title: Individual4_Blood_Tick

data_processing:
Partek Flow
RNA-seq data were trimmed and aligned to the human genome (hg38) using STAR (v2.7.3a).
The aligned reads were quantified to Ensembl Transcripts release 91 using the Partek E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization.
The gene-level data were normalized by dividing the gene counts by the total number of reads followed by the addition of a small offset (0.0001). The genes with p < 0.05, adjusted p < 0.05, and fold change ≥ 2 were considered as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include baseMean for each gene

source_name: Blood

extract_protocol:
Biopsied skin tissue was immediately frozen in tubes placed in dry ice. RNA extraction was performed using the RNAeasy plus kit (Qiagen, Valencia, CA).  For blood samples, red blood cells were removed from heparinized whole blood, and RNA was extracted using the miRNeasy Kit (Qiagen) following the instructions provided using a QIAcube (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All ticks were removed from the skin with forceps and the bite sites were biopsied under sterile conditions using a 3 mm punch immediately after removal of the tick. A control biopsy was collected from the corresponding location on the patient’s opposite, non-infested appendage. Blood was collected at acute and convalescent (after 2 months) time points. The human blood and biopsy samples were collected.

value: Blood

value: Tick bite


title: MCF7,ERα,DMSO, Biol Rep2

status: Public on Oct 16 2023

type: SRA

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

description: single

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Breast Cancer Cell

growth_protocol: MCF-7 human breast cancer cells (HTB-22, ATCC) were cultured in low-glucose (1 g/L) DMEM (Dulbecco’s modified Eagle’s media) supplemented with 1% (v/v) penicillin/streptomycin (P/S) either 10% (v/v) fetal bovine serum (FBS) or 5% dextran coated charcoal (DCC)-treated FBS.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen)
MicroPlex Library Preparation Kit from Diagenode

treatment_protocol: MCF-7 cells were treated with activated charcoal and subject to various ligands or DMSO for 1 hour and the ChIP sequencing experiment was done in triplicates.

tag: cell line

value: Human Breast Cancer Cell

tag: cell type

tag: chip antibody

value: ERα (Santa Cruz, #sc-542)


title: 2-Cell_32h_49

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Sequencing reads were aligned to the mm10 genome using bowtie2 (version 2.3.5) with the --local option. Duplicates were marked using samtools (version 1.9)and reads were filtered by keeping only properly paired reads, removing duplicates and selecting those whose mapping quality was higher or equal to 20. Bed files of the read coordinates were generated with bedtools (version 2.29.0) bamtobed command. Using bedtools intersect, read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM and then each bin by its respective average of all samples within the same stage, aiming to correct for the mappability biases intrinsic to the genomic regions. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.28.0) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 1.2.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
Assembly: mm10
Supplementary files format and content: tab-separated txt file with binary replication status
Library strategy: Single-cell Repli-seq

organism: Mus musculus

source_name: 2-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. For the parthenogenetic embryos and IVF-derived zygotes, the timing of S-phase was calculated based on the time after activation and insemination, respectively. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment. For the Repli-seq with physically isolated pronuclei, we distinguished maternal and paternal pronucleus based on their size and their relative position to the second polar body and isolated either of them using micromanipulation. The remaining zygote containing a single pronucleus was also collected after removal of polar body so that both pronuclei from the same zygote were further processed for Repli-seq.
Individual blastomeres or pronuclei were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

treatment_protocol: For induction of parthenogenetic embryos, MII-stage oocytes were collected from superovulated females without mating. After removal of cumulus cells, oocytes were treated with 10 mM Sr2+ for 2 hours in Ca2+-free CZB medium and then incubated in KSOM. For generation of IVF-derived zygote, MII oocytes from F1 female mice (C57Bl/6J × CBA) were inseminated with activated spermatozoa obtained from the caudal epididymides of adult DBA/2J male mice. To inhibit both minor and major ZGA, embryos were treated with 0.1mg/mL a-amanitin from 17 hphCG injection until their collection time.

tag: tissue

value: 2-cell embryo

tag: genotype

value: (C57BL/6J x CBA) x DBA/2J

tag: treatment


title: HUVEC_TGF-β1+IL-1β+acetate, rep3

city: St. Petersburg

first: JIANHUA

last: XIONG

state: FL

address: 501 6th Ave South, REB Bldg, 3rd Floor, Rm 3111, REB/Rm 3111

country: USA

institute: Johns Hopkins University/Johns Hopkins All Children's Hospital

library_source: transcriptomic

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads. Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping.
Assembly: GRCh38
Supplementary files format and content: The processed data file is in txt format and reports counts

molecule: total RNA

source_name: human umbilical vein endothelial cells (HUVECs)

growth_protocol: Primary human endothelial cells were cultured using Endothelial Cell Growth Medium MV2 Kit (C-22121; PromoCell).

extract_protocol:
Total RNAs were isolated using RNeasy Plus 96 Kit (74192, Qiagen).
RNA libraries for RNA-seq were constructed according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760L, New England BioLabs).

treatment_protocol: Primary human endothelial cells were treated with or without 10 ng/mL TGF-β1 and 1 ng/mL IL-1β, and with or without 40 mM acetate for 4 days.


title: Individual4_Blood_CTRL

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

country: China

institute: Zhejiang University


title: MCF7,ERα,DMSO, Biol Rep1

description: single


title: 16-Cell_80h_45

source_name: 16-cell embryo

value: 16-cell embryo


title: 16-Cell_80h_44


title: Individual3_Blood_Tick


title: HUVEC_TGF-β1+IL-1β+acetate, rep2

value: human umbilical vein endothelial cells (HUVECs)


title: Homogyzous chrIV–chrI(cen1∆),Input,Biol Rep 1

city: New York

first: Andreas

last: Hochwagen

state: New York

address: 100 Washington Square East, 1009 Silver Center

department: Biology

institute: New York University

data_processing:
ChIP-seq reads trimmed for low-quality sequence and mapped to a custom hybrid S288C/SK1 genome using bowtie v1.2.0 with parameters -q -m 1 -v 0 -p 8 -S
Peaks called using macs2 v2.1.1 command “callpeak” with parameters --keep-dup="auto" -B --nomodel --extsize 200 --SPMR -g 2.4e7
Normalized signal track produced by comparing ChIP treatment against input control using macs2 v2.1.1 command “bdgcmp” with parameter -m FE
Assembly: Genome_build: Custom hybrid S288C/SK1 genome built by concatenating recently published S288C and SK1 genome assemblies (Yue et al. Nat. Genet. 2017). For syn4 strains, the hybrid genome was built by concatenating genome assemblies of SK1 and S288C with the syn4 chromosome.
Supplementary files format and content: Supplementary_files_format_and_content: bedGraph files: Fold enrichment of ChIP signal track compared to input sample at each base position

organism: Saccharomyces cerevisiae

source_name: Cell suspension in synchronous meiosis

growth_protocol: Synchronous meiosis cultures were prepared by inoculating BYTA medium at OD600 = 0.3 and growing for 16.5 hours at 30°C. Cells were washed twice with water, resuspended in SPO medium at OD600 = 2.0 and incubated at 30°C.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using KAPA Hyper Prep Kit, with 3µM adapters. Input was 10ng and 9 PCR cycles were used to amplify the DNA. Amplified ChIP DNA between 300 and 500 bp was quantified using qPCR as well as an agilent 2200 TapeStation System. Fragments were sequenced on an illumine NextSeq 500 instrument using a 150-bp single-end sequencing protocol.

tag: time

value: meiotic time-point:3 hours

tag: strain code

tag: strain

value: chip antibody:input


title: 16-Cell_80h_43


title: 16-Cell_80h_42


title: MCF7,IgG,DMSO, Biol Rep1

description: single

value: IgG (Santa Cruz, #sc-2027)


title: Individual3_Blood_CTRL1


title: MCF7,AHR,DMSO, Biol Rep1

description: single

value: AHR (Santa Cruz, #sc-133088)


title: Individual3_Blood_CTRL2


title: HUVEC_TGF-β1+IL-1β+acetate, rep1


title: HUVEC_TGF-β1+IL-1β, rep3


title: MCF7,AHR,DMSO, Biol Rep3

description: single


title: Individual2_Skin_Tick

source_name: Skin

value: Skin


title: 16-Cell_80h_41


title: 16-Cell_80h_40


title: HUVEC_TGF-β1+IL-1β, rep1


title: Individual2_Skin_CTRL


title: MCF7,ERα,DIM, Biol Rep2

description: single


title: Individual1_Skin_Tick


title: Individual1_Skin_CTRL


title: MCF7,AHR,DMSO, Biol Rep2

description: single


title: MCF7,ERα,DIM, Biol Rep1

description: single


title: 16-Cell_80h_38


title: MCF7,AHR,DIM, Biol Rep3

description: single


title: HUVEC_control, rep2

value: Control


title: 16-Cell_80h_37


title: MCF7,AHR,DIM, Biol Rep2

description: single


title: HM_2_scATACseq

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
scRNA-seq
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz, v.3.0.0, hg19] were performed using a Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
The Cell Ranger count module was used to generate the raw gene expression matrix.
Genome_build: hg19
Supplementary_files_format_and_content: 10x cell ranger count output (raw gene expression matrix, cell barcode and gene information table)
scATAC seq
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-atac).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [https://cf.10xgenomics.com/releases/cell-atac/cellranger-atac-1.1.0.tar.gz, v.1.1.0, hg19] were performed using a Cell Ranger atac software (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
The Cell Ranger ATAC count module was used to generate the raw peak count matrix and transcription factors.
Genome_build: hg19
Supplementary_files_format_and_content: 10x cell ranger atac count output (raw peak count matrix, raw transcription factor count matrix, cell barcode, peak and transcription factor information table)

source_name: Hepatic organoids

extract_protocol:
Sample extraction was prepared using Chromium Single Cell ATAC Reagent Kits v1 (10X Genomics) according to the manufacturer’s protocols.
Sequencing library was prepared using Chromium Single Cell ATAC Reagent Kits v1 (10X Genomics) according to the manufacturer’s protocols.

value: hepatic medium


title: HUVEC_control, rep1


title: MCF7,AHR,DIM, Biol Rep1

description: single


title: HM_1_scATACseq


title: HUVEC_TGF-β1+IL-1β, rep2


title: 16-Cell_80h_35


title: DM_2_scATACseq

value: Differentiation medium


title: MCF7,ERα,DIM, Biol Rep3

description: single


title: DM_1_scATACseq


title: MCF-7 cells, Diindolylmethane, 6 hr, Biol Rep2

data_processing:
Sequence reads were trimmed for adaptor sequence using Trimmomatic with MINLEN:15
Hisat2 was used for alignment top human transcriptome using hg38 index file obtained for hisat2 sever
Samtools was used for to convert hisat generated SAM to BAM file and sort and index it
Ht-seq count was used to with -s reverse -t exon flag and aggregated at gene level with hg38 UCSC obtained GTF to get count by gene
Assembly: hg38
Supplementary files format and content: Read Count txt file titled

extract_protocol:
Total RNA was isolated with the Aurum™ total RNA mini kit (BioRad, Hercules, CA, USA), following the manufacturer’s protocol. The RNA yield was assessed with NanoDrop™ 1000 from Thermo Fisher Scientific.
RNA libraries for RNA-seq were prepared using Strand-specific TruSeq RNA-seq library Prep Kit following manufacturer's protocols.

treatment_protocol: MCF-7 cells were treated with activated charcoal and subject to various ligands or DMSO for 6 hours and the RNA sequencing experiment was done in triplicates.

value: breast cancer cell

value: WT

value: Diindolylmethane


title: Control_004_ribo

city: Los Angeles

first: Brooke

last: Hjelm

state: CA

address: 1450 Biggy Street

department: Translational Genomics

institute: USC

description: total RNA ribosomal depletion

data_processing:
For spatial transcriptomics, BAM files were generated using the 10x Genomics spaceranger pipeline (https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome). BAM files were converted to the three FASTQ files using the bamtofastq tool (https://support.10xgenomics.com/docs/bamtofastq).
For bulk RNA-Seq, paired-end FASTQ files (unprocessed) were used as input for the Splice-Break pipeline.
Assembly: NC_012920.1
Supplementary files format and content: top30matrix.txt: Tab-delimited text file which includes demographic information (diagnosis, sex, age), mitochondrial benchmark coverage, and deletion read % for each of the "Top 30" deletions and sum of the "Top 30" deletions. Deletion read %'s are after normalization to mitochondrial benchmark coverage.
Supplementary files format and content: top30matrix_ImputedLayers.txt: Tab-delimited text file which includes demographic information (diagnosis, sex, age), mitochondrial benchmark coverage, and deletion read % for each of the "Top 30" deletions and sum of the "Top 30" deletions for each imputed cortical layer from the spatial transcriptomics samples. Deletion read %'s are after normalization to mitochondrial benchmark coverage.
Supplementary files format and content: SpatialVISIUM_supp.tar.gz contains the following files for each spatial transcriptomics sample: (1) "SAMPLE_tissue_hires_image.png" = high resolution png images; (2) "SAMPLE_filtered_feature_bc_matrix.h5" = filtered feature gene by barcode count matrices in binary h5 format; (3) "SAMPLE_scalefactors_json.json" = JSON files with scaling factors for pixel positions in png images; (4) "SAMPLE_tissue_positions_list.txt" = text file with pixel coordinates for each barcode

source_name: middle temporal gyrus

extract_protocol:
Frozen MTG was microdissected into ~5mm3 blocks. Frozen tissue was affixed to cryostat chucks with OTC and sectioned sectioned with a Microm HM525 Cryostat at -20ºC to 10 µm slices.   For spatial transcriptomics samples, frozen tissue slides were adhered to the 10x Visium Spatial Gene Expression or Tissue Optimization slides following the manufacturer’s protocols.   For bulk RNA-Seq, sections were adhered to Selectfrost microscope slides, and RNA was extracted using using the Direct-Zol RNA mini prep kit.   All slides were frozen at -80ºC prior to library preparation.
For spatial transcriptomics, tissue optimization (i.e., permeabilization time) was tested according to the 10x Genomics protocols, with 12 min of permeabilization selected for spatial transcriptomics sequencing (data not shown). Two sections of each of the four subjects that were adhered to the 10X Visium Spatial Gene Expression were processed according to the 10x Genomics Visium protocols. Hematoxylin and eosin (H&E) imaging was performed at 20X magnification and auto-stitching using a Keyence BZ-X810 Microscope to generate high-resolution TIFF files. The cDNA was amplified using 12 cycles following Cq determination steps. Library size and quality was evaluated using the Agilent Tape Station-HS DNA Screen Tape and Tape Station; libraries were quantified with the KAPA qPCR library quantification kit. Spatial transcriptomics libraries were sequenced as paired-end 150-mer reads on an Illumina NovaSeq 6000 system using a NovaSeq S4 flowcell. Sequencing was performed by the USC Keck Genomics Platform (KGP).     For bulk RNA-Seq, RNA was quantified and qualified using the Agilent Tape Station-HS RNA Screen Tape and Tape Station, and had an RNA Integrity Number (RIN) of 5.6. 240ng of RNA was used as input for each bulk RNA-Seq prep, which utilized the NEBNext Ultra II Directional RNA library prep kit. The polyA (mRNA) library preparation used the NEBNext Poly(A) mRNA Magnetic Isolation Module, and the ribo depletion library preparation used the NEBNext rRNA Depletion Kit V2 and SBP beads. Libraries were barcoded with the NEBNext Multiplex Oligos for Illumina. Library size and quality was evaluated using the Agilent Tape Station-HS DNA Screen Tape and Tape Station; libraries were quantified with the KAPA qPCR library quantification kit. Both RNA-Seq libraries were sequenced as paired-end 100-mer reads on an Illumina NovaSeq 6000 system using a NovaSeq S1 flowcell. Sequencing was performed by the USC Keck Genomics Platform (KGP).

tag: subject id

value: middle temporal gyrus

tag: age (yrs)

tag: Sex

value: M

tag: diagnosis


title: 16-Cell_80h_39


title: HUVEC_control, rep3


title: HM_2_scRNAseq

growth_protocol: Organoids were routinely maintained in HM, and the medium was replaced every 3 days. The organoids were mechanically passaged every 7 days; they were washed with cold PBS to remove the Matrigel and split into small pieces by a surgical blade under a dissecting microscope. The passaged organoids were then resuspended in Matrigel at a 1:3–1:10 ratio.

extract_protocol:
Sample extraction was prepared using Chromium Single cell 3' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocols.
Sequencing library was prepared using Chromium Single cell 3' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocols.

treatment_protocol: For further differentiation of hepatic organoids, HM-cultured organoids were incubated under expansion medium (EM) supplemented with 20 ng/ml BMP7 (PeproTech; 120-03) for 2–3 days and then under differentiation medium (DM) for an additional 6 days.


title: 16-Cell_80h_33


title: 16-Cell_80h_34


title: MCF-7 cells, Diindolylmethane, 6 hr, Biol Rep3


title: PD_144113

description: 10x spatial transcriptomics

value: F

value: Parkinson's Disease (PD)


title: 16-Cell_80h_36

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: MCF-7 cells, Diindolylmethane, 6 hr, Biol Rep1


title: 16-Cell_80h_32


title: AD_144112

description: 10x spatial transcriptomics

value: Alzheimer's Disease (AD)


title: HM_1_scRNAseq


title: Control_002_poly

description: total RNA non ribosomal depletion (polyA)


title: MCF-7 cells, TCDD, 6 hr, Biol Rep3

value: TCDD


title: PD_144114

description: 10x spatial transcriptomics


title: DM_2_scRNAseq


title: 16-Cell_80h_31


title: MCF-7 cells, TCDD, 6 hr, Biol Rep1


title: 16-Cell_80h_30


title: DM_1_scRNAseq


title: MCF-7 cells, TCDD, 6 hr, Biol Rep2


title: 16-Cell_80h_29


title: Control_144108

description: 10x spatial transcriptomics


title: MCF-7 cells, Estradiol+TCDD, 6 hr, Biol Rep3

value: Estradiol + TCDD


title: 16-Cell_80h_28


title: AD_144111

description: 10x spatial transcriptomics


title: Control_144107

description: 10x spatial transcriptomics


title: H9-ESC-derived human microglia in vitro library 2, HTO-derived cDNA

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
2_R_barcodes.tsv.gz
2_R_features.tsv.gz
2_R_matrix.mtx.gz

data_processing:
Cell Ranger v3.0.2 (10x Genomics) was used to align reads to the hg38 human pre-mRNA reference genome and to generate feature-barcode matrices.
Further processing was done with Seurat v4.1.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, gene set enrichment analysis).
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: cell line

growth_protocol: We used in vitro human microglia-like cells generated from H9 embryonic stem cells (WA09, purchased from WiCell) according to the serum- and feeder-free protocol for hPSC-derived monocytes/macrophages70. Bohlen et al. optimized microglia medium conditions and developed TIC medium that mainly contains three astrocyte-derived key components TGF-β, IL-34 and cholesterol71. We adapted these two protocols described above to generate H9MG for the screen of γ-secretase substrates (Figure S1). Briefly, H9 embryonic stem cells were expanded in Essential 8 medium with its supplement (A1517001, Gibco) in matrigel-coated 6-well plates. At day 0, H9 stem cells were dissociated with Accutase (A6964, Sigma-Aldrich) and suspended in mTeSR-1 medium with its supplement (#85850, Stemcell Technologies). Then, ~1 million cells were seeded in a 96-well u-bottom ultra-low adherence plate (#650979, Greiner Bio-one) and supplemented with Rock inhibitor (Y-27632, Sigma-Aldrich) and cytokines (50 ng/mL BMP4, 20 ng/mL SCF and 50 ng/mL VEGF). We spun the plate at 100 g for 3 minutes to pellet cells on the bottom of the wells. From day 1 to day 3, the medium was daily changed. At day 4,  embryonic bodies (EBs) were collected from the plates and transferred to a T175 flask. Each flask contained 192 EBs in 40 mL differentiation medium (X-VIVO15, 100 ng/mL M-CSF, 25 ng/mL IL3, 2 mM Glutamax, 100 U/mL Pen/Strep and 0.055 mM β-mercaptoethanol). The differentiation medium was changed when it got yellow. From day 18 onward, the H9-derived monocyte-like cells (H9MC)  were visible in the supernatant, and the non-adherent H9MC could be collected weekly. All the H9MC used in this study were collected from day 18, day 25 and day 32. The harvested H9MC were then transferred to the microglia TIC medium (DMEM F12, 2 mM L-Glutamine, 5 µg/mL N-acetyl-L-cysteine, 5 µg/mL human insulin, 100 µg/mL apo-transferrin, 100 ng/mL sodium selenite, 1.5 µg/mL cholesterol, 1 µg/mL heparin sulfate, 50 ng/mL M-CSF, 50 ng/mL IL34, 25 ng/mL TGFβ1, 10 ng/mL CX3CL1) for 7-day further maturation to H9MG. All cytokines used in this study were purchased from Miltenyi. Using this combined protocol, we were able to generate ≥ 300 million H9MG in a T175 flask within 39 days.

extract_protocol:
For the collection, we added 500 μL Accutase (#07922, Stemcell) with 5 μM Actinomycin D (A1410, Sigma) in each well and incubated the plate at 37 ℃ for 6 min. We rinsed the cells with cold PBS with 5 μM ActD and collected cells in a clean Eppendorf tube on ice. We spun the cell suspension at 300g for 5min and suspended the cells with cold FACS buffer. We spun down the cell pellets and incubated each of the 12 samples with a specific hashtag antibody (A0251-A0260, A0262 and A0263, Biolegend) at 4 ℃. After 30 min, we washed the cells in cold FACS buffer. We spun down the cell pellets again and suspended cells in FACS buffer. We measured the concentration of the cell suspensions on a LUNA cell counter and eventually pooled ~2,000 cells from each of the 12 samples together (4 conditions: n = 3 samples per condition).
We equally divided the pool into 2 and prepared them into 2 cDNA libraries using the 10X Genomics single-cell gene expression profiling kit following the manufacturer’s instructions (CG000204_Chromium Single Cell 3' v3.1). All cDNA libraries were then sequenced on a DNBSEQ PE100 sequencing platform.
Equimolar pool of both RNA libraries. For each RNA library a hash library is included. Hash libraries are spiked in for 10% with the corresponding RNA library (90%). So as an example: the hash library 1_H was spiked in (10%) into the 1_R RNA library (90%).

treatment_protocol: We seeded H9MC collected from D25 as described above in 12-well plates (500,000 cells/well). We grow them in TIC medium for 7 days, TIC medium was refreshed every two days. At Day 7, we pre-treated H9MG with 2 μM Semagacestat or DMSO for 22 h. We added 200 ng/mL LPS or PBS during the last 6 hours of the experiment.

value: cell line

value: Microglia

tag: library type

value: mRNA

tag: antibodies/tags

tag: rounds of_sequencing


title: MCF-7 cells, Estradiol+TCDD, 6 hr, Biol Rep2


title: Control_144106

description: 10x spatial transcriptomics

value: Control


title: H9-ESC-derived human microglia in vitro library 1, HTO-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
1_R_barcodes.tsv.gz
1_R_features.tsv.gz
1_R_matrix.mtx.gz


title: 16-Cell_80h_26


title: MCF-7 cells, Estradiol+TCDD, 6 hr, Biol Rep1


title: H9-ESC-derived human microglia in vitro library 1, mRNA-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
1_R_barcodes.tsv.gz
1_R_features.tsv.gz
1_R_matrix.mtx.gz

library_source: other

molecule: protein

value: HTO

value: Anti CD298 and β2 microglobulin:Ctrl-1/TotalSeq-A0251 ; Sema-1/TotalSeq-A0252 ; LPS-1/TotalSeq-A0253 ; SemaLPS-1/TotalSeq-A0254 ; Ctrl-2/TotalSeq-A0255 ; Sema-2/TotalSeq-A0256 ; LPS-2/TotalSeq-A0257 ; SemaLPS-2/TotalSeq-A0258 ; Ctrl-3/TotalSeq-A0259 ; Sema-3/TotalSeq-A0260 ; LPS-3/TotalSeq-A0262 ; SemaLPS-3/TotalSeq-A0263


title: ATAC-Pool2-F4-noStim

city: Muenster

first: Michael

middle: J

last: Ziller

address: Busso-Peus-Str. 10

institute: University of Muenster

description:
Sample_ATACSeq19
ATACSeq_UnionPeakSet_rawCounts.txt

data_processing:
Paired-end raw ATAC-Seq reads were aligned against hg19 using bowtie 2 (Langmead and Salzberg, 2012) version 2.3.5. Subsequently, duplicates were removed using picard tools and peak calling was performed using macs2 and standard human genome size (hs parameter). Resulting peak files of all samples were then merged using diffbind, only retaining those peaks that were present in at least 6 samples, giving rise to the union peak set employed in all further analyses. Next, bedtools multicov function was used to count fragments overlapping with peaks by at least one base.
Assembly: hg19
Supplementary files format and content: raw count matrix for each peak and peak files from MACS2

source_name: in vitro iPSC

growth_protocol: iPSC derived neurons were generated via overexpression of pro-neural transcription factor Ngn2 plus small molecules and differentiated for 49 days on murine astrocytes.

extract_protocol:
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed on bulk cryopreserved cell pellets of one 12-well according to previously published protocols8. Neuronal networks were gently thawed in DMEM/F12, pelleted (400 x g, 5 min, 4°C) and washed with PBS. Detergents for the lysis buffer were added freshly to the basic RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and complete lysis buffer RSBI (RSB supplemented with 100 µg/ml digitonin, 1:100 Tween™20, 1:100 IGEPAL) and RSBII (1:100 Tween™20) were cooled down on ice. Cell pellets were resuspended in 50 µl RSBI with 4 mixes with the 200 µl pipette tip and then lysed on ice for 3 min. Afterwards, 1 ml of RSBII was added and the cell solution was gently mixed 4 times with a 1000 µl pipette tip. The nuclei were pelleted at 500 x g for 10 min at 4°C and counted (Luna-II).
50,000 nuclei were used for the transposition reaction at 37°C while shaking on a thermomixer (1000 rpm) for 30 min: 25 µl TD buffer (15027866, Illumina), 2.5 µl TDE1 tagment DNA enzyme (15027865, Illumina), 16.5 µl PBS, 0.5 µl Tween20, 0.5 µl digitonin [1% stock], and 5 µl water. Fragmented DNA was immediately column-purified and eluted in 22 µl EB provided with the kit. For the preparation of the library, 20 µl of the purified DNA was mixed with 25 µl NEBNext High-Fidelity master mix (M0541L, New England Biolabs), 2.5 µl FW (5’ AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG 3’) and 2.5 µl  barcoding (for barcodes see Table S7) RV primer (5’ CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGT 3’)9.   After the amplification, a double-sided bead cleanup with 0.55x of the volume and then 1x of the volume was performed. Before the pooling, libraries were quantified and verified for a successful transposition with the Bioanalyzer on a high sensitivity DNA chip. 10 libraries containing 10 different barcodes could therefore then be pooled equimolar for sequencing on a NovaSeq (50bp paired-end sequencing). Final pool was repurified with a right-left-cleanup of 0.5x and then 0.45x the volume.

treatment_protocol: iPSC derived neurons were stimulated by KCl-solution (170 mM KCl, 150 mM HEPES, 1 mM MgCl2, 2 mM CaCl2) for 5h on day 49 or untreated.

value: in vitro iPSC

value: iPSC derived neuron

value: baseline


title: Control_144105

description: 10x spatial transcriptomics

value: middle temporal gyrus


title: MCF-7 cells, Estradiol, 6 hr, Biol Rep3

value: breast cancer cell

value: WT

value: Estradiol


title: 16-Cell_80h_27

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: ATAC-Pool2_S4_noStim

description:
Sample_ATACSeq18
ATACSeq_UnionPeakSet_rawCounts.txt


title: 16-Cell_80h_25


title: Bl6, day3, macrophages, replicate 3

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive

department: Cell Biology

institute: Duke University

data_processing:
The reads from fastq files were aligned to GRCm38 reference genome using STAR v2.7.4a (parameter-sjdbOverhang: 99)
The bigwig files were generated using bamCoverage from alignment of reads (parameter-normalizeUsing:RPKM ).
Assembly: mm10
Supplementary files format and content: indexed binary format files include RPKM values for each sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer’s protocol.
First-strand reverse transcription and template switching was performed using an Oligo(dT) primer (dT30VN-ME-A), a locked nucleic acid-containing TSO (NotI-TSO), and Superscript IV reverse transcriptase (Invitrogen, # 18090050). PCR preamplification of cDNA was performed with IS PCR and Tn5ME-A-aHic using 2X KAPA PCR mix (Kapa Biosystem, KK2602) followed by cleanup using SPRISelect beads (Beckman Coulter, REF B23319). DNA was digested by NotI-HF (NEB, #R3189L), tagmented using Tn5 assembled with adaptors Tn5ME-A/Tn5MErev and Tn5ME-B/Tn5MErev. A Zymo DNA clean and concentrator kit (Zymo, R1014 ) was utilized (PMID: 24385147). Library PCR was performed using unique combinations of Nextera-PCR i5/i7 primers. DNA fragments between 400-600bp were selected by gel extraction using Zymoclean Gel DNA recovery kit (Zymo, #D4002).

treatment_protocol: Hindlimb ischemia surgery was performed on young adult male mice as previously described (PMID: 18285563). Macrophages from ischemic hindlimb skeletal muscle were isolated on post-op day 3 for RNA-seq analysis. Single-cell suspensions were generated from skeletal muscle tissue using mechanical dissociation and enzymatic digestion with 0.05% Pronase (Sigma, 537088) for one hour. Cells were blocked with purified anti-mouse CD16/32 antibody (Biolegend, #101301) for 10 minutes. Primary antibody staining was performed using anti-CD45-Alexa Fluor 488 (clone HI30, Invitrogen, MHCD4520), anti-CD11b (clone M1/70, Invitrogen, 12-0112-81), and anti-F4/80-biotin (clone A3-1, Bio-rad, MCA497BT) antibodies for 40 minutes. Streptavidin-PE/Cy7 (Biolegend, 405206) was used as a secondary reagent for anti-F4/80-biotin (PMID: 25896247). Macrophages were isolated by fluorescence-activated cell sorting (SonySorter SH800s) with gating for PI-/CD45+/CD11b+/F480+ cells. Approximately 100,000 macrophages for collected from one mouse for each biological replicate.

value: skeletal muscle

value: macrophages

value: Hindlimb ischemia surgery

tag: post-op timepoint

value: Day 3


title: MCF-7 cells, Estradiol, 6 hr, Biol Rep2

tag: cell line


title: Bl6, day3, macrophages, replicate 2

tag: cell type


title: H9-ESC-derived human microglia in vitro library 2, mRNA-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
2_R_barcodes.tsv.gz
2_R_features.tsv.gz
2_R_matrix.mtx.gz

value: cell line

value: Microglia


title: ATAC-Pool2_S1_noStim

description:
Sample_ATACSeq16
ATACSeq_UnionPeakSet_rawCounts.txt


title: Bl6, day3, macrophages, replicate 1


title: 16-Cell_80h_23


title: MCF-7 cells, Resveratrol, 6 hr, Biol Rep3

value: Resveratrol


title: 16-Cell_80h_22


title: ATAC-Pool2_S1_KCl

description:
Sample_ATACSeq15
ATACSeq_UnionPeakSet_rawCounts.txt

value: Kcl


title: Balbc, day3, macrophages, replicate 2

value: BALB/c


title: ATAC-Pool2_N1_KCl

description:
Sample_ATACSeq14
ATACSeq_UnionPeakSet_rawCounts.txt

value: in vitro iPSC

value: iPSC derived neuron


title: Balbc, day3, macrophages, replicate 1


title: MCF-7 cells, Resveratrol, 6 hr, Biol Rep1


title: 16-Cell_80h_21


title: 16-Cell_80h_20


title: Bl6, day7, replicate 2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The doublets detecting was made using the Python package scrublet v0.2.3 (https://github.com/swolock/scrublet)
The cell filtering, annotation and sample integration were made using the R package Seurat v4.0.1 (https://satijalab.org/seurat)
The R package DropletUtils v1.10.3 was used to create a directory containing the filtered gene barcode matrix in the 10x format.
Assembly: mm10 (or hg38)
Supplementary files format and content: Tab-separated annotation files and matrix files

source_name: Hindlimb skeletal muscle

extract_protocol:
Skeletal muscle tissue was processed to generate single-cell suspensions using mechanical dissociation and enzymatic digestion. Live cells (PI- cells) were isolated by fluorescence-activated cell sorting using a SonySorter SH800s. For mouse HLI experiments, an equal number of PI- cells and PI-/CD31-/CD45- cells were pooled for each sample to increase the representation of relatively scarce non-hematopoietic and non-endothelial cell-types of interest (e.g. muscle stem cells and fibro-adipogenic progenitors). A total of approximately 150,000 cells were sorted for each sample, precisely counted using a hemocytometer, and used for scRNA-seq analysis.
Single-cell RNA sequencing libraries were generated using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s protocol. Approximately 16,000 - 24,000 cells per sample were used for GEM creation.

value: Hindlimb skeletal muscle cells

value: Hindlimb skeletal muscle

value: day 7

tag: age

value: 10-12 weeks


title: MCF-7 cells, DMSO, 6 hr, Biol Rep3

value: breast cancer cell

value: WT

value: DMSO


title: Bl6, day7, replicate 1, scRNAseq

description: 10x Genomics

tag: tissue


title: ATAC-Pool2_F3_KCl

description:
Sample_ATACSeq12
ATACSeq_UnionPeakSet_rawCounts.txt

tag: genotype


title: 16-Cell_80h_24

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J

tag: treatment


title: 16-Cell_80h_18


title: MCF-7 cells, DMSO, 6 hr, Biol Rep2

tag: time


title: Bl6, day3, replicate 2, scRNAseq

description: 10x Genomics

value: day 3

value: Hindlimb ischemia surgery


title: 16-Cell_80h_19


title: ATAC-Pool2_F2_noStim

description:
Sample_ATACSeq11
ATACSeq_UnionPeakSet_rawCounts.txt

value: baseline


title: MCF-7 cells, DMSO, 6 hr, Biol Rep1


title: 16-Cell_80h_17


title: ATAC-Pool2_S4_KCl

description:
Sample_ATACSeq17
ATACSeq_UnionPeakSet_rawCounts.txt


title: Bl6, day3, replicate 1, scRNAseq

description: 10x Genomics


title: MCF-7 cells, Estradiol, 6 hr, Biol Rep1

value: Estradiol


title: ATAC-Pool2_F2_KCl

description:
Sample_ATACSeq10
ATACSeq_UnionPeakSet_rawCounts.txt

value: Kcl


title: MCF-7 cells, Resveratrol, 6 hr, Biol Rep2

value: Resveratrol


title: Down Syndrome human brain organoids, 24h post SARS-CoV-2 infection 3

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: MBS Bldg 76, Cooper Rd

department: School Of Chemistry And Molecular Biosciences

country: Australia

institute: The University of Queensland

data_processing:
Reads were trimmed using Trimmomatic software v.0.36.6 with the following parameters: ILLUMINACLIP : TruSeq3 - SE : 2 : 30 : 10, LEADING : 32 TRAILING : 32, SLIDINGWINDOW : 4 : 20, MINLEN : 16.
Trimmed reads were mapped to the genome assembly hg38 using HISAT2 v.2.2.1.
Feature counting was performed using featureCounts v2.0.1 with counting mode set to “Union”, strand to “Unstranded”, feature type was “exon”, and ID attribute was Gene_ID.
Assembly: hg38
Supplementary files format and content: tab-delimited text file that includes reads counts values for each Sample

source_name: Human brain organoids

growth_protocol: Patterned neural spheroids were embedded in Matrigel (StemCell Technologies, Cat. #354277) and maintained in the terminal differentiation medium DMEM-F12 (Gibco, Cat. #11320-33): Neurobasal medium (Gibco, Cat. #A35829-01) 0.5% N2 (Gibco, Cat. #17502-048), 12.5 µl of insulin in 50 ml media (Sigma), 1% GlutaMAX, 1% MEM Non-Essential Amino Acids (Gibco, Cat. #11140-050), 1% penicillin/streptomycin (Gibco, Cat. #15140148), 17.5 µl of β-mercaptoethanol in 50 ml media (Gibco, Cat. #21985-023), and 1% B-27 supplement (Gibco, Cat. # 17504044), supplemented with 3µM Chiron and 5ng/ml of BMP4. Organoids were cultured at 37C in humidified atmosphere of 95% air and 5%CO2. Fresh media was replaced three times a week.

extract_protocol:
RNA was isolated from the pools of three individual organoids using TRIreagent (Sigma, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Library preparation was performed using TrueSeq RNA Library Preparation Kit v2, Set A (Illumina, USA) according to the manufacturers instructions.

treatment_protocol: Organoids were incubated in 500 ul media containing 106 foci-forming units (FFU) of the virus for 6 hours at 37 ºC, then inoculum was removed, organoids were washed 3 times and then maintained in 1 ml of fresh medium. Virus used in the experiment was SARS-CoV-2 isolate QLD1517/2021 (alpha variant, GISAID accession EPI_ISL_944644) recovered from nasopharyngeal aspirates of an infected individual, which was provided by the Queensland Health Forensic and Scientific Services, Queensland Department of Health.

value: Human brain organoids

value: multiple cell types

value: Trisomy 21 (DS)

value: SARS-CoV-2 infection


title: ATAC-Pool2_F1_noStim

description:
Sample_ATACSeq9
ATACSeq_UnionPeakSet_rawCounts.txt

value: in vitro iPSC

value: iPSC derived neuron


title: 16-Cell_77h_9


title: Bl6, day1, replicate 2, scRNAseq

description: 10x Genomics

value: Hindlimb skeletal muscle cells

value: Hindlimb skeletal muscle

value: day 1

value: 10-12 weeks


title: Down Syndrome human brain organoids, 24h post SARS-CoV-2 infection 2


title: Bl6, day1, replicate 1, scRNAseq

description: 10x Genomics


title: 16-Cell_77h_8

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: ATAC-Pool2_H6_noStim

description:
Sample_ATACSeq13
ATACSeq_UnionPeakSet_rawCounts.txt


title: ATAC-Pool2_F1_KCl

description:
Sample_ATACSeq8
ATACSeq_UnionPeakSet_rawCounts.txt


title: 16-Cell_77h_7


title: Down Syndrome human brain organoids, 24h post SARS-CoV-2 infection 1


title: ATAC-Pool2_C8_noStim

description:
Sample_ATACSeq7
ATACSeq_UnionPeakSet_rawCounts.txt


title: Down Syndrome human brain organoids, uninfected 3

value: uninfected


title: ATAC-Pool2_C8_KCl

description:
Sample_ATACSeq6
ATACSeq_UnionPeakSet_rawCounts.txt


title: 16-Cell_77h_6


title: ATAC-Pool2_C7_noStim

description:
Sample_ATACSeq5
ATACSeq_UnionPeakSet_rawCounts.txt

value: baseline


title: 16-Cell_77h_5


title: Down Syndrome human brain organoids, uninfected 2


title: Bl6, sham, replicate 1, scRNAseq

description: 10x Genomics

value: day 0

value: no injury


title: Balbc, day7, replicate 2, scRNAseq

description: 10x Genomics

value: BALB/c

value: day 7

value: Hindlimb ischemia surgery


title: Balbc, day7, replicate 1, scRNAseq

description: 10x Genomics


title: ATAC-Pool2_C7_KCl

description:
Sample_ATACSeq4
ATACSeq_UnionPeakSet_rawCounts.txt

value: Kcl


title: 16-Cell_77h_56


title: Down Syndrome human brain organoids, uninfected 1

value: Human brain organoids

value: multiple cell types

value: Trisomy 21 (DS)


title: 16-Cell_77h_55


title: ATAC-Pool2_C3_noStim

description:
Sample_ATACSeq3
ATACSeq_UnionPeakSet_rawCounts.txt

value: in vitro iPSC

value: iPSC derived neuron


title: Euploid human brain organoids, 24h post SARS-CoV-2 infection 3

value: Euploid (wild type)

value: SARS-CoV-2 infection


title: Euploid human brain organoids, 24h post SARS-CoV-2 infection 2


title: Balbc, day3, replicate 2, scRNAseq

description: 10x Genomics

value: Hindlimb skeletal muscle cells

value: Hindlimb skeletal muscle

value: day 3

value: 10-12 weeks


title: 16-Cell_77h_54

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: Balbc, day3, replicate 1, scRNAseq

description: 10x Genomics

value: BALB/c


title: ATAC-Pool1_C3_KCl

description:
Sample_ATACSeq1
ATACSeq_UnionPeakSet_rawCounts.txt


title: Balbc, day1, replicate 2, scRNAseq

description: 10x Genomics

value: day 1


title: Euploid human brain organoids, uninifected 3

value: uninfected


title: Bl6, sham, replicate 2, scRNAseq

description: 10x Genomics

value: day 0

value: no injury


title: ATAC-Pool1_N1_noStim

description:
Sample_ATACSeq2
ATACSeq_UnionPeakSet_rawCounts.txt

value: baseline


title: CROPSeq_gRNA_libF

description:
Sample_scRNASeq12
CROPSeq_gRNA_merged_features.tsv.gz
CROPSeq_gRNA_merged_barcodes.tsv.gz
CROPSeq_gRNA_merged_matrix.tsv.gz

data_processing:
10X Single cell RNA-Seq data from iNeurons infected with the CROP-Seq gRNA library were processed using cellranger version 3.1.0. Data was aligned against a custom build reference genome based on GRCh38, including the gRNA sequences flanked by adjacent parts of the vector backbone sequence:  5’:CTGTTAGAGAGATAATTAGAATTAATTTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTG  3’:TAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTAAGCTTGGCGTAACTAGATCTTGAGACACTGCTTTTTGCTTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCT
Subsequently, data from all six independent 10X libraries was aggregated with cellranger aggr without depth normalization/downsampling. Individual gRNA amplicon libraries were processed in the same manner, except that reads were trimmed to remove the 18 leading bases of R2 prior to processing by cellranger.  Lastly, single cell RNA-Seq and gRNA amplicon libraries were merged and further processed in Seurat version 3.9.9
Assembly: GRCh38
Supplementary files format and content: gene feature, cell barcode and count matrix for each library as generate by cellranger.

extract_protocol:
At day 30, cells were incubated 5 min at 37°C with accutase and collected as single cell suspension.
The scRNA-seq protocol from 10x Genomics v3.0 was used to prepare 6 different scRNA-seq libraries from the same cell suspension following the manufacturer’s instructions.  sgRNA  enrichment for the produced scRNA-seq libraries was obtained following Genga et al protocol. The index libraries were gel purified and sequenced with the scRNA-seq libraries
scRNA-Seq, targeted scRNA-Seq for gRNA amplicons

treatment_protocol: N1-KRAB iPSCs were infected with the CROP-seq library virus and selected with blasticidin after 24hours. Infection was repeated after 120h from the first one and cells were selected again using blasticidin at day 6 after the first infection.  At day 8 post infection, the cells were differentiated using the iNeuron protocol and the acute infection was performed at day 15 of the differentiation.


title: 16-Cell_77h_52


title: 16-Cell_77h_51


title: Euploid human brain organoids, uninifected 2

value: Human brain organoids

value: multiple cell types


title: Balbc, sham, replicate 2, scRNAseq

description: 10x Genomics


title: CROPSeq_gRNA_libE

description:
Sample_scRNASeq11
CROPSeq_gRNA_merged_features.tsv.gz
CROPSeq_gRNA_merged_barcodes.tsv.gz
CROPSeq_gRNA_merged_matrix.tsv.gz

value: in vitro iPSC

value: iPSC derived neuron


title: 16-Cell_77h_53


title: Balbc, day1, replicate 1, scRNAseq

description: 10x Genomics

value: Hindlimb ischemia surgery


title: CROPSeq_gRNA_libD

description:
Sample_scRNASeq10
CROPSeq_gRNA_merged_features.tsv.gz
CROPSeq_gRNA_merged_barcodes.tsv.gz
CROPSeq_gRNA_merged_matrix.tsv.gz


title: CROPSeq_gRNA_libC

description:
Sample_scRNASeq9
CROPSeq_gRNA_merged_features.tsv.gz
CROPSeq_gRNA_merged_barcodes.tsv.gz
CROPSeq_gRNA_merged_matrix.tsv.gz


title: 16-Cell_77h_4


title: 16-Cell_77h_50


title: 16-Cell_77h_49


title: B6(CG)Tyr(c-2J)/J , CN6, rep 3

city: Minneapolis

first: Laura

middle: L

last: Johnson

state: Minnesota

address: 2001 6th ST SE

institute: University of Minnesota

data_processing:
The University of Minnesota Informatics Institute analyzed the RNA Seq output. 2 x 150bp FastQ paired-end reads for 32 samples (n=22.3 million average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (mm10) as reference
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: mm10

source_name: abducens motor neurons

extract_protocol: RNA was isolated using either the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) or RNeasy Lipid Tissue Mini Kit (Qiagen).

value: abducens motor neurons


title: Balbc, sham, replicate 1, scRNAseq

description: 10x Genomics

value: Hindlimb skeletal muscle cells

value: Hindlimb skeletal muscle


title: B6(CG)Tyr(c-2J)/J , CN6, rep 4


title: B6(CG)Tyr(c-2J)/J , CN6, rep 2


title: Euploid human brain organoids, 24h post SARS-CoV-2 infection 1

value: Euploid (wild type)

value: SARS-CoV-2 infection


title: ValLib_iNeuron_noKcl_R2

description: ValLib_countMatrix_final_barcode_raw.txt

data_processing:
Associating MPRA barcodes with sequence elements: In order to associate the 3’ barcodes with its corresponding sequence/variant tested, we performed paired end sequencing of the intermediate MPRA library prior to inserting the minP-nanoLuc cassette, sequencing 150 cycles from either end on a Illumina MiSeq. Resulting FASTQ files were the modified to clip the 16bp barcode at the end of the second read to be included in the sequence name. Subsequently, the reads were aligned against a custom build reference of the original sequences included in each MPRA library using bwa version 0.7.17(Li and Durbin, 2009) in paired end mode. Resulting .bam files were converted to table format, only retaining aligned reads harboring the expected variant at the center position and including less than 5 clipped or mismatched bases. Subsequently, reads were collapsed onto individual barcodes and only barcodes covered by at least 2 reads and uniquely associated with one sequence element were retained for further analysis.
Processing of 3’ sequencing data: 3’mRNA sequencing data obtained from MPRA experiments in iPSC derived neurons or primary mouse cortical cultures were processed with a custom python scripts to count occurence of individual barcodes discovered in the data. All reads were filtered based on quality metrics, only retaining reads with less than 5 bases below a phred score of 20 and proper backbone sequence elements at the expected positions of the read, e.g. presence of the restriction site TCT and GAC. Subsequently, all 16mer barcodes from the remaining reads were counted initially, but only those barcodes also present in the quality-controlled results of the barcode-pEE association sequencing of the MPRA plasmid library were kept for quantitative analysis.
Assembly: hg19
Supplementary files format and content: table with the following columns: Barcode – unique 16mer barcode of mRNA fragment  Eid – unique Id of reference enhancer element that this barcode associates to  variantMapped – Boolean variable indicating if the expected SNP was detected at the correct position in the association sequencing  reference_name – name of the reference sequence fragment, corresponds to fasta file for this library  chrom – chromosome of enhancer fragment  chromstart – start coordinate of putative enhancer fragment  chromend – end coordinate of putative enhancer fragment  allele – detected allele in this fragment   ref_bases – reference allele for SNP that is interrogated by this putative enhance fragment  alt_bases – alternative allele for SNP that is interrogated by this putative enhance fragment  type – type of fragment, e.g. control or SNP   count – tag count of this fragment in the original plasmid library, used for normalization  followed by observed tag counts for MPRA all tag  count libraries from the different cell types and conditions evaluated

source_name: iNeuron

growth_protocol: iPSC derived neurons were generated via overexpression of pro-neural transcription factor Ngn2 plus small molecules and differentiated for 49 days on murine astrocytes. NPCs were differentiated based on the protocol from (Qi et al., 2017) with slight modifications. Primary mouse cortical cultures were generated from E15.5 mice cultured in vitro over a total of 12 days.

extract_protocol:
All cell types were directly lysed with lysis buffer (Quick-RNA Miniprep Kit, R1054, Zymogen). To increase the yield of the total RNA purification, QIAshredder columns (79654, Qiagen) were used before total RNA isolation. On-column DNAse digest was performed to digest DNA residues. Concentration of total RNA was measured by NanoDrop before performing mRNA isolation with the Poly(A)Purist MAG kit (AM1922, ThermoFisher Scientific) according to manufacturer’s protocol. Purification with glycogen was omitted and mRNA was directly isolated from the beads.
Association Seq: The fragments were amplified at the pMPRA1-enhancer-barcode stage in order to associate enhancer and their respective barcodes. The same forward primer (5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3’) was used for all amplifications, while the reverse primer (5’CAAGCAGAAGACGGCATACGAGAT NNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGTGCCAGAACATTTCTCTG3’) was barcoded (for barcode sequences see Table S7). 100 pg plasmid DNA, 1x Q5 Hot Start High-Fidelity 2x Master Mix (M0494L, NEB) and 0.5 µM reverse and forward primer were mixed and DNA was amplified at the following conditions: 98°C for 30 s, 16 cycles of [98°C for 10 s, 60°C for 30 s, 72°C for 20 s], and a final extension step for 2 min at 72°C. 8 PCR reactions were pooled and purified with Agencourt Ampure XP magnetic beads (A63881, Beckman Coulter) with a double sided selection with 0.55x and subsequently 0.35x of the volume of the pooled PCR product. Purification and clean-up were performed according to manufacturer’s recommendations. The correct fragment size and the concentration of the library were analyzed with the Bioanalyzer (High Sensitivity DNA Analysis, 5067-4626, Agilent). Library quantification was performed in triplicates with an RT-qPCR on the Illumina sequencing adapters according to manufacturer’s protocol (KAPA Library Quantification) on a Roche LightCycler® 480 System. 6-10 % PhiX were spiked into the final library of 6-10 pmol. Paired-end (150 bp each side) sequencing was performed with the MiSeq Reagent Kit (v2, 300-cycles, MS-102-2002, Illumina).  TagCountSeq: 30 µl mRNA were reverse transcribed into cDNA with 2 µl SuperScript IV reverse transcriptase (18090050, ThermoFisher Scientific) and 8 µl SuperScript™ IV VILO™ Master Mix (11756050, ThermoFisher Scientific): 25°C for 10 min, 50°C for 30 min and 85°C for 5 min. In order to analyze the activity of the enhancer, the barcodes were amplified from the cDNA: The PCR protocol described beforehand was used, but the cycle number was increased from 16 to 22 cycles. 0.5 µl cDNA were used for each of the 8 individual PCR reactions. The reverse primer was barcoded (barcode sequences Table S7). Sequence of primers: FW 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3’ and RV 5’CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttatcgacgagcgcctg3. As described above, PCR reactions were pooled and purified. Libraries were pooled equimolar according to their concentrations measured with the bioanalyzer.

treatment_protocol: Human iPSC derived glutamatergic iNeurons were infected during the splitting procedure on day 4. 1.5 - 4 µl MPRA-virus per million cells was added to the dislocated neurons for half an hour at RT. Cell differentiation proceeded then normally. NPCs were infected on day5 and then cultivated for another 3 days. 15-25 million neurons, 8 million NPCs, or 8 million primary neurons were infected per condition.

value: iNeuron

value: iPSC derived neurons


title: Euploid human brain organoids, uninifected 1


title: ValLib_iNeuron_noKcl_R1


title: CROPSeq_gRNA_libB

description:
Sample_scRNASeq8
CROPSeq_gRNA_merged_features.tsv.gz
CROPSeq_gRNA_merged_barcodes.tsv.gz
CROPSeq_gRNA_merged_matrix.tsv.gz


title: 16-Cell_77h_3

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: eQTLLib_iNeuron_noKcl_R4

description: eQTLLib_countMatrix_final_barcode_raw.txt


title: CROPSeq_gRNA_libA

description:
Sample_scRNASeq7
CROPSeq_gRNA_merged_features.tsv.gz
CROPSeq_gRNA_merged_barcodes.tsv.gz
CROPSeq_gRNA_merged_matrix.tsv.gz


title: B6(CG)Tyr(c-2J)/J , CN6, rep 1


title: CROPSeq_scRNA_libF

description:
Sample_scRNASeq6
CROPSeq_scRNA_merged_features.tsv.gz
CROPSeq_scRNA_merged_barcodes.tsv.gz
CROPSeq_scRNA_merged_matrix.tsv.gz


title: eQTLLib_iNeuron_noKcl_R3


title: 16-Cell_77h_1


title: CROPSeq_scRNA_libE

description:
Sample_scRNASeq5
CROPSeq_scRNA_merged_features.tsv.gz
CROPSeq_scRNA_merged_barcodes.tsv.gz
CROPSeq_scRNA_merged_matrix.tsv.gz


title: eQTLLib_iNeuron_noKcl_R1


title: DevLib_NPC_R5

description: DevLib_countMatrix_final_barcode_raw.txt

source_name: Neural Progenitors

value: Neural Progenitors


title: 16-Cell_77h_16


title: C57BL/6, CN6, rep 2


title: C57BL/6, CN6, rep 3


title: 16-Cell_77h_15


title: CROPSeq_scRNA_libC

description:
Sample_scRNASeq3
CROPSeq_scRNA_merged_features.tsv.gz
CROPSeq_scRNA_merged_barcodes.tsv.gz
CROPSeq_scRNA_merged_matrix.tsv.gz


title: C57BL/6, CN6, rep 1


title: CROPSeq_scRNA_libD

description:
Sample_scRNASeq4
CROPSeq_scRNA_merged_features.tsv.gz
CROPSeq_scRNA_merged_barcodes.tsv.gz
CROPSeq_scRNA_merged_matrix.tsv.gz


title: 16-Cell_77h_2


title: B6(CG)Tyr(c-2J)/J , CN3, rep 4

source_name: oculomotor neurons

value: oculomotor neurons


title: CROPSeq_scRNA_libB

description:
Sample_scRNASeq2
CROPSeq_scRNA_merged_features.tsv.gz
CROPSeq_scRNA_merged_barcodes.tsv.gz
CROPSeq_scRNA_merged_matrix.tsv.gz

value: baseline


title: 16-Cell_77h_14


title: 16-Cell_77h_13


title: CROPSeq_scRNA_libA

description:
Sample_scRNASeq1
CROPSeq_scRNA_merged_features.tsv.gz
CROPSeq_scRNA_merged_barcodes.tsv.gz
CROPSeq_scRNA_merged_matrix.tsv.gz


title: DevLib_iNeuron_Kcl_R3

value: Kcl


title: 16-Cell_77h_12


title: DevLib_iNeuron_Kcl_R4


title: 16-Cell_77h_11


title: B6(CG)Tyr(c-2J)/J , CN3, rep 3


title: B6(CG)Tyr(c-2J)/J , CN3, rep 2


title: MUC18290_SCZ4_iN_B13_d52_Kclstimm

description:
Sample_RNASeq22
RNASeq_rawCounts.txt

data_processing:
Single-End raw RNA-Seq read sequences were aligned against the GRCh38 genome assembly with the GENCODE version 27 transcriptome definition using the STAR aligner (Dobin et al., 2013) version 2.7.3a with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM Unsorted SortedByCoordinate --quantMode GeneCounts --outSAMstrandField intronMotif. Subsequently, duplicates were marked and library quality metric were computed using picard tools (http://broadinstitute.github.io/picard/).  Following quality control, gene level read counts were obtained using the Rsubread package, collapsing exon level reads onto gene level features based on GENCODE version 27 with the following parameters: countMultiMappingReads=FALSE,ignoreDup=FALSE, sGTFAnnotationFile=TRUE,isPairedEnd=T.
Assembly: GRCh38
Supplementary files format and content: raw count matrix for each gene

extract_protocol:
For total RNA isolation, frozen network pellets, or living cultures were subjected to Qiazol. Total RNA was isolated following the instruction of the Quick-RNA Microprep Kit (Zymogen). DNA digestion was performed after RNA purification with TurboDnase free Kit (AM1907, ThermoFisher Scientific). Quality and concentration of the isolated RNA was checked on a NanoDrop or TapeStation.
For bulk 3’RNA sequencing, 500 ng total RNA were used to generated 3’ mRNA sequencing libraries following manufacturer’s protocol (QuantSeq 3' mRNA-Seq, 015.96, Lexogen). Libraries were single indexed. In order to normalize the libraries, spike-ins were added during library preparation (SIRV-Set3, 51.01, Lexogen). Libraries were amplified for sequencing with 14 PCR cycles. Each library was examined for correct size distribution and concentration separately with the Bioanalyzer or the tape station. Up to 50 libraries were pooled equimolar and then sequenced on a NovaSeq (single-end sequencing).


title: C57BL/6, CN6, rep 4


title: MUC18289_SCZ1_iN_B13_d52_Kclstimm

description:
Sample_RNASeq21
RNASeq_rawCounts.txt


title: DevLib_iNeuron_Kcl_R2


title: 16-Cell_77h_10


title: B6(CG)Tyr(c-2J)/J , CN3, rep 1


title: MUC18288_C8_iN_B13_d52_Kclstimm

description:
Sample_RNASeq20
RNASeq_rawCounts.txt


title: DevLib_NPC_R4


title: DevLib_iNeuron_noKcl_R4


title: DevLib_NPC_R3


title: C57BL/6, CN3, rep 3


title: E105_STZ_03 RNA-seq

city: San Francisco

first: Tomohiro

last: Nishino

state: California

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: Single-cell sequencing assay for transposase-accessible chromatin from cardiogenic region from E10.5 mouse embryo from STZ treated to induce hyperglycemic female

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (5.0.0) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v4 according to specifications in the tutorials (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: normalized gene-cellbarcode expression matrix in csv format

source_name: Embryonic mouse heart at E10.5

growth_protocol: Timed matings were set up between normal glycemic male mice and either Veh-pretreated normal glycemic female mice or STZ-pretreated hyperglycemic female mice. Morning of plug detection was considered embryonic day (E) 0.5 and embryos were harvested at E10.5

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes and resuspended in 35ul of PBS/1% FBS

value: wild type

tag: specific heart region

value: Cardiogenic region

tag: additional cell lineages present in dataset

value: Non-cardiac mesoderm, ectoderm and endoderm

value: STZ treated


title: MUC18287_C7_iN_B13_d52_Kclstimm

description:
Sample_RNASeq19
RNASeq_rawCounts.txt

value: in vitro iPSC

value: iPSC derived neuron


title: DevLib_iNeuron_noKcl_R3


title: E105_STZ_02 RNA-seq

tag: strain


title: MUC18286_C3_iN_B13_d52_Kclstimm

description:
Sample_RNASeq18
RNASeq_rawCounts.txt


title: C57BL/6, CN3, rep 2


title: MUC18285_F4_iN_B13_d52_KClstimm

description:
Sample_RNASeq17
RNASeq_rawCounts.txt


title: E105_STZ_01 RNA-seq


title: C57BL/6, CN3, rep 1


title: MUC18284_F3_iN_B13_d52_Kclstimm

description:
Sample_RNASeq16
RNASeq_rawCounts.txt


title: Normal SAP development D40, Bio_Rep4 , Bulk- RNAseq

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

institute: UGent

data_processing:
Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina Cat nr. TG-410-1002).
FASTQ files were mapped using STAR (v2.7.3a).
The counts per gene were normalized using DESeq2 (Love et al., 2014)
The counts for each gene in each sample is divided by the geometric mean of the gene across all samples.
The median of the ratios for the genes in a sample is the estimated size “scaling” size factor used to adjust the total mapped reads count from each sample.
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text files include STAR counts per sample

source_name: J2 (MRC5-IPSC)

growth_protocol: Stem cells were maintained in E8 medium with E8 supplement in humidified atmosphere with 5% CO2 at 37C. The cells were passaged biweekly by treatment with accutase for 15min. Accutase was neutralised with E8 medium in a ratio of 3:1. The cell suspension was counted and centrifuged at 120 x g for 3 min. Eventually, 20-30,000 cells/well were seeded on previously prepared Matrigel-coated six well plates.

extract_protocol:
Cell pellets were snapfrozen for analysis at selected time-points over the differentiation process. To extract RNA from the cells, phase separation in cells lysed in TRIzol Reagent was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 125-500ng of total RNA with an RNA integrity number varying from 7.8-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina, with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit.

treatment_protocol:
Stem cells were transitioned to truncal neural crest cells (truncal NCC) in a 16-day long process. First cells were seeded on geltrex coated 24 well plates at a concentration of 100k/cm² in medium consisting of E6 supplemented with 10µM Rock inhibitor. After allowing the cells to attach for 24hrs the medium was changed to E6 with 100ng/mL FGF2, 10µM SB431542, 3µM CHIR, 1ng/µL BMP4 for the following 2 days. Hereafter the medium was adjusted to E6 medium with 10µM SB431542 and 1,5µM CHIR which was used until D16 where we enriched for NCC using FACS sorting. After sorting the cells were centrifuged and resuspended in neurobasal medium with 1/50 B27 supplement, 1/100 N2 supplement, 2mM L-glutamine, 1/100 non assential amino acids, (together making up Basal NB medium), 10ng/mL FGF2 and 3µM CHIR. The cells were subsequently plated out on ultra-low attachment plates (Corning, Cat Nr. 3471) to generate spheres and allow for larger increase of cell numbers. The spheres were allowed to grow for 4 days after which they were plated on previously prepared PO/FN/LM coated 24 well plates.
24Hrs after plating out the spheres the medium was changed to NB basal medium with 50ng/mL BMP4 and 50ng/mL SHH for a total of 4 days, renewed every 2 days. Subsequently the medium is changed to NB basal medium with 200µM Ascorbic Acid. This was renewed every 4 days until the end of the differentiation.

value: J2 (MRC5-IPSC)

value: iPSC

value: WT

value: SAP differentiation

value: Day 40


title: E105_STZ_03 ATAC-seq

description: Single-cell sequencing assay for transposase-accessible chromatin from cardiogenic region from E10.5 mouse embryo from STZ treated that stimulated hyperglycemic female

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger-atac Suite (v2.0) from 10X genomics
Additional filtering, quality control and doublet removal was done using ArchR (v1.0.1) according to specifications in the tutorials (https://www.archrproject.com/)
Assembly: mm10

extract_protocol:
After doing transposition step using 5ul of single nucli suspensions, samples were loaded onto the Chromium controller (10X genomics) microfluidic chip for single nuclei droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (PN- 1000176) and Single Index Kit N Set A (PN-1000212).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes, and supernatatn were removed. Cell pellets were lysed with Lysis Buffer on ice for 5min and then wasded with Wash Buffer. Nuclei were centrifuged at 500 rcf for 5 min and resuspended in 10x Nuclei Buffer. For the latter Nuclei isolation steps were accoding to the manufacture's instruction from 10x Genomics.

value: Streptozotocin


title: E105_STZ_02 ATAC-seq


title: Normal SAP development D35, Bio_Rep4 , Bulk- RNAseq

value: Day 35


title: Normal SAP development D31,TH reporter , Bulk- RNAseq

source_name: TH-rep (WA01)

value: TH-rep (WA01)

value: Day 31


title: B6(CG)Tyr(c-2J)/J , TA, rep 3

source_name: tibialis anterior

value: tibialis anterior


title: E105_STZ_01 ATAC-seq


title: MUC18283_F2_iN_B13_d52_Kclstimm

description:
Sample_RNASeq15
RNASeq_rawCounts.txt

value: Kcl


title: B6(CG)Tyr(c-2J)/J , TA, rep 4


title: C57BL/6, CN3, rep 4

value: oculomotor neurons


title: E105_Veh_03 ATAC-seq

description: Single-cell sequencing assay for transposase-accessible chromatin from cardiogenic region from E10.5 mouse embryo from Veh treated normal glycemic female

value: Vehicle

value: Cardiogenic region


title: Normal SAP development D31, Bio_Rep4 , Bulk- RNAseq


title: MUC18281_HDF6_iN_B13_d52_Kclstimm

description:
Sample_RNASeq13
RNASeq_rawCounts.txt


title: B6(CG)Tyr(c-2J)/J , TA, rep 2


title: B6(CG)Tyr(c-2J)/J , TA, rep 1


title: Normal SAP development D27, Bio_Rep4 , Bulk- RNAseq

value: Day 27


title: E105_Veh_02 ATAC-seq

value: Non-cardiac mesoderm, ectoderm and endoderm


title: C57BL/6, TA, rep 4


title: E105_Veh_01 ATAC-seq


title: MUC18280_No1_iN_B13_d52_KClstimm

description:
Sample_RNASeq12
RNASeq_rawCounts.txt

value: in vitro iPSC

value: iPSC derived neuron


title: DevLib_iNeuron_noKcl_R5

value: iNeuron

value: iPSC derived neurons

value: baseline


title: Normal SAP development D25, Bio_Rep4 , Bulk- RNAseq

value: J2 (MRC5-IPSC)

value: iPSC

value: WT

value: SAP differentiation

value: Day 25


title: MUC18276_C8_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq11
RNASeq_rawCounts.txt


title: MUC18282_F1_iN_B13_d52_Kclstimm

description:
Sample_RNASeq14
RNASeq_rawCounts.txt


title: C57BL/6, TA, rep 3

value: tibialis anterior


title: MUC18275_C7_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq10
RNASeq_rawCounts.txt


title: C57BL/6, TA, rep 2


title: MUC18274_C3_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq9
RNASeq_rawCounts.txt


title: Normal SAP development D35, Bio_Rep3 , Bulk- RNAseq

value: Day 35


title: Normal SAP development D23, Bio_Rep4 , Bulk- RNAseq

value: Day 23


title: Bacteria, tol deletion, rep2

city: Seongnam

first: Shin-Yae

last: Choi

institute: CHA University

data_processing:
Average Q20 using BBDuk
Mapping using Bowtie2 to Reference genome Calculation read count using Bedtools
Quantile normalization using EdgeR
DEG master file production using ExDEGA
Assembly: Vibrio cholerae O1 biovar El Tor str. N16961

organism: Vibrio cholerae

source_name: Bacteria

extract_protocol:
RNA was extracted using a Qiagen RNA purification Kit and Qiagen RNA Clean-up Kit.
Clontech SMARTer Stranded RNA-Seq Kit

value: Bacteria

value: tol deletion


title: Bacteria, tet deletion, rep2

value: tet deletion


title: Bacteria, tox deletion, rep2

value: tox deletion


title: MUC18273_SCZ4_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq8
RNASeq_rawCounts.txt

value: in vitro iPSC


title: Normal SAP development D29, Bio_Rep3 , Bulk- RNAseq

value: Day 29


title: C57BL/6, TA, rep 1


title: Bacteria, No mutation, rep2

value: No mutation


title: B6(CG)Tyr(c-2J)/J , EOM, rep 3

source_name: extraocular muscles

value: extraocular muscles


title: Normal SAP development D29, Bio_Rep4 , Bulk- RNAseq


title: Bacteria, No mutation, rep1


title: Normal SAP development D31, Bio_Rep3 , Bulk- RNAseq

value: Day 31


title: MUC18272_SCZ1_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq7
RNASeq_rawCounts.txt

value: iPSC derived neuron

value: baseline


title: MUC18271_F4_iN_B13_d52_KClunstimm

description:
Sample_RNASeq6
RNASeq_rawCounts.txt


title: Normal SAP development D27, Bio_Rep3 , Bulk- RNAseq

value: J2 (MRC5-IPSC)

value: iPSC

value: WT

value: Day 27


title: Bacteria, tox deletion, rep1


title: B6(CG)Tyr(c-2J)/J , EOM, rep 1


title: MUC18270_F3_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq5
RNASeq_rawCounts.txt


title: Normal SAP development D25, Bio_Rep3 , Bulk- RNAseq

value: SAP differentiation

value: Day 25


title: Normal SAP development D23, Bio_Rep3 , Bulk- RNAseq

value: Day 23


title: Bacteria, tol deletion, rep1

value: Bacteria

value: tol deletion


title: Bacteria, tet deletion, rep1

value: tet deletion


title: MUC18269_F2_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq4
RNASeq_rawCounts.txt

value: in vitro iPSC


title: Normal SAP development D40, Bio_Rep2 , Bulk- RNAseq

value: hESC

value: Day 40


title: B6(CG)Tyr(c-2J)/J , EOM, rep 4

value: extraocular muscles


title: C57BL/6, EOM, rep 3


title: MUC18268_F1_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq3
RNASeq_rawCounts.txt


title: B6(CG)Tyr(c-2J)/J , EOM, rep 2


title: C57BL/6, EOM, rep 4


title: C57BL/6, EOM, rep 2


title: MUC18267_HDF6_iN_B13_d52_Kclunstimm

description:
Sample_RNASeq2
RNASeq_rawCounts.txt


title: MUC18266_No1_iN_B13_d52_KClunstimm

description:
Sample_RNASeq1
RNASeq_rawCounts.txt


title: ATAC-Seq - Hippocampus Aged Female Replicate 8

first: Kelsey

last: Martin

address: 615 Charles E Young Drive South

department: Biological Chemistry

institute: UCLA

data_processing:
Adapter content was trimmed using Scythe (https://github.com/vsbuffalo/scythe/) and ATAC-seq reads were mapped to the mouse genome (mm10) using Bowtie 2 (Langmead and Salzberg, 2012). Reads in blacklist regions (Amemiya et al., 2019; Dunham et al., 2012) and reads mapped to mitochondria were removed.
Peaks were called on each individual sample using MACS3 (with parameter settings --nomodel -f BAMPE and FDR cutoff of 0.05) (Zhang et al., 2008). For each sample, read pairs (fragments) were counted for each peak using featureCount (Liao et al., 2014) (with parameter settings -p --countReadPairs -M --fraction).
For quality control, we calculated a transcription start site (TSS) enrichment score using ATACseqQC (Ou et al., 2018) and a FRiP score (fraction of reads/fragments in peaks), and included samples showed a TSS enrichment score > 10 and a FRiP score > 0.2.
For each condition, narrow peak sets were merged, and peaks were included in consensus peak sets for each condition if there was at least a 50% overlap with a peak in at least two replicates . A total consensus peak set (92,233 peaks) was generated by merging the consensus peak sets from each condition.
Fragments were counted for each total consensus peak in each sample using featureCount as described above, and differential analysis was performed using DESeq2, including sequencing batch as a variable (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: Excel table with genomic annotation, normalized counts, fold changes and p-values for all ATAC-seq consensus peaks

source_name: hippocampus

growth_protocol: Mice were housed in groups under a 12:12 hr light/dark cycle with food provided ad libitum until they reached the age of 10 weeks (young adult) and 80 weeks (aged).

extract_protocol:
The hippocampus was homogenized with a Dounce tissue grinder (Wheaton 357544) in 2mL HB buffer (1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitor (Sigma-Aldrich 04693159001), 0.3% IGEPAL-630, 0.25 M sucrose, 25 mM MgCl2, 20 mM Tricine-KOH). The homogenate was then filtered through a 40 mm strainer. The filtrate was centrifuged over one volume of cushion buffer (0.5 mM MgCl2, 0.5 mM DTT, protease inhibitor, 0.88 M sucrose) at 2800 g for 10 minutes in a swinging bucket centrifuge at 4°C. The nuclei pellet was resuspended in 20 mL PBS. 1 mL of the nuclei sample was stained with Hoechst 33342 to calculate nuclei concentration, and 50,000 nuclei per sample were used for downstream library preparation.
Libraries were prepared using the Nextera DNA Library Prep kit (Illumina FC-121-1030) and quality was analyzed using the D1000 ScreenTape Assay (Agilent 5067-5582).

treatment_protocol: For sample collection, mice were deeply anesthetized with isoflurane and euthanized by cervical dislocation. The brain was quickly removed and cooled for one minute in ice-cold PBS before the hippocampus from each hemisphere was dissected on ice and processed immediately.

value: hippocampus

value: Aged

value: Female


title: C57BL/6, EOM, rep 1


title: FVB_DorsalLateral_2

city: Chicago

first: Mindy

middle: Kim

last: Graham

state: IL

address: 303 E. Superior Street Chicago

department: Urology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Cell Ranger (version 2.2.0) count pipeline was used to align reads to the mm10 mouse transcriptome and create a gene-by-cell count matrix.
To align transgene expression, Kallisto quant (v0.46.0) was used to align the reads against human MYC and mouse Myc reference sequences. Samtools (v0.1.19) was used to extract alignments from BAM files for each sample. An in-house Perl script was used to map the alignments to the original FASTQ reads and create a feature-barcode count matrix. The Cell Ranger matrices were merged with the custom count matrices containing human MYC and mouse Myc.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: FVB/NJ

extract_protocol:
Tissues were minced with razor blades and digested in 0.25% Trypsin-EDTA (Gibco 25200-072) for 10 min at 37°C, followed by incubation for 2.5 hours at 37°C with gentle agitation in DMEM containing 10% FBS, 1 mg/mL Collagenase Type I (Gibco 17100-017), and 0.1 mg/mL of DNase I (Roche 10104159001). Digested tissues were centrifuged at 400 x g for 5 minutes, washed with HBSS, and further incubated in 0.25% Trypsin-EDTA for 10 min at 37°C. Cells were suspended in DMEM containing 10% FBS and 0.4 mg/mL of DNase I and filtered through a 40 μm cell strainer.
Libraries for scRNA-seq were prepared using the 10x Genomics Chromium Single Cell 3’ Library and Gel bead Kit V2 (CG00052_RevF) according to the manufacturer’s protocol for each dissected mouse prostate lobe and each human prostatectomy tissue punch. The cDNA libraries were sequenced (150 bp paired-end) on the Illumina HiSeqX platform. Each sequenced library was demultiplexed to FASTQ files using Cell Ranger (10x Genomics).

value: FVB/NJ

tag: lobe

value: Dorsal & Lateral

tag: replicate

value: 10 months


title: RPA in DMC1-knockout B6CASTF1 PRDM9hc

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

country: United Kingdom

institute: Oxford University

data_processing:
Alignment with a modified BWA mapper (Khil et al., 2012)
Peaks were called using an in-house algorithm R code available athttps://github.com/anjali-hinch/hybrid-rescue
Alleles were called using an in-house algorithm (described in Hinch et al 2019)
Filtering of false-positive hotspots and overlap with PRDM9-independent H3K4me3 were performed using in-house algorithm (Hinch et al 2019)
Assembly: mm10
Supplementary files format and content: text file with column descriptions in commented header; each line corresponds to one hotspot

source_name: whole adult testis

growth_protocol: Data were generated from in vivo tissue samples from adult male mice - no culturing was performed.

extract_protocol:
Testes samples were stripped of the tunica and processed as described in Khil et al, Genome Research, 2012). Single-stranded DNA sequencing and double-strand break detection were performed using a modified ssDNA ChIPseq protocol. Full experimental procedures are reported in Hinch et al 2020.
Libraries were prepared according to Illumina's instructions

value: whole adult testis

value: testis

value: HUM/CAST


title: Normal SAP development D31, Bio_Rep2 , Bulk- RNAseq

value: WT

value: SAP differentiation

value: Day 31


title: FVB_DorsalLateral_1


title: Normal SAP development D27, Bio_Rep2 , Bulk- RNAseq

value: Day 27


title: HiMyc_FVB_Ventral_2

value: Ventral

value: Hi-Myc

value: 6 months


title: HiMyc_FVB_Ventral_1


title: HK2_siGLUT2_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: HK2 cells transfected with siGLUT2, biological replicate 4

data_processing:
The raw data were analyzed by Next Generation Diagnostics srl proprietary Digital mRNA-seq pipeline (v2.0) which involves a cleaning step by quality filtering and trimming, alignment to the reference genome and counting by gene(BBMap – Bushnell B. – sourceforge.net/projects/bbmap/; Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.; Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25. PubMed PMID: 25260700; PubMed Central PMCID: PMC4287950; Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: HK2 cell were cultured in DMEM/F12 supplemented with 5% FBS, 1% ITS, 2mM Glutammine and 1% Pen/Strep. Cells are kept at 37C in 5% CO2 until reaching 70-80% confluency and then harvested and counted.

extract_protocol:
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). RNA was quantified and mixed at 10ng/µl
Libraries were prepared from 125 ng of total RNA using the Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl, https://doi.org/10.1038/s41598-017-14892-x) which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).

treatment_protocol: Cells were then seeded in 6-well plates and transfected with 50nM siRNA by RNAimax tranfection reagent according to manufacturers instructions. 96h post transfection, cells were lysed and RNA was extracted.

value: Proximal tubule cells

value: HK2 cells transfected with siGLUT2


title: Normal SAP development D29, Bio_Rep2 , Bulk- RNAseq

value: hESC

value: Day 29


title: Normal SAP development D23, Bio_Rep2 , Bulk- RNAseq

value: Day 23


title: HK2_siGLUT2_3

description: HK2 cells transfected with siGLUT2, biological replicate 3


title: HK2_scr_4

description: HK2 cells transfected with siRNAs with a scrambled sequence, biological replicate 4


title: HK2_siGLUT2_2

description: HK2 cells transfected with siGLUT2, biological replicate 2


title: Normal SAP development D35, Bio_Rep1 , Bulk- RNAseq

value: Day 35


title: Normal SAP development D35, Bio_Rep2 , Bulk- RNAseq


title: ATAC-Seq - Hippocampus Aged Female Replicate 4

value: hippocampus

value: Aged

tag: Sex

value: Female


title: C57BL6_Ventral_3


title: Normal SAP development D31, Bio_Rep1 , Bulk- RNAseq


title: HK2_scr_2

description: HK2 cells transfected with siRNAs with a scrambled sequence, biological replicate 2


title: ATAC-Seq - Hippocampus Aged Female Replicate 5


title: HiMyc_C57BL6_Ventral_1


title: Normal SAP development D29, Bio_Rep1 , Bulk- RNAseq


title: HK2_scr_1

description: HK2 cells transfected with siRNAs with a scrambled sequence, biological replicate 1


title: ATAC-Seq - Hippocampus Aged Female Replicate 6


title: ATAC-Seq - Hippocampus Aged Female Replicate 3


title: FVB_Ventral_1

value: FVB/NJ


title: FVB_Ventral_2

value: WT


title: ATAC-Seq - Hippocampus Aged Female Replicate 7


title: ATAC-Seq - Hippocampus Aged Female Replicate 2


title: ATAC-Seq - Hippocampus Young Female Replicate 8

value: Young Adult


title: M16_MBC_NST

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

description: 10x Genomics 3' standard v1 Visium Spatial Gene Expression; spaceranger-1.3.0

data_processing:
spaceranger-1.2.2 for samples M1 to M11
spaceranger-1.3.0 for samples M13 to M16
Pathological annotations by V Cockenpot, breast pathologist at Centre Léon Bérard, Lyon (FR)
Assembly: GRCh38
Supplementary files format and content: per-sample matrix of counts per spot in hierarchical data format
Supplementary files format and content: pathological annotations, as annotated and exported via Loupe Browser
Library strategy: Spatial transcriptomics: single-spot UMI-based RNA-seq

source_name: Breast

extract_protocol:
After optimisation, RNA permeabilisation on the Visium slide was set to 12 minutes and processed according to the manufacturer's protocol (10X Genomics)
Visium 3' V1 protocol (10X Genomics)

value: Breast

value: Cancer

tag: cell subtype

value: Metaplastic


title: M15_MBC_chondroid


title: Normal SAP development D25, Bio_Rep1 , Bulk- RNAseq

value: SAP differentiation

value: Day 25


title: ATAC-Seq - Hippocampus Young Female Replicate 7


title: Normal SAP development D23, Bio_Rep1 , Bulk- RNAseq


title: HK2_scr_3

description: HK2 cells transfected with siRNAs with a scrambled sequence, biological replicate 3

value: Proximal tubule cells


title: Normal SAP development D27, Bio_Rep1 , Bulk- RNAseq

value: Day 27


title: Normal SAP development D25, Bio_Rep2 , Bulk- RNAseq

value: hESC


title: C57BL6_Ventral_2

value: Ventral

value: 6 months


title: ATAC-Seq - Hippocampus Aged Female Replicate 1


title: HiMyc_C57BL6_Ventral_2

value: Hi-Myc


title: ATAC-Seq - Hippocampus Young Female Replicate 5

value: hippocampus


title: HiMyc_FVB_Lateral_2

value: Lateral


title: M14_MBC_spindle2


title: ATAC-Seq - Hippocampus Young Female Replicate 4

value: Female


title: HiMyc_C57BL6_Lateral_2


title: Normal SAP development D21, Bio_Rep2 , Bulk- RNAseq

value: Day 21


title: C57BL6_Ventral_1

value: WT


title: Normal SAP development D7, Bio_Rep2 , Bulk- RNAseq

value: Day 7


title: M13_MBC_spindle1

value: Breast


title: Normal SAP development D16, Bio_Rep2 , Bulk- RNAseq

value: Day 16


title: ATAC-Seq - Hippocampus Young Female Replicate 6

value: Young Adult


title: HiMyc_FVB_Lateral_1

value: FVB/NJ


title: C57BL6_Lateral_3


title: M11_CL-like3

description: 10x Genomics 3' standard v1 Visium Spatial Gene Expression; spaceranger-1.2.2

value: Cancer

value: CL-like


title: FVB_Lateral_1


title: HiMyc_C57BL6_Lateral_1


title: M6_Unstable4

value: Unstable


title: M9_CL-like3

value: Normal


title: ATAC-Seq - Hippocampus Young Female Replicate 3


title: Normal SAP development D11, Bio_Rep2 , Bulk- RNAseq

value: hESC

value: SAP differentiation

value: Day 11


title: Normal SAP development D3, Bio_Rep2 , Bulk- RNAseq

value: Day 3


title: ATAC-Seq - Hippocampus Young Female Replicate 2

value: hippocampus


title: M8_CL-like2


title: ATAC-Seq - Hippocampus Young Female Replicate 1

value: Female


title: M7_CL-like4


title: Normal SAP development D21, Bio_Rep1 , Bulk- RNAseq

value: Day 21


title: M5_Unstable3


title: M4_Unstable2


title: C57BL6_Lateral_1

value: Lateral

value: WT

value: 6 months


title: ATAC-Seq - Hippocampus Aged Male Replicate 7

value: Aged

value: Male


title: M10_CL-like4

value: Breast


title: Normal SAP development D16, Bio_Rep1 , Bulk- RNAseq

value: Day 16


title: ATAC-Seq - Hippocampus Aged Male Replicate 5


title: ATAC-Seq - Hippocampus Aged Male Replicate 6


title: HiMyc_FVB_DorsalLateral_2

value: FVB/NJ

value: Dorsal & Lateral

value: Hi-Myc

value: 10 months


title: Normal SAP development D11, Bio_Rep1 , Bulk- RNAseq

value: hESC

value: SAP differentiation


title: Normal SAP development D7, Bio_Rep1 , Bulk- RNAseq

value: Day 7


title: FVB_Lateral_2


title: Normal SAP development D21, Bio_Rep4 , Bulk- RNAseq

value: J2 (MRC5-IPSC)

value: iPSC


title: Normal SAP development Start, Bio_Rep2 , Bulk- RNAseq

value: Day 0


title: Normal SAP development D31-32, cells, scRNAseq

description: 10x Genomics

data_processing:
The sequenced libraries were quantified with Cell Ranger software (version 6.0.0) (Zheng et al., 2017) with default parameters.
The standard reference provided with Cell Ranger (version 2020-A) was used. This version was build on a GRCh38 human genome (bundle 3.0.0) and a filtered version of Gencode v32.
In addition, HTO surface antibodies were quantified with the Cell Ranger count feature reference option. The feature reference file is provided on GitHub (https://github.ugent.be/DePreterLab/Sympatho-adrenergic-differentiation-track)
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated barcodes, features and matrix files

source_name: SAP developmental cells

extract_protocol:
Prior to scRNAseq the cells of selected time-points were hashed and pooled together for scRNAseq analysis. The time-points D25-26, D27-28, D29-30 and D31-32 were hashed for the WT cells. For the ALK mutant cells time-points D25-27-29-32 were hashed. After dissociating the cells with Accutase for 25 minutes we prepared a 50μl single cell suspension at a concentration between 1x105 cells/mL and 2x107 cells/mL for each hasing group in Cell Staining Buffer (BioLegend, Cat nr. 420201) for cell labelling. 5μl Of cell solution was used to record total cell count and cell viability using Trypan Blue. To the remaining 45μl, 0.1X volume (5 μL) of Human TruStain FcX (BioLegend, Cat nr. 422301) was added. This was allowed to incubate for 10 minutes at 4°C. During this incubation time a solution of 1μg /50μl was prepared for each hashing antibody (B0251 – B0256, see key resource table). The hashing antibody solution was centrifuged at 14,000g at 4°C for 10 minutes. The antibody solution was thereafter carefully withdrawn, whilst avoiding touching the bottom of the tube, and transferred on the corresponding cell solution. This was allowed to incubate for 30 minutes at 4°C, simultaneously the cell staining buffer was cooled down to 4°C. After incubation the cell solution was diluted 10 times by adding 0.9 mL cell staining buffer and transferred to a 12 x 75mm Falcon Round-Bottom Polystyrene Tube. Subsequently we added 2.5ml of cell staining buffer for a final dilution of 35 times. The cell solutions where thereafter  centrifuged at 400g at 4°C for 5 minutes. Next the supernatant was aspirated leaving 50-100μl, this was repeated two more times for a total of 3 washes. It is very important to perform these washes carefully, leaving as little supernatant as possible. After the last wash the different cell solutions (each with their own hashtag) were combined into one tube, centrifuged and resupsended in DMEM-F12, as this medium was compatible with the 10XGenomics pipeline, for a final concentration of 1000 cells/μl.
The single-cell RNA-Seq was performed on Chromium instrument (10X genomics) following the user guide manual (Reagent Kit 3’ v3.1). Each sample, containing approximately 10,000 cells at a final dilution of ~1,000 cells/µl was loaded onto the cartridge following the manual. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). The individual transcriptomes of encapsulated cells were barcoded during RT step and resulting cDNA purified with DynaBeads followed by amplification per manual guidelines. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters and indexed by PCR. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher).

value: iPSCs (J2)

value: SAP developmental cells

tag: library type

value: 3’end gene expression


title: Normal SAP development D3, Bio_Rep1 , Bulk- RNAseq

value: WT

value: Day 3


title: Normal SAP development D7, Bio_Rep4 , Bulk- RNAseq


title: Normal SAP development D29-30, cells, scRNAseq

description: 10x Genomics


title: HiMyc_FVB_DorsalLateral_1


title: M2_CL-like1

value: Breast

value: Cancer

value: CL-like


title: HiMyc_FVB_Dorsal_2

value: FVB/NJ

value: Dorsal

value: 6 months


title: Normal SAP development Start, Bio_Rep1 , Bulk- RNAseq

value: hESC


title: ATAC-Seq - Hippocampus Aged Male Replicate 2

value: hippocampus

value: Aged

value: Male


title: HiMyc_FVB_Dorsal_1

value: Hi-Myc


title: ALKR1275Q SAP development D25-32, cells, scRNAseq

description: 10x Genomics

value: ALKR1275Q mutant patient-specific IPSCs


title: ATAC-Seq - Hippocampus Aged Male Replicate 1


title: Normal SAP development D27-28, cells, scRNAseq

description: 10x Genomics

value: iPSCs (J2)


title: FVB_Dorsal_2


title: ATAC-Seq - Hippocampus Young Male Replicate 6

value: Young Adult


title: Normal SAP development D25-26, cells, scRNAseq

description: 10x Genomics

value: SAP developmental cells

value: 3’end gene expression


title: Normal SAP development Start, Bio_Rep4 , Bulk- RNAseq

value: J2 (MRC5-IPSC)

value: iPSC

value: WT

value: SAP differentiation

value: Day 0


title: ATAC-Seq - Hippocampus Aged Male Replicate 4


title: HiMyc_C57BL6_Dorsal_1

value: Dorsal


title: HiMyc_C57BL6_Dorsal_2

value: 6 months


title: ATAC-Seq - Hippocampus Young Male Replicate 3


title: ATAC-Seq - Hippocampus Aged Male Replicate 3


title: ATAC-Seq - Hippocampus Young Male Replicate 2


title: ATAC-Seq - Hippocampus Young Male Replicate 5


title: Normal SAP development D16, Bio_Rep4 , Bulk- RNAseq

value: Day 16


title: C57BL6_Dorsal_3


title: Normal SAP development D7, Bio_Rep3 , Bulk- RNAseq

value: Day 7


title: Normal SAP development D31-32, hashtag4 , scRNAseq

description: 10x Genomics

value: cell hashing


title: Normal SAP development D3, Bio_Rep4 , Bulk- RNAseq

value: Day 3


title: ATAC-Seq - Hippocampus Young Male Replicate 1

value: hippocampus

value: Male


title: C57BL6_Dorsal_2


title: C57BL6_Dorsal_1


title: FVB_Dorsal_1

value: FVB/NJ


title: Normal SAP development D3, Bio_Rep3 , Bulk- RNAseq


title: RAD51 in DMC1-knockout B6CASTF1 PRDM9hc

value: whole adult testis

value: testis

value: HUM/CAST


title: Normal SAP development D21, Bio_Rep3 , Bulk- RNAseq

value: J2 (MRC5-IPSC)

value: Day 21


title: ALKR1275Q SAP development D25-32, hashtag5 , scRNAseq

description: 10x Genomics

value: ALKR1275Q mutant patient-specific IPSCs

value: SAP developmental cells


title: HiMyc_FVB_Anterior_2

value: Anterior

value: Hi-Myc


title: Normal SAP development D27-28, hashtag2 , scRNAseq

description: 10x Genomics

value: iPSCs (J2)


title: Normal SAP development D25-26, hashtag1 , scRNAseq

description: 10x Genomics

data_processing:
The sequenced libraries were quantified with Cell Ranger software (version 6.0.0) (Zheng et al., 2017) with default parameters.
The standard reference provided with Cell Ranger (version 2020-A) was used. This version was build on a GRCh38 human genome (bundle 3.0.0) and a filtered version of Gencode v32.
In addition, HTO surface antibodies were quantified with the Cell Ranger count feature reference option. The feature reference file is provided on GitHub (https://github.ugent.be/PPOL/Sympatho-adrenergic-differentiation-track)
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated barcodes, features and matrix files


title: HiMyc_FVB_Anterior_1

value: 6 months