title: monkey M8020, xenograft biopsy tissue sample after xenotransplantation, day 267

data_processing:
ENSEMBL Sscrofa11.1 FASTA assembly and v105 GTF annotation were prepared as a reference by removing unplaced contigs/scaffolds, and then adding intended genetic alterations/payload sequences as a separate contig. ENSEMBL Macaca fascicularis 6.0 FASTA assembly and v105 GTF annotations with unplaced contigs/scaffolds removed were appended to the pig reference for aligning reads from samples with expected NHP transcripts.
Transcript sequences were generated with gffread (0.12.7) on these synthetic genome assemblies.
Indexing was performed on transcripts with salmon index (1.6.0) applying standard settings and the whole genome as a decoy. Salmon quant in mapping-based mode was used to quantify RNA-seq read abundance per transcript using custom settings: 100 bootstrap replicates, GC content and sequence bias correction applied. For the included study, only transcripts aligning to Sscrofa11.1 were retained and analyzed. Gene level aggregation on transcript abundance was performed with tximport (1.22.0).
Protein coding and lncRNA genes were retained and normalized rlog counts calculated using DESeq2 (1.36.0) with design including sample source (CUK, biopsy, necropsy) and pig identification number used as covariates.
Assembly: ENSEMBL Sscrofa11.1 and ENSEMBL Macaca fascicularis 6.0
Supplementary files format and content: TAR of standard Salmon quantification output. An R RDS file containing the DESeqDataSet with raw and rlog processed counts, and sample metadata. FASTA and GTF files for the KI transgenes used in RNA-seq quantificaiton.

source_name: Kidney biopsy cells

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74106) after passing the sample through homogenizing columns (Qiagen, 79656) and performing a DNAase digestion (Qiagen, 79256) according to manufacturer’s instructions. RNA integrity number and concentration was measured using an automated electronic electrophoresis system (Agilent, 4200 Tapestation) and reagents (Agilent, 5067-5578).
For those samples passing quality checks, 500ng of total RNA was carried into the Illumina Stranded mRNA kit library preparation (Illumina, 20040534). Libraries were characterized using the high sensitivity dsDNA assay (Invitrogen, Q33231) for Qubit 3 (Invitrogen, Q33216).

value: Kidney biopsy cells

value: EGEN2060 AKA PL17P

value: xenotransplanted in NHP

tag: time

value: Day 267


title: ATACseq_Lymphblastoid cells_D21_42C_rep2_technical1

status: Public on Apr 21 2023

type: SRA

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

country: USA

institute: University of Colorado

description:
Eric_D21
genomic DNA (ATAC-seq)
Eric42merged_peaks_clean.narrowPeak

library_source: genomic

data_processing:
ATAC-seq data was processed using the ChIP-Flow pipeline (https://github.com/Dowell-Lab/ChIP-Flow) version 1.0.
In short, this pipeline trimmed reads with BBDuk version 38.05 with the following settings: ktrim=r, qtrim=10, k=23, mink=11, hdist=1, maq=10, minlen=20. Reads were mapped to GRCh38 with HISAT2 version 2.1.0 with the following settings: --very-sensitive, --no-spliced-alignment. Sam files were converted to bam files using SAMtools version 1.8, and Picard Tools version 2.6.0 was used to identify duplicate reads and deduplicate. BEDtools version v2.28.0 was used to produce bedGraph files from bam files. IGV Tools version 2.3.75 was used to produce TDF files from bedgraphs. For quality control of libraries, the QC programs FastQC version v0.11.8, preseq version 2.0.3, RSeQC version 3.0.0, and Pileup from the BBMap Suite version 38.0 were used.
Peak calling ATAC-seq: MACS2 version 2.1.1 was used to call peaks (callpeak) with the following settings: --SPMR, -q 0.0001. The genomic DNA preparations were used as control samples for peak calling (-c controlbams). Peak calling using MACS was carried out on the full bam files for ATAC-seq runs, as well as repeated on bam files with Chr21, ChrEBV, and ChrM removed for all downstream MuMerge and TFEA analyses used to compare data directly between different cell lines. Bedtools version 2.25.0 was used to remove blacklist regions from the resulting peak files using the bedtools intersect command with the Encode consensus blacklist regions. All downstream analysis using MACs2 peaks used the ‘narrowPeak’ files.
As noted above: For the second replicate of experiments, two sets of technical replicates were prepared for each condition. These replicates were carried out on cells from separate wells of a plate, but the cells were from the same cell lineages and passage numbers, so at the level of bam files, these technical replicates were merged into a single file, to be used as one cohesive second replicate of data.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bedgraphs and bed peak files supplied for ATAC-seq.

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblastoid-EBV immortalized

growth_protocol: Cell lines were given pseudonyms Ethan and Eric for ease of use. Lymphoblastoid cells were grown in suspension in RPMI media supplemented with 20% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, and 2mM L-glutamine. Cell cultures were maintained in incubators with 5% CO2 at 37°C. Generally cells were grown in t25 or t75 flasks and split 1:10 every few days.

extract_protocol:
Suspension cells were then used to prepare an ATAC-seq library using the OMNI-ATAC-seq protocol. For control samples in calling ATAC-seq peaks, genomic DNA was extracted from each of the two cell lines using the Purelink genomic mini kit, then the genomic DNA was prepared for sequencing by carrying out the OMNI-ATAC protocol on this genomic DNA suspension.
For ATAC-seq, samples were pooled, size selected from 100-1000bp by blue pippen, SPRI bead cleaned up, and sequenced on a Nextseq V2 high output 75-cycle kit paired end 2x37 reads with dual 8bp indexes. For the second replicate of experiments, two sets of technical replicates were prepared for each condition. These replicates were carried out on cells from separate wells of a plate, but the cells were from the same cell lineages and passage numbers, so at the level of bam files, these technical replicates were merged into a single file, to be used as one cohesive second replicate of data.

treatment_protocol: The control 37C flasks were kept in incubator, while heat shock 42C flasks were floated in an external 42C waterbath for 1 hour prior to harvesting. For replicate 1 data, 1ml of each cell suspension containing approximately 50,000 cells was aliquoted into a 24 well tissue culture plate prior to the experiment. 1 plate of cells was then floated on a 42C waterbath for 1 hour, as the other control 37C plate remained in the cell incubator. 50 minutes into the heat shock/control treatment, all cell plates were collected and 2ul of DMSO was added to all samples before putting the control plate back in incubator and heat shock plate back in 42C waterbath. (The DMSO was a control for an unpublished experiment). After full hour of heat shock treatment has elapsed, both plates of cells were collected and placed on ice before spinning cells down and harvesting for ATAC-seq. For second replicate, heat shock or control treatment was carried out similarly but with approximately 30,000 cells per 1ml media in each 24 well plate well, and no DMSO was added during the experiment. For the second replicate of experiments, frozen S2 cells were spiked into the cell suspensions at approximately 1% after harvesting the cells but prior to the ATAC-seq experiment.

tag: cell type

value: lymphoblastoid

tag: genotype

value: disomic

tag: treatment

value: 42C 1 hour heat shock


title: monkey M8020, xenograft biopsy tissue sample after xenotransplantation, day 55

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

library_source: transcriptomic

molecule: polyA RNA

organism: Sus scrofa

value: Day 55


title: ATACseq_Lymphblastoid cells_D21_37C_rep2_technical1

description:
Eric_D21
genomic DNA (ATAC-seq)
Eric37merged_peaks_clean.narrowPeak

value: untreated (37C incubator)


title: ATACseq_Lymphblastoid cells_D21_37C_rep2_technical2


title: CDK13_R860Q_oe_R159

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to a custom version of the danRer10 genome that also contained the human CDK13 gene sequence using bowtie with parameters --library-type fr-unstranded --no-novel-juncs and -G set revision 90 of the Ensembl GRCz10 genes
Expression of revision 90 GRCz10 genes was quantified using htseq-count with parameters -r name -I gene_name --stranded=no -m intersection-strict
Supplementary_files_format_and_content: Counts files contain gene names and htseq-determined read counts

molecule: total RNA

organism: Danio rerio

source_name: Melanoma

growth_protocol: p53-/-; mitfa:BRAFV600E;Na-/- one-cell embryos were injected with either 20ng/uL control or experimental MiniCoopR (MCR) DNA along with tol2 in vitro transcribed RNA for integration. In all experiments, 20 zebrafish were raised per tank to control for density effects.  Zebrafish were scored for the emergence of raised melanoma lesions as published.  Zebrafish were sacrificed on ice and the tumors were dissected.

extract_protocol:
Library prepped with random priming (NEBNext Ultra RNA Library Prep Kit for Illumina, E7530), fragmentation time of 15min, 12 PCR cycles, and sequenced on an Illumina HiSeq 2000 (100bp paired end reads).
Melanomas were homogenized in RLT buffer, subjected to QIAshredder columns (Qiagen, 79656), and then RNA was isolated with a column based method with genomic DNA column removal (Qiagen, 74134).  RNA was ribodepleted (Illumina Ribozero Gold, MRZG12324).  Ribodepletion was confirmed with Agilent 4200 Tapestation.

tag: tissue

value: Melanoma

tag: cdk13 status


title: EGFP_oe_R162

value: Wild-type


title: EGFP_oe_R163


title: CDK13_R860Q_oe_R158


title: ATACseq_Lymphblastoid cells_T21_GenomicDNAprep_rep1

value: chromosome 21 trisomic


title: CDK13_R860Q_oe_R157


title: monkey M7519, xenograft biopsy tissue sample after xenotransplantation, day 243

value: Day 243


title: EGFP_oe_R164


title: ATACseq_Lymphblastoid cells_D21_GenomicDNAprep_rep1


title: EGFP_oe_R165


title: CDK13_R860Q_oe_R160


title: monkey M7519, xenograft biopsy tissue sample after xenotransplantation, day 53

value: Day 53


title: CDK13_R860Q_oe_R161


title: monkey M7519, xenograft biopsy tissue sample after xenotransplantation, day 166

value: Day 166


title: ATACseq_Lymphblastoid cells_D21_42C_rep2_technical2


title: CDK13_W878L_Ser2PolII

data_processing:
Raw reads were aligned twice: first to the dm6 revision of the D. melanogaster genome to remove exogenous spike-in reads using bowtie version 1.2.2 with parameters -k 1 -m 1; unmapped reads were then aligned to the danRer10 revision of the zebrafish genome.
danRer10
Supplementary_files_format_and_content: bigWig files were created from the alignment bam file using the R with the GenomicAlignments package and with gr.cov and export.bw from rtracklayer

growth_protocol: p53-/-; mitfa:BRAFV600E;Na-/- one-cell embryos were injected with either 20ng/uL control or experimental MiniCoopR (MCR) DNA along with tol2 in vitro transcribed RNA for integration. In all experiments, 20 zebrafish were raised per tank to control for density effects.  Zebrafish were scored for the emergence of raised melanoma lesions as published.  Zebrafish were sacrificed on ice and the tumors were dissected.  11 EGFP or 6 CDK13 W878L expressing melanomas were isolated between 18-19 weeks post fertilization.  Tumors were combined and minced.  Cells were collected and fixed in 1.1% formaldehyde solution for 10min at room temperature (RT).  Tumors were homogenized and filtered through a 100um filter, spun down, washed with 1X PBS, and cells were counted using a Neubauer Chamber (9.00E+07 for CDK13 W878L and 7.10E+07 for EGFP expressing melanomas).  For anti-CDK13 ChIP-sequencing from melanomas from mitfa:BRAFmut+/+; p53-/-; Na-/- zebrafish expressing either CDK13 R860Q + ccnT1 CRISPR or CDK13 R860Q + ctrl CRISPR as above, 4 melanomas were isolated from each condition at the same time point (19.1 weeks post fertilization) and the above protocol was replicated (Neubauer Chamber  7.90 E-7  for R860Q + ccnT1 CRISPR and 8.5 E-7 for R860Q + ctrl CRISPR.

extract_protocol:
Libraries were performed using the NEBNextMultiplex Oligos for Illumina kit (NEB) according to instructions.  Samples were sequenced with 100bp single end reads.
Nuclear cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200-400 bp were immunoprecipitated using different antibodies.

tag: chip antibody

value: Phospho Ser2-RNA PolII

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: antibody lot

tag: sg target


title: ATACseq_Lymphblastoid cells_T21_42C_rep1

description:
Ethan_T21
genomic DNA (ATAC-seq)


title: CDK13_W878L_input


title: ATACseq_Lymphblastoid cells_T21_37C_rep1

description:
Ethan_T21
genomic DNA (ATAC-seq)


title: CDK13_W878L_PolII

value: RNA Pol II


title: pig 21404, contralateral kidney sample at day0/procurement

value: Kidney biopsy cells

value: EGEN2734 AKA PL15S

value: none, contralateral kidney, untransplanted

value: Day 0/procurement


title: Zebrafish_melanoma_eGFP_3pSeq_rep2

description: RNA 3' end sequencing

data_processing:
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013)
Custom Python script to filter reads from each bam file based on the following parameters: 1) Proper mate pairing; 2) orientation of the putative 3’ cleavage end corresponding to the direction of transcription for the gene to which reads mapped; 3) concordant mapping to known chromosomes; 4) no soft clippings; 5) skipped regions must be longer than 70 nucleotides.
Bedtools cluster tool version 2.26.0 (Quinlan and Hall, 2010) and custom Python scripts were used to generate read clusters by grouping any 3’ end coordinates that fell within 40 nucleotides of one another into a single cluster.
Clusters present in >1 replicate were considered to be true termination sites (high confidence termination sites). High confidence termination site reads were reclusters to define a complete and non-redundant 3' cleavage map for all conditions.
3' cleavage site reads were quantified using DEX-seq (Anders et al, 2012).
Assembly: GRCz11
Supplementary files format and content: 3pSeq counts tables contain gene coordinates, a unique polyA-site identifier, strand, and read counts

source_name: melanoma

growth_protocol: Melanomas generated from CDK13R860Q (n=3) or EGFP (n=3) injected into p53-/-; mitfa:BRAFV600E; mitfa-/- zebrafish were isolated and approximately equal cell numbers were gathered.

extract_protocol:
Poly-A selection was undertaken (NEB, E7490). Tissue was disrupted (Qiagen, 79654), DNA was removed, and RNA was isolated (Qiagen, 741134).
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina, 016.24

value: melanoma

value: eGFP injection


title: EGFP_input


title: ATACseq_Lymphblastoid cells_D21_42C_rep1

description:
Eric_D21
genomic DNA (ATAC-seq)

value: lymphoblastoid

value: disomic

value: 42C 1 hour heat shock


title: pig 20215, contralateral kidney sample at day0/procurement

value: EGEN2060 AKA PL17P


title: monkey M8020, xenograft biopsy tissue sample after xenotransplantation, day 132

value: xenotransplanted in NHP

value: Day 132


title: EGFP_Ser2PolII

value: Melanoma

value: Wild-type


title: ATACseq_Lymphblastoid cells_D21_37C_rep1

description:
Eric_D21
genomic DNA (ATAC-seq)

value: untreated (37C incubator)


title: EGFP_PolII

value: Abcam


title: pig 20200, contralateral kidney sample at day0/procurement


title: A9161 Contralateral Kidney Cortex, TR2

library_source: transcriptomic single cell

data_processing:
A modified ENSEMBL Sscrofa11.1 FASTA assembly and v105 GTF annotation was generated by removing unplaced contigs/scaffolds and adding PL15S FASTA sequence and GTF annotation as a separate contig.
10X 3’ scRNA-seq was processed using STARsolo (2.7.9a) with additional settings –soloCellFilter EmptyDrops_CR, --soloMultiMappers EM, --clipAdapterType CellRanger4, --outFilterScoreMin 30, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloType Gene, --soloUMIdedup 1MM_CR, --soloUMIfiltering MultiGeneUMI_CR, and –soloUMIlen 12.
Counts were loaded into R (4.1.2) using DropletUtils (1.14.2) and cells filtered based on number of unique UMIs and detected features, percentage of mitochondrial UMIs, percentage of protein-coding and lncRNA UMIs, complexity (number of detected features versus total UMIs per cell), and doublet removal using scDblFinder (1.8.0).
Counts were normalized using scran quickCluster, computeSumFactors, and logNormCounts per scran (1.22.1) guidelines.
Cell-cycle was assigned using Seurat (4.1.0) CellCycleScoring.
Batch effects were removed using scVI (0.15.5) with mitochondrial UMI percentage, Seurat S and G2M phase cell cycle scores, porcine donor, and kidney region (i.e. cortex or medulla) as covariates.
Cells were clustered on the 20 latent dimensions from scVI using the bluster (1.4.0) louvain algorithm on shared nearest neighbors (k=3) via scran clusterCells.
UMAP manifold was created via scater (1.22.0) runUMAP with 20 nearest neighbors and a minimum distance of 0.2.
Cluster marker genes were computed using scran scoreMarkers and cell types assigned using known markers [PMID: 34843404] and the molecular signature database cell type signature enrichment using the fgsea (1.20.0) fora function on the top 50 features per cluster by minimum Cohen’s d log fold change
Supplementary files format and content: TAR archives of STARsolo 10X CellRanger-like output including raw count matrices (matrix market exchange), features (tab delimited), and barcodes (tab delimited) for unfiltered and filtered cells.
Supplementary files format and content: R RDS format file containing a SingleCellExperiment with metadata and both raw and normalized UMI counts.

source_name: contralateral kidney cortex

extract_protocol:
Prior to tissue processing, kidneys were recovered from donor animals and placed in cold RPMI (11875093, ThermoFisher) with 2% FBS (10438026, ThermoFisher) and 1X Penicillin-Streptomycin (15140122, Thermofisher). Kidneys were kept on ice, and the kidney capsule was removed. Forceps and scissors were used to collect an approximately 1-gram piece of kidney cortex and dissect medullary pyramids from the kidney parenchyma of each kidney. Both cortex and medulla samples were separately minced into 1-2 mm3 pieces until roughly homogenous. The minced tissues were transferred to 50 mL conical tubes containing 10 mL of digestion solution of 1X HBSS (MT-20023CV, ThermoFisher), with 2.5 mg/mL Collagenase Type 2 (LS004174, ThermoFisher), 7.5 mg/mL Native Bacillus licheniformis Protease (NATE0633, ThermoFisher), and 100 U/mL Benzonase Nuclease (E1014, Sigma). Cortex and medulla digestions were incubated at 12°C for 30 and 45 minutes, respectively, and were thoroughly mixed at 5-minute intervals. After incubation, digestions were terminated with 25 mL 1X HBSS containing 20% FBS, passed through a 70-µm cell strainer (130-098-462, Miltenyi Biotec, Bergisch Gladbach, Germany) and centrifuged at 350xg for 5 minutes at 4°C. Supernatants were aspirated, and cells were resuspended in 4 mL RBC lysis buffer (11814389001, Roche, Basel, Switzerland) on ice for 2 minutes. Lysis was terminated with 25 mL 1X HBSS with 20% FBS, and cells were recentrifuged, pellets were resuspended in 1X HBSS, and re-filtered through 70-µm filters. Cells were manually counted by trypan blue exclusion, and dead cell removal was performed using a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) following manufacturer instructions. After dead cell removal, cells were recounted and resuspended in complete medium at a concentration of 600-1200 cells/μL
Library construction was performed per manufacturers protocol: 10X Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) (1000121, 10x Genomics, Pleasanton, CA).

value: contralateral kidney cortex

value: POD 0

value: 3KO, PL15S, RI

value: Untransplanted

tag: pig id


title: DNA from liver from YoungHetRec5

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Adapter removal and quality trimming for the analysis of DNA methylation reads were performed using TrimGalore v0.4.1 following previously established protocols (Krueger and Andrews, 2011; Meer et al., 2018; Petkovich et al., 2017)
Trimmed reads were mapped to the mouse genome (GRCm38.p2/mm10) using Bismark v0.15.0. (Krueger and Andrews, 2011)
Coverage files outputted by Bismark were then used for further analyses.
Assembly: mm10
Supplementary files format and content: Bismark .cov files with methylation calls and coverage for each locus

organism: Mus musculus

source_name: liver

growth_protocol: This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol:
DNA from samples was isolated by using the DNeasy Blood & Tissue Kit (Qiagen 69506), and then eluted from columns in 100 μl of 10 mM TrisHCl buffer, pH 8.0. 2 μl of RNase A (Life Technologies) was added to each sample. Samples were incubated at room temperature for 2 min, and isolated genomic DNA was purified by using the Genomic DNA Clean & Concentrator™-10 kit (Zymo D4011). DNA was eluted in 25 μl of 10 mM Tris-HCl buffer, pH 8.0 and quantified using a Qubit 2.0 (Life Technologies AM2271).
RRBS libraries were prepared following the protocol previously established (Petkovich et al., 2017), using 100 ng of DNA for each sample. Each library included 10 samples. To avoid an overlap of batch effect and age-related changes, we randomized samples across libraries. The libraries were sequenced using an Illumina HiSeq2500, with 150bp paired-end reads. 20% of mouse genomic DNA library was spiked in to compensate for low complexity of the libraries.

treatment_protocol: Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis.

tag: mouse strain

value: C57BL/6 WT

value: liver

tag: age (years)

tag: mouseid

tag: condition

value: Young heterochronic recovery


title: MCF7 BIRC2 sg3 rep3

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Read counts were generated by HTSeq (v0.11.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

growth_protocol: MCF7 is cultured in DMEM supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37C

extract_protocol:
Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN, Cat. 74136).
Libraries were constructed using Illumina standard protocols.

tag: cell line

value: adenocarcinoma cells

value: BIRC2 KO


title: MCF7 BIRC2 sg4 rep1


title: MCF7 BIRC2 sg4 rep3


title: DNA from liver from YoungHetRec4


title: MCF7 BIRC2 sg3 rep1


title: A9161 Contralateral Kidney Cortex, TR1

tag: time


title: 21077 Contralateral Kidney Medulla

source_name: contralateral kidney medulla

value: contralateral kidney medulla

value: 3KO, PL15S


title: MCF7 BIRC2 sg3 rep2

tag: cell type


title: DNA from liver from YoungHetRec3


title: MCF7 GFP sg rep2

tag: genotype

value: WT


title: DNA from liver from YoungHetRec2


title: MCF7 GFP sg rep3


title: 21077 Contralateral Kidney Cortex

tag: treatment


title: M2420 Kidney Cortex Biopsy POD359

data_processing:
Transcript sequences were generated with gffread (0.12.7) using a modified ENSEMBL Sscrofa11.1 FASTA assembly and v105 GTF annotation with unplaced contigs/scaffolds removed, and PL15S FASTA sequence and GTF annotation added as needed as a separate contig. For samples derived from transplanted organs the ENSEMBL Macaca fascicularis 6.0 FASTA assembly and v105 GTF annotations with unplaced contigs/scaffolds removed were appended to the pig reference
RNA-seq read counts were quantified at the transcript level with Salmon (1.6.0) with custom settings: whole genome used as decoy, 100 bootstrap replicates, and GC content and sequence bias correction applied.
Transcript abundances were aggregated to gene level using tximport (1.22.0) and only protein coding and lncRNA genes were retained.
Normalized rlog counts were generated with DESeq2 (1.34.0) using sample collection source (i.e. contralateral, biopsy, etc.) and Pig ID as an unblinded covariates.
Assembly: Modified Sscrofa 11.1 FASTA and v105 GTF
Supplementary files format and content: TAR directory containing standard Salmon quantification output.
Supplementary files format and content: R RDS format file containing a DESeq2 dataset with metadata, raw, and rlog normalized counts.

source_name: kidney cortex, biopsy

extract_protocol:
Snap-frozen xenotissue collected from the contralateral kidney, biopsies or kidney at necropsy was pulverized using a pre-chilled BioPulverizer (59012MS, BioSpec). Total RNA was extracted using homogenizing columns (79656, Qiagen), DNAase digestion (79256, Qiagen) and the RNeasy kit (74106, Qiagen) according to manufacturer’s instructions.
RNA integrity and quantity was assessed using an automatic electronic Electrophoresis system (4200 Tapestation, Agilent) and reagents (5067-5578, Agilent), and spectrophotometer (DS-11 Spectrophotometer, DeNovix). Upon passing quality checks, library was generated using the Illumina Stranded mRNA kit (20040534, Illumina) on 500 ng of total RNA input. Library concentrations were quantified by using the Qubit 3 (Q33216, Invitrogen) high sensitivity dsDNA assay (Q33231, Invitrogen), diluted to a final loading concentration of 650 pM, and sequenced on an Illumina NextSeq 2000 using a P3 100 cycle reagent kit (20040559, Illumina).

tag: tissue

value: biopsy kidney cortex

value: POD 359

value: Xenotransplanted

tag: cynomolgus macaque_id


title: MCF7 GFP sg rep1


title: DPSC-si-MXRA5-2_2

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

country: Japan

institute: Okayama University

description:
KY453d
condenseGenes_raw-Genes_20220204_siMXRA5_2_diffOutput_GEOupload.xlsx

data_processing:
Adapter trimming was conducted with Trimmomatic with default setting and then aligned to a reference genome (hg38) using HISAT2. The gene expression at exons was quantified using `analyzeRepeast.pl ` command in HOMER using `-strand both` and `-count exons` to identify expressed genes. Then, differentialy expressed genes were identified using `getDiffExpression.pl` command in HOMER.
Assembly: hg38
Supplementary files format and content: FPKM values for all 4 samples in condenseGenes_raw-Genes_20220204_siMXRA5_1_diffOutput_GEOupload.xlsx
Supplementary files format and content: FPKM values for all 4 samples in condenseGenes_raw-Genes_20220204_siMXRA5_2_diffOutput_GEOupload.xlsx

source_name: dental pulp

growth_protocol: normal culture

extract_protocol:
RNA was isolated from DPSC with RNAiso plus. Purified RNA was DNase-treated and further used for RNA-seq analyses.
Input RNA was converted to cDNA libraries using the NEBNExt poly(A) mRNA magnetic isolation module. Libraries were sequenced using 150-bp paired-end reads on an illumine Novaseq instruments.

value: dental pulp

value: dental pulp stem cells

value: siRNA transfection


title: DPSC-si-MXRA5-2_1

description:
KY453c
condenseGenes_raw-Genes_20220204_siMXRA5_2_diffOutput_GEOupload.xlsx


title: DPSC-si-MXRA5-1_2

description:
KY453b
condenseGenes_raw-Genes_20220204_siMXRA5_1_diffOutput_GEOupload.xlsx


title: DNA from liver from YoungHetRec1


title: 4C-seq_UT308_TLX3-promoter

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: DpnII-Csp6I digested genomic DNA

data_processing:
Library strategy: 4C-seq
Sequencing reads were processed using pipe4C (https://github.com/deLaatLab/pipe4C). Raw reads were trimmed to keep the sequences after DpnII restriction site 'GATC' and including only reads that contain the Csp6I restriction site 'GTAC' ("nonblind" fragments). Trimmed reads were aligned to human hg19 genome assembly using Bowtie2. The top 2 fragments were excluded from normalization and the normalization factor was set to 1000000. Following normalization, the data was smoothed by averaging using a running mean with a window size set to 100-bp.
The bigwig files were generated by converting the output wig files using the wigToBigWig function.
Assembly: hg19
Supplementary files format and content: bigwig files

source_name: Leukemia patients

growth_protocol: Human leukemia cell lines were cultured in RPMI supplemented with 20% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For 4C-seq analysis using the Illumina NextSeq500, 5 x 106 cells were cross-linked with 2% formaldehyde and nuclei were collected after cell lysis. Fixed chromatin was digested in situ with DpnII followed by in situ proximity ligation using T4 DNA ligase. Chromatin was then reverse cross-linked and genomic DNA was purified using phenol/chloroform extraction followed by ethanol precipitation. Purified DNA was then digested with Csp6I followed by proximity ligation with T4 DNA ligase. 4C templates were purified using QIAquick Spin columns. First round of PCR was performed using reading and non-reading promoter viewpoint primers followed by second round of PCR with primers containing Illumina-compatible adapter sequences.

treatment_protocol: For 5-aza-dC treatments, 5 µM of 5-aza-dC was added to culture medium for 7 days. Every 24 hours, cells were collected by centrifugation and spent media was replaced with fresh cell culture medium and 5 µM of 5-aza-dC. DMSO diluted 1:10,000 was added to cell culture medium freshly in the same manner as for 5-aza-dC-treated cells to serve as negative control.

value: leukemia cells


title: DNA from liver from YoungHet5

value: Young heterochronic parabiosis


title: M2519 Kidney Cortex Biopsy POD169

value: POD 169


title: DPSC-si-MXRA5-1_1

description:
KY453a
condenseGenes_raw-Genes_20220204_siMXRA5_1_diffOutput_GEOupload.xlsx


title: DNA from liver from YoungHet4

value: C57BL/6 WT


title: LEC sorted replicate3

city: Copenhagen

first: Mirna

last: Perez-Moreno

address: Universitetsparken 13

department: Department of Biology

country: Denmark

institute: University of Copenhagen

data_processing:
This project used the filtering software  SOAPnuke Version v1.5.2 for filtering. The specific steps are the following: 1)  Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Filtered clean reads were aligned to the mouse reference genome (GCF_000001635.26_GRCm38.p6) using HISAT (v2.0.4)
Differential gene expression analysis was assessed using DeSeq2
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

source_name: imLEC

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) following manufacturer's protocol. 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Set following manufacturer's protocols.

value: imLEC

value: Lymphatic endothelial cells

value: Co-culture


title: LEC sorted replicate2


title: MCF7 BIRC2 sg4 rep2

value: adenocarcinoma cells

value: BIRC2 KO


title: DNA from liver from YoungHet3

value: liver


title: DPSC-si-control_1

description:
KY453e
condenseGenes_raw-Genes_20220204_siMXRA5_1_diffOutput_GEOupload.xlsx
condenseGenes_raw-Genes_20220204_siMXRA5_2_diffOutput_GEOupload.xlsx

value: control


title: M8220 Kidney Cortex Biopsy POD61

value: biopsy kidney cortex

value: POD 61

value: 3KO, PL15S


title: M6320 Kidney Cortex Necropsy POD45

source_name: kidney cortex, necropsy

value: necropsy kidney cortex

value: POD 45

value: Xenotransplanted


title: M2519 Kidney Cortex Biopsy POD394

value: POD 394


title: LEC sorted replicate1


title: DNA from liver from YoungHet1

value: Young heterochronic parabiosis


title: M8220 Kidney Cortex Necropsy POD103

value: POD 103


title: LEC replicate2

value: Single culture


title: DNA from liver from YoungIsoRec6

value: C57BL/6 WT

value: Young isochronic recovery


title: LEC replicate1

value: imLEC

value: Lymphatic endothelial cells


title: M7920 Kidney Cortex Biopsy POD55

value: POD 55


title: DNA from liver from YoungIsoRec5

value: liver


title: HaCa4 sorted replicate3

value: Skin squamous carcinoma cell line

value: Co-culture


title: M8320 Kidney Cortex Biopsy POD61

value: biopsy kidney cortex

value: POD 61


title: DNA from liver from YoungIsoRec4


title: DNA from liver from YoungIsoRec3


title: M6521 Kidney Cortex Biopsy POD57

value: POD 57

value: 3KO, PL15S, RI


title: DPSC-si-control_2

description:
KY453f
condenseGenes_raw-Genes_20220204_siMXRA5_1_diffOutput_GEOupload.xlsx
condenseGenes_raw-Genes_20220204_siMXRA5_2_diffOutput_GEOupload.xlsx

value: dental pulp

value: dental pulp stem cells

value: control

value: siRNA transfection


title: HaCa4 sorted replicate1


title: M7920 Kidney Cortex Necropsy POD64

value: necropsy kidney cortex

value: POD 64

value: 3KO, PL15S

value: Xenotransplanted


title: DNA from liver from YoungIsoRec2

value: C57BL/6 WT

value: Young isochronic recovery


title: HaCa4 replicate1

value: Single culture


title: M6121 Kidney Cortex Biopsy POD61


title: DNA from liver from YoungIsoRec1

value: liver


title: DNA from liver from YoungHet2

value: Young heterochronic parabiosis


title: LEC replicate3

value: imLEC

value: Lymphatic endothelial cells


title: M2420 Kidney Cortex Biopsy POD170

value: biopsy kidney cortex

value: POD 170


title: DNA from liver from YoungIso5

value: Young isochronic parabiosis


title: HaCa4 sorted replicate2

value: Skin squamous carcinoma cell line

value: Co-culture


title: M8320 Kidney Cortex Biopsy POD193

value: POD 193


title: DNA from liver from YoungIso3


title: M6320 Kidney Cortex Biopsy POD40

value: POD 40


title: hematopoietic stem and progenitor cells, young diet restricted mice, scATACseq

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

description: multiome nulcear RNA and nuclear ATAC

library_source: genomic single cell

data_processing:
base calling: cellranger-arc mkfastq (cellranger-arc-2.0.0; bcl2FastQ v2.20.0.422)
Assembly: mm10
Supplementary files format and content: Folders containing the raw gene by cell gene expression matrix
Supplementary files format and content: Folders containing the filtered gene by cell gene expression matrix
Supplementary files format and content: Tab-separated files containing fragment information
Supplementary files format and content: Index of the tab-separated files

source_name: bone marrow

growth_protocol: female mice were kept in groups of 3-5 littermates, in 12:12 hour light:dark cycle in 20-24°C and 40-60% air humidity, had adlibitum access to gamma-irradiated chow and autoclaved, unacidified drinking water until ~6 months old (young mice) or ~25 months old (old mice)

extract_protocol:
We were able to isolated 50,000 hematopoietic stem and multipotent progenitor cells from each mouse using antibody staining and FACS. Cell suspensions from two mice were pooled for nuclei isolation. Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing was performed according to protocol (PROTOCOL VERSION, lysis time 3 minutes).
Nuclei suspensions were loaded into separate channels of the Chromium Controller (10x Genomics) and processed with Single Cell Multiome ATAC + Gene Expression (v1 chemistry) following the manufacturer's protocol (Document Number CG000338 Rev E).     ATAC libraries: 7 cycles in sample index PCR reaction and evaluated using D5000 ScreenTape (Agilent 4200 TapeStation System) and DNA 7500 (Agilent 2100 Bioanalyzer).   Gene Expression libraries: cDNA was amplified in 7 cycles, total cDNA was assessed on high sensitivity DNA assay (Agilent 2100 Bioanalyzer), another 6 cycles of sample index PCR were performed and final libraries were evaluated using D5000 ScreenTape (Agilent 4200 TapeStation System).     Each type of library was pooled and sequenced using Illumina NovaSeq 6000 platform and two SP Reagent Kits v1.5 (100 cycles). scATAC-seq: Read 1 and Read 2 53 bp for DNA Insert, i7 8 bp for sample index and i5 24 bp for 10x Barcode and Spacer. scRNA-seq: Read 1 28 bp for 10x Barcode and UMI; Read 2 90 bp for Insert, i7 and i5 10 bp for sample index.

treatment_protocol: mice were single caged, their food consumptionw as measured over the course of a week after which the dietary restricted mice were fed once a day shortly before lights out with a food allotment corresponding to 70% of their normal food intake by weight.

value: bone marrow

value: hematopoietic stem and progenitor cells (LSK)

tag: strain

tag: diet

value: diet restricted

tag: age

value: young (6.5-6.7 months)


title: M2519 Kidney Cortex Biopsy POD49

value: POD 49

value: 3KO, PL15S

value: Xenotransplanted


title: hematopoietic stem and progenitor cells, old mice fed ad libitum , scATACseq

description: multiome nulcear RNA and nuclear ATAC

value: ad libitum

value: old (25-26.7 months)


title: M2420 Kidney Cortex Biopsy POD50

value: POD 50


title: hematopoietic stem and progenitor cells, young mice fed ad libitum , scATACseq

description: multiome nulcear RNA and nuclear ATAC


title: hematopoietic stem and progenitor cells, young diet restricted mice, scRNAseq

description: multiome nulcear RNA and nuclear ATAC


title: DNA from liver from YoungIso1

value: C57BL/6 WT

value: liver


title: M6121 Kidney Cortex Contralateral POD0

source_name: kidney cortex, contralateral

value: contralateral kidney cortex

value: POD 0

value: 3KO, PL15S, RI

value: Untransplanted


title: DNA from liver from YoungIso2

value: Young isochronic parabiosis


title: DNA from liver from YoungIso6


title: HaCa4 replicate2

value: Skin squamous carcinoma cell line

value: Single culture


title: hematopoietic stem and progenitor cells, old diet restricted mice , scATACseq

description: multiome nulcear RNA and nuclear ATAC

value: bone marrow

value: hematopoietic stem and progenitor cells (LSK)

value: diet restricted


title: M6521 Kidney Cortex Contralateral POD0


title: KO-F-Infection+Protein-4-X16

city: hershey

first: Nithyananda

last: Thorenoor

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

data_processing:
De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).  The differentially expressed miRNAs (DEG) between FA to O3, males and females were identified by using the edgeR (Robinson et al., 2010) and the TCC v1.14.0 R package (Sun et al., 2013) with false discovery rate (FDR) adjusted p value of 0.1 as a significance cutoff.
miRNAs with good correlation between mice (3 out of 4).  We used two different parameters (methods) to analyze the identified miRNA expression (fold change).  a) The expression levels (fold change) of miRNAs from KO (infection vs infection + Protien for males and females)were analyzed and differentially expressed miRNAs in KO males and females were identified in response to infection and exogenous protein.
Supplementary_files_format_and_content: Matrix- excel sheet

source_name: Femaale mouse exposed to bacteria +SP-A2 (1A0) protein and Aleveolar Macrophage (AM) cells isolated after 6 h

extract_protocol:
AM cells were isoalated from Broncho alveolar lavage, Total RNA extracted
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: The animals were exposed to infection and/or exogenou SP-A2(1A0) protein in parallel.   A group of 4 animals/sex/condition (infection, infection+protein), and alveolar macrophages (AM) were isolated after 6h of recovery

tag: exposure time

value: 6 hours

tag: Sex

value: Female


title: DNA from liver from YoungIso4


title: hematopoietic stem and progenitor cells, young mice fed ad libitum , scRNAseq

description: multiome nulcear RNA and nuclear ATAC

value: ad libitum

value: young (6.5-6.7 months)


title: KO-F-Infection+Protein-3-X15


title: M8220 Kidney Cortex Contralateral POD0

value: 3KO, PL15S


title: hematopoietic stem and progenitor cells, old diet restricted mice , scRNAseq

description: multiome nulcear RNA and nuclear ATAC

value: old (25-26.7 months)


title: hematopoietic stem and progenitor cells, old mice fed ad libitum , scRNAseq

description: multiome nulcear RNA and nuclear ATAC


title: liver, VP, rep3

city: Bethesda

first: Margaret

last: Cam

state: MD

address: 9000 Rockville Pike

institute: NCI

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v6.1.2 (Bcl2fastq 2.20.0)
Alignment was performed using cellranger v6.1.2 (STAR 2.7.2a)
Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: hs

extract_protocol:
mouse Tumor Dissociation Kit from Miltenyi Biotec (#130-093-237)
10x Genomics scRNA-Seq 3' v3.1: (12) captures and sequencing
3’ gene expression profiling

value: liver

value: tumor cells

value: verteporfin


title: KO-F-Infection+Protein-1-X13


title: liver, VP, rep2


title: KO-M-Infection+Protein-4-X12

source_name: Male mouse exposed to bacteria +SP-A2 (1A0) protein and Aleveolar Macrophage (AM) cells isolated after 6 h

value: Male


title: M7920 Kidney Cortex Contralateral POD0

value: contralateral kidney cortex

value: POD 0

value: Untransplanted


title: M6320 Kidney Cortex Contralateral POD0


title: M8320 Kidney Cortex Contralateral POD0


title: liver, VP, rep1


title: KO-M-Infection+Protein-3-X11


title: Genomic DNA from Buffy coat from Subject 22 at time point 4

type: genomic

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Raw idat methylation files were processed using the minfi R package (Aryee et al., 2014). Data were first preprocessed using noob normalization and then beta values were calculated using the getBeta function. Detection p values were calculated using the detectionP function with type = m+u.

label: Cy3, Cy5

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from human buffy coat samples at the Crimson Core facility (Mass General Brigham) using the QIAamp DNA Blood Mini Kit (Qiagen 51104) following the manufacturer’s protocol. Eluted DNA was concentrated using a speedvac.

tag: subject id

tag: time point

value: male

tag: duration of hospitalization (days)

tag: duration of intensive care (days)

tag: hydroxychloroquine treatment

tag: remdesivir treatment

tag: toclizumab treatment


title: M6120 Kidney Cortex Contralateral POD0

tag: time


title: KO-F-Infection+Protein-2-X14


title: M2420 Kidney Cortex Contralateral POD0

tag: genotype


title: KO-M-Infection+Protein-2-X10


title: liver, veh, rep3

tag: cell type

tag: treatment

value: vehicle


title: liver, veh, rep2

tag: tissue


title: M2519 Kidney Cortex Contralateral POD0

tag: cynomolgus macaque_id


title: KO-M-Infection+Protein-1-X9

tag: strain


title: liver, veh, rep1


title: Genomic DNA from Buffy coat from Subject 24 at time point 4

tag: age

value: female


title: Genomic DNA from Buffy coat from Subject 20 at time point 4


title: KO-F-Infection-4-X8

source_name: Female mouse exposed to bacteria and Aleveolar Macrophage (AM) cells isolated after 6 h

tag: exposure time


title: Lung, Dp16 + baricitinib; sample 4

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per-gene strand-specific fragment counts.
Supplementary files format and content: Tab-delimited text files containing per gene normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: lung

extract_protocol:
Total RNA was isolated using the AllPrep Kit (QIAGEN) per manufacturer instructions.
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: Mice 7-11 weeks old were treated with 10 mg/kg of baricitinib (or an equivalent volume of 0.5% methylcellulose vehicle) once a day via oral gavage for 17 days. Sham indicates a daily saline injection for comparison to animals treated with polyI:C (see PMID 33207208). Mice were euthanized by CO2 asphyxiation and cervical dislocation then immediately perfused with 1x PBS using a Perfusion Two Automated Perfusion Instrument (Leica).

value: lung

tag: Sex

value: 51 days post birth

value: Sham+baricitinib (10mg/kg)


title: Genomic DNA from Buffy coat from Subject 25 at time point 4

tag: subject id


title: Genomic DNA from Buffy coat from Subject 28 at time point 4

tag: time point


title: Genomic DNA from Buffy coat from Subject 27 at time point 4

tag: duration of hospitalization (days)


title: Lung, Dp16 + baricitinib; sample 3

value: 54 days post birth


title: KO-F-Infection-3-X7

value: 6 hours

value: Female


title: M2220 Kidney Cortex Necropsy POD8

value: necropsy kidney cortex

value: POD 8

value: 3KO, PL15S

value: Xenotransplanted


title: M10619 Kidney Cortex Contralateral POD0


title: Genomic DNA from Buffy coat from Subject 26 at time point 4

tag: duration of intensive care (days)


title: M10619 Kidney Cortex Biopsy POD9

value: biopsy kidney cortex

value: POD 9


title: Genomic DNA from Buffy coat from Subject 7 at time point 4

tag: hydroxychloroquine treatment


title: Genomic DNA from Buffy coat from Subject 23 at time point 4

tag: remdesivir treatment


title: Lung, Dp16 + baricitinib; sample 1

value: Male

value: 78 days post birth


title: Genomic DNA from Buffy coat from Subject 21 at time point 4

tag: toclizumab treatment


title: Genomic DNA from Buffy coat from Subject 15 at time point 4


title: KO-M-Infection-4-X4

source_name: Male mouse exposed to bacteria and Aleveolar Macrophage (AM) cells isolated after 6 h


title: Lung, Dp16 + vehicle; sample 4

value: 60 days post birth

value: Sham+Vehicle


title: KO-F-Infection-2-X6


title: Genomic DNA from Buffy coat from Subject 18 at time point 4

value: male


title: KO-F-Infection-1-X5


title: KO-M-Infection-3-X3


title: Lung, Dp16 + vehicle; sample 3

value: lung


title: Lung, Dp16 + vehicle; sample 2

value: 58 days post birth


title: KO-M-Infection-1-X1


title: Genomic DNA from Buffy coat from Subject 5 at time point 4


title: Genomic DNA from Buffy coat from Subject 13 at time point 4


title: Genomic DNA from Buffy coat from Subject 16 at time point 4

value: female


title: KO-M-Infection-2-X2


title: Genomic DNA from Buffy coat from Subject 14 at time point 4


title: Genomic DNA from Buffy coat from Subject 17 at time point 4


title: Genomic DNA from Buffy coat from Subject 6 at time point 4


title: Lung, Wild-type + baricitinib; sample 2

value: wild-type

value: 51 days post birth

value: Sham+baricitinib (10mg/kg)


title: Genomic DNA from Buffy coat from Subject 8 at time point 4


title: Lung, Dp16 + vehicle; sample 1


title: Antagomir_Neuronal_mir_21_Rep_2

type: RNA

city: London

first: David

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

country: United Kingdom

institute: King's College London

description: Nugen WTA Pico System V2 Kit

hyb_protocol: Following fragmentation (Encore Biotin Kit), cDNAs were hybridized for 18 hr at 45C on GeneChip Mouse 430 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 430 according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 7G scanner according to the manufacturer's instructions.

data_processing: The data were analyzed with Transcript Analysis Console (TACX) using Affymetrix default MAS% analysis settings

label: Biotin

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Encore Biotin kit according to the manufacturer's instructions.

growth_protocol: microarray analysis on peritoneal macrophages transfected with scramble control or antagomir-21, exposed to exosomes from sensory neurons overexpressing miR-21 or GFP-reporter

extract_protocol: Extraction of total RNA was performed using Agilent Absolutely RNA Microprep kit according to the manufacturer's instructions.

value: peritoneal macrophage

tag: treatment goup


title: Genomic DNA from Buffy coat from Subject 4 at time point 4


title: Genomic DNA from Buffy coat from Subject 12 at time point 4


title: Lung, Dp16 + baricitinib; sample 2

tag: genotype

value: Female

value: 67 days post birth


title: Lung, Wild-type + vehicle; sample 2


title: Lung, Wild-type + baricitinib; sample 1


title: M2220 Kidney Cortex Contralateral POD0

value: contralateral kidney cortex

tag: time

value: POD 0

value: 3KO, PL15S

value: Untransplanted


title: Lung, Wild-type + vehicle; sample 1

value: Male

tag: treatment


title: Genomic DNA from Buffy coat from Subject 2 at time point 4


title: Genomic DNA from Buffy coat from Subject 3 at time point 4


title: Lipofectamin_Neuronal_mir_21_Rep_2

description: Nugen WTA Pico System V2 Kit

treatment_protocol: microarray analysis on peritoneal macrophages transfected with scramble control or antagomir-21, exposed to exosomes from sensory neurons overexpressing miR-21 or GFP-reporter

tag: cell type


title: Scrambled_GFP_reporter_Rep_2

description: Nugen WTA Pico System V2 Kit

source_name: peritoneal macrophages transfected with scramble control or antagomir-21, exposed to exosomes from sensory neurons overexpressing miR-21 or GFP-reporter


title: Antagomir21_GFP_reporter_Rep_2

description: Nugen WTA Pico System V2 Kit


title: Genomic DNA from Buffy coat from Subject 11 at time point 4


title: Scrambled_Neuronal_mir_21_Rep_2

description: Nugen WTA Pico System V2 Kit


title: Antagomir21_GFP_reporter_Rep_1

description: Nugen WTA Pico System V2 Kit


title: Antagomir_Neuronal_mir_21_Rep_1

description: Nugen WTA Pico System V2 Kit


title: Genomic DNA from Buffy coat from Subject 10 at time point 4


title: Scrambled_GFP_reporter_Rep_1

description: Nugen WTA Pico System V2 Kit


title: Scrambled_Neuronal_mir_21_Rep_1

description: Nugen WTA Pico System V2 Kit


title: Lipofectamin_Neuronal_mir_21_Rep_1

description: Nugen WTA Pico System V2 Kit


title: Genomic DNA from Buffy coat from Subject 9 at time point 4


title: Lipofectamin_GFP_reporter_Rep_1

description: Nugen WTA Pico System V2 Kit


title: Lipofectamin_GFP_reporter_Rep_2

description: Nugen WTA Pico System V2 Kit


title: KD2_mESCs_serum_Rep3

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Quantification using RSEM
Assembly: mm9
Supplementary files format and content: RSEM quantification files

source_name: mESCs

growth_protocol: mESCs were routinely grown on gelatin-coated plates on MEFs in serum-based medium: DMEM (Gibco) containing 15% ES-grade fetal calf serum (Biological Industries), 1X Sodium pyruvate (Gibco), 1X Nonessential amino acids (Gibco), 0.1mM β-mercaptoethanol (Sigma), 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries), and 10ng/ml LIF (Weizmann Proteomics Unit). Cells were passaged with 0.25% Trypsin (Biological Industries) every 2–3 days.

extract_protocol:
Total RNA was extracted from cells using the Trizol reagent (TRI, Sigma-Aldrich) according to the manufacturer’s instructions.
Lexogen SENSE mRNA-Seq

tag: cell line

tag: genotype/perturbation

value: CRISPR/dCas9 KD of Meteor


title: Genomic DNA from Buffy coat from Subject 1 at time point 4

tag: age


title: Genomic DNA from Buffy coat from Subject 21 at time point 3


title: Genomic DNA from Buffy coat from Subject 20 at time point 3


title: KD1_mESCs_serum_Rep3


title: Genomic DNA from Buffy coat from Subject 23 at time point 3


title: Ctrl_mESCs_serum_Rep3

value: empty vector


title: Genomic DNA from Buffy coat from Subject 24 at time point 3


title: RNAseq_siZFC3H1_1_A375

data_processing:
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013).
Using splice junctions and the mapped 3' cleavage and adenylation sites from the 3'seq data, custom transcriptomic annotations were produced with our custom alpha3pseq pipeline software.  This produced a gtf file with intronic and alternative polyadenylation sites.
The annotation from alpha3pseq was used to count mapped reads above using the DEXseq/Htseq counting scripts. This produced the read counts tables in this dataset.
Assembly: GRCh38
Supplementary files format and content: Count tables

source_name: melanoma cell line

growth_protocol: A375 human melanoma cells were identity-verified via STR analysis. Mycoplasma testing was done within one week of every experiment using human cell lines (Lonza, Mycoalert PLUS, LT07-710). All cell lines were mycoplasma negative. Cells were grown in DMEM supplemented with 10% FBS, penicillin/streptomycin or selection antibiotics, and L-glutamine.

extract_protocol:
DNA was removed, and RNA was isolated (Qiagen, 741134). Poly-A selection was undertaken (NEB, E7490).
NEBNext® Ultra™ Directional RNA Library Prep Kit

treatment_protocol: Stable lines were untreated. Knockdown of ZFC3H1 (Dharmacon, L-020839-02-0005), ZC3H14 (Dharmacon, L-014468-01-0005), or a control knockdown (Dharmacon, D-001810-01-05) were completed on A375 CLOVER cells

tag: tissue

value: melanoma cell line


title: Hg38_A375_ZC3H14-S475A_CDK13R860Q_rep1

value: CLOVER ZC3H14-S475A_CDK13R860Q


title: Hg38_A375_CDK13R860Q_rep2

value: CLOVER_CDK13R860Q control


title: RNAseq_siZFC3H1_3_A375


title: Hg38_A375_CDK13R860Q_rep1


title: Hg38_A375_ZC3H14-S475A_CDK13R860Q_rep3


title: Hg38_A375_CDK13R860Q_rep3


title: Hg38_A375_ZC3H14-S475A_CDK13R860Q_rep2


title: KD2_mESCs_serum_Rep2


title: KD1_mESCs_serum_Rep2


title: RNAseq_siZFC3H1_2_A375


title: Genomic DNA from Buffy coat from Subject 22 at time point 3

tag: Sex

value: male


title: KD2_mESCs_serum_Rep1


title: RNAseq_siZC3H14_3_A375


title: KD1_mESCs_serum_Rep1


title: RNAseq_siZC3H14_1_A375


title: Genomic DNA from Buffy coat from Subject 25 at time point 3

tag: subject id


title: Genomic DNA from Buffy coat from Subject 28 at time point 3

tag: time point

value: female


title: Genomic DNA from Buffy coat from Subject 18 at time point 3

tag: duration of hospitalization (days)


title: Genomic DNA from Buffy coat from Subject 8 at time point 3

tag: duration of intensive care (days)


title: RNAseq_siCtrl_3_A375

value: siControl


title: Ctrl_mESCs_serum_Rep1


title: RNAseq_siCtrl_2_A375


title: Genomic DNA from Buffy coat from Subject 15 at time point 3

tag: hydroxychloroquine treatment


title: Genomic DNA from Buffy coat from Subject 17 at time point 3

tag: remdesivir treatment


title: Genomic DNA from Buffy coat from Subject 26 at time point 3

tag: toclizumab treatment


title: Ctrl_mESCs_serum_Rep2


title: RNAseq_siCtrl_1_A375


title: pInv_NPCs_Rep3

source_name: NPCs

growth_protocol: Neuronal differentiation was performed as previously described (Ying and Smith, 2003). Briefly, mESCs were grown for two passages in serum-based medium on MEF-free, gelatin-coated plates. Cells were then seeded on gelatin-coated plates (2x105 cells/6-well) in neuronal differentiation medium: 1:1 mixture of DMEM/F12 (Sigma) and Neurobasal medium (Gibco), supplemented with 0.5X B27 (Gibco), 0.5X N2 (Gibco), 1X Glutamax (Gibco), 0.1mM β-mercaptoethanol (Sigma), 25μg/ml BSA, and 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries). NPCs were collected after four days.

value: Meteor promoter inversion


title: Genomic DNA from Buffy coat from Subject 5 at time point 3


title: pKO1_NPCs_Rep3

value: Meteor promoter KO


title: CLOVER_ZC3H14_S475A_A375_RNAseq_2

value: CLOVER ZC3H14_S475A


title: Genomic DNA from Buffy coat from Subject 27 at time point 3


title: WT2_NPCs_Rep3

value: WT


title: CLOVER_ZC3H14_S475A_A375_RNAseq_1


title: CLOVER_ZC3H14_S475E_A375_RNAseq_3

value: CLOVER ZC3H14_S475E


title: WT1_NPCs_Rep3


title: Genomic DNA from Buffy coat from Subject 6 at time point 3


title: CLOVER_ZC3H14_S475E_A375_RNAseq_2


title: Genomic DNA from Buffy coat from Subject 29 at time point 3


title: pInv_NPCs_Rep2


title: Genomic DNA from Buffy coat from Subject 7 at time point 3


title: pKO2_NPCs_Rep2


title: Genomic DNA from Buffy coat from Subject 19 at time point 3


title: Genomic DNA from Buffy coat from Subject 13 at time point 3


title: pKO2_NPCs_Rep3


title: CLOVER_A375_RNAseq_3

value: CLOVER control


title: pKO1_NPCs_Rep2


title: Genomic DNA from Buffy coat from Subject 12 at time point 3


title: RNAseq_siZC3H14_2_A375


title: CLOVER_A375_RNAseq_2


title: CLOVER_ZC3H14_S475E_A375_RNAseq_1


title: WT2_NPCs_Rep2


title: CLOVER_A375_RNAseq_1


title: WT1_NPCs_Rep2


title: Genomic DNA from Buffy coat from Subject 16 at time point 3


title: siZFC3H1_3_A375_S9

description:
RNA 3' end sequencing
siZFC3H1

data_processing:
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013)
Custom Python script to filter reads from each bam file based on the following parameters: 1) Proper mate pairing; 2) orientation of the putative 3’ cleavage end corresponding to the direction of transcription for the gene to which reads mapped; 3) concordant mapping to known chromosomes; 4) no soft clippings; 5) skipped regions must be longer than 70 nucleotides.
Bedtools cluster tool version 2.26.0 (Quinlan and Hall, 2010) and custom Python scripts were used to generate read clusters by grouping any 3’ end coordinates that fell within 40 nucleotides of one another into a single cluster.
Clusters present in >1 replicate were considered to be true termination sites (high confidence termination sites). High confidence termination site reads were reclusters to define a complete and non-redundant 3' cleavage map for all conditions.
3' cleavage site reads were quantified using DEX-seq (Anders et al, 2012).
Assembly: GRCh38
Supplementary files format and content: Read count tables for each replicate at each identified cleavage site

source_name: A375 melanoma cell line

extract_protocol:
DNA was removed, and RNA was isolated (Qiagen, 741134). Poly-A selection was undertaken (NEB, E7490).
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina, 016.24

value: A375 melanoma cell line

value: siZFC3H1 treated


title: pInv_NPCs_Rep1


title: Genomic DNA from Buffy coat from Subject 4 at time point 3


title: Genomic DNA from Buffy coat from Subject 14 at time point 3


title: Genomic DNA from Buffy coat from Subject 3 at time point 3


title: pKO2_NPCs_Rep1


title: siZFC3H1_1_A375_S7

description:
RNA 3' end sequencing
siZFC3H1


title: siZC3H14_3_A375_S6

description:
RNA 3' end sequencing
siZC3H14

value: siZC3H114 treated


title: WT2_NPCs_Rep1


title: pKO1_NPCs_Rep1


title: siZC3H14_2_A375_S5

description:
RNA 3' end sequencing
siZC3H14


title: Genomic DNA from Buffy coat from Subject 11 at time point 3


title: siZFC3H1_2_A375_S8

description:
RNA 3' end sequencing
siZFC3H1


title: WT1_NPCs_Rep1


title: siZC3H14_1_A375_S4

description:
RNA 3' end sequencing
siZC3H14


title: pInv_mESCs_serum_Rep3


title: Genomic DNA from Buffy coat from Subject 2 at time point 3


title: siCtrl_3_A375_S3

description:
RNA 3' end sequencing
siControl

value: Control siRNA treated


title: pKO2_mESCs_serum_Rep3


title: Genomic DNA from Buffy coat from Subject 10 at time point 3


title: siCtrl_1_A375_S1

description:
RNA 3' end sequencing
siControl


title: pKO1_mESCs_serum_Rep3


title: Genomic DNA from Buffy coat from Subject 1 at time point 3


title: siCtrl_2_A375_S2

description:
RNA 3' end sequencing
siControl


title: WT2_mESCs_serum_Rep3


title: Genomic DNA from Buffy coat from Subject 23 at time point 2


title: pLENTI_CMV_blast_CDK13_R860Q_into_A375s_Rep2

description:
RNA 3' end sequencing
CMV CLOVER CDK13

value: CMV CLOVER CDK13


title: pLENTI_CMV_blast_CDK13_R860Q_into_A375s_Rep1

description:
RNA 3' end sequencing
CMV CLOVER CDK13


title: Genomic DNA from Buffy coat from Subject 21 at time point 2


title: pInv_mESCs_serum_Rep2


title: Genomic DNA from Buffy coat from Subject 9 at time point 3


title: Genomic DNA from Buffy coat from Subject 27 at time point 2


title: pLENTI_CMV_blast_CLOVER_into_A375s_Rep1

description:
RNA 3' end sequencing
CMV CLOVER empty

value: CMV CLOVER empty control


title: A375_CMVCDK13_SE_Ser2PolII

data_processing:
Raw reads were aligned twice: first to the dm6 revision of the D. melanogaster genome to remove exogenous spike-in reads using bowtie version 1.2.2 with parameters -k 1 -m 1; unmapped reads were then aligned to the hg19 revision of the human genome.
hg19
Supplementary_files_format_and_content: bigWig files were created from the alignment bam file using the R with the GenomicAlignments package and with gr.cov and export.bw from rtracklayer

growth_protocol: For ChIP-seq from human melanoma cells, one replicate (line 1) of A375 human melanoma cells expressing pLENTI-CMV CLOVER or pLENTI-CMV CDK13 R860Q as derived above in “Stable Human Cell Lines” from methods were used.  Cells were grown in DMEM with 10% FBS with glutamine/penicillin/streptomycin.  Equal cell number (approximately 40x106) were fixed and used for each IP.

extract_protocol:
Libraries were performed using the NEBNextMultiplex Oligos for Illumina kit (NEB) according to instructions.  Samples were sequenced with 100bp reads, either single or paired end depending on the experiment.
Nuclear cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200-400 bp were immunoprecipitated using different antibodies.

value: melanoma cell line

tag: chip antibody

value: Phospho Ser2-RNA PolII

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: antibody lot

tag: cdk13 status

value: overexpress CDK13 R860Q


title: WT2_mESCs_serum_Rep2

tag: cell line


title: pKO1_mESCs_serum_Rep2

tag: genotype/perturbation


title: pKO2_mESCs_serum_Rep2


title: WT1_mESCs_serum_Rep3


title: A375_CMVCDK13_SE_PolII

value: RNA Pol II


title: Genomic DNA from Buffy coat from Subject 20 at time point 2

tag: age

value: male


title: Genomic DNA from Buffy coat from Subject 24 at time point 2

value: female


title: WT1_mESCs_serum_Rep2


title: Genomic DNA from Buffy coat from Subject 26 at time point 2


title: Genomic DNA from Buffy coat from Subject 25 at time point 2


title: pInv_mESCs_serum_Rep1

value: Meteor promoter inversion


title: Genomic DNA from Buffy coat from Subject 28 at time point 2


title: A375_CMV_SE_Ser2PolII

tag: tissue

value: control (overexpress CLOVER)


title: A375_CMV_SE_PolII


title: Genomic DNA from Buffy coat from Subject 29 at time point 2

tag: Sex


title: A375_CMV_SE_input

extract_protocol:
Nuclear cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200-400 bp were immunoprecipitated using different antibodies.
Libraries were performed using the NEBNextMultiplex Oligos for Illumina kit (NEB) according to instructions.  Samples were sequenced with 100bp reads, either single or paired end depending on the experiment.


title: A375_CMVCDK13_SE_input


title: Genomic DNA from Buffy coat from Subject 7 at time point 2

tag: subject id


title: Genomic DNA from Buffy coat from Subject 15 at time point 2

tag: time point


title: WT1_mESCs_serum_Rep1

value: WT


title: Genomic DNA from Buffy coat from Subject 17 at time point 2

tag: duration of hospitalization (days)


title: pKO1_mESCs_serum_Rep1

value: Meteor promoter KO


title: RPM_SS_sgTMED2

last: Sherwood

institute: Brigham & Women's Hospital

data_processing:
RNA-seq reads were mapped using the Quantseq 3' mRNA mapping pipeline as described by Lexogen to GRCh38.p12. Briefly, reads were first trimmed using bbduk from the bbmap suite (v38.79)108 trimming for low quality tails, poly-A read-through and adapter contamination using the recommended parameters. Then, reads were mapped using the STAR aligner (v2.5.2b)109 with the recommended modified-Encode settings. Finally, HT-seq (v0.9.1) count was used to obtain per-gene counts110.
Within each cell line, we conducted differential expression analysis using DESeq2 1.26.0 to identify significantly differentially expressed genes for each gene KO with respect to the control condition.
Assembly: GRCh38.p12
Supplementary files format and content: Hepg2_rnaseq_RPM.csv: matrix table containing RPMs for all samples

growth_protocol: All cell lines were obtained from ATCC and were cultured in DMEM + 10% FBS

extract_protocol:
RNA was harvested from cells using the Qiagen RNEasy Plus mini kit or the Zymo Quick-RNA 96 kit
RNA libraries for RNA-seq were prepared for RNA-seq using the Lexogen QuantSeq-Pool kit, and sequenced using Illumina Nextseq at >1*10^6 reads/sample.

treatment_protocol: HepG2 Cas9NG-P2A-mChe KO cell lines were seeded at a density of 2.1x10^5 cells/cm2 on a 24 well plate with two biological replicates per serum condition and incubated overnight. The next day, the media was replaced with either DMEM + 10% FBS (serum condition) or optiMEM (serum-starved condition) and cells were incubated overnight.

tag: cell type

value: human hepatoma

tag: genotype

tag: treatment

value: SS

tag: time

value: Day 2


title: RPM_SS_sgYTHDC1


title: Genomic DNA from Buffy coat from Subject 18 at time point 2

tag: duration of intensive care (days)

tag: hydroxychloroquine treatment

tag: remdesivir treatment

tag: toclizumab treatment


title: Genomic DNA from Buffy coat from Subject 5 at time point 2


title: pKO2_mESCs_serum_Rep1


title: MusMS1

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

description: 10x Genomics

data_processing:
10X Cell Ranger pipeline (version 3.0.2) was used to demultiplex and align sequencing reads
Assembly: A custom “pre-mRNA” reference genome created from mouse reference genome RGCm38.98
Supplementary files format and content: H5 file; feature-barcode matrices

source_name: Superficial superior colliculus

extract_protocol:
Brains were harvested after rapid decapitation to avoid stress- or anesthesia-related changes in gene expression, cooled in ice-cold Hibernate-A for 2min, placed into a chilled stainless steel brain matrix and then sectioned coronally into 1mm thick slices containing the sSC (Bregma -3.0 mm to -5.0 mm). The sSC was then visualized under a dissecting microscope, micro-dissected approximately by knife cuts. Next, we homogenized the sSC in lysis buffer and separated nuclei from cellular debris using density gradient centrifugation. After resuspending the nuclei pellet, the concentration of nuclei was counted with propidium iodide by a CellDrop automated cell counter (DeNovix, Delaware, U.S.A.).
We used 10X Chromium Next GEM 3’ reagent kit v3.1 according to the manufacturer’s protocol (user guide revision D) to capture each nucleus’s poly-adenylated RNA in a droplet, process it into cDNA sequencing libraries, and sequenced them by Illumina Next-Seq 550 or Nova-Seq 6000 to an average of 35,998 mean reads per cell.
10X Chromium Next GEM 3’ reagent kit v3.1

value: Superficial superior colliculus

value: Male

value: Neural cells

value: Chat-GFP

value: 2-4 months


title: pLENTI_CMV_blast_CLOVER_into_A375s_Rep2

description:
RNA 3' end sequencing
CMV CLOVER empty

value: A375 melanoma cell line

value: CMV CLOVER empty control


title: RPM_SS_sgSOD1


title: RPM_SS_sgTEN1


title: Genomic DNA from Buffy coat from Subject 22 at time point 2


title: MusMS2

description: 10x Genomics


title: Genomic DNA from Buffy coat from Subject 16 at time point 2


title: Genomic DNA from Buffy coat from Subject 13 at time point 2


title: MusFS1

description: 10x Genomics

value: Female

value: Chat-Cre x H2b-TRAP


title: WT2_mESCs_serum_Rep1


title: RPM_SS_sgRBM14


title: BSHXF 2

city: Changsha

first: Kailin

last: Yang

state: Hunan

address: Xueshi Road No. 300

country: China

institute: Hunan University of Chinese Medicine

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (Mus musculus),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.

source_name: Ovary

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Ovary

tag: strain

value: Balb/c

value: POF+BSHXF


title: Genomic DNA from Buffy coat from Subject 14 at time point 2

value: male


title: RPM_SS_sgPREB

tag: cell line

value: sgPREB


title: RPM_SS_sgSLC39A3

value: human hepatoma


title: RPM_SS_sgOST4

value: SS


title: BSHXF 3


title: model 3

value: POF


title: RPM_SS_sgMYLIP

value: sgMYLIP

value: Day 2


title: model 2


title: Genomic DNA from Buffy coat from Subject 4 at time point 2

value: female


title: RPM_SS_sgMIR5089


title: BSHXF 1


title: Genomic DNA from Buffy coat from Subject 6 at time point 2


title: Genomic DNA from Buffy coat from Subject 2 at time point 2


title: empty 2

value: Blank


title: RPM_SS_sgLDLR

value: sgLDLR


title: model 1


title: RPM_SS_sgHYOU1


title: Genomic DNA from Buffy coat from Subject 8 at time point 2


title: RPM_SS_sgKLHDC3


title: empty 1


title: Genomic DNA from Buffy coat from Subject 3 at time point 2


title: Genomic DNA from Buffy coat from Subject 9 at time point 2


title: RPM_SS_sgHNF1A


title: RPM_SS_sgGBA

value: sgGBA


title: Genomic DNA from Buffy coat from Subject 10 at time point 2


title: RPM_SS_sgDEF6


title: Genomic DNA from Buffy coat from Subject 1 at time point 2


title: cortex, SOD1, 3 months

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

description:
Read1 contains cell barcode and UMI, Read2 covers the gene sequences
preprocessed_data.txt
processed_SoupX_corrected.txt
processed_SoupX_corrected_metadata.csv

data_processing:
The sequencing reads were mapped to the reference genome by STARsolo (STAR version 2.7.3a). EmptyDrops function (DropletUtils R package, 100 UMIs threshold, FDR <= 0.001) was applied to preserve only cell-containing droplets.
Seurat R package (version 4.1.1) was used for further analysis. The data were SCTransformed and integrated excluding mitochondrial and ribosomal genes prefixed by mt- or Rps/Rpl, respectively.  UMAP was used to visualize 17 principal components, which were subsequently clustered (FindNeighbors and FindClusters functions, UMAP resolution 0.5). Clusters were annotated based on the expression of the known marker genes of the expected cell populations, and their correspondence to the markers found by the FindAllMarkers function.
DoubletFinder package was used to identify droplets containing multiple cells. Clusters expressing ambiguous markers and containing a higher number of doublets were filtered out of the data set.
Sex (male, female) was assigned to individual cells based on expression of genes encoded by X (Xist) and Y chromosome and those not matching our criteria (male: counts of Xist < 1, nFeature_Y > 0; female: counts of Xist > 0, nFeature_Y < 2, nCount_Y < 2; nFeature_Y being a number of Y-encoded genes and nCount_Y being a number of transcripts mapping to Y chromosome) were excluded from the dataset.
The SoupX R package (version 1.5.2) was applied to remove contaminating RNA background. The unfiltered and annotated data were supplied as the input. The count values were subsequently corrected for the contamination and the analysis was repeated from the integration step.
Assembly: GRCm38
Supplementary files format and content: preprocessed_data.txt contains count matrix generated after the initial integration step, only EmptyDrops filtering was applied, rows represent genes and columns represent individual barcoded cells, values are not normalized
Supplementary files format and content: processed_SoupX_corrected.txt contains normalized matrix after doublet filtering, sex assignment and filtering and SoupX correction, rows represent genes and columns individual barcoded cells
Supplementary files format and content: processed_SoupX_corrected_metadata.csv table contains additional data to SoupX corrected matrix, rows represent barcoded cells and variables in columns include age, sex, cluster identity, cell type assigned during annotation, and others

source_name: cortex

extract_protocol:
The cortical tissue was isolated and dissociated following the Adult Brain dissociation protocol for mice and rats (Milteyni-Biotec, Germany), omitting the red blood cell removal. The cells were treated with actinomycin D to prevent activation of immediate early genes. After the debris removal, cells were layered on top of 5 ml of ovomucoid inhibitor solution (Worthington, NJ) and harvested by centrifugation (300×g for 6 min). Potential cell aggregates were removed by 70 μm cell strainers (Becton Dickinson, NJ). The final suspension was labeled with ACSA-2, Cd11b and O4 antibodies conjugated with allophycocyanin and phycoerythrin respectively to allow for enrichment of astrocytes, microglia and oligodendrocytes using FACS. The cells were collected into 200 μl of Advanced Dulbecco's Modified Eagle Medium, supplemented with 10% fetal bovine serum (ThermoFisher Scientific Waltham, MA). Four animals per condition (2 males and 2 females) were pooled for the preparation of cell suspension.
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics, Pleasanton, CA) was used to prepare the sequencing libraries and the protocol was performed according to the manufacturer’s instructions. Briefly, 10x Chromium platform was used to encapsulate individual cells into droplets along with beads covered in cell-specific 10x Barcodes, UMIs and poly(dT) sequences. After reverse transcription the cDNA libraries were amplified (13-14 cycles), fragmented and ligated to sequencing adaptors. SPRISelect magnetic beads were used for purification of the cDNA suspension and size selection of fragments. Concentration and quality of the libraries was measured using Qubit dsDNA HS Assay Kit (Invitrogen) and Fragment Analyzer HS NGS Fragment Kit (#DNF-474, Agilent). The libraries were pooled and sequenced in paired-end mode using Illumina NovaSeq 6000 SP Reagent Kit, Read 1 containing a barcode and a UMI and Read 2 covering the sequence of interest. Sequencing data comprised of approx. 100-200 million reads per sample.

value: cortex

value: 3 months

value: brain cells excluding neurons


title: cortex, control, 4 months

value: 4 months

value: WT


title: Genomic DNA from Buffy coat from Subject 19 at time point 1


title: RPM_SS_sgDDX28


title: RPM_SS_sgCTRL

value: sgCTRL


title: cortex, SOD1, 2 months

value: 2 months


title: Genomic DNA from Buffy coat from Subject 7 at time point 1

value: male


title: cortex, control, 2 months


title: P40_pIC_M6

city: Freiburg im Breisgau

first: Omar

last: Mossad

address: Breisacher str 64

department: Institute of Neuropathology

country: Germany

institute: University Hospital Freiburg

data_processing:
CASAVA1.8.2 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using STAR
read counts were extracted using featurecounts
differential gene expression analysis was performed using Deseq2 v.2.11.40.6
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: microglia

extract_protocol:
Mice were anesthetized and transcardially perfused with ice cold PBS. Brain hemispheres were homogenized and subjected to 37% / 70% percoll density gradient separation. Microglia cells were collected from the pellet of 37% percoll and washed extensively with FACS buffer (0.5% FBS in PBS) followed by staining with anti-CD11b (clone M1/70, eBioscience) and anti-CD45 (clone 30-F11, eBioscience) antibodies. Isolation of immune cells and flow cytometry.
Total RNA was extracted from FACS sorted CD11b+CD45lowLin- microglia cells using The ARCTURUS® PicoPure® RNA Isolation Kit (ThermoFisher) according to manufacturer’s protocol. The SMARTer v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 to 750 pg total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). One-hundered and fifty pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposase. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 or HiSeq 2000 System User Guide. Image analysis and base calling resulted in BCL files, which were converted into FATSQ files with the CASAVA1.8.2 software. Library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany).

value: Whole brain

value: Male


title: Genomic DNA from Buffy coat from Subject 15 at time point 1


title: cortex, SOD1, 1 month

value: 1 month


title: cortex, SOD1, 4 months


title: Genomic DNA from Buffy coat from Subject 13 at time point 1


title: RPM_SS_sgATP6V1G2

value: human hepatoma

value: SS


title: Genomic DNA from Buffy coat from Subject 11 at time point 2


title: cortex, control, 1 month


title: RPM_SS_sgACAD11

value: Day 2


title: Gbi24D_biol rep 2

city: Hangzhou

first: Yue

last: SUN

state: Zhejiang

address: Yuhangtang Rd

institute: Zhejiang University

data_processing:
All libraries were subjected to paired-end 150-bp sequencing on the Illumina HiSeq 4000 platform. Illumina short paired-end reads produced previously were trimmed using Trimmomatic (v.0.36) with default parameters. The high-quality reads were aligned to the G. bickii genome using HISAT2 (v.2.0.4). The counts of reads aligned to each transcript were calculated with HTSeq (v.0.6.0) software, and fragments per kilobase of transcript per million mapped fragments were used to estimate the expression level of each gene.
Assembly: Gossypium bickii (G1) genome JZU_v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Gossypium bickii

source_name: cotyledons

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA was used for cDNA library construction with the NEBNext Ultra RNA Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). All libraries were subjected to paired-end 150-bp sequencing on the Illumina HiSeq 4000 platform.

value: cotyledons

value: 24-hours after imbibition

value: in dark


title: RPM_SER_sgTMED2

city: Boston

first: Richard

value: SER


title: Gbi24D_biol rep 1


title: RPM_SER_sgTEN1


title: Genomic DNA from Buffy coat from Subject 17 at time point 1

first: Jesse

last: Poganik

institute: Brigham and Women's Hospital, Harvard Medical School

value: female


title: cortex, control, 3 months

value: cortex

value: 3 months

value: brain cells excluding neurons


title: Genomic DNA from Buffy coat from Subject 5 at time point 1


title: Genomic DNA from Buffy coat from Subject 12 at time point 2


title: Genomic DNA from Buffy coat from Subject 8 at time point 1


title: RPM_SS_sgATP13A1


title: Genomic DNA from Buffy coat from Subject 12 at time point 1


title: RPM_SER_sgSOD1


title: genomic DNA from Blood from mouse 280625RR at time point 4

description: Pregnant

data_processing: For mammalian microarray analysis, raw methylation data were first normalized and beta values were calculated using the SeSAMe R package .

growth_protocol: This experiment was approved by the Mass General Brigham IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially (5 mice/cage) except during the pregnancy studies wherein male mice were housed individually after mating. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol: DNA was isolated from whole blood using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: C57Bl/6 mice (11 weeks old) were obtained from Jackson Laboratories. Three days before mating, male mice were separated into individual cages and soiled bedding from male cages was added to female cages to induce estrus (Whitten, 1956). 1:1 mating pairs were set up in the evening and left overnight. Females were removed from male cages the following morning and inspected for copulatory plugs. Pregnant females were identified by daily tracking of body weight. Blood was collected in EDTA tubes by submandibular vein puncture every two weeks to create a series of four samples per mouse: (1) 10 days before mating; (2) 4 days after mating; (3) 18 days after mating; and (4) 32 days after mating, generally corresponding to ~2 weeks postpartum. Pups were humanely euthanized shortly after birth allowing mothers to recover from pregnancy without needing to nurse. Blood was snap-frozen in liquid nitrogen immediately after collection and stored at –80°C until needed.

value: Pregnant

tag: mousestrain

value: Whole blood


title: RPM_SER_sgSLC39A3


title: Gbi48L_biol rep 2

value: 48-hours after imbibition

value: under light


title: Genomic DNA from Buffy coat from Subject 6 at time point 1

tag: age


title: 12M_HBs-HepR, liver_rep3

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

institute: Institute of Immunology, USTC

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using hisat v2.1.0 with parameters --threads 28 --dta -t
Read counts were computed using Rsubread using default settings
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: liver tissue

extract_protocol:
liver tissue were harvested, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HBs-HepR mice was adoptively transferred with HBsAg+ hepatocytes from HBs-Tg mice for reconstruction, and B6-HepR mice was adoptively transferred with wildtype hepatocytes from C57BL/6J mice for reconstruction.

tag: tissue

value: liver

value: HBs-HepR mice adoptively transferred with HBsAg+ hepatocytes from HBs-Tg mice


title: Gbi48L_biol rep 1


title: 12M_HBs-HepR, liver_rep2


title: 12M_HBs-HepR-T, liver_rep1

value: liver tumor tissue


title: empty 3

value: Ovary

value: Balb/c

value: Blank


title: RPM_SER_sgPREB

value: human hepatoma

value: sgPREB

value: Day 2


title: Genomic DNA from Buffy coat from Subject 4 at time point 1

tag: Sex

value: female


title: 12M_HBs-HepR, liver_rep1


title: Genomic DNA from Buffy coat from Subject 3 at time point 1

tag: subject id


title: Gbi36L_biol rep 2

value: cotyledons

value: 36-hours after imbibition


title: 12M_HBs-HepR-T, liver_rep3


title: Genomic DNA from Buffy coat from Subject 11 at time point 1

tag: time point

value: male


title: RPM_SER_sgOST4

value: SER


title: 12M_B6-HepR, liver_rep3

value: B6-HepR mice adoptively transferred with wildtype hepatocytes from C57BL/6J mice


title: Gbi36L_biol rep 1


title: Genomic DNA from Buffy coat from Subject 1 at time point 1

tag: duration of hospitalization (days)


title: genomic DNA from Blood from mouse 280623N at time point 4

description: Not pregnant

value: Not pregnant

value: Whole blood


title: RPM_SER_sgMYLIP

tag: cell type

value: sgMYLIP


title: genomic DNA from Blood from mouse 280626R at time point 4

description: Pregnant

value: Pregnant


title: 12M_B6-HepR, liver_rep2

value: liver


title: genomic DNA from Blood from mouse 280626RR at time point 4

description: Not pregnant


title: Genomic DNA from Buffy coat from Subject 9 at time point 1


title: genomic DNA from Blood from mouse 280625L at time point 4

description: Pregnant


title: Gbi48L_biol rep 3

value: 48-hours after imbibition

value: under light


title: Gbi24L_biol rep 3

value: 24-hours after imbibition


title: RPM_SER_sgMIR5089

value: human hepatoma

tag: genotype


title: Gbi24D_biol rep 3

tag: treatment

value: in dark


title: genomic DNA from Blood from mouse 280623R at time point 4

description: Pregnant


title: 12M_HBs-HepR-T, liver_rep2

value: liver tumor tissue

tag: time

value: HBs-HepR mice adoptively transferred with HBsAg+ hepatocytes from HBs-Tg mice


title: genomic DNA from Blood from mouse 280624B at time point 4

description: Pregnant

value: female


title: Gbi24L_biol rep 2

value: cotyledons


title: Gbi24L_biol rep 1


title: 6M_HBs-HepR, liver_rep5


title: RPM_SER_sgLDLR

value: sgLDLR

value: Day 2


title: Gbi12L_biol rep 3

value: 12-hours after imbibition


title: genomic DNA from Blood from mouse 280623RR at time point 4

description: Not pregnant

value: Not pregnant


title: RPM_SER_sgKLHDC3

value: SER


title: 6M_HBs-HepR, liver_rep3


title: RPM_SER_sgINTS1


title: genomic DNA from Blood from mouse 280623L at time point 4

description: Pregnant

value: Whole blood


title: Genomic DNA from Buffy coat from Subject 16 at time point 1

tag: duration of intensive care (days)


title: Gbi12L_biol rep 2


title: Genomic DNA from Buffy coat from Subject 14 at time point 1

value: male

tag: hydroxychloroquine treatment


title: Gbi12L_biol rep 1


title: 6M_HBs-HepR, liver_rep2

value: liver


title: 6M_HBs-HepR, liver_rep4


title: RPM_SER_sgHNF1A


title: RPM_SER_sgHYOU1


title: genomic DNA from Blood from mouse 280625N at time point 4

description: Not pregnant


title: Genomic DNA from Buffy coat from Subject 10 at time point 1

tag: remdesivir treatment


title: genomic DNA from Blood from mouse 280623B at time point 4

description: Not pregnant


title: genomic DNA from Blood from mouse 280626B at time point 4

description: Pregnant

value: Pregnant


title: RPM_SER_sgGBA

value: sgGBA


title: Gbi0_biol rep 3

value: 0-hours after imbibition


title: 6M_HBs-HepR, liver_rep1


title: 6M_B6-HepR, liver_rep4

value: B6-HepR mice adoptively transferred with wildtype hepatocytes from C57BL/6J mice


title: Gbi0_biol rep 2


title: Genomic DNA from Buffy coat from Subject 2 at time point 1

tag: toclizumab treatment


title: Gbi0_biol rep 1


title: RPM_SER_sgDR1

value: human hepatoma


title: genomic DNA from Blood from mouse 280626N at time point 4

description: Pregnant


title: RPM_SER_sgRBM14


title: 6M_B6-HepR, liver_rep3

tag: strain


title: RPM_SER_sgDDX28

tag: cell line


title: 6M_B6-HepR, liver_rep2


title: 6M_B6-HepR, liver_rep1


title: Methylome capture of HG007 at lab C, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

description:
SAMN16727318
Whole genome bisufite converted DNA
202775690063_R04C01

hyb_protocol: Bisulfite conversion was performed using the EZ DNA Methylation Kit (Zymo Research) with 250 ng of DNA per sample. The bisulfite converted DNA was eluted in 15 μl according to the manufacturer’s protocol, evaporated to a volume of < 4 μl, and used for methylation analysis on the 850k array according to the manufacturer’s protocol (Illumina).

scan_protocol: standard Illumina protocol

data_processing: Data was normalized using several methods: No normalization (preprocessRaw minfi function) (raw.beta.txt.gz), Peak-based correction (Dedeurwaerder et al., 2011) (pbc.beta.txt.gz), SWAN (Maksimovic et al., 2012) (swan.beta.txt.gz), ENmix (Xu et al., 2016) + RCP (Niu et al., 2016) (enmix.beta.txt.gz), funnorm (Fortin et al., 2014) (funnorm.beta.txt.gz), SeSAMe (Zhou et al., 2018) (sesame.beta.txt.gz), dasen (Pidsley et al., 2013) (dasen.beta.txt.gz), dasen (Pidsley et al., 2013) + RCP (Niu et al., 2016) (dasen.rcp.beta.txt.gz).

source_name: Cell line

label_protocol: standard Illumina protocol

extract_protocol: not provided

value: HG007 at lab C


title: genomic DNA from Blood from mouse 280625RR at time point 3

address: 77 Avenue Louis Pasteur

description: Pregnant

tag: mousestrain


title: Methylome capture of HG007 at lab C, replicate 3 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727318
Whole genome bisufite converted DNA
202775690063_R06C01


title: Methylome capture of HG007 at lab C, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727318
Whole genome bisufite converted DNA
202775690063_R01C01


title: RPM_SER_sgCSK

value: sgCSK


title: RPM_SER_sgCTRL

value: sgCTRL


title: genomic DNA from Blood from mouse 280624B at time point 3

description: Pregnant

tag: age

value: female


title: RPM_SER_sgDEF6


title: Methylome capture of HG005 at lab C, replicate 3 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727316
Whole genome bisufite converted DNA
202775690018_R06C01

value: HG005 at lab C


title: genomic DNA from Blood from mouse 280625L at time point 3

description: Pregnant

tag: tissue