title: Aortic CD45+ cells library2, HTO

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

description:
HTO: read1 file contains cell barcode and UMI; read2 file contains Hastag Antibody derived tag reads
G4_2_filtered_feature_bc_matrix.tar.gz
G4_2_molecule_info.h5

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Aorta

extract_protocol:
Ldlr-/- mice were fed a HFD according to the “Continuous” or “Alternate” diet protocols. C57bl6/J mice were used as healthy controls. Before sacrifice, mice received an i.v. injection of 2.5µg anti-CD45.2 APC (clone 104, Biolegend, cat. #109814) under isoflurane anesthesia to exclude contaminating blood leukocytes during FACS sorting. Mice were killed by cervical dislocation under isoflurane anesthesia, perfused via intracardiac injection of PBS, and the aorta excised and cleaned of perivascular adipose tissue. Aortas from 2 mice were pooled to generate each sample for single cell RNA-seq (scRNA-seq). The aortas were digested for 1 hour at 37°C under agitation in RPMI containing 450U/ml collagenase I (Sigma-Aldrich, #C0130), 125U/ml Collagenase XI (Sigma-Aldrich, C7657), 60U/ml Hyaluronidase (Sigma-Aldrich, H3506), 60U/ml DNAse (Roche #11284932001). After washing with PBS supplemented with 1% FCS, aortic cell preparations were incubated on ice in PBS+1%FCS supplemented with 1:50 FcBlock (BioLegend TruStain FcXTM) for 10 minutes, and further incubated for 25 minutes with a mix of fluorochrome coupled antibodies (anti-CD45.2-Alexa488 1:300, anti-Ter119-PE-Cy7 1:300), a viability dye (ThermoFisher Fixable Viability Dye e780), TotalSeq-A CITE-seq (all from BioLegend) and mouse TotalSeq-A Hashtag antibodies (1:200; BioLegend). Cell preparations were labeled using the following scheme: Hashtag 1 to 5: 5 pools of 2 aortas from Ldlr-/- mice fed the “Continuous” diet protocol; Hashtag 6 to 10: 5 pools of 2 aortas from Ldlr-/- mice fed the “Alternate” diet protocol; Hashtag 11 to 13: 3 pools of 2 aortas from healthy C57BL6/J mice. After two washes, all cell preparations were pooled for simultaneous sorting. We sorted viable Ter119negCD45.2(i.v.)negCD45.2-Alexapos in PBS supplemented with 0.2% ultrapure BSA (ThermoFisher) using a FACS Aria III with a 100µm nozzle. After sorting and washing, cells were resuspended in PBS supplemented with 0.2% ultrapure BSA at a concentration of 500 cells/µl and loaded into the 10x Genomics Chromium in duplicate lanes (Single Cell 3’ v3 reagents, 10x Genomics) and scRNA-seq, ADT and HTO libraries prepared and sequenced as described in PMID: 35950218.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Aorta

value: not applicable

value: Ldlr-/-

value: various

tag: library type

value: HTO


title: WRAP53_Rep1_Input

status: Public on Apr 15 2024

type: SRA

city: Baltimore

first: Taeyoung

last: Hwang

state: MD

address: 855 N. Wolfe St, 3rd floor, Suite 300

country: USA

institute: Lieber Institute for Brain Development

library_source: other

data_processing:
The sequencing reads were assigned to the designed oligonucleotides by mapping barcode sequences. Barcode sequences can be retrieved from the provided oligo pool fasta file: it is 10 nucleotides long from the end following the removal of the final 17 nucleotides.
Sequencing reads were counted for a given oligonucleotide if they have less than or equal to 2 mismatches between a read and a designed target sequence. The designed target sequences can be retrieved from the provided oligo pool fasta file: it is the remaining sequence following the removal of the first 16 nucleotides and the final 27 nucleotides.
Assembly: Not applicable, using custom sequences
Supplementary files format and content: Tab-delimited files include sequencing read counts for oligonucleotides and samples.
Library strategy: Amplicon-seq

molecule: other

organism: Homo sapiens

growth_protocol: HEK293T cells cultured in DMEM plus 10% FBS, 1% Penicillin-streptomycin, and 1% GlutaMAX supplement (Gibco) were passaged onto 15-cm dishes.

extract_protocol:
For the reverse cross-linking reaction, lysates were mixed with 33 μL of reverse crosslinking buffer (3X PBS, 6% N-Lauroylsarcosine, 30 mM EDTA, 15 mM DTT), 10 μL of Proteinase K (Ambion), and 1 μL of RNaseOUT (Invitrogen) and incubated at 42C for 1 hour then 55C for 1 hour. TRIzol (Invitrogen) and chloroform, followed by RNeasy Plus Mini Kit (Qiagen), were used to isolate RNAs.
Sequencing libraries were generated using customized primers that anneal to the universal priming sites on the oligos and attach Illumina-compatible sequencing adapters: reverse primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), forward primer (caagcagaagacggcatacgagatCGTGATgtgactggagttcagacgtgtgctcttccgatctACTGGCCGCTTCACTG, CGTGAT is a Illumina truseq index and can be variable).
Amplicon sequencing was performed with a single-end run.

treatment_protocol: Oligo pools were transfected into HEK293T cells using X-tremeGENE HP DNA Transfection Reagent (Roche) according to manufacturer’s instruction. Cells were harvested 48 hours post-transfection by scraping, collected by centrifugation at 500 x g for 5 minutes at 4C, and washed once with cold PBS. Cells were cross-linked in cold PBS resuspension (~5 million cells/mL) with 0.1% formaldehyde for 10 minutes on a nutator at room temperature. To cease the reaction, glycine was added to cells with a final concentration of 125 mM followed by incubation for 5 minutes on a nutator at room temperature. Cross-linked cells were centrifuged at 500 x g for 5 minutes at 4C. Cross-linked cell pellets were washed twice with PBS including cOmplete Protease Inhibitor Cocktail (Roche), flash-frozen and stored at -80C until use.

tag: cell line

tag: frip antibody

value: Input

tag: overexpression

value: FLAG-GFP-CTCF


title: GR11 patient, snMultiome

city: Villejuif

first: Clémence

last: Henon

address: 114 rue Edouard Vaillant

country: France

institute: Gustave Roussy

description: 10x Genomics Multiome

data_processing:
Demultiplexing reads alignment, filtering, ATAC peak calling, and generation of feature-barcode matrices were done using Cell Ranger ARC.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Single-cell multiome

source_name: Tumor

extract_protocol:
The fresh DSRCT tumor specimen was collected into 4°C MACS Tissue Storage Solution with a delay of less than 30 minutes after surgery. The tissue sample was then cut into small chunks before proceeding to nuclei isolation and nuclei permeabilization according to 10x Genomics Demonstrated Protocol for Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + GEX Sequencing (CG000375 Rev B)
The appropriate volume of cell nuclei suspension was extracted to target the effective encapsulation of 5,000 nuclei. Further steps were performed following the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338).

tag: tissue

value: Tumor

tag: disease

value: Desmoplastic Small Round Cell Tumor


title: GR7 patient, site 2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting were performed using CellRanger software (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

extract_protocol:
Briefly, fresh DSRCT tumor and peritumor material was collected into RPMI 1640 medium with GlutaMAXTM Supplement (GibcoTM, reference 61870010) or MACS Tissue Storage Solution (Miltenyi Biotec, reference 130-100-008) with a delay of less than 30 minutes after surgery. Tissue samples were further cut into small chunks and incubated at 37°C in RPMI medium containing DNAse I (Sigma, reference DN25-100MG) at 2.2 µg/mL (final concentration) and LiberaseTM Thermolysin Low (TL) (Roche, reference 5401020001) at 4.5 µg/mL (final concentration) during 20 to 30 minutes. After tissue dissociation, the mixture was washed in 1x PBS + 0.04% BSA before centrifugation. To obtain a single-cell suspension, cells resuspended in 1x PBS + 0.04% BSA were filtered twice with a 70 mm and 30 mm cell strainer. After another round of centrifugation, cells were resuspended in 1x PBS + 0.04% BSA. When necessary, red blood cell lysis was performed with a 2 to 3 minutes incubation in 1X Red Blood Cell Lysis buffer (BioLegend, reference 420301) protected from light before washing in 10 mL PBS and performing a last round of centrifugation.
Cell concentration and viability were controlled with an automated cell counter using trypan blue, and cells were loaded into the 10x Genomics cassette for a targeted cell recovery of 5,000 cells per sample following the recommendations from the manufacturer’s protocol. Cell encapsulation, reverse transcription, and library generation were performed according to 10x Genomics standard protocols. Paired-end sequencing was performed on the Illumina NovaSeq 6000 sequencer for a targeted depth of 400 million reads per sample.

tag: patient

value: GR7 patient, site 2


title: CTCF_Rep3_IP

library_source: transcriptomic

data_processing:
The sequencing reads were assigned to the designed oligonucleotides by mapping barcode sequences. Barcode sequences can be retrieved from the provided oligo pool fasta file: it is 10 nucleotides long from the end following the removal of the final 17 nucleotides.
Sequencing reads were counted for a given oligonucleotide if they have less than or equal to 2 mismatches between a read and a designed target sequence. The designed target sequences can be retrieved from the provided oligo pool fasta file: it is the remaining sequence following the removal of the first 16 nucleotides and the final 27 nucleotides.
Assembly: Not applicable, using custom sequences
Supplementary files format and content: Tab-delimited files include sequencing read counts for oligonucleotides and samples.

tag: antibody

value: FLAG


title: CTCF_Rep3_Input


title: GR7 patient, site 1, scRNAseq

description: 10x Genomics

value: GR7 patient, site 1


title: IC patient, site 3, scRNAseq

description: 10x Genomics

value: IC patient, site 3


title: Aortic CD45+ cells library1, HTO

country: Germany

description:
HTO: read1 file contains cell barcode and UMI; read2 file contains Hastag Antibody derived tag reads
G3_2_filtered_feature_bc_matrix.tar.gz
G3_2_molecule_info.h5

organism: Mus musculus

tag: cell type

tag: genotype

tag: treatment


title: CTCF_Rep2_IP


title: Aortic CD45+ cells library1, ADT

description:
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody derived tag reads
G3_2_filtered_feature_bc_matrix.tar.gz
G3_2_molecule_info.h5

value: ADT


title: IC patient, site 2, scRNAseq

description: 10x Genomics

value: IC patient, site 2


title: CTCF_Rep2_Input


title: GR4 patient, post chemotherapy, scRNAseq

description: 10x Genomics

value: GR4 patient, post chemotherapy


title: IC patient, site 1, scRNAseq

description: 10x Genomics

source_name: Juxtatumor

value: Juxtatumor

value: IC patient, site 1


title: Aortic CD45+ cells library1, GEX

description:
GEX (3’ mRNA) library: bam file contains mapped reads
G3_2_filtered_feature_bc_matrix.tar.gz
G3_2_molecule_info.h5

molecule: polyA RNA

value: Aorta

value: not applicable

value: mRNA


title: GR4 patient, scRNAseq

description: 10x Genomics

value: GR4 patient


title: CTCF_Rep1_IP


title: WRAP53_Rep3_Input

value: Input


title: GR2 patient, site 4, scRNAseq

description: 10x Genomics

value: GR2 patient, site 4


title: hTR_Rep3_IP

value: FLAG-hTERT


title: CTCF_Rep1_Input

value: FLAG-GFP-CTCF


title: GR2 patient, site 3, scRNAseq

description: 10x Genomics

value: Tumor

value: GR2 patient, site 3

value: Desmoplastic Small Round Cell Tumor


title: Aortic CD45+ cells library2, ADT

description:
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody derived tag reads
G4_2_filtered_feature_bc_matrix.tar.gz
G4_2_molecule_info.h5

value: Ldlr-/-

value: various


title: 14d ApoEHom replicate 2

city: Salt Lake City

first: Alessandro

last: Venosa

state: UT

department: Pharmacology and Toxicology

institute: University of Utah

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
Genes that were detected in less than 3 cells were removed. Cell with a minimum 200 detected genes were used for analysis.
PCA analysis and differential gene expression analysis was performed using hciR package, using Seurat (version 4.0.4).
Assembly: mm10, M_musculus_Jun_2020, GRCm38
Supplementary files format and content: file with barcodes, matrix, features

source_name: lung primary cells

extract_protocol:
Lungs were lavaged with ice cold saline solution. This was followed by saline perfusion through the heart. Lungs were then incubated in collagenase D for 30 min (2mg/ml, 37C, 5%CO2), followed by single cell suspension through a 70um strainer. Red blood cells were lyzed, cells were counted, and submitted for library preparation and sequencing following the 10x genomics protocol.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing (400 M read-pairs)

treatment_protocol: Two oral gavage treatments with tamoxifen (175mg/kg, in corn oil, three days apart) excises neomycin cassette and boosts mutant SPC mutant expression. Corn oil gavage was used for controls

value: whole lung digest

tag: time point

value: tamoxifen treated


title: 14d ApoEHom replicate 3


title: hTR_Rep3_Input


title: 14d ApoEHom replicate 1


title: GR2 patient, site 2, scRNAseq

description: 10x Genomics

value: GR2 patient, site 2


title: Aortic CD45+ cells library2, GEX

description:
GEX (3’ mRNA) library: bam file contains mapped reads
G4_2_filtered_feature_bc_matrix.tar.gz
G4_2_molecule_info.h5


title: control ApoEHom replicate 1

value: control

value: oil treated


title: hTR_Rep2_IP

value: FLAG


title: GR2 patient, site 1, scRNAseq

description: 10x Genomics

value: GR2 patient, site 1


title: 14d ApoEHet replicate 3


title: hTR_Rep1_IP


title: hTR_Rep2_Input


title: 42d ApoEHet replicate 1


title: TIL sorted BTLA knockout CART19

city: Philadelphia

first: Puneeth

last: Guruprasad

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: 10X Genomics/Azenta

data_processing:
The de-multiplexing, barcoding, mapping,  gene coutning, and aggregation was performed using CellRanger (10X; v5.0.1 or higher)
Assembly: GRCh38
Supplementary files format and content: filtered matrix h5 files for input into Seurat, .csv files for Hashtag

source_name: OCI-Ly18 subcutaneous tumor (NSG)

extract_protocol:
FACS purified CART19 cells were washed 2x in PBS + 0.04% PBS, and then resuspended in the same solution prior to loading onto 10X Genomics chips.
Library was prepared according to manufacturers instructions for the 10X Genomics 5' v2 Chemistry GEX (+ Feature Barcoding for model 1). User Guide, CG000331 Revision E was used for library preparation steps. DNA quality was assessed prior to NGS via BioAnalyzer High Sensitivity DNA.

value: OCI-Ly18 subcutaneous tumor (NSG)

value: primary T cell

value: BTLA sgRNA+Cas9


title: TIL sorted mock electroporated CART19

description: 10X Genomics/Azenta

value: mock-electroporation (Cas9 only)


title: 14d ApoEHet replicate 1


title: hTR_Rep1_Input

value: Input

value: FLAG-hTERT


title: MS2_Rep3_HA

value: HA

value: FLAG-HA-MCP


title: control ApoEHet replicate 3


title: Individual Mouse Hashtag - PB BTLA KO CART19

description: 10X Genomics/Azenta

source_name: peripheral blood (NSG)

value: peripheral blood (NSG)

value: BTLA sgRNA+Cas10


title: Peripheral blood sorted BTLA knockout CART19

description: 10X Genomics/Azenta


title: MS2_Rep3_FLAG


title: Individual Mouse Hashtag - PB Mock CART19

description: 10X Genomics/Azenta


title: 42d replicate 1

value: whole lung digest


title: Peripheral blood sorted mock electroporated CART19

description: 10X Genomics/Azenta


title: MS2_Rep2_FLAG


title: Ovary,old-5,spatial

city: Wuhan

first: Shixuan

last: Wang

state: Hubei

address: Jiefang Avenue

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequence reads in FASTQ format from ovary samples were processed and aligned to the GRCh38 human reference transcriptome (https://www.10xgenomics.com/) using the Cellranger v4.0.0 pipeline (https://www.10xgenomics.com/) with default parameters.
Assembly: GRCh38
Supplementary files format and content: matrix files
Library strategy: spatial transcriptomic

source_name: ovary

extract_protocol:
Human ovary tissues were saved in tissue storage solution (Miltenyi, 130-100-008) at ice bath and transferred to laboratory within two hours. Then we get rid of damaged parts in light microscopy and cut out a ~1 cm3 piece for isolation. The tissue was washed with PBS (containing 0.04% BSA) and cut into 0.1 cm3 in 2 mg/ml IV collagenase. Then the tube containing IV collagenase and tissues was oscillated in water bath at 37℃ for 20 min. After centrifuged for 5 min on 1200 rpm the supernatant was discarded and resuspended in 0.5% trypsin. Then the tissues in 0.5% trypsin were oscillated in water bath at 37℃ for 10 min again. Digestion was stopped with DMEM containing 10% BSA and filtered with 40 μm cell strainer (Millipore). Finally, cells were incubated in red blood bell lysis buffer for 10 min then centrifuged and resuspended in 100-200 μL PBS containing 0.04% BSA. For spatial  transcriptome sequencing, ovary tissues were cut into about 10*10*5 mm piece and dried with lab blotting paper to prevent ice crystal formation. After that we embedded the tissue with opti-mum cutting temperature compound into the embedding box in dry ice and saved in -80 ℃.
Single-cell suspension for each ovary sample was loaded onto a separate channel of a Chromium 10x Genomics single cell 3’v3 library chip as per manufacturer’s protocol. cDNA sequencing libraries were prepared according to the manufacturer’s protocol and sequenced on an Illumina Novaseq 6000 (2x150bp paired-end reads). Spatial transcrintome seauencing libraries were prepared with 10xGenomics Visium Soatail Gene Exoression Slides & Reagent kit according to manufacturer's construction

value: ovary


title: MS2_Rep1_HA


title: Ovary,old-4,spatial


title: 42d replicate 2

value: tamoxifen treated


title: Ovary,old-3,spatial


title: 14d replicate 2


title: 14d replicate 3


title: MS2_Rep2_Input


title: MS2_Rep1_FLAG


title: Ovary,old-2,spatial


title: 14d replicate 1


title: Ovary,old-1,spatial


title: 14d ApoEHet replicate 2


title: Ovary,middle-5,spatial


title: PUM2_Rep3_IP


title: PUM2_Rep3_Input


title: control ApoEHet replicate 2

value: control


title: MS2_Rep3_Input


title: Ovary,middle-4,spatial


title: control ApoEHet replicate 1

value: oil treated


title: control replicate 2


title: PUM2_Rep2_IP


title: MS2_Rep2_HA


title: PUM2_Rep2_Input


title: PUM2_Rep1_IP


title: Ovary,middle-2,spatial


title: MS2_Rep1_Input


title: Ovary,middle-1,spatial


title: CD11b+ cells, LPS-treated PA14, Replicate 3, scRNA-seq

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description:
10X Genomics
LPS+PA14_3

data_processing:
Samples were processed using the CellRanger suite (V6.0), including demultiplexing, barcode processing, and gene counting. Samples were analyzed and integrated using a Seurat-based scRNA-seq pipeline (V4.3.0), including quality control, filtering of doublets and contaminated cells, and clustering. Custom R scripts were used for the downstream analysis of 46,826 high quality cells, including Gene Set Enrichment Analysis and cell type annotation. Cell type annotations can be found in the "custom.cluster.labels" column of the Seurat object metadata file.
Assembly: mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: Tab-separated values (.tsv) and matrix (.mtx) files

source_name: Lung (CD11b+ cells)

extract_protocol:
CD11b+ cells from lung single cell suspensions were purified using anti-CD11b magnetic microbeads, then passed through a 40-µM cell strainer and enumerated immediately before loading onto a 10x Chromium controller for cell capture (targeting 5000 cells per sample) using the Chromium Single Cell Immune Profiling v2- Dual index kits.
Libraries for gene expression were constructed following protocols from 10x Genomics. Final libraries were QCed by Agilent TapeStation and then sequenced using Illumina’s Novaseq 6000 targeting 50,000 reads per cell.

value: Lung (CD11b+ cells)

value: CD11b+ cells


title: CD11b+ cells, LPS-treated PA14, Replicate 1, scRNA-seq

description:
10X Genomics
LPS+PA14_1


title: control replicate 3


title: PUM2_Rep1_Input


title: Ovary,young-4,spatial


title: retinal endothelial cells, EC-Foxc1-KO, postnatal day 6, biological replicate 2

city: Chicago

first: Teena

last: Bhakuni

state: Illinois

address: 303 E Superior St

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw counts

source_name: retina

extract_protocol:
Retinas pooled from 3 - 6 neonates were digested in collagenase Type I solution (2 mg/mL) for 40 minutes at 37°C with gentle agitation. Cells were then filtered through a 70 μm cell strainer and the pellet was resuspended in Buffer 1(PBS, 0.1% BSA, 2 mM EDTA, pH 7.4). The cell suspension was then incubated with magnetic Dynabeads (Invitrogen) pre-coated with CD31 antibody to isolate the endothelial cell population. After several washes with Buffer 1, RNA was extracted from endothelial cells using RNA STAT solution (Tel-Test) followed by phenol-chloroform treatment.
Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per the manufacturer’s instructions

value: retina

value: endothelial cells


title: Ovary,young-5,spatial


title: CD11b+ cells, PA14, Replicate 2, scRNA-seq

description:
10X Genomics
PA14_2


title: CD11b+ cells, PA14, Replicate 1, scRNA-seq

description:
10X Genomics
PA14_1


title: CD11b+ cells, PA14, Replicate 3, scRNA-seq

description:
10X Genomics
PA14_3


title: Ovary,young-3,spatial


title: retinal endothelial cells, EC-Foxc1-KO, postnatal day 6, biological replicate 3


title: control replicate 1


title: retinal endothelial cells, EC-Foxc1-KO, postnatal day 6, biological replicate 1


title: Ovary,middle-3,spatial


title: retinal endothelial cells, WT, postnatal day 6, biological replicate 3

value: WT


title: Ovary,young-1,spatial


title: Meioc KO P15 testes, biological replicate 2, scRNAseq

city: Cincinnati

first: Maria

last: Mikedis

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
Alignment, filtering, barcode counting, and UMI counting were done via count function in Cell Ranger v.4.0.0 with default settings using Cell Ranger’s mm10-2020-A reference package (i.e., the GRCm38/mm10 mouse genome assembly with GENCODE vM23/Ensembl 98 annotation)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: rds file contains the processed data for all 4 samples from GSE230746 as a seurat object containing the count matrix, metadata, clustering results, and labeled cluster cell types.

source_name: testes

extract_protocol:
Single-cell sequencing libraries were prepared and sequenced in two batches, with each batch containing one P15 littermate pair comprised of one wild-type and one Meioc-null pup.  One mouse testis per P15 pup was enzymatically dissociated by first shaking vigorously for 30 seconds and incubating at 35˚C for 7 minutes in 900 ul of 0.1% collagenase type I (Worthington LS004196) in Hank’s Balanced Salt Solution (HBSS), supplemented with TURBO DNase (ThermoFisher Scientific AM2238) for a final concentration of 2U/mL. After allowing the sample to sit for 1 minute such that the seminiferous tubules settled to the bottom of the tube, the interstitium was removed by discarding the resulting supernatant, and the remaining sample was incubated at 35˚C for 25 minutes (with gently pipetting every 5 minutes) in 800 ul of 0.05% trypsin and 0.1% collagenase type I in HBSS, supplemented with TURBO DNase for a final concentration of 2U/mL. The cell suspension was then passed through a 40um nylon strainer, and cell suspension was allowed to digest for 35˚C for an additional 20 minutes. The digestion was quenched by adding 200ul fetal bovine serum (FBS) and gently mixing. The cell suspension was again passed through a 40um nylon strainer. The concentration of the resulting cell suspension was assessed using trypan blue on the Countess Cell Counter. Cells were pelleted at 500g for 4 minutes at room temperature, resuspended in 0.05% bovine serum albumin (BSA) in phosphate buffered saline (PBS) for a target concentration of 1000 cells per microliter, and placed on ice. Viability and concentration were re-assessed ~20 minutes prior to loading on the Chromium Controller using trypan blue on a Countess Cell Counter, at which point all samples had a minimum of 90% viability. Cell suspensions were loaded onto the Chromium Controller, aiming for recovery of 10,000 cells per sample.
Libraries were generated using the Chromium Next GEM Single Cell 3ʹ v3.1 (10x Genomics), according to manufacturer’s instructions

tag: strain

value: testes

tag: age

value: Postnatal day 15 (P15)

value: Meioc KO

tag: batch

value: batch 2


title: Ovary,old-3,scRNAseq

data_processing:
Raw sequence reads in FASTQ format from ovary samples were processed and aligned to the GRCh38 human reference transcriptome (https://www.10xgenomics.com/) using the Cellranger v4.0.0 pipeline (https://www.10xgenomics.com/) with default parameters.
Assembly: GRCh38
Supplementary files format and content: matrix files


title: wild-type P15 testes, biological replicate 2, scRNAseq

description: 10x Genomics

value: wild-type


title: retinal endothelial cells, WT, postnatal day 6, biological replicate 2


title: CD11b+ cells, LPS-treated PA14, Replicate 2, scRNA-seq

description:
10X Genomics
LPS+PA14_2


title: Ovary,old-2,scRNAseq


title: wild-type P15 testes, biological replicate 1, scRNAseq

description: 10x Genomics

data_processing:
Alignment, filtering, barcode counting, and UMI counting were done via count function in Cell Ranger v.4.0.0 with default settings using Cell Ranger’s mm10-2020-A reference package (i.e., the GRCm38/mm10 mouse genome assembly with GENCODE vM23/Ensembl 98 annotation)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: rds file contains the processed data for all 4 samples from GSE230746 as a seurat object containing the count matrix, metadata, clustering results, and labeled cluster cell types.

value: batch 1


title: preleptotene-enriched testes, Meioc KO, biological replicate 3

data_processing:
Reads were quality trimmed using cutadapt v1.8 (options: -q 30 --minimum-length 20 -b AGATCGGAAGAGC)
Expression levels of all transcripts in the mouse Gencode Basic vM15 gene annotation were estimated using kallisto v0.44.0 (Bray et al. 2016) with sequence-bias correction (--bias) and strand-specific pseudoalignment (--rf-stranded). Quantified transcripts were filtered for protein-coding genes, transcript-level estimated counts and transcripts per million (TPM) values were summed to the gene level, and TPMs were renormalized to transcript-per-million units
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: postnatal testes

extract_protocol:
Total RNA was extracted from 4 wild-type samples and 3 Meioc-null samples, using 1.5 synchronized testes from a single pup per sample. TRIzol Reagent (Thermo Fisher Scientific) was added to freshly thawed whole testes, and ERCC RNA ExFold RNA Spike-In Mix 1 and 2 (Thermo Fisher Scientific) were added to wild-type and Meioc-null samples, respectively, at a concentration of 1 l of a 1:100 dilution of spike-in mix per 1 mg of testis tissue. (Spike-in mixes were ultimately not used for data analysis.) Total RNA was then isolated with chloroform following the manufacturer’s protocol, precipitated via isopropanol, and resuspended in RNase-free water
RNA-seq libraries were prepared with the TruSeq Stranded Total RNA kit with the Ribo-Zero Gold rRNA Removal kit following manufacturer's protocols.

treatment_protocol: Spermatogenesis was synchronized using a protocol originally developed by Hogarth et al. (Hogarth et al. 2013) and modified by Romer et al. (Romer et al. 2018). Male mice were injected daily subcutaneously from postnatal day (P) 2 to P8 with WIN 18,446 (Santa Cruz Biotechnology) at 0.1mg/gram body weight and on P9 with retinoic acid (RA; MilliporeSigma) at 0.0125 mg/gram body weight. To obtain testes enriched for preleptotene cells, mice were euthanized and testes were collected at 6.75 days after the RA injection. For each pup, a small testis biopsy was collected for histology to confirm proper enrichment of the desired preleptotene cell type, and the rest of the testes were flash frozen as whole testes.

value: postnatal testes

tag: developmental stage

value: developmental synchronization to enrich for preleptotenes


title: Ovary,old-1,scRNAseq

value: ovary


title: WT Rep2 for CUT&RUN using Hnrnpk

city: Guangzhou

first: Yuyu

last: Chen

state: Guangdong

address: Zhongshan II road, 74th

institute: Sun Yat-sen University

description: Hnrnpk binding DNA

library_source: genomic

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For CUT&RUN: CutRunTools pipeline was used to peformed CUT&RUN processing and footprint analysis.
For CUT&RUN: CutRunTools pipeline was used to peformed CUT&RUN processing and footprint analysis.
Assembly: mm10

molecule: genomic DNA

source_name: mice limb bud cells

extract_protocol:
For CUT&RUN: The protein binding DNA was  isolated from cells using EpiTM CUT&RUN Assay Kit (Epibiotek, cat. no R1816).
For CUT&RUN: The protein binding DNA was  isolated from cells using EpiTM CUT&RUN Assay Kit (Epibiotek, cat. no R1816). Extract DNA was processed for library generation using the QIAseq Ultralow Input Library Kit (QIAGEN) following the manufacturer’s protocol.

value: mice limb bud cells


title: Ovary,middle-4,scRNAseq


title: IκBα KO, E14.5 LT-HSC Fetal liver, replicate 1, 10x scRNAseq

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 from 10xGenomics
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Fetal Liver

extract_protocol:
E14.5 fetal livers were lineage depleted and FACS sorted for the LSK population from pools of  Ikba 2 WT and 3 KO.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
10x Genomic scRNA-seq

value: LSK

value: Fetal Liver

value: I{kappa}B{alpha} KO


title: preleptotene-enriched testes, Meioc KO, biological replicate 2


title: Ovary,middle-3,scRNAseq


title: Chat-cre; CAG-Sun1/sfGFP mice NA

city: San Diego

first: Yujuan

last: Su

state: CALIFORNIA

address: 9500 Gilman Dr. MC0766 CMME, Room 1087

institute: UCSD

description: Raw data in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object.

data_processing:
Sequencing was carried out on NovaSeq (Illumina) platform at the Institute for Genomic Medicine, UCSD.
Cell Ranger package (version 3.0.2) was used to align the raw reads onto the mouse reference genome (GRCm38) with default parameters and generate the feature-barcode matrix.
R package Seurat (version 4.0) was used to perform data quality control, normalization, principal components analysis and uniform manifold approximation and projection  (UMAP method).
Cells with more than 200 unique feature counts were considered high quality cells and used for further analysis.
We firstly used SCTransform.The dataset was normalized, scaled, and then analyzed for variable genes using Seurat’s NormalizeData, ScaleData, and FindVariableFeatures functions, respectively. A total of 2,000 top variable features were identified by function FindVariableFeatures and selected for subsequent principal components analysis.
Top 20 significant components were chosen to conduct cell clustering by using the algorithm of uniform manifold approximation and projection (UMAP) with default settings. The expression level and feature of selected genes were profiled and visualize by R package ggplot2 (version 3.3.2).
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary files format and content: Raw data-Reads alignment files in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object (rds).

molecule: nuclear RNA

source_name: flash frozen nucleus ambiguous of the brainstem

growth_protocol: All Mice used in this experiment are bred in the standard facility of UCSD with approval protocol from IACUC

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics Chromium Controller (10x Genomics, Pleasanton, CA) to generate single cell GEMs. cDNA extraction and amilification were excecuted using Chromium Single Cell 3' Reagent Kits (v3 Chemistry, PN-1000075, 10X Genomics) folloing User Guide provided by 10X Genomics.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v3 (PN-1000075, 10x Genomics) following User Guide provided by 10X Genomics.

treatment_protocol: no treatment

tag: Sex

value: pooled male and female

value: Chat-cre; CAG-Sun1/sfGFP

value: no treatment


title: Meioc KO P15 testes, biological replicate 1, scRNAseq

description: 10x Genomics


title: preleptotene-enriched testes, wild-type, biological replicate 4

value: WT


title: Ovary,young-2,spatial


title: preleptotene-enriched testes, Meioc KO, biological replicate 1


title: Ovary,young-3,scRNAseq


title: Ovary,middle-2,scRNAseq


title: preleptotene-enriched testes, wild-type, biological replicate 2


title: preleptotene-enriched testes, wild-type, biological replicate 1


title: Ovary,young-4,scRNAseq


title: Ovary,young-1,scRNAseq


title: WT for CUT&RUN using H3K4me3, Rep2

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For CUT&RUN: CutRunTools pipeline was used to peformed CUT&RUN processing and footprint analysis.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&RUN

extract_protocol: For CUT&RUN: The protein binding DNA was  isolated from cells using EpiTM CUT&RUN Assay Kit (Epibiotek, cat. no R1816). Extract DNA was processed for library generation using the QIAseq Ultralow Input Library Kit (QIAGEN) following the manufacturer’s protocol.

tag: chip antibody

tag: molecule

value: H3K4me3 binding DNA


title: CKO for CUT&RUN using H3K4me3, Rep1

value: Hnrnpk CKO


title: CKO for CUT&RUN using H3K4me3, Rep2


title: PBMCs, M3

city: Shanghai

first: Mengqing

address: No. 415 Fengyang Road, Huangpu District, Shanghai, China

department: Department of Emergency and Critical Care

institute: Shanghai Changzheng Hospital of Naval Medical University

description: 10x Genomics

data_processing:
Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome), the official analysis software of 10x Genomics, was utilized to filter data, compare, quantify, and identify the recovered cells from the raw data. , quantification, and identification of recovered cells to finally obtain the gene expression matrix of each cell.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood mononuclear cell

extract_protocol:
Within two hours of collection, three blood samples were subject to timely PBMC separation using FICOLL PAQUE PLUS (STEMCELL Technologies, Vancouver, Canada). These samples were divided into two groups: experimental (MXF 1-3) and control (Control 1-3).
Single-cell suspensions, loaded onto a 10X Genomics Chromium instrument, were used to capture 8000 single cells following the manufacturer’s instructions for the 10X Genomics Chromium Single-Cell 3' kit V3 (10x Genomics, Pleasanton, CA 94588, USA). Subsequent cDNA amplification and library construction steps were performed as per the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology Co., Ltd, (Hangzhou, China) at a minimum depth of 20,000 reads per cell.

value: peripheral blood mononuclear cell

value: male

value: 24 year-old

value: MXF


title: preleptotene-enriched testes, wild-type, biological replicate 3

value: postnatal testes


title: Ikba_KO_LT-HSC_H3K27me3_3 [Cut&Tag]

description: Read length: 50bp

data_processing:
Followed steps for data preprocessing (i) Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap.
(ii) Trimmed reads were aligned to GRCm38 reference genome with Bowtie2 aligner tool (v2.4.4) (Langmead & Salzberg, 2012). Reference genome was retrieved from Ensembl FTP site (http://ftp.ensembl.org/pub/release-102/).
(iii) Bowtie2 was executed with following parameters: --no-mixed â??no-discordant â??dovetail â??very-sensitive-local. Multi-mapped reads and those reads showing MAPQ < 20 were filtered out.
(iv) [Only applicable for H3K27me3 samples] Peak calling was performed with SEACR (v1.3) in stringent mode without considering IgG control sample (Meers et al., 2019). For this purpose, required input bedgraph files were obtained from deduplicated BAM files using bedtools (v2.30) following SEACR authors guidelines (Quinlan & Hall, 2010). The top 0.5% of peaks were retrieved for downstream analysis.
(v) BigWig files were obtained from BAM files with duplicates using deepTools (v3.5.1)
Assembly: mm10
Supplementary files format and content: BigWig files and detected SEACR peaks in .bed files (only applicable for H3K27me3 experiments)
Library strategy: Cut&Tag

source_name: E14.5 Fetal liver LSKCD48-CD150+

growth_protocol: Primary E14.5 fetal liver LT-HSCs and AGM CD31+ cells were obstained by disecting fetal liver or AGMs from E14.5 or E11.5 embryos folled by FACS sorting.

extract_protocol:
cut and tag experiments were performed on lightly fixed cell suspension and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with unique index primers and NEBNext HiFi 2x PCR Master mix (cat#M0541S) as decribed in bentop cut and tag v3.
Illumina HiSeq 2500 paired end sequencing run

tag: developmental age

value: fetal liver

tag: cells

value: Tri-Methyl-Histone H3 (Lys27)

tag: antibody info.

value: C36B11, cell signaling


title: PBMCs, NC3

description: 10x Genomics

tag: tissue

value: NO


title: retinal endothelial cells, WT, postnatal day 6, biological replicate 1

value: retina

value: endothelial cells


title: Ikba_WT_LT-HSC_H3K27me3_3 [Cut&Tag]

description: Read length: 50bp


title: WT for CUT&RUN using H3K4me3, Rep1

value: mice limb bud cells


title: CKO for CUT&RUN using H3K4me1, Rep2

value: H3K4me1 binding DNA


title: IκBα WT, E14.5 LT-HSC Fetal liver, replicate 1, 10x scRNAseq

description: 10x Genomics

value: LSK

value: Fetal Liver

value: I{kappa}B{alpha} WT


title: PBMCs, M2

description: 10x Genomics

value: 26 year-old


title: Ikba_WT_LT-HSC_H3K27me3_1 [Cut&Tag]

description: Read length: 75bp


title: CKO for CUT&RUN using H3K4me1, Rep1

value: Hnrnpk CKO


title: WT for CUT&RUN using H3K4me1, Rep2

value: WT


title: PBMCs, NC2

description: 10x Genomics

value: peripheral blood mononuclear cell

value: male


title: Ikba_KO_LT-HSC_H3K27me3_1 [Cut&Tag]

description: Read length: 75bp


title: WT for CUT&RUN using H3K4me1, Rep1


title: Ikba_KO_LT-HSC_H3K27me3_2 [Cut&Tag]

description: Read length: 75bp


title: E11.5_Ikba_CD31_1 [Cut&Tag]

description: Read length: 50bp

source_name: E11.5 CD31+ cells

growth_protocol: Primary AGM CD31+ cells were obstained by disecting AGMs from E11.5 embryos folled by FACS sorting.

extract_protocol:
cut and tag experiments were performed on lightly fixed cell suspension and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with unique index primers and NEBNext HiFi 2x PCR Master mix (cat#M0541S) as decribed in bentop cut and tag v3.
Illumina HiSeq 2500  paired end sequencing run

value: AGM

value: rabbit anti IκB-α

value: C-21, santa cruz


title: TCam-2 mimic scrambled #4

city: Nottingham

first: Cinzia

last: Allegrucci

state: Notts

address: Science Road

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Assembly: GRCh38.83
Supplementary files format and content: Tab delimited text file contain gene expression in counts

source_name: Testis

growth_protocol: NTERA cells were maintained at 37C and 5% CO2in  DMEM medium supplemented with 10% fetal bovine serum and 2 mM L-Glutamine. TCAm-2 cells were maintained at 37C and 5% CO2 in RPMI medium supplemented with 10% fetal bovine serum , 2 mM L-Glutamine, 1% MEM non essential aminoacids and 1% sodium pyruvate.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini kit with oncolumn DNase treatment
NEBNext ULTRA TM RNA library prep kit for Illumina

treatment_protocol: cells were transfeted with miRNA mimics (MIR9-2-5p or scrambled) using the Transit-IT X2 transfection reagent. Cells were collected 3 days after transfection.

value: Testis

tag: cell line

value: Germ cells tumour cells

value: Male

value: mimic scrambled


title: Ikba_WT_LT-HSC_H3K27me3_2 [Cut&Tag]

description: Read length: 75bp

value: fetal liver

tag: antibody

value: Tri-Methyl-Histone H3 (Lys27)

value: C36B11, cell signaling


title: TCam-2 mimic scrambled #3

tag: cell type


title: CKO for CUT&RUN using Ctcf, Rep1

tag: genotype

value: mice limb bud cells

value: Ctcf

value: Ctcf  binding DNA


title: WT for CUT&RUN using Ctcf, Rep2


title: CKO for CUT&RUN using Ctcf, Rep2

value: Hnrnpk CKO


title: PBMCs, NC1

description: 10x Genomics

value: 24 year-old

tag: treatment

value: NO


title: WT for CUT&RUN using Ctcf, Rep1

value: WT


title: Tcam-2 mimic scrambled #2


title: Tcam-2 mimic scrambled #1


title: TCam-2 mimic MIR9-2-5p #4

value: mimic MIR9-2-5p


title: naive mice, biol rep1

first: Xin

last: Sun

state: CA

address: 9500 Gilman Dr., CMME, Room 1055

department: Department of Pediatrics, Department of Biological Sciences

institute: UNIVERSITY OF CALIFORNIA AT SAN DIEGO

description:
Raw data in fastq format. UMI count matrix files (h5) from cellranger. Seurat object in R object.
Reads alignment files in fastqs-intergrated_Yujuan_nTS_WT.rds

data_processing:
Sequencing was carried out on NovaSeq (Illumina) platform at the Institute for Genomic Medicine, UCSD.
Cell Ranger package (version 3.0.2) was used to align the raw reads onto the mouse reference genome (GRCm38) with default parameters and generate the feature-barcode matrix.
CellBender was used next to model and remove systematic biases and background noise, and to produce improved estimates of gene expression.
R package Seurat (version 4.0) was used to perform data quality control, normalization, principal components analysis and uniform manifold approximation and projection  (UMAP method).
For raw data from WT, Saline or HDM conditions, we firstly used SCTransform to regress our batch effects and did doublets removal separately. We then integrated all the data from three conditions (WT, Saline, HDM) using Harmony.
Cells with 3,500 to 5,500 unique feature counts were considered high quality cells and used for further analysis. The integrated dataset was normalized, scaled, and then analyzed for variable genes using Seurat’s NormalizeData, ScaleData, and FindVariableFeatures functions, respectively. A total of 2,000 top variable features were identified by function FindVariableFeatures and selected for subsequent principal components analysis.
Top 20 significant components were chosen to conduct cell clustering by using the algorithm of uniform manifold approximation and projection (UMAP) with default settings. The expression level and feature of selected genes were profiled and visualize by R package ggplot2 (version 3.3.2).
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary files format and content: For data from all conditions (WT, Saline or HDM-treated mice):  UMI count matrix files (h5) from cellranger. Seurat object in R object (single condition rds and also intergrated rds-labeled with merged_filtered8 rds which were used to generate figures (merged_filtered8.rds integrated all 4 samples; merged_filtered8_wt.rds integrated WT1 AND WT2 samples; merged_filtered8_saline_HDM.rds - integrated Saline and HDM samples)).

source_name: solitary nucleus of the brainstem

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics Chromium Controller (10x Genomics, Pleasanton, CA) to generate single cell GEMs. cDNA extraction and amilification were excecuted using Chromium Single Cell 3' Reagent Kits (v3 Chemistry, PN-1000075, 10X Genomics) folloing User Guide provided by 10X Genomics.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v3 (PN-1000075, 10x Genomics) following User Guide provided by 10X Genomics.
scRNA-seq library for 10X Genomics sequencing

treatment_protocol: Saline or house dust mite (HDM) intranasal delivery to the mice

value: solitary nucleus of the brainstem

value: 12 weeks

value: male

value: wild-type

value: no treatment


title: TCam-2 mimic MIR9-2-5p #1

value: Testis

value: Germ cells tumour cells

value: Male


title: CKO for HiC

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0. For ATAC-seq: The 150 bp paired-end reads were mapped to the reference genome by using bowtie2 (v2.11.1). For CUT&RUN: CutRunTools pipeline was used to peformed CUT&RUN processing and footprint analysis. For HiC: it-Hi-C was used for assigning statistical confidence estimates to intra-chromosomal contact maps.
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3). For ATAC-seq: Significant peak regions of each samples were identified using MACS2 (v2.1.2) with parameters "-q 0.05 --nomodel --shift -100 --extsize 200".
Genome_build: mm10

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction. For CUT&RUN: The protein binding DNA was  isolated from cells using EpiTM CUT&RUN Assay Kit (Epibiotek, cat. no R1816). Extract DNA was processed for library generation using the QIAseq Ultralow Input Library Kit (QIAGEN) following the manufacturer’s protocol. For ATAC-seq: The chromatin DNA was isolated from cells for library construction using EpiTM ATAC-seq kit(Epibiotek, cat. no EPI20180202) . For HiC: We used the HiC-pro pipeline (Servant et al. 2015) to process the Hi-C raw data.

value: interaction DNA


title: E11.5_Ikba_CD31_2  [Cut&Tag]

description: Read length: 75bp

data_processing:
Followed steps for data preprocessing (i) Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap.
(ii) Trimmed reads were aligned to GRCm38 reference genome with Bowtie2 aligner tool (v2.4.4) (Langmead & Salzberg, 2012). Reference genome was retrieved from Ensembl FTP site (http://ftp.ensembl.org/pub/release-102/).
(iii) Bowtie2 was executed with following parameters: --no-mixed –no-discordant –dovetail –very-sensitive-local. Multi-mapped reads and those reads showing MAPQ < 20 were filtered out.
(iv) [Only applicable for H3K27me3 samples] Peak calling was performed with SEACR (v1.3) in stringent mode without considering IgG control sample (Meers et al., 2019). For this purpose, required input bedgraph files were obtained from deduplicated BAM files using bedtools (v2.30) following SEACR authors guidelines (Quinlan & Hall, 2010). The top 0.5% of peaks were retrieved for downstream analysis.
(v) BigWig files were obtained from BAM files with duplicates using deepTools (v3.5.1)
Assembly: mm10
Supplementary files format and content: BigWig files and detected SEACR peaks in .bed files (only applicable for H3K27me3 experiments)
Library strategy: Cut&Tag

source_name: AGM

extract_protocol:
cut and tag experiments were performed on lightly fixed cell suspension and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with unique index primers and NEBNext HiFi 2x PCR Master mix (cat#M0541S) as decribed in bentop cut and tag v3.

tag: developmental time

value: AGM

value: rabbit anti IkB-a

tag: ab description

value: C-21, santa cruz


title: NTERA-2 mimic scrambled #4

value: mimic scrambled


title: Saline-treated mice

description:
Raw data in fastq format. UMI count matrix files (h5) from cellranger. Seurat object in R object.
Reads alignment files in fastqs-intergrated_Yujuan_nTS_Saline_HDM.rds

tag: strain

tag: age

value: Saline intranasal delivery to lung


title: WT for HiC

value: Hnrnpk WT

value: mice limb bud cells


title: TCam-2 mimic MIR9-2-5p #2

value: mimic MIR9-2-5p


title: naive mice, biol rep2

value: solitary nucleus of the brainstem


title: TCam-2 mimic MIR9-2-5p #3


title: NTERA-2 mimic scrambled #2


title: CKO for CUT&RUN using H3K4me3

data_processing:
Library strategy: CUT&RUN
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0. For ATAC-seq: The 150 bp paired-end reads were mapped to the reference genome by using bowtie2 (v2.11.1). For CUT&RUN: CutRunTools pipeline was used to peformed CUT&RUN processing and footprint analysis. For HiC: it-Hi-C was used for assigning statistical confidence estimates to intra-chromosomal contact maps.
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3). For ATAC-seq: Significant peak regions of each samples were identified using MACS2 (v2.1.2) with parameters "-q 0.05 --nomodel --shift -100 --extsize 200".
Genome_build: mm10

value: Hnrnpk CKO

value: H3K4me3 binding DNA


title: PGCs, F04, R3

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

data_processing:
Bismark v0.23.1 (https://doi.org/10.1093/bioinformatics/btr167) was used to align DNA reads to the bisulfite converted GRCm38 mouse genome then perform methylation calling.
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

source_name: PGCs, F04

extract_protocol:
PGCs (GOF18-GFP+SSEA1+) were isolated from E12.5 embryos carrying the GOF18-GFP reporter by FACS into lysis buffer (Qiagen RLT plus buffer)
WGBS-sequencing libraries were prepared according to the bulk version of the published scBS-seq protocol (https://www.nature.com/articles/nprot.2016.187). Briefly, cells were lysed in RLT plus buffer (Qiagen) then bisulfite converted using the Zymo EZ-Direct kit. Converted DNA was prepared for Illumina sequencing via two rounds of random primed synthesis using oligos containing Illumina adapter sequences followed by PCR to amplify and incorporate indexes.

value: Primordial germ cell

value: PCNA knockout


title: NTERA-2 mimic scrambled #1

value: Testis


title: PGCs, D05, R3

source_name: PGCs, D05

value: wildtype


title: HDM-treated mice

value: 12 weeks

value: male

value: wild-type

value: House dust mite (HDM) intranasal delivery to lung


title: NTERA-2 mimic MIR9-2-5p #4

value: Germ cells tumour cells

value: Male


title: NTERA-2 mimic MIR9-2-5p #3


title: WT for CUT&RUN using H3K4me1

value: H3K4me1 binding DNA


title: PGCs, D04, R3

source_name: PGCs, D04


title: PGCs, C04, R3

source_name: PGCs, C04


title: WT for CUT&RUN using H3K4me3

value: Hnrnpk WT


title: CKO for CUT&RUN using H3K4me1

value: mice limb bud cells


title: CKO for CUT&RUN using Ctcf

value: Ctcf  binding DNA


title: PBMCs, M1

description: 10x Genomics

value: peripheral blood mononuclear cell

value: 24 year-old

value: MXF


title: NTERA-2 mimic MIR9-2-5p #2

value: mimic MIR9-2-5p


title: WT for CUT&RUN using Ctcf


title: PGCs, B05, R3

source_name: PGCs, B05

value: Primordial germ cell


title: NTERA-2 mimic scrambled #3

value: Testis

value: mimic scrambled


title: NTERA-2 mimic MIR9-2-5p #1


title: Patient_6_Run2

description: 5' v1.1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Fresh tumor tissue was collected from lymph nodes of four adult patients with classical Hodgkin lymphoma. . Tumor biopsies were minced, fragmented into single-cell suspensions using a 0.45-μm filter, and washed 3X with 0.04% BSA in PBS. Single-cell suspensions were loaded onto the 10X Genomics Chromium Controller.
Gene expression libraries were prepared using the Chromium Single Cell 5′ Reagent Kit with v1.1 Chemistry (10X Genomics) according to the manufacturer's instructions.

treatment_protocol: Tumor tissue was not pretreated before mincing and flitering into single-cell suspension

value: Hodgkin lymphoma

value: lymph node


title: CKO Rep3 for ATAC-seq

value: Hnrnpk CKO

value: chromatin DNA


title: CKO Rep2 for ATAC-seq


title: WT for CUT&RUN using Hnrnpk

value: Hnrnpk binding DNA


title: Patient_2

description: 5' v1.1


title: PGCs, F04, R1

value: PCNA knockout


title: PGCs, D04, R1


title: PGCs, C04, R1


title: Patient_6_Run1

description: 5' v1.1


title: Patient_3

description: 5' v1.1


title: CKO Rep1 for ATAC-seq


title: PGCs, B05, R1

value: wildtype


title: Patient_1

description: 5' v1.1


title: WT Rep1 for ATAC-seq

value: Hnrnpk WT


title: WT Rep3 for ATAC-seq

value: mice limb bud cells


title: CKO Rep3 for RNA-seq

value: totalRNA


title: iPSC-derived neural graft, FTD, GF011

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description: 10X Genomics

data_processing:
All snRNA samples were processed with 10X genomics software Cell Ranger.
In each sample run (Batch), Cellranger v3 was used to map sequenced transcripts to a dual reference for human (GRCh38)
For each Batch, only genes expressed in at least 10 nuclei were kept. Batches were merged into one data object and percentages of human mitochondrial genes and ribosomal- related genes were assessed, after which mitochondrial related genes for human .
This merged data object was then filtered, keeping only nuclei with less than 5% mitochondrial related genes, more than 1,000 and less than 25,000 unique mapped transcripts (Unique Molecular Identifiers – UMIs).
For normalization of this merged data object, the Seurat function “SCTransform” was used to identify 3000 variable genes in all nuclei and regress out UMI counts, percent of mitochondrial genes and percent of ribosomal-related genes. 50 principal components and 20 neighbors were used to embed nuclei into a Uniform Manifold Approximation and Projection (UMAP) space for visualization and to identify cell clusters using the standard Louvain community detection algorithm implemented in Seurat.     Finally, the Seurat function “FindAllMarkers” was used to find gene markers for cell clusters among the 3000 variable genes identified by SCTransform.
Assembly: GRCh38 Ensemble 91
Supplementary files format and content: .txt files of count matrix

source_name: iPSC-derived neural graft

growth_protocol: Neural progenitor cells (NPCs) were generated and cultured as previously described (Hargus et al., 2014; Reinhardt et al., 2013). Briefly, iPSC colonies were detached from MEFs 3–4 days after splitting using 2 mg/ml collagenase IV. Pieces of colonies were collected by sedimentation and resuspended in human ESC media (without FGF2) supplemented with 10 μM SB-431542 (Ascent Scientific), 1 μM dorsomorphin (Tocris), 3 μM CHIR 99021 (Axon Medchem), and 0.5 μM purmorphamine (PMA; Alexis) and subsequently cultured as embryoid bodies (EBs) in Petri dishes. On day 2, media was changed to N2B27 media containing the same small-molecule supplements. N2B27 medium consisted of Dulbecco’s modified Eagle’s media (DMEM)-F12 (Invitrogen)/Neurobasal (Invitrogen) 50:50 with 1:200 N2 supplement (Invitrogen), 1:100 B27 supplement lacking vitamin A (Invitrogen) with1%penicillin/streptomycin/glutamine (PAA). On day 4, SB-431542 and dorsomorphin were withdrawn and 150 mM ascorbic acid (AA; Sigma) was added to the media. On day 6, EBs were triturated into smaller pieces and plated on Matrigel- coated (Matrigel, growth factor reduced, high concentration; BD Biosciences) 12-well plates (Nunc) in NPC expansion media (N2B27 with CHIR, PMA, and AA). Media was changed every other day and cells were typically split 1:10–1:15 every 5–6 days. For splitting, cells were digested to single cells for approximately 10 min at 37C using prewarmed Accutase (PAA). Cells were diluted in DMEM (PAA) and spun down at 1,000 rpm for 5 min. The cell pellet was resuspended in fresh NPC expansion media and plated on Matrigel-coated cell culture dishes.

extract_protocol:
(Post-mortem samples) Nuclei were isolated from frozen surgical resection specimen as described previously (Al- Dalahmah et al., 2020). Briefly, frozen tissue samples were homogenized using a dounce homogenizer in ice-cold 30% sucrose 0.1% Triton-X 100 based homogenization buffer. 10-15 strokes of the loose dounce pestle were followed by 10-15 strokes of the tight dounce pestle on ice. Mixing using a P1000 pipette followed before filtration through a BD Falcon 40um filters. Filtration was repeated after a 10-minute spin at 1000g at 4c. A cleanup step followed using a density gradient step as described (Krishnaswami et al., 2016)
For neuronal differentiation of NPCs, expansion media was changed 2 days after splitting to neuronal induction media consisting of N2B27 medium supplemented with 1 μM PMA, 200 μM AA and 3 μM CHIR 99021. After 6 days of differentiation the neuronal induction media was replaced by neuronal maturation media consisting of N2B27 with 20 ng/ml BDNF, 10 ng/ml GDNF, 1 ng/ml TGF-β3 (Peprotech), 200 μM AA, and 500 μM dbcAMP (Sigma Aldrich). Media was changed every other day and cultures were analyzed after three weeks in maturation conditions.
(Post-mortem samples) The nuclear pellet was suspended in 1% BSA in PBS resuspension buffer containing RNAse inhibitors. A final filteration step using 20um Flowmi TM filters followed before dilution to 700-1200 nuclei per ul in resuspension buffer. The nuclear suspensions were processed by the Chromium Controller (10x Genomics) using single Cell 3’ Reagent Kit v2 or v3 (Chromium Single Cell 3’ Library & Gel Bead  Kit v2, catalog number: 120237; Chromium Single Cell A Chip Kit, 48 runs, catalog number: 120236; 10x Genomics).
Grafts composed of human iPSC-derived neural cells were microdissected and submitted to nuclei isolation, followed by a standard single nucleus RNA-seq library preparation and sequencing.
snRNA (single-nuclei RNA sequencing)

value: iPSC-derived neural graft

tag: disease state

value: FTD


title: E14.5_Ikba_LT-HSC_1 [Cut&Tag]

description: Read length: 75bp

value: fetal liver

value: rabbit anti IκB-α

value: C-21, santa cruz


title: iPSC-derived neural graft, FTD, GF017

description: 10X Genomics


title: iPSC-derived neural graft, FTD, GF015

description: 10X Genomics


title: WT Rep2 for ATAC-seq


title: CKO Rep2 for RNA-seq


title: CKO Rep1 for RNA-seq


title: PGCs, D05, R1

value: Primordial germ cell


title: iPSC-derived neural graft, Ctrl , GF016

description: 10X Genomics

value: Ctrl


title: Ureter_UUO4d_Col17a1-KO3

type: RNA

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

hyb_protocol: Gene Expression Hybridization Kit (Agilent) was used, and 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 25x fragmentation buffer and 10x GE blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2600D) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Ver.12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Ureter at 4 day after UUO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

growth_protocol: All mice were maintained under specific pathogen-free conditions.

extract_protocol: Total RNA from cells was purified using RNeasy Mini Kit (Qiagen)  following the manufacturer's recommendations. RNA samples were checked for RNA integrity on a Bioanalyzer 2100 II (Agilent Technologies).

treatment_protocol: These mice were performed with UUO, and those ureters were collected 4 days after UUO.

value: C57BL/6N, Col17a1-KO

tag: gender

value: Female

value: 2 months

value: ureter


title: iPSC-derived neural graft, Ctrl , GF014

description: 10X Genomics


title: WT Rep3 for RNA-seq

source_name: mice limb bud cells


title: iPSC-derived neural graft, Ctrl , GF010

description: 10X Genomics


title: BE2C_mock

first: Qiangsong

last: Tong

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of empty vector

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: BE(2)-C stably transfected with empty vector

growth_protocol: Human neuroblastoma cell line BE(2)-C was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, 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 construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The GATA2-AS1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of puromycin.

value: neuroblastoma

tag: passages


title: BE2C_GATA2_AS1

description: Gene expression after stable transfection of GATA2-AS1

source_name: BE(2)-C stably transfected with GATA2-AS1


title: Ureter_UUO4d_Col17a1-KO2

value: Male


title: iPSC-derived neural graft, Ctrl , GF012

description: 10X Genomics


title: WT Rep1 for RNA-seq

tag: molecule


title: Ureter_UUO4d_Col17a1-KO1


title: WT Rep2 for RNA-seq


title: iPSC-derived neural graft, FTD, GF013

description: 10X Genomics


title: Postmortem human brain, Ctrl , HO013

description: 10X Genomics

source_name: Postmortem human brain

value: Postmortem human brain


title: Postmortem human brain, Ctrl , HO011

description: 10X Genomics


title: shPdgf-d mESCs-2

first: Weisi

last: Lu

address: No.7 Jinsui Road

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling.
Sequenced reads were trimmed for adaptor sequence by fastQC, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 mouse genome using Hisat2 software.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using StringTie and R software Ballgown package.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file include FPKM values for all Samples

source_name: shPdgf-d mESCs

growth_protocol: Mouse embryonic stem cells (mESCs) were maintained in culture dish coated with 0.1% gelatin in ESC medium, which contained Knockout DMEM medium and supplemented with 15% (v/v) fetal bovine serum , β–mercaptoethanol (0.1µM), GlutaMax-I supplement (2mM), MEM non-essential amino acids (0.1 mM), 1% (v/v) Penicillin-Streptomycin, LIF (1,000 U/ml), and 2 inhibitors (CHIR99021, PD325901 at 3 µM and 1 µM, respectively)

extract_protocol:
Total RNA was extracted from shControl or shPdgf-d mESCs by Trizol regent. 1 ∼ 2 µg of total RNA was used for the construction of sequencing libraries by KAPA Stranded RNA-Seq Library Prep Kit(Illumina).
RNA libraries for sequencing were prepared following standard Illumina protocols

treatment_protocol: To generate stable Pdgf-d knockdown mESCs, 1μg pLent-Pdgf-d-4in1-shRNA plasmids were transfected into HEK293T cells together with 2μg lentivirus packing plasmids pSPAX2 and pMD2G using Lipofectamine 2000. Supernatants containing the viral particles was collected and added to the mESCs. New ESC medium was added 6 hours later. Cells were selected by puromycin (2 μg/ml). pLent-4in1-shRNA-GFP-Puro was used as a negative control.

value: embryonic stem cells

tag: passage

value: passage 25

value: transfected with pLent-Pdgf-d-4in2-shRNA plasmids


title: shPdgf-d mESCs-3

value: transfected with pLent-Pdgf-d-4in3-shRNA plasmids


title: C&R,Zf5,Zld,Rep6

city: philadelphia

first: Mustafa

last: Mir

address: 3501 Civic Center Boulevard, CTRB 9030

institute: Children's Hospital of Philadelphia

data_processing:
For ATAC-seq and CUT&RUN, reads were aligned to the Berkeley Drosophila Genome Project (version six) reference genome using bowtie2 with the ‘--sensitive-local’ setting. Samtools was used to convert from .sam to .bam, index, sort, and remove duplicate, unmapped, and multi-mapped reads. For Cut and Run, peaks were called using macs2 using the ‘-f BAMPE’, ‘-g 129789873’, and ‘--bw 300’ settings using IgG as a control. For ATAC-seq, no IgG was used as a control and --nomodel --nolambda settings were used. Consensus peaks were called using the ‘diffbind’ package in R. Peaks were annotated using the CHIPseeker package and ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ annotation. Bigwig files were generated using the Bamcoverage function from the deeptools package using the a ‘--binSize 20’, ‘--smoothLength 60’, ‘--centerReads’, ‘--normalizeUsing RPKM’, ‘--effectiveGenomeSize 142573017’.
Assembly: DM6
Supplementary files format and content: .bw files with averaged RPKM with a bine size of 20
Library strategy: Cut and Run

organism: Drosophila melanogaster

extract_protocol:
Embryos were staged to NC12-NC13 and were placed and briefly dried on a double-sided tape . Using a sterile 18 gauge metal needle, embryos were popped into pools of the wash buffer previously described in Panday, A. 2022. Extracted contents were quickly moved in the wash buffer into a 1.5ul tube and temporarily stored at room temperature while samples were collected. Nuclei were collected by slow centrifugation at room temperature at 1500 RCF for 10 minutes.
Cut & Run libraries were made using NEBNext Ultra II NGS library kit and size selected using AMPure XP beads using manufacturer’s protocols.

value: mNG-ZF5 GLC

value: Zelda


title: shPdgf-d mESCs-1

value: transfected with pLent-Pdgf-d-4in1-shRNA plasmids


title: Postmortem human brain, Ctrl , HO009

description: 10X Genomics


title: C&R,Zf5,Zld,Rep5


title: C&R,Zf5,Zld,Rep4


title: Ureter_UUO4d_Col17a1-WT3

value: C57BL/6N, Col17a1-WT


title: Postmortem human brain, Ctrl , HO007

description: 10X Genomics


title: C&R,Zf5,Zld,Rep3


title: shControl mESCs-2

source_name: shControl mESCs

value: transfected with negtive control plasmids


title: Postmortem human brain, Ctrl , GO005

description: 10X Genomics

value: Ctrl


title: Ureter_UUO4d_Col17a1-WT2


title: C&R,Zf5,Zld,Rep2


title: shControl mESCs-1


title: C&R,Zf5,Zld,Rep1


title: Postmortem human brain, Ctrl , GO003

description: 10X Genomics


title: Ureter_UUO4d_Col17a1-WT1


title: Postmortem human brain, Ctrl , HO002

description: 10X Genomics


title: C&R,WT,Zld,Rep2

value: sfGFP-ZLD


title: Postmortem human brain, FTD, HO012

description: 10X Genomics

value: FTD


title: C&R,WT,Zld,Rep3


title: male_3d_3 (GRZ_GONAD_10b)

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_10b

data_processing:
Reads were extracted as FastQ sequences using bcl2fastq v1.8.4 (provided by Illumina).
The reads were filtered with sga (parameters: preprocess -q 30 -m 50 --dust; https://github.com/jts/sga).
Quality-passed reads were mapped to the N. furzeri reference genome (assembly version Nfu_20150522, gene annotation version 150922) using STAR (parameters: --alignIntronMax 100000) (PMID: 23104886)
Counts per sample and gene were obtained with the summarizeOverlaps function of the R package GenomicAlignments (PMID: 23950696)
Assembly: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de) (PMID: 26638077)
Supplementary files format and content: csv file containing raw read counts per gene over all samples

organism: Nothobranchius furzeri

source_name: trunk

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen) according to Baumgart et al., 2012 (PMID: 22487494)
Libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).

value: trunk

tag: Sex

value: male

value: 3 dph


title: Postmortem human brain, FTD, HO010

description: 10X Genomics


title: male_3m_1 (GRZ_GONAD_4)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_4

source_name: testis

value: testis

value: 3 month


title: shControl mESCs-3

value: embryonic stem cells


title: female_3m_1 (GRZ_GONAD_1)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_1

source_name: ovary

value: ovary

value: female


title: male_3d_1 (GRZ_GONAD_7b)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_7b


title: Postmortem human brain, FTD, HO008

description: 10X Genomics

value: Postmortem human brain


title: C&R,Zf5,IgG,Rep1

value: mNG-ZF5 GLC

value: IgG


title: C&R,WT,Zld,Rep1

value: Zelda


title: Postmortem human brain, FTD, GO004

description: 10X Genomics


title: C&R,Zf5,IgG,Rep2


title: Postmortem human brain, FTD, GO006

description: 10X Genomics


title: male_3d_2 (GRZ_GONAD_8b)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_8b


title: female_3d_2 (GRZ_GONAD_11b)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_11b


title: female_3d_1 (GRZ_GONAD_9b)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_9b


title: Postmortem human brain, FTD, HO001

description: 10X Genomics


title: female_3d_3 (GRZ_GONAD_12b)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_12b


title: iPSC neurons, FTDmetformin-2

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to the fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12) using kallisto (0.44.0) was performed.
Differentially expressed genes were identified using Sleuth or DESeq2, R packages designed to test differential expression between experimental groups from RNA-seq counts data.
Assembly: Human:GRCh38.p12
Supplementary files format and content: .csv file of count matrix of all samples in each column

source_name: iPSC-derived neurons

extract_protocol:
For neuronal differentiation of NPCs, expansion media was changed 2 days after splitting to neuronal induction media consisting of N2B27 medium supplemented with 1 μM PMA, 200 μM AA and 3 μM CHIR 99021. After 6 days of differentiation the neuronal induction media was replaced by neuronal maturation media consisting of N2B27 with 20 ng/ml BDNF, 10 ng/ml GDNF, 1 ng/ml TGF-β3 (Peprotech), 200 μM AA, and 500 μM dbcAMP (Sigma Aldrich). Media was changed every other day and cultures were analyzed after three weeks in maturation conditions.
Poly-A pull-down was applied to enrich for mRNAs from total RNA samples followed by library construction using Illumina TruSeq chemistry. Libraries were sequenced at the Columbia Genome Center using Illumina NovaSeq 6000. Samples were multiplexed in each lane yielding targeted number of paired-end 100bp reads for each sample.
bulk-RNA sequencing

treatment_protocol: Lentivirus expressing human SPP1 was obtained from VectorBuilder. Scrambled RNA lentiviral particles and shRNA lentiviral particles for the downregulation of SPP1 were purchased from Sigma. Three different SPP1-shRNAs were used. An MOI of 5 was applied for transduction of 50,000 NPCs or neurons, respectively.

value: iPSC-derived neurons

value: FTD with metformin


title: male_0d_3 (GRZ_GONAD_10_0)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_10_0

value: 0 dph


title: C&R,Zf5,Gaf,Rep1

value: sfGFP-ZLD

value: GAF


title: male_0d_1 (GRZ_GONAD_6_0)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_6_0

value: trunk


title: iPSC neurons, FTDvehicle-3

value: FTD

value: FTD with vehicle


title: male_0d_2 (GRZ_GONAD_8_0)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_8_0

value: male


title: iPSC neurons, FTDmetformin-1


title: male_10dpf_3 (GRZ_GONAD_12_10)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_12_10

source_name: embryo

value: embryo

value: 10 dpf


title: iPSC neurons, FTDvehicle-1


title: female_0d_1 (GRZ_GONAD_5_0)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_5_0


title: male_10dpf_2 (GRZ_GONAD_6_10)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_6_10


title: iPSC neurons, FTDvehicle-2


title: iPSC neurons, FTDscr-2

value: FTD with scrambled shRNA


title: iPSC neurons, FTDscr-4


title: male_10dpf_1 (GRZ_GONAD_1_10)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_1_10


title: iPSC neurons, FTDscr-1


title: iPSC neurons, FTDmetformin-3


title: female_10dpf_1 (GRZ_GONAD_7_10)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_7_10

value: female


title: female_10dpf_2 (GRZ_GONAD_8_10)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_8_10


title: iPSC neurons, FTDshSPP1-3

value: FTD with downregulation of SPP1


title: iPSC neurons, FTDshSPP1-4


title: iPSC neurons, FTDshSPP1-2


title: iPSC neurons, FTDshSPP1-1


title: JURKAT, Input

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Preprocessing of the raw sequence reads was done with PRINSEQ-lite (version 0.20.4).
The remaining high quality reads were aligned with BWA (version 0.7.15-r1140) against the human reference genome (GRCh38) and further processed to bam files with samtools (version 1.4).
The deepTools (version 3.5.1) bamCompare function was applied to create CPM normalized bigWig files.
These were then visualized in R (version 4.2.1) with rtracklayer (version 1.56.1).
ChIP-seq peaks were called with MACS27 (version 2.1.0) against the respective input controls.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

source_name: Lymphoid

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For each ChIP, 5 μg of antibody coupled to 2 μg of magnetic Dynabeads (Life Technologies) was added to 3 mL of sonicated nuclear extract from formaldehyde-fixed cells. Chromatin was immunoprecipitated overnight, cross-links were reversed, and DNA was purified by precipitation with phenol:chloroform:isoamyl alcohol. DNA pellets were resuspended in 25 μL of TE buffer.
Libraries for Illumina sequencing were prepared following the Illumina TruSeq DNA Sample Preparation v2 kit. Amplified libraries were size-selected using a 2% gel cassette in the Pippin Prep system from Sage Science set to capture fragments between 200 and 400 bp. Libraries were quantified by qPCR using the KAPA Biosystems Illumina Library Quantification kit according to kit protocols.

value: Lymphoid

value: JURKAT

tag: stat5 activation

value: low

value: precursor T-cell

value: WT

tag: chip antibody


title: iPSC neurons, CtrlGFP-4

value: iPSC-derived neurons

value: Ctrl

value: Ctrl with overexpression of GFP


title: female_0d_2 (GRZ_GONAD_12_0)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_12_0

tag: tissue

value: trunk

value: 0 dph


title: LOUCY, Input

tag: cell line

value: LOUCY


title: iPSC neurons, CtrlGFP-3

tag: cell type


title: iPSC neurons, FTDscr-3

value: FTD


title: female_10dpf_3 (GRZ_GONAD_9_10)

description:
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_9_10

value: embryo


title: iPSC neurons, CtrlGFP-2


title: iPSC neurons, CtrlGFP-1


title: SUP-T13, Input

value: high

tag: genotype


title: MG63 cells, Control

first: zheng

last: jianwei

address: School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 East Huanhuan Road, Guangzhou

institute: SYSU

data_processing:
sample1-7:single sequencing was performed with Illumina HiSeq 3000 (RiboBio Co, Ltd). TopHat2 and HTSeq were used for RNA-seq data analysis with GRCh38/hg19 as the reference genome. Differential analysis of the RNA-seq data was performed using DESeq2 analysis.
Assembly: hg38
Supplementary files format and content: sample1-7:tab-delimited text files include TPM values for each Sample

source_name: Homo sapiens

growth_protocol: 143B and MG63 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample1-7:Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
sample1-7:DNase I was used for column digestion to ensure RNA quality. RNA library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (E7420L). RNA libraries were prepared for paired-end sequencing using standard Illumina protocols.

treatment_protocol: 143B and MG63 cells were treated with XY018 or GSK805 for 48 h.

value: Homo sapiens

value: tumor cells

tag: treatment

value: Control


title: MG63 cells, GSK805


title: 143B cells,SR2211


title: iPSC neurons, CtrlSPP1-3

value: Ctrl with overexpression of SPP1


title: HSB-2, Input

value: Lymphoid


title: SUP-T13, STAT5B

value: R&D Sytems AF1584 (anti-STAT5B)


title: MG63 cells, XY018


title: iPSC neurons, CtrlSPP1-4


title: ATAC,Zf5,rep2

data_processing:
For ATAC-seq and CUT&RUN, reads were aligned to the Berkeley Drosophila Genome Project (version six) reference genome using bowtie2 with the ‘--sensitive-local’ setting. Samtools was used to convert from .sam to .bam, index, sort, and remove duplicate, unmapped, and multi-mapped reads. For Cut and Run, peaks were called using macs2 using the ‘-f BAMPE’, ‘-g 129789873’, and ‘--bw 300’ settings using IgG as a control. For ATAC-seq, no IgG was used as a control and --nomodel --nolambda settings were used. Consensus peaks were called using the ‘diffbind’ package in R. Peaks were annotated using the CHIPseeker package and ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ annotation. Bigwig files were generated using the Bamcoverage function from the deeptools package using the a ‘--binSize 20’, ‘--smoothLength 60’, ‘--centerReads’, ‘--normalizeUsing RPKM’, ‘--effectiveGenomeSize 142573017’.
Assembly: DM6
Supplementary files format and content: .bw files with averaged RPKM with a bine size of 20

extract_protocol:
Embryos were staged at NC12-NC13; placed on double-sided tape and rinsed before they were placed in 1.5 mL tube caps. Embryos were macerated with an 18-gauge needle in lysis buffer containing 10mM Tris-HCl pH7.5; 10mM NaCl, 3mM MgCl2; 0.1% Igepal-630.
ATAC libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Small Kit with Nextera DNA CD indexes following manuafactor's protocol and previously described methods from Blythe, SA and Buenrostro JD.

value: 5th Zinc Finger of Zelda deleted


title: 143B cells, XY018


title: iPSC neurons, CtrlSPP1-2


title: KYSE960 exosome hypoxia

city: Chiba-Shi

first: Yasunori

last: Matsumoto

state: Chiba

address: 1-8-1 Inohana, Chuo-Ku

department: Frontier Surgery

institute: Chiba University

hyb_protocol: Arrays were incubated with GeneChip™ Hybridization Oven 645 at 48°C for 18 hours (60 rpm) according to the protocol supplied with the kit. The arrays were cleaned using the GeneChip™ Fluidics Station 450 according to the protocol supplied with the kit.

scan_protocol: Arrays were scanned using the GeneChip™ Scanner 3000 7G according to the accompanying manual <GeneChip™ Command Console (AGCC) 4.0 User Manual>.

data_processing:
Arrays were read using a GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific, Inc.). Images were quantified and corrected using Expression Console™ Software (Thermo Fisher Scientific, Inc.). Normalization was performed by RMA-DABG, and quality flags were calculated by Affymetrix® Expression Console™ Software and are denoted as P: Probes with detectable transcripts and A: Probes with ambiguous transcript detection.
Up regulation (Ratio≥2) is defined when it is more than twice the control, or Down regulation (Ratio≤0.5) when it is less than 1/2 the control. Only data for which both "test,control" in the Quality flag are set to "P" are selected.

label: biotin

source_name: exosomal RNA 48h hypoxia

label_protocol: Biotin-labeled samples were prepared using the FlashTag™ Biotin HSR RNA Labeling Kit according to the protocol supplied with the kit.

growth_protocol: Cell lines were grown according to standard conditions up to 80% confluent. After that, the cells were incubated for 48 hours  under normoxia (O2: 20%) or hypoxia(O2: 1%).

extract_protocol: Exosomes were isolated from 10 ml of culture medium by ultracentrifuge (Optima TLX Ultracentrifuge, Beckman Coulter, CA, USA) at 10,000 g, 4°C for 90 min. Total Exosome RNA & Protein Isolation Kit ( Thermo Fisher Scientific, Inc, cat.#4478545) was used to extract total RNA from exosomes.

value: human esophageal  squamous cell carcinoma

tag: sample type

value: exosome

tag: stress

value: hypoxia


title: T.Tn exosome normoxia

source_name: exosomal RNA 48h normoxia

value: normoxia


title: ATAC,Zf5,rep1


title: HSB-2, STAT5B

value: precursor T-cell

value: WT


title: JURKAT, STAT5B

value: JURKAT

value: low


title: 143B cells, GSK805


title: DND-41, Input


title: KYSE960 exosome normoxia


title: iPSC neurons, CtrlSPP1-1

value: iPSC-derived neurons

value: Ctrl


title: ATAC,WT


title: 143B cells, Control

value: Homo sapiens


title: LOUCY, STAT5B

value: LOUCY


title: DND-41, STAT5B

value: high


title: T.Tn exosome hypoxia


title: H9_pericyte_a_d65

first: Ryan

last: Walsh

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC

description: 10x Genomics

data_processing:
Cellranger v6.1.2 was used for demultiplexing and generation of a count matrix
Assembly: GRCh38
Supplementary files format and content: comma separated count matrix

source_name: organoid

extract_protocol:
Organoids were dissociated with a papain dissociation system (Worthington) according to the manufacturer's protocol for 30min at 37C. The single cell suspension was washed, filtered and resuspended in 0.04% BSA/PBS + Ribolock RNase inhibitor for scRNAseq.
Libraries were constructed with the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to the manufacturer's protocol. In brief, single cell suspensions were loaded onto a Chromium Next GEM Chip G for GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 7,000-15,000 cells. cDNA amplification included 11-12 cycles and 30-240 ng of the material were used to prepare sequencing libraries with 10-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

value: organoid

value: progenitors & neurons

value: Pericyte


title: Patient #172, human colon organoids, differentiation (B+D) medium - calcitriol

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

data_processing:
Analyses were performed using Nextpresso RNAseq pipeline.
Sequencing read quality and cross-contamination analysis were performed by FastQC and FastqScreen softwares, respectively.
Raw reads were preprocessed using BBDuk software in order to trim polyA and trueseq adapters contaminant sequences
Raw reads were aligned to hg19 human genome assembly using Bowtie and TopHat aligners. Gene counts were generated from alignment maps using htseq-count function.
Differential expression analysis was performed as paired test using DeSEQ2 R package.
Assembly: hg19

source_name: colon

growth_protocol: Human colon normal organoids were seeded in Matrigel and grown in a culture medium enriched in stemness agents (PROL) according to Fernández-Barral et al. (FEBS J., 2020).

extract_protocol:
Macherey-Nagel RNA extraction Kit was used in combination with TRIZOL. Both large and small RNA was extracted. 500 ng of total RNA was used for the construction of sequencing libraries
RNA samples (500 ng; RQS/RIN average 8.6, range 7.3-9.6) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis.

treatment_protocol: Organoids growing in proliferation (PROL) medium for 5 days were washed twice in PBS and changed to either fresh PROL medium or differentiation (B+D) medium for additional 48 h in the presence of calcitriol (1,25(OH)2D3, 100 nM) or vehicle (ethanol).

value: colon

value: human colon epithelial stem cells

value: Male

value: Calcitriol (1,25(OH)2D3)


title: Patient #172, human colon organoids, differentiation (B+D) medium - control

value: Vehicle (ethanol)


title: Patient #172, human colon organoids, proliferation (PROL) medium - control


title: H9_Control_a_d65

description: 10x Genomics

value: Control


title: Patient #166, human colon organoids, differentiation (B+D) medium - calcitriol

value: Female


title: H9_H9_d100_LIF2

description: 10x Genomics

value: WT

value: LIF


title: Patient #166, human colon organoids, differentiation (B+D) medium - control


title: KOPT-K1, STAT5B

value: Lymphoid

value: precursor T-cell

value: R&D Sytems AF1584 (anti-STAT5B)


title: Patient #166, human colon organoids, proliferation (PROL) medium - control


title: H9_H9_d100_LIF1

description: 10x Genomics


title: H9_H9_d100_Control2

description: 10x Genomics


title: Patient #161, human colon organoids, differentiation (B+D) medium - calcitriol


title: Cardiomyocytes, DOX22h, C3

city: Bogota DC

first: Yohana

last: Dominguez

state: Bogota

address: El Dorado avenue 51-20

department: Sub-Direction of Scientific and Technological Research

country: Colombia

institute: National Institute of Health

data_processing:
Read quality assessment was performed using MultiQC and validated in Galaxy using FastQC. Alignments of reads ranging from 17 to 35 nucleotides in length were performed against the Homo sapiens reference genome.
Assembly: Homo sapiens maskedPAR (UCSC hg19)
Supplementary files format and content: Quality control and normalization of the resulting reads was performed using the BaseSpace® Small RNA v1.0 app (Illumina), with subsequent conversion of the sequences to FastQ files. and the quality of the readings was analyzed multiQC and confirmed in Galaxy by FastQC. The alignments for readings obtained between 17 and 35 nt against the reference genome for Homo sapiens.

organism: Cavia porcellus

source_name: Heart

extract_protocol:
Total R.N.A. extraction was conducted on isolated guinea pig ventricular cardiomy-ocytes exposed independently to 10 μM of DOX and to the vehicle control (DMSO) for 22 hours at room temperature. We used Trizol reagent to extract following the manufacturer's guidelines (Invitrogen). The extracted R.N.A. was resuspended in H2O DEPC (diethyl py-rocarbonate, Sigma–Aldrich) and quantified via spectrophotometry using the Nanodrop 2000 (Thermo Fisher Scientific).
A small R.N.A. library was constructed using the TruSeq Small R.N.A. Library Prep Kit (Illumina Inc., U.S.A.). . The quality control and the normalization of the readings obtained using the BaseSpace® App, Small RNA v1.0 (Illumina), the sequences converted into FastQ files, and the quality of the readings was analyzed multiQC and confirmed in Galaxy by FastQC (https://usegalaxy.org/).
TruSeq Small R.N.A. Library to miRNAs was sequenced on an Illumina HiSeq2500 platform. Quality control and normalization of the resulting reads was performed using the BaseSpace® Small RNA v1.0 app (Illumina), with subsequent conversion of the sequences to FastQ files.

value: Heart

value: Cardiomyocytes

value: Ventricular cardiomyocytes

value: Mature

value: DOX

tag: time point


title: H9_H9_d100_Control1

description: 10x Genomics

value: organoid

value: progenitors & neurons


title: H9_LIF2_d60

description: 10x Genomics


title: Cardiomyocytes, DMSO22h, C3

value: DMSO


title: KOPT-K1, Input

value: high


title: Patient #161, human colon organoids, differentiation (B+D) medium - control

value: colon

value: human colon epithelial stem cells

tag: age

value: Vehicle (ethanol)


title: Cardiomyocytes, DOX1h, C3


title: H9_LIF_a_d65

description: 10x Genomics

value: WT


title: iPSC derived neurons, Ctrl_C

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Human Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package (version 1.36.1) (Gautier et al., 2004) included in the Bioconductor software suite (version 2.11) (Gentleman et al., 2004) and an Entrez Gene- specific probeset mapping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan (Dai et al., 2005). Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0).

source_name: iPSC derived neurons from control patient tissue

label_protocol: GeneChipTM Human Gene 2.0 ST microarray procedure

extract_protocol: RNA from microdissected human nigral tissue or iPSC-derived neurons was extracted using RNeasy columns (QIAGEN)

tag: disease state

value: Ctrl

value: iPSC derived neurons


title: H9_LIF1_d60

description: 10x Genomics

value: LIF


title: iPSC derived neurons, FTD_C

source_name: iPSC derived neurons from FTD patient tissue

value: FTD


title: iPSC derived neurons, FTD_A


title: iPSC derived neurons, Ctrl_B


title: Cardiomyocytes, DMSO1h, C3

value: Heart


title: iPSC derived neurons, FTD_B