title: NWSN117

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_061

value: male


title: TOX_WT_P14_RNA_S4

status: Public on Mar 01 2025

type: SRA

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
scRNA-seq and scATAC-seq sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using 10x Cell Ranger pipeline (6.0.0) and mm10 genome.
Downstream scRNA-seq amd scATAC-seq analysis was performed in R using Signac and Archr packages
Union peak list was generated using peaks called in ArchR and using macs2 with sample bam files.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered feature-barcode matrices containing only cellular barcodes corresponding to gene expression and chromatin accessibility

molecule: polyA RNA

organism: Mus musculus

source_name: TOX WT CD8 T cells used as control

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
scRNAseq and scATACseq coAssay
The scRNAseq and scATACseq libraries were generated using 10x Genomics multiome coAssay according to the manufacturer’s protocol.

tag: tissue

value: Spleen

tag: genotype

value: WildType

tag: treatment

value: Tamoxifen


title: RNA-SeqofAML primary sample of patient 22

city: Jena

first: Faezeh

last: Ghazvini Zadegan

address: Hans-Knoll-Strase 2

department: Department of Hematology/Oncology, Clinic of Internal Medicine II

country: Germany

institute: Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB)

library_source: transcriptomic

data_processing:
usegalaxy.eu
Initial Assessment with FastQC tool to control the quality of raw sequencing data.
Cutadapt tool was used for trimming adapter sequences, removing low-quality bases, and filtering out sequences of inadequate length.
Aligning sequencing reads to a reference genome is accomplished using STAR (Spliced Transcripts Alignment to a Reference) tool.
Quantifying gene expression levels is performed using the featureCounts tool, while the identification of differentially expressed features is carried out using the DESeq2 tool.
Assembly: manipulation of de Bruijn graphs, via the removal of errors and the simplification of repeated regions
Supplementary files format and content: A tabular file containing normalized abundance measurements generated by the DESeq2 tool

molecule: total RNA

organism: Homo sapiens

source_name: Peripheralblood

value: Peripheralblood

tag: diagnosis

value: AML

tag: Sex

value: F

tag: age (year)


title: Naive_P14_RNA_S1

source_name: Naive CD8 T cells used as control


title: NWSN112

city: Marseille

first: Thibaud

last: Parpaite

address: 51 Bd Pierre Dramard

department: Neural basis of the Somatosensory System

country: France

institute: Aix-Marseille University

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_056

data_processing:
cDNAds libraries were sequenced on an Illumina HiSeq 4000 using single-end reads (50 pb) with an average depth of 4,7 million reads per cell. Image analysis and base calling were performed using RTA version 2.7.7. Demultiplexing was performed using bcl2fastq version 2.20.0.422 and quality control was performed using FastQC v0.11.5n.
Sequences were uniquely mapped to the mm10 genome using Subread (C version 1.4.6-p2) using default values.
Reads mapping to gene exons (GRCm38.90 gene assembly) were counted using featureCounts57 (C version 1.4.6-p2).
Read counts were analyzed in the R/Bioconductor environment (version 4.2.2; www.bioconductor.org). Genes with less than one read per cell on average were removed (n = 26,546 genes remaining) and the count data were normalized between samples by TMM (trimmed mean of the M-values) using the scran package in R Bioconductor (Lun et al., 2016). Quality control plots were performed using scran as described in Lun et al. (2016).
Relative abundance were obtained by sample normalization using TPM (transcripts per kilobase million).
Assembly: mm10
Supplementary files format and content: Text file containing tab-delimited matrices of Transcripts Per Million (TPM) transformed values.
Supplementary files format and content: Text file containing tab-delimited matrices of count data normalized by Trimmed Mean of the M-value (TMM).

source_name: sensory neuron

growth_protocol: All dorsal root ganglion (DRG) sensory neurons were carefully extracted and digested with 2mg/mL of collagenase type II, 5mg/mL of dispase and 5mM of CaCl2 in HBSS media (magnesium- and calcium- free) containing 5mM HEPES, 10mM D-Glucose and 1% penicillin/streptomycin, at pH 7.5 for 1h at 37°C. After removing the supernatant, DRGs were resuspended with Leibovitz-15 complete medium (L-15 supplemented with 5% FCS and 1% penicillin/streptomycin), and then mechanically dissociated with two glass Pasteur pipettes of decreasing diameter (1 and 0.5 mm). The resulting suspensions were subjected to a density gradient centrifugation through Percoll (onto 12.5 and 28% Percoll gradient in Leibovitz-15 complete medium) at a speed of 1300g (acc=6, break=3) for 20 minutes, to eliminate cell debris. Cells were washed with Leibovitz-15 complete medium and centrifuged at 900g (acc=7, break=8) for 5 minutes. Cells were then resuspended in Neurobasal complete medium (Neurobasal A medium supplemented with 2mM L-glutamine, 1% penicillin/streptomycin and B27 1X) containing the following factors: Nerve growth factor (NGF) at 50ng/mL, Glial cell-derived neurotrophic factor (GDNF) at 50ng/mL, Neurotrophin-3 (NT3) at 50ng/mL, Neurotrophin-4 (NT4) at 10ng/mL and Brain Derived Neurotrophic Factor (BDNF) at 5ng/mL. Cells were plated in a Poly-D-lysine- (50 µg/ml) Laminin- (10 µg/ml) coated ibidi Polymer Coverslip Bottom (ibidi μ−Dish 35 mm, high-81156) and incubated at 37°C for 24 hours.

extract_protocol:
After calcium imaging recording, the cytoplasmic content of the neuron was harvested using a glass pipette, transferred into a lysis solution (RNaseOUT 8 U.µl-1, 2% Triton X-100) and flash frozen. Reverse transcription was performed using a SMART-seq v4 Low Input Kit (Clontech) directly on the cell lysate according to the manufacturer’s protocol.
After cDNAds amplification, 50 μl of the sample were subjected to cDNA purification on AMPure XP beads. 0.5 ng of each purified cDNAds were used to construct the sequencing library using Nextera XT kit (Illumina) with fragments over 300-bp length from each neuron.

treatment_protocol: Primary neuronal cultures were stimulated with a focused ultrasound (FUS) transducer (Olympus V317-SM, central frequency of 20 MHz, active diameter of 6.32 mm, focal distance of 12.7 mm). The FUS transducer was tilted at an angle of approximately 20° relative to the axis perpendicular to the culture dish in order to reduce standing wave formation within the cavity formed by the transducer and the culture dish. In addition, an acoustic absorber (Aptflex F28, Precision Acoustics, UK) was attached to the transducer to avoid reflected waves at the water/air interface. The FUS stimulus consisted of a 20-MHz sinusoidal signal with peak positive pressure of 4 to 5 MPa and stimulus duration of 0.1 to 1 ms. Calcium responses were recorded before, during and after FUS stimulation. All experiments were performed at room temperature.

value: sensory neuron


title: H3K36me2 H2A.Z-CTR FGO rep1

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Library name: Sample1

library_source: genomic

data_processing:
*library strategy: CATCH-seq, CUT&RUN
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10, dm6
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: ovary

extract_protocol:
After ZP of SN-type FGOs were removed by acid tyrodes’ solution, ZP-free oocytes were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80C until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21C or 37C for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021).
CUT&RUN libraries were prepared as previously described (Hayashi and Inoue 2023). The antibodies used were mouse anti-H2A (1/100, MBL D210-3), rabbit anti-H2A.X (1/100, Abcam 11175), and rabbit anti-TH2A antibody (1/100) (Shinagawa et al. 2014). Protein A-MNase was provided by the Steven Henikoff Lab (Skene and Henikoff 2017). For CATCH-seq, 3 uL of rabbit anti-H2A.Z (Active motif 39113, 200 oocytes/library), 500 ng of mouse anti-H2A (MBL D210-3, 200 oocytes/library), 1 uL of rabbit anti-H2A.X (Abcam ab11175, 200 oocytes/library), 500 ng of rabbit anti-TH2A antibody (a gift from Shunsuke Ishii, 200 oocytes/library) (Shinagawa et al. 2014), 0.25 uL of rabbit anti-H3K4me3 (Active Motif 39159, 40 oocytes/library), 500 ng of rabbit anti-H3K27me3 (Diagenode C15410069, 80 oocytes/library), or 1.0 µl of rabbit anti-H2AK119ub1 antibody (Cell Signaling Technology 8240, 500 oocytes/library) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. The quality of these antibodies was validated in previous studies [H2A.Z (Murphy et al. 2018), H2A (Inoue and Zhang 2014), H2A.X (Inoue and Zhang 2014), TH2A (Shinagawa et al. 2014), H3K4me3 (Kaya-Okur et al. 2020), H3K27me3 (Inoue et al. 2018), H2AK119ub1 (Mei et al. 2021)]. After immunoprecipitation at 4C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 13-15 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37C for 2 hrs followed by heat inactivation at 65C for 20 min and purified by 0.9x SPRIselect beads.

treatment_protocol: Growing oocytes (GO) were collected from ovaries of 10-11 day-old BDF1 females. They were incubated in α-MEM/5% FBS containing 100 µM 5, 6-Dichloro-1-β-D-Ribofuranosyl-1H-Benzimidazole (DRB, Cayman Chemical 53-85-0), 0.2% DMSO (the solvent of DRB), or 100 µg/mL α-amanitin (Fiji-film 010-22961). For each CATCH-seq library construction, 250-300 GOs were collected at 24 hrs culture under the inhibitors.

value: ovary

tag: developmental stage

value: Full-grown oocyte

value: wild type


title: NWSN120

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_065


title: RNA-SeqofAML primary sample of patient 20

value: M


title: TOX_WT_P14_ATAC_S4

library_source: genomic single cell


title: NWSN110

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_054


title: TOX_iKO_P14_ATAC_S5

source_name: CD8 T cells from Inducibe cre for TOX KO mice 5 days post infection of LCMV chronic infection

value: Knockout


title: Naive_P14_ATAC_S1


title: RNA-SeqofAML primary sample of patient 19


title: NWSN108

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_052

value: female


title: NWSN106

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_049


title: NWSN105

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_048


title: day 3 post-infection brain, mouse 2

city: Birmingham

first: Rebecca

last: Drummond

state: Edgbaston

address: IBR 437, University of Birmingham

country: United Kingdom

institute: University of Birmingham

description:
10x genomics
Day3_m2

data_processing:
The demultiplexing of raw sequencing data was performed using CellRanger v3.0.1 (10X Genomics), using function mkfastq. Reads obtained from mkfastq were used as the input for ‘cellranger count’ (10X Genomics), in which reads were aligned to the mouse reference genome (mm10, v3.0.0; Ensembl 93). Pooling of the different samples was completed using ‘cellranger aggr’ (10X Genomics), in which the different chemistries used for different samples was accounted for and corrected.
Assembly: mm10
Supplementary files format and content: Tab-separated features and matrix files

source_name: Total myeloid CD11b+ cells from brain

extract_protocol:
Myeloid cells from the brain were sorted as live CD45+CD11b+ singlets, and collected into RPMI media supplemented with 10% FBS and 1% Pen/Strep, keeping cells cold during the sort. Sorted cells were spun down and resuspended into PBS supplemented with 0.04% BSA at a concentration of approximately 1000 cells/uL. Cells were loaded on a GemCode Single-Cell Instrument (10X Genomics) to generate single-cell gel bead-in emulsions (GEMs).
Library was constructed according to manufacturer's instructions (single cell 3' v2 or v3 protocol, 10x genomics)

tag: strain

tag: cell type

value: Total myeloid CD11b+ cells from brain

value: infected with C. neoformans (strain H99)

tag: time point

value: day 3  post-infection


title: H3K36me2 H2A.Z-CTR FGO rep2

description: Library name: Sample2


title: RNA-SeqofAML primary sample of patient 18


title: day 3 post-infection brain, mouse 1

description:
10x genomics
Day3_m1


title: day 6 post-infection brains, pooled mice

description:
10x genomics
Day6

value: day 6 post-infection


title: uninfected brain, mouse 2

description:
10x genomics
Day0_m2

value: uninfected


title: CD45+ isotype control

city: San Francisco

first: Miqdad

last: Dhariwala

state: California

address: 513 Parnassus

institute: University of Caifornia, San Francisco

description: 3' library, aligned to the genome mms10 with Cell Ranger

data_processing:
Cell Ranger
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: skin

extract_protocol:
Skin was minced and digested with collagenase. Cells (Live CD45+) were sorted and submitted for 10X
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics).

treatment_protocol: C57BL/6 mice were treated every other day between the ages of postnatal day 4 and 14 with either the anti-Gr-1 antibody or an isotype control antibody. Skin tissues were processed as described in the materials and methods section.

value: skin

tag: cell line

value: CD45+ immune cells

value: C57BL/6 (Wild Type)

value: Isotype Cotrol


title: NWSN104

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_047


title: NWSN102

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_044


title: RNA-SeqofAML primary sample of patient 17

value: Peripheralblood

value: AML

value: F


title: RNA-SeqofAML primary sample of patient 16


title: CD45+ aGr1


title: METTL3 KO-3-DP

city: wuhan

first: huiru

last: jing

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

country: China

institute: wuhan university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: thymus

extract_protocol:
Live cells were collected, and RNA was harvested using Trizol reagent. Direct-zol RNA Microprep Kits (Cat#R2061) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols.

value: thymus

value: METTL3 KO


title: NWSN91

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_013

value: sensory neuron

value: male


title: RNA-seq FGO H2A.Z DKO rep1

data_processing:
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
About 20 FGOs per sample were pooled to generate each RNA-seq library. The zona pellucida was removed by brief incubation in acidic Tyrode's solution. All samples for RNA-seq were washed three times in 0.2% BSA/PBS before being transferred into a 0.2-ml tube with ~0.5μl carryover.
For RNA-seq, libraries were prepared as previously described (Inoue et al., Genes Dev. 2018). Briefly, cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA, 634890) according to the manufacture's instructions. Two hundreds picograms of cDNA were used for the library construction by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to the manufacture's instructions.

value: ovary

value: Full-grown oocyte

value: H2A.Z.1 and H2A.Z.2 double knockout


title: RNA-seq FGO H2A.Z CTR rep1

value: wild type


title: METTL3 KO-1-DP


title: RNA-SeqofAML primary sample of patient 12

value: M


title: RNA-seq FGO H2A.Z DKO rep2


title: METTL3 KO-2-DP


title: RNA-SeqofAML primary sample of patient 21


title: RNA-SeqofAML primary sample of patient 15


title: NWSN85

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_006


title: NWSN87

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_009


title: uninfected brain, mouse 1

description:
10x genomics
Day0_m1

value: Total myeloid CD11b+ cells from brain

value: uninfected


title: WT-3-DP

value: WT


title: RNA-SeqofAML primary sample of patient 14


title: HEK293T, NS2A, rep2

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

institute: ISM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit following standard Illumina protocol

value: Human embryonic kidney

value: NS2A overexpression


title: WT-1-DP


title: RNA-SeqofAML primary sample of patient 13

value: Peripheralblood


title: RNA-seq FGO H2A.Z CTR rep2


title: young-METTL3 KO-3-DP

tag: group

value: young


title: NWSN83

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_004


title: NWSN86

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_008


title: RNA-SeqofAML primary sample of patient 11

value: AML

value: F


title: WT-2-DP

value: thymus


title: RNA-SeqofAML primary sample of patient 10


title: H3K27me3 H2A.Z-DKO FGO rep2

data_processing:
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10, dm6
Supplementary files format and content: bigwig


title: H3K27me3 H2A.Z-DKO FGO rep1


title: young-METTL3 KO-2-DP

value: METTL3 KO


title: NWSN82

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_003

value: sensory neuron

value: male


title: NWSN81

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_002


title: RNA-SeqofAML primary sample of patient 9


title: H3K27me3 H2A.Z-CTR FGO rep2

value: ovary

value: Full-grown oocyte


title: young-METTL3 KO-1-DP


title: NWSN172

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_127

value: female


title: RNA-SeqofAML primary sample of patient 7


title: H3K27me3 H2A.Z-CTR FGO rep1

value: wild type


title: RNA-SeqofAML primary sample of patient 8

value: M


title: H2AK119ub1 H2A.Z-DKO FGO rep2

value: H2A.Z.1 and H2A.Z.2 double knockout


title: old-3-DP

value: old

value: WT


title: old-1-DP


title: RNA-SeqofAML primary sample of patient 6


title: NWSN159

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_114


title: old-2-DP


title: NWSN130

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_076


title: old-4-DP


title: RNA-SeqofAML primary sample of patient 5


title: NWSN160

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_115


title: young-2-DP


title: H3K4me3 Mll2 KO FGO rep2

value: Mll2 knockout


title: RNA-SeqofAML primary sample of patient 3

value: Peripheralblood


title: H2AK119ub1 H2A.Z-DKO FGO rep1


title: NWSN132

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_079


title: H3K4me3 Mll2 KO FGO rep1


title: RNA-SeqofAML primary sample of patient 2


title: NWSN170

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_125


title: H2AK119ub1 H2A.Z-CTR FGO rep1


title: H2AK119ub1 H2A.Z-CTR FGO rep2


title: young-3-DP

value: young


title: young-1-DP


title: RNA-SeqofAML primary sample of patient 4

value: AML


title: NWSN114

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_058


title: NWSN119

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_064


title: H3K4me3 Mll2 WT FGO rep1


title: NWSN93

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_015


title: NWSN107

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_050


title: H3K4me3 H2A.Z-DKO FGO rep2


title: RKO WT_IP

city: nanjing

first: xian

last: luo

address: xianlin

institute: NJUCM

data_processing:
Fastp 0.19.11 software performs basic quality statistics for raw reads
QC analysis was used by  fastqc v0.11.5
burrows Wheeler aligner(0.7.12-r1039) can  compare reads to reference genome
Peak calling was performed by MACS22.1.0
The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1)

source_name: RKO

growth_protocol: Human CRC cell lines RKO were cultured in RPMI 1640 Medium  with 10% fetal bovine serum 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured in a humidified atmosphere of 5 % CO2 at 37℃.

extract_protocol:
~5-20 × 106 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of SRSF1 and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using a phenol-chloroform lysate to obtain a purified product.
RNA samples were fragmented by RNA fragmentation buffer (10 mM Tris-HCl [pH 7.0], 10 mM ZnCl2). Fragmented RNA was incubated for 2 hr at 4C with 0.5 mg/mL antim6A polyclonal antibody in IP buffer (150 mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl [pH 7.4]) supplemented with RNasin Plus RNase inhibitor (Promega). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H - ）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Illumina HiSeqTM 2500 system.

value: Colorectal cancer cells

value: Wild type

value: RKO

value: ZCCHC7 antibody


title: Input H2A.Z-CTR FGO rep1


title: H3K4me3 H2A.Z-CTR FGO rep2


title: RKO ZCCHC7-OE_IP

value: SRSF1 antibody


title: RKO ZCCHC7-OE_Input

value: input


title: RNA-SeqofAML primary sample of patient 1

value: F


title: ICN K+-rep2

city: Chicago

first: Matias

last: Alvarez-Saavedra

state: IL

address: 303 East Superior Street, Lurie 11-221303 East Superior Street, Lurie 11-221

department: Simpson Querrey Institute for BioNanotechnology

institute: Northwestern University

data_processing:
Raw FASTQ files were processed using the nf-core/rnaseq pipeline (v3.7). Adapter sequences were removed with Trim Galore. Reads were aligned with STAR to GRCm38/mm10 (mouse) and quantified to gene counts using RSEM.
Assembly: GRCm38/mm10 (mouse)
Supplementary files format and content: Excell file contains raw counts for each sample.

source_name: brain

extract_protocol:
Total RNA Purification was performed using TRIzol-extracted samples using the Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010).
Illumina Stranded mRNAPrep library kit.

treatment_protocol: Embryonic cortical neurons were allowed to settle overnight and on the next day, media was removed, 80ul of PAs were added on top of cells, and fresh media added. A 50% media change was performed at 48hrs after PA treatment.

value: brain

value: embryonic cortical neuron

value: 5mM Stock, 200uM Treatment


title: H3K4me3 Mll2 WT FGO rep2

value: ovary

value: Full-grown oocyte

value: wild type


title: NWSN92

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_014

value: sensory neuron

value: male


title: Control KPP biological rep1

city: Charleston

first: Denis

last: Guttridge

state: SC

address: 173 Ashley Ave

department: Pediatrics

institute: Medical University of South Carolina

description: 1386 ctrl

data_processing:
Basecalls were performed using bcl2fastq v2.20 with default settings. Read quality was assessed using FASTQC.
RNA-seq FASTQ files were transcriptomically aligned to the indexed mouse genome mm10 (UCSC) with Salmon package and quantified with k-mer counting. Salmon quantification files are attached
DESeq2 was used to quantify differential gene expression between samples with biological replicates of 2.
Assembly: mm10
Supplementary files format and content: Salmon_quantification, DESeq2_Tumor_vs_Control

source_name: TA muscle

extract_protocol:
TA muscles were snap frozen in either dry ice or liquid nitrogen and then homogenized in 1mL of Trizol.
Libraries were prepared by MUSC Translational Core using the New England Biolabs NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit from Illumina (Cat# 7760L). Dual indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 to a depth of approximately 25 million paired-end 150 bp reads per library.

treatment_protocol: Mice were injected with C26 cells subcutaneously, LLC cells intramuscularly, KPC or KPCML1 cells orthotopically, or tamoxifen to induce the genetic tumor model

tag: model

value: Genetic KPP Model No Tumor Control

value: TA muscle

tag: strain background


title: Input H2A.Z-DKO FGO rep2

value: H2A.Z.1 and H2A.Z.2 double knockout


title: KPP tumor bearing biological rep2

description: 3837 kpp

value: Genetic KPP Model Tumor


title: RKO ZCCHC7-OE_IP

value: Colorectal cancer cells

value: RKO


title: H3K4me3 H2A.Z-DKO FGO rep1


title: RKO WT_IP

value: Wild type

value: SRSF1 antibody


title: ICN K+-rep1


title: Control KPP biological rep2

description: 3051 ctrl


title: RKO WT_Input

value: input


title: ICN K+-rep3

value: brain


title: Control C26 biological rep2

description: Ctrl C26 4

value: C26 Xenograft Control (PBS)


title: KPP tumor bearing biological rep1

description: 2846 kpp


title: C26 tumor bearing biological rep1

description: C26 4

value: C26 Xenograft Tumor


title: C26 tumor bearing biological rep2

description: C26 3


title: NWSN113

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_057


title: H3K4me3 H2A.Z-CTR FGO rep1

value: ovary


title: Control C26 biological rep1

description: Ctrl C26 5


title: ICN Na+-rep3

value: embryonic cortical neuron

value: 5mM Stock, 200uM Treatment


title: H2A.Z H2A.Z-DKO FGO rep2

value: Full-grown oocyte


title: ICN Na+-rep2


title: KPC 50000 cell orthotopic injection biological rep2

description: M50 30

value: Orthotopic Model Tumor


title: KPC 50000 cell orthotopic injection biological rep1

description: M50 50


title: ICN Na+-rep1


title: 231 RIP-HNRNPC

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software(v0.11.7)
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt(v1.17)) were aligned to reference genome(GRCh37) using Hisat2 software(v2.1.0)
The transcript abundance for each sample was estimated with StringTie(v1.3.3), and the FPKM value for gene and transcript level was calculated with R package Ballgown(v2.10.0)
Assembly: GRCh37
Supplementary files format and content: the FPKM value of detected mRNA for each sample

growth_protocol: Cells were cultured L15 culture medium with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
LY6E-DT and HNRNPC was knocked down by respectivly transfection with HNRNPC  and LY6E-DT siRNA  in 231 cells
EZ-Magna RIP Kit (Millipore, USA) was used in RIP assay following the manufacturer’s protocols. MDA-MB-231 cells  were lysed with RIP lysis buffer, followed by incubated with RIP buffer containing magnetic beads conjugated with human anti- HNRNPC antibody, and IgG (Millipore).


title: H2A.Z H2A.Z-DKO FGO rep1


title: 231 RIP-INPUT

description: MDA-MB-231 cells were lysed with RIP lysis buffer


title: KPCML1 1000 cell orthotopic injection biological rep2

description: TM2 3


title: H2A.Z H2A.Z-CTR FGO rep1

value: wild type


title: PA-rep3


title: KPCML1 1000 cell orthotopic injection biological rep1

description: TM1 1

value: TA muscle


title: Input 28d FGO rep1


title: PA-rep2


title: Control Matrigel injected biological rep2

description: VEM1 5

value: Orthotopic Model Control (Matrigel Only)


title: 231 CELLS-si-LY6E-DT

description: LY6E-DT was knocked down by transfection with LY6E-DT Smart Silencer


title: Input 15d GO rep1

value: 15d growing oocyte


title: PA-rep1


title: Control Matrigel injected biological rep1

description: VEM1 3


title: SH-SY5Y_BioID-Flag-ERRg4

first: Rita

middle: M

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

data_processing:
Basecalls performed using CASAVA
TrimGalore! version 0.6.6 was used to trim primer adapter contamination from raw FASTQ files using parameters: --paired --trim-n
Trimmed FASTQ files were then aligned with STAR version 2.7.8a using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.3 using parameters: -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression was done by DESeq2 following their default parameters in their vignette
Assembly: Gencode GRCh38 p13 Release 36
Supplementary files format and content: tab-delimited text file containing Ensmebl IDs and raw count values for each sample

source_name: SH-SY5Y Cell line

growth_protocol: DMEM Media FBS 10% P/S 1% grown in 10 cm plates until 80% confluent before treatment

extract_protocol:
Total RNA isolated with Trizol/Chloroform/Isopropanol/Ethanol then quantified with nanodrop
rRNA depletion method
Addition of directional library preparation module to retain strand information in RNA library preparation

treatment_protocol: Cells were transfected with .5 ul of either BioID-GFP-NLS or BioID-Flag-Esrrg Adenovirus for 48 hours and then RNA was isolated

value: BioID-Flag-ERRg transfection

value: neuronal progenitor


title: Input 10d GO rep1

value: 10d growing oocyte


title: RKO ZCCHC7-OE_Input

value: Colorectal cancer cells

value: RKO


title: 231 CELLS-si-HNRNPC

description: HNRNPC was knocked down by transfection with SI-HNRNPC


title: H2A.Z H2A.Z-CTR FGO rep2


title: LLC tumor bearing biological rep2

value: LLC Xenograft Tumor


title: 231 CELLS-si-LY6E-NC

description: negative control


title: adult-spleen-treg-3

city: New York

first: Varun

last: Arvind

state: NY

address: 1 Gustave Levy Place

department: Orthopedics

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome (ENSEMBLE) using STAR aligner v.2.5.2b
Unique gene counts were calculated using featureCounts from Subread package v.1.5.2
After quantification of gene hit counts, differential gene expression analysis was performed using DESeq2
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample.

source_name: spleen

growth_protocol: Cells FACS sorted from murine tissue. Kept in FACS flow buffer on ice prior to RNA isolation.

extract_protocol:
RNA was isolated as per Arcturus PicoPure kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following FACS sorting cells were not treated and were immediately lysed for RNA purification.

value: Treg

tag: age

value: adult


title: adult-spleen-treg-2


title: SH-SY5Y_BioID-Flag-ERRg2


title: SH-SY5Y_BioID-Flag-ERRg3


title: LLC tumor bearing biological rep1


title: Input 5d GO rep1

value: ovary

value: 5d growing oocyte


title: Control LLC biological rep2

description: Ctrl LLC2

value: LLC Xenograft Control (PBS)


title: adult-tendon-treg-3

source_name: tendon


title: SH-SY5Y_BioID-Flag-ERRg1


title: H2A.Z 28d FGO rep2

value: Full-grown oocyte


title: Control LLC biological rep1

description: Ctrl LLC1


title: adult-tendon-treg-1


title: FLOX-2 Striatum

data_processing:
Basecalls performed using CASAVA
TrimGalore! version 0.6.5 was used to trim primer adapter contamination from raw FASTQ files using parameters: --paired --trim-n
Trimmed FASTQ files were then aligned with STAR version 2.7.3a using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.3 using parameters: -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression was done by DESeq2 following their default parameters in their vignette
Assembly: Gencode GRCm38 p6 Release M24
Supplementary files format and content: tab-delimited text file containing Ensmebl IDs and raw count values for each sample

source_name: Striatum

extract_protocol:
Brains were removed and striatum were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All mice were injected with AAV:CamKcre

value: Striatum

value: 4 months

value: Esrrg Flox


title: SH-SY5Y_BioID-GFP-NLS2

value: BioID-GFP-NLS Transfection


title: SH-SY5Y_BioID-GFP-NLS3


title: neonatal-spleen-treg-3

value: neonatal


title: H2A.Z 10d GO rep1

value: wild type


title: H2A.Z 15d GO rep2

value: 15d growing oocyte


title: SH-SY5Y_BioID-GFP-NLS1

value: neuronal progenitor


title: neonatal-spleen-treg-2


title: FLOX-3 Striatum


title: neonatal-spleen-treg-1


title: FLOX-1 Striatum


title: H2A.Z 5d GO rep2


title: SH-SY5Y_BioID-GFP-NLS4


title: WT-1 Striatum

value: Esrrg WT


title: neonatal-tendon-treg-3


title: H2A.Z 10d GO rep2

value: 10d growing oocyte


title: adult-tendon-treg-2


title: Mut2_VD2_rep3

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

description:
Smart-seq2
Full length

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.0 with the parameters “--cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 30 --length_required 30”
The clean reads were aligned to the human genome (GRCh38) using STAR (version 2.7.5c).
The reads aligned to exon were counted using featureCounts.
The reference transcript data and the gene annotation file for mouse was downloaded from GENCODE (release 36, https://www.gencodegenes.org/).
Genome_build: GRCh38
Supplementary_files_format_and_content: ReadCounts.xlsx: ReadCounts file generated using featureCounts.

source_name: iPS cell-derived cardiomyocytes

growth_protocol: iPS cell-derived cardiomyocytes were induced by sequential treatment with CHIR99021 (day 0-2) and IWP2 (day 2-4) in adherent culture and then purified using no-glucose lactic acid-containing medium. See below (J Mol Cell Cardiol. 2019 Mar;128:90-95. doi: 10.1016/j.yjmcc.2019.01.020. Epub 2019 Jan 23).

extract_protocol:
Total mRNA was extracted from iPSCMs with lysis buffer in Smart-seq2 protocol.
Libraries were generated using Smart-seq2 protocol.

treatment_protocol: DMSO (1:1000) or 1uM vitamin D2 (VD2) for 6 days.

value: iPS cell-derived cardiomyocytes

tag: lmna mutant

value: LMNA-mutant

value: vitamin D2


title: adult-spleen-treg-1

value: Treg

value: adult


title: H2A.Z 5d GO rep1

value: ovary

value: 5d growing oocyte


title: Mut2_VD2_rep2

description:
Smart-seq2
Full length


title: WT-2 Striatum

value: Striatum


title: H2A.Z 15d GO rep1


title: WT-3 Striatum

value: 4 months


title: TH2A CUT&RUN FGO rep1

value: Full-grown oocyte


title: Mut2_VD2_rep1

description:
Smart-seq2
Full length


title: H2A.Z 28d FGO rep1


title: neonatal-tendon-treg-2


title: J594I457

data_processing:
Basecalls performed using CASAVA
TrimGalore! version 0.6.5 was used to trim primer adapter contamination from raw FASTQ files using parameters: --paired --trim-n
Trimmed FASTQ files were then aligned with STAR version 2.7.3a using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.1 using parameters: -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression was done by DESeq2 following their default parameters in their vignette
Assembly: Gencode GRCm38 p4 Release M11
Supplementary files format and content: tab-delimited text file containing Ensmebl IDs and raw count values for each sample

source_name: Cortex

extract_protocol:
Brains were removed and two cortical hemispheres were flash frozen on dry ice, and RNA was harvested using the BAC-TRAP method of RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable

value: Brain

value: Pvcre;L10a;Esrrg WT


title: TH2A catch-seq FGO rep1

value: wild type


title: neonatal-tendon-treg-1

value: neonatal


title: J523J513

value: PVcre;L10a;Esrrg Flox


title: PBMC from healthy control, subject 9

type: RNA

first: Elisa

middle: Elisa

last: Oltra

state: VALÈNCIA

address: C/ Quevedo 2

department: Pathology

country: Spain

institute: Universidad Catolica de Valencia San Vicente Martir

description: HERV and gene expression data of PBMC from healthy control

hyb_protocol: The resulting target was mixed with standard hybridization controls and B2 oligonucleotides following supplier recommendations. The hybridization cocktail was heat-denatured at 95 ºC for 2 min, incubated at 50 ºC for 5 min, and centrifuged at 16,000 g for 5 min to pellet the residual salts. HERV-V3 microarrays were pre-hybridized with 200 μL of hybridization buffer and placed under stirring (60 rpm) in an oven at 50 C for 10 min. Hybridization buffer was then replaced by denatured hybridization cocktail. Hybridization was performed at 50 °C for 18 h in the oven under constant stirring (60 rpm). Washing and staining were carried out according to manufacturer´s protocol, using a fluidic station (GeneChip fluidic station 450, Affymetrix).

scan_protocol: Arrays were finally scanned using a fluorometric scanner (GeneChip scanner 3000 7G, Affymetrix).

data_processing: All bioinformatic analysis were performed with RStudio software version 4.2.1. Microarray CEL files were processed and analyzed using R oligo package (87). Data were normalized, adjusted for background noise, and summarized using the RMA (Robust Multi-Array) algorithm.

label: biotin

source_name: PBMC from healthy control

label_protocol: Five micrograms of purified ssDNA were enzymatically fragmented into 50–100 bp fragments and biotin-labeled with the Encore Biotin Module kit from Nugen according to manufacturer's instructions

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, MD, USA) according to the manufacturer's instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent). All RNA samples had an RNA Integrity number (RIN) above 7. cDNA was synthesized and amplified from 45 ng of RNA using the Ovation Pico WTA System V2 kit (Nugen) according to manufacturer's instructions. The resulting amplified ssDNA was purified using the QIAquick purification kit (Qiagen, MD, USA)

value: Healthy control


title: H2A.X CUT&RUN FGO rep1


title: PBMC from healthy control, subject 8


title: Mut2_DMSO_rep2

description:
Smart-seq2
Full length

value: DMSO


title: H2A.X catch-seq FGO rep1


title: Mut2_DMSO_rep3

description:
Smart-seq2
Full length

value: iPS cell-derived cardiomyocytes


title: PBMC from healthy control, subject 7


title: I444J746


title: I407I307


title: Mut1_VD2_rep3

description:
Smart-seq2
Full length

value: LMNA-mutant


title: Mut1_VD2_rep2

description:
Smart-seq2
Full length

value: vitamin D2


title: Mut2_DMSO_rep1

description:
Smart-seq2
Full length


title: PBMC from healthy control, subject 4


title: I445

value: L10a;Esrrg WT


title: PBMC from healthy control, subject 5


title: PBMC from healthy control, subject 6


title: I224I401


title: Mut1_VD2_rep1

description:
Smart-seq2
Full length


title: H2A CUT&RUN FGO rep1


title: Mut1_DMSO_rep2

description:
Smart-seq2
Full length


title: ZFHX3, ZT15, ChIP

city: Didcot

first: Akanksha

last: Bafna

address: Harwell Campus

institute: MRC HARWELL

data_processing:
Raw sequence data was quality assessed by removing low-quality bases (Phred < 20) and trimmed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic v0.36 (http://www.usadellab.org/cms/index.php?page=trimmomatic), respectively.
FASTQ files containing trimmed sequences were then aligned to mm10 genome assembly to generate binary alignment map (BAM) files and used for peak calling by MACS (Zhang et al., 2008) at a threshold of q < 0.01.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: SCN

extract_protocol:
WT C57BL/6J mice (aged between 8 to 12 weeks) were used for SCN tissue punch collection as described by Jagannath et al. (Jagannath et al., 2013) at  ZT3 and ZT15, where lights on at 7 am (ZT0) and lights off at 7 pm (ZT12), for ZFHX3-ChP-seq.
ChIP was conducted using the Active Motif ChIP‐IT enzymatic kit (https://www.activemotif.com/catalog/868/chip-it-high-sensitivity) according to the manufacturer’s instructions.

value: SCN

tag: chip antibody

value: WT

tag: time


title: Mut1_DMSO_rep3

description:
Smart-seq2
Full length


title: sc_Mm_LT_NPMc_Flt3ITD

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

data_processing:
Basecalls were performed using bcltofastq v2
Reads were aligned to the mm10 reference genome, annotated using the GENCODE vM16 annotation, and raw UMI counts for every cell-gene combination generated in a single analysis step using the STARsolo feature of STAR v2.7.0c.
Single mismatches in cellular barcode and UMI were corrected.
Cellular barcodes not reflecting actual cells (empty drops) were detected and filtered out using the "emptyDrops()" function of the DropletUtils R package v1.2.2 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: bone marrow

extract_protocol:
Bone marrow from posterior limbs, anterior limbs and sternum were crushed and recovered cells were stained. LT-HSCs have been FACS sorted and immediately processed by 10x technology
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

tag: tissue

value: long term hematopoietic stem cell

tag: genotype

value: 8-11 weeks


title: ZFHX3, Input

value: none (input)


title: sc_Mm_LT_Flt3ITD


title: PBMC from healthy control, subject 3

tag: diagnosis


title: H2A catch-seq FGO rep1

source_name: ovary

extract_protocol:
After ZP of SN-type FGOs were removed by acid tyrodes’ solution, ZP-free oocytes were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80C until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21C or 37C for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021).
CUT&RUN libraries were prepared as previously described (Hayashi and Inoue 2023). The antibodies used were mouse anti-H2A (1/100, MBL D210-3), rabbit anti-H2A.X (1/100, Abcam 11175), and rabbit anti-TH2A antibody (1/100) (Shinagawa et al. 2014). Protein A-MNase was provided by the Steven Henikoff Lab (Skene and Henikoff 2017). For CATCH-seq, 3 uL of rabbit anti-H2A.Z (Active motif 39113, 200 oocytes/library), 500 ng of mouse anti-H2A (MBL D210-3, 200 oocytes/library), 1 uL of rabbit anti-H2A.X (Abcam ab11175, 200 oocytes/library), 500 ng of rabbit anti-TH2A antibody (a gift from Shunsuke Ishii, 200 oocytes/library) (Shinagawa et al. 2014), 0.25 uL of rabbit anti-H3K4me3 (Active Motif 39159, 40 oocytes/library), 500 ng of rabbit anti-H3K27me3 (Diagenode C15410069, 80 oocytes/library), or 1.0 µl of rabbit anti-H2AK119ub1 antibody (Cell Signaling Technology 8240, 500 oocytes/library) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. The quality of these antibodies was validated in previous studies [H2A.Z (Murphy et al. 2018), H2A (Inoue and Zhang 2014), H2A.X (Inoue and Zhang 2014), TH2A (Shinagawa et al. 2014), H3K4me3 (Kaya-Okur et al. 2020), H3K27me3 (Inoue et al. 2018), H2AK119ub1 (Mei et al. 2021)]. After immunoprecipitation at 4C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 13-15 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37C for 2 hrs followed by heat inactivation at 65C for 20 min and purified by 0.9x SPRIselect beads.

value: ovary

value: Full-grown oocyte


title: ZFHX3, ZT3, ChIP


title: sc_Mm_LT_NPMc

value: NPMc+


title: PBMC from healthy control, subject 1


title: Mut1_DMSO_rep1

description:
Smart-seq2
Full length

tag: treatment


title: sc_Mm_LT_Mx

value: MxCRE


title: P21 Mouse retina bACE-seq Tet1/2/3 tcKO Replicate 3

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Library name: P21 Tet1/2/3 tcKO Replicate 3 bACE-seq

data_processing:
bACE-seq: Paired-end sequencing reads were processed with TrimGalore (v0.4.4_dev) to remove adapters and low-quality sequences using the parameters --paired --clip_R1 16 --clip_R2 16. The trimmed reads were independently aligned to the mouse genome (mm10) using Bismark (v0.18.2). Read 1 (R1) was aligned with Bowtie2 in PBAT mode (--pbat flag) and the following settings: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --directional. Read 2 (R2) was mapped using Bowtie2 with default parameters. Aligned reads were filtered to retain only those with a mapping quality score ≥ 10 using Samtools (v1.15.1) and PCR duplicates were removed using Picard’s MarkDuplicates tool (GATK v4.1.3). CpG methylation levels were extracted with MethylDackel (v0.6.1) using the --CHG and --CHH flags alongside default settings. Finally, strand-specific read counts were combined using a custom Python script.
WGBS: WGBS data were processed using the same pipeline as described for bACE-seq analysis (above), with modifications to the  alignment steps. Reads were aligned to the mouse genome (mm10) using Bismark (v0.18.2) with default alignment parameters (PBAT mode turned off).
Differentially Methylated Region (DMR) Analysis - DMRs were identified using DSS (v2.48.0). The DMLtest function was applied with smoothing=TRUE and default parameters. DMRs were called with a p-value threshold of 0.01. To define DMRs, a minimum length of 50 bp and at least 3 CpG sites were required, with DMRs within 50 bp merged (following DSS default settings). DMR annotation was performed using ChIPseeker (v1.36.0), with the transcription start site (TSS) Region set to +/- 2000 bp and default settings. Mouse gene annotations from TxDb.Mmusculus.UCSC.mm10.knownGene were used for the annotation process.
Assembly: mm10
Supplementary files format and content: diff.Methy .csv files
Library strategy: bACE-seq

source_name: Whole Retina

extract_protocol:
Retinas from P21 animals were dissected in PBS and homogenized in 1ml TRIZOL solution. 200µl of chloroform was added to homogenized TRIZOL solution, mixed by vortexing and incubated for 3 min at RT. Lysates were centrifuged for 10 min at 4C at max speed (16,000g). The aqueous phase with RNA was transferred into a fresh tube without disturbing the interphase. The rest of the volume, containing DNA and proteins was washed with 300µl 100% ethanol, inverted several times, and then centrifuged for 5 min at 4C at 2000g. The supernatant containing proteins was carefully removed so as to not disturb the precipitated DNA pellet. The DNA pellet was washed in 1mL of 100mM sodium citrate in 10% ethanol and incubated for 30 min at RT followed by centrifugation 5 min at 4ºC at 2000g and removal of the resulting supernatant. This step is repeated twice. 1.5mL of 75% ethanol was added to the DNA pellet and incubated for 20 min at RT using occasional mixing during the 20-minute incubation. The supernatant is discarded, and the DNA pellet is air dried for 10 min. 100µl of 8mM NaOH in 1mM EDTA pH 7-8 was added to resuspend the DNA pellet. After that, samples are centrifuged for 10 min at 4ºC and max speed (16,000g). The supernatant is transferred to a new tube and stored at -20ºC. DNA concentrations were measured in a Qubit fluorometer.
Genomic DNA was quantified using the Qubit fluorometer. 200ng of gDNA, including 0.2% Lambda DNA (N6-methyladenine-free; NEB) was fragmented in a final volume of 50uL using the Covaris LE220 targeting ~350bp inserts. A 1.5x AMPure clean-up was utilized after fragmentation to concentrate the sample. The fragmented gDNA was bisulfite converted with the EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research, Cat # D5043) according to the manufacturer’s recommendations. Bisulfite converted DNA was quantitated on the Qubit Fluorometer using the ssDNA Assay Kit (Thermo Fisher Scientific, Cat #Q10212). Whole genome bisulfite libraries were constructed with ~100ng of converted DNA using the xGen™ Methyl-Seq Library Prep Kit (Integrated DNA Technologies, Cat # 10009825) using unique dual indexes (IDT, 0008053) and eight PCR cycles for incorporation and amplification of indexed libraries, followed by a final 0.85x AMPure cleanup. Final libraries are quality checked for average library size and concentration. Molar concentration of libraries was determined using the KAPA Library Quantification kit (Roche Diagnostics). Libraries were sequenced on NovaSeq X using 150bp paired end reads.
bACE-seq: 10-15ng of RNAse treated, TRIZOL purified gDNA was used for each sample. Samples were diluted to 10µL in MilliQ water and pre-heated by incubating at 50C for 20 minutes on a thermocycler with a heated lid set to 95ºC. 32.5µL of CT Conversion Reagent (Zymo EZ DNA Methylation Direct Kit) was then added to each sample before running the the following program on a thermocycler (98ºC for 8min, 64ºC for 105 min, followed by 98ºC for 8 min, 64ºC for 105 min), with the lid set to 95ºC. Following the bisulfite reaction, the tubes were placed at -20ºC overnight, or for 16 hours. The bisulfite converted DNA was then purified using the Zymo EZ Methylation Direct Kit, eluting with 17µL of MilliQ water for a final elution volume of 16µL. Each sample was incubated at 95ºC for 3 minutes on a thermocycler, with the lid set to 105ºC. The samples were then immediately placed into a dry-ice ethanol bath to snap cool them and were left in the cooling bath for 5 minutes. The samples were then placed on a pre-chilled PCR rack and kept on ice. 8µL of premixed APOBEC reaction mixture (2.4µL APOBEC reaction buffer (E7134A, NEB), 0.48µL APOBEC (E7133AA, NEB), 0.48µL BSA (B9000S, NEB), water to 8µL) was added to each tube and samples were incubated at 37ºC on a thermocycler with the lid set to 95ºC. After 30 min, the samples were mixed and placed back on the thermocycler for two and a half hours at 37ºC with the lid set to 95ºC. DNA was purified from the reaction using 2X Agencourt AMPure XP SPRI beads (add 2X volume of SPRI beads, incubate at room temperature for 10 minutes, place samples on magnet and wash 2 times with fresh 80% ethanol, dry for 3 min, elute in 9µL Low EDTA TE (IDT). Sequencing libraries were constructed using the xGen Adaptase Module with minor modification. 250nM of random stubby index primer was added to each sample (xGen Adaptase Module, P5L_AD002_H). Samples were incubated at 95ºC on a thermocycler with the lid set to 105ºC for 3 min, then cooled on ice for 2 min. 10µL of BST-based random priming mixture (2µL 10X ISO AMP Buffer II (B0374S, NEB), 0.8µL BST 3.0 (M0374S, NEB), 1.2µL 200mM MgCl2, 2.8µL 10mM dNTP, 3.2 µL water) was then added to each sample and incubated at 60ºC for 1 hour on a thermocycler with the lid set to 95ºC. Fragment ends were blunted and dephosphorylated by adding 2µl Exonuclease I (M0293L, NEB) and 1µl shrimp alkaline phosphatase (M0371S, NEB) to each sample. The samples were then incubated at 37ºC for 30 min and purified using a 1.6X SPRI beads (add 1.6X volume of SPRI beads, incubate at room temperature for 10 minutes, place samples on magnet and wash 2 times with fresh 80% ethanol, dry for 3 min, elute) Samples were eluted in 10 µL Low EDTA TE (IDT). In brief, samples were denatured by incubating at 95ºC on a thermocycler with the lid set to 105ºC for 3 min, then cooled on ice for 2 min. Samples were indexed and amplified using the PCR protocol in the xGen Adaptase Module using 21 cycles. The indexed samples were purified using 1.6X SPRI beads (add 1.6X volume of SPRI beads, incubate at room temperature for 10 minutes, place samples on magnet and wash 2 times with fresh 80% ethanol, dry for 3 min, elute) and eluted in 12µL Low EDTA TE (IDT).

value: Whole Retina

value: C57 BL/6J

value: Tet tcKO


title: E18_scRNA_cerebella

city: Farmington

first: Nagham

last: Khouri-Farah

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
The raw reads were processed to molecule counts using the Cell Ranger pipeline with default setting
The raw UMI counts from Cell Ranger was processed by the Seurat R package.
The count matrix without filtering was uploaded.
Assembly: mm10
Supplementary files format and content: UMI counts in csv format

source_name: Cerebellum

extract_protocol:
Freshly disected cerebella from mouse embryos at embryonic stages (E16-E18) in ice-cold phosphate buffered saline. The dissected tissues were pooled and cut into pieces, smaller than 1 mm in dimension and processed according to 10X Genomics protocaol for scRNA-seq of embryonic mouse brain
10X Genomics Chromium Kits was used to create libraries.

value: Cerebellum

value: wild type


title: E16_2_scRNA_cerebella


title: PBMC from co-diagnosed individual, subject 15

description: HERV and gene expression data of PBMC from co-diagnosed individual

source_name: PBMC from co-diagnosed individual

value: Co-diagnosis


title: E11.5 KDR+/CD31+ tdTom+

city: Oxford

first: Oliver

last: Stone

address: Sherrington Road

institute: University of Oxford

description:
FACS sorted CD45-CD41-KDR+/CD31+ Pax3Cre;tdTomato+ve cells
integrated.rds
integrated.h5py
lymphatic.rds
subset_dynamic.h5ad

data_processing:
NextSeq500 sequencing
CellRanger 5.0.0 for cell calling and mapping to mm10 with the tdtomato gene added
Seurat 4.0 for normalisation and clustering
FastMNN for batch correction
PAGA-initiated FA2 for visualisation
Assembly: mm10
Supplementary files format and content: integrated.rds is a Seurat Object that contains all 6 samples
Supplementary files format and content: integrated_paga.h5py is a Scanpy Object that contains the PAGA analysis for all 6 samples
Supplementary files format and content: lymphatic.rds is a Seurat Object that contains the re-clustering of the LEC, LEC_Prog, Vein and Angioblast subset from the integrated object
Supplementary files format and content: subset_dynamic.h5ad is a Scanpy Object that contains the RNA velocity and CellRank analyses for the lymphatic subset

source_name: Angioblasts and endothelial cells

extract_protocol:
Embryos were dissociated using 2 mg/ml Collagenase IV and 0.2 mg/ml Dnase I in 10% FBS/PBS, stained with surface antibodies against CD41, CD45, KDR and CD31, then FACS sorted.
scRNA-seq libraries were produced using the 10x Genomics Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1

tag: lineage

value: paraxial mesoderm


title: Cor_DMSO_rep3

description:
Smart-seq2
Full length

value: iPS cell-derived cardiomyocytes

value: corrected

value: DMSO


title: PBMC from co-diagnosed individual, subject 13


title: P21 Mouse retina bACE-seq Cre- Replicate 3

description: Library name: P21 Cre- Replicate 3 bACE-seq

value: WT


title: E16_1_scRNA_cerebella


title: PBMC from co-diagnosed individual, subject 14


title: Cor_DMSO_rep1

description:
Smart-seq2
Full length


title: E11.5 KDR+/CD31+ tdTom-

description:
FACS sorted CD45-CD41-KDR+/CD31+ Pax3Cre;tdTomato-ve cells
integrated.rds
integrated.h5py
lymphatic.rds
subset_dynamic.h5ad

value: non-paraxial mesoderm


title: P21 Mouse retina bACE-seq Tet1/2/3 tcKO Replicate 2

description: Library name: P21 Tet1/2/3 tcKO Replicate 2 bACE-seq


title: PBMC from co-diagnosed individual, subject 12


title: E10.5 KDR+/CD31+ tdTom-


title: P21 Mouse retina bACE-seq Cre- Replicate 2

description: Library name: P21 Cre- Replicate 2 bACE-seq


title: PBMC from co-diagnosed individual, subject 11


title: P21 Mouse retina bACE-seq Tet1/2/3 tcKO Replicate 1

description: Library name: P21 Tet1/2/3 tcKO Replicate 1 bACE-seq


title: P21 Mouse retina bACE-seq Cre- Replicate 1

description: Library name: P21 Cre- Replicate 1 bACE-seq


title: PBMC from healthy control, subject 2

value: Healthy control


title: PBMC from co-diagnosed individual, subject 16


title: Cor_DMSO_rep2

description:
Smart-seq2
Full length


title: E9.5 KDR+ tdTom+

description:
FACS sorted CD45-CD41-KDR+ Pax3Cre;tdTomato+ve cells
integrated.rds
integrated.h5py
lymphatic.rds
subset_dynamic.h5ad


title: siScr.bGAL_rep2

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

organism: Rattus norvegicus

source_name: Primary isolated cells, Cardiomyocytes

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: Ventricular Cardiomyocytes were isolated from SD rats (P3) using SADO mix digestion buffer (HEPES, NaCl, KCl, Na2H2PO4, Glucose), pancreatin and collagenase enzymes. Cells were cultured in DMEM/F-12 supplemented with 5% horse serum and 20 μM cytosine β-arabinofuranoside for 48 hours on 1% gelatin coated 6 well plate. Overexpression was achieved by adenoviral infection of Smyd2 or LacZ constructs in DMEM/F-12 medium for 48 hours.

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: Cardiomyocytes  were treated by Si.RNA approach(Qiagen Flexitube) to knockdown/adenoviral approach for overexpression for total period of 48h followed by RNA isolation.

tag: overexpression

value: beta-galacttosidase


title: E10.5 KDR+/CD31+ tdTom+

tag: strain


title: P21 Mouse retina snRNA-seq Tet 1/2/3 tcKO

description: Library name: P21 Tet1/2/3 tcKO snRNA-seq

data_processing:
Fastq files were processed using pipseeker (v3.3.0) and aligned to the GRCm39 reference genome. To lessen the effects of ambient RNA contamination, resulting matrices from pipseeker outputs were processed using Cellbender v.0.3.0. The priors used for the --expected-cells and --total-droplets-included parameters were 1000 and 350,000, respectively. A “full” model was used for both samples with the model dimensions set to --z-dim 256 and --z-layers 2048. Each model was trained to 150 epochs using a learning rate of 1x10^-7. Only cells with a 0.99 probability were used in the downstream analysis.Resulting matrices from Cellbender were imported into Monocle3 for single-cell analysis. Cells containing greater than 500 and less than 10000 transcripts with less than 20% mitochondrial transcripts were utilized for downstream analyses. Dimension reduction was performed using a preprocessed matrix with PCA followed by UMAP dimension reduction using the first 16 PCA dimensions. Cell type annotations were performed using marker gene expression within clusters for known marker genes for retinal cell types as determined previously. Differential expression analysis by genotype was performed using the Monocle3 fit_models function performed on all genes expressed within at least 100 cells and a q-value threshold of 1e-20.
Assembly: GRCm39
Supplementary files format and content: .csv
Supplementary files format and content: .mtx

extract_protocol:
Dissected retina tissue was dissociated on ice in 500ul cold Homogenization Buffer (25mM KCl, 5mM MgCl2, 10mM Tris-HCl, 1mM DTT, cOmplete Mini Protease Inhibitor Cocktail (Roche)) with RNase inhibitors (200U/ml RNasin (Promega), 200U/ml SUPERaseIn (Invitrogen)) using a Dounce homogenizer, with 15 strokes each of pestles A and B. The lysate was strained through a 40um cell strainer, which was then rinsed with 9ml additional Homogenization Buffer. The strained lysate was centrifuged for 5 min at 500xg in a 4°C swinging-bucket centrifuge. After discarding the supernatant, the nuclei pellet was gently resuspended in 1ml cold Resuspension Buffer (25mM KCl, 3mM MgCl2, 50mM Tris-HCl, 1mM DTT) with RNase inhibitors (200U/ml RNasin (Promega), 200U/ml SUPERaseIn (Invitrogen)) using a wide-bore pipet tip. Nuclear concentration was quantified by Countess.
Appropriate numbers of nuclei were then processed according to the PIPseq T20 3’ Single Cell RNA Kit v4.0 (Fluent BioSciences). Completed libraries were sequenced on a NovaSeq X Plus (Illumina Inc) and reads processed using pipseeker (v3.3.0) and aligned to the GRCm39 reference genome.


title: PBMC from co-diagnosed individual, subject 10


title: siScr.Smyd2_rep2


title: siScr.Smyd2_rep1


title: PBMC from co-diagnosed individual, subject 9


title: umbilical cord plasma, overweight sample 3, female

city: Graz

first: Ursula

last: Hiden

address: Auenbruggerplatz 14

department: Obstetrics and Gynecology

country: Austria

institute: Medical University of Graz

description: microRNAs

library_source: other

data_processing:
Primary anaylsis was performed on GeneGlobe software (Quagen) using the RNA-seq Analysis & Biomarker Discovery Pipeline
FASTQ files were uploaded in the RNA-seq Analysis Portal 4.0 (Qiagen) and aligned against reference (miRBase_v22)
Assembly: miRBase_v22 homo sapiens (GRCh38.103)
Supplementary files format and content: tab-delimited text file includes raw counts and CPM for each sample

molecule: other

source_name: umbilical cord plasma

extract_protocol:
miRNeasy Serum/Plasma Advanced Kit (Qiagen)
library was constructed using QIAseq miRNA UDI Library Kit (Qiagen)

value: umbilical cord plasma

tag: maternal bmi

tag: neonatal sex

value: female


title: E3, T lym coculture with MSC-sEVs 3

city: Nes ziona

first: Batia

last: Avni

state: State*

address: 1 lotus st

country: Israel

institute: Hadassah medical center

data_processing:
Fastq files were created with bcl2fastq, v2.18.0.12. Cutadapt, v1.18, using parameters -q32,32 -O 1 --match-read-wildcards and -m 15, was used to trim low quality and adapter bases. Finally, fastq_quality_filter, from FASTX package v0.0.14, using parameters -q 20 -p 90, was used to filter low quality reads.
Alignment of processed reads against the GRCh38 human genome was done with Tophat, v2.1.1, using parameters -G genes.gtf (from Ensembl release 95) -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 18 --read-realign-edit-dist 3 --no-coverage-search and --library-type fr-firststrand.
Raw counts were obtained with htseq-count, v0.6.6, with parameters -s reverse. Counts from all 3 sequencing runs were summed to get the final raw counts per gene per sample.
Differential expression was done with the R (v3.5.2) package DESeq2, v1.22.2, after discarding genes with less than total 10 counts in all samples, using default parameters except not using the independentFiltering algorithm.
Assembly: GRCh38
Supplementary files format and content: Excel file with a header row, followed by a row for each gene. Columns include general gene details (A-I), raw counts per sample (J-N), normalized counts per sample (O-S), DESeq2 calculated baseMean (T), DESeq2 results for comparing T lymphocytes cocultured with MSC-sEVs to control T lymphocytes (U-Y).

source_name: human buffy coat

growth_protocol: BmMSCs were separated from the BM aspirates by filtration through nylon cell strainers with 70 µm pores and re-suspended in filter-sterilized  DMEM,  supplemented with 15% heat-inactivated fetal bovine serum, 1% L-glutamine and 1% Penicillin/ Streptomycin/ Neomycin .  For cell passaging, ~80% confluent cells were incubated for 2-3 minutes in 5 ml pre–warmed Trypsin EDTA Solution (0.25%), EDTA (0.05%) at 37ºC and plated in fresh growth medium. When cells reached 80-90% confluence between passages 1-3, they were re-suspended for 24 hours in growth medium supplemented with sEVs-depleted HI-FBS. Small EVs isolation and purification: medium was collected and differentially centrifuged at 300 x g for 10 minutes at room temperature (R.T.) and at 10,000 x g for 20 minutes at R.T. to eliminate cells and debris. The supernatant was filtered through 0.22 µm filter bottlesr, centrifuged at 100,000 x g for 1 hour at 4°C using a SW 28 rotor in an Optima L-90K ultracentrifuge. sEVs pellets were resuspended in PBS and ultra-centrifuged again at 100,000 x g for 1 hour at 4°C. sEVs were finally resuspended in PBS and stored at -80ºC for further analysis. Each batch of sEVs was isolated from a different MSC donor.

extract_protocol:
Lymphocyte RNA was extracted using the trizol method. For quality control of RNA extraction yield and library synthesis products, RNA Screen Tape kit (Agilent Technologies, Waldbronn, Germany), D1000 ScreenTape kit (Agilent Technologies, Waldbronn, Germany), Qubit® RNA HS Assay kit (Invitrogen, USA) and Qubit® DNA HS Assay kit (Invitrogen, USA) were used for each specific step.
For mRNA library preparation, poly A selection beads followed with NEXTflex™ Rapid Directional qRNA-Seq™ Kit were used (Bio Scientific, UK). In brief, one μg was used for the library construction; the library was eluted in 20 μl elution buffer. Libraries were adjusted and pooled to concentration of 4 nM. Multiplex samples Pool included PhiX 1.5% were loaded on NextSeq 500/550 High Output v2 kit (75 cycles) cartridge (Illumina, USA) and loaded on the NextSeq 500 System (Illumina, USA), with 75 cycles and single-Read Sequencing condition.

treatment_protocol: in vitro T cell isolation using the EasysepTM Human T Cell Enrichment cocktail was performed according to the manufacturer's protocol (Stem CellTM Technologies, Vancouver, Canada). T cell activation was performed by covering designated wells with 50 µl of 5 µg/ml anti CD3 (UCHT1) antibody (Tonbo Biosciences, CA, USA), followed by incubation at 37°C for 4 hours. Antibody solution in each well was replaced by 100 µl 10% sEVs free RPMI media for blocking. T Cells were added at a concentration of 1x105 cells per well and cultured with 0.4 µg per well of anti CD28 (CD 28.2) antibody (Tonbo Biosciences, CA, USA), in the presence or absence of purified bmMSC-sEVs (isolated from 1x106 MSCs, from three different donors), supplemented with 0.2 ml sEVs-depleted medium (containing RPMI with 10% sEVs-depleted FBS). After 4 days of culture, cells were collected for RNA extraction.

tag: agent

value: bmMSC derived sEVs


title: umbilical cord plasma, overweight sample 2, female

description: microRNAs


title: PBMC from co-diagnosed individual, subject 7


title: PBMC from co-diagnosed individual, subject 6


title: E1, T lym coculture with MSC-sEVs 1


title: P21 Mouse retina RNA-seq Tet1/2/3 Het Replicate 3

description: Library name: P21 Tet1/2/3 Het Replicate 3 RNA-seq

data_processing:
Quality control of raw sequencing reads was performed using FastQC (v0.11.9), with summaries generated by MultiQC (v1.19). Adapter trimming and removal of low-quality bases were conducted using Trim Galore (v0.6.7). Trimmed reads were aligned to the mm10 reference genome, using STAR (v2.7.0f) with default parameters optimized for paired-end data, followed by post-alignment processing, including sorting and indexing of BAM files, using Samtools (v1.9). Gene-level quantification was performed using HTSeq (v0.11.2), and genome-wide read coverage was visualized using deepTools (v3.5). Differential expression analysis was conducted in edgeR (v4.2.2) within R (v4.4.1), employing TMM normalization and statistical modeling, with significance thresholds set at |log2FC| ≥ 1 and FDR < 0.01.
Assembly: mm10
Supplementary files format and content: P21_Tet_tcKO_RNAseq.csv

extract_protocol:
Retinas from P21 animals were dissected in PBS and homogenized in 1ml TRIZOL solution. 200µl of chloroform was added to homogenized TRIZOL solution, mixed by vortexing and incubated for 3 min at RT. Lysates were centrifuged for 10 min at 4C at max speed (16,000g). The aqueous phase with RNA was transferred into a fresh tube without disturbing the interphase.
SMARTer Stranded Total RNA High Input (RiboGone Mammalian) (Takara) was used. Briefly, extracted RNA first undergoes ribosomal RNA removal. Then, we proceeded with cDNA synthesis and purification. Following, RNA-seq library was amplified by PCR. Total RNA was captured and purified from RNA samples using Illumina TruSeq stranded primers. RNA-libraries concentrations were measured in a Qubit fluorometer and using the Agilent 2100 Bioanalyzer.

value: Whole Retina

value: Heterozygous


title: P21 Mouse retina RNA-seq Tet1/2/3 tcKO Replicate 1

description: Library name: P21 Tet1/2/3 tcKO Replicate 1 RNA-seq

value: C57 BL/6J

value: Tet tcKO


title: E2, T lym coculture with MSC-sEVs 2


title: P21 Mouse retina snRNA-seq Cre-

description: Library name: P21 Cre- snRNA-seq


title: umbilical cord plasma, overweight sample 4, female

description: microRNAs


title: C2, T lym control 2


title: umbilical cord plasma, overweight sample 4, male

description: microRNAs

value: male


title: umbilical cord plasma, overweight sample 3, male

description: microRNAs


title: PBMC from co-diagnosed individual, subject 8

value: Co-diagnosis


title: PBMC from co-diagnosed individual, subject 5


title: P21 Mouse retina RNA-seq Tet1/2/3 Het Replicate 2

description: Library name: P21 Tet1/2/3 Het Replicate 2 RNA-seq


title: E9.5 KDR+ tdTom-

description:
FACS sorted CD45-CD41-KDR+ Pax3Cre;tdTomato-ve cells
integrated.rds
integrated.h5py
lymphatic.rds
subset_dynamic.h5ad


title: P21 Mouse retina RNA-seq Tet1/2/3 tcKO Replicate 2

description: Library name: P21 Tet1/2/3 tcKO Replicate 2 RNA-seq


title: P21 Mouse retina RNA-seq Tet1/2/3 tcKO Replicate 3

description: Library name: P21 Tet1/2/3 tcKO Replicate 3 RNA-seq


title: PBMC from co-diagnosed individual, subject 4


title: umbilical cord plasma, overweight sample 2, male

description: microRNAs


title: P21 Mouse retina RNA-seq Tet1/2/3 Het Replicate 1

description: Library name: P21 Tet1/2/3 Het Replicate 1 RNA-seq


title: PBMC from co-diagnosed individual, subject 3

description: HERV and gene expression data of PBMC from co-diagnosed individual


title: umbilical cord plasma, overweight sample 1, male

description: microRNAs


title: P21 Mouse retina RNA-seq Cre- Replicate 3

description: Library name: P21 Cre- Replicate 3 RNA-seq


title: PBMC from co-diagnosed individual, subject 2


title: PBMC from co-diagnosed individual, subject 1


title: P21 Mouse retina RNA-seq Cre- Replicate 2

description: Library name: P21 Cre- Replicate 2 RNA-seq


title: umbilical cord plasma, normal weight sample 7, female

description: microRNAs


title: HypoxiaSMC3

city: Boston

first: Ming

last: Zhai

state: Massachusetts

address: Avenue Louis Pasteur

department: Cardiovascular Division, Department of Medicine

institute: Brigham and Women's Hospital

description: Library name: Sample18

data_processing:
CLC genomics WORKbench v 11.0.1
Assembly: mm10
Supplementary files format and content: txt

source_name: primary SMC

extract_protocol:
We used the trizol to extract the RNA
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library prep kit following manufacturer's protocols

tag: cell type

value: primary SMC

value: Hypoxia


title: umbilical cord plasma, normal weight sample 8, female

description: microRNAs


title: PBMC from FM, subject 10

description: HERV and gene expression data of PBMC from FM

source_name: PBMC from FM

value: FM


title: umbilical cord plasma, overweight sample 1, female

description: microRNAs


title: TKPTS cell, FOXA1 antibody

city: Shenyang

first: Ling

last: Hou

email: 79594942@qq.com, houl@sj-hospital.org

address: No.36 Sanhao street

institute: China Medical University

data_processing:
At room temperature, collect fresh cells in an EP tube and count them; perform low-speed centrifugation and remove the supernatant.Add cell perforation buffer to the tube to resuspend the cells; perform low-speed centrifugation and remove the supernatant.Add cell perforation buffer to the tube again to resuspend the cells, gently shake, and then add Binding buffer-resuspended ConA magnetic beads, gently invert to mix for 5-10 minutes.
Quickly centrifuge the EP tube to bring down the liquid on the cap, then place the EP tube on a magnetic rack to precipitate the cells and remove the supernatant. Add pre-cooled antibody buffer to the EP tube to resuspend the cells, gently shake, and place the tube on ice. Add 1μl of primary antibody to each tube and gently shake. Incubate the EP tube on a shaker at room temperature for 2 hours.
Quickly centrifuge the EP tube to bring down the liquid on the cap, then place the EP tube on a magnetic rack to precipitate the cells and remove the supernatant. Dilute the secondary antibody 1:100 in perforation buffer, add it to the tube, and gently shake. Incubate the EP tube on a shaker at room temperature for 30-60 minutes. Quickly centrifuge the cells to bring down the liquid on the cap, then place the EP tube on a magnetic rack to precipitate the cells and remove the supernatant. Add 0.8-1 ml of perforation buffer to the tube, and invert it 10 times.
Quickly centrifuge the EP tube to bring down the liquid on the cap, then place the EP tube on a magnetic rack to precipitate the cells and remove the supernatant.Add 300μl of ChiTag activation buffer to the tube and gently shake.Incubate at 37ºC for 1 hour.
DNA extraction, PCR, DNA purification, and sequencing.
Assembly: mm10
Supplementary files format and content: bigwig, txt
Library strategy: CUT&Tag

source_name: TKPTS

growth_protocol: Mouse kidney proximal tubule cells (TKPTS) were from ATCC (CRL-3361, Manassas, VA) and were cultured in DMEM: F12 (Gibco, Carlsbad, CA) that was supplemented with 7% FBS (Gibco) and 6 μg/mL insulin (HY-P0035/CS-7905, MCE). These cells were maintained at 37 ℃ in a 5% CO2 atmosphere, and were passaged twice per day at a 1:7 ratio.

extract_protocol:
A total of 100,000 TKPTS cells were subjected to CUT&Tag sequencing analysis using the NovoNGS CUT&Tag4.0 High-Sensitivity Kit for Illumina (N259-YH01, Novoprotein, Suzhou, China), according to the specified protocol.
Use Qubit to accurately quantify the library concentration, and use the Agilent 2100 Bioanalyzer to determine the size distribution of the library fragments to assess whether it is suitable for sequencing.The CUT&Tag libraries were sequenced by Genesky Biotechnologies Inc. (Shanghai, China) using the Illumina Novaseq platform.

tag: cell line

value: TKPTS

value: renal proximal tubule cells

value: HNF-alpha (Abcam, #Ab170933)


title: NormoxiaSMC3

description: Library name: Sample21

value: Normoxia


title: HypoxiaSMC1

description: Library name: Sample16


title: PBMC from FM, subject 8


title: TKPTS cell, IgG control

value: IgG control from SimpleChIP Enzymatic Chromatin IP Kit (9003, Cell Signaling Technology, USA)


title: umbilical cord plasma, normal weight sample 4, male

description: microRNAs

value: umbilical cord plasma


title: siScr.bGAL_rep1

value: beta-galacttosidase


title: C1, T lym control 1


title: umbilical cord plasma, normal weight sample 3, male

description: microRNAs


title: 72 hours post inoculation, infected, biorep 4

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

country: Canada

institute: University of Manitoba

description:
Library name: 72hINF4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hINF4

data_processing:
Read quality was determined using FastQC
Reads were aligned using HISAT2 and raw counts were generated using featureCounts
DESeq2 was used to conduct differencial gene expression analysis
Assembly: C. sativa genome - RefSeq assembly accession: GCF_029168945.1 (Kim et al,. 2023)
Assembly: S. sclerotiorum genome - RefSeq assembly accession: GCF_000146945.2 (Amselem et al., 2011)
Supplementary files format and content: C.sativa_raw_counts.txt - tab delimited txt file including raw counts for each sample aligned to C. sativa
Supplementary files format and content: S.sclerotiorum_raw_counts.txt - tab delimited txt file including raw counts for each sample aligned to S. sclerotiorum

organism:
Cannabis sativa
Sclerotinia sclerotiorum

source_name: Inflorescence

extract_protocol:
RNA was extracted using Purelink Invitrogen PlantRNA reagent with the addition of Qiagen's on-column DNAse treatment. 1µg of RNA was sent to Genome Québec for library construction.
Genome Québec constructed cDNA libraries according to their mRNA stranded library preparation protocol. Paired-end 100bp reads were sequenced (Illumina NovaSeq 6000).

value: Inflorescence

value: Cultivar - Kona

value: 72h infected


title: CARMNWT3

description: Library name: Sample14

source_name: musculus gastrocnemius

value: musculus gastrocnemius

value: CARMN WT


title: CARMNWT4

description: Library name: Sample15


title: NormoxiaSMC1

description: Library name: Sample19


title: NormoxiaSMC2

description: Library name: Sample20


title: 72 hours post inoculation, infected, biorep 3

description:
Library name: 72hINF3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hINF3


title: PBMC from FM, subject 6


title: HypoxiaSMC2

description: Library name: Sample17


title: CARMNWT2

description: Library name: Sample13


title: PBMC from FM, subject 5


title: 72 hours post inoculation, infected, biorep 2

description:
Library name: 72hINF2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hINF2


title: umbilical cord plasma, normal weight sample 2, male

description: microRNAs

value: male


title: umbilical cord plasma, normal weight sample 1, male

description: microRNAs


title: PBMC from FM, subject 9


title: umbilical cord plasma, normal weight sample 6, female

description: microRNAs

value: female


title: umbilical cord plasma, normal weight sample 5, female

description: microRNAs


title: PBMC from FM, subject 7


title: PBMC from FM, subject 4


title: CARMNWT1

description: Library name: Sample12


title: Ts93, 1mM copper  [Treat3_3]

city: Nanchang

first: kehe

last: Fu

address: RuiXiang road No.889, Nanchang Changbei Economic Development Zone

department: life of science

institute: Nanchang Normal University

data_processing:
illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Bowtie v2.2.3
paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene
Differential expression analysis was performed using the DESeq R package (1.18.0)
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Trichoderma asperellum

source_name: Ts93, 1mM copper  [Treat3_3] []

extract_protocol:
RNA was harvested using Trizol reagent.RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina

value: Ts93, 1mM copper  [Treat3_3] []

value: wild type

value: 1mM copper ions


title: CARMNKO5

description: Library name: Sample11

value: CARMN knockout


title: CARMNKO4

description: Library name: Sample10


title: Ts93, 1mM copper  [Treat3_2]

source_name: Ts93, 1mM copper  [Treat3_2] []

value: Ts93, 1mM copper  [Treat3_2] []


title: 24 hours post inoculation, infected, biorep 4

description:
Library name: 24hINF4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hINF4

value: 24h infected


title: 24 hours post inoculation, infected, biorep 3

description:
Library name: 24hINF3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hINF3


title: PBMC from FM, subject 2

value: FM


title: CARMNKO3

description: Library name: Sample9


title: Ts93, 1mM copper  [Treat3_1]

source_name: Ts93, 1mM copper  [Treat3_1] []

value: Ts93, 1mM copper  [Treat3_1] []


title: PBMC from FM, subject 1


title: Ts93, control [Treat2_3]

source_name: Ts93, control [Treat2_3] []

value: Ts93, control [Treat2_3] []

value: CK


title: CARMNKO2

description: Library name: Sample8


title: PBMC from ME/CFS, subject 8

description: HERV and gene expression data of PBMC from ME/CFS

source_name: PBMC from ME/CFS

value: ME/CFS


title: 72 hours post inoculation, infected, biorep 1

description:
Library name: 72hINF1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hINF1

value: Inflorescence

value: Cultivar - Kona


title: 24 hours post inoculation, infected, biorep 2

description:
Library name: 24hINF2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hINF2


title: Ts93, control [Treat2_2]

source_name: Ts93, control [Treat2_2] []

value: Ts93, control [Treat2_2] []


title: PBMC from ME/CFS, subject 7


title: PBMC from FM, subject 3


title: PBMC from ME/CFS, subject 6


title: CARMNSMCWT3

description: Library name: Sample6

value: primary SMC

value: CARMN WT


title: 168 hours post inoculation, infected, biorep 4

description:
Library name: 168hINF4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hINF4

value: 168h infected


title: Ts93, control [Treat2_1]

source_name: Ts93, control [Treat2_1] []

value: Ts93, control [Treat2_1] []


title: PBMC from ME/CFS, subject 5


title: 168 hours post inoculation, infected, biorep 2

description:
Library name: 168hINF2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hINF2


title: 168 hours post inoculation, infected, biorep 3

description:
Library name: 168hINF3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hINF3


title: P21 Mouse retina RNA-seq Cre- Replicate 1

description: Library name: P21 Cre- Replicate 1 RNA-seq

source_name: Whole Retina

value: Whole Retina

value: C57 BL/6J

value: WT


title: CARMNSMCWT2

description: Library name: Sample5


title: PBMC from ME/CFS, subject 4


title: CARMNSMCWT1

description: Library name: Sample4


title: 168 hours post inoculation, infected, biorep 1

description:
Library name: 168hINF1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hINF1


title: Ts93, 0.5 mM BCS [Treat1_1]

value: wild type

value: 0.5 mM BCS


title: 120 hours post inoculation, infected, biorep 4

description:
Library name: 120hINF4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hINF4

value: 120h infected


title: Ts93, 0.5 mM BCS [Treat1_2]


title: 24 hours post inoculation, infected, biorep 1

description:
Library name: 24hINF1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hINF1

value: 24h infected


title: CARMNSMCKO3

description: Library name: Sample3

value: CARMN knockout


title: CARMNSMCKO2

description: Library name: Sample2


title: PBMC from ME/CFS, subject 3


title: 120 hours post inoculation, infected, biorep 3

description:
Library name: 120hINF3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hINF3


title: PBMC from ME/CFS, subject 2


title: VH_SV-2

city: Wuhan

first: Shengchi

last: Shi

address: Donghu South Road #7

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Library name: VH_SV-2

data_processing:
HISAT2
Assembly: ASM1834038v1
Supplementary files format and content: tab-delimited text fle includes raw fpkm for each Sample

organism: Cyprinus carpio

source_name: Epithelial cells

extract_protocol:
RNA was harvested using RNA 6000 nano kit (Agilent). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit followingmanufacturer's protocols.

value: Epithelial cells

value: SVCV infection


title: VH_SV-1

description: Library name: VH_SV-1


title: 120 hours post inoculation, infected, biorep 2

description:
Library name: 120hINF2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hINF2

value: Inflorescence


title: CARMNKO1

description: Library name: Sample7

value: musculus gastrocnemius


title: H-cyp_SV-2

description: Library name: H-cyp_SV-2

value: cyp17a2 overexpression


title: CARMNSMCKO1

description: Library name: Sample1

value: primary SMC


title: PBMC from ME/CFS, subject 1

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, MD, USA) according to the manufacturer's instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent). All RNA samples had an RNA Integrity number (RIN) above 7. cDNA was synthesized and amplified from 45 ng of RNA using the Ovation Pico WTA System V2 kit (Nugen) according to manufacturer's instructions. The resulting amplified ssDNA was purified using the QIAquick purification kit (Qiagen, MD, USA)

value: ME/CFS


title: Ts93, 0.5 mM BCS [Treat1_3]


title: H-cyp_SV-1

description: Library name: H-cyp_SV-1


title: HCC tumor, IMQNP_4

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

country: Taiwan

institute: National Tsing Hua University

description: Library name: IMQNP_4

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: tumor

growth_protocol: Murine HCC HCA-1 cells were orthotopically implanted in the liver of 6–8-week-old male C3H mice. 1 × 10^6 HCA-1 cells were injected in the subcapsular region through a 28-gauge needle.

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanting murine HCC (HCA-1) cells in C3H mice, followed by IV administration of PFSUV-IMQ on day 17. Subsequent transcriptome analysis of the tumors was performed after 3-hour circulation.

value: tumor

value: HCC


title: 120 hours post inoculation, infected, biorep 1

description:
Library name: 120hINF1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hINF1

value: Cultivar - Kona

tag: batch