title: Intact rat treated with DAPM 45


title: Cdh16Pos_P10

status: Public on Apr 01 2025

type: SRA

city: WenZhou

first: Jin

last: Wu

state: ZHejiang

address: Jingguan street 1#

country: China

institute: WenZhou Medical University

description:
Library name: Sample 2
10X Genomics

library_source: transcriptomic single cell

data_processing:
A total of 20,000 cells were processed using the 10x Genomics platform, following the manufacturer's protocol for cDNA and library preparation. Data analysis was performed using the Seurat R package (v4.0.0). Quality control steps were applied to remove doublets, multicellular aggregates, and apoptotic cells. The final dataset included 10,213 to 12,353 cells per sample, with UMI counts ranging from 10,553 to 11,249 per cell, and 3,025 to 3,226 genes identified per cell. Mitochondrial gene expression was consistent, with an average UMI ratio of 0.017 per cell. Quality control metrics ('nFeature_RNA', 'nCount_RNA', and 'percent_mt') were assessed for each cell. For data normalization, UMIs were normalized, scaled, and log-transformed across cells. Variable genes were selected for dimensionality reduction using PCA and UMAP. Batch effects were corrected by integrating multiple samples. Clustering dimensions were optimized using JackStraw and Elbow plot analyses, and cell clusters were identified with the Louvain method. Clusters were annotated based on tissue-specific markers, with epithelial fractions identified by known marker genes. Differential gene expression analysis was performed to identify cluster-specific RNA markers, aiding in cluster identification. Clusters were annotated using LungMAP (https://app.lungmap.net, accessed January 15, 2024). RNA velocity analysis was performed to infer the direction of gene expression changes in different clusters. The SCENIC software was used to identify transcription factor (TF)-target gene modules and calculate the regulon activity score (RAS) for each cell. The regulon specificity score (RSS) and connection specificity index (CSI) were calculated to assess regulon activity and co-regulation between regulons (https://github.com/aertslab/SCENIC, accessed February 15, 2024).
Assembly: Mouse mm10
Supplementary files format and content: The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell ranger for each sample".
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Embryonic lung

extract_protocol:
Lung tissues were harvested and placed in Hank’s Balanced Salt Solution (HBSS, Gibco), finely minced, and then digested in 0.25% collagenase IV mixed with dispase II (Gibco) in PBS at 37°C for 45 min. The resultant lung homogenates were strained through 100 μm, 70 μm and 40 μm cell strainers (BD Biosciences) to achieve single-cell suspensions. After centrifugation at 4°C and 1000 rpm for 10 min, cells were resuspended in MACS buffer and stained with anti-CD326 (APC-conjugated, 1:100, Biolegend) for 30 min on ice before washing with HBSS. Flow cytometry and subsequent cell sorting were conducted on a Moflo Astrios (Beckman), with tdTomatoPos cells identified within the CD326-APC population. Mesenchymal cells from adult C57BL/6 lungs were sorted as CD326Neg, CD31Neg, CD45Neg (APC-conjugated, 1:100) populations.
Library was performed according to the manufacter's instructions (single cell 3' v2protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loadedtogether with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM wasretrotranscripted to cDNA, which contains an llumina R1 primer sequence, UniqueMolecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was thencleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragmentswere selected with SPRlselect reagent for subsequent library construction. During thelibrary construction llumina R2 primer sequence, paired-end constructs with P5 and P7sequences and a sample index were added.

tag: tissue

value: Embryonic lung

tag: cell type

value: Lung alveolar epithelial cells

tag: genotype

tag: time point

value: postnatal day 10 (P10)

tag: batch


title: Cadmium Chloride sample tested at 1.05 uM (Replicate: 2, Control Batch Id: 8).

type: RNA

city: Mason

first: Bastian

middle: Gregory

last: Selman

state: Ohio

address: 8700 Mason Montgomery Rd

country: USA

institute: Procter & Gamble

hyb_protocol: 7.5 micrograms of labeled cRNA was fragmented manually and hybridized to Affymetrix Human Genome U219-96 arrays for 16 hr, washed, stained and scanned using an Affymetrix GeneTitan (Santa Clara, CA).

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan (Santa Clara, CA).

data_processing: The data were analyzed using the rma function in the affy package for R. This function uses RMA for background correction, performs probe specific correction, normalizes using quantile normalization and finally applies a median polish. Package citation: Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi:10.1093/bioinformatics/btg405.

label: biotin

organism: Homo sapiens

source_name: TK6 Human lymphoblastoid cells

label_protocol: Labeled cRNA was synthesized from 250 ng of total RNA using the Affymetrix (Santa Clara, CA) IVT-Express labeling kit according to manufacturer's instructions. Seven and a half micrograms of labeled cRNA was fragmented manually and hybridized to Affymetrix Human Genome U219-96 arrays for 16 hr, washed, stained and scanned using an Affymetrix GeneTitan (Santa Clara, CA).

growth_protocol: TK6 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, CRL-8015). Cells were cultured at 37C with 5% CO2 and 95% humidity in RPMI 1640 with 10% heat-inactivated FBS and 1% pen-strep. Cells were maintained at or below 1E6 cells/ml.

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Tissue XP beads (Beckman Coulter Inc., Danvers, MA) according to the manufacturer's protocol on the cell lysates. RNA integrity was validated using a NanoDrop 8000 Spectrophotometer (Wilmington, DE).

treatment_protocol: All chemicals were tested in triplicate to a top concentration of 10 mM, or the limit of solubility or cytotoxicity. The final concentration of the solvent in these studies was limited to 0.5% (vol/vol) DMSO or water, although in a few isolated cases 1% DMSO or 10% water was used at a top concentration, in accordance with the OECD guidelines.

value: Cadmium Chloride

value: sample

tag: solvent

value: Water


title: Cadmium Chloride sample tested at 1.05 uM (Replicate: 1, Control Batch Id: 8).


title: Cadmium Chloride sample tested at 1.58 uM (Replicate: 1, Control Batch Id: 8).


title: GBM-6425_D.1H12, single cell DNA methylation

city: Toronto

first: Federico

last: Gaiti

state: Ontario

address: 101 college street

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: GBM-6425_D.1H12

library_source: genomic

data_processing:
The single-cell DNA methylation sequencing data from Scale Biosciences was processed using the ScaleBio Seq Suite: Methylation Workflow (v1.1.0 pre-release) under default parameters.
Assembly: hg38
Supplementary files format and content: h5 files with matrices of DNA methylation status for each cell
Library strategy: sciMet

molecule: genomic DNA

source_name: GBM patient brain tissue

extract_protocol:
Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. Nuclei were fixed with 16% formaldehyde followed by nucleosome disruption. After gently mixing nucleosome disruption solution with nuclei suspension, nuclei were centrifuged with pellet resuspended for each biological sample. Nuclei inputs were normalized across samples, and the tagmentation-nuclei mix was prepared for each biological sample based on the number of reactions. Nuclei were distributed across the three 96-well Met Tagment Barcode Plates, using a total of 288 unique barcodes for nuclei tagmentation. Tagmented nuclei were gated for positive DNA staining and sorted for 24 nuclei per well on the sorting plate. Bisulfite Conversion Solution was added to each well to convert unmethylated cytosines to uracil and the post-reaction product was cleaned up through elution.
The sequencing library was prepared by adding amplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.

value: GBM patient brain tissue


title: Azidothymidine sample tested at 1870 uM (Replicate: 3, Control Batch Id: 7).

value: Azidothymidine


title: GBM-6425_D.1H11, single cell DNA methylation

description: Library name: GBM-6425_D.1H11


title: Cdh16Pos_E18.5

description:
Library name: Sample 1
10X Genomics


title: Ovariectomized rat treated with DAPM 36

city: Baton Rouge

first: Tammy

middle: R

last: Dugas

state: LA

address: Skip Bertman Drive

department: Comparative Biomedical Sciences

institute: LSU School of Veterinary Medicine

description: miRNA profiling was done in isolated RNA from pulmonary artery using NanoString nCounter Tumor Signaling 360 Panel.

hyb_protocol: An overnight hybridization was performed, followed by a two-step magnetic bead-based purification. The purified target/probes complexes were immobilized on the catridge for data collection in nCounter SPRINT Profiler.

scan_protocol: Digitial images were taken from immobilized target/probes complex and color-coded barcode were counted.

data_processing: Run files in RCC format were analyzed using nSolver software. Raw counts for mRNA were subjected to background substraction, followed by normalization using positive control normalization and CodeSet Content Normalization. Data were analyzed using two-way ANOVA to determine significance between groups and significant interactions between groups.

label: Biotin

organism: Rattus norvegicus

source_name: Pulmonary artery

label_protocol: 10 ng of tissue RNA were ligated with unique oligonucleotide tags. Then, tagged miRNA were labeled using oligonucleotide probes with color-coded signal in 5' end and biotin on its 3' end.

extract_protocol: RNA was extracted from pulmonary arteries with a miRNeasy mini kit (Qiagen).

tag: strain

value: Sprague Dawley

tag: Sex

value: Female

tag: age

value: 11-15 weeks


title: Ovariectomized rat treated with DAPM 38


title: RAW264.7 cells overexpressing HA-TLR3-anti-HA  [s0h-shang iCLIP-seq]

city: 东城区

first: 张仕坤

last: Zhang

state: 北京市

address: 东单三条五号

institute: 协和医学院基础医学研究所

library_source: transcriptomic

data_processing:
Primary sequencing data that produced by Illumina HiSeq 2500 , called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Raw data quality control was performed by FastQC, and raw data filter was performed by scripts.
Trimmomatic and Fastx-toolkit were used to trim adaptor contamination and low quality bases.
Clean data mapped to mm10 reference genome by HISAT2.
Assemble of RNA-Seq alignments into mm10 transcripts was processed by Stringtie.
Differential expression analysis between sample 1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: RAW264.7 cells overexpressing HA-TLR3

growth_protocol: RAW264.7 cells were cultured and passaged in DMEM with 10% (v/v) fetal bovine serum (FBS) (Gibco). TLR3 overexpression RAW264.7 cell line was obtained by transfecting RAW264.7 cells with the plasmid: pUNO1-mTLR3-3×HA (InvivoGen)

extract_protocol:
iCLIP was performed using anti-HA antibody, and the isolated RNA was further processed into iCLIP-seq library and then standard illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treamtment

tag: cell line

tag: genotype/variation

value: overexpressing HA-TLR3

tag: molecule subtype

value: HA-TLR3 binding RNA

tag: antibody

value: anti-HA antibody


title: Ovariectomized rat treated with DAPM 37


title: RAW264.7 cells overexpressing HA-TLR3-IgG [ctrl iCLIP-seq]

institute: 协和医学院基础医学研究所

extract_protocol:
iCLIP was performed using IgG antibody, and the isolated RNA was further processed into iCLIP-seq library and then standard illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: IgG binding RNA


title: Azidothymidine sample tested at 1870 uM (Replicate: 1, Control Batch Id: 7).


title: Intact rat treated with DAPM 44


title: Azidothymidine sample tested at 3740 uM (Replicate: 2, Control Batch Id: 7).


title: Azidothymidine sample tested at 3740 uM (Replicate: 1, Control Batch Id: 7).


title: Lgr5+ intestinal stem cells from a mouse treated with GSI (DBZ), biological replicate 3

city: New York

first: Teresa

last: Palomero

state: New York

address: 1130 St Nicholas Ave Rm 607

institute: Institute for Cancer Genetics -Columbia University

description: Gene expression data from Lgr5+ intestinal stem cells from mouse treated with DMSO

hyb_protocol: hybridized on Affymetrix Mouse 430A_2 arrays according to the manufacturer's instructions

scan_protocol: Standard Affymetix protocol

data_processing: We normalized interarray intensity differences with dCHIP and averaged the expression across triplicate samples.

source_name: Lgr5-EGFP-IRES-creERT2 mouse

label_protocol: RNA of each sample was amplified and labeled using the 3’ IVT Express Kit (Affymetrix)

growth_protocol: collected mouse small intestinal stem cells by sorting GFPhigh cells from Lgr5-EGFP-IRES-creERT2 mice treated with vehicle (DMSO) or DBZ (30 mol kg-1) for 24 hours

extract_protocol: We extracted the total RNA using RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.

value: intestine


title: Intact rat treated with DAPM 41


title: Intact rat treated with DAPM 43


title: GBM-6425_D.1H10, single cell DNA methylation

description: Library name: GBM-6425_D.1H10


title: Intact rat treated with DAPM 42


title: GBM-6431_B.2B07, single cell DNA methylation

description: Library name: GBM-6431_B.2B07


title: Azidothymidine sample tested at 1870 uM (Replicate: 2, Control Batch Id: 7).


title: Lgr5+ intestinal stem cells from a mouse treated with vehicle (DMSO), biological replicate 3


title: GBM-6425_D.1H06, single cell DNA methylation

description: Library name: GBM-6425_D.1H06


title: GBM-6425_D.1H09, single cell DNA methylation

description: Library name: GBM-6425_D.1H09


title: Azidothymidine sample tested at 935 uM (Replicate: 2, Control Batch Id: 7).


title: Lgr5+ intestinal stem cells from a mouse treated with GSI (DBZ), biological replicate 2


title: Azidothymidine sample tested at 935 uM (Replicate: 3, Control Batch Id: 7).


title: GBM-6425_D.1H08, single cell DNA methylation

description: Library name: GBM-6425_D.1H08


title: Lgr5+ intestinal stem cells from a mouse treated with GSI (DBZ), biological replicate 1


title: GBM-6425_D.1H04, single cell DNA methylation

description: Library name: GBM-6425_D.1H04


title: Ovariectomized rat treated with vehicle 32


title: Azidothymidine sample tested at 467.5 uM (Replicate: 2, Control Batch Id: 7).


title: HCT116, siTG2, rep1

city: Shenyang

first: Wanhua

last: Xie

address: Huanghe North Street 146

institute: Shenyang Medical college

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered reads were mapped to hg19 genome using STAR 2.7.0 with  parameters  --bamRemoveDuplicatesType UniqueIdentical
The reads on exon of each genes were counted using Htseq-count 0.12.4 with parameters -s no -t exon -i gene_id -m union
Normalization and differential analysis of gene counts were performed by the DESeq2 package in R
Assembly: hg38
Supplementary files format and content: xls files include DESeq2-normalied counts for every gene and every sample

molecule: polyA RNA

growth_protocol: McCoy's 5A medium cells were cultured in  high-glucose McCoy's 5A medium supplemented with 10% FBS (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37 °C, 5% CO2.

extract_protocol:
Total RNA was isolated using QIAzol reagent (Qiagen) and quantitated using a Bioan-alyzer 2100 (Agilent).  1 ug of total RNA was used to prepare seqencing library
VAHTS mRNA-seq V3 Library Prep Kit for Illumina  (Vazyme) was used to prepare the seqencing libraries.

treatment_protocol: HCT116 cells 48 hours after siRNA transfection were used to perform mRNA-seq and ChIP-seq. siRNA were transfected by Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: Human Colon Adenocarcinoma

value: TG2 knockdown

tag: treatment


title: Intact rat treated with DAPM 25


title: GBM-6425_D.1H07, single cell DNA methylation

description: Library name: GBM-6425_D.1H07


title: Intact rat treated with DAPM 26


title: GBM-6425_D.1H03, single cell DNA methylation

description: Library name: GBM-6425_D.1H03


title: HCT116, siTG2, rep3


title: HCT116, siRNF40, rep3

value: RNF40 knockdown


title: GBM-6425_D.1H05, single cell DNA methylation

description: Library name: GBM-6425_D.1H05


title: Azidothymidine sample tested at 935 uM (Replicate: 1, Control Batch Id: 7).


title: Azidothymidine sample tested at 467.5 uM (Replicate: 3, Control Batch Id: 7).


title: Ovariectomized rat treated with vehicle 33


title: HCT116, siTG2, rep2


title: Azidothymidine sample tested at 467.5 uM (Replicate: 1, Control Batch Id: 7).


title: Lgr5+ intestinal stem cells from a mouse treated with vehicle (DMSO), biological replicate 1


title: Lgr5+ intestinal stem cells from a mouse treated with vehicle (DMSO), biological replicate 2


title: Ovariectomized rat treated with vehicle 29


title: Azidothymidine sample tested at 233.75 uM (Replicate: 1, Control Batch Id: 7).


title: HCT116, siRNF40, rep1


title: GBM-6425_D.1G12, single cell DNA methylation

description: Library name: GBM-6425_D.1G12


title: GBM-6425_D.1H02, single cell DNA methylation

description: Library name: GBM-6425_D.1H02


title: Azidothymidine sample tested at 233.75 uM (Replicate: 3, Control Batch Id: 7).


title: Ovariectomized rat treated with vehicle 31


title: GBM-6425_D.1G11, single cell DNA methylation

description: Library name: GBM-6425_D.1G11


title: HCT116, siRNF40, rep2


title: Ovariectomized rat treated with vehicle 30


title: Ovariectomized rat treated with vehicle 34


title: HCT116, siControl, rep2

value: WT

value: siControl


title: Ovariectomized rat treated with vehicle 28


title: HCT116, siControl, rep1


title: Ovariectomized rat treated with vehicle 27


title: GBM-6425_D.1G09, single cell DNA methylation

description: Library name: GBM-6425_D.1G09


title: HCT116, siControl, rep3


title: Azidothymidine sample tested at 116.88 uM (Replicate: 3, Control Batch Id: 7).

value: sample


title: Intact rat treated with vehicle 21


title: Intact rat treated with vehicle 24


title: HCT116, H3Q5ser, Sigma, siRNF40, rep2

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered ChIP-seq reads were aligned to the hg19 genome using bowtie2 (Version 2.4.1) with   default parameters. PCR duplicates in bam files were moved by using Picard tool.
MACS2 (Version 2.2.7.1 43) was used to call narrow peaks for H2Bub1, H3K4me3, and H3Q5ser with the parameters (-q 0.001).
The ChIP signal was normalized by using bamCoverage function in deeptools 3.5.0 with the parameters ( --normalizeUsing CPM,  --ignoreDuplicates,  --minMappingQuality 30,  --minFragmentLength 50)
Assembly: hg38
Supplementary files format and content: bigWig (from both replicates), narrowPeak

extract_protocol:
10^6 cells were crosslinked in 1% formaldehyde for 10 minutes and quenched using 125mM of Glycine for 5 minutes. The chromosome was fragmented to the fragment range of 200-400 bp in the Bioruptor® Pico via sonicating 5 cycles. The fragmented histone-DNA complexes were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607)  was used with 5 ng of ChIP DNA of each sample for the construction of sequencing libraries.

tag: chip antibody

value: H3Q5ser (Sigma, #ABE1791)


title: Intact rat treated with vehicle 12


title: Ascorbic acid sample tested at 578 uM (Replicate: 3, Control Batch Id: 8).

value: Ascorbic acid

value: Water


title: GBM-6425_D.1G06, single cell DNA methylation

description: Library name: GBM-6425_D.1G06

value: GBM patient brain tissue


title: Azidothymidine sample tested at 116.88 uM (Replicate: 2, Control Batch Id: 7).

value: Azidothymidine


title: Azidothymidine sample tested at 233.75 uM (Replicate: 2, Control Batch Id: 7).


title: Azidothymidine sample tested at 116.88 uM (Replicate: 1, Control Batch Id: 7).


title: HCT116, H3Q5ser, Sigma, siRNF40, rep1


title: GBM-6425_D.1G05, single cell DNA methylation

description: Library name: GBM-6425_D.1G05


title: GBM-6425_D.1H01, single cell DNA methylation

description: Library name: GBM-6425_D.1H01


title: HCT116, H3Q5ser, Sigma, siControl, rep2


title: Gsdmd_KO_oxalate_3

city: München

first: Yoshihiro

last: Kusunoki

address: Ziemssenstr. 5

country: Germany

institute: LMU Klinikum

data_processing:
Raw reads were trimmed of adaptors and filtered for quality by BGI.
After QC, Fastq was mapped to the mm39 by hisat2. DESeq2 for downstream analyze.
Assembly: mm39
Supplementary files format and content: tab-delimited csv file includes raw counts for each sample
Supplementary files format and content: tab-delimited csv file includes RPKM values for each sample

source_name: kidney

extract_protocol:
Total RNA was isolated from kidneys using an RNA extraction kit (Invitrogen).
RNA libraries were conducted by Beijing Genomics Institute (BGI) using DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

value: kidney

tag: background strain

value: Gsdmd knockout

value: oxalate rich-diet


title: Ascorbic acid sample tested at 578 uM (Replicate: 1, Control Batch Id: 8).


title: GBM-6425_D.1G04, single cell DNA methylation

description: Library name: GBM-6425_D.1G04


title: HCT116, H3Q5ser, Sigma, siTG2, rep1


title: GBM-6425_D.1G10, single cell DNA methylation

description: Library name: GBM-6425_D.1G10


title: HCT116, H3Q5ser, Sigma, siControl, rep1


title: Gsdmd_KO_oxalate_1


title: HCT116, H3Q5ser, Sigma, siTG2, rep2


title: GBM-6425_D.1G08, single cell DNA methylation

description: Library name: GBM-6425_D.1G08


title: Intact rat treated with vehicle 23

value: Sprague Dawley

value: Female

value: 11-15 weeks


title: WT_oxalate_4

value: wild-type


title: GBM-6425_D.1G07, single cell DNA methylation

description: Library name: GBM-6425_D.1G07


title: GBM-6425_D.1G02, single cell DNA methylation

description: Library name: GBM-6425_D.1G02


title: Gsdmd_KO_oxalate_4


title: WT_oxalate_2


title: Gsdmd_KO_oxalate_2


title: GBM-6425_D.1G03, single cell DNA methylation

description: Library name: GBM-6425_D.1G03


title: Ascorbic acid sample tested at 400 uM (Replicate: 3, Control Batch Id: 7).


title: Ascorbic acid sample tested at 401 uM (Replicate: 2, Control Batch Id: 8).


title: Ascorbic acid sample tested at 482 uM (Replicate: 3, Control Batch Id: 8).


title: GBM-6425_D.1F11, single cell DNA methylation

description: Library name: GBM-6425_D.1F11


title: HCT116, H3K4me3, Abclonal, siControl, rep2

value: Human Colon Adenocarcinoma

value: H3K4me3 (ABclonal, #A2357)


title: Ascorbic acid sample tested at 578 uM (Replicate: 2, Control Batch Id: 8).


title: WT_control_ 4

value: control  diet


title: HCT116, H3K4me3, Abclonal, siTG2, rep2


title: Ascorbic acid sample tested at 401 uM (Replicate: 3, Control Batch Id: 8).


title: Ascorbic acid sample tested at 482 uM (Replicate: 1, Control Batch Id: 8).


title: Ascorbic acid sample tested at 482 uM (Replicate: 2, Control Batch Id: 8).


title: HCT116, H3K4me3, Abclonal, siTG2, rep1


title: GBM-6425_D.1F12, single cell DNA methylation

description: Library name: GBM-6425_D.1F12


title: GBM-6425_D.1G01, single cell DNA methylation

description: Library name: GBM-6425_D.1G01


title: Ascorbic acid sample tested at 400 uM (Replicate: 1, Control Batch Id: 7).


title: HCT116, H2Bub1, CST, siRNF40, rep2


title: HCT116, H3K4me3, Abclonal, siRNF40, rep1


title: WT_control_ 1

value: control diet


title: HCT116, H2Bub1, CST, siRNF40, rep1


title: Ascorbic acid sample tested at 401 uM (Replicate: 1, Control Batch Id: 8).

value: sample


title: WT_oxalate_1


title: HCT116, H3K4me3, Abclonal, siControl, rep1

value: siControl


title: GBM-6425_D.1F09, single cell DNA methylation

description: Library name: GBM-6425_D.1F09


title: HCT116, H2Bub1, CST, siControl, rep2


title: Ascorbic acid sample tested at 400 uM (Replicate: 2, Control Batch Id: 7).

value: Ascorbic acid


title: Ascorbic acid sample tested at 285.71 uM (Replicate: 3, Control Batch Id: 7).

value: Water


title: Zcchc8KO_rep2

city: Aarhus C

first: Katsutoshi

last: Imamura

address: Bissensgade 16, 4. tv

country: Denmark

institute: Aarhus University

data_processing:
Raw sequence reads from RNA-seq experiments quality checked using FastQC
Trimmed reads were mapped to mm10, using  bowtie2
Mapped files were sorted and checked for pairing using Samtools
Finally, reads were converted to bigwig (bw) files normalized to library sizes using bamCoverage
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: mESC

growth_protocol: cell lines were cultured on 0.2% gelatin-coated plates in 2i/LIF containing medium (1:1 mix of Neurobasal (Gibco) and DMEM/F12 (Gibco)) supplemented with 1x Pen-Strep (Gibco), 2 µM Glutamax, 50 µM -mercaptoethanol (Gibco), 0.1 mM Non-Essential Amino Acids (Gibco), 1 mM Sodium Pyruvate (Gibco), 0.5x N2 supplement (Gibco), 0.5x B27 supplement (Gibco), 3 µM GSK3i (CHIR99021), 1 µM MEKi (PD0325901) and Leukemia Inhibitory Factor (LIF, produced in house) at 37°C, 5% CO2.

extract_protocol:
RNA was extracted using TRIzol (Ambion) and then further treated with TURBO DNAse (Ambion), according to manufacturer’s recommendations
Library construction and sequencing is a paid service provided by the Beijing Genomics Institute (BGI), which cutting out 15-30 nt, prepared libraries and performed SE50 sequencing

value: mESC

value: Zcchc8 knockout

value: gRNA for Zcchc8


title: HCT116, H2Bub1, CST, siControl, rep1


title: GBM-6425_D.1F04, single cell DNA methylation

description: Library name: GBM-6425_D.1F04

value: GBM patient brain tissue


title: WT_control_ 2

value: kidney


title: Ascorbic acid sample tested at 285.71 uM (Replicate: 2, Control Batch Id: 7).


title: Sample 13_TW24-1

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk and FASTX-Toolkit.
mRNA-seq reads were aligned to the Triticum aestivum Chinesespring genome sequence (IWGSC) using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.4
Expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method. The normalized expression levels of different samples were converted to FPKM (fragments per kilobase transcriptome per million fragments)
Differential expression were analysed  using edgeR.
Genome_build: Triticum aestivum Chinesespring genome sequence (IWGSC)
Supplementary_files_format_and_content: Tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Triticum aestivum

source_name: wheat coleoptiles_after 24 hours control (0.5% Tween-20) treated coleoptiles

growth_protocol: Grow the wheat seedling in the growth chamber for 3 day under controlled environment conditions at 25 °C with a 12 h light/12 h dark photoperiod

extract_protocol:
Total RNA was isolated using EasyPure Plant RNA kit (Transgen biotech) according to the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrated number (RIN) value of 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For compound treatment: add 2μl fusaoctaxin B (0.5mM) or 0.5% tween-20 onto wound site of wheat coleoptiles.

tag: cultivars

value: Zhongyuan 98-68

tag: days post inoculation

tag: treatment/timepoint


title: Sample 15_TW24-3

value: after 24 hours control (0.5% Tween-20) treated coleoptiles


title: Sample 14_TW24-2


title: Ascorbic acid sample tested at 204.08 uM (Replicate: 1, Control Batch Id: 7).


title: GBM-6425_D.1F08, single cell DNA methylation

description: Library name: GBM-6425_D.1F08

tag: tissue


title: GBM-6425_D.1F07, single cell DNA methylation

description: Library name: GBM-6425_D.1F07


title: WT_control_ 3

tag: genotype


title: GBM-6425_D.1F10, single cell DNA methylation

description: Library name: GBM-6425_D.1F10


title: GBM-6425_D.1F02, single cell DNA methylation

description: Library name: GBM-6425_D.1F02


title: GBM-6425_D.1F06, single cell DNA methylation

description: Library name: GBM-6425_D.1F06


title: Ascorbic acid sample tested at 145.77 uM (Replicate: 1, Control Batch Id: 7).


title: Zcchc8KO_rep3

tag: cell type


title: GBM-6425_D.1F05, single cell DNA methylation

description: Library name: GBM-6425_D.1F05


title: Ascorbic acid sample tested at 204.08 uM (Replicate: 3, Control Batch Id: 7).

tag: solvent


title: HCT116, H3K4me3, Abclonal, siRNF40, rep2


title: Sample 11_FB24-2

source_name: wheat coleoptiles_after 24 hours fusaoctaxin B-treated coleoptiles


title: GBM-6425_D.1E12, single cell DNA methylation

description: Library name: GBM-6425_D.1E12


title: GBM-6425_D.1F03, single cell DNA methylation

description: Library name: GBM-6425_D.1F03


title: Zcchc8KO_rep1


title: Ascorbic acid sample tested at 285.71 uM (Replicate: 1, Control Batch Id: 7).


title: Control_rep3

value: WT


title: Non-stressed_C8_Rep1

city: Villeurbanne

first: Philippe

last: Veber

address: 16 rue Raphael Dubois

country: France

institute: CNRS

description: Aquatic microbial communities

data_processing:
transcriptome assembly
trinity 2.9.1 default options
transcript quantification
kallisto 0.43.0 default options, effective counts

organism: freshwater metagenome

source_name: Biofilm

growth_protocol: The inoculum was allowed to grow on glass slides (15.25 cm2) vertically disposed in glass-tanks of 20L. Microbial communities incubated for five weeks at constant conditions (22.1°C, 14:10h day:night cycle).

extract_protocol:
Samples were grinded into liquid nitrogen. Afterwards the RNeasy Plant Mini kit (QIAGEN, Inc., Valencia, CA) was used according to the manufacturer. RNA was eluted two times (30µL and 10µL) with 60°C elution buffer. Then, DNA contaminations were digested using the Ambion Turbo DNA-free kit (Thermo Fisher Scientific, Inc., Waltham, MA) following the instructions. To remove DNase buffer the RNA was precipitated by ethanol. The final dried pellet was dissolved into 20µL of RNase-free water and incubated for 8 minutes at 58°C. After cooling-down on ice, and a brief centrifugation, the RNA samples were stored at -80°C.
100 ng total RNA was used for rRNA depletion. Ribosomal RNAs were removed from total RNA using the Ribo-Zero Magnetic Kit (Illumina, San Diego, CA, USA) according to the manufacturer`s low input instructions. To improve rRNA depletion, rRNA probes from Ribo-Zero bacteria kit (MRZMB126) and plant kit (MRZPL1224) were combined. A strand-specific library for transcriptome sequencing was prepared using the ScripSeqv2 Kit (Illumina) following the manufacturer`s instructions. The library was checked by using the Agilent 2100 Bioanalyzer system with a High Sensitivity DNA Kit (Agilent) according to the manufacturer`s instructions. Library concentration was determined by using the Qubit 2.0 instrument using the Quant-iT dsDNA High Sensitivity kit (Thermo Fisher Scientific) according to the manufacturer`s instructions. Single libraries were normalized by equimolar pooling. The library pool was size-selected in a range of 150-600 bp using a preparative agarose gel in combination with MinElute gel extraction kit (Qiagen) according to the manufacturer’s protocol. 12 pmol of the library pool were clustered on 7 lanes of an Illumina paired-end flow cell and 2x100 bp were sequenced according to the manufacturer’s instructions using the v3 Cluster Generation and SBS Sequencing Kits (Illumina, San Diego, CA, USA) on a HiSeq2000 system.

treatment_protocol: First, stressed samples were exposed 5 weeks to 4µg/L of diuron (samples 1-17). After the 5 weeks of incubation all the samples were exposed 1 hour to diuron (to one of the 9 concentrations of the gradient, including control).

value: Only acute exposure

tag: acute


title: Control_rep2


title: Ascorbic acid sample tested at 145.77 uM (Replicate: 3, Control Batch Id: 7).


title: GBM-6425_D.1E11, single cell DNA methylation

description: Library name: GBM-6425_D.1E11


title: Sample 9_TW3-3

source_name: wheat coleoptiles_after 3 hours control (0.5% Tween-20) treated coleoptiles


title: Ascorbic acid sample tested at 145.77 uM (Replicate: 2, Control Batch Id: 7).


title: Non-stressed_C7_Rep2

description: Aquatic microbial communities

value: 50 ug/L


title: Control_rep1


title: WT_oxalate_3

value: wild-type

value: oxalate rich-diet


title: Ascorbic acid sample tested at 104.12 uM (Replicate: 3, Control Batch Id: 7).


title: Ascorbic acid sample tested at 104.12 uM (Replicate: 1, Control Batch Id: 7).


title: GBM-6425_D.1F01, single cell DNA methylation

description: Library name: GBM-6425_D.1F01


title: Ascorbic acid sample tested at 204.08 uM (Replicate: 2, Control Batch Id: 7).


title: Sample 10_FB24-1

value: after 24 hours fusaoctaxin B-treated coleoptiles


title: Sample 12_FB24-3


title: Ascorbic acid sample tested at 104.12 uM (Replicate: 2, Control Batch Id: 7).

value: sample


title: CCSER1_S_Body_R6

city: Singapore

first: Ajay

last: Mathuru

state: Singapore

address: 28 Medical Drive, #5-COR

department: Physiology

country: Singapore

institute: NUS

data_processing:
Raw reads were first processed by Novogene-AIT to remove adapter, poly-N sequences, and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy
Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software, v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner, default parameters, and subsequently filtered to a minimum mapping quality score of > 30.
Assembly: GRCz10 genome assembly by STAR aligned
Supplementary files format and content: STAR aligned

organism: Danio rerio

source_name: whole body

extract_protocol:
The quality of each sample was verified by gel electrophoresis and bio-analyser.
Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired-end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.

value: whole body


title: GBM-6425_D.1E09, single cell DNA methylation

description: Library name: GBM-6425_D.1E09


title: Sample 8_TW3-2

value: after 3 hours control (0.5% Tween-20) treated coleoptiles


title: GBM-6425_D.1E10, single cell DNA methylation

description: Library name: GBM-6425_D.1E10


title: CCSER1_S_Body_R5


title: Sample 7_TW3-1


title: Sample 6_FB3-3

source_name: wheat coleoptiles_after 3 hours fusaoctaxin B-treated coleoptiles


title: Non-stressed_C7_Rep1

description: Aquatic microbial communities


title: CCSER1_S_Body_R3


title: Non-stressed_C8_Rep2

description: Aquatic microbial communities


title: GBM-6425_D.1E08, single cell DNA methylation

description: Library name: GBM-6425_D.1E08


title: CCSER1_S_Body_R4


title: Sample 5_FB3-2

value: after 3 hours fusaoctaxin B-treated coleoptiles


title: GBM-6425_D.1E07, single cell DNA methylation

description: Library name: GBM-6425_D.1E07


title: Non-stressed_C6_Rep2

description: Aquatic microbial communities

value: 10 ug/L


title: Non-stressed_C5_Rep1

description: Aquatic microbial communities

value: 1 ug/L


title: GBM-6425_D.1E06, single cell DNA methylation

description: Library name: GBM-6425_D.1E06


title: Non-stressed_C6_Rep1

description: Aquatic microbial communities


title: CCSER1_S_Body_R2


title: Non-stressed_C5_Rep2

description: Aquatic microbial communities


title: GBM-6425_D.1E04, single cell DNA methylation

description: Library name: GBM-6425_D.1E04


title: CCSER1_M_Body_R6


title: Sample 4_FB3-1


title: Sample 2_BT-2

source_name: wheat coleoptiles_before compound treatment

value: before compound treatment


title: GBM-6425_D.1E03, single cell DNA methylation

description: Library name: GBM-6425_D.1E03

value: GBM patient brain tissue


title: Sample 3_BT-3


title: Non-stressed_C4_Rep1

description: Aquatic microbial communities


title: Non-stressed_C4_Rep2

description: Aquatic microbial communities


title: CCSER1_M_Body_R5


title: Sample 1_BT-1


title: CCSER1_M_Body_R4


title: GBM-6425_D.1E02, single cell DNA methylation

description: Library name: GBM-6425_D.1E02


title: Non-stressed_C3_Rep2

description: Aquatic microbial communities


title: CCSER1_M_Body_R3


title: eif6_3

city: Cleveland

first: Usua

last: Oyarbide

address: Cleveland Clinic, Lerner Research Institute NE6-205

institute: Cleveland Clinic

data_processing:
Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly, reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high-quality reads. Finally, reads were removed if they: (1) lacked a 3’ adapter sequence, (2) were 5’-3’ adapter ligation products, (3) were 5’-5’ adapter ligation products, (4) were shorter than 18 nt, or (5) contained only As (homopolymers). High-quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: -f -N 0 -M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19.
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: csv file. FPKM values and p and q values

source_name: whole larvae

extract_protocol:
RNA was harvested using TRIzol, following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA-seq library construction and deep sequencing.
BGISeq-500 sequencing platform

treatment_protocol: 5 dpf

value: whole larvae

value: 5 dpf

value: eif6 KO


title: GBM-6425_D.1E01, single cell DNA methylation

description: Library name: GBM-6425_D.1E01


title: Non-stressed_C3_Rep1

description: Aquatic microbial communities


title: GBM-6425_D.1E05, single cell DNA methylation

description: Library name: GBM-6425_D.1E05


title: GBM-6425_A.3H01, single cell DNA methylation

description: Library name: GBM-6425_A.3H01


title: CCSER1_S_Body_R1


title: CCSER1_M_Body_R1


title: eif6_2


title: CCSER1_M_Body_R2


title: Non-stressed_C2_Rep1

description: Aquatic microbial communities


title: eif6_1


title: wt3

value: eif6 wildtype


title: GBM-6425_A.3G11, single cell DNA methylation

description: Library name: GBM-6425_A.3G11


title: Non-stressed_C1_Rep2

description: Aquatic microbial communities

value: Only acute exposure


title: Non-stressed_C1_Rep1

description: Aquatic microbial communities


title: WT_Body_R5

value: WT


title: GBM-6425_A.3G10, single cell DNA methylation

description: Library name: GBM-6425_A.3G10


title: Non-stressed_C0_Rep2

description: Aquatic microbial communities

value: 0 ug/L


title: WT_Body_R6


title: wt2


title: GBM-6425_A.3G09, single cell DNA methylation

description: Library name: GBM-6425_A.3G09


title: wt1


title: WT_Body_R4


title: GBM-6425_A.3G08, single cell DNA methylation

description: Library name: GBM-6425_A.3G08


title: Non-stressed_C0_Rep1

description: Aquatic microbial communities


title: WT_Body_R3


title: WT_set40

city: Baltimore

first: Weidong

last: Wang

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging/NIH

data_processing:
RNA SEQ fastq files are first passed fastqc to remove potentially low quality bases
After cleaning, the fastq files are mapped to fly dm6 genome
The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function
The bam files are used to do further gene expression differential analysis by Tuxedo Suite  v2.2.1 pipleline to do genome structrte mapping, merging and gei siginificant defferential gene lists for each comparison.
The bed files are used to get gene raw counts data and fpkm normalized data for further analyses.
Assembly: dm6
Supplementary files format and content: bedGraph

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Normal growth condition (standard cornmeal food, 12/12 light cycle, 25'C temp). 4-7 days female matured ovary was dissected in PBS

extract_protocol:
RNA was extracted byTRizol following the product manual. For small RNA, total RNA was run using 15% TBE-urea gel, followed by cutting the 15-35 nt RNA fragments. RNA was extracted by incubating overnight in RNA gel extraction buffer (300 mM sodium acetate ( pH 5.5), 1.0 mM EDTA and 0.25% (wt/vol) SDS)
Library was constructed by standard Illumina protocol. Small RNA-seq library was generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs).

value: ovary

tag: Sex

value: female

tag: library type

value: RNA-seq


title: GBM-6425_A.3G07, single cell DNA methylation

description: Library name: GBM-6425_A.3G07


title: WT_Body_R2

value: whole body


title: WT_set37


title: Stressed_C8_Rep2

description: Aquatic microbial communities

value: Chronic+acute exposure


title: vas_set40


title: GBM-6425_A.3G06, single cell DNA methylation

description: Library name: GBM-6425_A.3G06


title: Stressed_C8_Rep1

description: Aquatic microbial communities


title: GBM-6425_A.3G04, single cell DNA methylation

description: Library name: GBM-6425_A.3G04


title: Stressed_C7_Rep1

description: Aquatic microbial communities

value: 50 ug/L


title: WT_Body_R1


title: CCSER1_S_3

source_name: whole brain

value: whole brain


title: vas_set37


title: Stressed_C6_Rep1

description: Aquatic microbial communities

value: 10 ug/L


title: CCSER1_S_2


title: Stressed_C5_Rep2

description: Aquatic microbial communities

value: 1 ug/L


title: Stressed_C5_Rep1

description: Aquatic microbial communities


title: CCSER1_S_1


title: GBM-6425_A.3G01, single cell DNA methylation

description: Library name: GBM-6425_A.3G01

value: GBM patient brain tissue


title: CCSER1_S_4


title: top3bvas_set40


title: top3bvas_set37


title: GBM-6425_A.3G02, single cell DNA methylation

description: Library name: GBM-6425_A.3G02


title: top3b26_set40


title: Stressed_C4_Rep1

description: Aquatic microbial communities


title: CCSER1_M_3


title: GBM-6425_A.3G05, single cell DNA methylation

description: Library name: GBM-6425_A.3G05


title: CCSER1_M_2


title: GBM-6425_A.3F09, single cell DNA methylation

description: Library name: GBM-6425_A.3F09


title: VitC scDam&T-seq Dam-LMNB1 (VAN10206.index28)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: VAN10206.index28

data_processing:
Dam&ChIC data processing is largely based on the workflow and scripts described in Rooijers et al., 2019 and Markodimitraki et al., 2020 (available at: https://github.com/KindLab/scDamAndTools), but adapted to allow for computational separation of scDamID and sortChIC derived reads and further processing of sortChIC reads.
All reads are demultiplexed by comparing their sample barcode (e.g. single-cell barcode) located at the start of each read (R1 in case of paired-end sequenced libraries) conform to the read layout of 5′-[3 nt UMI][8 nt barcode]TC[gDNA]-3′ for scDamID and 5′-[3 nt UMI][8 nt barcode]WN[gDNA]-3′ for sortChIC reads, to a reference list of barcodes and zero mismatches between the observed barcode and reference are allowed. Sample barcodes and UMIs are trimmed off the reads to only retain gDNA sequences. The UMI sequences were appended to the read name for downstream processing. Per sample barcode, scDamID and sortChIC reads remain mixed at this point.
After preprocessing, the reads were aligned to a reference genome using bowtie2 (v. 2.4.1) with parameters: ‘‘--seed 42 --very-sensitive -N 1’’. Before alignment a ‘GA’ dinucleotide was prepended to the reads that has effectively been digested off scDamID fragments during DpnI gDNA digestion. For human samples, reads were aligned to reference genome hg19 (GRCh37) and mouse samples to mm10 (GRCm38). For allele-specific processing for X-chromosome inactivation experiments, data were aligned to reference genomes generated by imputing 129S1/SvImJ and CAST/EiJ single nucleotide polymorphisms obtained from the Sanger Mouse Genomes project (Keane et al., 2011) onto the mm10 reference genome. The reads were assigned to either genotype by aligning reads to both references. Reads that aligned with lower edit distance (SAM tag ‘NM’) or higher alignment score (SAM tag ‘AS’) in case of equal edit distance to one of the genotypes were assigned to that genotype. Reads aligning with equal edit distance and alignment score to both genotypes were considered of ‘ambiguous’ genotype. Reads that yielded an alignment with mapping quality (BAM field ‘MAPQ’) lower than 10 were discarded.
Following read alignment with ‘GA’ prepended dinucleotide, reads were considered scDamID in case of perfect alignment on genomic GATC motifs. Residual reads were considered sortChIC and their original sequences (i.e., without prepended GA dinucleotide) were realigned using hisat2 (v. 2.1.0) with parameters: ‘‘--seed 42 --no-spliced-alignment --mp '2,0' --sp '4,0'”. These sortChIC-considered reads were further pruned given MNase’s strong adenine or thymidine-nucleotide cut preference; only sortChIC reads were kept that lead with an ‘A’ or ‘T’ base. In addition, we observed that a larger fraction of sortChIC reads (i.e., that do not map on a genomic GATC motif) are ‘TC’-dinucleotide leading in Dam&ChIC libraries than in sortChIC libraries and hence decided to exclude TC-leading reads from Dam&ChIC-derived sortChIC libraries.
Assembly: GRCm38
Supplementary files format and content: H5AD

source_name: Inner cell mass derived

growth_protocol: Mouse F1 hybrid Cast/EiJ x 129SvJ embryonic stem cells (mESCs; a kind gift from the Joost Gribnau laboratory) were cultured on a monolayer of irradiated feeders (MEFs) in CM+/+ (G-MEM + 10% FBS, 1% Pen/Strep, 1× GlutaMAX (Gibco), 1× NEVitaminC, 1× sodium pyruvate, 0.1 mM 2-ME and 1000 U/ml ESGROmLIF (EMD Millipore, ESG1107))

extract_protocol:
MESCs were fixed at -20C using 70% Ethanol and permeablised using 0.05% Tween. ProteinA-MN was targeted using antibodies against IgG, Lamin B1, H3, H3K4me1, H3K4me3, H3K9me3, H3K27me3 or H3K36me3 and cells were FACS sorted into 384 well plates.
MN was activated thorugh 2mM CaCl2 for 30min at 4C at inactivated by EGTA addition. Cells were lysed (protK + NP40), fragments end-repaired (Klenow) and adenine methylated sites were cut (DpnI). Dam and ChIC fragemnts are ligated to blunt end adaptors containing a cell barcode and unique molecular identifier and a T7 promoter. After pooling DNA is amplified by in vitro transcription, before rundom hexamer based reverse transcription and final indexing PCR for sequencing.

treatment_protocol: For mESCs 1mM IVitaminC was added 24h prior to induction, to ensure protein degradation.

value: Inner cell mass derived

tag: cell line

value: ESC

value: VitaminC differentiation

value: 129S1/SvImJ x CAST/Eij


title: Stressed_C3_Rep2

description: Aquatic microbial communities


title: VitC scDam&T-seq Dam-LMNB1 (VAN10206.index36)

description: Library name: VAN10206.index36


title: GBM-6425_A.3F08, single cell DNA methylation

description: Library name: GBM-6425_A.3F08

source_name: GBM patient brain tissue


title: VitC Dam&ChIC Dam-LMNB1/H2AK119Ub (KIN10162_xci.index48)

description: Library name: KIN10162_xci.index48


title: CCSER1_M_4


title: Stressed_C4_Rep2

description: Aquatic microbial communities


title: Stressed_C2_Rep2

description: Aquatic microbial communities


title: GBM-6425_A.3F05, single cell DNA methylation

description: Library name: GBM-6425_A.3F05


title: WT_2.


title: VitC Dam&ChIC Dam-LMNB1/H2AK119Ub (KIN10162_xci.index47)

description: Library name: KIN10162_xci.index47


title: VitC Dam&ChIC Dam-LMNB1/H2AK119Ub (KIN9826.index45)

description: Library name: KIN9826.index45


title: Stressed_C7_Rep2

description: Aquatic microbial communities


title: GBM-6425_A.3F12, single cell DNA methylation

description: Library name: GBM-6425_A.3F12


title: xrTestis_1M_macaque

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description: iPSC-derived macaque germ cells, transplanted 1 months

data_processing:
(SINGLE CELL) Raw data were demultiplexed with the mkfastq command in Cell Ranger (v7.1.0) to generate Fastq files. Trimmed sequence files were mapped to the reference genome for humans (GRCh38) or macaque (Mmul_10) as well as to the mouse (GRCm38) using Cell Ranger mkfastq. Read counts were obtained by using cellranger count.
(SINGLE CELL) Secondary data analyses were performed in Python with Scanpy 1.8.1 or in R (v.4.1.0) with the Seurat (v.4.3.0), SeuratObject (v4.1.3), SeuratWrappers (v0.3.2), tidyverse (v.1.3.2), destiny (v3.10.0), pheatmap (v1.0.12), plot3D (v1.4) and Matrix (v.1.5-1) packages and Excel (Microsoft).
(WGBS) Raw fastq files were demultiplexed with bcl2fastq2 (v.2.20). Barcode and index trimming was performed with Trim Galore (v.0.6.5) as follows: trim_galore --quality 30 --phred33 --illumina --stringency 1 --cores 4 -e 0.1 --fastqc --clip_R1 10 --three_prime_clip_r1 10 --length 20. The trimmed fastq files were then mapped to calJac4 from USCS with Bismark (v.0.22.3) as follows: bismark --parallel 4 --genome_folder $REF --non_directional --score_min L,0,–0.6.
(WGBS) CpG methylation was extracted and analyzed with methylKit (v.1.22.0). Covered CpG loci were included in the analysis. The genome was tiled in 2 kb windows, and DNA methylation levels were summarized with methyKit (v.1.22.0). Data were visualized with R (v.4.1.0).
Assembly: GRCh38/Mmul_10/GRCm38
Supplementary files format and content: h5 cell ranger output files for each sample
Supplementary files format and content: Seurat objects saved as .Robj files

organism: Macaca mulatta

source_name: xrTestis

extract_protocol:
(SINGLE CELL) xrTestis-derived cells were sorted via FACS for expression of AG/VT/PC and collected in CELLOTION. Cell clumps were removed by straining cell suspensions through a 70 µm nylon mesh and then the single-cell suspension was centrifuged at 300 × rcf for 5 min. Cells were resuspended in 0.1% BSA in PBS and counted. All samples had greater than 80% viability as determined by trypan blue staining. Encapsulation was performed using a 10X Genomics Chromium Controller according to the manufacturer’s protocol.
(WGBS) PGCLC aggregates were digested with 400 μl 0.25% trypsin for 15 min. Then, 100 μl FBS was used to stop digestion, and the lysates were pipetted well to obtain a single-cell suspension. The fractions of TFAP2C-eGFP, TFAP2C-eGFP+DDX4-tdTomato and DDX4-tdTomato were sorted for methylome analyses. Cells were collected and lysed in 50 mM Tris (pH 8.0), 10 mM EDTA, 0.5% SDS, and 100 μg/ml proteinase K.
(SINGLE CELL) The Cells were loaded into chromium microfluidic chips with the Chromium Single Cell 3ʼ Reagent Kit (v3.1 chemistry) and then used to generate single-cell gel bead emulsions (GEMs) using the Chromium Controller (10× Genomics) according to the manufacturer’s protocol. reverse transcription step was performed using a C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (Bio-Rad). All subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s protocol.
(SINGLE CELL) Chromium Single Cell 3ʼ Reagent (v3.1 chemistry) was used for library preparation
(WGBS) Crude DNA was used to build a sequencing library according to the protocol of the Pico Methyl-Seq Library Prep Kit (Zymo, #D5455). The libraries were sequenced on the Illumina 2200 platform.

value: xrTestis

tag: Stage


title: VitC scDam&T-seq Dam-LMNB1 (VAN10206.index34)

description: Library name: VAN10206.index34


title: Stressed_C0_Rep2

description: Aquatic microbial communities


title: VitC scDam&T-seq Dam-LMNB1 (VAN10206.index32)

description: Library name: VAN10206.index32


title: GBM-6425_A.3G03, single cell DNA methylation

description: Library name: GBM-6425_A.3G03


title: GBM-6425_A.3F10, single cell DNA methylation

description: Library name: GBM-6425_A.3F10


title: GBM-6425_A.3F03, single cell DNA methylation

description: Library name: GBM-6425_A.3F03


title: GBM-6425_A.3F06, single cell DNA methylation

description: Library name: GBM-6425_A.3F06


title: VitC scDam&T-seq Dam-LMNB1 (VAN10206.index30)

description: Library name: VAN10206.index30


title: CCSER1_M_1


title: VitC scDam&T-seq Dam-LMNB1 (VAN10206.index27)

description: Library name: VAN10206.index27


title: Stressed_C3_Rep1

description: Aquatic microbial communities


title: WT_3.

value: WT


title: xrTestis_6M_macaque

description: iPSC-derived macaque germ cells, transplanted 5 months


title: xrTestis_9M_macaque

description: iPSC-derived macaque germ cells, transplanted 9 months


title: GBM-6425_A.3F11, single cell DNA methylation

description: Library name: GBM-6425_A.3F11


title: Stressed_C2_Rep1

description: Aquatic microbial communities


title: PTEN knockout Svz replica 1 snRNAseq

city: New Haven

first: Kristopher

last: Kahle

state: Connecticut

address: 333 Cedar St

institute: Yale University Department of Neurosurgery

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)"
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subventricular zone

extract_protocol:
Animals were anesthetized with Ketamine/Xylazine and transcardially perfused with ice cold TBS before brain removal. Choroid plexi from bilateral lateral ventricles were microdissected in ice cold HBSS with 30uM Actinomycin D (ActD, Sigma, cat#A1410 ) and digested at 37oC for 20 min with Collagenases-I and -IV (10 U/mL, 400 U/mL final, Worthington, Cat# LS004194, and LS004184) and DNase I (30 U/mL, Roche, cat# 04716728001) and ActD (3uM). For Flow sorting, the cell suspension was blocked with CD16-CD32 antibodies (1:100, biolegend, cat#101302) and stained 30 min at 4oC with anti-rat CD45-PE/cy7 (1:100, biolegend, cat#202207) to and DAPI (50ug/mL). Cells were subsequently washed in FACS staining buffer (0.5% BSA, 2mM EDTA in PBS without Calcium/Magnesium) and centrifuged at 350 rcf for 5 minutes. Cells were resuspended in 300ul of FACS buffer and sorted by CD45 positivity on a BD ARIA instrument. CD45 positive and CD45 negative cells were collected in 0.4% BSA/PBS and 3uM ActD and sent for 10X 3prime library preparation and sequencing at Yale Center for Genome Analysis
Sequencing libraries were loaded on an Illumina HiSeq4000 flow cell with sequencing settings following the recommendations of 10x Genomics (read 1: 26 cycles; read 2: 98 cycles; index i7: eight cycles; index i5: no cycles; 2.1 pM loading concentration). The Cell Ranger pipeline was designed to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index. Read 2, containing the cDNA, was mapped to the reference genome (mouse mm10) using STAR

value: Subventricular zone

value: PTEN knockout


title: WT_1.


title: DOG 126

city: Chapel Hill

first: Liubov

last: Arbeeva

state: North Carolina

address: 3300 Thurston Bldg., CB# 7280

institute: UNC

description: Library name: R126-499381

data_processing:
Sequencing output was converted to fastq format and demultiplexed using Illumina bclconvert ver 4.2.4.
The resulting paired-end reads were processed with the QIIME ver.2.2022.2 wrapper for DADA2 including merging paired ends, quality filtering, error correction, and chimera detection.
Amplicon sequencing units from DADA2 were assigned taxonomic identifiers using the Silva 138 database.
Alpha diversities with respect to Shannon index, Phylogenetic Diversity, and Pielou’s Evenness index were estimated using QIIME2 at a rarefaction depth of 5,000 sequences per subsample.
Beta diversity estimates were calculated within QIIME2 using Weighted UNIFrac distance and Bray Curtis dissimilarity between samples at a subsampling depth of 5,000.
Assembly: Silva 138
Supplementary files format and content: feature-table.biom
Library strategy: 16S rRNA-seq

organism: Canis lupus familiaris

source_name: stool in ethanol

extract_protocol:
Samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA).
Mechanical lysis was performed for 20 minutes on a digital vortex mixer.
After 5 min centrifugation, 0.45 ml of supernatants were aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution.
The suspension was incubated at 4°C overnight.
After 5 min centrifugation, the supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads.
DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase-free water.
12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene.
Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with the Illumina sequencing platform
The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer, and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by cycling of denaturing at 95°C for 30 seconds, annealing at 55°C for 30 seconds, and a 30-second extension at 72°C (25 cycles), a 5-minute extension at 72°C and a final hold at 4°C.
Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN). In the next step, each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30-second extension at 72°C (8 cycles), a 5-minute extension at 72°C and a final hold at 4°C.
The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified, and normalized before pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer, and heat-denatured before loading on the MiSeq reagent cartridge (Illumina) and the MiSeq instrument (Illumina). Automated cluster generation and paired–end sequencing with dual reads were performed according to the manufacturer’s instruction

value: stool in ethanol

tag: age

tag: body composition_score

tag: mjoa

value: NO


title: Stressed_C1_Rep2

description: Aquatic microbial communities

tag: treatment


title: xrTestis_5M_macaque

description: iPSC-derived macaque germ cells, transplanted 6 months


title: Stressed_C1_Rep1

description: Aquatic microbial communities


title: xrTestis_2M_macaque

description: iPSC-derived macaque germ cells, transplanted 2 months


title: DOG 124

description: Library name: R124-482937


title: GBM-6425_A.3F07, single cell DNA methylation

description: Library name: GBM-6425_A.3F07

data_processing:
The single-cell DNA methylation sequencing data from Scale Biosciences was processed using the ScaleBio Seq Suite: Methylation Workflow (v1.1.0 pre-release) under default parameters.
Assembly: hg38
Supplementary files format and content: h5 files with matrices of DNA methylation status for each cell
Library strategy: sciMet

extract_protocol:
Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. Nuclei were fixed with 16% formaldehyde followed by nucleosome disruption. After gently mixing nucleosome disruption solution with nuclei suspension, nuclei were centrifuged with pellet resuspended for each biological sample. Nuclei inputs were normalized across samples, and the tagmentation-nuclei mix was prepared for each biological sample based on the number of reactions. Nuclei were distributed across the three 96-well Met Tagment Barcode Plates, using a total of 288 unique barcodes for nuclei tagmentation. Tagmented nuclei were gated for positive DNA staining and sorted for 24 nuclei per well on the sorting plate. Bisulfite Conversion Solution was added to each well to convert unmethylated cytosines to uracil and the post-reaction product was cleaned up through elution.
The sequencing library was prepared by adding amplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.


title: DOG 123

description: Library name: R123-264724

value: YES


title: MDTC-RP19 cells, mock-infected, 72hrs, rep1

city: Provo

first: Abraham

last: Quaye

state: UT

address: 4007 Life Sciences Building

department: Microbiology & Molecular Biology

institute: Brigham Young University

description: Library name: Sample 18

data_processing:
Reads were trimmed with the Trim-galore (v0.6.6) program to achieve an overall Mean Sequence Quality of 36
Trimmed reads were mapped to Meleagris gallopavo using Hisat2  (v 2.2.1) and output SAM files were converted to BAM files using samtools (v 1.21).
StringTie (v 2.2.1), set to expression estimation mode was used to generate normalized gene expression estimates from the BAM files for genes in the reference GTF file after which the prepDE.py3 script was used to extract read count information from the StringTie gene expression files, providing an expression-count matrix for downstream DEG analysis.
Differential gene expression analysis between mock- and THEV-infected samples was performed using DESeq2 (v1.42.0) R package
Assembly: melGal5
Supplementary files format and content: BAM files of reads mapped to the M. gallopavo genome for all replicates of each time point
Supplementary files format and content: comma-separated text file (csv) containing the FPKM values of all annotated M.gallopavo genes for each sample (gene count matrix)
Supplementary files format and content: comma-separated text files (csv) containing DESeq2 differential gene expression results (geneIDs/geneNames, sample names, log2fold changes, and adjusted p-values) for all timepoints 4, 12, 24, and 72 hours

organism: Meleagris gallopavo

growth_protocol: Mock and infected MDTC-RP19 cells were grown as suspension cultures in 1:1 complete Leibovitz's L-15/McCoy's 5A medium with 10% fetal bovine serum (FBS), 20% chicken serum (ChS), 5% tryptose phosphate broth (TPB), and 1% antibiotics solution (100 U/mL Penicillin and 100ug/mL Streptomycin), at 41C in a humidified atmosphere with 5% CO2. When infected or mock infected, cells were maintained in 1:1 serum-reduced Leibovitz's L15/McCoy's 5A media (SRLM) with 2.5% FBS, 5% ChS, 1.2% TPB, and 1% antibiotics solution (100 U/mL Penicillin and 100ug/mL Streptomycin)

extract_protocol:
Total RNA was extracted from infected cells using Thermofishers' RNAqueous™-4PCR Total RNA Isolation Kit (#AM1914) per manufacturer's instructions.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. 1ug of total RNA was used for this library construction

treatment_protocol: A commercially available THEV live vaccine was purchased from Hygieia Biological Labs. The stock virus was titrated using an in-house qPCR assay with titer expressed as genome copy number(GCN)/mL, similar to Mahshoub et al (https://doi.org/10.1016/j.jviromet.2016.11.002) with modifications. Cells were infected in triplicates at a multiplicity of infection (MOI) of 100 GCN/cell, incubate at 41 centigrade for 1 hour, and washed three times to get rid of free virion particles. Samples in triplicates were harvested at 4-, 12-, 24-, and 72-h.p.i for total RNA extraction and RNA-sequencing

value: B lymphocytes

value: mock-infected


title: GBM-6425_A.3F04, single cell DNA methylation

city: Toronto

first: Federico

last: Gaiti

address: 101 college street

description: Library name: GBM-6425_A.3F04


title: Stressed_C0_Rep1

description: Aquatic microbial communities

value: Chronic+acute exposure

value: 0 ug/L


title: xrTestis_4M_macaque

description: iPSC-derived macaque germ cells, transplanted 4 months


title: MDTC-RP19 cells, infected, 72hrs, rep3

description: Library name: Sample 17

value: Infected


title: DOG 128

description: Library name: R128-499762


title: PTEN knockout Svz replica 3 snRNAseq

description: 10x Genomics


title: GBM-6425_A.2H09, single cell DNA methylation

description: Library name: GBM-6425_A.2H09

value: GBM patient brain tissue


title: GBM-6425_A.3F02, single cell DNA methylation

description: Library name: GBM-6425_A.3F02


title: GBM-6425_A.2H08, single cell DNA methylation

description: Library name: GBM-6425_A.2H08


title: MDTC-RP19 cells, infected, 72hrs, rep2

description: Library name: Sample 16


title: PTEN knockout Svz replica 2 snRNAseq

description: 10x Genomics


title: GBM-6425_A.3F01, single cell DNA methylation

description: Library name: GBM-6425_A.3F01


title: GBM-6425_A.2H07, single cell DNA methylation

description: Library name: GBM-6425_A.2H07


title: PTEN knockout Cortex replica 1 snRNAseq

description: 10x Genomics

source_name: Cortex

value: Cortex


title: MDTC-RP19 cells, infected, 72hrs, rep1

description: Library name: Sample 15


title: VitC Dam&ChIC Dam-LMNB1/H2AK119Ub (KIN9826.index44)

description: Library name: KIN9826.index44

value: Inner cell mass derived

value: ESC


title: MDTC-RP19 cells, mock-infected, 24hrs, rep2

description: Library name: Sample 14


title: DOG 117

description: Library name: R117-498653


title: GBM-6425_A.2H11, single cell DNA methylation

description: Library name: GBM-6425_A.2H11


title: DOG 122

description: Library name: R122-497877


title: MDTC-RP19 cells, mock-infected, 72hrs, rep2

description: Library name: Sample 19


title: Control Svz replica 3 snRNAseq

description: 10x Genomics

value: Control


title: GBM-6425_A.2H10, single cell DNA methylation

description: Library name: GBM-6425_A.2H10


title: Control Svz replica 1 snRNAseq

description: 10x Genomics


title: DOG 121

description: Library name: R121-257847


title: GBM-6425_A.2H05, single cell DNA methylation

description: Library name: GBM-6425_A.2H05


title: DOG 120

description: Library name: R120-241016


title: GBM-6425_A.2H12, single cell DNA methylation

description: Library name: GBM-6425_A.2H12


title: DOG 119

description: Library name: R119-498656


title: Control Cortex replica 2 snRNAseq

description: 10x Genomics


title: PTEN knockout Cortex replica 3 snRNAseq

description: 10x Genomics


title: DOG 113

description: Library name: R113-264001


title: PTEN knockout Cortex replica 2 snRNAseq

description: 10x Genomics


title: Control Cortex replica 1 snRNAseq

description: 10x Genomics


title: DOG 115

description: Library name: R115-498143


title: PTEN knockout Choroid replica  scRNAseq

description: 10x Genomics

source_name: Choroid plexus

value: Choroid plexus


title: Control Cortex replica 3 snRNAseq

description: 10x Genomics


title: MDTC-RP19 cells, infected, 24hrs, rep3

description: Library name: Sample 12

value: WT


title: DOG 112

description: Library name: R112-264003


title: GBM-6425_A.2H02, single cell DNA methylation

description: Library name: GBM-6425_A.2H02


title: MDTC-RP19 cells, mock-infected, 12hrs, rep2

description: Library name: Sample 9


title: DOG 110

description: Library name: R110-497380


title: Control Choroid replica  scRNAseq

description: 10x Genomics


title: MDTC-RP19 cells, infected, 24hrs, rep1

description: Library name: Sample 10


title: GBM-6425_A.2H01, single cell DNA methylation

description: Library name: GBM-6425_A.2H01


title: Control Svz replica 2 snRNAseq

description: 10x Genomics

value: Subventricular zone


title: MDTC-RP19 cells, mock-infected, 24hrs, rep1

description: Library name: Sample 13


title: GBM-6425_A.2G12, single cell DNA methylation

description: Library name: GBM-6425_A.2G12


title: DOG 111

description: Library name: R111-497381


title: GBM-6425_A.2H04, single cell DNA methylation

description: Library name: GBM-6425_A.2H04


title: Cornea CB1-GFP rep2

first: Panteleimon

last: Rompolas

address: 421 Curie Blvd., BRB II/III Room 1014

department: Dermatology

institute: University of Pennsylvania

data_processing:
Cell Ranger (version 3.1.0) was used for primary data analysis (alignment, filtering, barcode and UMI counting) to determine transcript counts per cell (producing a gene-barcode matrix).
Downstream analysis was performed using the R Package Seurat, version 5.0.0 (Hao et al., 2023) for clustering and differential expression analyses. Low quality cells (>5% mitochondrial UMI counts, <1000 or >3000 features) were excluded to produce a dataset with 14,525 features across 2,370 total cells that were analyzed
Assembly: Transcripts were mapped to the mouse reference genome, GRCm38 (refdata-cellranger-mm10–2.1.0/GRCm38.84)
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (MEX Format)

source_name: Cornea

extract_protocol:
Dissected corneas were placed into 2.4 units/l of Dispase prepared in Keratinocyte Serum Free Medium and incubated overnight at 4C. For each cornea, the epithelium was gently peeled off, washed in 1 X PBS, and incubated in Trypsin-EDTA (0.25%) at 37C for 20 minutes. Following incubation, tissue was processed into a cell suspension via successive rounds of manual pipetting with a P1000 tip. 2 ml of FBS and 6 ml of 1 X PBS were added to the cell suspension and cells were spun down at 1000-1500 rpm for 5 minutes. Following centrifugation, the supernatant was aspirated, cells were resuspended in 1X PBS, and the entire volume was filtered through a 100 m cell strainer to obtain a single cell suspension. For cell staining, DAPI (1:1000) was added directly to the cell suspension and incubated for 10 minutes on ice. Following incubation, cells were spun down at 1000-1500 rpm for 5 minutes, supernatant was aspirated, and cells were resuspended for sorting in 2% FBS 5 mM EDTA in 1X PBS. Flow cytometry was performed on a BD LSRII cytometer (BD Biosciences), sorting on a BD FACS Aria II sorter (BD Biosciences). Only GFP+ live cells were collected from sorting. Flow cytometry data was collected and exported using BD FACs Diva software (BD Biosciences) and analyzed and plotted using FlowJo software
The FACS-generated cell suspension was used to generate a single-cell RNA-seq library according to the 10x Genomics protocol (Chromium Single Cell 3 Library & Gel Bead Kit v3, PN-1000075)

value: Cornea

value: Epithelium


title: GBM-6425_A.2G11, single cell DNA methylation

institute: Princess Margaret Cancer Centre

description: Library name: GBM-6425_A.2G11


title: MDTC-RP19 cells, infected, 12hrs, rep2

description: Library name: Sample 7


title: GBM-6425_A.2G10, single cell DNA methylation

description: Library name: GBM-6425_A.2G10


title: DOG 106

description: Library name: R106-493495

value: stool in ethanol

value: NO


title: MDTC-RP19 cells, infected, 24hrs, rep2

description: Library name: Sample 11

value: B lymphocytes


title: MDTC-RP19 cells, infected, 12hrs, rep1

description: Library name: Sample 6


title: DOG 105

description: Library name: R105-493494


title: GBM-6425_A.2G09, single cell DNA methylation

description: Library name: GBM-6425_A.2G09


title: Radiation-induced dermatitis mouse skin cells, no treatment (control), biol rep5

city: Bronx

first: Shaun

last: Wu

address: 1301 Morris Park Avenue, Room 355

institute: Shinoda Lab

data_processing:
Build the index in Kallisto from mouse reference genome
Run Kallisto quantification on raw data files to generate raw counts
Use DESeq2 to normalize and generate gene expression level
Use terminal commands to obtain list of differentially expressed genes
Assembly: GRCm38
Supplementary files format and content: TSV file includes estimated counts and transcripts per milion (tpm)

source_name: Whole skin

extract_protocol:
Qiagen RNeasy FFPE Kit according to the company's protocol
Targeting coding RNA using poly-T and random primers

treatment_protocol: Mouse IL-17/IL-17A Antibody from R&D SYSTEMS (Cat#MAB421)

value: Whole skin

value: Vehicle


title: Radiation-induced dermatitis mouse skin cells, no treatment (control), biol rep4


title: MDTC-RP19 cells, mock-infected, 4hrs, rep2

description: Library name: Sample 5

value: mock-infected


title: DOG 104

description: Library name: R104-217879


title: Radiation-induced dermatitis mouse skin cells, IL17ab treatment, biol rep4

value: IL-17 antibody


title: GBM-6425_A.2G07, single cell DNA methylation

description: Library name: GBM-6425_A.2G07

value: GBM patient brain tissue


title: DOG 102

description: Library name: R102-494719

value: YES


title: MDTC-RP19 cells, mock-infected, 4hrs, rep1

description: Library name: Sample 4


title: DOG 109

description: Library name: R109-494717


title: MDTC-RP19 cells, infected, 4hrs, rep3

description: Library name: Sample 3

value: Infected


title: Radiation-induced dermatitis mouse skin cells, IL17ab treatment, biol rep2


title: MDTC-RP19 cells, mock-infected, 12hrs, rep1

description: Library name: Sample 8


title: GBM-6425_A.2G06, single cell DNA methylation

description: Library name: GBM-6425_A.2G06


title: Radiation-induced dermatitis mouse skin cells, IL17ab treatment, biol rep3


title: Cornea CB1-GFP rep1


title: GBM-6425_A.2G05, single cell DNA methylation

description: Library name: GBM-6425_A.2G05


title: MDTC-RP19 cells, infected, 4hrs, rep2

description: Library name: Sample 2


title: Radiation-induced dermatitis mouse skin cells, IL17ab treatment, biol rep1


title: MDTC-RP19 cells, infected, 4hrs, rep1

description: Library name: Sample 1


title: DOG 099

description: Library name: R099-495053


title: DOG 100

description: Library name: R100-495048


title: DOG 098

description: Library name: R098-265788


title: GBM-6425_B.1D11, single cell DNA methylation

description: Library name: GBM-6425_B.1D11


title: C.elegans, PAS-seq 2, K-NAA-2

city: Tsingtao

first: li

middle: pan

last: feng

state: shandong

address: Ao Shan Wei Street

department: College of Life Sciences

institute: shandong university

description: Library name: Sample8

data_processing:
For RNA-seq analysis, raw sequencing reads were quality controlled and preprocessed using fastp (v0.24.0) with default parameters. The clean reads were aligned to the reference genome (WS250) using STAR (v2.7.11b) with the following parameters: --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1 --outSAMattribu tes NH HI AS nM --outSJfilterReads Unique. Gene expression quantification was performed using featureCounts (v2.0.3) with the parameters:-p --countReadPairs -s 2 -t exon. Differential expression analysis was conducted using DESeq2 (v1.40.2) with the lfcShrink function (lfcThreshold = 1, apeglm algorithm) to estimate moderated log2 fold changes. For PAS-seq 2 analysis, raw sequencing reads were merged into single-end reads and trimmed to remove adapter sequences and consecutive poly(A) sequences using fastp (v0.24.0). The processed reads were then aligned to the reference genome using STAR (v2.7.11b). Internal priming events were filtered by excluding reads mapped to genomic regions containing consecutive adenines, and the 3′ ends of the reads were compared to annotated poly(A) sites from the UTRome database. Global changes in alternative polyadenylation (APA) were analyzed using polyA-miner with the following parameters: -mode bam -p 20 -pa_p 0.6 -pa_a 3 -pa_m 1 -ip 30 -expNovel 0 -t BB.
Assembly: WS250
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Bigwig file for each Sample

organism: Caenorhabditis elegans

source_name: germline

growth_protocol: C.elegans were maintained on NGM (nematode growth medium) plates seeded with OP50 bacteria  or OP50 bacteria  including K-NAA at 20℃.

extract_protocol:
Total RNAs were extracted from Control and K-NAA oocyte at meiosis prophase I stage, using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample).
Poly(A) RNA was isolated from 5 μg of total RNA using the Oligo dT-Coated Magnetic Beads (YEASEN, 19820ES03) according to the manufacturer’s protocol. The eluted mRNA was diluted to a final volume of 45 μL with RNase-free water and kept on ice. For RNA fragmentation, 1 μg of total RNA was incubated with 10× RNA fragmentation reagent (Invitrogen, AM8740) at 70°C for 5 minutes in a thermal cycler. The reaction was stopped by adding Stop Solution (10×) and placed on ice. The fragmented RNA was precipitated using 3M sodium acetate, Glycogen (Invitrogen, AM9510), and 100% ethanol at -80°C for 1 hour, followed by washing with 75% ethanol and resuspension in 5 μL RNase-free water. Reverse transcription was performed using the SuperScript™ III First-Strand Synthesis System (Invitrogen, 18080051) with PAS-seq 2 oligo(dT) primer, dNTP mix, and a template switch oligo containing locked nucleic acid (LNA). To enhance efficiency, betaine and magnesium chloride were included in the reaction. The thermal cycling conditions were: 42°C for 90 min, 50°C for 2 min, 42°C for 2 min (repeated 9 times), followed by 72°C for 15 min. The resulting cDNA was purified using Hieff NGS ® Smarter DNA Clean Beads (YEASEN, 12600ES56) and eluted in 25 μL RNase-free water, with 23 μL of the supernatant transferred to a new tube. The cDNA was amplified using Phusion® High-Fidelity PCR Master Mix (NEB, M0531S) with TruSeq universal and indexed adapters. PCR conditions were: 98°C for 30 s, 19 cycles of 98°C for 10 s, 66°C for 30 s, and 72°C for 20 s, followed by 72°C for 5 min. DNA fragments ranging from 185 to 225 bp were recovered after electrophoresis on a 2.5% agarose gel. For RNA-seq library construction, we used the Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (YEASEN 12309ES24) following the manufacturer’s protocol. Sequencing was performed on the Illumina NovaSeq 6000 platform with a paired-end 150 bp (PE150) read configuration.

value: germline

value: meiosis prophase I

value: oocyte

value: knock-in

value: Auxin induced degradation

tag: batch


title: GBM-6425_B.1D12, single cell DNA methylation

description: Library name: GBM-6425_B.1D12


title: C.elegans, PAS-seq 2, K-NAA-1

description: Library name: Sample7


title: Radiation-induced dermatitis mouse skin cells, no treatment (control), biol rep3


title: Radiation-induced dermatitis mouse skin cells, no treatment (control), biol rep2


title: GBM-6425_B.1D10, single cell DNA methylation

description: Library name: GBM-6425_B.1D10


title: GBM-6425_A.2G08, single cell DNA methylation

description: Library name: GBM-6425_A.2G08


title: GBM-6425_A.2H06, single cell DNA methylation

description: Library name: GBM-6425_A.2H06


title: Radiation-induced dermatitis mouse skin cells, no treatment (control), biol rep1


title: C.elegans, PAS-seq 2, Control-2

description: Library name: Sample6

value: wide type


title: DOG 096

description: Library name: R096-494716


title: GBM-6425_B.1D09, single cell DNA methylation

description: Library name: GBM-6425_B.1D09


title: DOG 101

description: Library name: R101-493493


title: C.elegans, PAS-seq 2, Control-1

description: Library name: Sample5


title: GBM-6425_B.1D08, single cell DNA methylation

description: Library name: GBM-6425_B.1D08


title: DOG 095

description: Library name: R095-264093


title: VitC Dam&ChIC Dam-LMNB1/H3K9me3 (KIN8791_KIN8928_xci.index36)

description:
sc_damchic_mouse_binsize_100000.h5ad.gz
input_mouse_binsize_100000.h5ad.gz

data_processing:
Dam&ChIC data processing is largely based on the workflow and scripts described in Rooijers et al., 2019 and Markodimitraki et al., 2020 (available at: https://github.com/KindLab/scDamAndTools), but adapted to allow for computational separation of scDamID and sortChIC derived reads and further processing of sortChIC reads.
All reads are demultiplexed by comparing their sample barcode (e.g. single-cell barcode) located at the start of each read (R1 in case of paired-end sequenced libraries) conform to the read layout of 5′-[3 nt UMI][8 nt barcode]TC[gDNA]-3′ for scDamID and 5′-[3 nt UMI][8 nt barcode]WN[gDNA]-3′ for sortChIC reads, to a reference list of barcodes and zero mismatches between the observed barcode and reference are allowed. Sample barcodes and UMIs are trimmed off the reads to only retain gDNA sequences. The UMI sequences were appended to the read name for downstream processing. Per sample barcode, scDamID and sortChIC reads remain mixed at this point.
After preprocessing, the reads were aligned to a reference genome using bowtie2 (v. 2.4.1) with parameters: ‘‘--seed 42 --very-sensitive -N 1’’. Before alignment a ‘GA’ dinucleotide was prepended to the reads that has effectively been digested off scDamID fragments during DpnI gDNA digestion. For human samples, reads were aligned to reference genome hg19 (GRCh37) and mouse samples to mm10 (GRCm38). For allele-specific processing for X-chromosome inactivation experiments, data were aligned to reference genomes generated by imputing 129S1/SvImJ and CAST/EiJ single nucleotide polymorphisms obtained from the Sanger Mouse Genomes project (Keane et al., 2011) onto the mm10 reference genome. The reads were assigned to either genotype by aligning reads to both references. Reads that aligned with lower edit distance (SAM tag ‘NM’) or higher alignment score (SAM tag ‘AS’) in case of equal edit distance to one of the genotypes were assigned to that genotype. Reads aligning with equal edit distance and alignment score to both genotypes were considered of ‘ambiguous’ genotype. Reads that yielded an alignment with mapping quality (BAM field ‘MAPQ’) lower than 10 were discarded.
Following read alignment with ‘GA’ prepended dinucleotide, reads were considered scDamID in case of perfect alignment on genomic GATC motifs. Residual reads were considered sortChIC and their original sequences (i.e., without prepended GA dinucleotide) were realigned using hisat2 (v. 2.1.0) with parameters: ‘‘--seed 42 --no-spliced-alignment --mp '2,0' --sp '4,0'”. These sortChIC-considered reads were further pruned given MNase’s strong adenine or thymidine-nucleotide cut preference; only sortChIC reads were kept that lead with an ‘A’ or ‘T’ base. In addition, we observed that a larger fraction of sortChIC reads (i.e., that do not map on a genomic GATC motif) are ‘TC’-dinucleotide leading in Dam&ChIC libraries than in sortChIC libraries and hence decided to exclude TC-leading reads from Dam&ChIC-derived sortChIC libraries.
Library strategy: Dam&ChIC

growth_protocol: Human haploid KBM7 cells were cultured in suspension in IMDM medium (10% FBS and 1% Pen/Strep). Human HT-1080 cells were cultured in DMEM medium (10% FBS and 1% Pen/Strep). Mouse F1 hybrid Cast/EiJ x 129SvJ embryonic stem cells (mESCs; a kind gift from the Joost Gribnau laboratory) were cultured on a monolayer of irradiated feeders (MEFs) in CM+/+ (G-MEM + 10% FBS, 1% Pen/Strep, 1× GlutaMAX (Gibco), 1× NEVitaminC, 1× sodium pyruvate, 0.1 mM 2-ME and 1000 U/ml ESGROmLIF (EMD Millipore, ESG1107))

extract_protocol:
For Kbm7 cells nuclei were isolated using 0.05% Saponin. MESCs were fixed at -20C using 70% Ethanol and permeablised using 0.05% Tween. ProteinA-MN was targeted using antibodies against IgG, Lamin B1, H3, H3K4me1, H3K4me3, H3K9me3, H3K27me3 or H3K36me3 and cells were FACS sorted into 384 well plates.
MN was activated thorugh 2mM CaCl2 for 30min at 4C at inactivated by EGTA addition. Cells were lysed (protK + NP40), fragments end-repaired (Klenow) and adenine methylated sites were cut (DpnI). Dam and ChIC fragemnts are ligated to blunt end adaptors containing a cell barcode and unique molecular identifier and a T7 promoter. After pooling DNA is amplified by in vitro transcription, before rundom hexamer based reverse transcription and final indexing PCR for sequencing.

treatment_protocol:
Dam-POI induction: For Kbm7 cells 0.5 nM Shield-1 was added to stabilize the protein at the indicated timepoint. For mESCs 1mM IVitaminC was added 24h prior to induction, to ensure protein degradation.
double thymidine block: cells received 2 mM thymidine for 15 hours, followed by 9 hours of release, followed by a second thymidine block for 13 hours.
VitaminC: Cell culture was depleted from MEFs and 24-48 hours later confluent wells were passaged 1:15 in VitaminC differentiation medium (IMDM with 15% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X NEVitaminC, 50 μg/ml VitaminC and 0.1 mM 2ME).

value: Inner cell mass derived

value: ESC

value: VitaminC differentiation

value: 129S1/SvImJ x CAST/Eij


title: C.elegans, RNA-seq, K-NAA-2

description: Library name: Sample4


title: VitC Dam&ChIC Dam-LMNB1/H3K9me3 (KIN8791_KIN8928_xci.index37)


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8791_KIN8928_xci.index35)


title: GBM-6425_B.1D07, single cell DNA methylation

description: Library name: GBM-6425_B.1D07


title: C.elegans, RNA-seq, K-NAA-1

description: Library name: Sample3


title: DOG 093

description: Library name: R093-190133

value: stool in ethanol

value: NO


title: GBM-6425_B.1D06, single cell DNA methylation

description: Library name: GBM-6425_B.1D06


title: DOG 097

description: Library name: R097-494727


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8791_KIN8928_xci.index33)


title: GBM-6425_B.1D05, single cell DNA methylation

description: Library name: GBM-6425_B.1D05


title: DOG 090

description: Library name: R090-493739


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8791_KIN8928_xci.index34)


title: GE5184-6-NB3_7-320-5-368-H3_L001

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Short reads were trimmed with trimmomatic (v0.36). Quality control was performed with FastQC (v0.11.4) and MultiQC.
Reads were mapped to the Celegans genome (WBcel235) with STAR (v2.7.9a) and transcript abundance was quantified using RSEM (v1.3.1).
Differential expression analysis was performed usingDESeq2, with an FDR-corrected P-value threshold of 0.05. The output files were further filtered to extract transcripts showing a 2.0-fold change in either direction. Results were reported for protein-coding genes only, and for all transcript types.
Alternative splicing analysis was performed usingrMATSversion v4.1.0.
Assembly: WBcel235
Supplementary files format and content: genes.rawmatrix.csv: raw counts for each gene in each sample (tab-delimited)
Supplementary files format and content: transcripts.rawmatrix.csv: raw counts for each transcript in each sample (tab-delimited)
Supplementary files format and content: NA.vs.NB.allCodingDiff.csv: results of differential expression analysis for each gene (tab-delimited)

growth_protocol: Worms were synchronized and grown on OP50 on NGM plates until the late L4 to young adult stage

extract_protocol:
RNAqueous-Micro Total RNA isolation kit, ThermoFisher Scientific
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Worms were collected and washed in NGM buffer and then incubated with 25 μM chaetocin or DMSO vehicle control and heat-treated OP50 (OD600 1.8-2.2) in a total volume of 5 ml in 15 ml tubes in a rotator for 5 h.

value: whole animal

tag: strain

value: wild type

value: chaetocin

tag: biorep


title: DOG 091

description: Library name: R091-491411


title: GBM-6425_B.1D04, single cell DNA methylation

description: Library name: GBM-6425_B.1D04

value: GBM patient brain tissue


title: C.elegans, RNA-seq, Control-1

description: Library name: Sample1


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8791_KIN8928_xci.index31)


title: DOG 094

description: Library name: R094-494464


title: DOG 092

description: Library name: R092-491412


title: GE5184-5-NB2_7-319-5-367-G3_L001


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8791_KIN8928_xci.index32)


title: GBM-6425_B.1D02, single cell DNA methylation

description: Library name: GBM-6425_B.1D02


title: DOG 087

description: Library name: R087-493642

value: YES


title: DOG 088

description: Library name: R088-211704


title: GBM-6425_B.1D01, single cell DNA methylation

description: Library name: GBM-6425_B.1D01


title: C.elegans, RNA-seq, Control-2

description: Library name: Sample2

value: germline


title: VitC Dam&ChIC Dam-scFv-H3K27me3/LMNB1 (KIN8791_KIN8928_xci.index29)


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8791_KIN8928_xci.index30)


title: GE5184-4-NB1_7-318-5-366-F3_L001


title: GE5184-3-NA4_7-317-5-365-E3_L001

value: control


title: VitC Dam&ChIC Dam-scFv-H3K27me3/LMNB1 (KIN8791_KIN8928_xci.index28)


title: GBM-6425_B.1D03, single cell DNA methylation

description: Library name: GBM-6425_B.1D03


title: GE5184-2-NA3_7-316-5-364-D3_L001


title: DOG 083

description: Library name: R083-493426


title: GBM-6425_B.1C11, single cell DNA methylation

description: Library name: GBM-6425_B.1C11


title: GBM-6425_B.1C10, single cell DNA methylation

description: Library name: GBM-6425_B.1C10


title: GBM-6425_B.1C12, single cell DNA methylation

description: Library name: GBM-6425_B.1C12


title: VitC Dam&ChIC Dam-scFv-H3K27me3/LMNB1 (KIN8791_KIN8928_xci.index23)


title: GBM-6425_B.1C09, single cell DNA methylation

description: Library name: GBM-6425_B.1C09


title: VitC Dam&ChIC Dam-scFv-H3K27me3/LMNB1 (KIN8791_KIN8928_xci.index27)


title: Fish120

city: Ås

first: Linn

middle: Haug

last: Eide

address: Oluf Thesens vei 6

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Raw reads cleaned by BBDuk (v34.56) to trim low quality reads, adapter sequences and PhiX (Illumina spike-in).
Fragments counted using featureCounts (c1.4.6-pl)
Differentially expressed genes (DEGs) estimated using SARTools R package (v1.7.3).
DEGs were used in an enrichment analysis by CLueGo with term fusion in Cytoscape v.3.8.2.
Gene ontology databases for Atlantic salmon (biological process, cellular component, molecular function and immune system process were used to compare DEGs results, genes included in final results if 10 % of genes in each term were covered.
Assembly: Cleaned reads aligned to Salmo salar genome SSAL_v3.1 (GenBank assembly accession GCA_905237065.2
Supplementary files format and content: .counts files

organism: Salmo salar

source_name: distal intestine

extract_protocol:
RNA was isolated with 900 µL QIAzol lysis reagent (Qiagen, Hilden, Germany, cat. No. 79306) and a 5 mm  stainless steel bead (Qiagen, cat. No. 69989). The tissues were lysed with a Qiagen TissueLyser bead mill  (Retsch, Haan, Germany, cat. no. 85220)  at 20 Hz for 2 min (twice). 180 µL chloroform was added before  vortexing. Tubes were centrifuged at 12 000 rpm (4 °C) The upper phase containing RNA and water was  transferred to new tubes, and 450 µL isopropanol was added. Tubes were shaken by hand and incubated  for 10 min at room temperature, before centrifugation for 15 min. Excess liquid was removed and 200 µL  70 % ethanol was added before centrifugation at 10 min. The supernatant was removed, and the samples  were centrifugated for 3 min. With the lids open, the pellets dried for 5-10 min. The RNA was then  dissolved in 40 μL RNAse-free water, followed by a 10 min incubation at 55 °C. 20 ng/ul.
Poly A enrichment  and reverse transcription of cDNA.

value: distal intestine


title: GBM-6425_B.1C08, single cell DNA methylation

description: Library name: GBM-6425_B.1C08


title: Fish118


title: GBM-6425_B.1C07, single cell DNA methylation

description: Library name: GBM-6425_B.1C07


title: VitC Dam&ChIC Dam-scFv-H3K27me3/LMNB1 (KIN8791_KIN8928_xci.index21)


title: VitC Dam&ChIC Dam-LMNB1/H3K27me3 (KIN8433_xci.index20)


title: DOG 078

description: Library name: R078-255113


title: Fish117


title: GBM-6425_B.1C06, single cell DNA methylation

description: Library name: GBM-6425_B.1C06


title: Fish116


title: VitC Dam&ChIC Dam-LMNB1/H3K27me3 (KIN8433_xci.index19)


title: DOG 085

description: Library name: R085-493492


title: GBM-6425_B.1C05, single cell DNA methylation

description: Library name: GBM-6425_B.1C05


title: VitC Dam&ChIC Dam-LMNB1/H3K27me3 (KIN8433_xci.index18)


title: Fish115


title: DOG 076

description: Library name: R076-227105


title: DOG 082

description: Library name: R082-493425


title: VitC Dam&ChIC Dam-scFv-H3K27me3/LMNB1 (KIN8791_KIN8928_xci.index22)


title: Fish119


title: DOG 079

description: Library name: R079-255120


title: VitC Dam&ChIC Dam-LMNB1/H3K27me3 (KIN8433_xci.index16)


title: DOG 075

description: Library name: R075-258896


title: GBM-6425_B.1C03, single cell DNA methylation

description: Library name: GBM-6425_B.1C03


title: GE5184-1-NA1_7-315-5-363-C3_L001


title: Fish114


title: DOG 073

description: Library name: R073-232979


title: Fish113


title: DOG 074

description: Library name: R074-483211


title: GBM-6425_B.1C02, single cell DNA methylation

description: Library name: GBM-6425_B.1C02


title: VitC Dam&ChIC Dam-scFv-H3K27me3/H3K9me3 (KIN8403.index46)


title: DOG 077

description: Library name: R077-493413


title: VitC Dam&ChIC Dam-scFv-H3K27me3/H3K9me3 (KIN8403.index45)


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8403.index36)


title: Fish112


title: Fish111


title: DOG 070

description: Library name: R070-474029


title: DOG 072

description: Library name: R072-190432


title: GBM-6425_B.1B12, single cell DNA methylation

description: Library name: GBM-6425_B.1B12


title: GBM-6425_B.1C04, single cell DNA methylation

description: Library name: GBM-6425_B.1C04


title: DOG 068

description: Library name: R068-492548


title: Fish110


title: VitC Dam&ChIC Dam-LMNB1/LMNB1 (KIN8403.index35)


title: GBM-6425_B.1B11, single cell DNA methylation

description: Library name: GBM-6425_B.1B11


title: Fish109


title: VitC Dam&ChIC Dam-LMNB1/H3K27me3 (KIN8164.index15)


title: Fish108


title: GBM-6425_B.1B09, single cell DNA methylation

description: Library name: GBM-6425_B.1B09


title: DOG 066

description: Library name: R066-492165


title: DOG 067

description: Library name: R067-492166


title: LAIR-1-deficient, mouse 3

first: Akashdip

last: Singh

address: Lundlaan 6

institute: UMC Utrecht

data_processing:
Read 1 was used to identify the Illumina library index and CEL-seq sample barcode.
Read 2 was aligned to the mouse mm10 reference transcriptome using BWA MEM
Reads that mapped equally well to multiple locations were discarded.
Mapping and generation of count tables was done using the MapAndGo script.
Assembly: mm10
Supplementary files format and content: tsv file with count tables for genes per sample

source_name: naive CD8 T cells

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol
Sequencing libraries were prepared with Illumina Truseq small RNA primers

treatment_protocol: For RNA sequencing of naïve CD8+ T cells, spleens were isolated from 3 Lair1+/+ mice and 3 Lair1-/- mice, processed to single cell suspensions, followed by red blood cell lysis and multiple washing steps. Cells were then stained for 30 minutes on ice, washed and resuspended in FB. Afterwards, 100.000 CD45+CD3+CD8+CD62L+CD44- cells each were sorted on FACSAriaIII (BD). Cells were then spun down at 300xg, and resuspended in TRIzol (Invitrogen).

value: naive CD8 T cells


title: Fish107


title: GBM-6425_B.1B08, single cell DNA methylation

description: Library name: GBM-6425_B.1B08


title: GBM-6425_B.1C01, single cell DNA methylation

description: Library name: GBM-6425_B.1C01


title: LAIR-1-deficient, mouse 2


title: GBM-6425_B.1B10, single cell DNA methylation

description: Library name: GBM-6425_B.1B10


title: DOG 064

description: Library name: R064-492021


title: Fish106


title: GBM-6425_B.1B07, single cell DNA methylation

description: Library name: GBM-6425_B.1B07


title: LAIR-1-deficient, mouse 1


title: DOG 081

description: Library name: R081-493814


title: DOG 062

description: Library name: R062-491792


title: GBM-6425_B.1B06, single cell DNA methylation

description: Library name: GBM-6425_B.1B06


title: VitC Dam&ChIC Dam-LMNB1/H3K27me3 (KIN8164.index16)


title: wild type, mouse 3


title: DOG 061

description: Library name: R061-491793


title: Fish103


title: GBM-6425_B.1B04, single cell DNA methylation

description: Library name: GBM-6425_B.1B04


title: DOG 060

description: Library name: R060-491591


title: GBM-6425_B.1B03, single cell DNA methylation

description: Library name: GBM-6425_B.1B03


title: wild type, mouse 2


title: Fish104