title: SPF pancreas, AP, rep1

description:
Library name: SPF_AP_rep1
10x Genomics

value: pancreas

value: CD45+ immune cells;Acinal Cells

value: C57BL/6J WT

value: NovaSeq run 1


title: Erythroid-committed primary cells, scramble, day 12, rep2

status: Public on Aug 20 2025

type: SRA

city: Omaha

first: Meg

middle: A

last: Schaefer

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

country: USA

institute: University of Nebraska Medical Center

library_source: transcriptomic

data_processing:
RNA-seq data was aligned to the human genome, hg38, using STAR (v2.7.10b).
Sorted BAM files were obtained using samtools (v1.16.1), and normalized reads based on reads per kilobase per million mapped reads (TPM) were obtained using stringtie (v2.2.0).
Differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 results; raw counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Kit+ Erythroid-committed primary human cells

growth_protocol: CD34+ cells were cultured in serum free expansion media for 4 days containing a cocktail of recombinant human (rh) Flt-3, SCF, IL3, and IL-6, followed by an 8-day differentiation phase in IMDM containing 15% FBS, 500 μg/mL holotransferrin, 2 mM glutamine, 1.5% pen/strep, 1% BSA, 10 μg/mL rhinsulin, 1 μm dexamethasone, 1 μm β-estradiol, 5 ng/mL rhIL-3, 100 ng/mL rhSCF, and 6 U/mL EPO. Lentiviral infections with scramble and sgSAMD1 constructs were performed on day 2 of the differentiation phase by spinoculation. 48 hours after infection, infected cells were puromycin selected.

extract_protocol:
RNA was isolated by TRIzol extraction and purified with the Rneasy Plus Micro Kit (Qiagen).
RNA libraries were prepared using the Universal Plus mRNA-Seq with NuQuant kit.

tag: cell type

tag: condition

value: Scramble

tag: timepoint

value: Day 12


title: 20999X8 E0771 Obese secretome Rep2

city: Salt Lake City

first: Keren

last: Hilgendorf

state: Utah

address: 15 N Medical Drive East Rm 4100

department: Biochemistry

institute: University of Utah

description:
Library name: Sample 20
20999R_raw_counts.txt

data_processing:
Mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: Feature count output files combined into a tab-delimited count matrix

organism: Mus musculus

growth_protocol: E0771, NMuMG, and SkBr3 cells were plated at subconfluency and allowed to grow for 36 hours, before treatment addition. E0771 and SkBr3 cells were grown in DMEM with 10% FBS. NMuMG cells were grown in DMEM with 10% FBS, 4.5 g/L glucose and 10 mcg/ml insulin.

extract_protocol:
The cells (E0771, NMuMG, and SkBr3) were washed once post treatment with PBS then collected in RLT-bME buffer. The RNA was isolated using Qiagen RNeasy kit.
RNA was sequenced using Illumina Sequencing with Agilent RNA ScreenTape Assay for QC and NovaSeq S4 Reagent Kit v1.5_150x150 bp Sequencing (2500 M read-pairs/lane). The library was prepped using NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation with adapter read 1 (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) and adapter read 2 (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).

treatment_protocol: The treatments,  standard growth media, lean inguinal adipocyte secretome, or obese inguinal adipocyte secretome (50% secretome, 50% standard growth media) was added to the cells for 16 hours.

tag: cell line

value: Breast Cancer

tag: treatment

value: Obese Inguial Adipocyte Secretome


title: GF pancreas, AP, rep3

city: Nanchang

first: Yaoyu

last: Zou

state: Jiangxi

address: 17 Yong Waizheng Street, Donghu District

country: China

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: GF_AP_rep3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Step 1 – demultiplex & alignment: BCL files were demultiplexed and aligned to the mouse reference genome (GRCm39, Cell Ranger refdata-gex-mm10-2020-A) using Cell Ranger v7.0.1 (10x Genomics) with default parameters; filtered_feature_bc_matrix outputs were generated.
Step 2 – quality control: In Seurat v4.3.0, cells with < 200 detected genes, < 1 000 UMIs, log10(Genes/UMI) < 0.7, mitochondrial UMIs > 20 % or hemoglobin UMIs > 5 % were discarded. Doublets were predicted and removed using DoubletFinder v2.0.2.
Step 3 – normalisation & HVGs: Data were log-normalised (NormalizeData) and the 2 000 most variable genes identified (FindVariableFeatures).
Step 4 – dimensionality reduction & clustering: Scaled data (ScaleData) underwent PCA, and UMAP was computed on the top 30 PCs. Clusters were defined using the Louvain algorithm (resolution = 0.5) via FindNeighbors / FindClusters.
Step 5 – cell-type annotation: Cluster markers were identified with FindAllMarkers (Wilcoxon), and cell identities were assigned using SingleR v2.2.0 against the ImmGen mouse reference; acinar and immune subsets were confirmed with canonical markers.
Assembly: Mouse genome GRCm39 (Ensembl 109) / Cell Ranger reference “refdata-gex-mm10-2020-A
Supplementary files format and content: For each sample: filtered gene–barcode matrix (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz); combined Seurat object (seurat.rds) containing normalised counts, UMAP coordinates, cluster and cell-type metadata.
Supplementary files format and content: Integrated AnnData file (merged_anndata.h5ad) with expression matrix, dimensionality reductions and annotations; supplementary CSV of marker genes per cluster.

molecule: total RNA

source_name: pancreas

growth_protocol: Male C57BL/6J mice (7–8 weeks) were maintained under germ-free (GF) or specific-pathogen-free (SPF) conditions in individually ventilated isolators at 22 ± 2 °C, 50–60 % humidity, 12 h light/dark cycle with autoclaved chow and sterile water ad libitum.

extract_protocol:
Fresh pancreas was minced (~0.5 mm³) in DMEM + 10 % FBS and digested at 37 °C for 60 min in DMEM containing 0.25 % trypsin and 1 mg ml⁻¹ collagenase I/II/IV with gentle agitation. The digest was filtered through a 100 µm strainer and centrifuged (300 g, 5 min). Red blood cells were removed with MACS RBC lysis buffer (4 °C, 10 min). Cells were washed, resuspended in PBS + 0.04 % BSA, and viability was assessed on a Luna counter; suspensions were adjusted to 700–1 200 cells µl⁻¹ for library preparation.
Single-cell libraries were generated using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10x Genomics, PN 1000268) following the manufacturer’s instructions, targeting 8 000 cells per sample. GEM generation, reverse transcription, cDNA amplification and indexing PCR were performed on a Chromium Controller. Finished libraries were quantified (Qubit dsDNA HS) and quality-checked (Agilent 2100). Sequencing was carried out on an Illumina NovaSeq 6000 (paired-end 2 × 150 bp).

treatment_protocol: Acute pancreatitis (AP) was induced by intraperitoneal injections of cerulein (100 µg kg⁻¹) administered hourly for 10 h. Control animals received sterile saline. Mice were euthanized 24 h after the final injection; GF or SPF status was preserved throughout the experiment.

tag: tissue

tag: genotype

value: cerulein 100 µg kg-1 ×10, GF

tag: batch


title: Nrf2-peptide-linked fumarate rep3

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: Sample 15

data_processing:
The adapters were trimmed with fastp 0.21.1 (Chen et al., 2018).
Reads were mapped with STAR 2.7.7a (Dobin et al., 2013).
Count matrix was generated with featureCount tool from ssubread-2.0.1 aligner (Liao et al., 2013, 2014).
Assembly: GENCODE release 37 GRCh38.primary assembly.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: Neuroblastoma SH-SY5Y cells were grown in 6-well plates in 2 mL medium per well up to 80% confluence. The medium consisted of DMEM/F12 (Thermo Fisher Scientific) containing 10% FBS (Thermo Fisher Scientific), 100 U/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
Cells were lysed with the QIAzol Lysis Reagent (Qiagen, Germany). RNA isolation was performed using miRNeasy Micro Kit (Qiagen, Germany) according to the manufacturer's protocol. Nanodrop ND-1000 (Thermo Fisher Scientific, USA) was used to assess quantity and purity of the extracted RNA. Total RNA samples were also QC-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using Illumina Stranded mRNA Library Prep Kit (Illumina, USA).

treatment_protocol: The samples were prepared and added as follows: Fish oil (50 uL) diluted 6-fold in DMSO, incubated for an hour, and 10 uL of the stock solution added to the well; 50 mg dry caviar-derived supplement suspended in 500 uL DMSO, incubated for an hour, centrifuged to remove the precipitate, and 10 uL supernatant added to the well;  50 mg dry caviar-derived supplement suspended in 500 uL PBS, incubated for an hour, centrifuged to remove the precipitate, and 10 uL supernatant added to the well; 2 mg peptide diluted into 600 uL water, incubated for an hour, and 200 uL added to the well; 10 uL DMSO was used for the control well, and 10 uL DMSO was added to the wells with peptide and water extract of dry caviar-derived supplement. The medium was removed after 5h incubation, the cells were washed with DPBS tree times and lysed.

value: Nrf2-peptide-linked fumarate in water plus DMSO


title: Erythroid-committed primary cells, scramble, day 12, rep1

value: Kit+ Erythroid-committed primary human cells


title: 20999X17 NMuMG Obese secretome Rep2

description:
Library name: Sample 29
20999R_raw_counts.txt

source_name: NMuMG

value: NMuMG


title: 20999X15 NMuMG Lean secretome Rep3

description:
Library name: Sample 27
20999R_raw_counts.txt

value: Lean Inguinal Adipocyte Secretome


title: 20999X6 E0771 Lean secretome Rep3

description:
Library name: Sample 18
20999R_raw_counts.txt


title: 20999X5 E0771 Lean secretome Rep2

description:
Library name: Sample 17
20999R_raw_counts.txt


title: Nrf2-peptide-linked fumarate rep2

description: Sample 14


title: Nrf2-peptide-linked fumarate rep1

description: Sample 13


title: Erythroid-committed primary cells, scramble, day 12, rep4


title: 20999X4 E0771 Lean secretome Rep1

description:
Library name: Sample 16
20999R_raw_counts.txt


title: Control rep3

description: Sample 6

value: DMSO


title: 20999X3 E0771 Control Rep3

description:
Library name: Sample 15
20999R_raw_counts.txt

value: Control


title: Control rep1

description: Sample 4


title: Soft V+ siPiezo1_3

city: Barcelona

first: Mariana

last: Azevedo Gonzalez Oliva

state: Barcelona

address: Ed. Clúster – Lab EMS1C54, Av. Gregorio Marañon, 6, Rampa 2

country: Spain

institute: IBEC Parc Cientific Barcelona

description: Library name: 42

data_processing:
Trimming and alignment was performed using Kallisto 0.46.1
Assembly: Homo-sapiens.GrCh.cdna
Supplementary files format and content: normcounts_stiff.csv is a csv file containing EnsemblD and normalised counts for each condition

source_name: hTERT-BMSC clone Y201, cell line

growth_protocol: Y201 cells were routinely passaged in DMEM + 10% FBS (Corning T75 flasks), cells were transfected with Piezo1 siRNA (siPiezo1) or ctrl RNA (scRNA) using the standard RNAimax protocol

extract_protocol:
Total RNA was isolated using a commercial kit (Qiagen RNAeasy) with DNAse treatment to remove genomic contaminations.
Strand-specific RNA-Seq libraries were prepared using the Illumina Stranded mRNA (poly A selected) library preparation kit with a NextSeq2000 system. In total, 100x100 bp paired end reads and an average of 30M total reads were generated for each sample.

treatment_protocol: Post transfection, scRNA and siPiezo1 cells were seeded on FN coated hydrogels (stiff V- and stiff V+) and cultured on the gels for 48h. Post 48h, cells were washed with PBS and harvested

value: hTERT-BMSC clone Y201, cell line

value: mesenchymal stem cell

value: Soft viscoelastic substrate


title: 20999X2 E0771 Control Rep2

description:
Library name: Sample 14
20999R_raw_counts.txt


title: Soft V+ scRNA3

description: Library name: 39

value: scRNA


title: 20999X1 E0771 Control Rep1

description:
Library name: Sample 13
20999R_raw_counts.txt


title: Soft V+ siPiezo1_1

description: Library name: 40


title: Soft V+ siPiezo1_2

description: Library name: 41


title: Soft V+ scRNA2

description: Library name: 38


title: Soft V- siPiezo_3

description: Library name: 36

value: Soft elastic substrate


title: Soft V- siPiezo_2

description: Library name: 35


title: Soft V- siPiezo_1

description: Library name: 34


title: Th1 cells, CBS+66, CTCF-binding site+66 deletion

city: Fukushima

first: Masayuki

last: Sekimata

address: Fukushima-shi

country: Japan

institute: FukushimaMedical University

description: Library name: Sample2

library_source: genomic

data_processing:
Sequencing reads were aligned to the mouse mm10 assembly and processed into normalized contact maps with the HiC-Pro v3.1.0 pipeline (Servant et al., 2015) .
Default settings were used to remove duplicate reads, assign reads to restriction fragments, filter for valid pairs, and generate raw and ICE normalized interaction matrices at a range of resolutions.
For visualization by Juicebox (v2.15) valid pairs were converted to .hic files using the script “hicpro2juicebox.sh”.
Assembly: mm10/GRCm38
Supplementary files format and content: hic

molecule: genomic DNA

source_name: spleen

growth_protocol: Th1 cells were cultured with IMDM with plate-bound anti-CD3 (10 µg/mL, clone 145-2C11) and anti-CD28 (10 µg/mL, clone 37.51) under Th1 cell conditions: IL-12 (10 ng/mL) and anti-IL-4 (10  ug/mL, clone 11B11) for 3 days.

extract_protocol:
Cells were crosslinked with 3 mM disuccinimidyl glutarate and 1% formaldehyde. Intact nuclei were extracted with Micro-C Buffer #1 and digested with 20 U MNase for 10 minutes. Digested chromatin was washed twice with MB#2 and incubated in end-repair reactions for 15 minutes. To generate 5’ fragment overhangs for end-blunting and labeling, 50 U Klenow Fragment was added and incubated for 15 minutes. A mixture of dNTPs in end-labeling buffer was added and incubated for 45 minutes. Samples were washed with MB#3 and proximity ligation was performed in a ligation reaction. To remove biotinylated dNTPs, samples were digested by Exonuclease III for 15 minutes. To prepare ligated DNA for library preparation, dinucleosome-sized DNA fragments (250 to 400 bp) were gel-extracted and purified with Dynabeads MyOne Streptavidin C1.
Illumina library preparation was performed using the NEBNext Ultra II kit (NEB) and NEB Multiplex Oligos for Illumina. 120-mer probes were designed to tile end-to-end across the capture locus (mm10, chr10:118,369,795-118,508,916), and capture enrichment was performed according to the xGen Hybrid Capture protocol (Integrated DNA Technologies). Pooled libraries were sequenced with 150 bp paired-end reads using NovaSeq (Illumina).

value: spleen

value: T helper type1 cells

value: Th1 differentiation


title: Th1 cells, CBS-70, CTCF-binding site-70 deletion

description: Library name: Sample3


title: Soft V- scRNA3

description: Library name: 33


title: control siPiezo1 3

description: Library name: KD3

data_processing:
Trimming and alignment was performed using Kallisto 0.46.1
Assembly: Homo-sapiens.GrCh.cdna
Supplementary files format and content: normcounts_Glass.csv is a csv file containing EnsemblD and normalised counts for each condition

extract_protocol:
total RNA was isolated using a commercial kit (Qiagen RNAeasy) with DNAse treatment to remove genomic contaminations.
Strand-specific RNA-Seq libraries were prepared using the Illumina Stranded mRNA (poly A selected) library preparation kit with a NextSeq2000 system. In total, 100x100 bp paired end reads and an average of 30M total reads were generated for each sample.

value: FN Glass


title: control siPiezo1 1

description: Library name: KD1


title: Soft V- scRNA1

description: Library name: 31


title: control scRNA 2

description: Library name: Ctrl2


title: Soft V- scRNA2

description: Library name: 32


title: Th1 cells, WT

description: Library name: Sample1

value: WT


title: Stiff V+ siPiezo1_3

description: Library name: Stiff V K3

value: Stiff viscoelastic substrate


title: Th1 cells, CBS-70, CTCF-binding site-70 deletion-1

description:
Library name: L70-4
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : L70

data_processing:
RNA-seq reads were mapped using the nf-core RNA-seq pipeline v3.18.0 with the default alignment options (STAR and Salmon). The reads were mapped to the mm10 genome.
Transcription abundance estimates generated by Salmon.
Assembly: mm10/GRCm38
Supplementary files format and content: salmon.merged.gene_counts.tsv file generated by Salmon: tab-delimited txt file containing gene counts results for reads aligned to the standard mm10 genome.
Supplementary files format and content: salmon.merged.gene_tpm.tsv file generated by Salmon: tab-delimited txt file containing TPM results for reads aligned to the standard mm10 genome. Quantification is done on the transcript level.

extract_protocol:
RNA was purified using the FastGene RNA Premium Kit (Nippon Genetics) and NEBNext rRNA Depletion Kit v2 (NEB).
Purified total RNA (250 ng) was used to generate cDNA using the NEBNext UltraExpress RNA Library Prep Kit (NEB, #E3330).


title: Th1 cells, CBS-70, CTCF-binding site-70 deletion-2

description:
Library name: L70-5
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : L70


title: control siPiezo1 2

description: Library name: KD2


title: Control rep2

description: Sample 5


title: Th1 cells, CBS-70, CTCF-binding site-70 deletion-3

description:
Library name: L70-6
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : L70


title: Stiff V+ scRNA3

description: Library name: Stiff V C3

value: scrambled RNA (scRNA)


title: control scRNA 1

description: Library name: Ctrl1


title: Stiff V+ siPiezo1_2

description: Library name: Stiff V K2


title: Th1 cells, CBS+66, CTCF-binding site+66 deletion-2

description:
Library name: L66-8
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : L66


title: Stiff V+ scRNA1

description: Library name: Stiff V C1


title: control scRNA 3

description: Library name: Ctrl3


title: Th1 cells, CBS+66, CTCF-binding site+66 deletion-3

description:
Library name: L66-9
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : L66


title: Th1 cells, WT-3

description:
Library name: WT-3
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : WT


title: Soft V+ scRNA1

description: Library name: 37


title: Th1 cells, CBS+66, CTCF-binding site+66 deletion-1

description:
Library name: L66-7
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : L66


title: Stiff V+ siPiezo1_1

description: Library name: Stiff V K1


title: Th1 cells, WT-2

description:
Library name: WT-2
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : WT


title: Stiff V- siPiezo_2

description: Library name: Stiff E K2

value: Stiff elastic substrate


title: Stiff V- siPiezo_1

description: Library name: Stiff E K1


title: Th1 cells, WT-1

description:
Library name: WT-1
Column name in salmon_merged_gene_counts.tsv and slmon_merged_gene_tpm.tsv : WT


title: Stiff V- scRNA2

description: Library name: Stiff E C2


title: Stiff V- scRNA3

description: Library name: Stiff EC3


description: Library name: Sample3

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.5.4.
Aligned reads are converted to BAM files using samtools v1.21.
BAM files are subsequently converted to bigWig files using samtools and deepTools v3.5.5.
Assembly: mm10/GRCm38
Supplementary files format and content: bigWig

source_name: Spleen

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was treated with Mnase.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit  (NEB) and NEBNext Multiplex Oligos for Illumina (NEB). Briefly, 70 ng ChIP DNA fragments were end-repaired, indexed, and amplified. Libraries were sequenced with 150-bp paired-end reads on a NovaSeq platform.

value: Spleen

tag: chip antibody

value: CTCF (CST#3418)


title: 092523-4A-August-CoCl2-Estrogen_S4

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: Library name: 092523-4A-August-CoCl2-Estrogen_S4

data_processing:
Genome alignment, quality control, and differential gene expression were analyzed using Partek Flow (Partek, St. Louis, MO, USA).
Contaminants were removed using Bowtie 2 v2.2.5, and the reads were aligned to the refernce genome (hg38 for human; mm10 for mouse) using STAR 2.7.8a.
Aligned reads were quantified using RefSeq Transcripts 96. Features (genes) were filtered to retain only those with at least five reads in ≥ 80% of the samples.
Assembly: hg38 (HepG2 cells); mm10 (mouse tissues)
Supplementary files format and content: .txt

growth_protocol: HepG2 cells were cultured overnight in EMEM media for cell culture and %10 FBS, washed, and treated with 17 b Estradiol or CoCl2 under normal or hypoxic conditions.

extract_protocol:
RNA was purified using the QIAGEN RNeasy Mini Kit
The libraries were generated using Illumina Stranded Total RNA prep with Ribo-Zero Plus library preparation kit

treatment_protocol: For in vivo analyses, C57BL/6 female mice were purchased from Charles River laboratory and were blindly randomized into 4 groups with 10 mice in each group as follows: lean (L), lean+estrogen-pelleted (L+P), obese (O), and obese+estrogen-pelleted (O+P). Two groups were fed a normal chow diet while the other two groups were fed a high fat diet (HFHSD; 29% Fat Kcal, Teklad) for 3 months, and the body weight of each mouse was recorded until the experiments were completed. The obese mice were administered with a subcutaneous 17 β Estradiol tablet 800 µg/mouse (Innovative Research of America; E-121, FL, USA). Livers were collected. For in vitro assays, HepG2 (1x106) cells were seeded out into a 6-well plate and allowed to attach overnight and treated with β-Estradiol (25 nM) and CoCl2 (50 µM) for 4 hours. RNA was extracted

value: Cell Line


title: 092523-4C-August-CoCl2-Estrogen_S12

description: Library name: 092523-4C-August-CoCl2-Estrogen_S12


description: Library name: Sample2


title: 0092523-4B-August-CoCl2-Estrogen_S8

description: Library name: 0092523-4B-August-CoCl2-Estrogen_S8


title: Stiff V+ scRNA2

description: Library name: Stiff V C2


title: Stiff V- scRNA1

description: Library name: Stiff E C1


title: 092523-3B-August-Estrogen_S7

description: Library name: 092523-3B-August-Estrogen_S7

value: Estrogen


title: 092523-3C-August-Estrogen_S11

description: Library name: 092523-3C-August-Estrogen_S11


title: Th1 cells, WT

description: Library name: Sample1


title: Stiff V- siPiezo_3

description: Library name: Stiff E K3

value: hTERT-BMSC clone Y201, cell line


title: 092523-4C-Sept-Obese-Estrogen_S24

description: Library name: 092523-4C-Sept-Obese-Estrogen_S24

source_name: Liver

value: Liver

value: High Fat Diet + 17 B Estradiol


title: 092523-2B-August-CoCl2_S6

description: Library name: 092523-2B-August-CoCl2_S6


title: 092523-1A-August-Ctrl_S1

description: Library name: 092523-1A-August-Ctrl_S1

value: Control


title: 092523-2A-August-CoCl2_S2

description: Library name: 092523-2A-August-CoCl2_S2


title: 092523-2C-August-CoCl2_S10

description: Library name: 092523-2C-August-CoCl2_S10


title: maxillae bone, adult, Day14, rep3

city: Wuhan

first: Rui

last: Zhang

address: 237 Luoyu Road

department: Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology

institute: School & Hospital of Stomatology, Wuhan University

description: Library name: Sample18

data_processing:
mRNA was isolated from total RNA using oligo (dT) beads and subsequently fragmented chemically.
The fragmented mRNA underwent double-stranded cDNA synthesis, end repair, 3’-end adenylation and sequencing adapter ligation, followed by DNA purification with magnetic beads and PCR amplification.
The PCR products were purified using the AMPure XP system, and the quality of the libraries was assessed using the Agilent Bioanalyser 2100 system.
The libraries were sequenced using the Illumina NovaSeq platform, resulting in the generation of 150-bp paired-end reads.
Each sample achieved a sequencing depth of 8 gigabase pairs (Gbp).
Raw data in Fastq format was first processed through custom Perl scripts. In this step, clean data were obtained by eliminating reads containing adapters, poly-N sequences and low-quality reads from raw dataset.
Assembly: UCSC cDNA transcripts (mouse assembly mm10)
Supplementary files format and content: zip files include TPM values for each example

source_name: maxillae bone

extract_protocol:
TRIzol reagent (catalog number 10296010, Invitrogen) was utilized for RNA extraction from each sample in accordance with the manufacturer’ s instructions. The RNA purity was evaluated using a NanoPhotometer® spectrophotometer (IMPLEN) by measuring the absorbance ratio at 260/280nm and 260/230nm with acceptable values being greater than 1.8 and 2.0, respectively. RNA integrity was determined using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies), selecting samples with an RNA integrity number (RIN) exceeding 7 for subsequent library construction.
RNA sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB), following the manufacturer’ s guidelines.

treatment_protocol: A NiTi closed-coil spring was attached between the upper left first molar and the upper incisors, exerting a force of approximately 30g to induce the mesial movement of the first molar over periods of 7 days and 14 days. The upper right first molar was utilized as a control in this study.

value: maxillae bone

tag: Sex

value: female

tag: age

value: 6 months

value: orthodontic tooth movement

tag: time

value: 14 days


title: maxillae bone, adult, Day14, rep1

description: Library name: Sample16


title: maxillae bone, adult, Day7, rep2

description: Library name: Sample14

value: 7 days


title: maxillae bone, adult, Day7, rep3

description: Library name: Sample15


title: maxillae bone, adult, Day7, rep1

description: Library name: Sample13


title: 092523-3C-Sept-Obese_S21

description: Library name: 092523-3C-Sept-Obese_S21

value: High Fat Diet


title: 092523-1B-August-Ctrl_S5

description: Library name: 092523-1B-August-Ctrl_S5


title: 092523-4B-Sept-Obese-Estrogen_S23

description: Library name: 092523-4B-Sept-Obese-Estrogen_S23


title: 092523-4A-Sept-Obese-Estrogen_S22

description: Library name: 092523-4A-Sept-Obese-Estrogen_S22


title: 092523-3A-Sept-Obese_S19

description: Library name: 092523-3A-Sept-Obese_S19


title: 092523-3B-Sept-Obese_S20

description: Library name: 092523-3B-Sept-Obese_S20


title: 092523-3A-August-Estrogen_S3

description: Library name: 092523-3A-August-Estrogen_S3


title: 092523-1C-August-Ctrl_S9

description: Library name: 092523-1C-August-Ctrl_S9


title: 092523-2B-Sept-Lean-Estrogen_S17

description: Library name: 092523-2B-Sept-Lean-Estrogen_S17

value: normal chow diet + 17 b Estradiol


title: maxillae bone, adult, control, rep2

description: Library name: Sample11


title: maxillae bone, adult, Day14, rep2

description: Library name: Sample17


title: 092523-2C-Sept-Lean-Estrogen_S18

description: Library name: 092523-2C-Sept-Lean-Estrogen_S18


title: maxillae bone, young, Day14, rep3

description: Library name: Sample9

value: 6 weeks


title: 092523-1A-Sept-Lean_S13

description: Library name: 092523-1A-Sept-Lean_S13

value: normal chow diet


title: 092523-1B-Sept-Lean_S14

description: Library name: 092523-1B-Sept-Lean_S14


title: Goblet-Y/T, replicate 3

city: Boston

first: Xaralabos

last: Varelas

state: MA

address: 72 E. Concord St

department: Department of Biochemistry and Cell biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: 10x Genomics

data_processing:
Samples were processed using the standard CellRanger pipeline
Reads were mapped to mm10
The data is processed using 10X Genomics’ Cell Ranger pipeline
QC was done using SingleCellTK package (version 2.7.1)
Downstream analysis and additional QC and filtering were done on Seurat (version 5.0.1)
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Lung

extract_protocol:
Lung tissues were harvested from mice and incubated with digestion media (RPMI, 2mg/ml collagenase A, and 0.1mg/ml DNaseI) at 37°C for 20 minutes on a rocker. The resulted single cell suspension was filtered through a 70um filter, then subsequently incubated with ACK lysis buffer for 3 minutes. Cells were stained with viability dye and were resuspend in FACS staining buffer (PBS, 2% FBS, 0.1% sodium azide). Cells were then stained with conjugated anti-CD45 and antiEpcam antibody for 30 minutes at 4°C. Cells then were sorted to live CD45+/Epcam- populations. For each sample, 10,000 cells were collected for scRNA-seq.
Libraries were generated with Chromium Single Cell 3' Reagent Kits.

treatment_protocol: Mice were administered tamoxifen (75 mg/kg) via intraperitoneal injection for five consecutive days. Lung tissues were harvested seven days after the final tamoxifen dose.

value: Lung

value: Tamoxifen


title: maxillae bone, young, Day14, rep1

description: Library name: Sample7


title: Ctrl, replicate 2

description: 10x Genomics


title: Ctrl, replicate 3

description: 10x Genomics


title: maxillae bone, young, Day14, rep2

description: Library name: Sample8


title: 092523-1C-Sept-Lean_S15

description: Library name: 092523-1C-Sept-Lean_S15


title: Ctrl, replicate 1

description: 10x Genomics


title: Goblet-Y/T, replicate 1

description: 10x Genomics


title: maxillae bone, adult, control, rep1

description: Library name: Sample10


title: Goblet-Y/T, replicate 2

description: 10x Genomics


title: maxillae bone, young, Day7, rep3

description: Library name: Sample6


title: Primary hepatocyte, day 5, exoWNT3A/RSPO1 treatment, rep1

city: Guangzhou

first: Shixiang

middle: Clover

last: Wang

state: Guangdong

address: Guanzhou street

institute: Guangzhou national labratory

description:
Library name: Sample 29
PHH_WR_5d_rep1
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low- quality sequence, then mapped to reference genome using Hisat2(v2.0.5). For HE cells, human hepatic organoids and primary hepatocytes, reads were aligned against the GRCH38 human reference genome, while for mouse livers, reads were aligned against the mm10 mouse reference genome. Reads numbers mapped to each gene was calculated using featureCounts (v1.5.0-p3).
Assembly: For HE cells, human hepatic organoids and primary hepatocytes, reads were aligned against the GRCH38 human reference genome, while for mouse livers, reads were aligned against the mm10 mouse reference genome.
Supplementary files format and content: CSV files containing raw read count values (integer counts) for each gene across all samples. Each file includes a header row with sample identifiers and the first column listing gene IDs or gene symbols.

source_name: liver

extract_protocol:
Treated cell lines, organoids and mice livers were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: Primary hepatocyte

value: WT


title: Primary hepatocyte, day 5, exoWT treatment, rep2

description:
Library name: Sample 28
PHH_WT_5d_2
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv


title: maxillae bone, young, Day7, rep1

description: Library name: Sample4


title: Primary hepatocyte, day 5, exoWNT3A/RSPO1 treatment, rep2

description:
Library name: Sample 30
PHH_WR_5d_rep2
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv


title: Primary hepatocyte, day 5, exoWT treatment, rep1

description:
Library name: Sample 27
PHH_WT_5d_1
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv


title: maxillae bone, adult, control, rep3

description: Library name: Sample12


title: 092523-2A-Sept-Lean-Estrogen_S16

description: Library name: 092523-2A-Sept-Lean-Estrogen_S16

value: Liver


title: maxillae bone, young, control, rep3

description: Library name: Sample3


title: Primary hepatocyte, day 1, exoWNT3A/RSPO1 treatment, rep1

description:
Library name: Sample 25
PHH_WR_1d_rep1
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv


title: Primary hepatocyte, day 1, exoWNT3A/RSPO1 treatment, rep2

description:
Library name: Sample 26
PHH_WR_1d_rep2
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv


title: Primary hepatocyte, day 1, exoWT treatment, rep2

description:
Library name: Sample 24
PHH_WT_1d_2
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv


title: maxillae bone, young, control, rep2

description: Library name: Sample2


title: Hepatic organoid, day 14, Chir99021 treatment, rep2

description:
Library name: Sample 22
HO_CHIR_rep2
raw_count_HO_Chir_vs_WR.csv

value: Patient-derived hepatic organoid


title: maxillae bone, young, control, rep1

description: Library name: Sample1

value: maxillae bone


title: Hepatic organoid, day 14, Chir99021 treatment, rep1

description:
Library name: Sample 21
HO_CHIR_rep1
raw_count_HO_Chir_vs_WR.csv


title: Hepatic organoid, day 14, exoWNT3A/RSPO1 treatment, rep1

description:
Library name: Sample 19
HO_WR_rep1
raw_count_HO_Chir_vs_WR.csv


title: Hepatic organoid, day 14, exoWT treatment, rep2

description:
Library name: Sample 18
HO_WT_rep2
raw_count_HO_Chir_vs_WR.csv


title: mESC,H2AZ1KIflag,3

city: Richmond

first: Xiangyu

last: Shen

state: Virginia

address: 101N 5th street ,Apt1513,Richmond,VA2321, 1513

institute: Henan University

description: Library name: H2AZ1_rep3

data_processing:
Raw sequencing data were uploaded. Processed data include bigwig of H2AZ1 CUT&Tag and Ring1B CUT&Tag
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data include bigwig of H2AZ1 CUT&Tag and Ring1B CUT&Tag
Library strategy: CUT&Tag

growth_protocol: Mouse ESC lines were maintained in ESC medium, which consists of DMEM supplemented with 50 U/ml penicillin-streptomycin, 15% defined murine ESC FBS (R&D System, S10250), 1% GlutaMax (Gibco, 35050-061), 1 X non-essential amino acids (Corning, NY, MT-25-025-CI), 1 X nucleoside (Millipore, ES-008-D), 0.007% β-mercaptoethanol (Sigma, M3148), and 1,000 U/ml mLIF (Millipore, ESGRO) at 37oC in a humidified incubator with 5% CO2. ESCs were culture on 0.1% gelatin-coated plates or irradiated mouse embryonic fibroblasts (Fisherbrand, A34181)

extract_protocol:
Cells were washed with PBS and permeabilized using the reagents provided in the Vazyme CUT&Tag Assay Kit (Cat# TD904), following the manufacturer’s protocol. Primary antibody was incubated with the cells overnight at 4°C. After washing, cells were incubated with the secondary antibody according to the kit instructions.
Following tagmentation using the Vazyme CUT&Tag Assay Kit (Cat# TD904), DNA was purified and used for library construction with the Vazyme VAHTS Universal DNA Library Prep Kit for Illumina (Cat# TD202), according to the manufacturer’s protocol. Libraries were PCR-amplified with indexed primers, size-selected, and sequenced on an Illumina platform.

treatment_protocol: Cells were transfected with siRNA targeting H2AZ1, H2AZ2, or non-targeting control siRNA. After 48 hours, cells were harvested for CUT&Tag.

value: mESC


title: Hepatic endoderm, differentitated, day 7, exoWNT3A/RSPO1 treatment, rep2

description:
Library name: Sample 16
HE_differentiated_exoWR_rep2
raw_count_HE_Chir_vs_WR_vs_W+R.csv

source_name: bone marrow

value: bone marrow

value: iPSC12-derived hepatic endoderm


title: Hepatic organoid, day 14, exoWT treatment, rep1

description:
Library name: Sample 17
HO_WT_rep1
raw_count_HO_Chir_vs_WR.csv


title: mESC,H2AZ1KIflag,2

description: Library name: H2AZ1_rep2


title: mESC, H2AZ1KIflag,1

description: Library name: H2AZ1_rep1


title: Hepatic endoderm, differentitated, day 7, Chir99021 treatment, rep2

description:
Library name: Sample 14
HE_differentiated_Chir_rep2
raw_count_HE_Chir_vs_WR_vs_W+R.csv


title: N129_CD11b_BMT

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

description: Library name: XY04

data_processing:
Adapter and quality read trimming was performed using Skewer (version 0.2.1) and alignments were performed using Star Aligner (v2.7.3a) against the murine primary assembly transcriptome (GRCm39 v110). Counts tables were then generated using featureCounts (subread v1.6.2).
For only the stroma samples, since these libraries were run twice (technical replicates), the total counts from the two runs were combined for the raw counts table.
CD11b samples were from WT control and BMT recipients that were 52 weeks post transplantation.  Cells were isolated from cells there were both CD45.1+ and CD11b+.
TPM File was generated using RSEM (1.3.3) with aligned bam files. For Stroma samples the average TPM between the two runs was included in the txt table.
Assembly: GRCm39 v110
Supplementary files format and content: tab-delimited text file includes raw counts
Supplementary files format and content: tab-delimited text file includes transcripts per million (TPM)

source_name: Bone Marrow

extract_protocol:
RNA was isolated using guanidinium thiocyanate-phenol-chloroform extraction (TRIzol®) from sorted BM samples. Due to the low numbers of cells isolated from the sorted bone marrow stroma RNA, samples was concentrated using SPRIselect magnetic beads (Beckman Coulter).
For the hematopoietic samples: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. 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 were pooled and sequenced on Illumina NovaSeq6000 at PE150. Each library was sequenced to 6G (20 million paired-end reads).  For the Stromal Samples: Libraries were created using the NEBNext Low Input RNA Library Prep Kit (E6420S, New England Biolabs) and indexed using the NEBNext Multiplex Oligos dual index primers (E6440S, New England Biolabs). Libraries were sequenced at Novogene (Sacramento, CA) using the NovaSeq X system to generate 150bp paired end reads.

treatment_protocol: To isolate bone marrow (BM) from bone marrow transplant (BMT) recipients and donor animals they were euthanized via CO2 administration and secondary cervical dislocation. Bones were isolated, manually cleaned with sterile gauze, and stored in 4C dissection media (phosphate buffered saline without calcium and magnesium (1x PBS, Corning), 0.5% albumin bovine fraction V (BSA, RPI research products international), and 2mM EDTA (Invitrogen)).  Bones included were pelvic (2x), fibula (2x), tibia (2x), femur (1x), humerus (2x), scapula (2x), and sternum (1x).  After extraction of bones from euthanized animals, they were lightly crushed once in a mortar and pestle and collected into 3ml of Liberace TM (0.2 mg/ml), DNase I (200 U/ml, benzonase) and 1x PBS. Bones and cell suspension were then allowed to digest in an incubator at 37°C for 60 min on a tube rotator in a 5mL conical tube. Contents were then poured through a 70µm filter on a 50mL conical tube and washed with additional 45ml dissection media to collect released BM cells and quench the digestion. This was followed by peleting the cells at 485g for 10 minutes at 4C. Supernatant was discarded, and the cell pellet was resuspended into 7mL of  RBC lysis buffer for mouse (Boston BioProducts) and incubated on a tube rotator (Rotator Genie) for 15 minutes at room temperature. RBC lysis was quenched with the addition of 43mL of dissection media, tubes were lightly inverted to mix, and the suspension was spun down again at 485g for 5-10 minutes at 4C. Cells were resuspended into 3ml 1x PBS + 1µL/mL benzonase and counted to determine concentration.  Once cells were counted, they were concentrated into 1mL of 1x PBS where they were stained with zombie violet viability dye for 10 minutes at room temperature in the dark followed by quenching in FACS buffer (0.5% FBS in 1X PBS) and pelleted at 300g at 4C for 5 minutes. Cells were then resuspended into 15ml conical tubes at concentrations of 2.0x10^6 cells/100µL and blocked with Rat anti-mouse CD16/CD32 (Fc Block, BD Biosciences) for 10 minutes at room temperature in the dark on a tube revolver (FisherBrand). The samples were then diluted with an antibody cocktail to a concentration of 1.0x10^6 cells/100µL. This cocktail contained anti-CD45.1 (A20)-FITC (BioLegend), and anti-CD45.2 (104)-APC (BioLegend) along with biotinylated lineage markers: anti-B220 (RA3-6B2, BioLegend), CD4, (GK1.5, BioLegend), CD8 (53-6.7, BioLegend), NK1.1 (PK136, BioLegend), Ly-6G/Ly-6C (RB6-8C5, BioLegend), TER119 (BioLegend), and CD11b (M1/70, BioLegend).  Cell suspension was allowed to incubate on a tube revolver in the dark at room temperature for 30 minutes. Cells were then spun down (300g for 5min) and washed. Cells were spun down again and resuspended at 1.0x10^6 cells/100µL of FACs buffer with PE streptavidin (BD Biosciences) and allowed to incubate at room temperature on a rotator in the dark for 15 minutes. Cells were again spun down, washed, and resuspended into FACs buffer for sorting. Matched unstained BM was also kept aside to be run alongside the stained BM during sorting. Stained BM was then put through FACs tube 35µm strainer caps (Alkali Scientific) just prior to cell sorting. All sorted cells were collected into collection media. The workflow for sorting the BM proceeded as follows. To isolate hematopoietic BM, live singlets were sorted using gates that isolated CD45.2 donor-derived (FITC-positive/APC-negative) or CD45.1 recipient-derived (FITC-negative/APC-positive) BM. Concurrently, CD45.1/CD45.2 double negative cells were gated to observe the PE-stained combined lineage makers. A sorting gate was then used to collect the lineage-negative stromal-enriched cells. While performing the sorting only two populations were being isolated at a time to reduce the chance of contamination by positioning the collection tubes on either side of the sorting stream. The stromal isolation tube was always present during the sorting on one side since the frequency was always very low, while the other side would be used for the hematopoietic donor- or recipient-derived collection tubes. Starting with the recipient-derived material we would sort until 5.0x106 cells were collected before pausing the sorting and switching out collection tubes to collect 4.0-5.0x106 donor-derived cells. Wild-type no-BMT cells were sorted with the same gating paradigm but no CD45.2 cells were collected. Once isolated, cells were pelleted down (300g for 10 minutes) and resuspended into 1mL of TRIZOL and stored at -80C until RNA isolation.

value: Bone Marrow

value: MALE

tag: animal id

tag: source

value: Recipient-Derived Cells CD45.1+/CD11b+

value: Bone Marrow Transplant

tag: euthansia date


title: Hepatic endoderm, differentitated, day 7, exoWNT3A/RSPO1 treatment, rep1

description:
Library name: Sample 15
HE_differentiated_exoWR_rep1
raw_count_HE_Chir_vs_WR_vs_W+R.csv


title: maxillae bone, young, Day7, rep2

description: Library name: Sample5

value: female

value: 6 weeks

value: orthodontic tooth movement

value: 7 days


title: N128_CD11b_Control

description: Library name: XY03

value: Wild-type Control Cells CD45.1+/CD11b+

value: Wild-Type Control


title: Hepatic endoderm, differentitated, day 7, exoWNT3WLS+exoRSPO1 treatment, rep2

description:
Library name: Sample 10
HE_differentiated_exoWNT3+exoRSPO1_rep2
raw_count_HE_WNTs.csv

value: WT


title: Hepatic endoderm, differentitated, day 7, exoWNT3AWLS+exoRSPO1 treatment, rep1

description:
Library name: Sample 11
HE_differentiated_exoWNT3A+exoRSPO1_rep1
raw_count_HE_WNTs.csv


title: Hepatic endoderm, differentitated, day 7, exoWNT3WLS+exoRSPO1 treatment, rep1

description:
Library name: Sample 9
HE_differentiated_exoWNT3+exoRSPO1_rep1
raw_count_HE_WNTs.csv


title: Hepatic endoderm, differentitated, day 7, exoWNT3AWLS+exoRSPO1 treatment, rep2

description:
Library name: Sample 12
HE_differentiated_exoWNT3A+exoRSPO1_rep2
raw_count_HE_WNTs.csv


title: Hepatic endoderm, differentitated, day 7, Chir99021 treatment, rep1

description:
Library name: Sample 13
HE_differentiated_Chir_rep1
raw_count_HE_Chir_vs_WR_vs_W+R.csv


title: Hepatic endoderm, differentitated, day 7, exoRSPO1WLS treatment, rep2

description:
Library name: Sample 8
HE_differentiated_exoRSPO1_rep2
raw_count_HE_WNTs.csv


title: N116_CD11b_BMT

description: Library name: XY02


title: N112_CD11b_Control

description: Library name: XY01


title: Primary hepatocyte, day 1, exoWT treatment, rep1

description:
Library name: Sample 23
PHH_WT_1d_1
raw_count_PHH_WR_vs_WT_day 1 and day 5.csv

value: liver

value: Primary hepatocyte


title: Hepatic endoderm, differentitated, day 7, exoRSPO1WLS treatment, rep1

description:
Library name: Sample 7
HE_differentiated_exoRSPO1_rep1
raw_count_HE_WNTs.csv


title: Hepatic endoderm, differentitated, day 7, exoWNT3AWLS treatment, rep2

description:
Library name: Sample 6
HE_differentiated_exoWNT3A_rep2
raw_count_HE_WNTs.csv


title: N187_CD11b_BMT

description: Library name: XY08


title: Hepatic endoderm, differentitated, day 7, exoWNT3AWLS treatment, rep1

description:
Library name: Sample 5
HE_differentiated_exoWNT3A_rep1
raw_count_HE_WNTs.csv


title: Hepatic endoderm, differentitated, day 7, exoWNT3WLS treatment, rep2

description:
Library name: Sample 4
HE_differentiated_exoWNT3_rep2
raw_count_HE_WNTs.csv


title: N168_CD11b_Control

description: Library name: XY07


title: Hepatic organoid, day 14, exoWNT3A/RSPO1 treatment, rep2

description:
Library name: Sample 20
HO_WR_rep2
raw_count_HO_Chir_vs_WR.csv

value: Patient-derived hepatic organoid


title: Hepatic endoderm, differentitated, day 7, exoWT treatment, rep2

description:
Library name: Sample 2
HE_differentiated_exoWT_rep2
raw_count_HE_WNTs.csv


title: Hepatic endoderm, differentitated, day 7, exoWNT3WLS treatment, rep1

description:
Library name: Sample 3
HE_differentiated_exoWNT3_rep1
raw_count_HE_WNTs.csv


title: E53 human metatarsal, digit 5, rep 4

city: Cambridge

first: Terence

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

description: Library name: FM5_early_rep4

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3
Alignment to hg38 with Bowtie2 v2.3.4.1
duplicate removal with picard v2.9.0
mitochondrial read filtering with removeChrom.py
peak calling with MACS2 v2.1.1.2 -f bampe --nolambda –bdg --verbose
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Assembly: hg38
Supplementary files format and content: bed format; contains the coordinates of the peaks called

source_name: Metatarsal, digit V

growth_protocol: in vivo collected human autopod chondrocytes from E53-E74

extract_protocol:
Embryonic tissue was microdissected under a light microscope in 5% fetal bovine serum in Dulbecco’s Modified Eagle Medium (DMEM) on ice. The pooled phalanges (proximal and distal for digit I; proximal, intermediate, and distal for digits II-V) and metapodials were collected separately for all digits in both the fore- and hind limbs. The right and left sides of each element were pooled together. ATAC-seq protocol was performed as described in Young et al., 2022. After ATAC-seq, samples were then sent out for 1-2 rounds of sequencing on an Illumina NovaSeq 6000 at the Harvard Bauer Core in order to obtain at least 40 million reads per sample.
ATAC-seq protocol was performed as described in Young et al., 2022.

treatment_protocol: Human products of conception were collected from late first-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: Metatarsal, digit V

value: chondrocytes

value: Male


title: E53 human metatarsal, digit 4, rep 4

description: Library name: FM4_early_rep4

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: ADT expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well4

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

description:
Library name: Well 4_PB.FB
ADT expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well4

data_processing:
All raw input data were distributed across 4 wells, meaning each well contained a portion of the sequencing data for all samples. The Cell Ranger pipeline (version 7.2.0) from 10x Genomics was used to process the raw sequencing data, including quality filtering, alignment to the human reference genome (GRCh38), cell barcode assignment, and generation of unique molecular identifier (UMI) counts to produce the gene expression matrix. Data from all wells were then aggregated to generate a unified H5 gene expression file for each individual sample. The generated H5 files were uploaded to the Partek Flow (Illumina) cloud platform for single-cell analysis.
Assembly: hg38
Supplementary files format and content: h5 files includes gene expression

source_name: CD34 cell

growth_protocol: Human G-CSF–Mobilized HSC Isolation Leukopaks from four G-CSF–mobilized healthy adult donors (two female, two male) were obtained from BIOIVT. Each sample was diluted 1:6 in FACS buffer containing 2% fetal bovine serum (FBS) and 1 mM EDTA, then layered over Lymphoprep™ density gradient medium (StemCell Technologies) and centrifuged at 800 × g for 30 min. The mononuclear cell (MNC) fraction was collected and processed for CD34⁺ hematopoietic stem cell (HSC) isolation using the EasySep™ Human CD34 Positive Selection Kit II (StemCell Technologies). Purity was assessed by flow cytometry with anti-CD34 antibody (clone 561), targeting ≥80% CD34⁺ cells with ≥90% viability. Pre-isolation CD34⁺ frequency was approximately 2%, and the final enriched fraction exceeded 80% CD34⁺ with 95% viability, yielding ~45% recovery.  Bone Marrow–Derived HSC Isolation Fresh human whole bone marrow aspirates (100 mL; StemCell Technologies) were processed in parallel. Samples were diluted 1:6 in FACS buffer (2% FBS, 1 mM EDTA), followed by MNC separation via Lymphoprep™ density gradient centrifugation. CD34⁺ HSCs were then isolated using the EasySep™ Human CD34 Positive Selection Kit II. Final preparations contained >80% CD34⁺ cells with 95% viability, meeting our quality control criteria.

extract_protocol:
After incubation with exosomes, cells were harvested, washed, and stained with the TotalSeq™-C anti-human Hashtag antibodies (BioLegend), following the manufacturer’s recommended titration and staining protocol.The isolated RNA, was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).
For single cell RNA-seq, following staining, cells were counted and loaded onto the Chromium X system (10x Genomics) using the Chromium Single Cell 5′ High Throughput (HT) Immune Profiling Kit. Single-cell Gel Bead-In-Emulsions (GEMs) were generated, and barcoded cDNA libraries, including gene expression and antibody-derived tag (ADT) libraries, were constructed according to the manufacturer’s instructions. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform using an S4 flow cell to a targeted depth of ~50,000 reads per cell.

treatment_protocol: Bone marrow–derived and mobilized peripheral blood (mPB) CD34⁺ hematopoietic stem cells (HSCs) were incubated with lung-derived exosomes for 48 hours. Following treatment, cells were washed and stained with a TotalSeq™-C antibody panel (BioLegend) targeting CD34, CD38, CD90, CD45RA, and CD49f, along with TotalSeq™-C hashtag antibodies for sample multiplexing. Antibody amounts were used according to the manufacturer’s recommended titrations. After labeling, the cells were loaded onto the 10x Genomics Chromium platform using the 5′ High-Throughput (HT) Immune Profiling Kit for downstream single-cell library preparation.

value: CD34 cell


title: ADT expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well1

description:
Library name: Well 1_PB.FB
ADT expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well1


title: ADT expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well2

description:
Library name: Well 2_PB.FB
ADT expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well2


title: Gene expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well2

description:
Library name: Well 2_PB.gex
Gene expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well2


title: Gene expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well4

description:
Library name: Well 4_PB.gex
Gene expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well4


title: E53 human metatarsal, digit 2, rep 4

description: Library name: FM2_early_rep4

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E53 human metatarsal, digit 3, rep 4

description: Library name: FM3_early_rep4

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: Liver of Acetaminophen vehicle treated mice at 6h of ALF induction biol rep2

city: Derqui

first: Juan

last: Bayo

state: Buenos Aires

address: Av Peron 1500

department: IIMT

country: Argentina

institute: Universidad Austral-Conciet

description:
Library name: APAP vehicle biol rep2
Column name in count_matrix_APAP.txt : AD3

data_processing:
RNA-seq reads were mapped to mouse genome version GRCm39 and aligned using St. Jude Cloud RNAseq Standard v2 pipeline (https://github.com/stjudecloud/workflows).
Assembly: GRCm39
Supplementary files format and content: tab-delimeted file includes raw counts for each sample

growth_protocol: C57BL/6J mice (six-to-eight weeks old), purchased from the Instituto de Medicina Experimental (Consejo Nacional de Investigaciones Científicas y Técnicas - Academia Nacional de Medicina, Argentina). Animals were maintained at our Animal Resources Facilities in accordance with institutional guidelines and conformed to requirement of the state authority for animal research conduct.

extract_protocol:
RNA was extracted with TRIzol method.
TruSeq stranded mRNA library method

treatment_protocol: Concanavalin-A ALF model: Mice were fasted overnight and treated with Con-A [30 mg/kg] (Sigma-Aldrich) diluted in saline solution (0.9% NaCl) by a single tail vein injection. Treatment with 1D-142 [10 mg/ kg] was given intraperitoneally (i.p.) 30 min after Con-A injection, and mice were euthanized 3 hours after acute liver failure induction. Acetaminophen ALF model : APAP (Sigma-Aldrich) was dissolved in 70 °C warm PBS, incubated in a water bath at 60 °C for 30 min and i.p. injected at 55 °C into overnight fasted mice (600 mg/kg). One hour after APAP administration, a group of mice received 1D-142 [10 mg/kg] or vehicle i.p. All animals were euthanized 3 hours after acute liver failure induction.

value: Liver

value: To induce acute liver failure mice were fasted for 16 hours, followed by intraperitoneal administration of acetaminophen  (600 mg/kg).

value: Vehicle (12.5% DMSO, 12.5% Cremophor, 75% H₂O) was administered intraperitoneally 60 minutes after acetaminophen injection.


title: Liver of Acetaminophen 1D-142 treated mice at 6h of ALF induction  biol rep1

description:
Library name: APAP 1D-142 biol rep1
Column name in count_matrix_APAP.txt : AR3

value: 1D-142 (10 mg /kg) disolved in vehicle (12.5% DMSO, 12.5% Cremophor, 75% H₂O) was administered intraperitoneally 60 minutes after acetaminophen injection.

value: 3 hours after acute liver failure induction


title: Liver of Acetaminophen 1D-142 treated mice at 6h of ALF induction  biol rep2

description:
Library name: APAP 1D-142 biol rep2
Column name in count_matrix_APAP.txt : AR4


title: Liver of Acetaminophen 1D-142 treated mice at 6h of ALF induction  biol rep3

description:
Library name: APAP 1D-142 biol rep3
Column name in count_matrix_APAP.txt : AR5


title: Liver of Acetaminophen vehicle treated mice at 6h of ALF induction biol rep1

description:
Library name: APAP vehicle biol rep1
Column name in count_matrix_APAP.txt : AD1


title: ADT expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well3

description:
Library name: Well 3_BM.FB
ADT expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well3


title: ADT expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well4

description:
Library name: Well 4_BM.FB
ADT expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well4


title: E53 human metatarsal, digit 1, rep 4

description: Library name: FM1_early_rep4

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: Liver of Concanavalin A 1D-142 treated mice at 6h of ALF induction  biol rep3

description:
Library name: ConA 1D-142 biol rep3
Column name in count_matrix_CONA.txt : CR6

value: To induce acute liver failure mice were fasted for 16 hours, followed by intravenous administration of concanavalin A (30 mg/kg).

value: 1D-142 (10 mg /kg) disolved in vehicle (12.5% DMSO, 12.5% Cremophor, 75% H₂O) was administered intraperitoneally 30 minutes after concanavalin A injection.


title: E53 human foot phalanges, digit 5, rep 4

description: Library name: FP5_early_rep4

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: ADT expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well1

description:
Library name: Well 1_BM.FB
ADT expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well1


title: ADT expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well2

description:
Library name: Well 2_BM.FB
ADT expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well2


title: Hepatic endoderm, differentitated, day 7, exoWT treatment, rep1

description:
Library name: Sample 1
HE_differentiated_exoWT_rep1
raw_count_HE_WNTs.csv

value: bone marrow

value: iPSC12-derived hepatic endoderm

value: WT


title: Liver of Concanavalin A 1D-142 treated mice at 6h of ALF induction  biol rep2

description:
Library name: ConA 1D-142 biol rep2
Column name in count_matrix_CONA.txt : CR5

value: Male


title: Gene expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well4

description:
Library name: Well 4_BM.gex
Gene expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well4


title: ADT expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well3

description:
Library name: Well 3_PB.FB
ADT expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well3


title: Gene expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well3

description:
Library name: Well 3_BM.gex
Gene expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well3


title: Liver of Acetaminophen vehicle treated mice at 6h of ALF induction biol rep3

description:
Library name: APAP vehicle biol rep3
Column name in count_matrix_APAP.txt : AD4


title: Gene expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well3

description:
Library name: Well 3_PB.gex
Gene expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well3


title: Gene expression of CD34 PB cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well1

description:
Library name: Well 1_PB.gex
Gene expression of CD34 cells  extracted from Peripheral Blood samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Peripheral Blood CD34 cells sample, Well1


title: Gene expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well2

description:
Library name: Well 2_BM.gex
Gene expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well2


title: E53 human foot phalanges, digit 3, rep 4

description: Library name: FP3_early_rep4

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III

value: chondrocytes


title: Gene expression of CD34 BM cells samples treated by cancers and primary tissue exosomes and one untreated sample, Well1

description:
Library name: Well 1_BM.gex
Gene expression of CD34 cells  extracted from Bone Marrow samples treated by exosomes extracted from different cancers cell-lines, three different primary tissues and one untreated Bone Marrow CD34 cells sample, Well1

value: CD34 cell


title: 19009 CD82+/ERBB3+/NGFR+ cells cultured in NGF

city: Minneapolis

first: Elise

last: Engquist

state: MN

address: 2231 6th St SE

department: Lillehei Heart Institute and Department of Pediatrics

institute: University of Minnesota

description: Library name: 19009NP4

data_processing:
Raw reads were trimmed with Trim Galore (v0.6.10) using Cutadapt (v5.0) to remove Illumina Sequencing adapters (AGATCGGAAGAGC) from the 3’ end. An additional 15 bases were trimmed from the 5’ end of reads due to biased per base sequence content. Human genome sequence GRCh38 (v113) was downloaded from Ensembl, and reads were mapped to the human transcriptome using Salmon (v1.10.3), employing the GC bias correction flag. Transcript-level reads were aggregated to the gene-level in R using the tximeta package (v1.22.1).
Assembly: GRCh38
Supplementary files format and content: 19009_rawcounts.csv file contains raw counts for each sample.
Supplementary files format and content: 19009_deseq2counts.csv contains DESeq2 normalized counts for each sample.

source_name: 19-009 (human iPSC)

extract_protocol:
RNA was extracted using Zymo Quick-RNA Miniprep kit per manufacturer instructions.
Library preparation was performed by Azenta.

value: 19-009 (human iPSC)

value: teratoma-derived myogenic progenitors

value: NGF


title: Liver of Concanavalin A vehicle treated mice at 6h of ALF induction biol rep3

description:
Library name: ConA vehicle biol rep3
Column name in count_matrix_CONA.txt : CD5

value: Liver

value: Vehicle (12.5% DMSO, 12.5% Cremophor, 75% H₂O) was administered intraperitoneally 30 minutes after concanavalin A injection.


title: 19009 CD82+/ERBB3+/NGFR+ cells cultured in EGF

description: Library name: 19009EP4

value: EGF


title: E53 human foot phalanges, digit 2, rep 4

description: Library name: FP2_early_rep4

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: 19009 CD82+/ERBB3+/NGFR+ cells cultured in all 3 GFs (bFGF+EGF+NGF)

description: Library name: 19009AP4

value: bFGF + EGF + NGF


title: Liver of Concanavalin A vehicle treated mice at 6h of ALF induction biol rep1

description:
Library name: ConA vehicle biol rep1
Column name in count_matrix_CONA.txt : CD3

value: To induce acute liver failure mice were fasted for 16 hours, followed by intravenous administration of concanavalin A (30 mg/kg).

value: 3 hours after acute liver failure induction


title: Liver of Concanavalin A vehicle treated mice at 6h of ALF induction biol rep2

description:
Library name: ConA vehicle biol rep2
Column name in count_matrix_CONA.txt : CD4


title: E53 human foot phalanges, digit 1, rep 4

description: Library name: FP1_early_rep4

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: OCI-AML2 sgsc-1

city: Tianjin

first: Tingting

address: Tianjin,Heping district,288 Nanjing road.Institute of Hematology and Blood Diseases Hospital

description: Library name: sgsc-1

data_processing:
Illumina NovaSeq X Plus
Fastp (version 0.23.2) was used to trim sequences.
Reads were aligned to the human reference genome (GRCh38/hg38) using bowtie2 (v2.4.5).
PCR duplicates were removed using sambamba markdup -r (v1.0.1).
Reads with flag 12 (unmapped or secondary) and mapping quality < 10 were filtered using samtools(v1.18).
Final BAM files were converted to bigWig format using bamCoverage (v4.0.5) with --binSize 10 and --normalizeUsing RPKM.
Assembly: GRCh38
Supplementary files format and content: bigwig(.bw) file normalized ATAC-seq signal tracks for visualization.
Supplementary files format and content: BED(.narrowPeak) files:MACS2-called peaks indicating accessible chromatin regions.

growth_protocol: OCI-AML2 Cells were cultured in MEM Alpha medium (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
DNAs were extracted using ATAC DNA Extract Beads.
Nuclei were isolated and transposed using the Hyperactive ATAC-Seq Library Prep Kit for Illumina, following the manufacturer’s instructions. Briefly, nuclei were incubated with Tn5 transposase to simultaneously fragment DNA and add sequencing adapters. Libraries were amplified using PCR and purified for sequencing on the Illumina platform.

treatment_protocol: Control and CHD7-depleted OCI-AML2-Cas9 cells were cultured in MEM Alpha medium (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin. Cells were then collected for DNA extraction.

value: AML

value: wide type


title: E53 human metacarpal, digit 5, rep 4

description: Library name: HM5_early_rep4

source_name: Metacarpal, digit V

value: Metacarpal, digit V

value: Male


title: OCI-AML2 sgCHD7-5-1

institute: Institute of Hematology and Blood Diseases Hospita

description: Library name: sgCHD7-5-1

value: CHD7 knockout


title: E53 human metacarpal, digit 4, rep 4

description: Library name: HM4_early_rep4

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV

value: chondrocytes


title: midbrainOrganoid, PSP, d120, rep3

city: Catanzaro

first: Elvira

middle: Immacolata

last: Parrotta

state: Catanzaro

address: Viale Europa, 1

country: Italy

institute: University Magna Greacia of Catanzaro

description: Library name: PSPd120_3

data_processing:
Raw sequencing data in FASTQ format were processed using custom Perl and Python scripts. Clean reads were obtained by filtering out low-quality sequences, poly-Ns, adapter contaminants, insert tags, and homopolymeric stretches. Quality metrics such as Q20, Q30, and GC content were used to assess data quality.  Clean small RNA tags were aligned to the reference genome using Bowtie, allowing up to one mismatch.
Known miRNAs were identified using miRBase v22.0, while novel miRNAs and secondary structures were predicted with modified mirDeep2 and srna-tools-cli. Custom scripts quantified miRNA expression and assessed nucleotide bias. To exclude non-miRNA sequences, reads were mapped against RepeatMasker, Rfam, and species-specific annotations to remove tags from repeats, rRNAs, tRNAs, snRNAs, snoRNAs, and protein-coding genes.
Assembly: GRCh38
Supplementary files format and content: Raw_counts.tsv first column contains miRNA mature id while the other columns contain sample's raw read counts.
Supplementary files format and content: TPM.tsv first column contains miRNA mature id while the remaining columns contain sample's expression in TPM.

source_name: midbrain organoid

growth_protocol: iPSCs were cultured in 60-mm Matrigel-coated dishes in mTesR+ medium, disloged in Accutase and differentiated in midbrain organoids following the protocol of Sozzi and collegues (Sozzi et al.,Curr Protoc. 2022).

extract_protocol:
Total RNA was extracted from at least 3 organoids for each replicate using TRIzol reagent according to the manufacturer's instruction
Adapters were first ligated to the 3′ and 5′ ends of the small RNA molecules. Following adapter ligation, first-strand complementary DNA (cDNA) synthesis was performed via reverse transcription primer hybridization. The resulting cDNA was then PCR-amplified to generate double-stranded cDNA libraries. Libraries were purified and size-selected to enrich for fragments with insert sizes between 18 and 40 base pairs. Final libraries were prepared for single-end sequencing (SE50, NEBNext® Multiplex Small RNA Library Prep Set for Illumina) with a read length of 50 bases. Library quality and concentration were assessed using a Qubit fluorometer (Thermo Fisher Scientific) and real-time PCR. Fragment size distribution was verified using a Bioanalyzer (Agilent Technologies). Qualified libraries were pooled based on effective concentration and desired sequencing depth, then sequenced on Illumina platforms for downstream analysis.

value: midbrain organoid

value: PSP-RS

value: 120 days


title: Wild-type (biol rep 3)

city: Shanghai

first: Yueqi

address: 150 Jimo Road, Pudong New Area,Shanghai

institute: Shanghai East Hospital, School of Medicine, Tongji University

description: Library name: WT3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. The clean  reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Cartilage

extract_protocol:
Total RNA from WT and Apoe-KO chondrocyteswas extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Cartilage

value: Wild-type


title: Wild-type (biol rep 2)

description: Library name: WT2


title: midbrainOrganoid, PSP, d120, rep1

description: Library name: PSPd120_1


title: E53 human metacarpal, digit 3, rep 4

description: Library name: HM3_early_rep4

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E53 human foot phalanges, digit 4, rep 4

description: Library name: FP4_early_rep4

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: midbrainOrganoid, PSP, d90, rep3

description: Library name: PSPd90_3

value: 90 days


title: OCI-AML2 sgCHD7-2-3

description: Library name: sgCHD7-2-3


title: Liver of Concanavalin A 1D-142 treated mice at 6h of ALF induction  biol rep1

description:
Library name: ConA 1D-142 biol rep1
Column name in count_matrix_CONA.txt : CR3

source_name: Liver

value: Liver

value: To induce acute liver failure mice were fasted for 16 hours, followed by intravenous administration of concanavalin A (30 mg/kg).

value: 1D-142 (10 mg /kg) disolved in vehicle (12.5% DMSO, 12.5% Cremophor, 75% H₂O) was administered intraperitoneally 30 minutes after concanavalin A injection.

value: 3 hours after acute liver failure induction


title: Wild-type (biol rep 1)

description: Library name: WT1


title: midbrainOrganoid, PSP, d90, rep2

description: Library name: PSPd90_2


title: midbrainOrganoid, PSP, d120, rep2

description: Library name: PSPd120_2


title: E53 human metacarpal, digit 2, rep 4

description: Library name: HM2_early_rep4

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: midbrainOrganoid, PSP, d90, rep1

description: Library name: PSPd90_1


title: Apoe-KO (biol rep 3)

description: Library name: KO3

value: Apoe-KO


title: Apoe-KO (biol rep 2)

description: Library name: KO2


title: E53 human hand phalanges, digit 5, rep 4

description: Library name: HP5_early_rep4

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V

value: Male


title: Apoe-KO (biol rep 1)

description: Library name: KO1

value: chondrocytes


title: midbrainOrganoid, PD, d120, rep2

description: Library name: PDd120_2

value: midbrain organoid

value: PD


title: midbrainOrganoid, PSP, d60, rep3

description: Library name: PSPd60_3

value: PSP-RS

value: 60 days


title: 19009 CD82+/ERBB3+/NGFR+ cells cultured in bFGF

description: Library name: 19009BP4

value: 19-009 (human iPSC)

value: teratoma-derived myogenic progenitors

value: bFGF


title: midbrainOrganoid, PD, d90, rep3

description: Library name: PDd90_3

value: 90 days


title: midbrainOrganoid, PD, d120, rep3

description: Library name: PDd120_3

value: 120 days


title: midbrainOrganoid, PSP, d60, rep1

description: Library name: PSPd60_1


title: E53 human hand phalanges, digit 4, rep 4

description: Library name: HP4_early_rep4

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: midbrainOrganoid, PD, d120, rep1

description: Library name: PDd120_1


title: LacZ_TGFB_Replicate3

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

description: Library name: LacZ_TGFB_3

data_processing:
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
Assembly: mm10/GRCm38.93
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: cardiac fibroblast

growth_protocol: Isolated cardiac fibroblasts from TAK1fl/fl mice were maintained in DMEM/F12 + 10% fetal bovine serum + 1% insulin transferrin selenium + 20 ng/ml human bFGF + 1% penicillin/streptomycin/amphotericin B. All cells were used for treatment at passage 1

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Micro Kit (74004)
NEBNext Ultra II RNA Library Prep Kit for Illumina was used for library prep

treatment_protocol: Isolated cardiac fibrobalsts from TAK1fl/fl mice were treated with either LacZ or iCre to induce TAK1 knockdown. Then, cells were treated under serum-starved conditions with bFGF (20 ng/ml), TGFb (10ng/ml), TNFa (10ng/ml), or IL-1b (15ng/ml) for 24 h prior to RNA isolation

value: cardiac fibroblast


title: E53 human hand phalanges, digit 3, rep 4

description: Library name: HP3_early_rep4

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: midbrainOrganoid, PD, d90, rep2

description: Library name: PDd90_2


title: midbrainOrganoid, PD, d90, rep1

description: Library name: PDd90_1


title: E53 human hand phalanges, digit 2, rep 4

description: Library name: HP2_early_rep4

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: midbrainOrganoid, PD, d60, rep3

description: Library name: PDd60_3


title: E53 human metacarpal, digit 1, rep 4

description: Library name: HM1_early_rep4

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: LacZ_TGFB_Replicate2

description: Library name: LacZ_TGFB_2


title: E53 human hand phalanges, digit 1, rep 3

description: Library name: HP1_early_rep4

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: LacZ_TGFB_Replicate1

description: Library name: LacZ_TGFB_1


title: midbrainOrganoid, PSP, d60, rep2

description: Library name: PSPd60_2


title: midbrainOrganoid, HC, d120, rep3

description: Library name: HCd120_3

value: HC


title: midbrainOrganoid, PD, d60, rep2

description: Library name: PDd60_2


title: midbrainOrganoid, HC, d120, rep1

description: Library name: HCd120_1


title: E59 human metatarsal, digit 5, rep 3

description: Library name: FM5_early_rep3

source_name: Metatarsal, digit V

value: Metatarsal, digit V

value: chondrocytes

value: Male


title: midbrainOrganoid, PD, d60, rep1

description: Library name: PDd60_1

value: midbrain organoid

value: PD


title: midbrainOrganoid, HC, d120, rep2

description: Library name: HCd120_2


title: LacZ_SS_Replicate4

description: Library name: LacZ_SS_4


title: midbrainOrganoid, HC, d90, rep3

description: Library name: HCd90_3


title: LacZ_TGFB_Replicate4

description: Library name: LacZ_TGFB_4


title: E59 human metatarsal, digit 4, rep 3

description: Library name: FM4_early_rep3

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E59 human metatarsal, digit 3, rep 3

description: Library name: FM3_early_rep3

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: LacZ_SS_Replicate3

description: Library name: LacZ_SS_3


title: midbrainOrganoid, HC, d90, rep1

description: Library name: HCd90_1


title: midbrainOrganoid, HC, d90, rep2

description: Library name: HCd90_2


title: LacZ_SS_Replicate2

description: Library name: LacZ_SS_2


title: midbrainOrganoid, HC, d60, rep3

description: Library name: HCd60_3

value: 60 days


title: LacZ_SS_Replicate1

description: Library name: LacZ_SS_1


title: E59 human metatarsal, digit 1, rep 3

description: Library name: FM1_early_rep3

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: midbrainOrganoid, HC, d60, rep1

description: Library name: HCd60_1

source_name: midbrain organoid


title: OCI-AML2 Venetoclax WT-3

description:
Library name: Vsgsc-3
column name in gene_count_matrix.txt:Vsgsc.3

data_processing:
Illumina NovaSeq X Plus
Fastp (version 0.23.2) was used to trim sequences.
Raw sequencing reads were aligned to the human genome (GRCh38) using Hisat2(version 2.2.1).
Normalized expression levels of genes and transcripts were computed using StringTie (version 2.1.7).
Raw feature counts were normalized and differential expression analysis using DESeq2.
Weighted Gene Co-expression Network Analysis (WGCNA) was performed with the WGCNA package.
Assembly: GRCh38
Supplementary files format and content: gene_count_matrix.txt

extract_protocol:
RNA was extracted from cells using the RNeasy kit (Sparkjade, AC0205-B) following the manufacturer’s instructions.
RNA-seq

treatment_protocol: Control and CHD7-depleted OCI-AML2-Cas9 cells were cultured in MEM Alpha medium (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin, and treated under three different conditions (DMSO, gilteritinib, and venetoclax) for three days. Cells were then collected for RNA extraction.

value: AML

value: CHD7 knockout

value: Venetoclax


title: E59 human metatarsal, digit 2, rep 3

description: Library name: FM2_early_rep3

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: LacZ_ILB_Replicate4

description: Library name: LacZ_ILB_4

value: cardiac fibroblast


title: OCI-AML2 Venetoclax WT-2

description:
Library name: Vsgsc-2
column name in gene_count_matrix.txt:Vsgsc.2


title: E59 human foot phalanges, digit 5, rep 3

description: Library name: FP5_early_rep3

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: LacZ_ILB_Replicate3

description: Library name: LacZ_ILB_3


title: E59 human foot phalanges, digit 4, rep 3

description: Library name: FP4_early_rep3

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: OCI-AML2 Venetoclax sgCHD7-5-2

description:
Library name: VsgCHD7-5-2
column name in gene_count_matrix.txt:VsgCHD7.5.2


title: OCI-AML2 Venetoclax sgCHD7-5-3

description:
Library name: VsgCHD7-5-3
column name in gene_count_matrix.txt:VsgCHD7.5.3


title: OCI-AML2 Venetoclax WT-1

description:
Library name: Vsgsc-1
column name in gene_count_matrix.txt:Vsgsc.1


title: E59 human foot phalanges, digit 3, rep 3

description: Library name: FP3_early_rep3

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: OCI-AML2 Venetoclax sgCHD7-2-3

description:
Library name: VsgCHD7-2-3
column name in gene_count_matrix.txt:VsgCHD7.2.3


title: LacZ_ILB_Replicate2

description: Library name: LacZ_ILB_2


title: OCI-AML2 Venetoclax sgCHD7-2-2

description:
Library name: VsgCHD7-2-2
column name in gene_count_matrix.txt:VsgCHD7.2.2


title: E59 human foot phalanges, digit 2, rep 3

description: Library name: FP2_early_rep3

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: OCI-AML2 Venetoclax sgCHD7-5-1

description:
Library name: VsgCHD7-5-1
column name in gene_count_matrix.txt:VsgCHD7.5.1


title: LacZ_FGF_Replicate4

description: Library name: LacZ_FGF_4


title: OCI-AML2 Venetoclax sgCHD7-2-1

description:
Library name: VsgCHD7-2-1
column name in gene_count_matrix.txt:VsgCHD7.2.1


title: OCI-AML2 Gilteritinib WT-3

description:
Library name: Gsgsc-3
column name in gene_count_matrix.txt:Gsgsc.3

value: Gilteritinib


title: LacZ_ILB_Replicate1

description: Library name: LacZ_ILB_1


title: E59 human foot phalanges, digit 1, rep 3

description: Library name: FP1_early_rep3

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I

value: chondrocytes

value: Male


title: OCI-AML2 Gilteritinib WT-2

description:
Library name: Gsgsc-2
column name in gene_count_matrix.txt:Gsgsc.2


title: LacZ_FGF_Replicate3

description: Library name: LacZ_FGF_3


title: midbrainOrganoid, HC, d60, rep2

description: Library name: HCd60_2

value: midbrain organoid

value: HC


title: E59 human metacarpal, digit 5, rep 3

description: Library name: HM5_early_rep3

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: OCI-AML2 Gilteritinib sgCHD7-5-3

description:
Library name: GsgCHD7-5-3
column name in gene_count_matrix.txt:GsgCHD7.5.3


title: LacZ_FGF_Replicate2

description: Library name: LacZ_FGF_2

source_name: cardiac fibroblast


title: OCI-AML2 Gilteritinib sgCHD7-5-1

description:
Library name: GsgCHD7-5-1
column name in gene_count_matrix.txt:GsgCHD7.5.1


title: OCI-AML2 Gilteritinib sgCHD7-5-2

description:
Library name: GsgCHD7-5-2
column name in gene_count_matrix.txt:GsgCHD7.5.2


title: LacZ_FGF_Replicate1

description: Library name: LacZ_FGF_1


title: E59 human metacarpal, digit 3, rep 3

description: Library name: HM3_early_rep3

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: OCI-AML2 Gilteritinib sgCHD7-2-3

description:
Library name: GsgCHD7-2-3
column name in gene_count_matrix.txt:GsgCHD7.2.3

value: AML


title: OCI-AML2 Gilteritinib sgCHD7-2-2

description:
Library name: GsgCHD7-2-2
column name in gene_count_matrix.txt:GsgCHD7.2.2

value: CHD7 knockout


title: iCre_TGFB_Replicate4

description: Library name: iCre_TGFB_4


title: OCI-AML2 Gilteritinib sgCHD7-2-1

description:
Library name: GsgCHD7-2-1
column name in gene_count_matrix.txt:GsgCHD7.2.1


title: iCre_TGFB_Replicate3

description: Library name: iCre_TGFB_3


title: E59 human metacarpal, digit 2, rep 3

description: Library name: HM2_early_rep3

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: OCI-AML2 DMSO WT-2

description:
Library name: Csgsc-2
column name in gene_count_matrix.txt:Csgsc.2

value: DMSO


title: OCI-AML2 DMSO WT-1

description:
Library name: Csgsc-1
column name in gene_count_matrix.txt:Csgsc.1


title: E59 human metacarpal, digit 1, rep 3

description: Library name: HM1_early_rep3

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: OCI-AML2 DMSO WT-3

description:
Library name: Csgsc-3
column name in gene_count_matrix.txt:Csgsc.3


title: iCre_TGFB_Replicate2

description: Library name: iCre_TGFB_2

value: cardiac fibroblast


title: OCI-AML2 DMSO sgCHD7-5-3

description:
Library name: CsgCHD7-5-3
column name in gene_count_matrix.txt:CsgCHD7.5.3


title: E59 human hand phalanges, digit 4, rep 3

description: Library name: HP4_early_rep3

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: OCI-AML2 Gilteritinib WT-1

description:
Library name: Gsgsc-1
column name in gene_count_matrix.txt:Gsgsc.1


title: OCI-AML2 DMSO sgCHD7-5-2

description:
Library name: CsgCHD7-5-2
column name in gene_count_matrix.txt:CsgCHD7.5.2


title: E59 human hand phalanges, digit 5, rep 3

description: Library name: HP5_early_rep3

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: iCre_SS_Replicate4

description: Library name: iCre_SS_4


title: iCre_TGFB_Replicate1

description: Library name: iCre_TGFB_1


title: OCI-AML2 DMSO sgCHD7-2-3

description:
Library name: CsgCHD7-2-3
column name in gene_count_matrix.txt:CsgCHD7.2.3


title: E59 human hand phalanges, digit 3, rep 3

description: Library name: HP3_early_rep3

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: E59 human metacarpal, digit 4, rep 3

description: Library name: HM4_early_rep3

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: OCI-AML2 DMSO sgCHD7-2-2

description:
Library name: CsgCHD7-2-2
column name in gene_count_matrix.txt:CsgCHD7.2.2


title: MKL-1, JNJ-64619178, biol rep 4, Illumina NovaSeq X

city: Durham

first: Joseph

middle: L

last: Sevigny

state: NH

address: 35 Colovos Rd.

institute: Hubbard Center for Genome Studies

description: Library name: JNJ_8_illumina

data_processing:
Adapter and quality trimming with Fastp v0.23.4. Reads with a quality score below 20 and reads shorter than 30 bp after trimming were discarded.
Alignment using salmon v1.10.3 with the options ‘—validateMappings’, ‘-l A’, and the ‘gcBias’ flag.
Assembly: GENCODE Human Release 39 (GRCh38.p13) Transcript sequences, gencode.v39.transcripts.fa.gz
Supplementary files format and content: Quantifications are from salmon quant files and include raw counts and TPM.

growth_protocol: MKL-1 cells were maintained in RPMI-1640 medium supplemented with 10% FBS, 1% GlutaMAX, and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen)
Strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit, following the manufacturer's instructions. ≥400 ng of total RNA (measured by Qubit) was used. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis with dUTP instead of dTTP to maintain strand specificity. The strand-specific libraries then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Size selection was performed using AMPure XP beads to isolate fragments of approximately 300 bp. Library quality was assessed using Qubit and real-time PCR for quantification and a Bioanalyzer for size distribution analysis. Equimolar amounts of each quantified library were pooled for sequencing on the Illumina NovaSeq X Plus Series platform, generating paired-end 150 bp reads with 18 GB of raw data per sample (60 million reads).

treatment_protocol: Cells were treated with DMSO or 12 nM JNJ-64619178 for 4 days

value: virus-positive Merkel cell carcinoma cells

value: WT


title: OCI-AML2 DMSO sgCHD7-2-1

description:
Library name: CsgCHD7-2-1
column name in gene_count_matrix.txt:CsgCHD7.2.1


title: iCre_SS_Replicate3

description: Library name: iCre_SS_3


title: MKL-1, JNJ-64619178, biol rep 3, Illumina NovaSeq X

description: Library name: JNJ_7_illumina


title: MKL-1, JNJ-64619178, biol rep 2, Illumina NovaSeq X

description: Library name: JNJ_6_illumina


title: iCre_SS_Replicate2

description: Library name: iCre_SS_2


title: MKL-1, JNJ-64619178, biol rep 1, Illumina NovaSeq X

description: Library name: JNJ_5_illumina


title: iCre_SS_Replicate1

description: Library name: iCre_SS_1


title: E59 human hand phalanges, digit 1, rep 3

description: Library name: HP1_early_rep3

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I

value: chondrocytes

value: Male


title: MKL-1, DMSO, biol rep 3, Illumina NovaSeq X

description: Library name: DMSO_3_illumina


title: E58 human metatarsal, digit 5, rep 2

description: Library name: FM5_early_rep2

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: aim3-50

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

department: Endocrinology Department

institute: University of Chicago

description: Library name: IA1119

library_source: other

data_processing:
Adaptor trimming performed with sRNAbench from SRNAtoolbox version 0.0.4, with adapter minimum length of 10, adapter sequence "TGGAATTCTCGGGTGCCAAGG", no recursive trimming, and 1 allowed mismatch in the adapter.
Read Mapping to known libraries of Human miRNA was performed  using sRNAbench from SRNAtoolbox version 0.0.4. Wth hsa library as reference, species set for GRCh38_p13_mp, minimum read count of 2, number of mitmatches set to 1, seed = 19, hierarchical alignment type, isoMIR set to false.
Assembly: GRCh38_p13
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped to mature miRNA from sense strand summarized by sRNAbench.

molecule: other

source_name: Blood plasma

extract_protocol:
RNAs was extracted using an RNA isolation kit (miRNeasy Serum/Plasma Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using commercially available Illumina small RNA-Seq kits (San Diego, California, USA),

value: Blood plasma

tag: disease state

value: Healthy Old


title: hma442

description: Library name: IA1117


title: E58 human metatarsal, digit 4, rep 2

description: Library name: FM4_early_rep2

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: OCI-AML2 DMSO sgCHD7-5-1

description:
Library name: CsgCHD7-5-1
column name in gene_count_matrix.txt:CsgCHD7.5.1

value: AML

value: CHD7 knockout


title: hma445

description: Library name: IA1116


title: E58 human metatarsal, digit 3, rep 2

description: Library name: FM3_early_rep2

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: iCre_ILB_Replicate2

description: Library name: iCre_ILB_2

value: cardiac fibroblast


title: iCre_ILB_Replicate4

description: Library name: iCre_ILB_4


title: E59 human hand phalanges, digit 2, rep 3

description: Library name: HP2_early_rep3

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: hma435

description: Library name: IA1118


title: iCre_ILB_Replicate3

description: Library name: iCre_ILB_3


title: MKL-1, DMSO, biol rep 2, Illumina NovaSeq X

description: Library name: DMSO_2_illumina

value: DMSO


title: aim3-14

description: Library name: IA1115


title: iCre_ILB_Replicate1

description: Library name: iCre_ILB_1


title: E58 human metatarsal, digit 2, rep 2

description: Library name: FM2_early_rep2

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: MKL-1, DMSO, biol rep 4, Illumina NovaSeq X

description: Library name: DMSO_4_illumina


title: aim3-16

description: Library name: IA1112


title: E58 human metatarsal, digit 1, rep 2

description: Library name: FM1_early_rep2

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: aim3-15

description: Library name: IA1111


title: E58 human foot phalanges, digit 4, rep 2

description: Library name: FP4_early_rep2

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: mb429

description: Library name: IA1114


title: iCre_FGF_Replicate4

description: Library name: iCre_FGF_4

source_name: cardiac fibroblast


title: hma437

description: Library name: IA1113


title: aim3-31

description: Library name: IA1110


title: MKL-1, DMSO, biol rep 1, Illumina NovaSeq X

description: Library name: DMSO_1_illumina

value: virus-positive Merkel cell carcinoma cells

value: WT


title: E58 human foot phalanges, digit 5, rep 2

description: Library name: FP5_early_rep2

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V

value: chondrocytes


title: iCre_FGF_Replicate2

description: Library name: iCre_FGF_2


title: iCre_FGF_Replicate3

description: Library name: iCre_FGF_3


title: E58 human foot phalanges, digit 3, rep 2

description: Library name: FP3_early_rep2

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III

value: Male


title: iCre_FGF_Replicate1

description: Library name: iCre_FGF_1


title: aim3-2

description: Library name: IA1108

value: Blood plasma

value: HMA


title: aim3-44

description: Library name: IA1109


title: aim3-1

description: Library name: IA1105


title: aim3-29

description: Library name: IA1107


title: Aim3-27

description: Library name: IA1102


title: E58 human foot phalanges, digit 2, rep 2

description: Library name: FP2_early_rep2

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E58 human metacarpal, digit 5, rep 2

description: Library name: HM5_early_rep2

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: aim3-45

description: Library name: IA1106


title: aim3-13

description: Library name: IA1100


title: aim3-21

description: Library name: IA1103


title: Ctrl5

city: Chongqing

first: Guo

middle: Jing

last: Ma

address: Yuzhong Road

institute: Chongqing medical university

description: Library name: HC-5

data_processing:
SnRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform (www.novelbrain.com). We applied fastp  with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. Cells contained over 200 expressed genes and mitochondria UMI rate below 10% passed the cell quality filtering and mitochondria genes were removed in the expression table.
The 'Ctrl vs Dep DEGs.tsv' files included all DEGs; We identified DEGs between the groups and used functional FindMarkers under the following criteria: 1. log2 |FC| > 0.25; 2. FDR < 0.05 (Bonferroni correction); 3. min.pct > 0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: prefrontal cortex

extract_protocol:
Briefly, the frozen tissue was homogenized in NLB buffer which contain 250 mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton X-100 (SigmaAldrich, USA), 0.1 mM EDTA, 0.2U/μL RNase Inhibitor (Takara, Japan). Various concentration of sucrose was used to purify the nucleus. The concentration of nucleus was adjusted to about 1000 nuclei / μL for snRNA-Seq.
The snRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3' V3 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to 1000 nuclei/μL than loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent, USA). All libraries were sequenced by Novaseq6000 (Illumina, USA) on a 150 bp paired-end run.

value: prefrontal cortex

tag: group

value: healthy control