6.2 and scDAPP v1.2.2 (https://github.com/bioinfoDZ/scDAPP).
genome build/assembly: Mouse mm10
processed data files format and content: tab separated value files and matrix files

extract_protocol:
Embryos were collected at E9.5 and microdissected in 1x PBS at 4 °C. Dissected tissue was maintained in DMEM (Dulbecco’s Modified Eagle Medium, GIBCO 11885084) at 4°C while genotyping was performed. Microdissections included the pharyngeal region from PA1 onwards and included the heart. Embryos were pooled by genotype and then incubated in 1 ml of 0.25% Trypsin-EDTA (GIBCO, 25200056) containing 50 U/ml of DNase I (Millipore, 260913-10MU), at room temperature for 7 min with occasional pipetting to break up the tissue. 100 uL of FBS (fetal bovine serum, ATCC, 30-2021) kept at 4°C was added to stop the reaction at a final concentration of 10%. Dissociated cells were centrifugated for 5 min at 300 × g at 4 °C and the supernatant was removed. Cells were then resuspended in 1x PBS (without Ca2+ and Mg2+, Coming, 21-031-cv) containing 10% FBS at 4 °C. These preparations were then filtered with a 100-μm cell strainer and 1 μl DAPI (1 mM) (Thermo Fisher Scientific, D3571) was added to each sample. Cells were FACS (Fluorescence Activated Cell Sorting) purified using a BD FACSAria II (BD Biosciences) system and BD FACSDiva 8.0.1 software in order to collect EGFP-positive and DAPI negative living cells in 1x PBS containing 10% FBS at 4°C. Following collection, these cells were centrifuged at 4 °C for 5 min at 300 × g. Finally, supernatant was removed and the cells were resuspended in 50 μl of 10% FBS.
Library preparation was performed using standard manufacter's instructions using the 10X Genomic Chromium GEM-X Single Cell 3ʹ Kit v4.1 PN-1000691.  Libraries were indexed using the Dual Index Kit TT Set A  PN-1000215 and standard Illumina adaptors. The sequencing primers are standard Illumina, i5 and i7.

value: pharyngeal region and heart

value: outbred SwissWebster

value: E9.5 embryos

value: Tbx1Cre/+; Kmt2d F/+; GFP F/+

value: Conditional Heterozygote


title: THP-1 cells, control siRNA, LPS, 24 h, biological replicate 2

description: Library name: THP1LPSCtrlsi02


title: HPMEC_RA_40min_rep1


title: HPMEC_RA_0h_rep1

description: Gene expression data from HPMECs treated with RA at t = 0 h


title: HPMEC_EtOH_0h_rep2

description: Gene expression data from HPMECs treated with EtOH at t = 0 h


title: THP-1 cells, control siRNA, LPS, 24 h, biological replicate 3

description: Library name: THP1LPSCtrlsi03


title: Control-2

description: Library name: 24h_c_14_S2


title: 3 pooled E9.5 microdissected Tbx1Cre/+; Kmt2d F/F; GFP F/+ Embryos

description:
Library name: Mutant2- Kmt2d-cKO-E95
10X Genomics

value: Tbx1Cre/+; Kmt2d F/F; GFP F/+

value: Conditional Knockout


title: HPMEC_RA_4h_rep1

description: Gene expression data from HPMECs treated with RA at t = 4 h

value: lung


title: HPMEC_EtOH_4h_rep1

description: Gene expression data from HPMECs treated with EtOH at t = 4 h


title: HPMEC_EtOH_40min_rep1

description: Gene expression data from HPMECs treated with EtOH at t = 40 min


title: Control-1

description: Library name: 24h_c_13_S1


title: THP-1 cells, control siRNA, LPS, 24 h, biological replicate 1

description: Library name: THP1LPSCtrlsi01

value: acute monocytic leukemia cell line


title: RNA-seq_Control_Rep4

status: Public on Jul 01 2026

city: Hung Hom

first: Xiaofan

last: Xu

address: 11 Yuk Choi Rd

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Library name: RNA-seq_Control_Rep4

data_processing:
Sequencing reads were aligned to the human reference genome using STAR (Spliced Transcripts Alignment to a Reference) with default parameters for paired-end data.
Read pairs mapping to exons were quantified and summarized at the gene level using featureCounts from the Subread package.
The GENCODE v45 primary assembly GTF was used as the reference annotation for both the alignment index and the feature counting step.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing raw, unnormalized integer read counts per gene across all samples. Columns correspond to individual sample library names and rows correspond to Ensembl Gene IDs.

extract_protocol:
For adherent cells, remove the culture medium, wash once with PBS, and add 1 mL of TRIzol per 10 cm² of growth area; for suspension cells, pellet approximately 5×10⁶ cells and resuspend directly in 1 mL of TRIzol. Lyse the cells by repeated pipetting and incubate at room temperature for 5 min to ensure complete dissociation of nucleoprotein complexes. Transfer the lysate to a 1.5‑mL RNase‑free tube, add 0.2 mL of chloroform per 1 mL of TRIzol, cap tightly, shake vigorously for 15 s, let stand for 2–3 min, and then centrifuge at 12,000×g for 15 min at 4°C to separate the mixture into a lower organic phase, an interphase, and a colorless upper aqueous phase containing the RNA. Carefully transfer the upper aqueous phase (about 400–500 µL) to a fresh RNase‑free tube without disturbing the interphase, add 0.5 mL of isopropanol per 1 mL of TRIzol used, mix by inversion, incubate at room temperature for 10 min, and centrifuge at 12,000×g for 10 min at 4°C to pellet the RNA. Discard the supernatant, wash the gel‑like white pellet with 1 mL of 75% ethanol (prepared with DEPC‑treated water) by vortexing, centrifuge at 7,500×g for 5 min at 4°C, and remove the supernatant as completely as possible (repeat the wash if desired). Air‑dry the pellet for 5–10 min until the ethanol has evaporated but avoid over‑drying, then dissolve the RNA in 20–50 µL of RNase‑free water or DEPC‑treated water, with optional incubation at 55–60°C for 10 min to aid solubilization. Finally, assess the RNA purity and concentration by measuring A₂₆₀/A₂₈₀ (expected 1.8–2.1) and A₂₆₀/A₂₃₀ (>2.0) on a spectrophotometer, and check integrity by agarose gel electrophoresis, where a clear 28S and 18S rRNA bands with a ratio of approximately 2:1 indicates good quality. All operations must be carried out with RNase‑free consumables, gloves, and a clean workspace to prevent contamination.
Total RNA (1 μg) from each sample was depleted for rRNA using the Ribo−Zero rRNA Removal Kit (EPICENTRE, USA). The sequencing library was then constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina, USA).

treatment_protocol: Prior to transfection, HSC3 cells were seeded in 6-well plates at a density of 1 × 10^5 cells per well and allowed to adhere overnight. The following day, cells were transfected with si-Col1a1 or si-NC using Lipofectamine 3000 reagent according to the manufacturer’s instructions. Briefly, 100 pmol of siRNA was mixed with 5 µL of Lipofectamine 3000 in 200 µL of Opti-MEM medium and incubated for 20 minutes at room temperature. The transfection mixture was then added dropwise to the cells, and the cells were incubated for 48 hours post-transfection.

value: human oral squamous cell carcinoma cell lines


title: RNA-seq_Control_Rep3

description: Library name: RNA-seq_Control_Rep3


title: RNA-seq_Control_Rep2

description: Library name: RNA-seq_Control_Rep2


title: RNA-seq_Control_Rep1

description: Library name: RNA-seq_Control_Rep1


title: HPMEC_EtOH_0h_rep1


title: RNA-seq_KD_Rep3

description: Library name: RNA-seq_KD_Rep3


title: RNA-seq_KD_Rep4

description: Library name: RNA-seq_KD_Rep4


title: RNA-seq_KD_Rep2

description: Library name: RNA-seq_KD_Rep2


title: RNA-seq_KD_Rep1

description: Library name: RNA-seq_KD_Rep1


title: P12_LPS_2: CD45+ brain immune cells, P12 LPS-1

city: zhengzhou

first: jinjin

last: zhu

address: Kangfu steet

institute: zhengzhou university

description: Library name: P12_LPS_2

data_processing:
Raw sequencing reads were processed to generate FASTQ files and aligned to the mouse reference genome (mm10). Gene expression matrices were generated for downstream analysis.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data are provided as gzip-compressed 10x Genomics Matrix Exchange (MEX) files for each sample. The matrix.mtx.gz files contain filtered gene-by-cell UMI count matrices; the features.tsv.gz files contain the gene identifiers and gene symbols corresponding to matrix rows; and the barcodes.tsv.gz files contain the cell barcodes corresponding to matrix columns.

source_name: CD45+ brain immune cells from neonatal mouse

extract_protocol:
Brain tissues from neonatal mice were enzymatically dissociated to obtain single-cell suspensions. CD45+ immune cells were enriched by fluorescence-activated cell sorting (FACS) prior to library preparation.
Single-cell RNA-seq libraries were prepared using the SeekOne® Digital Droplet Single Cell 3' Library Preparation Kit following the manufacturer's instructions. Barcoded cDNA was generated in microfluidic droplets and subsequently amplified for sequencing.

value: brain

value: CD45+ brain immune cells

value: LPS


title: P7_LPS_2: CD45+ brain immune cells, P7 LPS-2

description: Library name: P7_LPS_2


title: P3_LPS_1: CD45+ brain immune cells, P3 LPS-2

description: Library name: P3_LPS_2


title: P12_LPS_1: CD45+ brain immune cells, P12 LPS-2

description: Library name: P12_LPS_1


title: P7_LPS_1: CD45+ brain immune cells, P7 LPS-1

description: Library name: P7_LPS_1


title: P3_LPS_1: CD45+ brain immune cells, P3 LPS-1

description: Library name: P3_LPS_1


title: CD45+ brain immune cells, P12 control-2

description: Library name: P12_NS_2

value: Control


title: CD45+ brain immune cells, P7 control-2

description: Library name: P7_NS_2


title: CD45+ brain immune cells, P7 control-1

description: Library name: P7_NS_1


title: CD45+ brain immune cells, P3 control-1

description: Library name: P3_NS_1


title: CD45+ brain immune cells, P3 control-2

description: Library name: P3_NS_2


title: CD45+ brain immune cells, P3 control-3

description: Library name: P3_NS_3


title: Orthotopic PDAC, MRTX1133+anti-PD1 treatment, 2w

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description: Library name: Hy-MRTX-aPD1

library_source: genomic single cell

data_processing:
Raw data were processed with Cell Ranger ATAC version 2.1.0
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz and filtered_feature_bc_matrix.h5

source_name: PDAC

growth_protocol: complete RPMI

extract_protocol:
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit
Bulk nuclei transposition, GEM generation, Barcoding & Reverse Transcription, Quenching, Cleanup & Pre-Amplification, ATAC library amplification

value: PDAC

value: Orthotopic KPC-2 primary tumors

value: Sorted CD45+ cells

value: LSL-KrasG12D/+, P53F/+, P48-Cre


title: CD45+ brain immune cells, P12 control-1

description: Library name: P12_NS_1


title: Orthotopic PDAC, MRTX1133+anti-CTLA4 treatment, 2w

description: Library name: Hy-MRTX-aCTL4


title: Orthotopic KPC2 PDAC, Veh/Iso, 2w

description: Library name: Hy-Veh

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1
GEM-RT, cDNA amplification, library contruction

value: Orthotopic KPC2 primary PDAC tumor

value: Veh/Iso


title: Orthotopic KPC2 PDAC, RMC6236+anti-CTLA4, 2w

description: Library name: Hy-RMC6236-aCTLA4


title: Orthotopic KPC3 PDAC, MRTX1133+anti-CTLA4, 10d

description: Library name: KPC-T-1133-CTLA4

value: Orthotopic KPC3 primary PDAC tumor

value: Sorted Live cells

value: Pdx1-cre, LSL-KrasG12D/+, Trp53R172H/+


title: Orthotopic KPC2 PDAC, RMC6236, 2w

description: Library name: Hy-RMC6236


title: Orthotopic KPC3 PDAC,MRTX1133, 10d

description: Library name: KPC-T-MRTX


title: Orthotopic PDAC, MRTX1133 treatment, 2w

description: Library name: Hy-MRTX


title: Orthotopic PDAC, Veh treatment, 2w

description: Library name: Hy-Veh

value: Veh


title: Orthotopic KPC2 PDAC, RMC6236+anti-PD1, 2w

description: Library name: Hy-RMC6236-aPD1


title: Orthotopic KPC1 PDAC, MRTX1133, 2w

description: Library name: MRTX1133343P

value: Orthotopic KPC1 primary PDAC tumor

value: Pdx1-cre, LSL-KrasG12D/+, Trp53R172H/+; Rosa-LSL-EYFP


title: Multiome, central amygdala, RT00942N, mouse_AUD, mouse, GEX

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

description: Library name: RT00942N_GEX

data_processing:
Multiome files were demultiplexed using Cellranger-arc mkfastq
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5,  atac_fragments.tsv.gz

source_name: Brain

extract_protocol:
Nuclei were isolated from fresh-frozen human central amygdala tissue and purified to generate single-nucleus suspensions for simultaneous chromatin accessibility and gene-expression profiling.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, which constructs matched ATAC-seq (genomic DNA accessibility) and gene-expression (polyA nuclear RNA) libraries from the same nucleus.

value: Brain

value: ethanol (2 g/kg IP)


title: Multiome, central amygdala, RT00942N, mouse_AUD, mouse, ATAC

description: Library name: RT00942N_ATAC


title: Multiome, central amygdala, RT00941N, mouse_CON, mouse, ATAC

description: Library name: RT00941N_ATAC

value: saline control


title: Orthotopic KPC1 PDAC, Veh, 2w

description: Library name: Vehicle_343P


title: Orthotopic KPC3 PDAC, anti-CTLA4, 10d

description: Library name: KPC-T-CTLA4


title: Kidney tissue from patient 5, healthy

city: Zaragoza

first: Maria del Mar

last: Encabo Berzosa

address: San Juan Bosco

institute: IACS

description:
Library name: Kidney_tissue_healthy_5
Column name in raw_counts.txt and in TPMs_matrix.txt: B6

data_processing:
The quality of the raw reads was assessed using FastQC. Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuck.
Trimmed sequence reads were mapped to GRCh38 using STAR software.
Gene and transcript expression levels were subsequently quantified using RSEM.
Gene annotation was performed in R by using org.Hs.eg.db (version 3.19.1) and AnnotationDbi (version 1.66.0) libraries.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: kidney

growth_protocol: Kidney-derived organoids were cultured in BME-II matrix in kidney organoid medium for 7 days post-passaging. Prior to RNA extraction, tubuloids were dissociated using dispase, centrifuged at 300 xg for 5 minutes at room temperature, and the resulting pellet was immediately snap-frozen. The frozen organoid pellet was then resuspended in Qiazol Lysis Reagent before proceeding with the miRNeasy protocol.

extract_protocol:
RNA was harvested using the miRNeasy Mini Kit (Qiagen). 250 ng of total RNA were used for the construction of sequencing libraries.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: kidney

tag: individual

value: patient 5


title: Multiome, central amygdala, RT00941N, mouse_CON, mouse, GEX

description: Library name: RT00941N_GEX


title: Kidney organoid derived from patient 5, healthy, passage 5, 7 days culture

description:
Library name: Kidney_organoid_healthy_5
Column name in raw_counts.txt and in TPMs_matrix.txt: B7

source_name: tubuloids

value: tubuloids

value: healthy


title: Multiome, central amygdala, RT00938N, mouse_AUD, mouse, ATAC

description: Library name: RT00938N_ATAC


title: Multiome, central amygdala, RT00937N, mouse_CON, mouse, ATAC

description: Library name: RT00937N_ATAC


title: Kidney tissue from patient 1, tumor

description:
Library name: Kidney_tissue_tumor_1
Column name in raw_counts.txt and in TPMs_matrix.txt: B4

value: patient 1


title: Multiome, central amygdala, RT00938N, mouse_AUD, mouse, GEX

description: Library name: RT00938N_GEX


title: Kidney organoid derived from patient 4, healthy, passage 1, 6 days culture

description:
Library name: Kidney_organoid_healthy_4
Column name in raw_counts.txt and in TPMs_matrix.txt: B3

value: patient 4


title: Kidney organoid derived from patient 1, tumor, passage 2, 7 days culture

description:
Library name: Kidney_organoid_tumor_1
Column name in raw_counts.txt and in TPMs_matrix.txt: B5

value: tumoral


title: Kidney tissue from patient 4, healthy

description:
Library name: Kidney_tissue_healthy_4
Column name in raw_counts.txt and in TPMs_matrix.txt: B2


title: Kidney organoid derived from patient 3, tumor, passage 2, 7 days culture

description:
Library name: Kidney_organoid_tumor_3
Column name in raw_counts.txt and in TPMs_matrix.txt: B1

value: patient 3


title: Multiome, central amygdala, RT00937N, mouse_CON, mouse, GEX

description: Library name: RT00937N_GEX


title: Multiome, central amygdala, RT00934N, mouse_AUD, mouse, ATAC

description: Library name: RT00934N_ATAC


title: Kidney tissue from patient 3, tumor

description:
Library name: Kidney_tissue_tumor_3
Column name in raw_counts.txt and in TPMs_matrix.txt: A9


title: Multiome, central amygdala, RT00934N, mouse_AUD, mouse, GEX

description: Library name: RT00934N_GEX


title: Kidney tissue from patient 3, healthy

description:
Library name: Kidney_tissue_healthy_3
Column name in raw_counts.txt and in TPMs_matrix.txt: A7


title: Kidney organoid derived from patient 2, tumor, passage 1, 13 days culture

description:
Library name: Kidney_organoid_tumor_2
Column name in raw_counts.txt and in TPMs_matrix.txt: A6

value: patient 2


title: Kidney organoid derived from patient 3, healthy, passage 2, 7 days culture

description:
Library name: Kidney_organoid_healthy_3
Column name in raw_counts.txt and in TPMs_matrix.txt: A8


title: Multiome, central amygdala, RT00933N, mouse_CON, mouse, ATAC

description: Library name: RT00933N_ATAC


title: Multiome, central amygdala, RT00933N, mouse_CON, mouse, GEX

description: Library name: RT00933N_GEX


title: Multiome, central amygdala, RT00930N, mouse_CON, mouse, ATAC

description: Library name: RT00930N_ATAC


title: Multiome, central amygdala, RT00930N, mouse_CON, mouse, GEX

description: Library name: RT00930N_GEX


title: Kidney tissue from patient 2, tumor

description:
Library name: Kidney_tissue_tumor_2
Column name in raw_counts.txt and in TPMs_matrix.txt: A5


title: Kidney organoid derived from patient 2, healthy, passage 2, 6 days culture

description:
Library name: Kidney_organoid_healthy_2
Column name in raw_counts.txt and in TPMs_matrix.txt: A4


title: Multiome, central amygdala, RT00929N, mouse_CON, mouse, ATAC

description: Library name: RT00929N_ATAC


title: NEG_EVT_Rep3

status: Public on Jul 03 2026

city: Seattle

first: Meagan

middle: Nicole

last: Esbin

state: WA

address: 850 Republican St. S280

department: Obstetrics & Gynecology

institute: University of Washington School of Medicine

description: Library name: Sample 13

data_processing:
Plasmidsaurus performed read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp
Plasmidsaurus aligned reads to the human hg38 reference genome using STAR aligner v2.7.1181 with non-canonical splice junction removal and output of unmapped reads.
Plasmidsaurus performed gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook with filtering for low-expressed genes with edgeR::filterByExpr. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by Ensembl Gene ID
Supplementary files format and content: Comma separated values file containing differential gene expression analysis output from EdgeR with the Log2 Fold-Change (logFC), p-value (pValue) and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) comparing NEG (non-targeting sgRNA transfected) hTSCs to ZBTB10 KO hTSCs in Undifferentiated, STB-differentiated, and EVT-differentiated conditions. Comparisons are noted as (_KOvsWT) where positive FC values indicates higher gene expression in ZBTB10 KO cells compared to NEG control.

source_name: hTSC

growth_protocol: Naïve-derived human trophoblast stem cells were established previously and cultured in hypoxic conditions (37°C, 5% CO2, 5% O2) in TSC Media (DMEM/F12 supplemented with 0.1 mM β-mercaptoethanol, 0.2% FBS (Sigma, F4135), 0.5% Penicillin-Streptomycin (P/S; Gibco, 15140122), 0.3% BSA, 1% ITS-X (Gibco, 41400045), 1.5 μg/mL L-ascorbic acid, 50 ng/mL EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA, and 5 μM Y-27632).51 Media was changed every other day and TSCs were passaged using TrypLE Express (Gibco, 12605010) when 80% confluent (approximately every 4 days) at a ratio of 1:4–6 on Cultrex-coated plates. Cells from passage 10-25 were used.

extract_protocol:
hTSC RNA was harvested using the RNeasy mini kit (Qiagen, 74104).
RNA-sequencing was performed by Plasmidsaurus using Illumina Sequencing Technology with custom analysis and annotation.

treatment_protocol: Human hTSCs were plated at a density of 1E5 cells/well in Cultrex-coated 6-well plates and differentiated for 6 days into EVT or STB and harvested at Day 7, or if undifferentiated were harvested when confluent at Day 4. For the induction of EVTs, Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to EVT1 medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 100ng/mL NRG1, 7.5uM A83-01, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) supplemented with 1% Geltrex (Day 1). On day 3, the medium was replaced with EVT2 medium (EVT1 medium without NRG1) supplemented with 0.5% Geltrex. On day 5, the medium was replaced with EVT2 medium. For the induction of STBs, TSCs were seeded identically as above. Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to STB medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 2.5 μM forskolin, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) on Day 1. The medium was replaced on day 4.

value: hTSC

value: naive pluripotent stem cell derived human trophoblast stem cells

value: NEG (polyclonal nucleofected with Cas9+non-targeting sgRNA)

value: 6 day EVT differentiation


title: Multiome, central amygdala, RT00929N, mouse_CON, mouse, GEX

description: Library name: RT00929N_GEX


title: Kidney organoid derived from patient 1, healthy, passage 2, 6 days culture

description:
Library name: Kidney_organoid_healthy_1
Column name in raw_counts.txt and in TPMs_matrix.txt: A2


title: Kidney tissue from patient 2, healthy

description:
Library name: Kidney_tissue_healthy_2
Column name in raw_counts.txt and in TPMs_matrix.txt: A3


title: JZ24023244-785_SN_WTA-785_SN_WTA

city: Shenyang

first: Yani

address: General Hospital of Northern Theater Command, Wenhua Road 83

department: State Key Laboratory of Frigid Zone Cardiovascular Diseases, Department of Cardiology and Cardiovascular Research Institute

description: Library name: Sample5

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCm39.106

source_name: Ventricular muscle

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1) the target RNA was interrupted by adding ion-interrupting reagent and random primer, and the random primer was combined with the target RNA; 2) the target RNA was reversely transcribed into cDNA by adding 1-strand reverse transcription reagent, and the hybrid chain of RNA and cDNA was formed; 3) the RNA in cDNA and RNA hybrid chain was cleaved by adding 2-strand synthetic reagent, and the double-stranded cDNA was synthesized by using the remaining RNA as the primer; 4) the double-stranded cDNA synthesis product was subjected to end-padding and a-addition; the“Y”-shaped linker was ligated; 5) the linker self-connecting fragment was removed by magnetic bead screening; 6) the library template was enriched by PCR amplification; 7) the library was recovered by magnetic beads. Reagent: VAHTS Universal V 8rna-seq Prep Library Kit for Illumina

value: Ventricular muscle

value: SnRNA-seq was performed on cardiac tissue from a mouse model of sorafenib-induced cardiotoxicity


title: JZ24023245-786_SN_WTA-786_SN_WTA

institute: General Hospital of Northern Theater Command

description: Library name: Sample6

value: control


title: Female,Adlib,Saline,Adult,rep10

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: 9B.7_Female_Adlib_Saline_mPFC_Adult
9B.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

source_name: Medial prefrontal cortex

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: Kidney tissue from patient 1, healthy

description:
Library name: Kidney_tissue_healthy_1
Column name in raw_counts.txt and in TPMs_matrix.txt: A1

value: kidney


title: JZ24023243-781_SN_WTA-781_SN_WTA

description: Library name: Sample4


title: NCCIT cells, scrambled control siRNA, replicate 1

city: Farmington

first: Ching

middle: C

last: Lau

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description: Library name: NCCIT_SCsiRNA_replicate1

data_processing:
Raw sequencing data was processed using the nf-core rnaseq (v3.18.0, https://nf-co.re/rnaseq/3.18.0/parameters/) pipeline via Nextflow (v24.10.4), with default options.
Assembly: GRCh38
Supplementary files format and content: Length-corrected Salmon-derived gene read counts provided, with samples provided on the columns.

source_name: NCCIT

growth_protocol: NCCIT and NEC8 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (Denville), 1% penicillin-streptomycin (PS, Gibco), 1% GlutaMax (Thermo Fisher Scientific), 1% non-essential amino acids (NEAA,Gibco) under standard condition (37°C and 5% CO₂).

extract_protocol:
Total RNA was extracted from siRNA-treated cells using the RNeasy Kit (Qiagen) following the manufacturer’s instructions. RNA was quantified using a NanoDrop spectrophotometer.
Sequencing was performed on 1,000 ng total RNA per sample and Poly(A) library preparation, quality control, and sequencing were done by GENEWIZ by Azenta Life Sciences.

treatment_protocol: Silencer Select siRNAs (Thermo Fisher Scientific) targeting PRDM14 and CBFA2T2 or a scrambled non-targeting control siRNA were transfected directly into 3×105 cells per well of a 6-well plate using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific) and Opti-MEM (Gibco). A final concentration of 10 nM siRNA was used. Transfected cells were incubated for 96 hours prior to analysis.

value: NCCIT

value: embryonal carcinoma

value: scrambled control


title: NCCIT cells, siPRDM14, replicate 2

description: Library name: NCCIT_PRDM14siRNA_replicate2

value: PRDM14 knockdown


title: JZ24023242-780_SN_WTA-780_SN_WTA

description: Library name: Sample3


title: NCCIT cells, scrambled control siRNA, replicate 2

description: Library name: NCCIT_SCsiRNA_replicate2


title: JZ24023240-777_SN_WTA-777_SN_WTA

description: Library name: Sample1


title: NCCIT cells, siPRDM14, replicate 1

description: Library name: NCCIT_PRDM14siRNA_replicate1


title: MPL

city: Aachen

first: Mohamed

last: Saad

address: Pauwelsstraße 30

department: Institut für Zell- und Tumorbiologie

institute: Uniklinik RWTH Aachen

description: Library name: PW7

data_processing:
The Cell Ranger Software (version 7.0.0) implemeted
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz : list of barcodes
Supplementary files format and content: features.tsv.gz : list of gene Ids
Supplementary files format and content: matrix.mtx.gz : gene expresion count data in Matrix Market Exchange Format

source_name: Spleen

growth_protocol: BM cells from CD45.1 donor (male and female) mice were isolated 48h prior to transplantation. C-kit enriched cells were transduced with 1) ThPO lentivirus or  empty vector (EV) control lentivirus, or with 2) MPL retrovirus or EV control retrovirus, depending on mouse model. Gli1CreERT;tdTomato recipients (male and female) were injected with tamoxifen (4x30mg, every 48h) in corn oil/ 3% ethanol intraperitoneally. Three weeks after the last tamoxifen injection, 15-20 week old recipients were 1) lethally irradiated using twice 5Gy, 4h apart, or 2) sublethally irradiated using 5Gy before receiving 0.5 x106 transduced C-kit+ donor cells by intravenous injection. Blood was collected biweekly starting 4 weeks after transplantation and basic blood parameters were measured. Remaining blood was further processed for flow cytometry. For the ThPO model, spleen volume was measured by weekly ultrasound under isoflurane anesthesia using the Visualsonics Vevo3100 starting 4 weeks after transplantation. The software Vevo LAB (v5.7.1) was used for analysis. Mice were sacrificed at 1) 4 weeks (early) or 8-10 weeks (late/endstage) post-transplant or at 2) 4-5 weeks post-transplant. For each analysis, a control group, sacrificed on the same day, was used for comparison.

extract_protocol:
Splenocytes were isolated and RBC lysis was performed as described below. CD3+, CD19+, Ly6G+, NK1.1+ and Ter119+ cells were magnetically depleted using biotinylated antibodies in combination with Anti-Biotin MicroBeads (Miltenyi Biotech). Immune (CD45+), stromal (CD45- CD31-) and endothelial cells (CD31+) were sorted by fluorescence-activated cell sorting (FACS) using BD FACSMelody and pooled in a specific ratio. For stromal enrichment, CD45+ splenocytes were magnetically depleted followed by FACS for stromal cells (Ter119-, CD45-, CD31-). 25,000 cells were used per sequencing reaction.
All libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1): Library Construction Kit and Gel Bead Kit (PN-1000268), Chromium Next GEM Chip G Single Cell Kit (PN-1000127) and Dual Index Kit TT Set A (PN-1000215), and following the Chromium Next GEM Single Cell 3ʹ v3.1(Dual Index) User Guide (CG000315, Rev F). Finalized libraries were sequenced aiming for a minimum of 20.000 reads/cell using the 10x Genomics recommended number of cycles (28-10-10-90 cycles).

value: Spleen

tag: sample group

value: MPL


title: NCCIT cells, siCBFA2T2, replicate 1

description: Library name: NCCIT_CBFA2T2siRNA_replicate1

value: CBFA2T2 knockdown


title: EV_2

description: Library name: PW6

value: EV


title: JZ24023241-779_SN_WTA-779_SN_WTA

description: Library name: Sample2


title: NCCIT cells, siCBFA2T2, replicate 2

description: Library name: NCCIT_CBFA2T2_replicate2


title: NEC8 cells, scrambled control siRNA, replicate 2

description: Library name: NEC8_SCsiRNA_replicate2


title: ThPO_2

description: Library name: PW5

value: ThPO


title: NEC8 cells, scrambled control siRNA, replicate 1

description: Library name: NEC8_SCsiRNA_replicate1


title: ZBTB10KO_STB_Rep1

description: Library name: Sample 10

value: hTSC

value: naive pluripotent stem cell derived human trophoblast stem cells

value: polyclonal ZBTB10 KO

value: 6 day STB differentiation


title: NEC8 cells, siPRDM14, replicate 1

description: Library name: NEC8_PRDM14siRNA_replicate1


title: NEC8 cells, siPRDM14, replicate 2

description: Library name: NEC8_PRDM14siRNA_replicate2


title: EV_1

description: Library name: PW1


title: 52-week PBMC-sec-treated mouse dorsal skin

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

description:
Library name: 52wk_Apo
10x Genomics

data_processing:
Raw base call files were demultiplexed and converted to FASTQ files using the 10x Genomics Cell Ranger pipeline.
Sequencing reads were aligned to the mouse reference genome using Cell Ranger count. The 10x Genomics mouse reference refdata-gex-mm10-2020-A was used, corresponding to mm10/GRCm38 with GENCODE vM23/Ensembl 98 gene annotation.
Cell Ranger was used for cellular barcode detection, UMI counting, and generation of gene-barcode count matrices for each sample.
Assembly: Mus musculus mm10/GRCm38 reference genome assembly using the 10x Genomics refdata-gex-mm10-2020-A reference package with GENCODE vM23/Ensembl 98 annotation.
Supplementary files format and content: Tab separated value files and matrix files

source_name: Dorsal skin

growth_protocol: Male C57BL/6 mice were maintained under standard animal facility conditions until 8, 26 or 52 weeks of age.

extract_protocol:
Three animals were pooled per condition. Immediately after collection, tissues were enzymatically dissociated using the gentleMACS Whole Skin Dissociation Kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) according to the manufacturer's instructions on a gentleMACS Octo Dissociator (Miltenyi Biotec). Cell suspensions were filtered sequentially through 100 µm and 40 µm strainers and washed in PBS containing 0.04% bovine serum albumin (BSA; Sigma-Aldrich, St. Louis, MO, USA). Cell viability and concentration were assessed with the Acridine Orange/Propidium Iodide (AO/PI) Cell Viability Kit (Logos Biosystems, Anyang-si, Gyeonggi-do, Korea) on a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems), and the concentration was adjusted to 0.7–1.2 × 10⁶ cells/ml.
Gel beads-in-emulsion (GEMs) were generated, and GEM formation, barcoding, clean-up, cDNA amplification, and library preparation were performed according to the manufacturer's instructions using the Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1, the Chromium Next GEM Chip G Single Cell Kit, and the Single Index Kit T Set A (10x Genomics, Pleasanton, CA, USA). Sequencing, demultiplexing, and read counting were performed by the Biomedical Sequencing Facility of the Center for Molecular Medicine (CeMM, Vienna, Austria).

treatment_protocol: For untreated control samples, dorsal skin from 8-week, 26-week and 52-week-old C57BL/6 mice was processed directly after collection. For treatment samples, freshly collected dorsal skin from age-matched mice was treated ex vivo with the secretome of γ-irradiated peripheral blood mononuclear cells (PBMC-sec) prior to tissue dissociation and single-cell RNA-sequencing. Following treatment, tissue was enzymatically dissociated using the same protocol as untreated samples. Three animals were pooled per condition.

value: Dorsal skin

value: Whole skin cells

value: wildtype

value: PBMCsec

value: male


title: ThPO_1

description: Library name: PW2


title: 26-week PBMC-sec-treated mouse dorsal skin

description:
Library name: 26wk_Apo
10x Genomics


title: 52-week untreated control mouse dorsal skin

description:
Library name: 52wk_ctrl
10x Genomics

value: Untreated


title: 26-week untreated control mouse dorsal skin

description:
Library name: 26wk_ctrl
10x Genomics


title: NEC8 cells, siCBFA2T2, replicate 1

description: Library name: NEC8_CBFA2T2siRNA_replicate1

value: embryonal carcinoma


title: NEC8 cells, siCBFA2T2, replicate 2

description: Library name: NEC8_CBFA2T2_replicate2