title: WT - TT E. coli, OD05, rep1

description: Library name: Sample 1


title: MG pQCXIP exp1

status: Public on Oct 15 2025

type: protein

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
Isaac_Witz__Sivan_Izraely_37
559
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.

hyb_protocol: Each slide was probed with one antibody. The detection system used was a GenPoint-based staining kit from Agilent.

scan_protocol: Array-Pro Analyzer

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curve from the “standard curve” (supercurve) of the slide (Ab). Supercurve is constructed by a script in R written by Bioinformatics (“Supercurve Fitting” developed by the Department of Bioinformatics and Computational Biology in MD Anderson Cancer Center, http://bioinformatics.mdanderson.org/Software/supercurve). The raw spot intensity data were adjusted to correct spatial bias before model fitting. The protein concentrations of each set of slides were then normalized by median polish, which was corrected across samples by the linear expression values using the median expression levels of all Ab experiments to calculate a loading correction factor for each sample. These values (given as log2 values) are defined as Supercurve Log2 (Raw) values. All the data points were normalized for protein loading and transformed to linear values.

label: DAB

molecule: protein

organism: Homo sapiens

source_name: Immortalized human microglia-SV40 cells (ABM, Milton, Canada)

label_protocol: Samples were probed with Ab by CSA amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: Cells were maintained in RPMI-1640 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS), 2 mmol/ml L-glutamine, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 12.5 units/ml nystatin. 0.5% FBS supplemented medium was used for starvation in all the experiments. Cells were cultured in an incubator with humidified air with 5% CO2 at 37°C.

extract_protocol: Cell lysate was extracted using RIPA buffer (Sigma-Aldrich).

treatment_protocol:
The JunBlo microglia cells were established by using a mixture of three different pGIPZ vectors containing shRNA sequences targeting JUNB mRNA (RHS4430-200225817, RHS4430-200229510 and RHS4430-200246702; Dharmacon, Lafayette, CO, USA). A sh-non-silencing pGIPZ vector (RHS4531, Dharmacon) was used as a negative control. The variants are referred as MG conlo, MG JunBlo. All microglia variants were selected using 6 μg/ml puromycin (AG Scientific Inc.) as selection antibiotics, except for GFP-labeled MG conhi and MG JunBhi, which were also selected using 800 μg/ml G-418 disulfate (AG Scientific Inc.)
0.5X10 microglia cells were seeded on collagen coated plates in Prigrow III supplemented with 10% FCS for 24hrs. Then the cells were washed twice with ice cold PBS and frozen at -80° until protein extraction.

tag: cell type

value: Microglia cell line

tag: treatment

value: Control


title: Healthy, S3, normal2

type: SRA

city: Singapore

first: Catherine Wei Min

last: Ong

state: Singapore

address: 14 Medical Drive, MD6, Centre for Translational Medicine, #15-02

country: Singapore

institute: National University of Singapore

description: microdissected RNA-Seq

library_source: transcriptomic

data_processing:
Alignment was performed using Kallisto (version 0.46), with sequence based bias correction.
Data was annotated using ensembldb package (version 2.24.0). The transcript abundance was summarized to gene level using Sleuth (version 0.30).
Raw counts from RNA sequencing were processed using edgeR, Bioconductor version 3.17, with 3 variance estimated and size factor normalised using Trimmed Mean of M-values (TMM).
Assembly: GRCm39, M. tb strain H37Rv transcriptome
Supplementary files format and content: CSV table with counts and TPM as estimated by Kallisto

molecule: polyA RNA

organism: Mus musculus

source_name: Normal brain tissue

growth_protocol: Not applicable

treatment_protocol: Not applicable

tag: tissue

value: Normal brain tissue


title: CNSTB, S1, inflammatory1

description: microdissected RNA-Seq

source_name: M.tb H37Rv-infected brain tissue

value: M.tb H37Rv-infected brain tissue


title: Fortified folic acid, wild type 3

city: Boulder

first: David

last: Engelhardt

state: CO

address: 347 UCB

department: MCDB

country: USA

institute: CU Boulder

description: Processed matrix column 12

data_processing:
Samples were processed simultaneously using the nf-core RNA-seq pipeline.
https://nf-co.re/rnaseq/3.14.0/
Assembly: mm10
Supplementary files format and content: tab separated values file includes tpm counts for all samples by column
Supplementary files format and content: tab separated values file includes raw counts for all samples by column

source_name: primary

growth_protocol: Mouse embryonic fibroblasts were cultured in DMEM containing either 225ng/mL folic acid (moderate) or 3600ng/mL folic acid (fortified)

extract_protocol:
RNA was isolated using a trizol/chloroform extraction
library was constructed using the TECAN Universal Plus mRNA-Seq kit.

treatment_protocol: F3 mice were maintained on either 2ppm folic acid (moderate) or 10 ppm folic acid (fortified)

tag: developmental stage

tag: cell line

value: primary

value: mouse embryonic fibroblasts

tag: genotype

value: wt

value: fortified folic acid


title: M_WT_1698RP

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV. De-multiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic (Bolger et al., 2014) was used for cleaning.
R package “QuasR” (Gaidatzis et al., 2015) was used for the read alignment to the mouse genome (mm10) followed by counting at the gene level.
Assembly: mm10
Supplementary files format and content: Excel file include raw counts

molecule: total RNA

source_name: spinal cord

extract_protocol:
RNAs were isolated using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: spinal cord

tag: Sex

value: male

value: microglia

value: Wildtype

value: EAE


title: M_cKO_1675RELP

value: Kdm6a cKO


title: H3K27me3_lhp1_rep1

city: Uppsala

first: Miyuki

last: Nakamura

address: Ulls Grand1

country: Sweden

institute: Swedish University of Agricultural Sciences

library_source: genomic

data_processing:
Following quality trimming, the first 80 nucleotides from the forward reads were aligned to the reference genome using Bowtie2 with the 'best' option.
Processed data files were prepared with the bamCoverage command in the deepTools(v3.3.2) with option '-bs 1 --normalizeUsing CPM  --ignoreDuplicates' to calculate normalized  coverage of reads.
Assembly: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 12 days seedlings

growth_protocol: Plants were grown on1/2 Murashige-Skoog medium plate for 12 days under long-day condition (8h/16h: dark/light) at 22±1 ˚C.

extract_protocol:
Frozen seedlings were ground into fine powder. Suspension in nuclei isolation buffer and then crosslinked with 1% formaldehyde. After fiitering through a 40 µm nylon cell strainer, isolated nuclei were centrifuged and resuspended in nuclear isolation buffer. The nuclear pellets were lysed using a buffer containing detergen and sonicated using a focused-ultrasonicator. Following immunoprecipitation processes, DNA was decrosslinked from the beads by incubating overnight at 65 °C in elution buffer. Genomic DNA were recovered and purified after Proteinase K and RNase treatment.
The  libraryies were made using the ThruPLEX DNA-seq Kit (Takara) with manufacturer's protocol

treatment_protocol: Whole plants were harversted 1 hour before dark.

value: 12 days seedlings

value: lhp1 mutant

value: anti-H3K27me3 antibody


title: H3K27me3_lhp1_rep2


title: CNSTB, S4, granuloma4

description: microdissected RNA-Seq


title: M_cKO_1675LW


title: F_WT_1720RC

value: female


title: Fortified folic acid, wild type 1

description: Processed matrix column 10


title: H3K27me3_dekQ_rep2

value: dek quadruple mutant


title: CNSTB, S4, granuloma3

description: microdissected RNA-Seq


title: Fortified folic acid, mutant 3

description: Processed matrix column 9


title: F_cKO_1675RC


title: H3K27me3_dekQ_rep1


title: CD

city: Guang zhou

first: chen

last: jian

address: No. 1838, North Guangzhou Avenue

country: China

institute: Southern Medical University，Nanfang Hospital

data_processing:
Quality control and mapping
Gene-level quantification, analysis of differentially expressed genes (DEGs), clusteranalysis, GO and KEGG enrichment Transcript-level quantification, analysis of differentially expressed transcript (DEGs),cluster analysis, GO and KEGG enrichment
Alternatively splicing analysis and SNP-INDEL calling
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited txt files include FPKM values for each sample

source_name: dermis

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion)
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,CA, USA) according to the manufacturer’ s instructions

value: dermis

value: the skin of old mice injected with liposomes


title: CNSTB, S4, granuloma2

description: microdissected RNA-Seq

value: M.tb H37Rv-infected brain tissue


title: Fortified folic acid, mutant 2

description: Processed matrix column 8

value: primary

value: mouse embryonic fibroblasts


title: H3K27me3_Wt_rep1

value: wild-type


title: D

value: deletion  macrophage in the old skin


title: CNSTB, S3, granuloma4

description: microdissected RNA-Seq


title: H3K27me3_Wt_rep2


title: CNSTB, S4, granuloma1

description: microdissected RNA-Seq


title: Fortified folic acid, mutant 1

description: Processed matrix column 7

value: fortified folic acid


title: Fortified folic acid, wild type 2

description: Processed matrix column 11

value: wt


title: Moderate folic acid, wild type 3

description: Processed matrix column 6

value: moderate folic acid


title: Moderate folic acid, wild type 2

description: Processed matrix column 5


title: H3_lhp1dekT_rep1

value: lhp1;dek2;3;4 quadruple mutant

value: anti-H3 antibody


title: CNSTB, S3, granuloma3

description: microdissected RNA-Seq


title: Moderate folic acid, wild type 1

description: Processed matrix column 4


title: H3_lhp1dekT_rep2

value: 12 days seedlings


title: CNSTB, S3, granuloma1

description: microdissected RNA-Seq


title: H3_lhp1_rep2

value: lhp1 mutant


title: Moderate folic acid, mutant 3

description: Processed matrix column 3


title: CNSTB, S3, granuloma2

description: microdissected RNA-Seq


title: H3_lhp1_rep1


title: CNSTB, S2, granuloma2

description: microdissected RNA-Seq


title: Moderate folic acid, mutant 2

description: Processed matrix column 2


title: H3_dekQ_rep2


title: CNSTB, S2, granuloma1

description: microdissected RNA-Seq


title: H3_dekQ_rep1


title: CNSTB, S1, granuloma1

description: microdissected RNA-Seq


title: Healthy, S4, normal2

description: microdissected RNA-Seq

value: Normal brain tissue


title: pl_2wpm_juvenile_J3_snRNAseq

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

description: Library name: J3_S3

library_source: transcriptomic single cell

data_processing:
P. lividus genome version 1.0 annotation gene models were extended in the 3’ direction by 5 kilobases (kb).
snRNA-seq reads were mapped to this genome and modified annotation using the Cell Ranger Software Suite v7.1.0 with --include-introns=true, --no-bam, --nosecondary and --force-cells=N flags, where N is number of cells to force for each sample.
Cell Ranger output matrices, features and barcodes were used for further analysis using the R package Seurat v 4.4.0.
Seurat objects were created by excluding from the analysis genes that are transcribed in less than three cells and cells that have less than a minimum range of 350-500 and a maximum of 5000 transcribed genes.
Generated datasets were normalized and variable genes were found using the variance stabilizing transfer (VST) method with a maximum of 2000 variable features.
The three different objects corresponding to the three independent libraries were integrated through identification of gene anchors (FindIntegrationAnchors) between the different datasets.
The integration of the datasets was followed by scaling and principal component analysis (PCA). Jackstraw was used to evaluate PCA significance. A Sharing Nearest Neighbor (SNN) graph was computed with 50 dimensions (resolution 1.0).
Uniform Manifold Approximate and Projection (UMAP) was used to perform clustering dimensionality reduction.
The FindAllMarkers command was used to identify differentially expressed marker genes.
Sub-clustering analysis of the PRCs was performed using the subset function available in Seurat, by using all the clusters corresponding to the nervous system and only the cells that express at least one of the seven opsin genes encoded by the P. lividus genome. The subsetted objects were further analyzed by means of calculation of variable genes, scaling, and PCA analysis. Jackstraw was used to determine the number PCAs to be used for clustering. 19 PCAs were selected and clustering dimensionality reduction was performed.
To compare the S. purpuratus 3dpf larva single cell atlas and the P. lividus juvenile single nucleus atlas, SAMap v1.02 was used.
Assembly: GCA_940671915.1
Supplementary files format and content: R object file, analysed integrated Seurat object
Supplementary files format and content: R object file, analysed subsetted Seurat object for photoreceptors (PRCs)

molecule: nuclear RNA

organism: Paracentrotus lividus

source_name: dissociated juvenile

growth_protocol: For snRNA-seq adult P. lividus individuals were collected from the Bay of Villefranche-sur-Mer (France) and were housed at Institut de la Mer de Villefranche (IMEV), in circulating seawater aquaria. Gametes were collected from dissected gonads. For fertilization, sperm was diluted 1:1000 and added to a beaker containing unfertilized oocytes in approximately 100 mL of natural filtered sea water (FSW). Embryos and larvae were reared at a concentration of, respectively, 70 embryos and 1 larva per mL at 18°C under constant mechanical stirring and fed five times per week with a mixture of Dunaliella salina and Rhodomonas salina. Three times per week, two-third of the culture sea water was exchanged with fresh FSW.

extract_protocol:
Juveniles were placed in the lid of a 5 mL Protein LoBind tube (Eppendorf, #0030108302) containing 560 μL of pre-chilled Homogenization Buffer. Homogenization Buffer is a hypotonic buffer composed of 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM tris buffer (pH 8.0), 1 mM dithiothreitol, 1× protease inhibitor (Sigma-Aldrich, #11873580001), 0.4 U/μL ribonuclease inhibitor (Invitrogen, #AM2682), 0.2 U/μL SUPERase-In ribonuclease inhibitor (Invitrogen, #AM2694), 1 mM spermine, and 0.3% Triton X-100. For each library, the  six juveniles were cut in half using a microsurgical knife (Electron Microscopy Sciences, #72047-30), while the tissues from three of them were further gently scraped using a microsurgical blade and fine forceps (Fine Science Tools, #10316-14 and #11251-20, respectively) under a dissecting microscope. Juvenile large fragments were transferred, using a P1000 micropipette, into a clean 1.5 mL Protein LoBind tube. The rest of the supernatant, was filtered through a 40 μm cell strainer (PluriSelect Mini strainer), to remove debris. Nuclei were extracted through application of mechanical force via pipette aspiration for 10 times using a P1000 micropipette and 15 times using a P200 micropipette. Samples were left until the large juvenile fragments settled and the supernatant containing the isolated nuclei was transferred into a new clean 1.5 mL Protein LoBind tube. Isolated nuclei were spun down for 10 min at 500 g and 4°C using a 5424 R Eppendorf microcentrifuge. The presence of pellets was visually confirmed (brown colored pellets). All the supernatant was discarded except from 50 μL (surrounding the pellet). 600 μL of Wash Buffer [1x Dulbecco’s phosphate-buffered saline (DPBS), 2% BSA, 0.2 U/μL SUPERase-In ribonuclease inhibitor, 1 mM spermine and 5 mM MgCl2] was carefully added  using a P200 micropipette, in order not to disrupt the pellet. Next, the nuclei pellets were resuspended through pipette aspiration for 5 times, ensuring that the resuspended nuclei stay close to the bottom of the tube. Isolated nuclei were once more spun down for 10 min at 500 g and 4°C using a 5424 R Eppendorf microcentrifuge. Most of the supernatant was discarded apart from 25 μL (covering the pellet). Lastly, 25 μL of Resuspension Buffer [3x DPBS, 2% BSA, 0.4 U/μL ribonuclease inhibitor, 0.2 U/μL SUPERase-In ribonuclease inhibitor and 1 mM spermine] were added to the pellet. Pellet was resuspended through gentle pipette aspiration for 20-30 times using a P200 micropipette. Nuclei suspensions were filtered through a 10 μm cell strainer (PluriSelect Mini strainer) to avoid aggregates. The nuclei quality and numbers were estimated by Trypan blue and hemocytometer, respectively.
Isolate nuclei (25,000 per library) were loaded on the 10x Genomics Chromium Controller according to the manufacturer's instructions. cDNA libraries were prepared using the Chromium Single Cell 3’ Reagent Kit (v3.1 Chemistry Dual Index). Libraries were sequenced by the IGFL sequencing platform (Plateforme de Séquençage de l'IGFL) using the Illumina NextSeq 500.

treatment_protocol: Upon induced metamorphosis using Dibromomethane, the juveniles were transferred to new containers and kept at 16°C under constant sea water flow. Once the mouth was formed the juveniles were fed with Tetraselmis suecica algae until they reached the 2 wpm stage.

value: dissociated juvenile

value: all 2 wpm juvenile cells

value: 2 wpm juvenile cells

value: wild type

value: 2 wpm juvenile


title: pl_2wpm_juvenile_J2_snRNAseq

description: Library name: J2_S2


title: H3_Wt_rep1


title: P20-23_PDO_Matrigel

status: Public on Oct 14 2025

city: Basel

first: Romuald

last: Parmentier

address: Schönbeinstrasse 40

department: Department of Biomedicine

country: Switzerland

institute: University Hospital Basel

description:
Library name: SR12_sample6
Chromium Flex single cell gene expression library of patient P20-23 organoids grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

data_processing:
Chromium Flex gene expression: Genome alignment, UMI counting, and sample demultiplexing were performed with Cell Ranger multi (v7.2.0) using default parameters and hg38/Ensembl 98 reference. Downstream processing was carried out in R (v4.2.2) with Bioconductor (v3.16). Cell QC was performed with scuttle (v1.8.4) by filtering low-quality cells (<2000 reads, <1000 genes, >10% mitochondrial, or scDblFinder doublets v1.12.0). Normalization was applied per sample using scran (v1.26.2) with quickCluster/computeSumFactors and logNormCounts.
Chromium Next GEM Single Cell 3’ (v3.1): Reads were aligned to hg38 using STARsolo (v2.7.10a) with a custom GTF file (Ensembl 104, with protein_coding, lncRNA, B/TCR transcripts only). Downstream processing was performed in R (v4.2.2) with Bioconductor (v3.16). Empty droplets were removed with DropletUtils (v1.18.1, niters = 5000). Cells with <10,000 reads, <1,000 genes, >25% mitochondrial content, or identified as doublets by scDblFinder were excluded. Normalization was applied per sample using scran (v1.26.2) with quickCluster/computeSumFactors and logNormCounts.
Assembly: hg38
Supplementary files format and content: Cell ranger output: SRXX_sampleXX_barcodes.tsv,  SRXX_sampleXX_features.tsv,  SRXX_sampleXX_matrix.mtx (see README.txt file)
Supplementary files format and content: Integrated samples: integration_barcodes.tsv,  integration_features.tsv,  integration_matrix.mtx, integration_metadata.csv (see README.txt file)

source_name: Transurethral resection

growth_protocol: For Matrigel-based culture, patient samples were processed and embedded in Matrigel following previously-published protocols 7. For Matrigel-free culture, patient samples were processed the same way and cells were seeded at 20,000 cells/cm2 in ultra-low adherence plates (Corning Costar). The organoid medium was identical to the previously published composition (PMID: 33934365), and was changed every 3 days, supplemented with either 1 nM DHT or 0.1 nM DHT for hormone-sensitive PCa (HSPC) or castration-resistant PCa (CRPC) samples, respectively. Organoid cultures were passaged after 7-14 days of culture, depending on doubling time.

extract_protocol:
Following organoid or tissue digestion into single-cell suspensions (see Methods: Tissue processing for organoid culture & Organoid passaging), cell count and viability was assessed using Trypan Blue staining with automated cell counting. For samples with viability below 60%, an Annexin-V-based magnetic sorting assay (Miltenyi Biotech, 130-090-101) was used to enrich for live cells. After this step, samples with viability below 80% or with fewer than 50,000 viable cells were considered not suitable for scRNA-seq experiments. As 10X genomics protocols for scRNA-seq require clumps to be absent from the loaded cell suspension, a filtering step using a pre-separation filter of 30µm (Milenyi Biotec, Cat: 130-101-812) was used, whenever needed. For this purpose, cells were first transferred to a 15mL tube, resuspended in a total volume of 5mL of adDMEM/F-12 and passed through the filter. Finally, cells were spun down at 350 G for 5 min, the supernatant was discarded and cells were resuspended in 1mL of the same media and counted again with Trypan Blue before being loaded in the appropriated chip at the appropriated concentration.
Chromium Flex gene expression libraries: Sequencing libraries were prepared according to the Chromium Fixed RNA Profiling Multiplexed Samples User Guide (10x Genomics, Revision D). Briefly, samples meeting viability and cell number criteria were fixed at 4°C for 20 hours and stored at -80°C, following the manufacturer’s guidelines (Fixation of cells & nuclei for Chromium Fixed RNA Profiling). Batches of four samples were multiplexed using the Human Transcriptome 4 probe set. Following probe hybridization and washing, fixed cells were counted using Trypan Blue for each sample within a batch and then pooled in equal numbers to achieve a concentration of 1,750–2,500 cells/µL. Each batch of four samples was loaded into a Chromium Microfluidic Chip Q to target a recovery of 40,000 cells (10,000 cells per sample). Immediately after Gel Beads-in-Emulsion (GEM) generation, ligation and extension of captured mRNA were performed to incorporate Unique Molecular Identifiers (UMIs), 10x GEM Barcodes, and partial Read 1T sequences. Pre-amplification of ligated products was performed after breaking the GEMs and SPRIselect beads (Beckman Coulter, B23317) were used to select for pre-amplified products. Finally, libraries were constructed by adding Illumina P5/P7 adapters and i5/i7 sample indexes, along with the Illumina TruSeq Read 1 (Read 1T) and Small Read 2 (Read 2S) sequences, via Sample Index PCR (8 cycles).
Chromium Next GEM Single Cell 3’ (v3.1): Single-cell gene expression libraries were prepared according to the Chromium Next GEM Single Cell 3’ v3.1 Dual Index User Guide (10x Genomics, Revision B). Briefly, samples meeting viability and cell number criteria were resuspended at a concentration of 700–1,200 cells/µL and then loaded into the Chromium Next GEM Chip G to reach a recovery of 10,000 cells per sample. Immediately following GEM generation, reverse transcription of captured mRNA was performed to incorporate barcoded primers, including Unique Molecular Identifiers (UMIs) and 10x GEM Barcodes to the captured mRNA. Following Post-GEM-RT cleanup, PCR amplification of the first-strand cDNA was performed by PCR (11 cycles), followed by SPRIselect bead-based size selection (Beckman Coulter, B23317) to enrich for cDNA fragments of the desired size. Enzymatic fragmentation, end repair, A-tailing and ligation steps were performed immediately after. Finally, libraries were constructed by adding Illumina P5/P7 adapters and i5/i7 sample indexes via Sample Index PCR (9-10 cycles).

value: Transurethral resection

value: Epithelial cells from patient-derived prostate cancer organoids

tag: culture conditions

value: Matrigel

tag: batch


title: P24-14_Parental_Tumor

description:
Library name: SR12_sample7
Chromium Flex single cell gene expression library of patient P24-14 parental tumor tissue
Dolgos_Matched_Tissue_PDOs_barcodes.tsv
Dolgos_Matched_Tissue_PDOs_features.tsv
Dolgos_Matched_Tissue_PDOs_matrix.mtx
Dolgos_Matched_Tissue_PDOs_metadata.csv

value: Epithelial and stromal cells isolated from human prostate cancer tissue

value: Non applicable


title: pl_2wpm_juvenile_J1_snRNAseq

description: Library name: J1_S1


title: P20-23_PDO_Matrigel_free

description:
Library name: SR12_sample5
Chromium Flex single cell gene expression library of patient P20-23 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

value: Matrigel-free


title: P24-14_PDO_Matrigel_free

description:
Library name: SR12_sample8
Chromium Flex single cell gene expression library of patient P24-14 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv
Dolgos_Matched_Tissue_PDOs_barcodes.tsv
Dolgos_Matched_Tissue_PDOs_features.tsv
Dolgos_Matched_Tissue_PDOs_matrix.mtx
Dolgos_Matched_Tissue_PDOs_metadata.csv


title: P24-12_PDO_Matrigel

description:
Library name: SR12_sample4
Chromium Flex single cell gene expression library of patient P24-12 organoids grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

source_name: Radical prostatectomy

value: Radical prostatectomy


title: P24-06_Parental_Tumor

description:
Library name: SR12_sample1
Chromium Flex single cell gene expression library of patient P24-06 parental tumor tissue
Dolgos_Matched_Tissue_PDOs_barcodes.tsv
Dolgos_Matched_Tissue_PDOs_features.tsv
Dolgos_Matched_Tissue_PDOs_matrix.mtx
Dolgos_Matched_Tissue_PDOs_metadata.csv


title: P24-06_PDO_Matrigel_free

description:
Library name: SR12_sample2
Chromium Flex single cell gene expression library of patient P24-06 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv
Dolgos_Matched_Tissue_PDOs_barcodes.tsv
Dolgos_Matched_Tissue_PDOs_features.tsv
Dolgos_Matched_Tissue_PDOs_matrix.mtx
Dolgos_Matched_Tissue_PDOs_metadata.csv


title: P20-11_PDOXO_Matrigel

description:
Library name: SR11_sample4
Chromium Flex single cell gene expression library of patient P20-11 PDOXOs grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

source_name: Lung metastasis resection

value: Lung metastasis resection


title: P24-06_PDO_Matrigel

description:
Library name: SR12_sample3
Chromium Flex single cell gene expression library of patient P24-06 organoids grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv
Dolgos_Matched_Tissue_PDOs_barcodes.tsv
Dolgos_Matched_Tissue_PDOs_features.tsv
Dolgos_Matched_Tissue_PDOs_matrix.mtx
Dolgos_Matched_Tissue_PDOs_metadata.csv


title: Moderate folic acid, mutant 1

description: Processed matrix column 1

value: primary

value: mouse embryonic fibroblasts

value: moderate folic acid


title: P23-53_PDO_Matrigel_free

description:
Library name: SR11_sample2
Chromium Flex single cell gene expression library of patient P23-53 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

source_name: Prostate biopsy

value: Prostate biopsy


title: P22-36_PDO_Matrigel

description:
Library name: SR06_sample1
Chromium Next GEM single cell gene expression library of patient P22-36 organoids grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv


title: MSK_PCa2_PDO_Matrigel

description:
Library name: SR10_sample4
Chromium Flex single cell gene expression library of patient MSK_PCa2 organoids grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

source_name: Bone metastasis resection

value: Bone metastasis resection


title: Healthy breast tissue control, replicate 2

city: Beijing

first: Junyue

last: Wang

address: No. 23, Art Museum Back Street, Dongcheng District.

department: Department of Breast

institute: Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University

description:
Library name: Sample 5
10X Chromium

data_processing:
Cell Ranger v3 (3.1.0) was used to demultiplex cellular barcodes.Raw scRNA-seq data were integrated and filtered using the Seurat R package (v3.0.0). The NormalizeData function was employed to normalize the sequencing data, and 2000 highly variable genes were selected for scaling and principal component analysis (PCA). The Harmony R package (v0.1.0) was utilized to correct for batch effects. The appropriate dimensions of Harmony embeddings were then used for downstream uniform manifold approximation and projection (UMAP) visualization and clustering.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Breast tissue

extract_protocol:
Fresh tissue samples were surgically obtained.
Tissue samples from the 3 GLM patients and 3 healthy controls were  profiled using the 10X Genomics Chromium Single Cell 3′V3. Barcoded cDNA libraries were prepared using the Single Cell 3′mRNA kit.

value: Breast tissue

tag: disease

value: Healthy


title: P23-51_PDO_Matrigel_free

description:
Library name: SR11_sample1
Chromium Flex single cell gene expression library of patient P23-51 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv


title: Healthy, S4, normal1

description: microdissected RNA-Seq

value: Normal brain tissue


title: P23-36_PDO_Matrigel_free

description:
Library name: SR10_sample1
Chromium Flex single cell gene expression library of patient P23-36 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv


title: MSK_PCa2_PDO_Matrigel_free

description:
Library name: SR10_sample3
Chromium Flex single cell gene expression library of patient MSK_PCa2 organoids grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv


title: H3_Wt_rep2

value: 12 days seedlings

value: wild-type

value: anti-H3 antibody


title: P23-36_PDO_Matrigel

description:
Library name: SR10_sample2
Chromium Flex single cell gene expression library of patient P23-36 organoids grown in Matrigel
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

value: Epithelial cells from patient-derived prostate cancer organoids

value: Matrigel


title: Granulomatous lobular mastitis, replicate 3

description:
Library name: Sample 3
10X Chromium

value: Granulomatous lobular mastitis


title: Granulomatous lobular mastitis, replicate 1

description:
Library name: Sample 1
10X Chromium


title: Healthy breast tissue control, replicate 3

description:
Library name: Sample 6
10X Chromium


title: P20-11_PDOXO_Matrigel_free

description:
Library name: SR11_sample3
Chromium Flex single cell gene expression library of patient P20-11 PDOXOs grown in Matrigel-free conditions
Dolgos_Early_Passage_PDOs_barcodes.tsv
Dolgos_Early_Passage_PDOs_features.tsv
Dolgos_Early_Passage_PDOs_matrix.mtx
Dolgos_Early_Passage_PDOs_metadata.csv
Atlas_PCa_PDOs_barcodes.tsv
Atlas_PCa_PDOs_features.tsv
Atlas_PCa_PDOs_matrix.mtx
Atlas_PCa_PDOs_metadata.csv
scRNAseq_metadata.csv

value: Matrigel-free


title: Healthy breast tissue control, replicate 1

description:
Library name: Sample 4
10X Chromium


title: SK-UT-1 treated with Hoechst for 6h, rep 3

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

institute: University of Udine

description: Library name: 20-S6H

data_processing:
Raw reads were clipped from their adapter sequences using the Trimmomatic software (v0.39). Reads with an average Phred quality lower than 28 and length < 36 bp were discarded
Transcripts were quantified from raw reads with STAR (v2.7.3a) on the human transcriptome GRCh38 (Ensembl 107). Quantifications were summarized to gene level with StringTie (v2.1.5).
Differential expression analysis was performed with DESeq2 package (v1.46.0)). Genes were considered differentially expressed if FDR <0.05 and abs(log2(FoldChange)) >1.
Assembly: GRCh38 (Ensembl 107)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample and quantified gene
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

growth_protocol: Cells were maintained in culture at 37°C with an atmosphere of 5 % CO2 in Dulbecco modified Eagle medium (DMEM) supplemented with 10% of fetal bovine serum (FBS) (Sigma-Aldrich), L-glutamine (2mM, Euroclone), penicillin (100 U/ml), streptomycin (10 mg/ml) solution (Euroclone), and amphotericin B (250 μg/mL, Thermo Fisher Scientific).

extract_protocol:
RNA was extracted with the Quick-RNA MagBead kit (Zymo Research) following the manufacturer’s instructions.
cDNA libraries were prepared from poly(A) selected RNA following Illumina specifications

treatment_protocol: HUtSMC and SK-UT-1 cells were seeded at a concentration of 1 x 10*5 cells/mL and treated the next day with 10 µM XMH95 or 10 µM Hoechst 33258, for 6 or 18 hours.

value: leiomyosarcomas cell lines

value: aneuploid

value: Hoechst

tag: time

value: 6 h

tag: replicate

value: round 3


title: SK-UT-1 treated with Hoechst for 6h, rep 2

description: Library name: 16-S6H

value: round 2


title: SK-UT-1 treated with XMH95 for 18h, rep 1

description: Library name: 13-S18X

value: round 1


title: SK-UT-1 treated with XMH95 for 18h, rep 2

description: Library name: 17-S18X


title: Granulomatous lobular mastitis, replicate 2

description:
Library name: Sample 2
10X Chromium

value: Breast tissue


title: SK-UT-1 UNTREATED, rep 3

description: Library name: 18-SC

value: UNTREATED

value: 0 h


title: SK-UT-1 treated with XMH95 for 6h, rep 3

description: Library name: 19-S6X


title: SK-UT-1 treated with Hoechst for 6h, rep 1

description: Library name: 12-S6H


title: SK-UT-1 treated with XMH95 for 6h, rep 2

description: Library name: 15-S6X


title: SK-UT-1 UNTREATED, rep 1

description: Library name: 10-SC


title: hutsmc treated with XMH95 for 18h, rep 3

description: Library name: 9-U18X

source_name: HUtSMC

value: HUtSMC

value: human uterine smooth muscle cells

value: diploid


title: SK-UT-1 UNTREATED, rep 2

description: Library name: 14-SC


title: hutsmc UNTREATED, rep 3

description: Library name: 7-UC


title: hutsmc treated with XMH95 for 18h, rep 2

description: Library name: 6-U18X


title: hutsmc UNTREATED, rep 1

description: Library name: 1-UC


title: hutsmc treated with XMH95 for 6h, rep 1

description: Library name: 2-U6X


title: hutsmc UNTREATED, rep 2

description: Library name: 4-UC


title: SK-UT-1 treated with XMH95 for 18h, rep 3

description: Library name: 21-S18X


title: hutsmc treated with XMH95 for 18h, rep 1

description: Library name: 3-U18X


title: eAML7PB TCR

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: Pool129-1_17
5' scRNA-seq 10x Genomics

library_source: other

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list, feature list in csv file format and QC file in html format for gene expression (GEX)
Supplementary files format and content: High-level descriptions of each clonotype, high-level and detailed annotations of each clonotype consensus sequence, high-level annotations of each high-confidence contigs from cell-associated barcodes, and high-level and detailed annotations of all contigs (from cell and background barcodes) in csv file format for T cell receptor sequencing (TCR)
Library strategy: TCR-Seq

molecule: other

source_name: peripheral blood

extract_protocol:
Digestion of tissue and cryopreservation in FCS with 10% DMSO until analysis. Thawing in PBS supplemented with 10% FCS and 10% bovine DNase I, grade II. Resuspension in PBS with 0.04% ultra-pure BSA.
Standard 5' 10x Genomics single cell RNA sequencing protocol according to manufacturer's instructions. TCR-seq using V(D)J amplification kit.

value: peripheral blood


title: eAML7.2 TCR

description:
Library name: Pool129-1_16
5' scRNA-seq 10x Genomics

source_name: tissue

value: tissue


title: eAML7PB GEX

description:
Library name: Pool129-1_2
5' scRNA-seq 10x Genomics

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list, feature list in csv file format and QC file in html format for gene expression (GEX)
Supplementary files format and content: High-level descriptions of each clonotype, high-level and detailed annotations of each clonotype consensus sequence, high-level annotations of each high-confidence contigs from cell-associated barcodes, and high-level and detailed annotations of all contigs (from cell and background barcodes) in csv file format for T cell receptor sequencing (TCR)


title: eAML4.2 TCR

description:
Library name: Pool124_69
5' scRNA-seq 10x Genomics


title: eAML4PB.3 GEX

description:
Library name: Pool124_33
5' scRNA-seq 10x Genomics


title: eAML4.2 GEX

description:
Library name: Pool124_34
5' scRNA-seq 10x Genomics


title: SK-UT-1 treated with XMH95 for 6h, rep 1

description: Library name: 11-S6X


title: eAML7.1 GEX

description:
Library name: Pool123_1
5' scRNA-seq 10x Genomics


title: eAML7.1 TCR

description:
Library name: Pool123_31
5' scRNA-seq 10x Genomics


title: eAML1.6 TCR

description:
Library name: Pool121_55
5' scRNA-seq 10x Genomics


title: eAML1.4 TCR

description:
Library name: Pool121_53
5' scRNA-seq 10x Genomics


title: eAML1.2 TCR

description:
Library name: Pool121_51
5' scRNA-seq 10x Genomics


title: hutsmc treated with XMH95 for 6h, rep 3

description: Library name: 8-U6X


title: eAML1.3 TCR

description:
Library name: Pool121_52
5' scRNA-seq 10x Genomics


title: eAML1.5 TCR

description:
Library name: Pool121_54
5' scRNA-seq 10x Genomics


title: eAML5.2 TCR

description:
Library name: Pool121_49
5' scRNA-seq 10x Genomics


title: eAML6 TCR

description:
Library name: Pool121_50
5' scRNA-seq 10x Genomics


title: hutsmc treated with XMH95 for 6h, rep 2

description: Library name: 5-U6X


title: eAML5.1 TCR

description:
Library name: Pool121_48
5' scRNA-seq 10x Genomics


title: eAML4PB.2 TCR

description:
Library name: Pool121_47
5' scRNA-seq 10x Genomics


title: eAML3.2 TCR

description:
Library name: Pool121_46
5' scRNA-seq 10x Genomics


title: eAML1.6 GEX

description:
Library name: Pool121_25
5' scRNA-seq 10x Genomics


title: eAML1.4 GEX

description:
Library name: Pool121_23
5' scRNA-seq 10x Genomics


title: eAML6 GEX

description:
Library name: Pool121_20
5' scRNA-seq 10x Genomics


title: eAML1.2 GEX

description:
Library name: Pool121_21
5' scRNA-seq 10x Genomics


title: eAML3PB TCR

description:
Library name: Pool121_44
5' scRNA-seq 10x Genomics


title: eAML1.3 GEX

description:
Library name: Pool121_22
5' scRNA-seq 10x Genomics


title: eAML7.2 GEX

description:
Library name: Pool129-1_1
5' scRNA-seq 10x Genomics


title: eAML1.5 GEX

description:
Library name: Pool121_24
5' scRNA-seq 10x Genomics


title: eAML4PB.3 TCR

description:
Library name: Pool124_68
5' scRNA-seq 10x Genomics


title: eAML5.2 GEX

description:
Library name: Pool121_19
5' scRNA-seq 10x Genomics


title: eAML5.1 GEX

description:
Library name: Pool121_18
5' scRNA-seq 10x Genomics


title: eAML4PB.2 GEX

description:
Library name: Pool121_17
5' scRNA-seq 10x Genomics


title: eAML3.2 GEX

description:
Library name: Pool121_16
5' scRNA-seq 10x Genomics


title: eAML2PB GEX

description:
Library name: Pool121_15
5' scRNA-seq 10x Genomics


title: eAML3PB GEX

description:
Library name: Pool121_14
5' scRNA-seq 10x Genomics


title: eAML4PB.1 TCR

description:
Library name: Pool119-61
5' scRNA-seq 10x Genomics


title: eAML3.1 TCR

description:
Library name: Pool117-14
5' scRNA-seq 10x Genomics


title: eAML4PB.1 GEX

description:
Library name: Pool119-15
5' scRNA-seq 10x Genomics


title: eAML2 TCR

description:
Library name: Pool117-13
5' scRNA-seq 10x Genomics


title: eAML4.1 GEX

description:
Library name: Pool119-2
5' scRNA-seq 10x Genomics


title: eAML2 GEX

description:
Library name: Pool117-4
5' scRNA-seq 10x Genomics


title: eAML3.1 GEX

description:
Library name: Pool117-5
5' scRNA-seq 10x Genomics


title: snRNA-seq of child (1-4 yo) human macular region of retina donor_MMD_23_22486

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

data_processing:
The fastq files from the snRNA-seq 3' were processed into a raw count matrix using Cell Ranger count v7.0.1. The fastq files from the snATAC-seq were processed into a raw count matrix using Cell Ranger atac v2.1.0. The fastq files from the multiome GEX and ATAC libraries from each sample were processed into a single raw count matrix with both gene expression and ATAC peak counts using Cell Ranger arc v2.0.2. raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol,genomic coordinates; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI,fragment ends
Supplementary files format and content: fragments_file_format:tsv, fragments_file_content:per unique fragment information, fragments_file_tbi_content:fragment index

source_name: macula lutea

extract_protocol:
Samples included in this study were retinal tissues of 59 postmortem donors from the Utah Lions Eye Bank and other sources. All donors were screened for medical history, and only the ones with no of retinal diseases were used in this study. Post-mortem phenotyping with OCT were performed to confirm that there were no drusen, atrophy, or any other disease phenotypes on retina. One eye was collected from each donor. All eye tissues were collected and dissected within 6 hours post-mortem. With 4mm and 6mm disposable biopsy punches, macula and peripheral retina were collected and flash frozen in liquid nitrogen, and stored at -80°C before nuclei isolation. Nuclei for snRNA-seq were isolated by fresh-made pre-chilled RNase-free lysis buffer. The frozen tissue was resuspended and triturated in lysis buffer and homogenized with a WheatonTM Dounce Tissue Grinder.
Single cell Gene Expression Library was prepared according to Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics). Single cell ATAC Library was prepared according to Chromium Next GEM Single cell ATAC Reagent kit v1.1 (10x Genomics). The multiome GEX and ATAC libraries were prepared with Chromium Next GEM Single Cell Multiome GEM kit (10x Genomics) following the manufacturer’s protocols.

value: macula lutea

tag: assay

value: male

tag: ethnicity

value: European

tag: age

value: 3 years

value: FALSE

tag: donor id

tag: raw matrix_feature_keys

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: eAML1.1 GEX

description:
Library name: Pool117-3
5' scRNA-seq 10x Genomics

tag: tissue


title: snRNA-seq of adult human macular region of retina donor_MMD_23_21999

value: African American

value: 17 years


title: eAML2PB TCR

description:
Library name: Pool121_45
5' scRNA-seq 10x Genomics


title: snRNA-seq of adult human macular region of retina donor_MMD_23_20181

value: 16 years


title: snRNA-seq of juvenile (5-14 yo) human macular region of retina donor_MMD_23_17738

value: female

value: 10 years


title: snRNA-seq of adult human macular region of retina donor_MMD_23_16055

value: 18 years


title: snRNA-seq of adult human macular region of retina donor_MMD_23_02177

value: Hispanic or Latin American

value: 27 years


title: snRNA-seq of adult human macular region of retina donor_MMD_22_38453

value: macula lutea

value: 43 years


title: snRNA-seq of adult human macular region of retina donor_MMD_23_01524


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_38453

value: male

tag: suspension enrichment_factors

value: NeuN


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_38029

tag: Sex

value: 82 years

value: FALSE


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_38453

source_name: peripheral region of retina

value: peripheral region of retina

value: gene symbol

value: GENCODE 32


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_38029

value: UMI

value: snRNA-seq


title: eAML4.1 TCR

description:
Library name: Pool119-60
5' scRNA-seq 10x Genomics

value: tissue


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_37117

value: South Asian

value: 77 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_37089 1

value: female

value: 68 years


title: eAML1.1 TCR

description:
Library name: Pool117-12
5' scRNA-seq 10x Genomics


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_37089 2

value: Hispanic or Latin American


title: snRNA-seq of adult human macular region of retina donor_MMD_22_37089

value: macula lutea


title: snRNA-seq of adult human macular region of retina donor_MMD_22_34032

value: European

value: 34 years


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_37089


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_33472 1

value: African American

value: 71 years

value: NeuN


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_33472 3

value: FALSE


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_33472

value: peripheral region of retina

value: gene symbol


title: snRNA-seq of adult human macular region of retina donor_MMD_23_21623

value: male

value: 15 years

value: GENCODE 32

value: UMI


title: snRNA-seq of adult human macular region of retina donor_MMD_22_33472

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_33472 2

value: female


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_32888 1

value: 52 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_32888 2


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_25357

value: 77 years


title: snRNA-seq of adult human macular region of retina donor_MMD_22_25357

value: macula lutea


title: snRNA-seq of adult human macular region of retina donor_MMD_22_38029

value: Hispanic or Latin American

value: 82 years


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_25357

value: African American


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_21878

value: 72 years


title: snRNA-seq of adult human macular region of retina donor_MMD_22_21878


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20372 2

value: 65 years

value: NeuN


title: snRNA-seq of adult human macular region of retina donor_MMD_22_37117

value: South Asian

value: FALSE


title: snRNA-seq of adult human macular region of retina donor_MMD_22_20372

value: gene symbol


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_20372

value: peripheral region of retina


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20357 s2_3

value: 64 years

value: GENCODE 32


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_32888

value: male

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20357 s2_2

value: female


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20357 s2_1

value: macula lutea


title: snRNA-seq of adult human macular region of retina donor_MMD_22_32888

value: 52 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_37117

value: 77 years


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_21878

value: African American


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_20357


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_18633

value: 67 years


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_20137

value: Hispanic or Latin American

value: >89 years


title: snATACseq of adult human macular region of retina donor_MMD_22_20137

library_source: genomic single cell

value: 10x scATAC-seq

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20137 1

value: FALSE

value: NeuN

value: gene symbol


title: snRNA-seq of adult human macular region of retina donor_MMD_22_18633

value: male

value: South Asian

value: GENCODE 32

value: UMI


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_18633

value: peripheral region of retina

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina donor_MMD_22_20357

value: macula lutea

value: female

value: African American

value: 64 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_17939

value: 71 years


title: snRNA-seq of adult human macular region of retina donor_MMD_22_17464

value: 81 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_17464


title: snATACseq of adult human macular region of retina donor_MMD_22_17939

value: 10x scATAC-seq

value: genomic coordinates

value: fragment ends


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20372 1

value: 65 years

value: FALSE

value: NeuN


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_17464

value: gene symbol


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_17939

value: GENCODE 32


title: snRNA-seq of adult human macular region of retina donor_MMD_22_20137

value: male

value: Hispanic or Latin American

value: >89 years

value: UMI


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_17017

value: macula lutea

value: female

value: South Asian

value: 86 years

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina donor_MMD_22_17017


title: snATACseq of adult human macular region of retina donor_MMD_22_17464 s1

value: 10x scATAC-seq

value: African American

value: 81 years

value: snATAC-seq


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_17017

value: peripheral region of retina

value: FALSE


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_20137 2

value: NeuN

value: gene symbol


title: snATACseq of adult human macular region of retina donor_MMD_22_17017 s2

value: genomic coordinates

value: fragment ends


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_16860

value: 60 years

value: GENCODE 32


title: snATACseq of adult human macular region of retina donor_MMD_22_17017 s3

value: macula lutea


title: snATACseq of adult human macular region of retina donor_MMD_22_16608 s1

value: male

value: Hispanic or Latin American


title: snRNA-seq of adult human macular region of retina donor_MMD_22_16860

value: female

value: UMI


title: snRNA-seq of adult human macular region of retina donor_MMD_22_16477

value: 85 years

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_16608

value: 81 years


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_16860

value: African American


title: Multiome-GEX of adult human macular region of retina donor_MMD_22_16477

data_processing:
The fastq files from the snRNA-seq 3' were processed into a raw count matrix using Cell Ranger count v7.0.1. The fastq files from the snATAC-seq were processed into a raw count matrix using Cell Ranger atac v2.1.0. The fastq files from the multiome GEX and ATAC libraries from each sample were processed into a single raw count matrix with both gene expression and ATAC peak counts using Cell Ranger arc v2.0.2. raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol,genomic coordinates; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI,fragment ends
Supplementary files format and content: fragments_file_format:tsv, fragments_file_content:per unique fragment information, fragments_file_tbi_content:fragment index
Library strategy: Multiome-GEX

value: 10x multiome

value: gene symbol,genomic coordinates

value: UMI,fragment ends

value: snRNA-seq,snATAC-seq


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_16477

value: FALSE

value: NeuN

value: gene symbol


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_16608

value: peripheral region of retina

value: GENCODE 32


title: snRNA-seq of adult human macular region of retina donor_MMD_22_16608

value: macula lutea

value: male


title: snATACseq of adult human macular region of retina donor_MMD_22_16477 s2

value: 10x scATAC-seq

value: female

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_14307

value: African American

value: 63 years

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina donor_MMD_22_17939

value: 71 years


title: snATACseq of adult human macular region of retina donor_MMD_22_16608 s2

value: Hispanic or Latin American

value: 81 years

value: FALSE


title: Multiome-ATAC of adult human macular region of retina donor_MMD_22_16477

data_processing:
The fastq files from the snRNA-seq 3' were processed into a raw count matrix using Cell Ranger count v7.0.1. The fastq files from the snATAC-seq were processed into a raw count matrix using Cell Ranger atac v2.1.0. The fastq files from the multiome GEX and ATAC libraries from each sample were processed into a single raw count matrix with both gene expression and ATAC peak counts using Cell Ranger arc v2.0.2. raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol,genomic coordinates; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI,fragment ends
Supplementary files format and content: fragments_file_format:tsv, fragments_file_content:per unique fragment information, fragments_file_tbi_content:fragment index
Library strategy: Multiome-ATAC

value: 10x multiome

value: 85 years

value: gene symbol,genomic coordinates

value: UMI,fragment ends

value: snRNA-seq,snATAC-seq


title: snATACseq of adult human macular region of retina donor_MMD_22_17464 s2

value: macula lutea

value: 10x scATAC-seq

value: female


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_16477

value: peripheral region of retina

value: gene symbol

value: GENCODE 32


title: snATACseq of adult human macular region of retina donor_MMD_22_16477 s1

value: African American

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: snRNA-seq of adult human macular region of retina donor_MMD_22_14307

value: male

value: 63 years

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_14307

value: FALSE


title: snATACseq of adult human macular region of retina donor_MMD_22_17017 s1

value: South Asian

value: 86 years


title: snRNA-seq of adult human macular region of retina donor_MMD_22_02443

value: macula lutea

value: Hispanic or Latin American

value: 75 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_02443

value: NeuN


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_02443

value: peripheral region of retina

value: gene symbol


title: snRNA-seq of adult human peripheral lobe region of retina donor_MMD_22_13066

value: African American

value: 72 years

value: GENCODE 32


title: snRNA-seq of adult human macular region of retina donor_MMD_22_13066


title: Multiome-ATAC of adult human macular region of retina donor_MMD_22_02443

value: 10x multiome

value: gene symbol,genomic coordinates

value: UMI,fragment ends

value: snATAC-seq,snRNA-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1556 s2

source_name: fovea centralis

value: fovea centralis

value: female

value: European

value: 69 years

value: UMI

value: snRNA-seq


title: snATAC-seq of adult human macular region of retina donor_MMD_22_02443 s2

value: macula lutea

value: 10x scATAC-seq

value: male

value: Hispanic or Latin American

value: 75 years

value: FALSE

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: Multiome-GEX of adult human macular region of retina donor_MMD_22_02443

value: 10x multiome

value: gene symbol,genomic coordinates

value: GENCODE 32

value: UMI,fragment ends


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_MMD_22_13066

value: African American

value: 72 years

value: NeuN

value: gene symbol


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0792

value: fovea centralis

value: female

value: 69 years

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0578

value: European

value: FALSE


title: snATAC-seq of adult human macular region of retina donor_MMD_22_02443 s1

value: macula lutea

value: 10x scATAC-seq

value: male

value: Hispanic or Latin American

value: 75 years

value: genomic coordinates

value: fragment ends


title: snATAC-seq of adult human macular region of retina donor_MMD_22_02443 s3

value: snATAC-seq


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_23_0574

value: 46 years

value: GENCODE 32


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0313

value: fovea centralis

value: 60 years

value: gene symbol


title: HEK293T_danoprevir_mRNA_bio_rep_3_SRS

city: New Haven

first: Alexandra

last: Bergfort

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

description: Library name: sample33

data_processing:
mRNA-Illumina: Paired-end read mates were generated in .fastq format. Illumina adapters were trimmed using fastp 0.24.0. Reads were mapped to the GRCh38.p14 genome (GENCODE release 44) using STAR 2.7.11b with settings  --runMode alignReads -outSAMtype BAM SortedByCoordinate. Resulting .bam files were indexed with samtools 1.21. Splicing was quantified running whippet on fastp outputs. Gene expression was determined using featureCounts(subread 2.0.8) followed by DESeq2 analysis. All downstream analyses were carried out using custom python scripts that utilize the output files from DESeq2 and whippet.
nRNA-Illumina: Paired-end read mates were generated in .fastq format. Illumina adapters were trimmed using fastp 0.24.0. Reads were mapped to the GRCh38.p14 genome (GENCODE release 44) using STAR 2.7.11b with settings  --runMode alignReads –outSAMattributes All --outSAMtype BAM --SortedByCoordinate. Resulting .bam files were indexed with samtools 1.21. Junction reads were quantified using splice-q 1.0.0 and splicing per intron (SPI) values were calculated using a custom python script using the splice-q output files. Splicing order was calculated using insplico with the STAR outputs as input files.
mRNA-PacBio: Adapters were trimmed and data pre-processed using fastplong 0.2.2. Reads were mapped to the GRCh38.p14 genome (GENCODE release 44) using flair align 2.0.0.
Assembly: GRCh38.p14 genome (GENCODE release 44)
Supplementary files format and content: whippet outputs as comma delimited files, providing Percent Spliced In (PSI) values for the different treatment conditions.
Supplementary files format and content: FeatureCount output as txt files providing read counts for the hg38 genome. Input for DESeq2.
Supplementary files format and content: DESeq2 results as comma delimited files, providing change in gene expression between different treatment conditions.
Supplementary files format and content: splice-q outputs as tab delimited files providing info aboout read numbers over splice junctions
Supplementary files format and content: insplico outputs as comma delimited files providing info about splicing order of introns surrounding the listed exons.
Supplementary files format and content: block_junction_coverage as a comma delimited file, providing info about coordinates of blocks of exons spliced collectively and the read coverage of the respective block skipping junctions

growth_protocol: All cells were cultivated at 37°C in Dulbecco's modified Eagle's medium (DMEM) GLutaMAX (Thermo Fisher Scientific, 10569010) supplemented with 10% fetal bovine serum (Gibco, A5670701) and 1% penicillin/streptomycin (Thermo Fisher Scientific, 15140122). In addition, medium for SMASh-EIF4A3 cells was supplemented with 1 ug/mL Puromycin (Thermo Fisher Scientific, A1113803) and 10 ug/mL Blasticidine (Thermo Fisher Scientific, A1113903). Medium for 293 Flp-In T-REx  – EIF4A3 cells was supplemented with 15 ug/mL Blasticidine and 150 ug/mLHygromycin (Thermo Fisher Scientific, 10687010).

extract_protocol:
mRNA: To harvest, cells were washed off the 6-wells with 500 uL ice cold PBS and then centrifuged for 1 minute at 1000g in a tabletop centrifuge. PBS was removed, cells were resuspended in 1 mL TRIzol (Thermo Fisher Scientific, 15596018) and RNA extracted according to the manufacturer protocol. Subsequently RNA was further purified via the RNeasy Mini Kit (Qiagen, 74104), including DNase digestion (RNase-Free DNase Set, Qiagen, 79254).
Nascent RNA (nRNA): Cells were fractionated and nascent RNA was extracted from chromatin as described in Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). For Illumina short read sequencing, the protocol was followed until step 40 (including poly(A)+ depletion but excluding ribosomal RNA (rRNA) depletion) and samples were subsequently used for library preparation, that included rRNA depletion (see below). For PacBio long-read sequencing of nascent RNA, rRNA depletion was carried out following the complete protocol.
mRNA-Illumina sequencing: Extracted RNA was used to prepare RNA-seq libraries using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). The RNA-seq library was sequenced on the Illumina Novaseq X Plus platform generating ~25 milliion paired-end reads per sample.
nRNA-Illumina sequencing:  Extracted RNA was used to prepare RNA-seq libraries using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems). The RNA-seq library was sequenced on the Illumina Novaseq X Plus platform generating ~100 milliion paired-end reads per sample.
mRNA-PacBio: The Iso-Seq libraries were prepared according to PacBio’s Preparing Iso-Seq® Libraries using SMRTbell® Prep Kit 3.0 manual. 1.05x SMRTbell clean-up was done to size select 500bp and above fragments and one SMRT library was prepared and run on two SMRTcells. Primer annealing and polymerase binding reactions were prepared using the Binding Calculator from PacBio, based on sample volume, concentration, and insert size using default settings. The SMRTbell libraries were annealed to sequencing primers and then bound to polymerase using the Sequel® II Binding Kit 3.1 before being loaded onto the PacBio Sequel II sequencer. Sequencing was performed for 24 hours of movie time.

treatment_protocol: EIF4A3 overexpression (OE) in 293 Flp-In T-REx  – EIF4A3 cells  was induced with 0.1 mg/mL Doxycycline in PBS for 48 hours. EIF4A3 depletion in SMASh-EIF4A3 cells was induced by treatment with 1.5 uM Danoprevir for 24 hours. Control cells were treated with the same volume DMSO.

tag: cell line

tag: cell type

value: Human embryonic Kidney

tag: genotype

value: WT

tag: treatment

value: 1.5 uM Danoprevir, 24 hrs


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1340 2

value: African American

value: 62 years

value: FALSE

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1340 1

value: male


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1556 s1

value: female

value: European

value: 69 years


title: snRNA-seq of adult human fovea region of retina donor_BCM_24_0080

value: 24 years


title: HEK293T_danoprevir_mRNA_bio_rep_1_SRS

description: Library name: sample31

tag: batch


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0131

tag: assay

value: Hispanic or Latin American

value: 16 years

value: GENCODE 32


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0890

value: fovea centralis

tag: ethnicity

value: Indian

value: 64 years

value: gene symbol


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0574 s2

tag: age

value: 46 years


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0896

value: 62 years

tag: donor id


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0867

value: 58 years

value: FALSE

tag: raw matrix_feature_keys


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0358

value: 34 years

tag: raw matrix_cellranger_assay_chemistry

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0574

value: female

value: European

tag: raw matrix_genome_annotation


title: HEK293T_dmso_mRNA_bio_rep_2_SRS

description: Library name: sample29

value: Human embryonic Kidney

value: WT

value: DMSO, 24 hrs


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0231

value: male

value: 69 years

value: GENCODE 32

tag: raw matrix_value_units


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_23_0131

value: peripheral region of retina

value: Hispanic or Latin American

value: 16 years

tag: raw matrix_assays


title: HEK293T_danoprevir_mRNA_bio_rep_2_SRS

description: Library name: sample32

value: 1.5 uM Danoprevir, 24 hrs


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0334

tag: tissue

value: fovea centralis

value: 62 years

value: gene symbol


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_0334 s2

value: FALSE

value: UMI


title: eif4a3_OE_mRNA_bio_rep_2_SRS

description: Library name: sample23

source_name: HEK293 Flp-In Trex

value: HEK293 Flp-In Trex

value: WT + EIF4A3

value: 0.1ug/mL Doxyxycline, 48 hrs


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0784 2

value: macula lutea

value: female

value: African American

value: 43 years

value: snRNA-seq


title: HEK293T_dmso_mRNA_bio_rep_3_SRS

description: Library name: sample30

value: Human embryonic Kidney

value: WT

value: DMSO, 24 hrs


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0784 1

tag: suspension enrichment_factors

value: NeuN

value: GENCODE 32


title: eif4a3_OE_ctr_mRNA_bio_rep_3_SRS

description: Library name: sample21

value: untreated


title: HEK293T_dmso_mRNA_bio_rep_1_SRS

description: Library name: sample28


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0849

value: fovea centralis

tag: Sex

value: Hispanic or Latin American

value: 69 years

value: gene symbol


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0784 2

value: FALSE

value: UMI


title: snATAC-seq of adult human fovea region of retina donor_BCM_22_0784

value: 10x scATAC-seq

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: eif4a3_OE_mRNA_bio_rep_3_SRS

description: Library name: sample24

tag: cell line

value: HEK293 Flp-In Trex

value: WT + EIF4A3

value: 0.1ug/mL Doxyxycline, 48 hrs


title: eif4a3_OE_mRNA_bio_rep_1_SRS

description: Library name: sample22

tag: cell type

value: Human embryonic Kidney


title: eif4a3_OE_ctr_mRNA_bio_rep_1_SRS

description: Library name: sample19

tag: genotype


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0784 1

value: macula lutea

value: female

value: African American

value: 43 years

value: snRNA-seq


title: snATAC-seq of adult human peripheral lobe region region of retina donor_BCM_22_0784

value: peripheral region of retina


title: snRNA-seq of juvenile (5-14 yo) human peripheral lobe region of retina donor_BCM_22_0769

value: male

value: European

value: 11 years

value: gene symbol

value: GENCODE 32


title: smash_eif4a3_danoprevir_nRNA_bio_rep_1_SRS

description: Library name: sample10

tag: treatment

value: 1.5 uM Danoprevir, 24 hrs


title: smash_eif4a3_danoprevir_nRNA_bio_rep_3_SRS

description: Library name: sample12

tag: batch


title: smash_eif4a3_dmso_nRNA_bio_rep_3_SRS

description: Library name: sample9

value: DMSO, 24 hrs


title: smash_eif4a3_danoprevir_nRNA_bio_rep_2_SRS

description: Library name: sample11


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0458 1

tag: assay

value: Hispanic or Latin American

value: 25 years

value: FALSE

value: NeuN

value: UMI


title: eif4a3_OE_ctr_mRNA_bio_rep_2_SRS

description: Library name: sample20

value: HEK293 Flp-In Trex

value: Human embryonic Kidney

value: WT + EIF4A3

value: untreated


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0458 2

value: macula lutea

value: female

tag: ethnicity

value: snRNA-seq


title: smash_eif4a3_danoprevir_mRNA_bio_rep_3_SRS

description: Library name: sample6


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0500

value: fovea centralis

value: male

value: European

tag: age

value: 64 years


title: smash_eif4a3_dmso_nRNA_bio_rep_2_SRS

description: Library name: sample8

value: DMSO, 24 hrs


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0458 2

value: Hispanic or Latin American

tag: donor id

value: gene symbol

value: GENCODE 32


title: smash_eif4a3_dmso_mRNA_bio_rep_3_SRS

description: Library name: sample3


title: smash_eif4a3_dmso_nRNA_bio_rep_1_SRS

description: Library name: sample7


title: smash_eif4a3_danoprevir_mRNA_bio_rep_2_SRS

description: Library name: sample5

value: 1.5 uM Danoprevir, 24 hrs


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0458 1

value: 25 years

value: FALSE

tag: raw matrix_feature_keys

value: UMI


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0784

value: peripheral region of retina

value: African American

value: 43 years

tag: raw matrix_cellranger_assay_chemistry


title: Multiome-GEX of adult human fovea region of retina donor_BCM_22_0458 s3

value: 10x multiome

value: female

value: gene symbol,genomic coordinates

tag: raw matrix_genome_annotation

value: UMI,fragment ends

value: snATAC-seq,snRNA-seq


title: smash_eif4a3_danoprevir_mRNA_bio_rep_1_SRS

description: Library name: sample4

value: Human embryonic Kidney


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0458

tag: raw matrix_value_units

value: snRNA-seq


title: Multiome-ATAC of adult human fovea region of retina donor_BCM_22_0458 s2

value: fovea centralis

value: Hispanic or Latin American

tag: raw matrix_assays


title: smash_eif4a3_dmso_mRNA_bio_rep_1_SRS

description: Library name: sample1

value: DMSO, 24 hrs


title: RRBS_Suz12KO_WT_Rep3

city: London

first: Aina

middle: Maria

last: Mas

address: Chester Beatty Laboratories, 237 Fulham Rd.

country: United Kingdom

institute: Institute of Cancer Research

data_processing:
RRBS sequencing reads were trimmed using v0.4.5 of TrimGalore with --rrbs setting enabled to remove 2bp from the 3´end of Read 1 and 5´end of Read 2 in addition to adaptor contamination. Raw reads were filtered for quality and adapter content using TrimGalore with a quality setting of 20 and running v1.15 of Cutadapt and v0.11.5 of FastQC.
Trimmed reads were then aligned to the mm10 in silico bisulfite transformed genome with the bisulfite sequencing aligner Bismark v0.19.0 (https://www.bioinformatics.babraham.ac.uk/ projects/bismark/) using default Bowtie2 (v2.3.4.1) settings within Bismark.
Duplicated reads were discarded, and the remaining alignments were used for cytosine methylation calling by Bismark methylation extractor. Initial visualization with principle component analysis revealed no outliers or batch effects.
Differentially methylated CpGs (DMCs) were identified using DSS R-package v2.42.0 using the dispersion shrinkage method followed by Wald statistical test for beta-binomial distributions. Any CpGs with FDR < 0.05 and methylation percentage differences greater than 10% were considered significant DMCs. Custom annotation was built from the H3K27me3 peak-set using the R-package Annotatr v1.20.0, and DMCs were filtered for direct PRC2 target DMCs. Annotatr was then used to add annotations for CpG-type, gene, and transcriptional rescue groups to each DMC.
Custom DMRs were called by grouping DMCs based on shared identifiers by combining the gene ID with CpG type, resulting in up to 4 DMRs per gene (CpG-island, CpG-shore, CpG-shelf, and CpG-opensea). Mean methylation (%) was then calculated for each DMR
Assembly: mm10
Supplementary files format and content: BigWig coverage and BigWig Methyl

growth_protocol: Mouse embryonic stem cells were cultured in serum/LIF medium (Glasgow Minimum Essential Media (GMEM) supplemented with 10% heat-inactivated Fetal Bovine Serum (HI-FBS), 1% Penicillin/Streptomycin, 2mM L-glutamine, 1 mM Sodium Pyruvate (Gibco), 0.1 mM MEM Non-essential amino acids (Gibco), 100μM ß-Mercaptoethanol (Gibco) and Leukemia Inhibitory Factor (LIF, produced in the lab))

extract_protocol:
DNA was extracted from cells using DNeasy Blood and Tissue kit (Qiagen), and concentrations were quantified with Qubit dsDNA HS assay kit. For each sample, 2ug genomic DNA was spiked with 2ng unmethylated Lambda DNA (Promega) to allow assessment of the bisulfite-conversion reaction efficiency before DNA was ingested for 5 hours at 37°C using a methylation-insensitive restriction enzyme, MspI.
Library preparation was performed using NEXTFLEX Bisulfite-Seq kit (Bioo Scientific) with methylated adaptors (Bioo Scientific) and 1µg input DNA according to manufacturer’s protocol. DNA was quantified again using Qubit dsDNA HS assay kit before bisulfite conversion was performed with EZ DNA Methylation-Lightning kit (Zymo Research). Bisulfite-converted DNA was PCR amplified and purified following the protocol of NEXTFLEX Bisulfite-Seq kit (Bioo Scientific). RRBS libraries were quantified with Qubit dsDNA HS assay kit, and size distributions were analyzed on TapeStation 2200 (Agilent Technologies). Libraries were first pooled based on molar concentrations and then combined with RNA-seq or CUT&RUN samples to compensate for the inherently low ATGC complexity of RBBS libraries. The final library pools were denatured, loaded onto an Illumina Nextseq 550 with SE75 high-output kits, and sequenced as paired-end 36/36 cycles.

treatment_protocol: Cells were treated with either dTAG13 or DMSO for 24hrs. KDM4-specific inhibitor QC6352 treatment for 96hrs

value: Mouse embryonic stem cells

value: Suz12 KO + WT


title: RRBS_Suz12KO_Rep3

value: Suz12 KO


title: Multiome-GEX of adult human fovea region of retina donor_BCM_22_0458 s1_2

tag: tissue

value: 25 years

value: FALSE

value: GENCODE 32


title: Multiome-GEX of adult human fovea region of retina donor_BCM_22_0458 s1_1


title: RRBS_WT_mESC_Rep3

value: WT


title: Multiome-ATAC of adult human fovea region of retina donor_BCM_22_0458 s1_1

value: 10x multiome


title: Multiome-ATAC of adult human fovea region of retina donor_BCM_22_0458 s1_2

value: female


title: snRNA-seq of juvenile (5-14 yo) human fovea region of retina donor_BCM_22_0769

value: male

value: European

value: 11 years

value: gene symbol

value: UMI


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0458

value: fovea centralis

value: snRNA-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1448

value: Hispanic or Latin American

value: 50 years


title: RRBS_Suz12KO_S12NSUV2dead_Rep3

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2*


title: RRBS_Suz12KO_S12NSUV2_Rep3

value: Suz12 KO + S12N:SUV2


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0434

value: peripheral region of retina

value: African American

value: 32 years

value: FALSE


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0434 2

value: macula lutea

value: female

tag: suspension enrichment_factors

value: NeuN

value: GENCODE 32


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0434

tag: Sex

value: gene symbol


title: RRBS_Suz12KO_WT_Rep2

tag: cell line

value: Suz12 KO + WT


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0434 1

value: UMI


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1401 2

value: fovea centralis

value: male

value: European

value: 71 years

value: snRNA-seq


title: BMP10-treated_vEHT_5, Day_10

city: Hamburg

first: Laura

last: Sommerfeld

address: Martinistr. 52

country: Germany

institute: UKE Hamburg

description:
Library name: Sample 10_BMP10
1.3.4 D

data_processing:
RNA-seq raw reads were processed using R (version 4.2, BlueBEAR portal with bio module). Quality-controlled FASTQ files were aligned in parallel with two pipelines:
Genome-based alignment: Reads were aligned to the human reference genome (Ensembl GRCh38) using STAR. Resulting SAM files were converted to BAM format using SAMtools, and read counts per gene were obtained with CountSAM.R
Transcriptome-based quantification: Reads were mapped and quantified against the Ensembl transcriptome using RSEM
Reference genome sequence (FASTA) and annotation (GTF) were obtained from the Ensembl database (https://www.ensembl.org/info/data/index.html)
Assembly: GRCh38.110
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Engineered Heart Tissue

extract_protocol:
RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, USA).
RIN >9.2 was confirmed for all samples on an Agilent Tapestation device. Library preparation was carried out with the NEBNext Ultra II Directional RNA kit (New England Biolabs).

value: Engineered Heart Tissue

value: UKEi001-A (RRID:CVCL_A8PR)

tag: cell type

value: hiPSC-derived cardiomyocytes

value: 100 nM human recombinant BMP10


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0395

value: Hispanic or Latin American

value: 58 years

value: FALSE


title: smash_eif4a3_dmso_mRNA_bio_rep_2_SRS

description: Library name: sample2

value: Human embryonic Kidney

tag: genotype

value: DMSO, 24 hrs


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0434

value: female

value: African American

value: 32 years

value: gene symbol

value: GENCODE 32


title: BMP10-treated_vEHT_4, Day_10

description:
Library name: Sample 9_BMP10
1.3.4 C

tag: treatment


title: snRNA-seq of adult human peripheral lobe region region of retina enriched for neurons donor_BCM_22_0389

value: peripheral region of retina

value: male

value: European

value: 67 years

value: NeuN

value: UMI


title: RRBS_WT_mESC_Rep2

value: Mouse embryonic stem cells

value: WT


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0389

value: snRNA-seq


title: RRBS_Suz12KO_Rep2

value: Suz12 KO


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0389

value: fovea centralis

value: FALSE


title: BMP10-treated_vEHT_3, Day_10

description:
Library name: Sample 8_BMP10
1.3.4 A

value: Engineered Heart Tissue

value: UKEi001-A (RRID:CVCL_A8PR)

value: hiPSC-derived cardiomyocytes

value: 100 nM human recombinant BMP10

tag: batch


title: BMP10-treated_vEHT_2, Day_10

description:
Library name: Sample 7_BMP10
1.1.1 C


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0200 s3

value: macula lutea

tag: assay

value: female

value: Hispanic or Latin American

value: 43 years

value: gene symbol

value: GENCODE 32


title: RRBS_Suz12KO_S12NSUV2_Rep2

value: Suz12 KO + S12N:SUV2


title: RRBS_Suz12KO_S12NSUV2dead_Rep2

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2*


title: snATAC-seq of adult human peripheral lobe region region of retina donor_BCM_22_0389

value: peripheral region of retina

value: 10x scATAC-seq

value: male

tag: ethnicity

value: European

value: 67 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_23_1401 1

value: fovea centralis

tag: age

value: 71 years

value: FALSE

value: UMI

value: snRNA-seq


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0200 s1_1

value: macula lutea

value: female

value: Hispanic or Latin American

value: 43 years

tag: donor id

value: gene symbol

value: GENCODE 32


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0200

value: NeuN

tag: raw matrix_feature_keys


title: RRBS_Suz12KO_WT_Rep1

value: Mouse embryonic stem cells

value: Suz12 KO + WT


title: RRBS_WT_mESC_Rep1

value: WT


title: BMP10-treated_vEHT_1, Day_10

description:
Library name: Sample 6_BMP10
1.1.1 A

value: Engineered Heart Tissue

value: UKEi001-A (RRID:CVCL_A8PR)

value: hiPSC-derived cardiomyocytes

value: 100 nM human recombinant BMP10


title: Multiome-GEX of adult human fovea region of retina donor_BCM_22_0200 2

value: fovea centralis

value: 10x multiome

value: FALSE

value: gene symbol,genomic coordinates

tag: raw matrix_cellranger_assay_chemistry

value: UMI,fragment ends

value: snATAC-seq,snRNA-seq


title: Control_vEHT_4, Day_10

description:
Library name: Sample 4_Control
1.3.5 A

value: Vehicle


title: Multiome-ATAC of adult human fovea region of retina donor_BCM_22_0200 2

value: female

value: Hispanic or Latin American

value: 43 years

tag: raw matrix_genome_annotation


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0200 s2_1

value: macula lutea

value: gene symbol

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

value: snRNA-seq


title: Multiome-GEX of adult human fovea region of retina donor_BCM_22_0200 1

tag: raw matrix_assays


title: Control_vEHT_3, Day_10

description:
Library name: Sample 3_Control
1.3.3 C

tag: tissue

value: Engineered Heart Tissue

value: UKEi001-A (RRID:CVCL_A8PR)

value: hiPSC-derived cardiomyocytes


title: Multiome-ATAC of adult human fovea region of retina donor_BCM_22_0200 1

value: fovea centralis

value: 10x multiome


title: RRBS_Suz12KO_S12NSUV2dead_Rep1

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2*


title: Control_vEHT_2, Day_10

description:
Library name: Sample 2_Control
1.3.3 B


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0183 2

value: male

value: European

value: 21 years

value: FALSE

tag: suspension enrichment_factors

value: NeuN


title: RRBS_Suz12KO_S12NSUV2_Rep1

value: Suz12 KO + S12N:SUV2


title: snATAC-seq of adult human fovea region of retina donor_BCM_22_0389

value: 10x scATAC-seq

tag: Sex

value: 67 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0200,BCM_23_0491

value: female

value: Hispanic or Latin American,African American

value: 43 years,16 years

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: Control_vEHT_5, Day_10

description:
Library name: Sample 5_Control
1.3.5 D

value: Engineered Heart Tissue

tag: cell line

value: UKEi001-A (RRID:CVCL_A8PR)

value: hiPSC-derived cardiomyocytes

value: Vehicle


title: Control_vEHT_1, Day_10

description:
Library name: Sample 1_Control
1.3.3 A

tag: cell type


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0183 2

value: macula lutea

value: male

value: European

value: 21 years

value: FALSE


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0183 1


title: RRBS_Rbbp5_FKBP_dTAG_rep2

value: Mouse embryonic stem cells

tag: genotype


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0183 s3

value: peripheral region of retina


title: Suz12 knockout + Suz12 dVEFS (S12N) fused to HP1a chromodomain_Replicate 2

description: Library name: S12N-Hp1_R2

data_processing:
RNA sequencing reads were 3’ trimmed for base quality with a setting of 20 and adapter sequences using Trimmomatic and reads were then aligned to mouse assembly mm10 using HISAT2 with default parameters.
Assembly: mm10
Supplementary files format and content: feature counts

extract_protocol:
Total RNA was extracted from fresh cell pellets in biological triplicates using RNeasy Plus Mini kit (Qiagen). RNA integrity was assessed on TapeStation 2200 (Agilent Technologies) using High Sensitivity RNA Screentape assay, and RNA was quantified with Qubit RNA HS assay kit
Libraries of mRNA were prepared using NEBNext UltraII Library prep kit according to the manufacturer’s instructions using 1µg input RNA. Libraries were quantified with Qubit dsDNA HS assay kit, and size distributions were analyzed on a Tape Station 2200 (Agilent Technologies). Libraries were pooled based on molar concentrations, denatured, loaded onto an Illumina Nextseq 2000, and sequenced as paired-end 60/60 cycles.

tag: treatment


title: Suz12 knockout + Suz12 dVEFS (S12N) fused to HP1a chromodomain_Replicate 3

description: Library name: S12N-Hp1_R3


title: RRBS_Suz12KO_Rep1

value: Suz12 KO


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0183 s1


title: RRBS_RS_S12NSUV2_dTAG_rep2+C48

value: Suz12 KO + S12N:SUV2


title: RRBS_R-Suz12KO_dTAG_rep2

value: RBBP5-FKBP + Suz12 KO (RS)


title: Suz12 knockout + Suz12 dVEFS (S12N) fused to HP1a chromodomain_Replicate 1

description: Library name: S12N-Hp1_R1


title: snRNA-seq of adult human peripheral lobe region region of retina enriched for neurons donor_BCM_22_0183

value: NeuN

value: gene symbol

value: GENCODE 32


title: RRBS_Rbbp5_FKBP_DMSO_rep2

value: DMSO


title: snRNA-seq of adult human fovea region of retina donor_BCM_22_0183

value: fovea centralis

value: UMI

value: snRNA-seq


title: Suz12 knockout + Suz12 Full length_Replicate 3

description: Library name: FL_R3

value: Suz12 knockout + Suz12 Full length


title: snATAC-seq of adult human peripheral lobe region region of retina donor_BCM_22_0183 s1

value: 10x scATAC-seq

value: male

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: snATAC-seq of adult human fovea region of retina donor_BCM_22_0183

value: European

value: 21 years

value: FALSE


title: snRNA-seq of adult human macular region of retina donor_BCM_22_0047

value: macula lutea

value: 70 years


title: snRNA-seq of adult human macular region of retina enriched for neurons donor_BCM_22_0183 1

value: NeuN

value: gene symbol


title: snATAC-seq of adult human peripheral lobe region region of retina donor_BCM_22_0183 s2

value: peripheral region of retina


title: RRBS_R-Suz12KO_DMSO_rep2

value: Mouse embryonic stem cells

value: RBBP5-FKBP + Suz12 KO (RS)

value: DMSO


title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0183 s2

value: GENCODE 32

value: UMI

value: snRNA-seq


title: Suz12 knockout + Suz12 Full length_Replicate 2

description: Library name: FL_R2

value: Suz12 knockout + Suz12 Full length


title: Multiome-GEX of adult human macular region of retina donor_BCM_22_0047 s2

value: 10x multiome

value: male

value: gene symbol,genomic coordinates

value: UMI,fragment ends

value: snRNA-seq,snATAC-seq


title: Suz12 knockout + Suz12 Full length_Replicate 1

description: Library name: FL_R1


title: Multiome-ATAC of adult human macular region of retina donor_BCM_22_0047 s2

value: macula lutea

value: European

value: FALSE


title: RRBS_Rbbp5_FKBP_dTAG_rep1


title: Suz12 knockout + Suz12 dVEFS (S12N)_Replicate 3

description: Library name: dVEFS_R3

value: Suz12 knockout + Suz12 dVEFS (S12N)


title: Multiome-GEX of adult human macular region of retina donor_BCM_22_0047 s1

value: 70 years

value: snATAC-seq,snRNA-seq


title: Multiome-ATAC of adult human macular region of retina donor_BCM_22_0047 s1


title: RRBS_RS_S12NSUV2_dTAG_rep1

value: Mouse embryonic stem cells

value: RS + S12N:SUV2


title: Multiome-ATAC of adult human fovea region of retina donor_BCM_22_0047

value: fovea centralis

value: GENCODE 32


title: Multiome-GEX of adult human fovea region of retina donor_BCM_22_0047


title: Suz12 knockout + Suz12 dVEFS (S12N)_Replicate 2

description: Library name: dVEFS_R2


title: snRNA-seq of adult human fovea region of retina donor_A23_5566

value: >89 years

value: gene symbol

value: UMI

value: snRNA-seq


title: RRBS_R-Suz12KO_dTAG_rep1

value: RBBP5-FKBP + Suz12 KO (RS)


title: RRBS_RS_S12NSUV2_DMSO_rep2

value: Suz12 KO + S12N:SUV2

value: DMSO


title: Human6_081

city: Leiden

first: Evita

last: van de Steeg

address: Sylviusweg 71

department: Metabolic Health Research

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Human: Homo_sapiens.GRCh38.gencode.v29, Pig: GCF_000003025.6_Sscrofa11.1_genomic
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: liver

extract_protocol:
After total RNA isolation from liver tissue, RNA quality was evaluated using a Fragment Analyzer (tot.RNA conc. & RQN) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). Next Generation Sequencing (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~18-26 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: - Porcine livers (of 6 ~6 months old male pigs, 2.1-2.5 kg/liver) were procured, preserved  and perfused for 360 min at 37°C as previously published*. Standard perfusion protocol consisted of infusion with TCA at a fixed rate of 0.2g/hr (0.39 mmol/hr). Porcine liver samples were taken at t=0min and t=360min for RNAseq analysis. *Stevens LJ, Zhu AZ, Chothe PP, Chowdhury SK, Donkers JM, Vaes WH, Knibbe CA, et al. Evaluation of normothermic machine perfusion of porcine livers as a novel preclinical model to predict biliary clearance and transporter-mediated drug-drug interactions using statins. Drug Metabolism and Disposition 2021;49:780-789.  - Human explanted and discarded livers (from adults, Male & Female, 1 healthy and 5 with various liver diseases, ~2kg/liver) were perfused for 360 min at 37°C as previously published**. Standard perfusion protocol consisted of infusion with TCA at a fixed rate of 0.2g/hr. The samples (perfusate, bile and tissue) used in this research with TCA infusion were derived from a study which was previously published**. Human liver samples were taken at t=0min and t=360min for RNAseq analysis. **Stevens LJ, Dubbeld J, Doppenberg JB, van Hoek B, Menke AL, Donkers JM, Alsharaa A, et al. Novel explanted human liver model to assess hepatic extraction, biliary excretion and transporter function. Clinical Pharmacology & Therapeutics 2023.

value: liver

tag: subject id

tag: treatorganism

value: H

tag: treatperfusionhr

tag: treat(non)cirrhotic

value: Nc

tag: diagn

value: HL

tag: diagnosis


title: Suz12 knockout mESCs_Replicate 3

description: Library name: S12KO_R3

value: Suz12 knockout


title: RRBS_RS_S12NSUV2_DMSO_rep1


title: RRBS_Rbbp5_FKBP_DMSO_rep1


title: RRBS_R-Suz12KO_DMSO_rep1


title: Suz12 knockout mESCs_Replicate 2

description: Library name: S12KO_R2


title: Suz12 knockout + Suz12 dVEFS (S12N)_Replicate 1

description: Library name: dVEFS_R1

value: Suz12 knockout + Suz12 dVEFS (S12N)


title: Human4_057

value: HBHC


title: Human4_049


title: Human3_040

value: C

value: ALD


title: Suz12 knockout mESCs_Replicate 1

description: Library name: S12KO_R1

value: Mouse embryonic stem cells


title: RRBS_Rbbp5-FKBP_dTAG_rep3


title: Wild type mESCs_Replicate 3

description: Library name: WT_R3

value: Wild type


title: RRBS_R-Suz12KO_dTAG_rep3


title: Human2_025

value: NASH