title: pUC19, mock-treated, rep1

status: Public on Mar 15 2024

first: David

middle: J.

last: Clark

state: MD

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
The raw pacbio subreads are called using the default pipeline by BLASR using SMRT analysis 6.0 with default settings, and the reads are aligned using pbalign using the SMRT Analysis 10.2 software.
The aligned subreads were grouped by ZMW and we predicted consensus m6A sites for each ZMW using the ipdSummary package from SMRT Analysis 10.2 with default parameters. We also computed the CCS reads from the raw subreads using the SMRT Analysis 10.2 with default parameters, and filtered the ZMWs with minimal average base quality score=90 in the CCS reads.
Supplementary files format and content: Bam format (with _m6A suffix). The m6A sites in the consensus reads are annotated as insertions at A sites, and the subread coverage of the consensus read is stored in the dp tag.
We predicted nucleosome footprints and accessible regions in each read using our own program (described in the paper), and stored the per-read nucleosome footprints and accessible regions in bed files and bam files.
Note from submitter: The . bam files  allow the user to visualise our nucleosome predictions in a viewer such as IGV. These processed bam files are much more informative than the bed files: m6A bases are annotated as insertions; nucleosomes are annotated as substitutions; ambiguous regions are annotated as deletions, and accessible regions are annotated as matches.  These files show both the data and the predictions of our bioinformatic pipeline and represent the main point of our paper.
Assembly: sacCer3 for yeast data and SmaI linearized pUC19 for pUC19 data
Supplementary files format and content: Bed format. Each track represents one consensus read; accessble regions and nucleosomes are annotated as blocks in each track.
Supplementary files format and content: Bam format (with _Nucleosome suffix). More detailed information is stored In the bam file: m6A sites are annotated as insertions; nucleosomes are annotated as substitutions; ambiguous regions are annotated as deletions, and accessible regions are annotated as matches, suitable for IGV (2.9.2) visualization.
Supplementary files format and content: Bigwig format. The average m6A fraction at in reference location.
Library strategy: m6A-Seq

organism: Escherichia coli

growth_protocol: Yeast strain YDC111 was grown at 30°C in synthetic complete (SC) medium (2% D-glucose, 6.7 g/l yeast nitrogen base (Sunrise Science Products 1501-250) and 0.79 g/l Complete Supplement Mixture with adenine (Sunrise Science Products 1128-010) to an OD A600 ~0.2 and arrested in G1 by the addition of ɑ-factor (FDA Core Facility) to 10 μg/ml. Arrest was monitored by observance of the "shmoo" phenotype in a light microscope. After 2.5 h, the cells were harvested by filtration and stored at -80°C.

extract_protocol:
Genomic DNA samples were sheared to ~2 kb in a total volume of 200 µl using a Covaris miniTube Clear on the Covaris M220 with shearing conditions as follows: Peak Incident Power: 8 W, Duty Factor: 20%, Cycles per Burst: 1000, Treatment time: 900 s. Sonicated DNA was purified using AMPure XP beads (Beckman-Coulter) at a 1:1 ratio, eluted in 22.5 µl AMPure Elution Buffer and checked for quality using the DNA12000 assay in an Agilent BioAnalyzer.
SMRTbell libraries were prepared using PacBio barcoded adapters according to the manufacturer's instructions.
PacBio long-read SMRT sequencing

treatment_protocol: Spheroplasts were prepared from ~100 A600 units of cells in 15 ml SM Buffer (SC medium with 1 M sorbitol, 50 mM Tris-HCl pH 8.0, 20 mM 2-mercaptoethanol) by digestion with ~19,000 units of lyticase (Sigma L-2524) at 30°C for 10 min. Digestion of the cell wall was monitored by measuring the A600 of 30 μl cell suspension in 1 ml 1% SDS and considered complete when the A600 decreased to < 10% of the initial value. Spheroplasts were spun down in a pre-cooled Sorvall SA600 rotor (7,500 rpm for 5 min at 4°C) and washed once with 25 ml cold ST Buffer (1 M sorbitol, 50 mM Tris-HCl pH 8.0). Spheroplasts were lysed by resuspension in 20 ml cold F Buffer (18% w/v Ficoll-PM400 (GE Healthcare 17-0300-50), 40 mM potassium phosphate, 1 mM magnesium chloride, pH 6.5; protease inhibitors (Roche 05056489001) and 5 mM 2-mercaptoethanol were added just before use). The lysate was applied to a step gradient of 15 ml cold FG Buffer (7% w/v Ficoll-PM400, 20% glycerol, 40 mM potassium phosphate, 1 mM magnesium chloride, pH 6.5, with protease inhibitors and 5 mM 2-mercaptoethanol as above) and spun in the SA600 rotor (12,500 rpm for 20 min at 4°C). To perform methylation, the pellet of crude nuclei was resuspended in 4.8 ml pre-warmed NEB buffer 2.1 (50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, 0.1 mg/ml BSA, pH 7.9) with 1.2 mM S-adenosylmethionine (SAM) and protease inhibitors, and divided into ten 425 µl aliquots. M.EcoGII (24 µl; 600 units at 25 units/µl; New England Biolabs M0603B-HC1) or 24 µl water was added to each of five aliquots, mixed thoroughly but gently, and incubated at 30°C for 20 min. Methylation was stopped by adding 50 μl 200 mM EDTA, 10% SDS and incubating at 25°C for 5 min. Genomic DNA was purified by addition of 27.5 μl 10% SDS, mixing, addition of 133 μl 5 M potassium acetate, followed by two extractions with an equal volume of chloroform, precipitation with 0.7 vol. isopropanol, and one wash with 75% ethanol. The purified genomic DNA was dissolved in 20 μl 10 mM Tris-HCl pH 8.0, 0.5 mg/ml RNase A and incubated at 37°C for 4 h. To verify methylation, purified genomic DNA was digested with either DpnI, which only cleaves when its recognition site (GATC) is methylated, or MboI, which recognises the same site but is blocked by methylation, and evaluated by gel electrophoresis. Genomic DNA positive control samples (gDNA) were obtained by subjecting genomic DNA purified from yeast cells as above to three rounds of M.EcoGII treatment to maximise methylation (28 μg DNA in 160 μl NEB buffer 2.1 with 0.8 mM SAM, incubated with 96 units M.EcoGII at 37oC for 4 h). The DNA was purified after each round.

tag: cell line

value: E. coli (NEB C2925I)

tag: genotype

value: dam- dcm-

tag: treatment

value: Mock-treated


title: pUC19, dam-treated, rep2

type: SRA

city: Bethesda

country: USA

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: cell type

value: Treated with dam


title: pUC19, mock-treated, rep2


title: WGBS of MRV sample 1

status: Public on Apr 02 2024

city: Zhuhai

first: Mincong

last: Liang

state: Guangdong

address: No. 2 Daxue Road

department: School of Marine Sciences

country: China

institute: Sun Yat-sen University

data_processing:
The raw data were trimmed and filtered by Trimmomatic v0.39 (“ILLUMINACLIP:TruSeq3-PE-2:2:30:10:8:true SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:36
Clean data were mapped to the MRV genome, deduplicated and methylation extracted (--ignore_r2 2) using Bismark v0.24.2, Bowtie2 v2.5.2 and SAMtools v1.17.
Assembly: MG941005.3
Supplementary files format and content: The number of methylations and unmethylations counts for each cytosines in MRV genome based on the WGBS data.

organism: Mandarin fish ranavirus

source_name: Virion

extract_protocol:
The total DNA from the purified virions was extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit following the manufacturer's protocol (Vazyme, China).
Libraries were prepared using kit following to the manufacturer's protocol.

value: Virion

value: inoculating Mandarin fish fry (MFF-1) cells with MRV


title: pUC19, M.EcoGII-treated, rep2

value: Treated with M.EcoGII


title: pUC19, dam-treated, rep1


title: Genomic DNA, M.EcoGII-treated, rep2

organism: Saccharomyces cerevisiae

source_name: W303 background

value: W303 background

value: strain YDC111

value: haploid

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1


title: Genomic DNA, M.EcoGII-treated, rep1


title: Nuclei, M.EcoGII-treated, rep2


title: Nuclei, M.EcoGII-treated, rep1


title: Nuclei, mock-treated, rep2


title: Nuclei, mock-treated, rep1


title: pUC19, M.EcoGII-treated, rep1


title: athero_human_13

status: Public on Mar 05 2024

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic single cell

data_processing:
Demultiplexing with bcl2fastq
Removal of adapter sequencing with TrimGalore
Alignment against the mouse GRCm38 build using Bowtie2
Removal of duplets using samtools
Generation of a count matrix with FeatureCounts from the SubRead package
Assembly: GRCm38
Supplementary files format and content: Count files, with every column a cell and every row a gene.

molecule: polyA RNA

organism: Homo sapiens

source_name: Carotid Atherosclerotic Plaque

extract_protocol:
FACS into 384well plate of single cells from dissociation of human carotid atherosclerotic plaque
RNA libraries were prepared using standard SmartSeq2 protocol

value: Carotid Atherosclerotic Plaque

tag: subject status

value: Asymptomatic patient


title: athero_human_12

value: Symptomatic patient


title: athero_human_10


title: athero_human_9


title: athero_human_15


title: athero_human_14


title: athero_human_8


title: athero_human_6


title: athero_human_7


title: athero_human_4


title: athero_human_3


title: athero_human_2


title: athero_human_5


title: athero_human_1


title: Retina, adult, rep2

status: Public on Mar 04 2024

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Pmarinus_7.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Petromyzon marinus

source_name: Retina

extract_protocol:
Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. They were dissociated in papain, followed by FACS sorting.
Single cell libraries were generated using the Chromium 3’ V3 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single cells were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.

value: Retina

tag: developmental stage

value: adult

value: retinal cell types


title: MEN_patient6_EC_bulkRNA-seq

status: Public on Feb 29 2024

city: London

first: Thomas

last: Wälchli

state: London

address: Paul O'Gorman Building, 72 Huntley St

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

library_source: transcriptomic

data_processing:
For bulk RNA-seq analysis the cells were sorted directly into RLT Plus lysis buffer and RNA was extracted using RNeasy Plus Micro Kit (Cat No. 74034, Qiagen, Hilden, Germany). RNA sequencing of endothelial cells was performed by the Functional Genomics Center Zurich. The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolarly and sequenced in an Illumina NovaSeq sequencer (single- end 100 bp) with a depth of around 20 Mio reads per sample. For mapping and trimming of FASTQ format sequences was performed using Trimmomatic v0.3.3, and sequence quality control was assessed using FastQC. Alignment to the Ensembl Homo_sapiens GRCh38.p10 reference genome (Release_91-2018-02-26) was performed using the STAR aligner. Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GRCh38.p13
Supplementary files format and content: text files holding raw counts

source_name: meningioma

growth_protocol: The sequenced cells are freshly isolated cells

extract_protocol:
Isolation of FACS-sorted human fetal and adult endothelial cells and of unsorted human fetal and adult endothelial and perivascular cells for single cell RNA-seq Endothelial cells were isolated from human fetal and adult tissues using tissue digestion and subsequent CD31 + / CD45- FACS sorting whereas human endothelial and perivascular cells (all cells) were isolated from the unsorted fraction. Briefly, both fetal and adult tissues were quickly minced in a petri dish on ice, using two surgical blades. For CD31+ / CD45- FACS sorting, a cell suspension was obtained upon digesting the tissue in 2 mg/ml Dispase II (D4693, Sigma- Aldrich, Steinheim, Germany), 2 mg/ml Collagenase IV (#1710401, Thermo Fisher Scientific, Zurich, Switzerland) and 2 mM CaCl2 PBS solution for 40 min at 37°C with occasional shaking. The suspension was filtered sequentially through 100/70/40 μm cell strainers (#431751, Corning, New York, USA) to remove large cell debris. Cells were then centrifuged 500 RCF for 5 min at 4°C. In case of a visible myelin pellet 5 ml 25% Bovine Serum Albumin (BSA) (ice cold) was overlayed with 5 ml of the sample, centrifuged at 2000 RCF for 20 min (4°C). The supernatant was removed (including the lipid phase) and the pellet was resuspended in 9 ml PBS, followed by another round of centrifugation at 500 RCF for 5 min (4°C). Supernatant was subsequently discarded, while the cell pellets were resuspended in 3 ml of ACK hemolytic buffer at room temperature for 3 minutes. To stop the reaction, 30 ml of ice- cold PBS was added to the mixture and centrifuged at 500 RCF for 5 min at 4⁰C. The cell pellets were resuspended in FACS buffer (PBS + 1% Bovine Serum Albumin), a volume is taken for unsorted scRNA-seq analysis. For CD31+ / CD45 - FACS sorting, the cells were stained with anti-CD31 PE conjugated antibody in a concentration of 1:20 (#566125, clone MBC78.2, BD Pharmingen) and anti-CD45 APC conjugated antibody in a concentration of 1:20 (#17-0459- 42, clone HI30, eBiosciences) for 30 min at 4⁰ C, protected from light. Thereafter the cells were washed with 1ml of FACS buffer, centrifuged in a tabletop centrifuge at 500 RCF at 4⁰C for 5 min. Finally, the cell pellets were resuspended in appropriate volumes of FACS buffer (PBS + 1% Bovine Serum Albumin) and the suspension was passed through a 35 μm cell strainer of a FACS sorting tube (#352235, Corning). Immediately before sorting, SYTOXTM blue was added in 1:1000 (Thermo Fisher Scientific, #S34857) to exclude dead cells from further analysis. Cell debris were excluded via a forward scatter-area/side scatter-area (FSC-A/SSC-A) gating, while singlets were selected for using a forward scatter-area (FSC-A)/ FSC-height (FSC-H) gating strategy. Viable (SYTOXTM blue negative) endothelial cells were FACS-sorted by endothelial marker CD31 positivity and negative selection for the brain microglia and macrophages marker CD45, whereas unsorted endothelial and perivascular cells were obtained from the SYTOXTM blue- fraction. Cells were sorted by a FACS Aria III (BD Bioscience) sorter using the four-way purity sorting mode directly in EGM2 medium (#CC-3162, Lonza, Basel, Switzerland).
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.

treatment_protocol: there was no treatment done on the cells

value: meningioma

value: Endothelial cells

value: Adult

value: Meningioma

value: diseased


title: MEN_patient4_EC_bulkRNA-seq


title: MEN_patient5_EC_bulkRNA-seq


title: MEN_patient3_EC_bulkRNA-seq


title: MEN_patient2_EC_bulkRNA-seq


title: MET_patient4_EC_bulkRNA-seq

source_name: brain metastasis

value: brain metastasis

value: Lung brain metastasis


title: MET_patient5_EC_bulkRNA-seq


title: MET_patient2_EC_bulkRNA-seq


title: MET_patient1_EC_bulkRNA-seq


title: MET_patient3_EC_bulkRNA-seq


title: athero_human_11


title: MEN_patient1_EC_bulkRNA-seq


title: GBM_patient6_EC_bulkRNA-seq

source_name: high grade glioma / glioblastoma (GBM)

value: high grade glioma / glioblastoma (GBM)

value: High grade glioma


title: GBM_patient3_EC_bulkRNA-seq


title: GBM_patient1_EC_bulkRNA-seq


title: GBM_patient2_EC_bulkRNA-seq


title: GBM_patient4_EC_bulkRNA-seq


title: GBM_patient5_EC_bulkRNA-seq


title: LGG_patient2_EC_bulkRNA-seq

source_name: lower grade glioma

value: lower grade glioma

value: Lower grade glioma


title: LGG_patient4_EC_bulkRNA-seq


title: AVM_patient7_EC_bulkRNA-seq

source_name: brain arteriovenous malformations

value: brain arteriovenous malformations

value: Arteriovenous malformations


title: LGG_patient3_EC_bulkRNA-seq


title: Retina, adult, rep1

description: 10X Genomics

value: Retinal cell types


title: AVM_patient3_EC_bulkRNA-seq


title: LGG_patient1_EC_bulkRNA-seq


title: TL_patient2_EC_bulkRNA-seq

source_name: adult/control brain

value: adult/control brain

value: Temporal lobe

value: control


title: AVM_patient4_EC_bulkRNA-seq


title: AVM_patient1_EC_bulkRNA-seq


title: TL_patient3_EC_bulkRNA-seq


title: FETAL_brain_6_all cells

description: 10x Genomics

data_processing:
Chromium data was demultiplexed with cellranger mkfastq
Gene-cell count matrix was generated by cellranger count against Ensembl GRCh38.p13 reference genome.
Assembly: GRCh38.p13
Supplementary files format and content: Filtered count matrix from cellranger count is stored in three files: barcodes.tsv.gz, genes.tsv,gz and matrix.mtx.gz

source_name: fetal brain - GW12.4

extract_protocol:
Isolation of FACS-sorted human fetal and adult endothelial cells and of unsorted human fetal and adult endothelial and perivascular cells for single cell RNA-seq Endothelial cells were isolated from human fetal and adult tissues using tissue digestion and subsequent CD31 + / CD45- FACS sorting whereas human endothelial and perivascular cells (all cells) were isolated from the unsorted fraction. Briefly, both fetal and adult tissues were quickly minced in a petri dish on ice, using two surgical blades. For CD31+ / CD45- FACS sorting, a cell suspension was obtained upon digesting the tissue in 2 mg/ml Dispase II (D4693, Sigma- Aldrich, Steinheim, Germany), 2 mg/ml Collagenase IV (#1710401, Thermo Fisher Scientific, Zurich, Switzerland) and 2 mM CaCl2 PBS solution for 40 min at 37°C with occasional shaking. The suspension was filtered sequentially through 100/70/40 μm cell strainers (#431751, Corning, New York, USA) to remove large cell debris. Cells were then centrifuged 500 RCF for 5 min at 4°C. In case of a visible myelin pellet 5 ml 25% Bovine Serum Albumin (BSA) (ice cold) was overlayed with 5 ml of the sample, centrifuged at 2000 RCF for 20 min (4°C). The supernatant was removed (including the lipid phase) and the pellet was resuspended in 9 ml PBS, followed by another round of centrifugation at 500 RCF for 5 min (4°C). Supernatant was subsequently discarded, while the cell pellets were resuspended in 3 ml of ACK hemolytic buffer at room temperature for 3 minutes. To stop the reaction, 30 ml of ice- cold PBS was added to the mixture and centrifuged at 500 RCF for 5 min at 4⁰C. The cell pellets were resuspended in FACS buffer (PBS + 1% Bovine Serum Albumin), a volume is taken for unsorted scRNA-seq analysis. For CD31+ / CD45 - FACS sorting, the cells were stained with anti-CD31 PE conjugated antibody in a concentration of 1:20 (#566125, clone MBC78.2, BD Pharmingen) and anti-CD45 APC conjugated antibody in a concentration of 1:20 (#17-0459- 42, clone HI30, eBiosciences) for 30 min at 4⁰ C, protected from light. Thereafter the cells were washed with 1ml of FACS buffer, centrifuged in a tabletop centrifuge at 500 RCF at 4⁰C for 5 min. Finally, the cell pellets were resuspended in appropriate volumes of FACS buffer (PBS + 1% Bovine Serum Albumin) and the suspension was passed through a 35 μm cell strainer of a FACS sorting tube (#352235, Corning). Immediately before sorting, SYTOXTM blue was added in 1:1000 (Thermo Fisher Scientific, #S34857) to exclude dead cells from further analysis. Cell debris were excluded via a forward scatter-area/side scatter-area (FSC-A/SSC-A) gating, while singlets were selected for using a forward scatter-area (FSC-A)/ FSC-height (FSC-H) gating strategy. Viable (SYTOXTM blue negative) endothelial cells were FACS-sorted by endothelial marker CD31 positivity and negative selection for the brain microglia and macrophages marker CD45, whereas unsorted endothelial and perivascular cells were obtained from the SYTOXTM blue- fraction. Cells were sorted by a FACS Aria III (BD Bioscience) sorter using the four-way purity sorting mode directly in EGM2 medium (#CC-3162, Lonza, Basel, Switzerland).
Library construction was performed according to the 10x Chromium Single Cell 3' Reagent Kit v2.

value: fetal brain - GW12.4

value: Endothelial, perivascular and other tissue derived cells

value: Fetal

value: Fetal brain

value: healthy


title: TL_patient1_EC_bulkRNA-seq

value: Endothelial cells

value: Adult


title: AVM_patient2_EC_bulkRNA-seq

value: diseased


title: AVM_patient6_EC_bulkRNA-seq


title: AVM_patient5_EC_bulkRNA-seq


title: GBM_patient8_EC

description: 10x Genomics

value: high grade glioma / glioblastoma (GBM)

value: High grade glioma


title: GBM_patient6_EC

description: 10x Genomics


title: GBM_patient7_EC

description: 10x Genomics


title: LGG_patient5_EC

description: 10x Genomics

value: lower grade glioma

value: Lower grade glioma


title: TL_patient10_all cells_1

description: 10x Genomics


title: LGG_patient6_EC

description: 10x Genomics


title: TL_patient10_EC_1

description: 10x Genomics


title: FETAL_brain_8_all cells

description: 10x Genomics

source_name: fetal brain - GW9.1

value: fetal brain - GW9.1


title: TL_patient10_all cells_2

description: 10x Genomics


title: TL_patient7_EC

description: 10x Genomics


title: TL_patient10_EC_2

description: 10x Genomics


title: TL_patient9_all cells_1

description: 10x Genomics


title: MEN_patient4_all cells

value: meningioma

value: Meningioma


title: MEN_patient5_all cells


title: TL_patient9_all cells_2

description: 10x Genomics

value: adult/control brain

value: Temporal lobe


title: MEN_patient3_all cells


title: MET_patient4_all cells

value: brain metastasis

value: Lung brain metastasis


title: MET_patient5_all cells

value: Endothelial, perivascular and other tissue derived cells


title: MET_patient3_all cells


title: GBM_patient4_all cells


title: GBM_patient6_all cells


title: GBM_patient7_all cells


title: LGG_patient5_all cells

value: Low grade glioma


title: GBM_patient5_all cells


title: LGG_patient4_all cells


title: LGG_patient6_all cells


title: AVM_patient4_all cells

value: brain arteriovenous malformations

value: Arteriovenous malformations


title: TL_patient9_EC_2

description: 10x Genomics

value: Endothelial cells

value: Adult

value: control


title: AVM_patient3_all cells

value: diseased


title: TL_patient8_all cells_3


title: LGG_patient3_all cells

value: lower grade glioma


title: TL_patient8_all cells_2


title: TL_patient6_all cells


title: AVM_patient5_all cells


title: FETAL_brain_4_all cells

source_name: fetal brain - GW18

value: fetal brain - GW18

value: Fetal

value: Fetal brain

value: healthy


title: FETAL_brain_3_all cells

source_name: fetal brain - GW16.4

value: fetal brain - GW16.4


title: TL_patient5_all cells

value: adult/control brain

value: Temporal lobe


title: FETAL_brain_5_all cells

source_name: fetal brain - GW15.5

value: fetal brain - GW15.5


title: FETAL_brain_1_all cells

source_name: fetal brain - GW9

value: fetal brain - GW9

value: Endothelial, perivascular and other tissue derived cells


title: FETAL_brain_2_all cells

source_name: fetal brain - GW14.4

value: fetal brain - GW14.4


title: MEN_patient2_EC

value: meningioma

value: Meningioma


title: MEN_patient1_EC

value: Endothelial cells

value: Adult


title: GBM_patient3_all cells

value: high grade glioma / glioblastoma (GBM)

value: High grade glioma

value: diseased


title: MEN_patient5_EC


title: TL_patient9_EC_1

description: 10x Genomics

value: control


title: MET_patient5_EC

value: brain metastasis

value: Lung brain metastasis


title: MET_patient4_EC


title: MET_patient2_EC


title: TL_patient7_all cells


title: MET_patient3_EC


title: TL_patient8_all cells_1


title: GBM_patient4_EC


title: GBM_patient3_EC


title: GBM_patient2_EC


title: LGG_patient4_EC

value: lower grade glioma

value: Lower grade glioma


title: GBM_patient1_EC


title: LGG_patient3_EC


title: LGG_patient2_EC


title: LGG_patient1_EC


title: MEN_patient4_EC


title: MEN_patient3_EC


title: AVM_patient4_EC

value: brain arteriovenous malformations

value: Arteriovenous malformations


title: AVM_patient5_EC


title: AVM_patient2_EC


title: AVM_patient1_EC


title: TL_patient6_EC

value: adult/control brain

value: Temporal lobe


title: TL_patient4_EC


title: FETAL_periphery_IND6_EC_arm

source_name: fetal periphery organs - GW12.4 - arm

value: fetal periphery organs - GW12.4 - arm

value: Fetal

value: Fetal periphery organs

value: healthy


title: TL_patient5_EC

value: Endothelial cells

value: Adult


title: TL_patient2_EC


title: TL_patient3_EC


title: FETAL_periphery_IND5_EC_arm

source_name: fetal periphery organs - arm - GW15.5

value: fetal periphery organs - arm - GW15.5


title: GBM_patient5_EC

value: high grade glioma / glioblastoma (GBM)

value: High grade glioma

value: diseased


title: FETAL_periphery_IND5_EC_kidney

source_name: fetal periphery organs - kidney - GW15.5


title: FETAL_periphery_IND4_EC_leg

source_name: fetal periphery organs - leg - GW18

value: fetal periphery organs - leg - GW18


title: FETAL_periphery_IND5_EC_throat

source_name: fetal periphery organs - throat - GW15.5


title: MET_patient1_EC

source_name: brain metastasis

value: brain metastasis

value: Lung brain metastasis


title: FETAL_periphery_IND3_EC_kidney

source_name: fetal periphery organs - kidney - GW16.4


title: TL_patient1_EC

value: control


title: FETAL_brain_IND5_EC

value: fetal brain - GW15.5

value: Fetal brain


title: FETAL_brain_IND2_IND3_EC

source_name: fetal brain - GW14.4-16.4

value: fetal brain - GW14.4-16.4


title: FETAL_periphery_IND2_EC_kidney

source_name: fetal periphery organs - kidney -  GW14.4


title: FETAL_brain_IND1_EC

value: fetal brain - GW9


title: AVM_patient3_EC

source_name: brain arteriovenous malformations

value: brain arteriovenous malformations

value: Arteriovenous malformations


title: mouse 3, unsort, RNAseq projectome library

status: Public on Feb 25 2024

city: Shanghai

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

description: bar.mat.drop.csv

data_processing:
Demultiplexing of projection index barcode was performed using deMULTIplex R package (v1.0.2) (https://github.com/chris-mcginnis-ucsf/MULTI-seq) with modifications. Briefly, we have revised the MULTIseq.align function to count the UMI of each projection barcode separately. We adopted a minimal Hamming distance of 2 for the MULTIseq.align function to improve the matching accuracy between detected and designed barcodes. Tag parameters in 'MULTIseq.preProcess' function were adjusted according to our user-defined position of index barcode length and position. Based on our primer design, the expected format is: cell barcode in Read 1 (bases 1-16), UMI in Read 1 (bases 17-28), and projection barcode in Read 2 (bases 31-45). To determine valid barcoded cells,  we first calculated the 95th percentile of the total number of unique molecular identifiers (nUMI) that are mapped with five barcodes, and removed the unusually high numbers of UMIs, which might indicate doublets or PCR-biased amplification. Next, we used two set of cells as negative control, that is, cells supposed not to contain projection barcodes. First set of negative control cells we used is non-neuronal cells classified by coarse clustering based on single-cell transcriptome (Tervo et al., 2016). Second set of negative control cells we used is 'EGFP-negative' cells in FAC-sorted dataset. Basically, we calculated the total five projection barcodes counts determined by cellranger of FAC-sorted dataset, then we assigned the cells with zero projection barcodes (nUMI of EGFP RNA = 0) counts as 'EGFP-negative' cells. For two set of negative control cells, we searched for the value in the empirical cumulative distribution function (ECDF) that is closest to the 99.9th percentile agains each projection barcode, respectively. We selected the higher UMI threshold from the two given sets of threshold values. A cell is determined to be validly barcoded if the number of the barcode UMIs within the cell is larger than the threshold. For example, the calculated threshold of UMIs for barcode 0 (AI) is 28, which means if a cell contains more than 28 UMIs of barcode 0, then this cell is validly barcoded by AI. UMIs threshold for DMS, 101; for MD, 114; for BLA, 35; for LH, 103. Finally, we dropped UMI counts of determined non-barcoded cells to zero to obtain the index barcode counts matrix used for downstream analysis. Binary projection patterns were calculated by five projection targets set intersections of corresponding barcoded cells. Only the top 10 frequent binary and collateral projection patterns were kept for reliable inference.
Supplementary files format and content:
Output files of 'MULTIseq.preProcess'  function in deMULTIplex R package: An nRead x 3 dataframe with columns correpsonding to (1) cell barcode, (2) UMI, and (3) retro-AAV barcode sequences, including readTable_pfc_*.csv
Output files of MULTIseq.align function in deMULTIplex R package: sample barcode UMI count matrix, including bar.table_pfc_*_v2_hd2.csv
bar.mat.drop_ecdf.0.999.filter_top.05.quantile.csv: processed index barcode counts matrix by droping barcodes that are below the threshold to zero.
pfc_all_meta_barcoded.csv is the file  that marks whether an cellis validly barcoded to a certain downstream target.
exn_meta_valid.csv is the file that marks whether an excitatory neuron is validly barcoded to a certain downstream target.
Assembly: mm10-3.0.0

organism: Mus musculus

source_name: retrograde labeled vmPFC neurons

extract_protocol:
For mice without FAC-sorting, three mice that had been injected with virus were anaesthetized and then subjected to transcranial perfusion with ice-cold oxygenated self-made dissection buffer (in mM: 92 Choline chloride, 2.5 KCl, 1.2 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 Glucose, 5 Sodium ascorbate, 2 Thiourea, 3 Sodium pyruvate, 10 MgSO4.7H2O, 0.5 CaCl2.2H2O, 12 N-Acetyl-L-Cysteine). The brain was removed, 300 µm vibratome sections were collected, and the PrL and IL regions were microdissected under a stereo microscope with a cooled platform. Brain slices were incubated in dissection buffer with 10 µM AMPA receptor antagonist CNQX (Abcam, Cat #ab120017) and 50 µM NMDA receptor antagonist D-AP5 (Abcam, Cat #ab120003) at 33°C for 30 min. The pieces were dissociated first using the ice-cold oxygenated dissection buffer added papain (20 units/ml, Worthington, Cat #LS003126), 0.067 mM 2-mercaptoethanol (Sigma, Cat #M6250), 1.1 mM EDTA (Invitrogen, Cat #15575020), L-Cysteine hydrochloride monohydrate (Sigma, Cat #C7880) and Deoxyribonuclease I (Sigma, Cat #D4527), with 30-40 min enzymatic digestion at 37°C, followed by 30 min 1 mg/ml protease (Sigma, Cat #P5147) and 1 mg/ml dispase (Worthington, Cat #LS02106) enzymatic digestion at 25°C. Supernatant was removed and digestion was terminated using dissection buffer containing 2% fetal bovine serum (FBS, Bioind, Cat #04-002-1A). Single-cell suspension was generated by manual trituration using fire-polishing pasteur pipettes and filtered through a 35 µm DM-equilibrated cell strainer (Falcon, Cat #352052). Cells were then pelleted at 400 g for 5 min. The supernatant was carefully removed and resuspended in 1-2 ml dissection buffer containing 2% FBS. The suspension was then subjected to the debris removal step using the Debris Removal Solution (Miltenyi, Cat #130-109-398). Cell pellets were resuspended and 48,000 cells were loaded into 3 lanes to perform 10X Genomics sequencing. For mice with FAC-sorting, PrL and IL regions were microdissected and dissociated as mice without FAC-sorting, cells were sorted to enrich for EGFP-positive retro-AAV-labeled cells. About 4893 EGFP-positive cells were captured and loaded to perform 10X Genomics sequencing.
Parallel PCR reactions were performed containing 50 ng of post cDNA amplification reaction cleanup material as a template. P5-Read1 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC) and P7-index-Read2-EGFP (CAAGCAGAAGACGGCATACGAGATAGGATTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGgCATGGACGAGCTGTACAAG) (200 nM each) were used as primers with the NEBNext Ultra II Q5 Master Mix (NEB, Cat #M0544L). Amplification was performed using the following PCR protocol: (1) 33°C for 1 min, (2) 98° for 10 s, then 65°C for 75 s (20-24 cycles), (3) 75°C for 5 min. Reactions were re-pooled during 1X SPRI selection (Beckman, Cat #B23317), which harvested virus projection barcodes library. 431-437bp (with 120bp adaptors) libraries were sequenced using Illumina HiSeq X Ten.

value: retrograde labeled vmPFC neurons

tag: strain

tag: Sex

value: Male

tag: age

value: 8 weeks


title: mouse 4-6, FAC-Sorted, RNAseq projectome library

description: bar.mat.drop.csv


title: FETAL_brain_IND4_EC

value: fetal brain - GW18

value: Endothelial cells

value: Fetal

value: healthy


title: mouse 1, unsort, RNAseq projectome library

description: bar.mat.drop.csv


title: mouse 2, unsort, RNAseq projectome library

description: bar.mat.drop.csv


title: THP-1, 48hr, 200UMNase

status: Public on Feb 06 2024

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

library_source: other

data_processing:
adapter sequences and poor quality reads were removed with Trimmomatic (version 0.39)
Bowtie2 was used to align the sequences to the T2T reference human genome with the --end-to-end --no-mixed --no-discordant flags
Mitochondrial and duplicate reads were filtered with samtools (version 1.10) and picardtools (version 2.27.3)
Nucleosome footprints (>120bp) for light and heavy digests were calculated with DANPOS3 and the log2 ratio of quantile normalized light to heavy digests was calculated for each time point with deeptools (version 3.5.1) to determine nucleosome sensitivity to MNase digest.
Small fragments (<110bp) from light digests were used for regulatory factor footprinting. Peaks were called with MACS3. Xstreme was used to identify enriched motifs under small fragment footprints and FIMO was used to identify the locations of specific motifs
Assembly: T2T
Supplementary files format and content:
bigwig files of light and heavy digests
bigwig file of small fragments from light digests
bigwig files of nucelosome occupancy and sensitivity to MNase digestion

molecule: other

growth_protocol: Cells were grown in RPMI-1640 media (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO2

extract_protocol:
Cells were crosslinked in 1% v/v formaldehyde (Sigma-Aldrich) and incubated for 10 minutes at room temperature while rocking. Excess formaldehyde was quenched with 125mM glycine and cells were washed twice in PBS. Cells were resuspended in nuclei isolation buffer (10mM HEPES at pH 7.8, 2mM MgOAc2, 0.3M sucrose, 1mM CaCl2 and 1% Triton-X) and pelleted by centrifugation at 1000×g for 10 min at 4°C. Nuclei were washed twice in nuclei isolation buffer and chromatin was digested with either 5U or 200U MNase for 10 minutes at 37°C. MNase reactions were halted with 50mM EDTA. Protein-DNA crosslinks were reversed by treating the MNase-digested nuclei with 0.2 mg/mL proteinase K and 1% sodium dodecyl sulfate, and incubating overnight at 65°C. DNA was isolated using guanidinium-isopropanol and washed with ethanol on a silica column. Mononucleosomal and sub-mononucleosomal DNA was isolated from a 2% agarose gel slice and purified by glycogen precipitation.
MNase sequencing libraries were prepared for each replicate using the Accel-NGS®2S Plus DNA Library Kit (Swift) for Illumina® using 10ng of input DNA from each digestion. Libraries were indexed with the Accel-NGS 2S Unique Dual Indexing Kit and normalized with Normalase. We used a previously validated custom designed Roche Nimblegen SeqCap EZ Library SR to capture 2000 bp regions flanking the Transcription Start Site (TSS) for every pol II gene in the human genome(Druliner et al. 2016; Sexton et al. 2016). The TSS sequences were repeat masked using human COT DNA and library adapters were masked with universal blocking oligos. Biotinylated sequence capture oligos were hybridized to input libraries for 48 hours and purified with streptavidin beads. Enriched sequences were amplified in a 15 cycle PCR amplification using TruSeq primers.

treatment_protocol: Cells were exposed to 25nM phorbol 12-myristate 13-acetate (Sigma-Aldrich) for 48 hours and recovered in complete medium for 24 hours following differentiation

value: PMA derived macrophage

value: PMA

tag: time point

value: 48hr post PMA


title: THP-1, 48hr, 5UMNase


title: THP-1, 12hr, 5UMNase

value: PMA treated monocyte

value: 12hr post PMA


title: THP-1, 24hr, 5UMNase

value: 24hr post PMA


title: THP-1, 12hr, 200UMNase


title: FETAL_periphery_IND5_EC_heart

source_name: fetal periphery organs - Heart - GW15.5

value: fetal periphery organs - Heart - GW15.5

value: Fetal periphery organs


title: THP-1, 4hr, 5UMNase

value: 4hr post PMA


title: THP-1, 8hr, 200UMNase

value: 8hr post PMA


title: THP-1, 8hr, 5UMNase


title: THP-1, 1hr, 200UMNase

value: 1hr post PMA


title: THP-1, 1hr, 5UMNase


title: THP-1, 0hr, 200U MNase

value: monocyte

value: untreated; 0hr


title: THP-1, 0hr, 5U MNase


title: THP-1, 72hr, 5UMNase

value: 72hr post PMA


title: S6_Pericyte

status: Public on Dec 30 2023

city: Chicago

first: Issam

middle: A

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

data_processing:
Nextflow pipeline: nf-core/rnaseq 3.8.1
Raw sequencing QC assessement: FastQC v0.11.9
Adapter trimming: trimgalore 0.6.5
Unique molecules extraction: UMI-tools 1.1.2
Pseudo-alignment and counts: Salmon v1.9.0
Differentially expressed miRNA analysis: Limma 3.52.0 with R version 4.2.1
Assembly: GRCh38.34
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped per gene

source_name: Pericyte

extract_protocol:
RNAs was extracted using TRIzol (Thermo Fisher Scientific, Waltham, United States)
RNA libraries were prepared for sequencing using commercially available SMARTer® Stranded Total RNA-Seq Kit-3-Pico Input (Takara, Shiga, Japan)

value: Pericyte

tag: disease state

value: CCM

tag: disease group

value: Sporadic


title: S6_Neuroglia

source_name: Neuroglia

value: Neuroglia


title: S5_Neuroglia


title: S5_Endothelial

source_name: Endothelial

value: Endothelial


title: C4_Endothelial

value: Control


title: THP-1, 24hr, 200UMNase

value: PMA treated monocyte

value: PMA


title: S4_Pericyte

value: Familial


title: S4_Endothelial


title: C3_Neuroglia


title: C4_Neuroglia


title: S3_Neuroglia


title: C3_Endothelial


title: S3_Endothelial


title: THP-1, 72hr, 200UMNase

value: PMA derived macrophage


title: S3_Pericyte


title: THP-1, 4hr, 200UMNase


title: S2_Pericyte


title: S1_Neuroglia


title: S1_Pericyte


title: S2_Endothelial


title: C2_Pericyte


title: S4_Neuroglia


title: S5_Pericyte


title: C2_Endothelial


title: C1_Neuroglia


title: C4_Pericyte


title: C1_Pericyte


title: C1_Endothelial


title: meningeal CD45+ cells, AAV-Control treated mice, exp1

status: Public on Dec 29 2023

city: Paris

first: Ruchith

last: Singhabahu

address: 47 bd de l'Hôpital

country: France

institute: Institut du Cerveau

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.10.11) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: Dura mater

extract_protocol:
RNA extractions were performed using the Direct-zol™ RNA Microprep kit (R2061) according to the manufacturer’s instructions
RNA library preparation was realized following manufacturer’s recommendations (SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian from Takara).

value: Dura mater

value: Meningeal CD45+ immune cells

value: WT

value: AAV-Control


title: C3_Pericyte


title: meningeal CD45+ cells, AAV-Control treated mice, exp2


title: S2_Neuroglia


title: Ecloacae_SCVGenta_rep1

status: Public on Oct 18 2023

first: Avinash

middle: R

last: Shenoy

address: Rm 4.40A Flowers Bldg, Armstrong Road

department: Dept of Infectious Disease

institute: Imperial College London

description:
SHE3654A7_S56
SRA Run accession: SRR25054839

data_processing:
Sequencing reads were mapped to the E. cloacae ATCC 13047 genome (GCA_000025565, genome assembly ASM2556v1 from Ensembl) using kallisto. Subsequent analyses used Bioconductor packages by importing the output of kallisto using tximport to generate length scaled TPM counts mapped to genes in E. cloacae.
Subsequently, edgeR was used to generate a DGElist object, filter genes with > 1 TPM in all 9 samples, normalise data using the TMM method and log2-transformation.
Analyses used Experiment as a blocking factor for fitting a model using the limma package functions voomWithQualityWeights, duplicateCorrelation and lmFit. Two contrasts were set (SCV vs Control and SCVGenta vs SCV) followed by smoothening in eBayes and the genelist was extracted using topTable. All genes with adjusted P values < 0.01 sorted by "t" are listed.
Assembly: ASM2556v1
Supplementary files format and content: Four processed files are provided as below.
Supplementary files format and content: (1) log2-transformed normalised counts using cpm from edgeR are provided in file "Ecloacae_logCPMnorm_counts.csv".
Supplementary files format and content: (2) Output of tximport using "lengthScaledTPM" option are provided in the file "Ecloacae_lSTPM_counts.csv"
Supplementary files format and content: (3) Fold-change for genes in the SCV vs Control comparison in file "SCV_vs_Control_FC.scv"
Supplementary files format and content: (4) Fold-change for genes in the SCVGenta vs SCV comparison in file "SCVGenta_vs_SCV_FC.scv"

organism: Enterobacter cloacae subsp. cloacae ATCC 13047

source_name: gentamicin-associated petite E. cloacae

growth_protocol: Exponentially growing cultures of bacteria in LB (50 mL LB in a 250 mL flask), shaking 180 rpm, 37C, up to OD600 of 0.5. "Control" and "SCV" were grown similarly.

extract_protocol:
Experiments were performed on three separate occasions to collect biologically independent samples and purified together using Qiagen RNeasy kit following manufacturer’s protocol.
RNA sequencing was performed at the Advanced Sequencing facility at the Francis Crick Institute. Samples were normalised to 500 ng and ribosomal RNA was depleted with RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Invitrogen, Cat no. A47335), followed by library preparation with KAPA RNA HyperPrep kit (Roche, kit code KK8541), as according to manufacturer instructions.
The adapter concentration was 7 µM and the libraries were amplified by 9 cycles of PCR. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent Technologies). Libraries were pooled and sequenced on the Illumina NovaSeq6000 in Single read 100 configuration to a read depth of at least 22 M.

treatment_protocol: SCV culture was treated with gentamicin (8 mg/L) for 2 h to collect "SCV_Genta" samples. Other samples were untreated.

value: gentamicin-associated petite E. cloacae

value: wild type

value: gentamicin


title: 7DAP endosperm, replicate 1, scRNAseq

status: Public on Nov 28 2023

city: Beijing

first: Qiang

last: Huo

address: Yuanmingyuan West Road

institute: China Agricultural University

description: 10x Genomics

data_processing:
Raw data were compared, barcoded and quantified by UMI using the Chromium 10x Cell Ranger software package. Samples were normalized and cell clusters were determined using Seurat.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Zea mays

source_name: Endosperm

growth_protocol: B73 inbried line kernels cultivated in the greenhouse of China Agricultural University (Beijing, China)

extract_protocol: Endosperm from maize 80-100 maize kernels from 6 to 8 DAP. Endosperm were incubated in a enzymatic solution to digest cell walls and produce protoplasts. Protoplasts were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' V3 pipeline. Libraries were prepared using Chromium Single Cell 3' Reagent Kit V3.

value: Endosperm

tag: cultivar

value: 7 DAP


title: Ecloacae_SCV_rep2

description:
SHE3654A5_S54
SRA Run accession: SRR25054840

value: untreated


title: Ecloacae_SCV_rep3

description:
SHE3654A6_S55
SRA Run accession: SRR25054840


title: Ecloacae_SCVGenta_rep3

description:
SHE3654A9_S58
SRA Run accession: SRR25054839


title: Ecloacae_Control_rep2

description:
SHE3654A2_S51
SRA Run accession: SRR25054841

source_name: control

value: control


title: Ecloacae_SCVGenta_rep2

description:
SHE3654A8_S57
SRA Run accession: SRR25054839


title: Ecloacae_Control_rep1

description:
SHE3654A1_S50
SRA Run accession: SRR25054841


title: Ecloacae_SCV_rep1

description:
SHE3654A4_S53
SRA Run accession: SRR25054840


title: G17_42_Mutant

status: Public on Aug 09 2023

first: Sigolène

middle: M

last: Meilhac

address: 24 boulevard du Montparnasse

institute: Institut Imagine, Institut Pasteur

description: res_DEseq2.0_(Mut_G17)_vs_(Ctrl_G17).xlsx

data_processing:
Base Calling: Illumina base calling software
Alignement: Hisat2
Abundance mesurement: FeatureCount (R Subread package)
Normalisations / statistical analysis: DESeq2 (R package)
Assembly: Mouse GRCm38
Supplementary files format and content: normalized read counts in G3 or G17 mutant line. For each gene analyzed, the table presents the normalized number of reads for each sample, a mean of the mutant or the wild-type group normalized reads, a ratio of those means and a delta. “Flags_g1” and “Flag_g2” columns represent the number of samples in both groups (mutant and wild-type) for which the gene is considered based on the normalized read count. For all genes, a non-corrected p-value and 2 corrected p-values (Benjamini-Hochberg and Bonferroni) are given.

source_name: microdissected cardiac region

extract_protocol:
Total RNA was extracted in TRIzol-Chloroform and purified using the RNeasy micro Kit (QIAGEN) including DNAse treatment. RNA quality and quantity were assessed by capillary electrophoresis using High Sensitivity RNA reagents with the Fragment Analyzer (Agilent Technologies) and RNA concentration was measured both by spectrophometry using Fragment Analyzer capillary electrophoresis. All RINs were higher than 9.0 and RNA concentration was between xx and yy per sample.
An equimolar pool of the final indexed RNA-Seq libraries was prepared, using the NuQuant system (Nugen), and sequenced on a NovaSeq6000 from Illumina with paired-end reads of 100 bases and a mean sequencing depth of 50 millions per sample

treatment_protocol: Heart regions were microdissected and the tissue was flash frozen in liquid nitrogen

value: E8.5e embryo


title: S1_Endothelial

value: Endothelial

value: CCM


title: G17_41_Mutant


title: G17_33_Mutant


title: C2_Neuroglia

value: Neuroglia

value: Control


title: G17_37_Control

value: WT littermate


title: meningeal CD45+ cells, AAV-VEGF-C treated mice, exp2

value: Dura mater

value: AAV-VEGF-C


title: G17_35_Control


title: G17_29_Control


title: G3_30_Mutant


title: G3_29_Mutant


title: G3_23_Mutant


title: G3_31_Mutant


title: Ecloacae_Control_rep3

description:
SHE3654A3_S52
SRA Run accession: SRR25054841


title: G3_21_Control


title: G3_20_Control


title: G3_18_Control


title: G3_16_Control


title: meningeal CD45+ cells, AAV-VEGF-C treated mice, exp1

value: Meningeal CD45+ immune cells

value: WT


title: G17_36_Mutant


title: no_nic_T3_R1

status: Public on Aug 07 2023

city: Iași

first: Marius

last: Mihasan

state: Iași

address: Bulevardul Carol I, nr. 20 A

department: Biology

country: Romania

institute: Alexandru Ioan Cuza University of Iasi

description: No nicotine, 24 HAI, replicate 1

data_processing:
Raw data was basecalled using Guppy_6.3.2 with high accuracy (configuration file rna_r9.4.1_70bps_hac.cfg).
Basecalled data was analysed (quality checks to differential gene expression analysis) using the nf-core/nanoseq v 3.1.0 pipeline (10.1038/s41587-020-0439-x) and the stringtie2 branch for transcript reconstruction.
Assembly: Genome Build: ASM2191934v1 / NCBI_Assembly:GCA_021919345.1
Supplementary files format and content: stringtie.merged.gtf: extended annotation that combines provided reference GTF with GTF file from each sample via StringTie2 Merge (takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts; this mode is used in the differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples).
Supplementary files format and content: counts_gene.txt: gene expression estimates calculated by featureCounts.
Supplementary files format and content: deseq2.results.txt: a TXT file that contains differential gene expression

organism: Paenarthrobacter nicotinovorans

growth_protocol: The strain was grown on citrate medium consisting of 0.2% Na-citrate, 34 mM Na2HPO4, 22 mM KH2PO4, 0.2% (NH4)2SO4, pH 7.0, 5% mineral solution (doi: 10.1515/bchm2.1961.323.1.236), 0.1 mg mL–1 biotin, and 35 μg mL–1 kanamycin.

extract_protocol:
Native RNA was extracted with the Promega SV Total RNA Isolation System (after 8.C., step 7 were added 8 µl of Proteinase K 20 mg/ml (Promega) and samples were incubated at 37⁰ C for 10 min before proceeding with 4.E, Steps 1–9).
Native RNA was polyadenylated using the Lucigen Poly(A) Polymerase Tailing Kit. Library preparation was performed with the Oxford Nanopore Technologies (ONT) Direct RNA sequencing kit (SQK-RNA002) and an adapted protocol for the MinION Flongle flowcells (https://www.protocols.io/view/flongle-directrna-library-preparation-kqdg35847v25/v1 ).

treatment_protocol: Cultures were grown without nicotine (no_nic samples) or supplemented with 0.3 mM nicotine (nic samples)

value: control, no nicotine

tag: time

value: 24 hours


title: no_nic_T2_R2

description: No nicotine, 10 HAI, replicate 2

value: 10 hours


title: nic_T3_R3

description: Nicotine, 24 HAI, replicate 3

value: nicotine 0.3 mM


title: nic_T3_R4

description: Nicotine, 24 HAI, replicate 4


title: no_nic_T1_R2

description: No nicotine, 5 HAI, replicate 2

value: 5 hours


title: no_nic_T3_R2

description: No nicotine, 24 HAI, replicate 2


title: no_nic_T1_R1

description: No nicotine, 5 HAI, replicate 1


title: nic_T3_R1

description: Nicotine, 24 HAI, replicate 1


title: nic_T3_R2

description: Nicotine, 24 HAI, replicate 2


title: G17_20_Control


title: nic_T2_R3

description: Nicotine, 10 HAI, replicate 3


title: nic_T2_R2

description: Nicotine, 10 HAI, replicate 2


title: nic_T2_R4

description: Nicotine, 10 HAI, replicate 4


title: nic_T1_R4

description: Nicotine, 5 HAI, replicate 4


title: nic_T2_R1

description: Nicotine, 10 HAI, replicate 1


title: nic_T1_R3

description: Nicotine, 5 HAI, replicate 3


title: nic_T1_R2

description: Nicotine, 5 HAI, replicate 2


title: nic_T1_R1

description: Nicotine, 5 HAI, replicate 1


title: hMF.413.D500uM

status: Public on Jul 01 2023

city: Madrid

first: Lisardo

last: Bosca

state: Madrid

address: Arturo Duperier 4

department: Metabolism and cellular Signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang etal,2014) for removing the low-quality reads and trimming the Illumina adapter.
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
Assembly: hg38
Supplementary files format and content: Excel file includes Entrez Gene ID and Log2 Fold Change values for differential expression of case vs control

source_name: Monocyte-derived macrophages

growth_protocol: Monocyte-derived human macrophages were isolated from buffy coats by a ficoll gradient, cells were seeded 1h in DMEM without FBS and then cell media was replaced by DMEM+10%FBS for a week until differentiation was observed visually.

extract_protocol:
Total RNA was extracted using TRI Reagent TM Solution (Invitrogen) protocol.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Differentiated macrophages were treated with CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF)20ng/mL for 24h, DETANONOATE 500µM (D500µM) 24h or CK (1h)+DETANONOATE 500µM 24h (D500µM) in RPMI+2%FBS or vehicle (controls RPMI+2%FBS)

tag: group

value: Monocyte-derived macrophages

value: DETA NONOATE 500µM 24h


title: hMF.413.CKs

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 24h


title: no_nic_T3_R3

description: No nicotine, 24 HAI, replicate 3


title: no_nic_T2_R3

description: No nicotine, 10 HAI, replicate 3


title: no_nic_T2_R1

description: No nicotine, 10 HAI, replicate 1


title: Colon Naive ZT20 rep 4

status: Public on Mar 15 2023

city: Manchester

first: Julie

middle: Elizabeth

last: Gibbs

address: Oxford Road

department: FBMH

institute: University of Manchester

data_processing:
Sequencing library preparation and sequencing was performed by the University of Manchester Genomic Technologies Core Facility.  Sample quality was determined using a 2200 TapeStation (Agilent Technologies).  Libraries were generated using the TruSeq Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol.  The multiplexed libraries were analysed by paired-end sequencing on a HiSeq 4000 instrument (76 + 76 cycles, plus indices), then demultiplexed and converted using bcl2fastq software (v2.17.1.14, Illumina).
Adaptors were removed and ends trimmed using Trimmomatic (v0.36), then reads were mapped against the mouse genome (mm10/GRCm38) using STAR (v2.5.3).
Reads were counted in R using the Rsubread (v1.28.1),
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colon

extract_protocol:
A 5mm section of mid-colon was snap frozen and prepared for RNA Seq.  Tissue was transferred to a Lysing matrix D tube containing Trizol.  Tissue was homogenized using a Bead Mill homogenizer.  RNA was extracted using chloroform then precipitated using isopropanol.  After washing with 75% ethanol, the RNA pellet was re-suspended in RNase free water (50mg/ml).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male DBA/1 mice (Envigo, 9–10 weeks) were immunised (day 0) with intradermal injections (50μL in two separate sites above the tail) of bovine type II collagen (MD biosciences, Switzerland) emulsified in Complete Freund’s adjuvant (CFA, MD biosciences) at 1mg/ml. A boost of bovine type II collagen (diluted to 1mg/ml in saline) was administered intraperitoneally on day 21. Both the immunisation and the boost were administered in the mid-light phase (ZT6). Disease developed from day 18 (peak incidence at day 23 – day 29) and animals were scored for disease severity on a scale of 0–4 per limb (59). Colonic tissue samples were collected at ZT0, ZT4, ZT8, ZT12, ZT16 or ZT20, 7 days after the development of disease symptoms in CIA mice or at matched time points in naïve co-housed  mice.

value: Colon

value: Naïve


title: Colon Naive ZT20 rep 3


title: Colon Naive ZT20 rep 5


title: no_nic_T1_R3

description: No nicotine, 5 HAI, replicate 3


title: Colon Naive ZT20 rep 2


title: Colon Naive ZT20 rep 1


title: Colon Naive ZT16 rep 5


title: Colon Naive ZT16 rep 4


title: Colon Naive ZT16 rep 3


title: Colon Naive ZT12 rep 5


title: Colon Naive ZT16 rep 2


title: Colon Naive ZT16 rep 1


title: Colon Naive ZT12 rep 4


title: Colon Naive ZT12 rep 2


title: Colon Naive ZT12 rep 3


title: Colon Naive ZT8 rep 5


title: Colon Naive ZT12 rep 1


title: Colon Naive ZT8 rep 3


title: Colon Naive ZT8 rep 4


title: Colon Naive ZT8 rep 1


title: Colon Naive ZT4 rep 4


title: Colon Naive ZT4 rep 3


title: Colon Naive ZT4 rep 5


title: Colon Naive ZT4 rep 2


title: Colon Naive ZT4 rep 1


title: Colon Naive ZT0 rep 1


title: Colon Naive ZT0 rep 4


title: Colon CIA ZT20 rep 4

value: CIA


title: Colon Naive ZT0 rep 2


title: Colon CIA ZT20 rep 1


title: Colon CIA ZT20 rep 3


title: Colon Naive ZT8 rep 2


title: Colon CIA ZT20 rep 2


title: Colon CIA ZT16 rep 5


title: Colon CIA ZT20 rep 5


title: Colon CIA ZT16 rep 3


title: Colon CIA ZT12 rep 5


title: Colon CIA ZT16 rep 4


title: Colon CIA ZT16 rep 2


title: Colon CIA ZT12 rep 1


title: Colon CIA ZT12 rep 3


title: Colon CIA ZT12 rep 2


title: Colon CIA ZT16 rep 1


title: Colon CIA ZT8 rep 5


title: Colon CIA ZT8 rep 4


title: Colon CIA ZT8 rep 3


title: Colon CIA ZT8 rep 1


title: Colon CIA ZT4 rep 4


title: Colon CIA ZT8 rep 2


title: Colon CIA ZT4 rep 5


title: Colon Naive ZT0 rep 3


title: Colon CIA ZT4 rep 3


title: Colon CIA ZT4 rep 2


title: Colon CIA ZT0 rep 5


title: Colon CIA ZT4 rep 1


title: Colon CIA ZT0 rep 4


title: Colon Naive ZT0 rep 5


title: Colon CIA ZT0 rep 3


title: Colon CIA ZT12 rep 4


title: Colon CIA ZT0 rep 1


title: IL08_Pool5

status: Public on Dec 18 2022

city: Lausanne

first: Elia

last: Magrinelli

state: Canto Vaud

address: Rue du Bugnon 9

department: Department of Neuroscience

country: Switzerland

institute: University of Lausanne

description: Excitatory cell from a P7 mouse cerebral cortex S1 area born at E13.5, as identified from a FlashTag injection

data_processing:
While capturing cells we recorded the radial position of each cell as a measure of the distance from the white matter and the pia.
Before capturing the cells we measured membrane resistance, Ih current and capacitance
RNAseq reads were aligned to the GRCm38 genome assembly using STAR aligner
The number of reads per transcript was calculated with the open-source HTSeq Python library
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files containing count table for every replicated sample per condition

source_name: P7 mouse cerebral cortex S1 E13.5 born cortical cells

extract_protocol:
P7 E13.5 born Cortical neurons where captured by preparing 300um thick acute coronal brain slices maintained in aCSFcontaining 119 mM NaCl, 2.5 mM KCl, 1.3 mM MgCl2, 2.5 mM CaCl2, 1.0 mM NaH2PO4, 26.2 mM NaHCO3 and 11 mM glucose, bubbled with 95% O2 and 5% CO2. Slices were maintained 30 minutes in bath at 32°C and then at room temperature. The whole-cell voltage-clamp recording technique was used (30–32 °C, 2–3 ml min−1, submerged slices) to measure the holding currents and Ih current of GFP+ FlashTag neurons. The internal solution contained 140 mM KCH3O3S, 4 mM NaCl, 2 mM MgCl2, 0.2 mM EGTA, 10 mM HEPES, 3 mM Na2ATP, 5 mM sodium creatine phosphate, 0.33 mM GTP and 1µl of 1U/mL of RNase inhibitor (Takara). After recording the cells were acquired by manual suction until visual confirmation of the capture of the cytosolic volume.
cDNA libraries were prepared for sequencing using standard Illumina protocols using SMART-Seq v4 3’ DE kit (Clontech, # 635040) and sequenced using HiSeq 4000 in 100 pairbase length fragments for a minimum of 1 million reads per sample.

value: CD1 Wild type

value: cortical cells

tag: radial position (0=white matter, 1=pia)

tag: membrane resistance (mv)

tag: ih current (pa)

tag: capacitance (pf)


title: IL12_Pool1

tag: genotype


title: IL09_Pool2

tag: cell type


title: IL10_Pool5


title: IL10_Pool1


title: IL08_Pool3


title: IL08_Pool4


title: IL09_Pool3


title: IL09_Pool4


title: IL11_Pool1


title: IL08_Pool2


title: IL09_Pool1


title: IL08_Pool1


title: IL09_Pool5


title: IL07_Pool5


title: IL07_Pool4


title: IL07_Pool2


title: IL07_Pool3


title: IL07_Pool1


title: IL06_Pool5


title: IL06_Pool4


title: Colon CIA ZT0 rep 2

tag: tissue

tag: treatment


title: IL06_Pool3

tag: strain


title: IL05_Pool5


title: IL06_Pool1


title: IL05_Pool3


title: IL05_Pool4


title: IL06_Pool2


title: IL05_Pool2


title: IL04_Pool3


title: IL04_Pool2


title: IL04_Pool5


title: IL03_Pool5


title: IL03_Pool3


title: IL04_Pool1


title: IL04_Pool4


title: IL03_Pool2


title: IL02_Pool4


title: IL03_Pool1


title: IL02_Pool3


title: IL02_Pool2


title: IL05_Pool1


title: IL02_Pool1


title: IL01_Pool4


title: IL01_Pool2


title: IL01_Pool1


title: IL01_Pool5


title: IL01_Pool3


title: Putamen_PD4

status: Public on Dec 05 2022

city: St. Louis

first: Guoyan

last: Zhao

state: MO

address: 660 South Euclid Ave.

department: Genetics & Neurology

institute: Washington University

data_processing:
Cellranger v3.0.2 (10x Genomics) was used to align reads to reference genome and generate feature-barcode matrices.
Seurat v3.08 was used for cell quality control, cell clustering, marker gene detection and differential expressed gene identification.
Genome_build: hg38 human pre-mRNA reference genome
Supplementary_files_format_and_content: barcodes.tsv.gz , barcode for cells
Supplementary_files_format_and_content: features.tsv.gz , feature names and identifiers
Supplementary_files_format_and_content: matrix.mtx.gz , Matrix table with raw gene counts for every gene and every cell in the sample.

source_name: Putamen

extract_protocol:
The putamen tissue (~50 mg) was carefully dissected out with a scalpel at -20 °C using the autoradiography images of dopaminergic biomarkers. Nuclei suspension was prepared following 10X protocol.
Purified nuclei were used to generate 10X Genomics libraries using Chromium Single Cell 3′ V3 Reagent Kits  according to the 10X Genomics protocol.

tag: brain

value: brain

value: Putamen

tag: diagnosis

value: Parkinson disease (PD)


title: Putamen_PD3


title: Putamen_AD4

value: Alzheimer disease (AD)


title: Putamen_AD3


title: Putamen_PD1


title: Putamen_AD2


title: Putamen_CTRL4

value: control


title: Putamen_AD1


title: Putamen_PD2


title: IL03_Pool4

tag: age


title: IL02_Pool5


title: DSF12 post-treatment1

status: Public on Nov 27 2022

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of sample DSF011 were processed as follows.  Adapter trimming of sequencing data was performed by using cutadapt 2.10.Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.14.0.Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.7.Associated cDNA reads were mapped to reference RNA (build GRCh38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 2 -N 1 –very-sensitive-local –norc –seed 656565 –reorder. Then, cell barcode information of each read were added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted by using mawk. Resulted count data was converted to genes x cells matrix file and inflection threshold of the knee-plot was detected by using DropletUtils package in R 3.6.3.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix_inflection*.txt.gz file

source_name: gastric tumor biopsy

extract_protocol:
Single cell suspensions were prepared form tumor tissue specimens by enzymatic digestion and subjected to single-cell RNA preparation using BD Rhapsody.
10000 cells were loaded onto BD Rhapsody cartrige and captured cell number was asessed by BD Rhapsody scanner. Cell lysis, mRNA trap, cDNA synthesis, and primer digestion were performed according to the manufacture's instruction.
cDNA amplification was performed by TAS-Seq protocol (Shichino et al BioRxiv 2021). Sequencing libraries from amplified cDNAs were produced by using NEB UltraII FS Kit (New England Biolabs) with some modifications. Sequencing was performed by using a Novaseq S2 200 cycle kit and a Novaseq 6000 sequencer (Illumina) according to the manufacture's instructions. 20% PhiX spike-in was used for sequencing.
BD Rhapsody WTA

treatment_protocol: Patients were treated orally disulfiram 3 times daily with intravenous nivolumab every two weeks with one cycle as four weeks.

value: gastric tumor biopsy

tag: disease state

value: gastric cancer

value: CD45+ single cell suspension

tag: Sex

value: female

tag: organ

value: stomach

tag: mmr

value: pMMR

value: disulfiram (160mg) plus nivolumab

tag: outcome

value: SD


title: Putamen_CTRL2


title: DSF13 post-treatment

value: male

value: PR


title: Putamen_CTRL3


title: Putamen_CTRL1


title: DSF13 pre-treatment


title: DSF12 post-treatment2


title: DSF07 pre-treatment

value: dMMR


title: DSF07 post-treatment


title: DSF12 pre-treatment


title: DSF11 post-treatment


title: DSF11 pre-treatment


title: DSF10 post-treatment

value: NE


title: DSF08 pre-treatment

value: PD


title: DSF06 post-treatment

value: dMMR (MSS)


title: DSF10 pre-treatment


title: DSF06 pre-treatment


title: DSF05 pre-treatment


title: DSF03 pre-treatment


title: DSF02 post-treatment


title: DSF04 pre-treatment


title: DSF01 post-treatment


title: DSF02 pre-treatment


title: DSF03 post-treatment


title: DSF01 pre-treatment


title: CTX_12_HD_8wk

status: Public on Nov 14 2022

city: Irvine

first: Jie

last: Wu

address: Sprague Hall 332

department: Biological Chemistry

institute: University of California, Irvine

description: 8wk R6/2 cortex single nuclei RNAseq

data_processing:
Illumina Casava 1.8 software was  used for basecalling.
Sequenced reads were aligned to mm10 whole transcriptome using cellranger v3.0.2:  cellranger count  --transcriptome=ref_premrna/mm10_premrna/
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in every cell in every sample

source_name: Cortex

extract_protocol:
Single nuclei were isolated from ½ hemisphere striatal or cortex in Nuclei EZ Lysis buffer (Cat#NUC101-1KT, Sigma-Aldrich) and incubated for 5 min. Samples were passed through a 70μm filter and incubated in additional lysis buffer for 5 min and centrifuged at 500 g for 5 min at 4°C before two washes in Nuclei Wash and   Resuspension buffer (1xPBS, 1% BSA, 0.2U/μl RNase inhibitor). Nuclei were FACS sorted using DAPI to further isolate single nuclei and remove additional cellular debris. These nuclei were run on the 10x Chromium Single cell 3’ gene expression v3 platform.
RNA libraries were prepared for sequencing using 10x Genomics single cell v3 and standard Illumina protocols

value: Cortex

tag: condition

value: 8week old


title: CTX_10_WT_8wk

description: 8wk NT cortex single nuclei RNAseq

value: NT


title: CTX_11_HD_8wk

description: 8wk R6/2 cortex single nuclei RNAseq


title: CTX_9_WT_8wk

description: 8wk NT cortex single nuclei RNAseq


title: CTX_8_HD_12wk

description: 12wk R6/2 cortex single nuclei RNAseq

value: 12 week old


title: CTX_7_HD_12wk

description: 12wk R6/2 cortex single nuclei RNAseq


title: CTX_5_WT_12wk

description: 12wk NT cortex single nuclei RNAseq


title: CTX_6_WT_12wk

description: 12wk NT cortex single nuclei RNAseq


title: CTX_2_HD_12wk

description: 12wk R6/2 cortex single nuclei RNAseq


title: CTX_4_HD_8wk

description: 8wk R6/2 cortex single nuclei RNAseq


title: STR_12_HD_8wk

description: 8wk R6/2 striatum single nuclei RNAseq

source_name: Striatum

value: Striatum


title: STR_10_WT_8wk

description: 8wk NT striatum single nuclei RNAseq


title: STR_4_HD_8wk

description: 8wk R6/2 striatum single nuclei RNAseq


title: STR_11_HD_8wk

description: 8wk R6/2 striatum single nuclei RNAseq


title: STR_3_WT_8wk

description: 8wk NT striatum single nuclei RNAseq


title: STR_8_HD_12wk

description: 12wk R6/2 striatum single nuclei RNAseq


title: STR_6_WT_12wk

description: 12wk NT striatum single nuclei RNAseq


title: STR_2_HD_12wk

description: 12wk R6/2 striatum single nuclei RNAseq


title: STR_7_HD_12wk

description: 12wk R6/2 striatum single nuclei RNAseq


title: STR_9_WT_8wk

description: 8wk NT striatum single nuclei RNAseq


title: STR_1_WT_12wk

description: 12wk NT striatum single nuclei RNAseq


title: cdk8K185_3

status: Public on Nov 09 2022

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

data_processing:
RNA-Star alignment to dm6 reference with default setting
Gathering counts with FeatureCount with default setting
DESeq2 to normalize counts and generate differential gene expression table with p.adj < 0.05 filter
ClusterProfiler for pathway enrichment
Assembly: dm6
Supplementary files format and content: csv, count table
Supplementary files format and content: excel, differential gene expression table

organism: Drosophila melanogaster

source_name: whole 3rd instar larvae

extract_protocol:
The total RNA from ten third-instar larvae of w1118 (as the wild-type control) and Cdk8K185 homozygotes at the wandering stage (triplicate for each genotype) was extracted using 1.0 ml TRIzol Regent (Invitrogen), and then purified using an RNeasy Mini Kit (Qiagen, 74104) following the manufacturer instructions.
Standard RNA-seq preparation with Illumina RNA-seq kit

value: whole 3rd instar larvae


title: w1118_3


title: w1118_1


title: w1118_2


title: cdk8K185_1


title: cdk8K185_2


title: SOR1

status: Public on Nov 01 2022

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

data_processing:
Raw files were processed with spaceranger-1.2.2.
Outputs for each samples are provided in tar.gz files.
Assembly: mm10
Supplementary files format and content: Compressed directory containing spaceranger output. _filtered_feature_bc.matrix.h5 contains expression data. Images are provided as low and high resolution PNG, and scaling information is provided in scalefactors_json.json. Mapping between image coordinates and spot identifiers are provided in tissue_positions_list.csv.

source_name: brain

extract_protocol:
Mouse brain section per mouse was cut at 10 µm thickness and mounted onto each Visium slide capture area. After H&E staining, each bright-field image was taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 18 minutes, as established in the tissue optimization assay.  The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.
Libraries were constructed according to the 10x Visium library construction protocol and sequenced by Illumina NovaSeq6000.

value: brain

value: spatial object recognition training


title: SOR3


title: HC3

value: home cage


title: CTX_3_WT_8wk

description: 8wk NT cortex single nuclei RNAseq


title: CTX_1_WT_12wk

description: 12wk NT cortex single nuclei RNAseq


title: STR_5_WT_12wk

description: 12wk NT striatum single nuclei RNAseq


title: HC1


title: HC2


title: Ageing, H3K9me3, Paired-Tag, RNA#10

status: Public on Sep 13 2022

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

description:
Processed data file(s):
paired_tag_h3k9me3_bigwig.tar
paired_tag_rna_2020_09_21_remove_lowqual.RDS

data_processing:
Library strategy: Paired-Tag
base-calling use bcl2fastq
Alignment was performed using bowtie2 for snATAC-seq and subsequently analyzed using SnapATAC package. snRNA-seq was analyzed by cellranger and Seurat. Paired-tag analysis was carried out with the scripts available from https://github.com/cxzhu/Paired-Tag.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for snATAC-seq and DNA part of paired-tag; seurat object for snRNA-seq and RNA part of paired-tag. barcode_list files contain the p7 and p5 barcodes for demultiplexing snATAC-seq libraries. Sample_demultiplex_info file contains the meta information (barcode file and range) for demultiplexing snATAC-seq libraries.
Supplementary_files_format_and_content: List of files:
Supplementary_files_format_and_content: barcodes_hiSeq2500.txt (barcode_list)
Supplementary_files_format_and_content: barcodes_nextSeq_comp.txt (barcode_list)
Supplementary_files_format_and_content: barcodes_nextSeq_comp_768_p7.txt (barcode_list)
Supplementary_files_format_and_content: demultiplex.sample_info.txt (sample_demultiplex_info)
Supplementary_files_format_and_content: DH_final_seurat_object.RDS (Seruat.Object)
Supplementary_files_format_and_content: FC_final_seurat_object.RDS (Seruat.Object)
Supplementary_files_format_and_content: paired_tag_rna_2020_09_21_remove_lowqual.RDS (Seruat.Object)
Supplementary_files_format_and_content: BM.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: DH.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: FC.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: HT.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: LM.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: paired_tag_h3k9me3_bigwig.tar (bigWig)

source_name: Mix of Dorsal Hippocampus and Frontal Cortex

extract_protocol: Single-cell suspension were prepared from douncing of the frozen tissues, in Doucing Buffer with Protease/RNase Inhibitor cocktail (DBI: 0.25 M sucrose [Sigma, S7903], 25 mM KCl [Sigma, P9333], 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT [Sigma, D9779], 1X Protease Inhibitor, 0.5 U/µL RNase OUT and 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X 100 (Sigma T9284). The cell suspension was then filtered by 30 µm Cell-Tric (Sysmex) and spun-down for 10 min, 1,000 g at 4 °C. After washing the cell pellets with DBI and spun-down again, NIB with 0.2% IGEPAL CA-630 were added to resuspend the nuclei pellets and rotate for 10 min at 4 °C. The nuclei were counted by BioRad TC20 cell counter and proceed to Paired-tag experiments immediately.Libraries were constructed by Paired-tag workflow, briefly: First, permeabilized nuclei were incubated with antibodies targeting chromatin regions of interest to trigger the targeted binding of protein A-fused Tn5. Tagmentation reaction and reverse transcription (RT) were then sequentially performed: specifically, reactions were carried out in 12 different wells, with the same set of barcodes in transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy was used to introduce the 2nd and 3rd rounds of barcodes to nuclei, by sequential attaching well-specific DNA barcodes from 96-well plates to the 5’-end of both DNA fragments and cDNA from RT. Lastly, barcoded nuclei were divided into sub-libraries and lysed, the DNA/cDNA was purified and subjected to an optimized “amplify-and-split” strategy based on that we previously developed, to give rise DNA and RNA libraries for sequencing

value: mix

tag: sequencing method

value: paired-tag


title: Ageing, H3K9me3, Paired-Tag, RNA#11

value: Mix of Dorsal Hippocampus and Frontal Cortex

value: male


title: Ageing, H3K9me3, Paired-Tag, RNA#7


title: Ageing, H3K9me3, Paired-Tag, RNA#5


title: Ageing, H3K9me3, Paired-Tag, RNA#8


title: Ageing, H3K9me3, Paired-Tag, RNA#3


title: Ageing, H3K9me3, Paired-Tag, RNA#6


title: Ageing, H3K9me3, Paired-Tag, RNA#2


title: Ageing, H3K9me3, Paired-Tag, RNA#1


title: Ageing, H3K9me3, Paired-Tag, DNA#8

tag: chip antibody


title: Ageing, H3K9me3, Paired-Tag, DNA#11


title: Ageing, H3K9me3, Paired-Tag, DNA#7


title: Ageing, H3K9me3, Paired-Tag, DNA#9


title: Ageing, H3K9me3, Paired-Tag, DNA#10


title: SOR2


title: Ageing, H3K9me3, Paired-Tag, DNA#6


title: Ageing, H3K9me3, Paired-Tag, DNA#2


title: Ageing, H3K9me3, Paired-Tag, DNA#5


title: Ageing, H3K9me3, Paired-Tag, DNA#1


title: RNA.FC.18.rep2

description:
Processed data file(s):
FC_final_seurat_object.RDS

data_processing:
base-calling use bcl2fastq
Alignment was performed using bowtie2 for snATAC-seq and subsequently analyzed using SnapATAC package. snRNA-seq was analyzed by cellranger and Seurat. Paired-tag analysis was carried out with the scripts available from https://github.com/cxzhu/Paired-Tag.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for snATAC-seq and DNA part of paired-tag; seurat object for snRNA-seq and RNA part of paired-tag. barcode_list files contain the p7 and p5 barcodes for demultiplexing snATAC-seq libraries. Sample_demultiplex_info file contains the meta information (barcode file and range) for demultiplexing snATAC-seq libraries.
Supplementary_files_format_and_content: List of files:
Supplementary_files_format_and_content: barcodes_hiSeq2500.txt (barcode_list)
Supplementary_files_format_and_content: barcodes_nextSeq_comp.txt (barcode_list)
Supplementary_files_format_and_content: barcodes_nextSeq_comp_768_p7.txt (barcode_list)
Supplementary_files_format_and_content: demultiplex.sample_info.txt (sample_demultiplex_info)
Supplementary_files_format_and_content: DH_final_seurat_object.RDS (Seruat.Object)
Supplementary_files_format_and_content: FC_final_seurat_object.RDS (Seruat.Object)
Supplementary_files_format_and_content: paired_tag_rna_2020_09_21_remove_lowqual.RDS (Seruat.Object)
Supplementary_files_format_and_content: BM.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: DH.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: FC.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: HT.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: LM.bigwigs.tar (bigWig)
Supplementary_files_format_and_content: paired_tag_h3k9me3_bigwig.tar (bigWig)

source_name: Frontal Cortex

extract_protocol: Droplet-based Chromium Single Cell 3’ solution (10x Genomics, v3 (hippocampus) and v3.1 chemistry (frontal cortex); Zheng et al., 2017) was used to generate snRNA-seq libraries as described (Wang et al 2020, Hocker et al. 2021).

value: Frontal Cortex

value: 18 month

value: single-nucleus RNA-seq


title: RNA.FC.18.rep1


title: Ageing, H3K9me3, Paired-Tag, DNA#3


title: RNA.FC.10.rep2

value: 10 month


title: Ageing, H3K9me3, Paired-Tag, RNA#9


title: RNA.FC.03.rep2

value: 3 month


title: RNA.FC.10.rep1


title: Ageing, H3K9me3, Paired-Tag, RNA#4


title: RNA.FC.03.rep1


title: 3 factor-PC

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

description: droplet-based single cells

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v0.5.3) used for cell barcode and UMI counting
STAR (v2.5.3a_modified) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.1) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: txt files include UMI counts for each cell barcode and genes

growth_protocol: PCs were cultured in pericyte medium. MEFs were cultured in MEF medium. pOPCs and iOPCs were cultured in OPC medium. The cells were cultured in a humidified incubator at 37°C under 5% CO2.

extract_protocol:
Trypsin-EDTA dissociated single cells were counted using Luna-II automated cell counter (Logos Biosystems) and captured using the ddSEQ system (Illumina-BioRad).
Libraries were prepared according to the manufacturer’s instructions using SureCell WTA 3′ Library Prep Kit (Illumina)
3' single cell RNA-Seq using cell barcodes and unique molecular identifiers (UMIs).

treatment_protocol: PC and MEFs were transduced with virues containing Olig2/Sox10 or Olig2/Sox10/Nkx6.2

value: primary mouse cerebral pericytes (PC)

value: transduced with virues containing Olig2/Sox10/Nkx6.2


title: RNA.DH.18.rep2

description:
Processed data file(s):
DH_final_seurat_object.RDS

source_name: Dorsal Hippocampus

value: Dorsal Hippocampus


title: 2 factor-PC

description: droplet-based single cells

value: transduced with virues containing Olig2/Sox10


title: 3 factor-MEF

description: droplet-based single cells

value: embryo

value: mouse embryonic fibroblasts (MEF)


title: RNA.DH.18.rep1


title: Ageing, H3K9me3, Paired-Tag, DNA#4


title: primary mouse cerebral pericytes

description: droplet-based single cells

source_name: PC

value: brain


title: RNA.DH.10.rep2


title: RNA.DH.10.rep1


title: Ageing, H3K9me3, Paired-Tag, RNA#25, batch2


title: ATAC.FC.rep1

description:
Processed data file(s):
FC.bigwigs.tar
barcodes_hiSeq2500.txt
demultiplex.sample_info.txt

extract_protocol: Combinatorial barcoding snATAC-seq was performed as described previously (Cusanovich et al., 2015, Fang et al. 2021, Hocker et al. 2021, Wang et al. 2020) and the protocol for library preparation can be found here:  https://www.protocols.io/edit/snatac-seq-library-generation-using-combinatorial-bpwcmpaw

value: single-nucleus ATAC-seq


title: ATAC.BM

description:
Processed data file(s):
BM.bigwigs.tar
barcodes_nextSeq_comp_768_p7.txt
demultiplex.sample_info.txt

source_name: Bone Marrow

value: Bone Marrow

value: mix


title: Ageing, H3K9me3, Paired-Tag, RNA#28, batch2

value: Mix of Dorsal Hippocampus and Frontal Cortex

value: paired-tag


title: RNA.DH.03.rep1

value: male


title: RNA.DH.03.rep2


title: ATAC.LM.rep1

description:
Processed data file(s):
LM.bigwigs.tar
barcodes_nextSeq_comp.txt
demultiplex.sample_info.txt

source_name: Leg Muscle

value: Leg Muscle


title: Ageing, H3K9me3, Paired-Tag, RNA#23, batch2


title: Ageing, H3K9me3, Paired-Tag, RNA#21, batch2


title: Ageing, H3K9me3, Paired-Tag, DNA#26, batch2


title: Ageing, H3K9me3, Paired-Tag, DNA#24, batch2


title: Ageing, H3K9me3, Paired-Tag, DNA#25, batch2


title: Ageing, H3K9me3, Paired-Tag, DNA#22, batch2


title: mouse embryonic fibroblasts

description: droplet-based single cells

source_name: MEF


title: Ageing, H3K9me3, Paired-Tag, RNA#24, batch2


title: 2 factor-MEF

description: droplet-based single cells


title: ATAC.FC.rep2

description:
Processed data file(s):
FC.bigwigs.tar
barcodes_nextSeq_comp.txt
demultiplex.sample_info.txt

value: Frontal Cortex


title: ATAC.HT.rep1

description:
Processed data file(s):
HT.bigwigs.tar
barcodes_nextSeq_comp.txt
demultiplex.sample_info.txt

source_name: Heart

value: Heart


title: Ageing, H3K9me3, Paired-Tag, RNA#26, batch2


title: ATAC.DH.rep1

description:
Processed data file(s):
DH.bigwigs.tar
barcodes_nextSeq_comp.txt
demultiplex.sample_info.txt


title: ATAC.LM.rep2


title: Ageing, H3K9me3, Paired-Tag, DNA#27, batch2


title: ATAC.DH.rep2


title: Ageing, H3K9me3, Paired-Tag, DNA#23, batch2


description: droplet-based single cells

source_name: pOPC

value: primary oligodendrocyte progenitor cells (pOPC)


title: Ageing, H3K9me3, Paired-Tag, DNA#28, batch2


title: Ageing, H3K9me3, Paired-Tag, RNA#27, batch2


title: Ageing, H3K9me3, Paired-Tag, RNA#22, batch2


title: S379_DNA methylation [203229450268_R08C01]

status: Public on Jul 06 2022

type: genomic

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

institute: University of Massachusetts Amherst

description: normal sperm sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Sperm DNA methylation was assessed using Illumina's EPIC Infinium Methylation Beadchip. Raw idat files were imported into R and within-array normalization and dye-bias equalization of Type I and Type II probes was performed using normal-exponential convolution method (Noob) via  minfi package. Batch effects were corrected with the ComBat function in the sva package while cross-hybridizing probes were removed using the DMRcate package. probes with detection pvalue >0.01 were also exluced prior to downstream analysis.
Processed matrix contains the NOOB-normalized beta values representing the percent CpG methylation for all the CpGs that passed the preprocessing method.

label: Cy3, Cy5

source_name: sperm

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

treatment_protocol: Sperm from semen was extracted using 40% gradient method and purified DNA was isolated our previously developed method of beads, RLT and TCEPS

value: sperm

tag: tag

value: normal

tag: basename

tag: average beta

tag: detection pval


title: S376_DNA methylation [203229450268_R05C01]

description: normal sperm sample

tag: tissue


title: Ageing, H3K9me3, Paired-Tag, DNA#21, batch2

tag: strain


title: S378_DNA methylation [203229450268_R07C01]

description: normal sperm sample


title: S375_DNA methylation [203229450268_R04C01]

description: normal sperm sample


title: S377_DNA methylation [203229450268_R06C01]

description: normal sperm sample


title: ATAC.HT.rep2


title: WBM_4

status: Public on Jul 12 2022

city: New York

first: Anna

last: Yeaton

state: New York

address: 550 1st ave

department: Pathology

institute: NYU Langone

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software.
ADTs and HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome.

source_name: bone marrow

extract_protocol:
Bone marrow cells were isolated from the spine, hips, femur and tibia of mice. A single-cell suspension was generated after red blood cell lysis ACK buffer. Cells were tagged with cell hashing (Stoeckius et al, 2018) oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions and pooled on a 10x Chromium instrument (10x Genomics) to generate barcoded single-cell beads-in emulsion (GEM) according to the manufacturer’s protocol. scRNA-seq libraries were prepared using the Chromium Single-Cell’ v3 Reagent Kit (10x Genomics) following the direction of the manufacturer. The libraries were quantified using Qubit fluorometric quantification (Thermo Fisher Scientific). The quality was assessed on an Agilent Bioanalyzer 2000, obtaining an average library size of 455 bp. Libraries were pooled and normalized to 2 nmol/L and clustered on a HiSeq4000 high output mode on a paired-end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs). Followed by 8 cycles of i7 index (sample index), and 98 bases on R2 (transcript), with a coverage around 130M reads per sample.
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000157; Single Cell 3’ Chip Kit v3 PN-1000123 and i7 Multiplex Kit PN-220103(10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions.

tag: cell type

value: bone marrow cells


title: WBM_2b


title: WBM_3b


title: WBM_2c


title: S374_DNA methylation [203229450268_R03C01]

description: normal sperm sample


title: S369_DNA methylation [203229450256_R06C01]

description: normal sperm sample


title: S368_DNA methylation [203229450256_R05C01]

description: normal sperm sample


title: S370_DNA methylation [203229450256_R07C01]

description: normal sperm sample


title: S373_DNA methylation [203229450268_R02C01]

description: normal sperm sample


title: S366_DNA methylation [203229450256_R03C01]

description: normal sperm sample


title: S371_DNA methylation [203229450256_R08C01]

description: normal sperm sample


title: S367_DNA methylation [203229450256_R04C01]

description: normal sperm sample


title: S364_DNA methylation [203229450256_R01C01]

description: normal sperm sample


title: S365_DNA methylation [203229450256_R02C01]

description: normal sperm sample


title: S361_DNA methylation [203229450243_R06C01]

description: normal sperm sample


title: S360_DNA methylation [203229450243_R05C01]

description: normal sperm sample


title: S358_DNA methylation [203229450243_R03C01]

description: normal sperm sample


title: WBM_1

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software.
ADTs and HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome.
Supplementary_files_format_and_content: WBM_1.hashtags.tsv contains information required to demultiplex the single-cell RNAseq data. It is a matrix of reads mapping to hashtags per cell.


title: WBM_2a


title: S355_DNA methylation [203229450226_R08C01]

description: normal sperm sample


title: S357_DNA methylation [203229450243_R02C01]

description: normal sperm sample


title: S356_DNA methylation [203229450243_R01C01]

description: normal sperm sample


title: S351_DNA methylation [203229450226_R04C01]

description: normal sperm sample


title: S353_DNA methylation [203229450226_R06C01]

description: normal sperm sample


title: S354_DNA methylation [203229450226_R07C01]

description: normal sperm sample


title: S349_DNA methylation [203229450226_R02C01]

description: normal sperm sample


title: S352_DNA methylation [203229450226_R05C01]

description: normal sperm sample


title: S372_DNA methylation [203229450268_R01C01]

description: normal sperm sample


title: S350_DNA methylation [203229450226_R03C01]

description: normal sperm sample


title: S348_DNA methylation [203229450226_R01C01]

description: normal sperm sample


title: S363_DNA methylation [203229450243_R08C01]

description: normal sperm sample


title: S347_DNA methylation [203229450223_R08C01]

description: normal sperm sample


title: S362_DNA methylation [203229450243_R07C01]

description: normal sperm sample


title: S343_DNA methylation [203229450223_R04C01]

description: normal sperm sample


title: S344_DNA methylation [203229450223_R05C01]

description: normal sperm sample


title: S359_DNA methylation [203229450243_R04C01]

description: normal sperm sample


title: S338_DNA methylation [203229450210_R06C01]

description: normal sperm sample


title: S336_DNA methylation [203229450210_R04C01]

description: normal sperm sample


title: S339_DNA methylation [203229450210_R07C01]

description: normal sperm sample


title: S345_DNA methylation [203229450223_R06C01]

description: normal sperm sample


title: S340_DNA methylation [203229450210_R08C01]

description: normal sperm sample


title: S335_DNA methylation [203229450210_R03C01]

description: normal sperm sample


title: S334_DNA methylation [203229450210_R02C01]

description: normal sperm sample


title: S341_DNA methylation [203229450223_R01C01]

description: normal sperm sample


title: S333_DNA methylation [203229450210_R01C01]

description: normal sperm sample


title: S332_DNA methylation [203229450206_R08C01]

description: normal sperm sample


title: S331_DNA methylation [203229450206_R07C01]

description: normal sperm sample


title: S330_DNA methylation [203229450206_R06C01]

description: normal sperm sample


title: S328_DNA methylation [203229450206_R04C01]

description: normal sperm sample


title: S329_DNA methylation [203229450206_R05C01]

description: normal sperm sample


title: S326_DNA methylation [203229450206_R02C01]

description: normal sperm sample


title: S346_DNA methylation [203229450223_R07C01]

description: normal sperm sample


title: S327_DNA methylation [203229450206_R03C01]

description: normal sperm sample


title: S324_DNA methylation [203229450196_R08C01]

description: normal sperm sample


title: S342_DNA methylation [203229450223_R03C01]

description: normal sperm sample


title: S321_DNA methylation [203229450196_R05C01]

description: normal sperm sample


title: S320_DNA methylation [203229450196_R04C01]

description: normal sperm sample


title: S337_DNA methylation [203229450210_R05C01]

description: normal sperm sample


title: S323_DNA methylation [203229450196_R07C01]

description: normal sperm sample


title: S318_DNA methylation [203229450196_R02C01]

description: normal sperm sample


title: S314_DNA methylation [203229450192_R06C01]

description: normal sperm sample


title: S317_DNA methylation [203229450196_R01C01]

description: normal sperm sample


title: S315_DNA methylation [203229450192_R07C01]

description: normal sperm sample


title: S310_DNA methylation [203229450192_R02C01]

description: normal sperm sample


title: S316_DNA methylation [203229450192_R08C01]

description: normal sperm sample


title: S309_DNA methylation [203229450192_R01C01]

description: normal sperm sample


title: S308_DNA methylation [203229450190_R08C01]

description: normal sperm sample


title: S313_DNA methylation [203229450192_R05C01]

description: normal sperm sample


title: S307_DNA methylation [203229450190_R07C01]

description: normal sperm sample


title: S306_DNA methylation [203229450190_R06C01]

description: normal sperm sample


title: S305_DNA methylation [203229450190_R05C01]

description: normal sperm sample


title: S325_DNA methylation [203229450206_R01C01]

description: normal sperm sample


title: S304_DNA methylation [203229450190_R04C01]

description: normal sperm sample


title: S303_DNA methylation [203229450190_R03C01]

description: normal sperm sample


title: S319_DNA methylation [203229450196_R03C01]

description: normal sperm sample


title: S299_DNA methylation [203229450185_R07C01]

description: normal sperm sample


title: S300_DNA methylation [203229450185_R08C01]

description: normal sperm sample


title: S301_DNA methylation [203229450190_R01C01]

description: normal sperm sample


title: S298_DNA methylation [203229450185_R06C01]

description: normal sperm sample


title: S302_DNA methylation [203229450190_R02C01]

description: normal sperm sample


title: S296_DNA methylation [203229450185_R04C01]

description: normal sperm sample


title: S297_DNA methylation [203229450185_R05C01]

description: normal sperm sample


title: S322_DNA methylation [203229450196_R06C01]

description: normal sperm sample


title: S295_DNA methylation [203229450185_R03C01]

description: normal sperm sample


title: S294_DNA methylation [203229450185_R02C01]

description: normal sperm sample


title: S311_DNA methylation [203229450192_R03C01]

description: normal sperm sample


title: S293_DNA methylation [203229450185_R01C01]

description: normal sperm sample


title: S292_DNA methylation [203229450176_R08C01]

description: normal sperm sample


title: S291_DNA methylation [203229450176_R07C01]

description: normal sperm sample


title: S288_DNA methylation [203229450176_R04C01]

description: normal sperm sample


title: S286_DNA methylation [203229450176_R02C01]

description: normal sperm sample


title: S312_DNA methylation [203229450192_R04C01]

description: normal sperm sample


title: S284_DNA methylation [203229450174_R08C01]

description: normal sperm sample


title: S287_DNA methylation [203229450176_R03C01]

description: normal sperm sample


title: S290_DNA methylation [203229450176_R06C01]

description: normal sperm sample


title: S283_DNA methylation [203229450174_R07C01]

description: normal sperm sample


title: S289_DNA methylation [203229450176_R05C01]

description: normal sperm sample


title: S285_DNA methylation [203229450176_R01C01]

description: normal sperm sample


title: S282_DNA methylation [203229450174_R06C01]

description: normal sperm sample


title: S280_DNA methylation [203229450174_R04C01]

description: normal sperm sample


title: S279_DNA methylation [203229450174_R03C01]

description: normal sperm sample


title: S281_DNA methylation [203229450174_R05C01]

description: normal sperm sample


title: S278_DNA methylation [203229450174_R02C01]

description: normal sperm sample


title: S274_DNA methylation [203229450163_R06C01]

description: normal sperm sample


title: S273_DNA methylation [203229450163_R05C01]

description: normal sperm sample


title: S275_DNA methylation [203229450163_R07C01]

description: normal sperm sample


title: S276_DNA methylation [203229450163_R08C01]

description: normal sperm sample


title: S272_DNA methylation [203229450163_R04C01]

description: normal sperm sample


title: S270_DNA methylation [203229450163_R02C01]

description: normal sperm sample


title: S271_DNA methylation [203229450163_R03C01]

description: normal sperm sample


title: S277_DNA methylation [203229450174_R01C01]

description: normal sperm sample


title: S266_DNA methylation [203229450158_R06C01]

description: normal sperm sample


title: S264_DNA methylation [203229450158_R04C01]

description: normal sperm sample


title: S268_DNA methylation [203229450158_R08C01]

description: normal sperm sample


title: S265_DNA methylation [203229450158_R05C01]

description: normal sperm sample


title: S263_DNA methylation [203229450158_R03C01]

description: normal sperm sample


title: S262_DNA methylation [203229450158_R02C01]

description: normal sperm sample