title: multiome, E15.5 back skin from 3 control embryos (pooled), ATAC, pool 1

status: Public on Mar 11 2025

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

description:
Library name: CTRL_E15.5_SKIN_ATAC_1
ATAC

library_source: genomic single cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using the Illumina bcl2fastq software. scRNA and scATAC-seq reads were processed and aligned to the mm10 reference genome using the Cell Ranger Count function. Further analysis and visualization was performed using Seurat (v4.3) (Hao et al., 2021) and Signac (v1.9) (Stuart et al., 2021). Briefly, peaks were unified between conditions and filtered based on length (20-10,000). EnsDb.Mmusculus.v79 was used for gene annotations. Cells underwent manual filtering to ensure cells used were between nCount_ATAC (100-50,000), nCount_RNA (100-25,000), nucleosome_signal <4, and TSS_enrichment >1. scRNA-seq separately underwent an additional SCTransform analysis. scATAC-seq underwent FindTopFeatures, RunTFIDF, and RunSVD. Datasets were then intersected using FindIntegrationAnchors (1:30, k.anchors=5) and IntegrateData (1:30). SCTransform, RunTFIDF, FindTopReatures, and RunSVD were rerun after integration. FindMultiModal neighbors using PCA (1:50) and LSI (2:50) was performed prior to FindClusters to generate the final UMAP. Trajectory analysis was performed with Monocle3 (Trapnell et al., 2014). Gene signature scoring was performed with UCell (Andreatta and Carmona, 2021). Cell cycle analysis was performed using CellCycleScoring with the cc.genes.updated.2019 converted to mouse format by Gprofiler2 (Kolberg et al., 2020). GO ontology analysis was performed using GO Biological Process and plotted using ShinyGO 0.8 (Ge et al., 2020).
For BigWig files, clusters were parsed into epidermis (2,3,5,7,8,10), dermis (0,1,4,6,9,18), and other (11,12,13,14,15,16,17,19,20,21,22) groups based on the cluster identities within Recka et al. 2025 supplemental figures 6-8. Epidermal or hair follicle related lineages were further subset into basal (2/5), spinous (3/10), differentiated (7), hair follicle (8), and dermal condensate (18). Reads originating from cells belonging to the described cell identities (clusters) were extracted via barcodes to create pseudobulk alignments. RNAseq and ATACseq were normalized using RPKM and read count, respectively, and tile size of 25 bp was used to generate final tracks.
Assembly: mm10
Supplementary files format and content: Cell Ranger Output Files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: bigwig files of mRNA expression or ATAC-seq peaks in individual clusters

source_name: back skin

extract_protocol:
For single cell multiome-sequencing experiments, embryos were collected at E15.5 from multiple litters. Yolk-sac tissue was lysed quickly using the Extract-N-Amp Tissue PCR Kit (Sigma-Aldrich) and embryos quickly genotyped using Phusion High-Fidelity DNA Polymerase (New England Biolabs) and shortened PCR cycling parameters. During genotyping, the back skin from all E15.5 mouse embryos was dissected and immediately transferred to ice cold DEPC-PBS (Millipore Sigma). Samples were incubated in 0.25% Trypsin (ThermoFisher) for 30-45 mins at 37°C with frequent pipette mixing. Once cells reached a single cell suspension, the reaction was quenched with 10% FBS (ThermoFisher), passed through a 40 µM cell strainer (Flomi Cell Strainers, SP Bel-Art), and triplicates of each genotype (CRE-negative controls or Prmt5 cKOs, based on quick-genotyping results) pooled. 500,000 cells from each pooled sample were incubated with lysis buffer (10mM Tris HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) for 5 mins on ice, nuclei extracted and quantified using trypan blue.
scRNA-Seq and scATAC-Seq sequencing libraries were prepared by the University of Iowa’s Iowa Institute of Human Genetics Genomics Division Laboratory. Briefly, 10,000 nuclei were targeted for bulk transposition before individual nuclei were encapsulated in oil droplets along with the 10X GEM code beads in the Chip J cartridge (P/N: 1000234) using the 10X Genomics Single Cell iX Chromium Controller. Generation of gel beads in emulsion (GEMs), barcoding, pre-amplification PCR, and ATAC library construction were all performed as recommended by the manufacturer (10X Genomics, Chromium Next GEM Single Cell Multiome + ATAC Reagent Kit, Rev F, P/N:1000283). The gene expression libraries were pooled and sequenced on a NovaSeq 6000 to give at least 20,000 reads per nuclei. The ATAC-Seq libraries were pooled and sequenced on a NovaSeq 6000 to give at least 25,000 reads per nuclei.

value: back skin

value: Mixed - epidermis/dermis

value: control

tag: batch


title: RNAseq, EPP2 cells, Ctu1KO, Torin1, replicate6

status: Public on Feb 19 2025

type: SRA

city: Heidelberg

first: Andres

last: Elia

state: Baden-Württemberg

address: Im Neuenheimer Feld 223

country: Germany

institute: DKFZ

library_source: transcriptomic

data_processing:
The adaptor sequences were trimmed using cutadapt (v3.4).
Alignment was performed against mm10 using STAR with “--twopassMode Basic --twopass1readsN -1 --outSAMtype BAM Unsorted SortedByCoordinate --limitBAMsortRAM 100000000000 --outBAMsortingThreadN=1 --outSAMstrandField intronMotif --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3 --chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15  --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20 --quantMode TranscriptomeSAM GeneCounts --outSAMmapqUnique 0”
Raw counts were determined with a custom script quantifying sorted, transcriptome-based BAM files from RNAseq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts

molecule: cytoplasmic RNA

organism: Mus musculus

growth_protocol: EPP2 were cultured in DMEM/F-12 supplemented with 10 % FBS and 2 mM glutamine and maintained at 37 °C and 5 % CO2

extract_protocol:
RNA was harvested by Trizol-chloroform extraction and isopropanol precipitation.
RNA libraries for RNA seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer´s instructions

treatment_protocol: KO was induced by doxycycline (300ng/mL) 4 days prior to the experiment. Torin1 (300 nM) or DMSO treatment was for 2 hours.

tag: cell line

tag: cell type

value: pancreatic cancer

tag: genotype

tag: treatment

value: Torin


title: MDX594 Olaparib

status: Public on Mar 03 2025

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

description:
Library name: MDX594 Olaparib
10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq (scRNA-seq) data were analyzed through the CellRanger Single-Cell Software Suite (v6.0.1).
Assembly: Sequencing reads from mouse  cells were mapped with the genome references for mouse (gex-mm10).
Supplementary files format and content: Cell Ranger output: matrix, barcodes and features

molecule: polyA RNA

source_name: Breast cancer Mouse Derived Allograft

extract_protocol:
Single-cells were loaded to the 10×Genomics Chromium Controller to be partitioned into Gel Beads-in-emulsion (GEMs). The cDNA sequencing libraries were prepared using the Chromium Single Cell 5´ Library and Gel Bead Kit (10X Genomics, Cat. N. 1000006) following manufacturer's instructions. Briefly, after GEM generation and reverse transcription (RT), GEM-RT were cleaned up and cDNA was amplified during 13 cycles to be subjected to quality control and quantification on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies).
To construct the Gene expression (GEX) library, 25-50 ng of the amplified cDNA were fragmented, end repaired, A-tailed, and sample indexed using the Chromium Single Cell 5’ Library Construction Kit (10x genomics, 1000020).

tag: tissue

value: Breast cancer Mouse Derived Allograft

value: Olaparib (PARPi) sensitive

value: Olaparib (PARPi)


title: RNAseq, EPP2 cells, Ctu1KO, Torin1, replicate5


title: RNAseq, EPP2 cells, Ctu1KO, Torin1, replicate4


title: RNAseq, EPP2 cells, Ctu1KO, Torin1, replicate3


title: RNAseq, EPP2 cells, Ctu1KO, Torin1, replicate1


title: RNAseq, EPP2 cells, Ctu1KO, Torin1, replicate2


title: Ascl1_sample2_rep2_demultiplex_required

status: Public on Mar 16 2025

city: Brisbane

first: Lachlan

middle: Ian

last: Harris

state: QLD

address: 300 Herston Road

department: Cancer Research Program

country: Australia

institute: QIMR Berghofer MRI

data_processing:
scRNA-seq: CellRanger Count (Ver. 7.0.1) CUT&RUN The nf-core/cutandrun pipeline was used (v3.2). The uniquely mapped reads were aligned to the mm10 reference genome using Bowtie2. Peak calling was performed using SEACR with 0.01 seacr_peak_threshold. The BigWig file was visualized using the Integrative Genomics Viewer (IGV).
Assembly: scRNA-seq: refdata-gex-mm10-2020-A or Mycn data was mapped to a custom version of this genome, which had the Mycn gene deleted and replaced with two new contigs, corresponding to exon1 of the Mycn gene (Mycnex1) and exon 2/3 (Mycnex3). The gene encoding eGFP was also added to the custom genome. The genome was made with the cellRanger mkref command. CUT&RUN: mm10.
Supplementary files format and content: scRNA-seq: output from CellRanger Count (Ver. 7.0.1). CUT&RUN: bigWig files.

source_name: hippocampal neural stem cells (FLOW-enriched)

extract_protocol:
scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions (10x Genomics Chemistry, Single Cell version 3.0.1).  CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000  cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C  for 10 min. DNA was then purified using a DNA cleanup kit.
scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100.


title: RNAseq, EPP2 cells, Ctu1KO, DMSO, replicate4

value: DMSO


title: RNAseq, EPP2 cells, Control, Torin1, replicate6

value: WT


title: RNAseq, EPP2 cells, Ctu1KO, DMSO, replicate2


title: RNAseq, EPP2 cells, Ctu1KO, DMSO, replicate1


title: RNAseq, EPP2 cells, Control, Torin1, replicate2


title: RNAseq, EPP2 cells, Control, Torin1, replicate1


title: RNAseq, EPP2 cells, Ctu1KO, DMSO, replicate5


title: RNAseq, EPP2 cells, Control, Torin1, replicate3


title: RNAseq, EPP2 cells, Ctu1KO, DMSO, replicate3


title: Huwe1_cKO_rep1

value: hippocampal neural stem cells (FLOW-enriched)


title: Mycn_cKO_rep2


title: RNAseq, EPP2 cells, Control, DMSO, replicate6


title: RNAseq, EPP2 cells, Control, Torin1, replicate4


title: RNAseq, EPP2 cells, Control, Torin1, replicate5


title: RNAseq, EPP2 cells, Control, DMSO, replicate3


title: RNAseq, EPP2 cells, Control, DMSO, replicate1


title: RiboSeq, EPP2 cells, Ctu1KO, Torin1, replicate6

data_processing:
The adaptor sequences were trimmed using cutadapt (v3.4) and demultiplexed with barcode splitter from FASTX-toolkit (Cold Spring Harbor Laboratory, Hannon Lab, by Assaf Gordon)
Unique molecular identifiers (UMIs) were extracted with umi_tools (v1.1.1) and the rRNA discarded with BLAST-Like Alignment Tool (BLAT, v36x2).
Remaining reads were aligned to GRCm38/mm10 mouse genome by Spliced Transcripts Alignment to a Reference (STAR, v2.5.3a).
Raw counts were determined with a custom script quantifying sorted, transcriptome-based BAM files from RiboSeq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts
Library strategy: Ribo-Seq

extract_protocol:
RNA was harvested by Trizol-chloroform extraction and isopropanol precipitation.
Cytoplasmic RNA from ribosome protected fragments (RPFs) were isolated from cytosolic cell lysate. Isolates were RNaseI-treated  and monosome were purified using TRIzol reagent. Libraries were constructed according to McGlincy NJ and Ingolia NT.  Methods. 2017


title: RNAseq, EPP2 cells, Control, DMSO, replicate5


title: RNAseq, EPP2 cells, Control, DMSO, replicate2


title: RiboSeq, EPP2 cells, Ctu1KO, DMSO, replicate5


title: RiboSeq, EPP2 cells, Ctu1KO, Torin1, replicate1


title: RiboSeq, EPP2 cells, Ctu1KO, Torin1, replicate3


title: RiboSeq, EPP2 cells, Ctu1KO, DMSO, replicate4


title: RiboSeq, EPP2 cells, Ctu1KO, DMSO, replicate2


title: RiboSeq, EPP2 cells, Ctu1KO, Torin1, replicate2


title: RiboSeq, EPP2 cells, Ctu1KO, DMSO, replicate1


title: RiboSeq, EPP2 cells, Control, Torin1, replicate6


title: RNAseq, EPP2 cells, Control, DMSO, replicate4


title: RiboSeq, EPP2 cells, Control, Torin1, replicate3


title: RiboSeq, EPP2 cells, Control, Torin1, replicate5


title: RiboSeq, EPP2 cells, Control, Torin1, replicate1


title: RiboSeq, EPP2 cells, Control, Torin1, replicate2


title: RiboSeq, EPP2 cells, Control, DMSO, replicate6


title: RiboSeq, EPP2 cells, Ctu1KO, Torin1, replicate4


title: RiboSeq, EPP2 cells, Control, DMSO, replicate4


title: RiboSeq, EPP2 cells, Control, DMSO, replicate5


title: 44_ALS (Donor ID 5974) [snRNAseq]

status: Public on Feb 10 2025

city: Cambridge

first: Timothy

middle: R

last: Hammond

state: MA

address: 350 Water Street

country: USA

institute: Sanofi

description: Library name: Sample9

data_processing:
cellranger-5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: .h5 matrix files

organism: Homo sapiens

source_name: cervical spinal cord

extract_protocol:
Nuclei isolation kit followed by DAPI+ FACS isolation
10x Genomics Next GEM Single Cell 3′ v3.1

value: cervical spinal cord


title: 47_ALS (Donor ID 6350) [snRNAseq]

description: Library name: Sample12


title: RiboSeq, EPP2 cells, Control, DMSO, replicate3


title: 42_ALS (Donor ID 5951) [snRNAseq]

description: Library name: Sample8


title: 37_control (Donor ID 13446) [snRNAseq]

description: Library name: Sample4


title: RiboSeq, EPP2 cells, Control, DMSO, replicate1


title: 35_control (Donor ID 13394) [snRNAseq]

description: Library name: Sample3


title: RiboSeq, EPP2 cells, Control, DMSO, replicate2


title: 41_ALS (Donor ID 5867) [snRNAseq]

description: Library name: Sample7


title: 46_ALS (Donor ID 6314) [RNAseq]

description: Library name: 175_S175

data_processing:
Data were analyzed with Array Studio (Version 11, Omicsoft Corporation). Reads were mapped to the human B38 reference genome with the Ensembl R109 gene model using the Omicsoft Aligner 4 (OSA4). Quantification was performed at gene level to obtain count-level information using the Expectation-Maximization (EM) algorithm. Genes were removed from the analysis if their counts equaled 0 for 9 or more samples.
Assembly: Human B38 reference genome
Supplementary files format and content: Counts matrix, Deseq2 normalized counts

extract_protocol:
RNeasy lipid tissue mini kit
NEBNext Ultra II Directional RNA Library Prep Kit + NEBNext Ultra II Directional RNA Library Prep Kit


title: 47_ALS (Donor ID 6350) [RNAseq]

description: Library name: 176_S176


title: 44_ALS (Donor ID 5974) [RNAseq]

description: Library name: 173_S173


title: RiboSeq, EPP2 cells, Ctu1KO, DMSO, replicate3


title: 40_ALS (Donor ID 5781) [snRNAseq]

description: Library name: Sample6


title: 39_ALS (Donor ID 5724) [snRNAseq]

description: Library name: Sample5


title: RiboSeq, EPP2 cells, Ctu1KO, Torin1, replicate5


title: 32_control (Donor ID 13122) [snRNAseq]

description: Library name: Sample2


title: 42_ALS (Donor ID 5951) [RNAseq]

description: Library name: 172_S172


title: 29_control (Donor ID 13085) [snRNAseq]

description: Library name: Sample1


title: 37_control (Donor ID 13446) [RNAseq]

description: Library name: 168_S168


title: 46_ALS (Donor ID 6314) [snRNAseq]

description: Library name: Sample11


title: 39_ALS (Donor ID 5724) [RNAseq]

description: Library name: 169_S169


title: RiboSeq, EPP2 cells, Control, Torin1, replicate4


title: 45_ALS (Donor ID 6290) [snRNAseq]

description: Library name: Sample10


title: 41_ALS (Donor ID 5867) [RNAseq]

description: Library name: 171_S171


title: 35_control (Donor ID 13394) [RNAseq]

description: Library name: 167_S167


title: 45_ALS (Donor ID 6290) [RNAseq]

description: Library name: 174_S174


title: 40_ALS (Donor ID 5781) [RNAseq]

description: Library name: 170_S170


title: scc15 cells, cav2koTG1A

status: Public on Feb 04 2025

city: tianjin

first: Zhang

last: ze

address: Huanhu Xi Road, Tiyuan Bei, Hexi District, Tianjin

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

description:
Library name: sample4
fpkm_scc15cav2koTG1A

data_processing:
To show the gene amount under different FPKM value, we calculate the gene amount under three different FPKM ranges(FPKM <= 1、FPKM 1~10、FPKM >= 10).
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
Used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.
We used Bowtie2 to align the clean reads to the reference genes.
Assembly: Homo_sapiens NCBI   GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Excel file includes FPKM, TPM, read count values for each Sample

molecule: total RNA

source_name: HNSCC

growth_protocol: For the transwell co-culture model, HNSCC cells were seeded in the upper chamber and ganglia (three TGs) were implanted in the low chamber of a 24-well transwell device with 0.4um pore size (Corning Incorporated). The same medium of 1:1 mix of DEME/F12 and neurobasal medium enriched with B-27 supplement was added to the upper and lower parts of the chamber.

extract_protocol:
RNA was harvested using SPARKeasy cell RNA rapid extraction kit
The cDNA library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions.  Adaptor ligation, size selection, and PCR amplification were performed, and the final library was quantified using Qubit and qPCR before sequencing on the sequencing platform.

treatment_protocol: Cav2 +/- mice (C57BL/6 background) were procured from Cyagen Biosciences (S-KO- 01350, Cyagen Biosciences) and subsequently bred to yield Cav2+/+ , Cav2 +/- and Cav2 - /- offspring for utilization in in vivo studies, as well as for in vitro experiments necessitating TG. SCC15 cells co-culture with wild TG or Cav2 -/- TG.

value: HNSCC

value: Epithelial Cell

value: co-culture with Cav2 -/- TG


title: 32_control (Donor ID 13122) [RNAseq]

description: Library name: 166_S166


title: scc15 cells, cav2koTG3A

description:
Library name: sample6
fpkm_scc15cav2koTG3A


title: scc15 cells, cav2koTG2A

description:
Library name: sample5
fpkm_scc15cav2koTG2A


title: Si2, Mouse dental papilla cells were transfected with Setd2-targeted siRNA

status: Public on Feb 03 2025

city: Wuhan

first: 佳欣

last: 牛

state: 洪山区

address: State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology

institute: Wuhan University

description: Library name: Sample 4

library_source: genomic

data_processing:
High-throughput sequencing was performed by Anoroad (Beijing). The raw data underwent quality control using Skewer (version 0.2.2) with the -m pe parameter to filter out adapter and low-quality reads, followed by FastQC (version 0.11.5) for raw data quality assessment. Filtered reads were aligned to the spike-in genome using Bowtie2 (version 2.2.9) with the following parameters: -p 8--very-sensitive-local --no-unal --no-mixed --no-discordant -- phred33 -l 10 -X 700 -x spike_in_genome.fa. Clean reads were then aligned to the Mus musculus reference genome (GRCm39) (Ensembl) using BWA (version 0.7.12-r1039) with parameters: -T 25 -k 18. For spike-in normalization, clean reads were mapped to the spike-in genome, and the number of mapped spike-in reads was quantified using samtools: samtools view -bF 4 -c. The sample with the lowest spike-in reads (NC1) was used as the reference, and the scaling factor for each sample was calculated as the ratio of the reference spike-in reads to the sample spike-in reads:
SCALE=`echo "scale=5; least_reads_count/sample_reads_count" | bc`
For example, the scaling factor for NC2 was calculated as follows:
Total_reads_A=`samtools view -bF 4 -c ../spike_in/NC1.bam`
Total_reads_B=`samtools view -bF 4 -c ../spike_in/NC2.bam`
SCALE=`echo "scale=5; $Total_reads_A/$Total_reads_B" | bc`
Peak Calling and Visualization
Peak calling was performed using MACS2 (version 2.1.2) with the following parameters:
-p 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all.
For peak visualization, the following MACS2 command was used to generate bedGraph files:
macs2 pileup -i ../mapping/NC2uni.dedup.bam --extsize 200 -o NC2.old.bdg1
The scaling factor was then applied to the signal in the bedGraph files:
awk -v SCALE=$SCALE '{print $1"\t"$2"\t"$3"\t"$4*SCALE}' NC2.old.bdg > NC2.bdg
Finally, the scaled bedGraph files were converted to bigWig format using:
bedGraphToBigWig NC2.bdg ..\ref\genome.chrom.sizes \ NC2.bw
DeepTools (version 3.0.2) was used to visualize the distribution of reads from 5-kb upstream of the TSS to 5-kb downstream of the TES, with the Pearson correlation method (--corMethod pearson).
Assembly: Ensembl; Mus_musculus.GRCm39
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: mouse dental papilla cells

extract_protocol:
The mDPCs were transfected with Setd2-targeted siRNA or scramble siRNA and cultured for 5 days under odontoblastic induction conditions. CUT&Tag was performed as described previously (Kaya-Okur et al., 2019), with modifications using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, China, cat. no. TD904). In brief, 1×105 cells were harvested, and after isolating the nuclei, they were incubated with Con A-coated beads at RT for 10 min. After removing the supernatant, the bead-bound cells were resuspended in 50 μL antibody buffer containing 1 μg rabbit anti-H3K36me3 antibody (Abcam) and incubated at 4°C overnight. The beads were then sequentially incubated with anti-rabbit IgG antibody, pA/G-Transposome Mix, and underwent fragmentation. DNA Spike-in was added to the samples. The reaction was terminated, and DNA fragments were extracted using PCI, followed by PCR amplification with indexed P5 and P7 primers.
The library products were enriched, quantified, and finally sequenced using the Illumina NovaSeq 6000 platform in PE150 mode.

value: mouse dental papilla cells

value: siSetd2, induced for odontoblastic differentiation for 5 days.

tag: cut&tag antibody

value: H3K36me3 (Abcam, ab9050)


title: scc15 cells, TGWT1A

description:
Library name: sample1
fpkm_scc15TGWT1A

value: co-culture with wild TG


title: Si1, Mouse dental papilla cells were transfected with Setd2-targeted siRNA

description: Library name: Sample 3


title: scc15 cells, TGWT3A

description:
Library name: sample3
fpkm_scc15TGWT3A


title: scc15 cells, TGWT2A

description:
Library name: sample2
fpkm_scc15TGWT2A


title: NC2, Mouse dental papilla cells were transfected with scramble siRNA

description: Library name: Sample 2

value: si Scramble, induced for odontoblastic differentiation for 5 days.


title: 29_control (Donor ID 13085) [RNAseq]

description: Library name: 165_S165


title: DAN-0319_XBxC_-+_XX_9w_Br

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

department: Institute of Pharmacology and Toxicology

institute: Technical University of Munich

description: instrument name: 64215e

data_processing:
The demultiplexing, barcode processing, and processing into full-length reads was made using SMRTLink 11.0
full-length reads were aligned using pbmm2 (1.10) with defaults options and the sort flag
aligned file was tagged according to haplotype using whatshap (1.17) subcommand haplotag (parameters: ignore linked reads, skip missing contigs)
bam file was separated by the haplotype given from the previous step using whatshap (1.17) subcommand split
counts were obtained from htseq-count (from htseq 0.12.4) for both alleles (parameters: stranded, sorted by position, bam file input)
Assembly: mm10
Supplementary files format and content: tab-delimited text file include counts for the maternal B6 allele and its corresponding BAM files containing the aligned long-read isoforms for genome browser visualization such as IGV
Supplementary files format and content: tab-delimited text file include counts for the paternal CAST allele and its corresponding BAM files containing the aligned long-read isoforms for genome browser visualization.
Supplementary files format and content: bed file contains the SNPs used in this study.

source_name: Whole brain

extract_protocol:
RNA was extracted from the tissue sample according to the manufacturers’ instructions for Invitrogen TRIzol Reagent.
cDNA libraries were prepared according to the Procedure & Checklist - Iso-Seq™ Express Template Preparation for Sequel® and Sequel II Systems protocol. Briefly, 300 ng of total RNA was used to generate full-length cDNA using oligo-dT primers and the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module (New England Biolabs). cDNA amplification was performed using unique barcoded forward and reverse primers. The brain sample used in this study was pooled equimolarly with eleven other samples, followed by end repair and adapter ligation. Primer and polymerase binding was performed according to the SMRT Link Sample Setup using the Sequel II Binding Kit 2.1. The entire pool was sequenced on one SMRT cell on the Sequel II sequencing platform using the Sequel II Sequencing Kit 2.0 (Pacific Biosciences) with a 4-hour pre-extension and 20-hour running time.
PacBio HiFi long-read seq

value: Whole brain

tag: background

value: delta Xist -/+

tag: Sex

value: female

tag: age

value: 9 weeks


title: WT_OPC_2

status: Public on Feb 01 2025

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw reads were passed through adapter filtration and process for potential rRNA contaminants clearance
The clean data were then aligned to GRCm38 for genome reference
Normalization of gene expression was performed by transferring the read counts to FPKM values, and both the read counts and FPKM values were used in visualization
Assembly: GRCm38
Supplementary files format and content: csv file includes baseMean, log2Foldchange, lfcSE, p-value, and adjusted p-value as WT vs. APC KO for OPC samples
Supplementary files format and content: excel files includes TPM, FPKM, Read Count and Normalized Read Count for each sample

source_name: Central Nervous System

extract_protocol:
RNA was extracted from the isolated cells by Trizol (Thermo, Cat No. 15596026) according to the manufacturer’s protocol
All EASY-RNAseq libraries were sequenced through the Illumina HiSeq platform with a 150-bp pair-end model.

value: Central Nervous System

value: Primary oligodendrocyte precursor cell culture

value: Apc-fl/fl


title: NC1, Mouse dental papilla cells were transfected with scramble siRNA.

description: Library name: Sample 1


title: parasites selected using KIR2DL1-Fc from RIFIN library 2 of P. falciparum lek79

status: Public on Jan 15 2025

city: Suita

first: Shiroh

last: Iwanaga

state: Osaka

address: 3-1 Yamadaoka

department: Molecular protozoology

country: Japan

institute: RIMD, Osaka University

description: Library name: lek79-k2d1-2

library_source: other

data_processing:
The reads containing the variable regions were isolated from the obtained fastq files using the seqkit program
The plasmid backbone sequence was trimmed using trimomatic-0.39-2 program
After confirming the quality of the trimmed reads, they were mapped to the reference genome sequence of Plasmodium falciparum 3D7, downloaded from PlasmoDB (version 62), or to the genomes of P. falciparum Lek174 and Lek79 strains, with accession numbers JBMVIM000000000 and JBMVIN000000000, respectively, using the Bowtie2 tool.
The number of reads for each RIFIN gene was then quantified using featureCounts.
Assembly: JBMVIN000000000
Supplementary files format and content: tab-delimited text  file includeds raw counts for each sample.

molecule: other

organism: Plasmodium falciparum

growth_protocol: P. falciparum was cultured with human RBCs (type O blood, hematocrit 2%) in complete medium (CM). This medium consisted of RPMI-1640 medium containing 10% human serum and 10% AlbuMAXI (Invitrogen), along with 25 mM HEPES, 0.225% sodium bicarbonate, and 0.38 mM hypoxanthine. Additionally, the medium was supplemented with 10 mg/ml gentamicin. Cultures were maintained under an atmosphere containing 90% N2, 5% CO2, and 5% O2.

extract_protocol:
DNA purified using conventional method using phnol/chroloform.
Amplicon seq library was prepared by conventional PCR with sequence-tagged primers. Sequence tags were used for illumina seq.

treatment_protocol: The parasite expressing KIR2DL1-binding RIFIN are selected using KIR2DL1-Fc.

value: Aseuxal blood stage


title: parasites selected using KIR2DL1-Fc from RIFIN library 2 of P. falciparum lek174

description: Library name: lek174lib-k2dl1-2

data_processing:
The reads containing the variable regions were isolated from the obtained fastq files using the seqkit program
The plasmid backbone sequence was trimmed using trimomatic-0.39-2 program
After confirming the quality of the trimmed reads, they were mapped to the reference genome sequence of Plasmodium falciparum 3D7, downloaded from PlasmoDB (version 62), or to the genomes of P. falciparum Lek174 and Lek79 strains, with accession numbers JBMVIM000000000 and JBMVIN000000000, respectively, using the Bowtie2 tool.
The number of reads for each RIFIN gene was then quantified using featureCounts.
Assembly: JBMVIM000000000
Supplementary files format and content: tab-delimited text  file includeds raw counts for each sample.


title: parasites selected using KIR2DL1-Fc from RIFIN library 1 of P. falciparum lek79

description: Library name: lek79-k2d1-1


title: parasites selected using KIR2DL1-Fc from RIFIN library 2 of P. falciparum 3D7

description: Library name: rif_lib1_2_K2DL1

data_processing:
The reads containing the variable regions were isolated from the obtained fastq files using the seqkit program
The plasmid backbone sequence was trimmed using trimomatic-0.39-2 program
After confirming the quality of the trimmed reads, they were mapped to the reference genome sequence of Plasmodium falciparum 3D7, downloaded from PlasmoDB (version 62), or to the genomes of P. falciparum Lek174 and Lek79 strains, with accession numbers JBMVIM000000000 and JBMVIN000000000, respectively, using the Bowtie2 tool.
The number of reads for each RIFIN gene was then quantified using featureCounts.
Assembly: PlasmoDB-62_Pfalciparum3D7
Supplementary files format and content: tab-delimited text  file includeds raw counts for each sample.


title: parasites selected using KIR2DL1-Fc from RIFIN library 1 of P. falciparum lek174

description: Library name: lek174lib-k2dl1-1


title: all parasites from RIFIN library1 of P.falcuparum 3D7

description: Library name: rif_lib_1-1_before


title: all parasites from RIFIN library2 of P.falcuparum 3D7

description: Library name: rif_lib_1-2_before


title: C: Uninjured No-treatment Control Spinal Cord Tissue, Biological Replicate 1

status: Public on Jan 05 2025

city: Rochester

first: Isobel

last: Scarisbrick

state: MN

address: 200 First St SW

institute: Mayo Clinic

data_processing:
Quality assessment of paired-end reads (.fastq files) using FASTQC (version 0.12.1).
Sequence reads were trimmed for adaptor sequence/low-quality sequences using Trimmomatic (version 0.38) with the following parameter: ILLUMINACLIP:TruSeq3-PE:2:30:10.
Trimmed reads were aligned to the mouse reference genome (mm10) using STAR (version 2.5.4b) to produce .bam files.
Gene expression quantification of STAR .bam files was performed using RSEM (version 1.3.1 with parameter: –star-sjdboverhang 150) to calculate transcripts per million (TPM).
Gene annotations for mm10 were sourced from UCSC Genome Browser (2023, genome.ucsc.edu).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample (raw_counts.txt)
Supplementary files format and content: tab-delimited text file includes transcripts per kilobase million (TPM) counts for each Sample (TPMs.txt)

source_name: Spinal cord

growth_protocol: Female C57BL/6J mice were aged to 12-weeks following standard housing conditions (12-hour light/dark cycle) between 22-24C.

extract_protocol:
At six weeks post-injury, experimental mice were euthanized with a terminal dose of pentobarbital (60 mg/kg), perfused with ice-cold saline, and spinal cords were isolated. Two uninjured control mice were similarly euthanized and perfused. From each mouse, a 5 mm section centered around the T9-T10 injury site or the corresponding site in uninjured mice was immediately preserved in RNAlater and stored at -80°C. RNA extraction was carried out with Trizol (Invitrogen) following purification with RNeasy Mini Kit (Qiagen), with on-column DNase treatment to eliminate genomic DNA.
RNA libraries for RNA-seq were constructed using SMARTer Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio) following the manufacturer's protocol.

treatment_protocol: At 12 weeks of age, experimental mice were anesthetized with xylazine (10 mg/kg) and ketamine (100 mg/kg) and underwent a 0.25 mm lateral compression model of spinal cord injury at the T8-9 vertebral level. Starting two weeks post-injury, experimental mice received daily for four weeks atorvastatin (10 mg/kg) dissolved in a vehicle of composed of 2% dimethyl sulfoxide (DMSO), 35% polyethylene glycol (PEG) 400, 2% Tween 80, and 61% saline—and a control group received the vehicle alone. Daily treatment continued until six weeks post-injury.

value: Spinal cord

value: C:Uninjured No-treatment Control


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 6

value: B:SCI + Vehicle


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 7


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 3


title: C: Uninjured No-treatment Control Spinal Cord Tissue, Biological Replicate 2


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 4


title: parasites selected using KIR2DL1-Fc from RIFIN library 1 of P. falciparum 3D7

description: Library name: rif_lib1_1_K2DL1


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 2


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 1


title: B: SCI plus Vehicle Spinal Cord Tissue, Biological Replicate 5


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 5

value: A:SCI + Atorvastatin


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 7


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 2


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 3


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 1


title: PRD, AL foamy, s087

status: Public on Jan 02 2025

city: Amsterdam

first: Alida

last: Chen

address: Meibergdreef 47, 1105 BA

country: Netherlands

institute: Netherlands Institute for Neuroscience

description:
Library name: 104898-001-087
104898-001-087

data_processing:
Adapter sequences were trimmed using Trimmomatic (version 0.39).
Trimmed reads were mapped to the human GRCh38 genome using HISAT2 (version 2.2.1) on default settings
Feature counts of reads mapped to genes were determined using HTSeq (version 1.99.2) with the ‘Homo_sapiens.CRCh38.105.gtf’ file (options: -m union -f bam -r name -s no -a 10 -t exon -i gene_id)
Resulting counts of both datasets were analyzed separately using R (version 4.1.0) and Bioconductor (version 3.13)
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file containing raw, unnormalised counts for each sample

source_name: AL foamy

extract_protocol:
All samples were collected in TRIsure and stored at -80°C until further processing. Total RNA was isolated with the RNeasy micro kit (QIAGEN) according to the manufacturers’ instructions.
rRNA depletion using QIAseq FastSelect kit (Qiagen)

treatment_protocol: MS lesions and NAWM samples were isolated from frozen post-mortem brain tissue

tag: donor

value: PRD

value: AL foamy

tag: diagnosis

value: Multiple Sclerosis

value: Male

tag: ms type

value: PP

tag: rin value


title: ERD, AL foamy_NAWM, s083

description:
Library name: 104898-001-083
104898-001-083

source_name: AL foamy_NAWM

value: ERD

value: AL foamy_NAWM


title: ERD, AL foamy_NAWM, s080

description:
Library name: 104898-001-080
104898-001-080

value: SP


title: PRD, AL foamy_NAWM, s093

description:
Library name: 104898-001-093
104898-001-093


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 4


title: ERD, AL foamy, s074

description:
Library name: 104898-001-074
104898-001-074


title: ERD, AL foamy, s073

description:
Library name: 104898-001-073
104898-001-073


title: ERD, AL foamy_NAWM, s079

description:
Library name: 104898-001-079
104898-001-079


title: ERD, AL foamy, s072

description:
Library name: 104898-001-072
104898-001-072


title: ERD, AL foamy, s071

description:
Library name: 104898-001-071
104898-001-071


title: ERD, AL foamy_NAWM, s078

description:
Library name: 104898-001-078
104898-001-078


title: PRD, AL ram-amo_NAWM, s068

description:
Library name: 104898-001-068
104898-001-068

source_name: AL ram-amo_NAWM

value: AL ram-amo_NAWM


title: PRD, AL ram-amo, s059

description:
Library name: 104898-001-059
104898-001-059

source_name: AL ram-amo

value: AL ram-amo


title: PRD, AL ram-amo_NAWM, s069

description:
Library name: 104898-001-069
104898-001-069


title: PRD, AL ram-amo_NAWM, s066

description:
Library name: 104898-001-066
104898-001-066


title: PRD, AL ram-amo, s062

description:
Library name: 104898-001-062
104898-001-062


title: ERD, AL foamy_NAWM, s081

description:
Library name: 104898-001-081
104898-001-081


title: ERD, AL ram-amo_NAWM, s055

description:
Library name: 104898-001-055
104898-001-055


title: PRD, AL ram-amo, s061

description:
Library name: 104898-001-061
104898-001-061


title: A: SCI plus Atorvastatin Spinal Cord Tissue, Biological Replicate 6


title: ERD, AL foamy, s076

description:
Library name: 104898-001-076
104898-001-076


title: ERD, AL ram-amo, s048

description:
Library name: 104898-001-048
104898-001-048


title: ERD, AL ram-amo, s046

description:
Library name: 104898-001-046
104898-001-046


title: PRD, RL_NAWM, s041

description:
Library name: 104898-001-041
104898-001-041


title: ERD, AL ram-amo, s044

description:
Library name: 104898-001-044
104898-001-044


title: ERD, AL ram-amo, s049

description:
Library name: 104898-001-049
104898-001-049

value: PR


title: PRD, RL_NAWM, s040

description:
Library name: 104898-001-040
104898-001-040


title: PRD, RL, s033

description:
Library name: 104898-001-033
104898-001-033

source_name: RL

value: RL


title: PRD, RL, s029

description:
Library name: 104898-001-029
104898-001-029


title: ERD, RL_NAWM, s027

description:
Library name: 104898-001-027
104898-001-027


title: ERD, RL, s021

description:
Library name: 104898-001-021
104898-001-021


title: ERD, RL_NAWM, s026

description:
Library name: 104898-001-026
104898-001-026


title: ERD, RL, s020

description:
Library name: 104898-001-020
104898-001-020


title: PRD, RL_NAWM, s036

description:
Library name: 104898-001-036
104898-001-036


title: ERD, AL ram-amo_NAWM, s053

description:
Library name: 104898-001-053
104898-001-053


title: ERD, RL, s019

description:
Library name: 104898-001-019
104898-001-019


title: ERD, RL, s007

description:
Library name: 104898-001-007
104898-001-007


title: ERD, AL ram-amo_NAWM, s051

description:
Library name: 104898-001-051
104898-001-051


title: ERD, RL, s001

description:
Library name: 104898-001-001
104898-001-001


title: ERD, RL_NAWM, s028

description:
Library name: 104898-001-028
104898-001-028


title: ERD, RL_NAWM, AL ram-amo_NAWM, s008

description:
Library name: 104898-001-008
104898-001-008

source_name: RL_NAWM/AL ram-amo_NAWM

value: RL_NAWM/AL ram-amo_NAWM


title: ERD, RL_NAWM, s014

description:
Library name: 104898-001-014
104898-001-014


title: PRD, RL, s034

description:
Library name: 104898-001-034
104898-001-034


title: B30

status: Public on Jan 01 2025

type: genomic

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected and quantile normalized aided by control probes

label: cy3, cy5

source_name: Biopsy-derived tumor sample

label_protocol: Standard Illumina labeling protocol

extract_protocol: For Human Methylation  EPIC Array, genomic DNA were extracted using QIAmp DNA Mini Kit.

value: Biopsy-derived tumor sample

tag: patient race (phenotype)

value: Black


title: W26

value: White


title: B34


title: B23


title: B25


title: W31


title: B26


title: B32


title: B24


title: B29


title: B28


title: B33


title: B19


title: W34


title: W33


title: B21


title: B35


title: B20


title: B31


title: B17


title: W23


title: W25


title: B22


title: B27


title: B18


title: W32


title: W24


title: W22


title: W35


title: W21


title: W20


title: B13


title: B6


title: B14


title: B15


title: B8


title: B16


title: W18


title: B12


title: W6


title: W15


title: W9


title: B11


title: B10


title: W19


title: B4


title: W5


title: SCC25,LIS1,short hairpin-2

city: DaLian

first: YiDing

last: Liu

address: wwde

institute: Dalian Medical University

description:
Library name: sh-LIS1-2
Column name in count.annot.xlsx:sh-LIS1-2

data_processing:
FASTQ
Remove adapter sequences from the reads
If the number of 'N' bases in a read exceeds 10% of the total read length, remove these paired reads
If the number of low-quality bases (Q ≤ 20) in a read exceeds 50% of the total read length, remove these paired reads
Assembly: hg38
Supplementary files format and content: xlsx files include counts values for each Sample

source_name: tongue

extract_protocol:
To extract RNA from samples, the Trizol method was used. After successful extraction, the RNA was dissolved in 50 µL of DEPC-treated water. Then, the total RNA was identified and quantified using a Qubit fluorometer and a Qsep400 high-throughput fragment analyzer.
Library construction involves enriching polyA-tailed mRNA using Oligo(dT) beads, fragmenting the mRNA, and synthesizing first strand cDNA with random hexamer primers. The second strand is synthesized with dUTP for strand specificity. After ligating adapters, the library is amplified via PCR and purified. Finally, concentration is measured with Qubit, fragment size analyzed with Qsep400, and effective concentration quantified by qPCR.

value: tongue

value: epithelial cells

value: Knockdown


title: W17


title: W14


title: SCC25,LIS1,short hairpin-3

description:
Library name: sh-LIS1-3
Column name in count.annot.xlsx:sh-LIS1-3


title: B5


title: SCC25,LIS1,short hairpin-1

description:
Library name: sh-LIS1-1
Column name in count.annot.xlsx:sh-LIS1-1


title: SCC25,NC-3

description:
Library name: control-3
Column name in count.annot.xlsx:control-3

value: Control


title: B3


title: W11


title: W16


title: SCC25,NC-1

description:
Library name: control-1
Column name in count.annot.xlsx:control-1


title: W7


title: W12


title: W35

data_processing: genes.results Hg38 genome build was used.

extract_protocol:
For RNA sequencing, total RNA was extracted with TRI Reagent (Sigma, Cat# T9424). DNA was removed by using a RNeasy MinElute Cleanup Kit (QIAGEN) with RNase-Free DNase Set (QIAGEN).
RNA-seq Libraries were prepared with a NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs Inc., Ipswich, MA) as described in the manufacturer’s protocol. RNA was extracted with QIAGEN RNeasy RNA isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: facility

value: NU

tag: patient race_(phenotype)

tag: disease

value: HGSOC


title: W34

tag: batch


title: W33


title: W31


title: SCC25,NC-2

description:
Library name: control-2
Column name in count.annot.xlsx:control-2

tag: cell line

tag: cell type


title: B33


title: W32


title: W13


title: B9


title: B36


title: B31


title: B35


title: B32


title: B34


title: W9


title: W7


title: W10


title: W5


title: B7


title: W6


title: B2


title: W8


title: W4


title: W26


title: W3


title: W3


title: W1


title: W24


title: W25


title: W23


title: W22


title: W20


title: W2


title: W19


title: W18


title: W21


title: B10

value: UC


title: W8


title: W16


title: W17


title: W14


title: W15


title: W1


title: W4


title: W13


title: B7


title: B4


title: B1


title: B29

value: USI


title: B9


title: W10


title: B30


title: B3


title: W11


title: B6


title: B25


title: B8


title: B24


title: W2


title: B5


title: B28

value: IU


title: B23


title: B21


title: B22


title: B20


title: B26


title: B2


title: B18


title: B17


title: B19


title: B16


title: B15


title: B11


title: No-TBI biological replicate 3, scRNAseq

status: Public on Dec 02 2024

city: Milwaukee

first: Ankan

last: Gupta

state: WI

address: 8701 W Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: h5 files contain filtered gene count matrices

source_name: Brain

extract_protocol:
Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer’s recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation.
Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X.  Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method.

value: 14 week

value: Male

value: Brain

tag: num cells_called

tag: genotype

tag: treatment

value: No injury control

tag: time

value: No-TBI


title: B13

tag: tissue

value: Biopsy-derived tumor sample


title: No-TBI biological replicate 4, scRNAseq

tag: age

tag: Sex


title: B1

value: Black


title: Post-TBI day 7 biological replicate 4, scRNAseq

value: Closed skull cortical impact


title: B12


title: No-TBI biological replicate 2, scRNAseq


title: Post-TBI day 28 biological replicate 4, scRNAseq


title: Post-TBI day 1 biological replicate 4, scRNAseq


title: Post-TBI day 28 biological replicate 3, scRNAseq


title: Post-TBI day 28 biological replicate 2, scRNAseq


title: Post-TBI day 1 biological replicate 2, scRNAseq


title: Post-TBI day 7 biological replicate 2, scRNAseq


title: B27


title: Post-TBI day 1 biological replicate 1, scRNAseq


title: neonatal Wistar rats treated with vehicle (PBS): DRG's were isolated 16 days post-treatment: Rat2

status: Public on Nov 25 2024

city: Nottingham

first: Mark

middle: John

last: Paul-Clark

state: Nottinghamshire

address: Clifton Campus

department: Bioscience

country: United Kingdom

institute: Nottingham Trent University

description:
PBS model control
Veh2

data_processing:
Mapping_hisat2_2.0.5_Default
Assembly_Stringtie_1.3.3b_Default
Quantification_featureCounts_1.5.0-p3_Default
Differential Analysis_DESeq2_1.20.0_log2(FoldChange)| >= 1 & padj <= 0.05_edgeR_3.22.5_log2(FoldChange)| >= 1 & padj <= 0.05
Enrichment Analysis_clusterProfiler_3.8.1_padj < 0.05
Enrichment Analysis_clusterProfiler_3.8.1_padj < 0.05
GSEA Analysis_gsea_v3.0_Default
Protein-Protein Interaction Analysis_diamond_0.9.14_e-value = 1e-10
Alternative splicing_rMATS_4.1.0_Default
Alternati"SNP/InDel Analysis_GATK 4.1.4.1_MQ < 40.0 and QD < 2.0 and FS > 30.0 and DP < 10 and QUAL < 20_snpEff_4.3q_Default"ve splicing_rMATS_4.1.0_Default
Assembly: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file includes FPKM cvalues for each sample

organism: Rattus norvegicus

source_name: dorsal root ganglia

growth_protocol: All experimental studies involving animals were performed following consultation with local Animal Welfare and Ethics Review Board at Nottingham Trent University and in accordance with UK Home Office animals (Scientific procedures) Act 1986 and ARRIVE guidelines. Animals hadad libitum access to standard chow and were housed under 12:12h light:dark conditions.

extract_protocol:
RNA was isloated using RNA mini plus kit (Qiagen). 1.3 ug of total RNA was used for the contruction of sequence libraries
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: 2 neonatal Wistar rats treated with vehicle (PBS) and 2 neonatal Wistar rats treated with cisplatin (Sigma-Aldrich; 0.3mg/kg). DRG's were isolated 16 days post-treatment.

value: dorsal root ganglia

value: tissue

value: control

value: WT

value: vehicle


title: B14

value: HGSOC


title: Post-TBI day 7 biological replicate 1, scRNAseq


title: Post-TBI day 1 biological replicate 3, scRNAseq


title: No-TBI biological replicate 1, scRNAseq


title: neonatal Wistar rats treated with vehicle (PBS): DRG's were isolated 16 days post-treatment: Rat1

description:
PBS model control
Veh1


title: neonatal Wistar rats treated with cisplatin (Sigma-Aldrich; 0.3mg/kg): DRG's were isolated 16 days post-treatment: Rat1

description:
cisplatin-induced neonatal CIPN
Cis4

value: disease state

value: cisplatin


title: Post-TBI day 28 biological replicate 1, scRNAseq


title: neonatal Wistar rats treated with cisplatin (Sigma-Aldrich; 0.3mg/kg): DRG's were isolated 16 days post-treatment: Rat2

description:
cisplatin-induced neonatal CIPN
Cis6


title: Post-TBI day 7 biological replicate 3, scRNAseq


title: IPIKID126.T1.rna.tcell

status: Public on Nov 08 2024

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

data_processing:
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Assembly: GRCh38
Supplementary files format and content: FASTQ files

source_name: Primary tumor

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified
The dsDNA went through tagmentation, amplification and clean up with  AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem

value: Primary tumor


title: IPIKID127.T1.rna.tcell


title: IPIKID123.T1.rna.tcell


title: IPIKID125.T1.rna.tcell


title: IPIKID116.T1.rna.tcell


title: IPIKID119.T1.rna.tcell


title: IPIKID115.T1.rna.tcell


title: IPIKID114.T1.rna.tcell


title: IPIKID046.T1.rna.tcell


title: IPIKID128.T1.rna.tcell


title: IPIHNSC091.T1.rna.tcell


title: IPIHNSC090.T1.rna.tcell


title: IPIHNSC081.T1.rna.tcell


title: IPIGYN145.T1.rna.tcell


title: IPIHNSC095.T1.rna.tcell


title: IPIHNSC080.T1.rna.tcell


title: IPIGYN148.T1.rna.tcell


title: IPIGYN137.T1.rna.tcell


title: IPIGYN140.T1.rna.tcell


title: IPIGYN136.T1.rna.tcell


title: IPIHNSC066.T1.rna.tcell


title: IPIGYN134.T1.rna.tcell


title: IPIHNSC097.T1.rna.tcell


title: IPIGYN130.T1.rna.tcell


title: IPIGYN133.T1.rna.tcell


title: IPIGYN126.T1.rna.tcell


title: IPIGYN129.T1.rna.tcell


title: IPIGYN123.T1.rna.tcell


title: IPIGYN131.T1.rna.tcell


title: IPIGYN121.T1.rna.tcell


title: IPIGYN120.T1.rna.tcell


title: IPIKID081.T1.rna.tcell


title: IPIGYN152.T1.rna.tcell


title: IPIGYN111.T1.rna.tcell


title: IPIGYN073.T1.rna.tcell


title: IPIGYN055.T1.rna.tcell


title: IPIGYN056.T1.rna.tcell


title: IPIHNSC088.T1.rna.tcell


title: IPICRC111.T1.rna.tcell


title: IPIGYN065.T1.rna.tcell


title: IPIGYN062.T1.rna.tcell


title: IPICRC125.T1.rna.tcell


title: IPIGYN024.T1.rna.tcell


title: IPIGYN038.T1.rna.tcell


title: IPIGYN142.T1.rna.tcell


title: IPICRC105.T1.rna.tcell


title: IPICRC106.T1.rna.tcell


title: IPIGYN090.T1.rna.tcell


title: IPICRC101.T1.rna.tcell


title: IPICRC117.T1.rna.tcell


title: IPIGYN036.T1.rna.tcell


title: IPICRC099.T1.rna.tcell


title: IPICRC103.T1.rna.tcell


title: IPICRC096.T1.rna.tcell


title: IPIGYN114.T1.rna.tcell


title: IPILUNG088.T1.rna.tcell


title: IPILUNG087.T1.rna.tcell


title: IPILUNG057.T1.rna.tcell


title: IPIKID101.T1.rna.tcell


title: IPILUNG024.T1.rna.tcell


title: IPIGYN112.T1.rna.tcell


title: IPIKID059.T1.rna.tcell


title: IPIKID073.T1.rna.tcell


title: IPIKID029.T1.rna.tcell


title: IPIKID054.T1.rna.tcell


title: IPIHNSC076.T1.rna.tcell


title: IPIKID032.T1.rna.tcell


title: IPIGYN100.T1.rna.tcell


title: IPIGYN032.T1.rna.tcell


title: IPIHNSC072.T1.rna.tcell


title: IPIKID025.T1.rna.tcell


title: Lung, BLM, CreERT2, biol rep2

status: Public on Nov 01 2024

city: Logroño

first: Jose

middle: Garcia

last: pichel

state: La Rioja

address: Piqueras 98

department: Oncology

institute: FUNDACIÓN RIOJA SALUD - CIBIR

data_processing:
The quality of RNA-seq reads was assessed using FastQC.
Raw reads were trimmed, filtered with a Phred quality score of at least 25 and all adapters removed with Trimmomatic software.
Clean reads were aligned to the Mus musculus GRCm38.p6 reference genome by using HiSat2 with default parameters.
Resulting alignment files were quality-assessed with Qualimap2 and sorted and indexed with Samtools.
Reads on gene features were counted with FeatureCounts.
Assembly: GRCm38.p6
Supplementary files format and content: For each sample, a tab-delimited .txt file which contains raw counts on gene features is provided (Ensembl gene Ids).

source_name: Lung

growth_protocol: Mice were bred and maintained under specific pathogen-free (SPF) conditions in laminar flow caging at the CIBIR animal facility. UBC-CreERT2; Igf1rfl/fl mice were crossed with Igf1rfl/fl mice to directly generate descendants in equal proportions in the same litter.

extract_protocol:
Inferior right lung lobes were homogenized in 1 mL of Trizol (Invitrogen) and total RNA was isolated with a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared by following the TruSeq Stranded mRNA Library Preparation Kit (Illumina Inc.) from 1 μg of total RNA.

treatment_protocol:
Tamoxifen was daily administered for five consecutive days to four-week-old mice of both genotypes to induce a postnatal Igf1r gene conditional deletion in UBC-CreERT2; Igf1rfl/fl, thus generating Igf1r-deficient mice (CreERT2 mutants).
Six-week-old Igf1rfl/fl (control) and CreERT2 (IGF1R-deficient) female mice were intra-tracheally instilled with either a single dose of 2.5 µL/g body weight of BLM sulfate (5 U/kg) (EMD Millipore) in saline (SAL) (2 U/mL) or SAL alone. 3 days later, mice were eutanized and lungs dissected and stored for subsequent analyses.

value: Lung

value: Bleomycin


title: IPIGYN066.T1.rna.tcell


title: IPIHNSC017.T1.rna.tcell


title: Lung, BLM, CreERT2, biol rep1


title: IPIGYN012.T1.rna.tcell


title: IPIKID111.T1.rna.tcell


title: IPIGYN030.T1.rna.tcell


title: IPIGYN072.T1.rna.tcell


title: Lung, BLM, Igf1rfl/fl, biol rep2


title: IPICRC032.T1.rna.tcell


title: Lung, BLM, Igf1rfl/fl, biol rep1


title: IPICRC003.T1.rna.tcell


title: Lung, SAL, CreERT2, biol rep3

value: Saline


title: IPIHNSC005.T1.rna.tcell


title: IPIGYN096.T1.rna.tcell


title: IPICRC053.T1.rna.tcell


title: IPICRC093.T1.rna.tcell


title: Lung, BLM, Igf1rfl/fl, biol rep3


title: Lung, SAL, CreERT2, biol rep2


title: Lung, SAL, CreERT2, biol rep1


title: Lung, BLM, CreERT2, biol rep3


title: Lung, SAL, Igf1rfl/fl, biol rep3


title: Lung, SAL, Igf1rfl/fl, biol rep1


title: Lung, SAL, Igf1rfl/fl, biol rep2


title: S115_RNA

status: Public on Oct 16 2024

city: Oxford

first: Julian

last: Knight

address: Roosevelt Drive, Headington

department: Wellcome Centre for Human Genetics

institute: University of Oxford

description: mRNA

data_processing:
Gene expression data were aligned using STARsolo (v2.7.9a) (GRCh38) and spliced and unspliced counts produced. Unfiltered files were used for cell calling (emptyDrops function, DropletUtils (v1.10.3)) with a UMI threshold of 100 and FDR of 0.5%.
Abseq reads were trimmed with Trimmomatic (v0.39) to the 12bp UMI + 36bp Abseq nucleotide sequence and aligned to an artificial reference of the Abseq nucleotide sequences using STARsolo.  http://abseq-ref-gen.genomics.bd.com/
Cells expressing <100 or >4000 genes, >10% mitochondrial reads, >2% hemoglobin reads or a log10(UMI/gene) <0.6 were removed. Genes expressed in <10 cells or with a total count <3 were removed. Scrublet (v.0.2.3) and doublet detect (v3.0) were both used on default settings to remove doublets with automatic thresholds
Data were log normalized and 4000 highly variable genes (HVGs) identified using the Seurat vst algorithm (scanpy v1.7.2). Multi-modal dimensionality reduction was performed with TotalVI (scvi-tools v0.10.0) on default settings with all 30 proteins and HVGs with each individual sample set as a batch (as all samples were processed separately).
Unsupervised clustering was performed on the 20 TotalVI latent dimensions (Seurat FindNeighbors (k=30) and FindClusters (smart local moving algorithm)). Clustering resolution was evaluated by cluster neighborhood purity, cluster average silhouette width and a 30 iteration bootstrap to determine cluster stability with respect to sampling noise (bluster v1.0). Additionally, we inspected top markers per cluster to match with known biology and understand potential value in merging vs. splitting clusters. Combining these elements, the default clustering resolution 0.8 was chosen, with one immature neutrophil cluster split into two (MPO+ immature neutrophils/progenitors and PADI4+ immature neutrophils) based on resolution 1.1
Assembly: GRCh38
Supplementary files format and content: Seurat object with count matrix and metadata

source_name: Whole blood

extract_protocol:
Whole blood red blood cell lysis
BD Rhapsody whole transcriptome amplicification + Abseq

value: Whole blood

value: Total leukocytes

tag: disease state

value: Sepsis acute


title: CS14_RNA

description: mRNA

value: Post cardiac surgery


title: S094_CONV_PRO

description: Abseq

data_processing:
Gene expression data were aligned using STARsolo (v2.7.9a) (GRCh38) and spliced and unspliced counts produced. Unfiltered files were used for cell calling (emptyDrops function, DropletUtils (v1.10.3)) with a UMI threshold of 100 and FDR of 0.5%.
Abseq reads were trimmed with Trimmomatic (v0.39) to the 12bp UMI + 36bp Abseq nucleotide sequence and aligned to an artificial reference of the Abseq nucleotide sequences using STARsolo.  http://abseq-ref-gen.genomics.bd.com/
Cells expressing <100 or >4000 genes, >10% mitochondrial reads, >2% hemoglobin reads or a log10(UMI/gene) <0.6 were removed. Genes expressed in <10 cells or with a total count <3 were removed. Scrublet (v.0.2.3) and doublet detect (v3.0) were both used on default settings to remove doublets with automatic thresholds
Data were log normalized and 4000 highly variable genes (HVGs) identified using the Seurat vst algorithm (scanpy v1.7.2). Multi-modal dimensionality reduction was performed with TotalVI (scvi-tools v0.10.0) on default settings with all 30 proteins and HVGs with each individual sample set as a batch (as all samples were processed separately).
Unsupervised clustering was performed on the 20 TotalVI latent dimensions (Seurat FindNeighbors (k=30) and FindClusters (smart local moving algorithm)). Clustering resolution was evaluated by cluster neighborhood purity, cluster average silhouette width and a 30 iteration bootstrap to determine cluster stability with respect to sampling noise (bluster v1.0). Additionally, we inspected top markers per cluster to match with known biology and understand potential value in merging vs. splitting clusters. Combining these elements, the default clustering resolution 0.8 was chosen, with one immature neutrophil cluster split into two (MPO+ immature neutrophils/progenitors and PADI4+ immature neutrophils) based on resolution 1.1
Assembly: GRCh38
Supplementary files format and content: Seurat object with count matrix and metadata
Library strategy: Ab-seq

molecule: protein

value: Sepsis convalescent


title: S117_PRO

description: Abseq


title: S113_PRO

description: Abseq


title: S119_PRO

description: Abseq


title: HV69_PRO

description: Abseq

value: Healthy


title: S119_RNA

description: mRNA


title: S090_CONV_PRO

description: Abseq


title: S090_CONV_RNA

description: mRNA


title: HV69_RNA

description: mRNA


title: S115_PRO

description: Abseq


title: S082_RNA

description: mRNA


title: CS11_RNA

description: mRNA


title: S105_RNA

description: mRNA


title: S113_RNA

description: mRNA


title: HV68_RNA

description: mRNA


title: CS14_PRO

description: Abseq


title: S094_CONV_RNA

description: mRNA


title: S105_PRO

description: Abseq


title: S098_CONV_PRO

description: Abseq


title: S107_PRO

description: Abseq


title: CS11_PRO

description: Abseq


title: S109_PRO

description: Abseq


title: HV68_PRO

description: Abseq


title: S095_CONV_PRO

description: Abseq


title: S117_RNA

description: mRNA


title: S098_CONV_RNA

description: mRNA


title: S095_CONV_RNA

description: mRNA


title: S082_PRO

description: Abseq


title: S107_RNA

description: mRNA


title: S109_RNA

description: mRNA


title: S104_CONV_PRO

description: Abseq


title: CS08_RNA

description: mRNA


title: S099_PRO

description: Abseq


title: HV78_RNA

description: mRNA


title: S066_CONV_PRO

description: Abseq


title: S066_PRO

description: Abseq


title: S099_CONV_PRO

description: Abseq


title: S104_CONV_RNA

description: mRNA


title: CS08_PRO

description: Abseq


title: S099_RNA

description: mRNA


title: CS03_RNA

description: mRNA


title: S104_RNA

description: mRNA


title: S066_RNA

description: mRNA


title: S099_CONV_RNA

description: mRNA


title: HV78_PRO

description: Abseq


title: S091_CONV_PRO

description: Abseq


title: S089_CONV_PRO

description: Abseq


title: HV58_RNA

description: mRNA


title: S101_RNA

description: mRNA


title: S103_PRO

description: Abseq


title: HV58_PRO

description: Abseq


title: S102_PRO

description: Abseq


title: S066_CONV_RNA

description: mRNA


title: S101_PRO

description: Abseq


title: CS05_PRO

description: Abseq


title: S091_CONV_RNA

description: mRNA


title: S104_PRO

description: Abseq


title: S103_RNA

description: mRNA


title: CS05_RNA

description: mRNA


title: S076_RNA

description: mRNA


title: S098_PRO

description: Abseq


title: S094_PRO

description: Abseq


title: CS02_RNA

description: mRNA


title: S090_PRO

description: Abseq


title: CS03_PRO

description: Abseq


title: S076_PRO

description: Abseq


title: HV96_RNA

description: mRNA


title: HV96_PRO

description: Abseq


title: S078_RNA

description: mRNA


title: CS02_PRO

description: Abseq


title: S089_RNA

description: mRNA


title: S094_RNA

description: mRNA


title: S080_RNA

description: mRNA


title: S089_CONV_RNA

description: mRNA


title: S090_RNA

description: mRNA


title: CS01_RNA

description: mRNA


title: S097_PRO

description: Abseq


title: S096_PRO

description: Abseq


title: HV89_RNA

description: mRNA


title: S102_RNA

description: mRNA


title: S098_RNA

description: mRNA


title: S095_PRO

description: Abseq


title: S072_RNA

description: mRNA


title: S080_PRO

description: Abseq


title: S089_PRO

description: Abseq


title: S072_PRO

description: Abseq


title: S078_PRO

description: Abseq


title: CS01_PRO

description: Abseq


title: HV89_PRO

description: Abseq


title: S097_RNA

description: mRNA


title: S091_RNA

description: mRNA


title: gPlexD_RNA

description:
Sample represents both sepsis patients and healthy controls.
gex_obj.rds

data_processing:
Raw FASTQ files of scRNA-seq and scATAC-seq were aligned to the GRCh38 reference genome using 10X-arc (v2). Genetic demultiplexing and doublet removal was performed for each batch with vireo. HSPC multi-omic data were input into ArchR (v1.0.2) with mintss=4 and minFrags=1000. Homotypic doublets were removed (removeDoublet)
Cells expressing <100 or >6000 genes, >25000 UMIs or with a log10(UMI/gene) <0.8 were removed. Cells with TSS enrichment < 7 and <1000 unique fragments were also filtered out. Genes expressed in <10 cells or <3 in total count were removed.
We assigned identity of HSPCs and contaminating cells by mapping our scRNA-seq data to two healthy donor reference bone marrow mononuclear cell scRNA-seq datasets from Hao et al (2021) (reference datasets 1, supervised PCA) and Granja et al (2019) (reference dataset 2, PCA) with Seurat (v4.0). Cells with non-HSPC labels from either mapping were filtered out.
Multi-modal dimensionality reduction for HSPCs was performed (iterativeLSI) for scRNA (gene expression matrix) and scATAC (tile matrix). Both modalities were batch corrected  (Harmony) and combined (addCombinedDims) before clustering on the combined dimensions. HSPC identity was finalized by assigning the majority RNA mapping identity from reference dataset 1 per cluster.
Each individual sample was pseudobulked for peak calling with MACS2 and iterative peak overlapping removal within ArchR . We re-performed dimensionality reduction and batch correction on the gene expression and peak matrices before reclustering HSCs on combined dimensions.
Assembly: GRCh38
Supplementary files format and content: RNA count matrix (single cell experiment object)
Supplementary files format and content: ATAC peak matrix (single cell experiment object)

molecule: nuclear RNA

source_name: PBMC

extract_protocol:
PBMCs were isolated from patients and healthy volunteers by Ficoll density gradient centrifugation. Cells were cropreserved in 10% DMSO + 90% FCS and thawed for use on the day of the experiment. Cells were enriched for CD34+ via MACS twice, before being FACS sorted for CD34+CD45+ live singlets, and then nuclei were isolated for 10X multiome
10X multiome protocol
scRNA-seq + scATAC-seq

value: PBMC

value: Hematopoietic stem and progenitor cells

value: sepsis patients and healthy volunteers


title: gPlexE_RNA


title: gPlexC_ATAC

description:
Sample represents both sepsis patients and healthy controls.
peak_obj.rds


title: S095_RNA

description: mRNA


title: gPlexC_RNA


title: E16.R1.5.AI: Endometrium_IVD Conceptus Co-Culture_Rep 10

status: Public on Jun 30 2024

city: Knoxville

last: Mathew

state: TN

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

data_processing:
The RNA-Seg raw sequences (fastq) underwent adaptor removal and quality trimming using Trimmomatic and quality reads were aligned to the bovine reference genome (ARS-UCD1.2.103) using the STAR aligner program for the endometrial sequences and Hisat2 mapper program for conceptus sequences (Dobin et al., 2013; Kim et al., 2015). The sorted binary alignment maps and the NCBI gene annotation assembly were subjected to FeatureCounts to quantify read counts of genes for each sample (Liao et al., 2014).
Assembly: ARS-UCD1.2.103
Supplementary files format and content: Gene FeatureCounts in Excel

organism: Bos taurus

source_name: Intercaruncle Endometrium

extract_protocol:
Endometrial total RNA was extracted and analyzed using RNA-Sequencing (RNA-Seq). Endometrial total RNA extraction was achieved using 5 mm stainless steel beads (Qiagen) and a bead mill homogenizer (Bead Mill 4; ThermoFisher) and Trizol (Invitrogen) in combination with an on-column method (RNeasy Mini Kit; Qiagen) involving a DNase step as previously described by Mathew et al. 2019. The resulting RNA quality and quantity were assessed using the 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 (NanoDrop Technologies), respectively. Endometrial RNA integrity numbers (RIN) ranged from 5.2 – 9.3 and total endometrial RNA was analyzed using RNA-Sequencing (RNA-Seq) for the following culture tissues: 1) Endo (n=13; mono-culture); and 2) Endo-Conceptus Endo (n=15; co-culture). Conceptus RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) with the optional on-column DNase digestion step according to the manufacturer’s recommendations. The RNA quantity and quality were assayed using a NanoDrop 1000 and RNA Screen Tape (Agilent Technologies). The conceptus RIN ranged from 7.5 – 10. Conceptus section total RNA was assayed using RNA-Seq for the following culture tissues: Conceptus (n=8; mono-culture) and Endo-Conceptus Conceptus (n=9; co-culture).
Library preparation including poly (A) enrichment and RNA-Seq of the explant and conceptus total RNA was performed by the University of Missouri DNA Core facility (Columbia, MO). The cDNA libraries were prepared using the Stranded RNA Prep Ligation Kit (Illumina) as described by the manufacturer. The final amplified cDNA constructs were purified by addition of Axyprep Mag PCR Clean-up beads (Corning) and the final construct of each purified library was evaluated using a Fragment Analyzer automated electrophoresis system (Agilent), quantified using the Invitrogen Qubit HS dsDNA assay kit and Qubit fluorometer, and diluted according to Illumina’s standard protocol for sequencing on the NovaSeq 6000 (Illumina).

value: Intercaruncle Endometrium

value: Female

value: RPMI Medium + IVD Conceptus


title: E14.R1.8.AI: Endometrium_IVD Conceptus Co-Culture_Rep 6


title: gPlexA_RNA


title: E14.T1.26.AI: Endometrium_IVD Conceptus Co-Culture_Rep 7


title: gPlexB_ATAC


title: E69.R1.71.AI: Endometrium_IVD Conceptus Co-Culture_Rep 12


title: E56.R1.5.AI: Endometrium_IVD Conceptus Co-Culture_Rep 11


title: S096_RNA

description: mRNA


title: gPlexA_ATAC


title: gPlexE_ATAC


title: E39.R1.8.AI: Endometrium_IVD Conceptus Co-Culture_Rep 8


title: E38.R1.50.AI: Endometrium_IVD Conceptus Co-Culture_Rep 14


title: E19.R1.22.AI: Endometrium_IVD Conceptus Co-Culture_Rep 3


title: E38.T1.66.AI: Endometrium_IVD Conceptus Co-Culture_Rep 15


title: E70.R1.71.AI: Endometrium_IVD Conceptus Co-Culture_Rep 13


title: gPlexB_RNA


title: E19.T1.47.AI: Endometrium_IVD Conceptus Co-Culture_Rep 4


title: S091_PRO

description: Abseq


title: E39.T1.26.AI: Endometrium_IVD Conceptus Co-Culture_Rep 9


title: gPlexD_ATAC


title: E54.T1.47.AI: Endometrium_IVD Conceptus Co-Culture_Rep 5


title: E53.R2.10.AI: Endometrium_IVD Conceptus Co-Culture_Rep 2


title: E45.R2.10.AI: Endometrium_IVD Conceptus Co-Culture_Rep 1


title: E38.P1: Endometrium_Mono-Culture_Rep 13

value: RPMI Medium


title: E69.P1: Endometrium_Mono-Culture_Rep 11


title: E56.P1: Endometrium_Mono-Culture_Rep 10


title: E16.P1: Endometrium_Mono-Culture_Rep 9


title: E45.P2: Endometrium_Mono-Culture_Rep 3


title: E53.P2: Endometrium_Mono-Culture_Rep 4


title: E15.P1: Endometrium_Mono-Culture_Rep 1


title: E19.P1: Endometrium_Mono-Culture_Rep 5


title: E14.P1: Endometrium_Mono-Culture_Rep 7


title: E54.P1: Endometrium_Mono-Culture_Rep 6


title: Healthy_H_4982

status: Public on Jun 25 2024

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
The Seurat R software package (version 3.0) in R (version 3.6.2) was utilized for analysis of scRNA seq-data. Cells with nCount_RNA > 50000, nFeature > 1500, and External RNA Control Consortium (ERCC) RNA Spike-In < 15% were included in the analysis. Normalized datasets were integrated, scaled, followed by principal component analysis. Two-dimensional map coordinates were generated using the ‘RunUMAP’ procedure. Cluster analysis was performed using the ‘FindNeighbors’ and ‘FindClusters’ functions. Marker genes for clusters were identified using the ‘FindMarkers’ function. The Wilcoxon rank-sum test was used to identify differentially expressed genes (DEGs) among clusters to define cell states and was then repeated for each resultant cell type to further characterize subpopulations. The online tool EnrichR was used to perform Gene Ontology (GO) Biological Processes (BP) analysis on the significantly DEGs extracted from different pairs of comparision21. CIM-seq analysis22, an unsupervised method to analyze direct physical cell–cell interactions, was performed on RNAseq data from identified doublets/multiplets with FSC-W values exceeding 300.
Assembly: hg38
Supplementary files format and content: count matrix

source_name: Skin

extract_protocol:
Four-mm full-depth punch biopsies were obtained from lesional and non-lesional skin of five untreated psoriasis patients and three sex- and age-matched healthy donors. Skin biopsies were enzymatically digested with dispase (5 U/ML, Gibco) overnight to separate the epidermis from the dermis, followed by dissociation of the epidermis to single cells using a protocol optimized to achieve partial dissociation (0.5 % trypsin, 1 U ul−1 DNase, Gibco) for 7 min at 37 °C to obtain both single cells and multiplets. In the single-cell suspensions, cells were counted and diluted to 1 × 106 cells per 100 ul with ice-cold FACS buffer, followed by incubation with dye-conjugated antibodies, including anti-CD45 (APC, eBioscience). After sorting into 384-well plates with hypotonic lysis buffer using a SONY SH800S sorter, both CD45-positive and CD45-negative cells were sorted, excluding dead/dying cells, and stored at -80 °C.
cDNA synthesis was based on the Smart-seq2 protocol as implemented in (Andrews et al. Nat. Meth. 2021). In summary, single-cell lysates were thawed on ice in 384-well plates, followed by primer annealing at 72°C for 3 minutes. Subsequently, a reverse transcription (RT) mix of 3 ul was added (0.05 ul of Maxima H Minus Reverse Transcriptase [Thermo Scientific, EP0751], 0.125 ul of Recombinant RNase Inhibitor [Takara Bio, 2313B], 1 ul of 5x First strand buffer, 0.25 ul of 100mM DTT [Thermo Fisher 707265ML], 1 ul of 5M Betaine [Sigma-Aldrich, B0300-5VL], 0.03 ul of 1M MgCl2, 0.05 ul of 100uM TSO [IDT 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′], and 0.495 ul of H2O). The RT reaction was 42°C for 90 minutes, followed by 70°C for 5 minutes and a 4°C hold. Next, 7.5 ul of cDNA pre-amplification mix was added, consisting of 1.068 ul of H2O, 6.25 ul of 2X Kapa HiFi HotStart ReadyMix (Roche 07958927001), 0.125 ul of 10 uM IS_PCR primer (IDT 5′-AAGCAGTGGTATCAACGCAGAGT-3′), and 0.056 ul of Lambda Exonuclease (ThermoFisher EN0561). The PCR program was 37°C for 30 minutes, 95°C for 3 minutes, followed by [98°C for 20 seconds, 67°C for 15 seconds, 72°C for 4 minutes] repeated for 21 cycles, and a final step of 72°C for 5 minutes, with a 4°C hold. Post-PCR, cDNA clean-up was performed using 0.7X volume SPRI beads and a magnetic 384-well rack. For tagmentation, 1 ul of diluted cDNA (150 pg/ul) was mixed with 1.5 ul of tagmentation buffer (0.5 ul TAP-PEG buffer [50mM TAPS, 25mM MgCl2, 40% PEG 8k) with 0.75 ul H2O)] and 0.25 ul of Tn5 (Vasilios 2020), followed by incubation at 55°C for 10 minutes. Upon completion, Tn5 was inactivated by adding 1 ul of 0.1% SDS (Teknova S0287). Barcoding PCR was performed on the same plate by adding 19.5 ul of PCR mix (Roche7958846001, 13.25 ul of H2O, 5 ul of 5X buffer, 0.75 ul of dNTPs, and 0.5 ul of KAPA HiFi DNA Polymerase) and 2 ul of primers. The total volume of 25 ul underwent the following PCR cycling: 72°C for 3 minutes, 95°C for 30 seconds, [95°C for 15 seconds, 55°C for 30 seconds, 72°C for 45 seconds] repeated for 12 cycles, and a 10°C hold. Finally, 2 ul per well was pooled and subjected to SPRI bead clean-up at 0.9X volume twice. The finished libraries were sequenced on an Illumina NextSeq 550 sequence paired-end 37bp with 8bp dual index.

value: Skin

tag: ncount rna

tag: nfeature rna

tag: donor

tag: diagnosis

tag: region

value: H

tag: class

value: singlet

tag: seurat clusters

tag: celltype

value: Suprabasal keratinocytes I


title: Healthy_H_4984

value: Mitotic keratinocytes


title: Healthy_H_4981


title: Healthy_H_4980

value: Basal keratinocytes II


title: Healthy_H_4983

value: Transition keratinocytes


title: Healthy_H_4978

value: Basal keratinocytes III


title: Healthy_H_4985


title: Healthy_H_4979

value: Melanocytes


title: Healthy_H_4988

value: Healthy


title: Healthy_H_4986


title: Healthy_H_4987


title: Healthy_H_4977


title: Healthy_H_4974


title: Healthy_H_4973


title: Healthy_H_4972


title: Healthy_H_4975

value: Basal keratinocytes I


title: Healthy_H_4976


title: E70.P1: Endometrium_Mono-Culture_Rep 12


title: Healthy_H_4971


title: E39.P1: Endometrium_Mono-Culture_Rep 8


title: E17.P1: Endometrium_Mono-Culture_Rep 2


title: Healthy_H_4970


title: Healthy_H_4969


title: Healthy_H_4968


title: Healthy_H_4965

value: Suprabasal keratinocytes II


title: Healthy_H_4966


title: Healthy_H_4967


title: Healthy_H_4964


title: Healthy_H_4960


title: Healthy_H_4952


title: Healthy_H_4953


title: Healthy_H_4958


title: Healthy_H_4961


title: Healthy_H_4956


title: Healthy_H_4962


title: Healthy_H_4955


title: Healthy_H_4949

value: Activated Transition keratinocytes


title: Healthy_H_4950


title: Healthy_H_4947


title: Healthy_H_4957


title: Healthy_H_4948


title: Healthy_H_4946


title: Healthy_H_4945

value: Progenitor keratinocytes


title: Healthy_H_4954


title: Healthy_H_4943


title: Healthy_H_4942


title: Healthy_H_4944


title: Healthy_H_4959


title: Healthy_H_4951


title: Healthy_H_4939


title: Healthy_H_4940


title: Healthy_H_4941


title: Healthy_H_4963


title: Healthy_H_4938


title: Healthy_H_4937


title: Healthy_H_4936


title: Healthy_H_4935


title: Healthy_H_4932


title: Healthy_H_4933


title: Healthy_H_4934


title: Healthy_H_4929


title: Healthy_H_4928


title: Healthy_H_4930


title: Healthy_H_4927


title: Healthy_H_4931


title: Healthy_H_4921


title: Healthy_H_4924


title: Healthy_H_4920


title: Healthy_H_4919


title: Healthy_H_4925


title: Healthy_H_4923


title: Healthy_H_4918


title: Healthy_H_4922


title: Healthy_H_4915


title: Healthy_H_4916


title: Healthy_H_4910


title: Healthy_H_4912


title: Healthy_H_4914


title: Healthy_H_4909


title: Healthy_H_4907


title: Healthy_H_4906


title: Healthy_H_4904


title: Healthy_H_4926


title: Healthy_H_4908


title: Healthy_H_4901


title: Healthy_H_4899


title: Healthy_H_4900


title: Healthy_H_4898


title: Healthy_H_4902


title: Healthy_H_4896


title: Healthy_H_4894


title: Healthy_H_4891


title: Healthy_H_4893


title: Healthy_H_4897


title: Healthy_H_4905

value: Channel keratinocytes


title: Healthy_H_4895


title: Healthy_H_4892


title: Healthy_H_4911


title: Healthy_H_4913


title: Healthy_H_4889


title: Healthy_H_4890


title: Healthy_H_4888


title: Healthy_H_4887


title: Healthy_H_4885


title: Healthy_H_4884


title: Healthy_H_4886


title: Healthy_H_4903


title: Healthy_H_4883


title: Healthy_H_4882


title: Healthy_H_4881


title: Healthy_H_4917


title: Healthy_H_4880


title: Healthy_H_4879


title: Healthy_H_4878


title: Healthy_H_4877


title: Healthy_H_4875


title: Healthy_H_4876


title: Healthy_H_4874


title: Healthy_H_4873


title: Healthy_H_4871


title: Healthy_H_4872


title: Healthy_H_4869


title: Healthy_H_4866


title: Healthy_H_4865


title: Healthy_H_4868


title: Healthy_H_4861


title: Healthy_H_4863


title: Healthy_H_4862


title: Healthy_H_4860


title: Healthy_H_4864


title: Healthy_H_4858


title: Healthy_H_4857


title: Healthy_H_4859


title: Healthy_H_4856


title: Healthy_H_4855


title: Healthy_H_4854


title: Healthy_H_4853


title: Healthy_H_4849


title: Healthy_H_4870


title: Healthy_H_4848


title: Healthy_H_4847


title: Healthy_H_4867


title: Healthy_H_4850


title: Healthy_H_4851


title: Healthy_H_4845


title: Healthy_H_4844


title: Healthy_H_4840


title: Healthy_H_4841


title: Healthy_H_4843


title: Healthy_H_4842


title: Healthy_H_4839


title: Healthy_H_4837


title: Healthy_H_4834


title: Healthy_H_4833


title: Healthy_H_4838


title: Healthy_H_4831


title: Healthy_H_4835


title: Healthy_H_4836


title: Healthy_H_4832


title: Healthy_H_4830


title: Healthy_H_4829


title: Healthy_H_4828


title: Healthy_H_4826


title: Healthy_H_4852


title: Healthy_H_4827


title: Healthy_H_4846


title: Healthy_H_4824


title: Healthy_H_4821


title: Healthy_H_4820


title: Healthy_H_4823


title: Healthy_H_4825


title: Healthy_H_4819


title: Healthy_H_4818


title: Healthy_H_4816


title: Healthy_H_4815


title: Healthy_H_4814


title: Healthy_H_4817


title: Healthy_H_4811


title: Healthy_H_4813


title: Healthy_H_4810


title: Healthy_H_4808


title: Healthy_H_4807


title: Healthy_H_4809


title: Healthy_H_4806


title: Healthy_H_4812


title: Healthy_H_4805


title: Healthy_H_4804


title: Healthy_H_4822


title: Healthy_H_4802


title: Healthy_H_4801


title: Healthy_H_4803


title: Healthy_H_4797


title: Healthy_H_4800


title: Healthy_H_4799


title: Healthy_H_4798


title: Healthy_H_4792


title: Healthy_H_4793


title: Healthy_H_4795


title: Healthy_H_4796


title: Healthy_H_4790


title: Healthy_H_4794


title: Healthy_H_4777


title: Healthy_H_4784


title: Healthy_H_4788


title: Healthy_H_4787


title: Healthy_H_4785


title: Healthy_H_4786


title: Healthy_H_4780


title: Healthy_H_4783


title: Healthy_H_4778


title: Healthy_H_4781


title: Healthy_H_4776


title: Healthy_H_4789


title: Healthy_H_4773


title: Healthy_H_4774


title: Healthy_H_4791


title: Healthy_H_4772


title: Healthy_H_4769


title: Healthy_H_4767


title: Healthy_H_4764


title: Healthy_H_4770


title: Healthy_H_4768


title: Healthy_H_4771


title: Healthy_H_4766


title: Healthy_H_4782


title: Healthy_H_4763


title: Healthy_H_4779


title: Healthy_H_4765


title: Healthy_H_4762


title: Healthy_H_4775


title: Healthy_H_4761


title: Healthy_H_4757


title: Healthy_H_4759


title: Healthy_H_4754


title: Healthy_H_4758


title: Healthy_H_4751


title: Healthy_H_4749


title: Healthy_H_4746


title: Healthy_H_4750


title: Healthy_H_4745


title: Healthy_H_4760


title: Healthy_H_4742


title: Healthy_H_4744


title: Healthy_H_4741


title: Healthy_H_4740


title: Healthy_H_4743


title: Healthy_H_4739


title: Healthy_H_4738


title: Healthy_H_4736


title: Healthy_H_4748


title: Healthy_H_4734


title: Healthy_H_4735


title: Healthy_H_4756


title: Healthy_H_4753


title: Healthy_H_4752


title: Healthy_H_4755


title: Healthy_H_4737


title: Healthy_H_4732


title: Healthy_H_4730


title: Healthy_H_4729


title: Healthy_H_4726


title: Healthy_H_4725


title: Healthy_H_4724


title: Healthy_H_4722


title: Healthy_H_4721


title: Healthy_H_4723


title: Healthy_H_4719


title: Healthy_H_4720


title: Healthy_H_4718


title: Healthy_H_4716


title: Healthy_H_4713


title: Healthy_H_4733


title: Healthy_H_4715


title: Healthy_H_4717


title: Healthy_H_4731


title: Healthy_H_4712


title: Healthy_H_4710


title: Healthy_H_4714


title: Healthy_H_4711


title: Healthy_H_4727


title: Healthy_H_4706


title: Healthy_H_4709


title: Healthy_H_4705


title: Healthy_H_4707


title: Healthy_H_4704


title: Healthy_H_4708


title: Healthy_H_4728


title: Healthy_H_4701


title: Healthy_H_4700


title: Healthy_H_4699


title: Healthy_H_4698


title: Healthy_H_4696


title: Healthy_H_4694


title: Healthy_H_4693


title: Healthy_H_4692


title: Healthy_H_4691


title: Healthy_H_4695


title: Healthy_H_4689


title: Healthy_H_4690


title: Healthy_H_4684


title: Healthy_H_4688


title: Healthy_H_4747


title: Healthy_H_4703


title: Healthy_H_4685


title: Healthy_H_4702


title: Healthy_H_4682


title: Healthy_H_4681


title: Healthy_H_4676


title: Healthy_H_4687


title: Healthy_H_4675


title: Healthy_H_4683


title: Healthy_H_4678


title: Healthy_H_4680


title: Healthy_H_4679


title: Healthy_H_4697


title: Healthy_H_4672


title: Healthy_H_4673


title: Healthy_H_4670


title: Healthy_H_4668


title: Healthy_H_4669


title: Healthy_H_4667


title: Healthy_H_4686


title: Healthy_H_4666


title: Healthy_H_4663


title: Healthy_H_4677


title: Healthy_H_4664


title: Healthy_H_4660


title: Healthy_H_4662


title: Healthy_H_4674


title: Healthy_H_4658


title: Healthy_H_4656


title: Healthy_H_4655


title: Healthy_H_4657


title: Healthy_H_4653


title: Healthy_H_4659


title: Healthy_H_4651


title: Healthy_H_4671


title: Healthy_H_4652


title: Healthy_H_4649


title: Healthy_H_4650


title: Healthy_H_4647


title: Healthy_H_4648


title: Healthy_H_4646

value: ILC


title: Healthy_H_4645


title: Healthy_H_4661


title: Healthy_H_4643


title: Healthy_H_4642


title: Healthy_H_4654


title: Healthy_H_4644


title: Healthy_H_4641


title: Healthy_H_4665


title: Healthy_H_4639


title: Healthy_H_4640


title: Healthy_H_4638


title: Healthy_H_4637


title: Healthy_H_4636


title: Healthy_H_4635


title: Healthy_H_4633


title: Healthy_H_4634


title: Healthy_H_4627


title: Healthy_H_4628


title: Healthy_H_4631


title: Healthy_H_4625


title: Healthy_H_4626


title: Healthy_H_4624


title: Healthy_H_4623


title: Healthy_H_4630


title: Healthy_H_4621


title: Healthy_H_4622


title: Healthy_H_4619


title: Healthy_H_4620


title: Healthy_H_4618


title: Healthy_H_4616


title: Healthy_H_4614


title: Healthy_H_4613


title: Healthy_H_4612


title: Healthy_H_4609


title: Healthy_H_4610


title: Healthy_H_4611


title: Healthy_H_4608


title: Healthy_H_4632


title: Healthy_H_4629


title: Healthy_H_4605


title: Healthy_H_4604


title: Healthy_H_4606


title: Healthy_H_4607


title: Healthy_H_4603


title: Healthy_H_4600


title: Healthy_H_4601


title: Healthy_H_4599


title: Healthy_H_4595


title: Healthy_H_4597


title: Healthy_H_4591


title: Healthy_H_4592


title: Healthy_H_4617


title: Healthy_H_4602


title: Healthy_H_4615


title: Healthy_H_4593


title: Healthy_H_4590


title: Healthy_H_4596


title: Healthy_H_4594


title: Healthy_H_4583


title: Healthy_H_4585


title: Healthy_H_4588


title: Healthy_H_4584


title: Healthy_H_4598


title: Healthy_H_4581


title: Healthy_H_4582


title: Healthy_H_4580


title: Healthy_H_4579


title: Healthy_H_4576


title: Healthy_H_4586


title: Healthy_H_4575


title: Healthy_H_4578


title: Healthy_H_4573


title: Healthy_H_4572


title: Healthy_H_4571


title: Healthy_H_4568


title: Healthy_H_4569


title: Healthy_H_4566


title: Healthy_H_4574


title: Healthy_H_4589


title: Healthy_H_4587


title: Healthy_H_4564


title: Healthy_H_4562


title: Healthy_H_4565


title: Healthy_H_4570


title: Healthy_H_4567


title: Healthy_H_4577


title: Healthy_H_4558


title: Healthy_H_4561


title: Healthy_H_4553


title: Healthy_H_4555


title: Healthy_H_4560


title: Healthy_H_4554


title: Healthy_H_4547


title: Healthy_H_4557


title: Healthy_H_4548


title: Healthy_H_4545


title: Healthy_H_4546


title: Healthy_H_4550


title: Healthy_H_4551


title: Healthy_H_4559


title: Healthy_H_4544


title: Healthy_H_4538


title: Healthy_H_4541


title: Healthy_H_4556


title: Healthy_H_4539


title: Healthy_H_4543


title: Healthy_H_4542


title: Healthy_H_4536


title: Healthy_H_4563


title: Healthy_H_4540


title: Healthy_H_4535


title: Healthy_H_4534


title: Healthy_H_4549


title: Healthy_H_4532


title: Healthy_H_4531


title: Healthy_H_4530


title: Healthy_H_4529


title: Healthy_H_4528


title: Healthy_H_4523


title: Healthy_H_4533


title: Healthy_H_4526


title: Healthy_H_4516


title: Healthy_H_4517


title: Healthy_H_4511


title: Healthy_H_4514


title: Healthy_H_4537


title: Healthy_H_4527


title: Healthy_H_4519


title: Healthy_H_4509


title: Healthy_H_4510


title: Healthy_H_4552


title: Healthy_H_4522


title: Healthy_H_4520


title: Healthy_H_4508


title: Healthy_H_4524


title: Healthy_H_4513


title: Healthy_H_4518


title: Healthy_H_4512


title: Healthy_H_4507


title: Healthy_H_4506


title: Healthy_H_4525


title: Healthy_H_4521


title: Healthy_H_4505


title: Healthy_H_4502


title: Healthy_H_4503


title: Healthy_H_4515


title: Healthy_H_4501


title: Healthy_H_4504


title: Healthy_H_4499


title: Healthy_H_4492


title: Healthy_H_4491


title: Healthy_H_4489


title: Healthy_H_4500


title: Healthy_H_4485


title: Healthy_H_4498


title: Healthy_H_4486


title: Healthy_H_4490


title: Healthy_H_4495


title: Healthy_H_4494


title: Healthy_H_4497


title: Healthy_H_4484


title: Healthy_H_4496


title: Healthy_H_4493


title: Healthy_H_4488


title: Healthy_H_4481


title: Healthy_H_4487


title: Healthy_H_4480


title: Healthy_H_4479


title: Healthy_H_4478


title: Healthy_H_4477


title: Healthy_H_4475


title: Healthy_H_4476


title: Healthy_H_4471


title: Healthy_H_4473


title: Healthy_H_4474


title: Healthy_H_4472


title: Healthy_H_4469


title: Healthy_H_4466


title: Healthy_H_4464


title: Healthy_H_4482


title: Healthy_H_4463


title: Healthy_H_4465


title: Healthy_H_4468


title: Healthy_H_4470


title: Healthy_H_4461


title: Healthy_H_4459


title: Healthy_H_4454


title: Healthy_H_4452


title: Healthy_H_4460


title: Healthy_H_4456


title: Healthy_H_4462


title: Healthy_H_4455


title: Healthy_H_4467


title: Healthy_H_4457


title: Healthy_H_4451


title: Healthy_H_4450


title: Healthy_H_4449


title: Healthy_H_4453


title: Healthy_H_4458


title: Healthy_H_4446


title: Healthy_H_4447


title: Healthy_H_4445


title: Healthy_H_4448


title: Healthy_H_4443


title: Healthy_H_4444


title: Healthy_H_4442


title: Healthy_H_4440


title: Healthy_H_4438


title: Healthy_H_4437


title: Healthy_H_4436


title: Healthy_H_4434


title: Healthy_H_4433


title: Healthy_H_4435


title: Healthy_H_4483


title: Healthy_H_4428


title: Healthy_H_4427


title: Healthy_H_4429


title: Healthy_H_4430


title: Healthy_H_4431


title: Healthy_H_4432


title: Healthy_H_4426


title: Healthy_H_4423


title: Healthy_H_4422


title: Healthy_H_4424


title: Healthy_H_4421


title: Healthy_H_4420


title: Healthy_H_4419


title: Healthy_H_4441


title: Healthy_H_4417


title: Healthy_H_4415


title: Healthy_H_4416


title: Healthy_H_4414


title: Healthy_H_4411


title: Healthy_H_4409


title: Healthy_H_4439


title: Healthy_H_4408


title: Healthy_H_4425


title: Healthy_H_4401


title: Healthy_H_4404


title: Healthy_H_4406


title: Healthy_H_4398


title: Healthy_H_4400


title: Healthy_H_4397


title: Healthy_H_4394


title: Healthy_H_4418


title: Healthy_H_4396


title: Healthy_H_4395


title: Healthy_H_4393


title: Healthy_H_4413


title: Healthy_H_4388


title: Healthy_H_4391


title: Healthy_H_4389


title: Healthy_H_4407


title: Healthy_H_4390


title: Healthy_H_4410


title: Healthy_H_4412


title: Healthy_H_4387


title: Healthy_H_4384


title: Healthy_H_4383


title: Healthy_H_4385


title: Healthy_H_4386


title: Healthy_H_4403


title: Healthy_H_4405


title: Healthy_H_4392


title: Healthy_H_4402


title: Healthy_H_4381


title: Healthy_H_4380


title: Healthy_H_4378


title: Healthy_H_4377


title: Healthy_H_4379


title: Healthy_H_4373


title: Healthy_H_4372


title: Healthy_H_4375


title: Healthy_H_4399


title: Healthy_H_4370


title: Healthy_H_4376


title: Healthy_H_4367


title: Healthy_H_4365


title: Healthy_H_4371


title: Healthy_H_4368


title: Healthy_H_4366


title: Healthy_H_4382


title: Healthy_H_4364


title: Healthy_H_4363


title: Healthy_H_4360


title: Healthy_H_4361


title: Healthy_H_4357


title: Healthy_H_4356


title: Psoriasis_PN_4354

value: Psoriasis

value: PN


title: Psoriasis_PN_4353

value: Skin


title: Psoriasis_PN_4351

value: singlet


title: Psoriasis_PN_4349


title: Psoriasis_PN_4350


title: Healthy_H_4374

value: H


title: Healthy_H_4369


title: Psoriasis_PN_4348

value: Suprabasal keratinocytes I


title: Psoriasis_PN_4347


title: Psoriasis_PN_4344


title: Psoriasis_PN_4343

value: Mitotic keratinocytes


title: Healthy_H_4359


title: Healthy_H_4355

value: Basal keratinocytes II


title: Healthy_H_4358


title: Psoriasis_PN_4339


title: Psoriasis_PN_4338


title: Psoriasis_PN_4337


title: Psoriasis_PN_4336


title: Psoriasis_PN_4352


title: Psoriasis_PN_4331

value: Basal keratinocytes III


title: Psoriasis_PN_4334

value: Melanocytes


title: Psoriasis_PN_4330


title: Psoriasis_PN_4332


title: Psoriasis_PN_4333


title: Psoriasis_PN_4329


title: Psoriasis_PN_4327


title: Psoriasis_PN_4326


title: Psoriasis_PN_4328


title: Psoriasis_PN_4346

value: Transition keratinocytes


title: Healthy_H_4362

value: Healthy


title: Psoriasis_PN_4324


title: Psoriasis_PN_4325


title: Psoriasis_PN_4323


title: Psoriasis_PN_4345


title: Psoriasis_PN_4342


title: Psoriasis_PN_4321


title: Psoriasis_PN_4340


title: Psoriasis_PN_4320


title: Psoriasis_PN_4322

value: Basal keratinocytes I


title: Psoriasis_PN_4318


title: Psoriasis_PN_4317


title: Psoriasis_PN_4315


title: Psoriasis_PN_4316


title: Psoriasis_PN_4319


title: Psoriasis_PN_4314


title: Psoriasis_PN_4313


title: Psoriasis_PN_4312


title: Psoriasis_PN_4311


title: Psoriasis_PN_4306


title: Psoriasis_PN_4308


title: Psoriasis_PN_4309


title: Psoriasis_PN_4341


title: Psoriasis_PN_4307


title: Psoriasis_PN_4305


title: Psoriasis_PN_4302


title: Psoriasis_PN_4303


title: Psoriasis_PN_4297


title: Psoriasis_PN_4298


title: Psoriasis_PN_4301


title: Psoriasis_PN_4335


title: Psoriasis_PN_4299


title: Psoriasis_PN_4296


title: Psoriasis_PN_4295


title: Psoriasis_PN_4293


title: Psoriasis_PN_4292


title: Psoriasis_PN_4294


title: Psoriasis_PN_4291


title: Psoriasis_PN_4290

value: T lymphocytes


title: Psoriasis_PN_4310


title: Psoriasis_PN_4289

value: Suprabasal keratinocytes II


title: Psoriasis_PN_4287


title: Psoriasis_PN_4288


title: Psoriasis_PN_4285


title: Psoriasis_PN_4279


title: Psoriasis_PN_4281


title: Psoriasis_PN_4304


title: Psoriasis_PN_4278


title: Psoriasis_PN_4280


title: Psoriasis_PN_4283

value: Progenitor keratinocytes


title: Psoriasis_PN_4284


title: Psoriasis_PN_4286


title: Psoriasis_PN_4300


title: Psoriasis_PN_4277


title: Psoriasis_PN_4276


title: Psoriasis_PN_4274


title: Psoriasis_PN_4273


title: Psoriasis_PN_4268


title: Psoriasis_PN_4271


title: Psoriasis_PN_4267


title: Psoriasis_PN_4266


title: Psoriasis_PN_4265


title: Psoriasis_PN_4264


title: Psoriasis_PN_4263


title: Psoriasis_PN_4275


title: Psoriasis_PN_4261


title: Psoriasis_PN_4260


title: Psoriasis_PN_4269


title: Psoriasis_PN_4282


title: Psoriasis_PN_4270