title: NB-1 treated with mock

description: Gene expression in mock-treated cells

value: mock


title: A30 scWAT

status: Public on Jul 23 2021

type: SRA

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
All read mapping and analysis was performed using the CLC Genomics Workbench v20.0.2 (CLC Bio-Qiagen).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Total counts.
Supplementary_files_format_and_content: TPM

molecule: total RNA

organism: Mus musculus

source_name: subcutaneous white adipose tissue

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: subcutaneous white adipose tissue

tag: strain

tag: age

value: 28 weeks

tag: genotype

value: Adipo-HuR KO


title: methylation_biotin

type: genomic

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: SAMPLE 3

hyb_protocol: Bisulphite converted DNA with EZ-DNA Methylation Kit (ZYMO RESEARCH, CA, USA) was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN scanner using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software V2011.1, Methylation Mudule 1.9.0

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: pluripotent stem cell

label_protocol: Standard Illumina Protocol

growth_protocol: The iPSCs were maintained under feeder-free condition using mTeSR1 (STEMCELL Technologies, Vancouver, Canada) in a dish coated with 0.5 μg/cm2 of Laminin511-E8 (iMatrix-511, Nippi, Tokyo, Japan).

extract_protocol: Total genomic DNA was extracted from treated-human iPSCs using DNeasy Blood & Tissue Kit (QIAGEN, Hilden, Germany).

treatment_protocol: Human iPSCs were exposed to DMSO (control), 1 μM biotin, 1 nM etoposide, 1 μM propyl gallate, 1 μM theophylline, 30 nM bisphenol A, and 1 μM thalidomide for 48 hours.

tag: cell tpye

value: pluripotent stem cell

tag: cell line

value: HPS0063 (Riken BRC, 201B7)


title: SAM24329574 CD4 aE- CD4 AphaE_negative

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were based on Refseq canonical transcript alignments to GRCh38. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from human intestinal biopsy

extract_protocol: Single T cells were sorted into individual wells of 96 well plates. SMART-seq v4 kit was used to generate cDNA from the sorted cells. Samples were assessed by PicoGreen assay at this point, and only wells with detectable DNA were included in the library preparation. Libraries were prepared with the Nextera kits using 1ng of cDNA per cell, according to manufacturer's specifications. Samples in each plate were uniquely barcoded, and pooled. Each plate was pooled individually. Pooled libraries were QC'd by Bioanalyzer and Qubit. Pooled libraries were then sequenced on one lane of an Illumina HiSeq4000 (Illumina) to generating an average of ~260M of paired end 75 base pair reads per pool.

value: CD4 aE-


title: A26 scWAT


title: ChIP-seq Smchd1-/- clone 1 EZH2

city: Boston

first: Chen-Yu

last: Wang

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
ChIP-seq: Input and ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT1, WT clone 1. KO1, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads.

source_name: neural progenitor cells

growth_protocol: ES cell–derived neural progenitor cell clones were cultured on poly-L-ornithine (0.001%) and laminin (1μg/ml) coated plates with N2 media (DMEM/F-12, GlutaMAX™ supplement, 1X N2 supplement, 1X B27 supplement, 1X Pen/Strep) supplemented with FGF2 (20ng/ml), EGF (20ng/ml), laminin (1μg/ml), and heparin (10μg/ml).

extract_protocol:
ChIP-enriched DNA was extracted with phenol:chloroform.
ChIP-seq libraries were generated by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina.

tag: cell type

value: ESC-derived clonal neural progenitor cells

tag: chip antibody

value: Ezh2 (D2C9) XP Rabbit mAb (Cell Signaling 5246S)


title: SAM24329736 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: methylation_etoposide

description: SAMPLE 4


title: SAM24329759 CD4 aE- CD4 AphaE_negative


title: SAM24329845 CD4 aE- CD4 AphaE_negative


title: methylation_control-2

description: SAMPLE 2


title: SAM24329606 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: A24 scWAT


title: ChIP-seq WT clone 1 EZH2

value: WT


title: methylation_bisphenol A

description: SAMPLE 7


title: A14 scWAT

value: wild-type


title: methylation_theophylline

description: SAMPLE 6


title: A12 scWAT


title: Lung_5_WT

first: Areum

last: Han

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

data_processing:
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.02).
Then, the cleaned reads were aligned to the mouse genome/transcriptome (mm10 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (library-type=fr-unstranded, min-intron-length=10, microexon-search, min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene using a htseq-count tool with the following parameters (--stranded=no --idattr=gene_id -t exon -i transcript_id).
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated from the htseq-count and edgeR tools. The text files have gene expression estimates, RPKM values.

source_name: whole lung

extract_protocol:
Total RNA was collected using Trizol (Invitrogen) according to the manufacturer's instructions.
RNA-seq libraries were constructed following the standard protocol (The SMARTer® Ultra™ Low Input RNA Kit by Clontech).

treatment_protocol: Lin28a and b double knockout was acheived in the lung using tamoxifen to induce recombination of exon 2 flanked with loxP sites.

value: whole lung

value: C57BL/6J/mixed background


title: Lung_7_DKO_1

value: Lin28a and Lin28b KO


title: Lung_9_DKO_2


title: SAM24329692 CD4 aE+ CD4 AphaE_positive


title: A8 scWAT


title: A7 scWAT


title: SAM24329784 CD4 aE+ CD4 AphaE_positive


title: A5 scWAT


title: D90-hROs scRNA-Seq

city: Wenzhou

first: dandan

last: Fan

address: 270 Xueyuan West Road

country: China

institute: Wenzhou Medical University

description: scRNA-Seq

data_processing:
Raw 10x Genomics data were processed with the standard Cell Ranger pipeline (v3.0.2). Mapping to the GRCh38 human genome, quality control and read counting of Ensembl genes was performed to generate a single cell gene count matrix.
Normalization, variance estimation, dimensionality reduction and clustering of single cells were performed by the monocle R package (v2.10.1). We set monocle to use the negative binomial distribution with fixed variance in downstream statistical tests and estimated size factors and dispersion. Genes with a minimum expression value of 0.5 that were detected in at least 10 cells were retained for subsequent analyses. There were 9,665 and 12,218 cells covering 19,997 genes in hRBO and hRO, respectively. On average, we detected ~1,500 genes per cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel files include count and log fold change values for each cluster ...

source_name: human embryonic stem cells

growth_protocol: Human retinal and Rb organoids differentiation were performed as previously described with minor modifications. On day 0, RB1Wt/Wt and RB1Mut/Mut hESCs maintained on Matrigel-coated plates were pretreated with 10 μM Y-27632 for 2h, and then carefully dissociated into single-cell suspensions using TrypLE Select (containing 0.05 mg/ml DNase I and 20 μM Y-27632), plated at a density of 12,000 live cells per well in 96-well low-attachment V-bottom plates in retinal differentiation medium I containing 44% Iscove’s modified Dulbecco’s medium, 44% Hams F12, 10% KnockOut Serum Replacement, 1% GlutaMAX-I, 1% Penicillin-Streptomycin (10,000 U/ml), and 20 μM Y-27632. 1.5nM (55 ng/ml) recombinant human BMP4 was added to the culture on day 6, and its concentration was semi-reduced with half medium change every 3 days. Retinal differentiation media Ⅱ [DMEM/F12-Glutamax medium containing 10% Fetal Bovine Serum, 1% N2 supplement, 1% Penicillin-Streptomycin (10,000 U/ml), 0.5 μM retinoic acid and 0.1 mM taurine] was exchanged until day 18 when the aggregate bodies were transferred to 9 cm nonadherent dishes (30 bodies per dish) for further long-term culture in a 37℃, 5% CO2/40% O2 incubator, and half of the volume changed with fresh retinal differentiation media Ⅱ every 5 days. The state and morphology of organoids was monitored in real time using the inverted fluorescence microscope.

extract_protocol:
Cells were loaded onto the 10x Chromium Single Cell Platform as described in the manufacturer’s protocol.
Samples were processed (including generation of Gel Bead in Emulsion & Thermal cycling, Post Cycling Cleanup & cDNA Amplication, and Library Preparation & Quantification) following the manufacturer’s protocol and sequenced on an Illumina X-ten instrument using 150-base-pair paired-end reads.

treatment_protocol: Organoids were washed with PBS and carefully trypsinized in dissociation solution (2.4 mL 0.25% Trypsin-EDTA supplemented with 1.6 mL Accumax (Stem Cell Technologies, 07921) and 0.05 mg/mL DNase I (Roche, 11284932001) and incubated at 37°C in a 5% CO2/40% O2 incubator for 1 h. The cell suspension was then centrifuged for 5 min at 300 RCF, and the resuspended to prepare a suitable cell concentration of 700~1,200 cells/μL.

tag: organoids

value: human ES-derived retinal organoids

tag: developmental/tumor stage

value: day 90

value: WT hESCs


title: methylation_thalidomide

description: SAMPLE 8


title: SAM24329907 CD8 aE+ CD8 AphaE_positive


title: methylation_control-1

description: SAMPLE 1


title: Responder (Y00-0)

city: Auroa

first: Xiao Jing

state: CO

department: Pathology

institute: University of Colorado AMC

description:
single-cell RNA sequencing data
Raw_UMI_Matrix.tsv
NormalizedUMI_Matrix.tsv
Metadata.tsv

data_processing:
Sequenced reads were mapped to the CellRanger genome build mm10 (v1.2.0) with CellRanger (v3.0.1) using "cellranger count" with the following parameters: --expect-cells=10000. Sample IDs (N11-3, N12-2, Y10-3, and Y00) were generated with the --ID function of cellranger.
This and all following steps were performed in Seurat (v3.1.5). Outputs from cellranger count assigned sample IDs ("N11-3", "N12-2", "Y10-3", "Y00") using the Read10X function.
Samples were aggregated into a single Seurat object using CreateSeuratObject with the following parameters: min.cells = 10, min.features = 200, names.field = 2, names.delim = "\\-").
Cells with greater than 20% mitochondrial gene expression were excluded with the subet command: subset(experiment2.aggregate, subset = nFeature_RNA > 200 & nFeature_RNA < 9000 & percent.mt < 20).
Responder status ("yes" or "no") and sample ID were added as metadata for each UMI read.
Samples were then split by their responder status into responder and non-responder categories using the Seurat function: SplitObject(experiment.aggregate, split.by = "responder")
Raw counts were normalized using the NormalizeData() function in Seurat.
Samples were integrated using FindIntegrationAnchors() and IntegrateData(), reads were scaled with ScaleData(), and then clustered by UMAP with runPCA() followed by runUMAP() using PCA reduction, FindNeighbors() using UMAP reduction, and FindClusters(). Arbitrary UMAP clusters are listed in the supplementary metadata file.
UMAP clusters were phenotyped by comparing gene expression in each cluster to the Panglao Database of single-cell RNA sequencing data, and cluster phenotypes were added to the metadata file.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI reads ($RNA@counts in the Seurat object) are saved in the supplementary data file, "Raw_UMI_Matrix.tsv"
Supplementary_files_format_and_content: Normalized UMI reads ($integrated@data in the Seurat object) can be found in the supplementary data file, "NormalizedUMI_Matrix.tsv".
Supplementary_files_format_and_content: The supplementary metadata file ("Metadata.tsv") contains the following notable categories for each UMI read: "orig.ident" (sample ID), "nCount_RNA" (number of reads), "nFeature_RNA" (number of genes), "percent.mt" (percent mitochondrial genes), "responder" (responder status of "yes" or "no"), "Seurat_clusters" (UMAP cluster ID number), and "clusters.named" (UMAP clusters after phenotyping).

source_name: Tumor

growth_protocol: A223 tumors (K15-Cre-delta-PR1.Smad4-/-KrasG12D) were injected into 6-8 week old female C57BL/6 mice and allowed grow for 12 days to a size of 100-200mm^3 before treatment start.

extract_protocol:
Tumors were excised on day 15 post-transplant, digested with Liberase TL, shredded with Miltenyi C-tubes, ground through a 100um strainer, red blood cells lysed with eBioscience RBC lysis buffer, and then strained through a 70um strainer. Cells were counted and then dead cells were excluded by Miltenyi Dead Cell Exclusion Kit, counted, and submitted for single-cell RNAseq capture.
Single-cell RNA libraries were prepared for sequencing using standard 10X Genomics protocols. Single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics). Raw paired-end fastq outputs were concatenated into a single R1 and R2 fastq file for each sample.

treatment_protocol: Mice were treated with 492ug of bintrafusp alfa diluted to 100ul in PBS by IP injection on days 12 and 14 post-transplant.

tag: treatment

value: Bintrafusp alfa

tag: tumor type

value: A223 SCC

tag: responder status

value: Responder


title: SAM24329680 CD4 aE+ CD4 AphaE_positive


title: methylation_propyl gallate

description: SAMPLE 5

value: pluripotent stem cell

value: HPS0063 (Riken BRC, 201B7)


title: SAM24329803 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: Non-responder (N12-2)

value: Non-responder


title: D90-hRBOs scRNA-Seq

description: scRNA-Seq

value: human ES-derived retinoblastoma organoids

value: RB1 mutation knock-in hESCs


title: SAM24329580 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: Rami_WT_EAE2_S2

city: Pittsburgh

first: Sarah

last: Gaffen

state: PA

address: 200 lothrop street

institute: University of Pittsburgh

description: Mice were immunized in the left flank with the MOG in CFA to induce EAE

data_processing:
Raw data was processed and quality check was performed using CLC Genomics Workbench v21.0.4 QC tool with default parameters
Then the filtered reads were aligned against the mouse reference genome mm10 and also Ensembl annotations v86 using default parameters of “RNA-Seq Analysis” tool of CLC Genomics Workbench v12.
Differentially expressed genes (DEGs) were identified between Imp2 Ko and WT using “Differential Expressions in Two Groups” tool provided by CLC Genomics Workbench v21 (Qiagen Inc) .
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include both raw read counts and normalized counts for each Sample
Supplementary_files_format_and_content: count matrix table with raw gene counts for every gene and every sample

source_name: Ingunial Lymph node

extract_protocol:
Inguinal lymph nodes were harvested at day 7 and RNA was isolated using Tryzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were immunized subcutaneously in 2 sites on the back with 100 μg MOG peptide (35–55) (Biosynthesis) emulsified with Complete Freund’s Adjuvant (CFA) with M. tuberculosis strain H37Ra (DIFCO Laboratories). Mice also received 100 ng pertussis toxin (List Biological Laboratories) i.p. on day 0 and day 2.

value: Ingunial Lymph node

value: 10 weeks

value: Imp2 wild type

value: EAE


title: VPA

city: Higashi-Hiroshima

first: Yasuhiro

last: Ishihara

state: Hiroshima

address: 1-7-1 Kagamiyama

department: Graduate School of Integrated Sciences for Life

institute: Hiroshima University

data_processing:
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with  count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Genome_build: mm9_male
Supplementary_files_format_and_content: Tab-delimited text file includ CPM (FPKM, peak) values for each sample.

source_name: Hippocampus

extract_protocol:
RNA was extracted from the hippocampus using a High Pure RNA Isolation Kit (Roche Diagnostics K.K., Tokyo, Japan).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: ICR

value: Hippocampus


title: Rami_WT_EAE3_S3


title: SAM24329866 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: 293T_KuDNA-PKcs+/- + siKuDNA-PKcs_rep3

city: Moscow

first: Andrey

last: Anisenko

address: Leninskye Gory, 1/40

department: Chemistry department

country: Russia

institute: Lomonosov Moscow State University

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A21

data_processing:
Read mapping on hg38 human genome with Ensemble gene annotation by STAR with default parameters.
Read counting by STAR with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using DESeq2 R library.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human embryonic kidney 293T cells

growth_protocol: 293T cells and their derivatives were cultured in DMEM medium supplemented with 10% FBS and 100 I.U./mL penicillin/100 μg/mL streptomycin solution (all obtained from Invitrogen). Preparation of 293T cells with monoallelic knockout of Ku70, Ku80 and DNA-PKcs genes (Ku70+/-, Ku80+/- and DNA-PKcs+/-) was described in (E. Knyazhanskaya et al., Retrovirology, 2019).

extract_protocol:
Total RNA from all samples (3 repeats for each coditions) was extracted using TRIzol reagent (Life Technologies) following the manufacturer’s protocol 72h after siRNA transfection. 1 µg of total RNA was fragmented by incubation at 900C for 6 min in 40 µL of 100 mM Tris-HCl pH 8.0 and 8 mM MgCl2. After isopropanol precipitation RNA was dissolved in 12 µL and subjected to ribosomal RNA depletion by NEBNext rRNA depletion kit (E6310L, New England Biolabs) according manufacturer’s protocol. mRNA sequencing libraries were prepared by NEBNext Ultra II Directional RNA library Prep kit for Illumina (E7760S, New England Biolabs) according to the manufacturer’s protocol. NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set1) (E7600S, New England Biolabs) were used for adaptor ligation. Quality control of the libraries was carried out on Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To transfect cells with siRNAs, 50 pmol of pre-annealed siRNA duplex in OptiMem transfection medium was mixed with Lipofectamine RNAiMAX reagent (Invitrogen) according to manufacturer’s protocol and then added to 293T cells seeded in a 12-well plate in 1 mL of growth medium for 72 h incubation.

value: human embryionic kidney cells

value: treated with 50 nM siDNA-PKcs for 72 hours


title: Rami_WT_EAE1_S1


title: vehicle


title: 20L004209: Het_Input_Rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: 8 weeks animals under normal diet

data_processing:
ChIP-seq datasets were mapped to GRCm38/Mm10 with default paired-end parameters from snakePipes version 2.1.2 (Bhardwaj et al. 2019). Peaks were called with MACS2 (Galaxy version 2.1.1.20160309.3), and bandwidth was set to 200, lower mfold bound to 5, upper mfold bound to 500, and the q-value to 0.1. Input was used as control to call peaks. Peaks from each cell type were merged using cat, BEDtools sort (Galaxy version 2.27.0.0) and piped to BEDtools merge with a distance of 1000 bp. BamCompare (Galaxy version 2.5.1.0.0) with a bin size of 50 bp. The data were normalized as log2 fold change over H3 immunoprecipitation. For plotting heatmaps were generated using deepTools2 compute matrix and plotHeatmap function from DeepTools2 version 3.5.0 (Ramírez et al. 2016). Box-plots were generated using DeepTools2 multiBigwigSummary scores. The Bioconductor package ChIP-Seeker (Yu et al. 2015). was used to retrieve the nearest genes around the peak, annotate the genomic region of the peak, and peak features annotation. GO term analysis was performed using the Metascape (Zhou et al. 2019) platform and the ShinyGo v0.61 database (Ge et al. 2020).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files having log2-fold change scores
Supplementary_files_format_and_content: peak bedfiles

source_name: Visceral white adipocyte tissue

extract_protocol:
WAT of 8 week old SD treated animals was minced and transferred into a Dounce homogenizer (loose pestle), covered with 1% formaldehyde in PBS, and dissociated, followed by 15 min incubation at room temperature (RT). During incubation, the tissue suspension was filtered using a nylon 70 µM cell strainer (Falcon, 352350). 125 mM glycine final was added to the sample, incubated at RT for 5 min and the suspension was pelleted for 5 min at 500 g. Cell pellets were washed twice in ice cold PBS and pelleted for 5 min at 500 g. For NEXON based nuclei isolation cell pellets were resuspended in 1ml of lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal, protease inhibitor cocktail. Cell suspension was transferred into Covaris MilliTube (cat. No. 520130) and sonicated in Covaris instrument (E220) for 30 sec at peak power 75W, duty factor 10% and 200 cycles/burst. Nuclei were pelleted at 1000g at 20°C for 5min. Pellets were resuspended in 0.5% SDS and incubated at RT for 10min. Sample was diluted 1:5 in the digestion buffer (1.1% Triton, 1x CutSmart buffer , H2Odest). Up to 1*10^6 nuclei were digested with Cvik1 (5U/100.000 cells) at 25°C for 17hrs, shaking at 800rpm. Nuclei were pelleted for 5min at 1000g and washed in a nuclei wash solution (10mM Tris-HCl pH 8, 0.25% Triton, 0.2mg/ml BSA ) until residual fat was removed. Nuclei were pelleted at 5000g for 10min, resuspend in the shearing buffer (10mM Tris-HCl pH 8, 0.1% SDS, 1mM EDTA), transferred into Covaris MicroTube (cat. No. 520052) and sonicated for 6min at peak power 105W, duty factor 2% and 200 cycles/burst. Sample was diluted 1:6 in 1x iC1 buffer (iDeal ChIP-seq, Diagenode) and incubated with 2ug of antibody o/n at 4°C. The next day protein G Dynabeads were added and incubated for 3 hrs at 4°C. Beads were washed and DNA was eluted according to manufacturer's instructions (iDeal ChIP-seq, Diagenode). DNA was purified using MinElute PCR purification kit (Qiagen) for further analysis
Libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina according to the manufacturer’s instructions (New England Biolabs, #E7645). ChIP libraries were sequenced using an Illumina NovaSeq6000 sequencer with 2 × 100 base paired-end reads.

treatment_protocol: Standart Diet

value: Mof heterozygous

value: Visceral white adipocyte

value: Input


title: SAM24329591 CD4 aE+ CD4 AphaE_positive


title: Non-responder (N11-3)

value: Bintrafusp alfa

value: A223 SCC


title: Responder (Y10-3)

value: Responder


title: 20L004208: Het_Input_Rep1

description: 8 weeks animals under normal diet


title: Rami_KO_EAE3_S6

value: Imp2 Konckout


title: 293T_KuDNA-PKcs+/- + siKuDNA-PKcs_rep1

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A19


title: 20L004207: WT_Input_Rep2

description: 8 weeks animals under normal diet

value: wild type


title: 293T_KuDNA-PKcs+/- + siKuDNA-PKcs_rep2

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A20


title: Rami_KO_EAE2_S5

value: Ingunial Lymph node


title: SAM24329582 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: 293T_KuDNA-PKcs+/- + siControl_rep3

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A18

value: treated with 50 nM siControl for 72 hours


title: 20L004206: WT_Input_Rep1

description: 8 weeks animals under normal diet


title: 20L004205: Het_H3_ChIP_Rep2

description: 8 weeks animals under normal diet


title: CM_14: uninfected rep 4

city: Charlottesville

first: Chelsea

last: Marie

state: VA

address: 345 Crispell Drive

department: Medicine

institute: University of Virginia School of Medicine

data_processing:
Basecalling was done with illumina software RTA v2
Cutadapt was used to trim the adapter sequences
Quality of the reads was assessed by FastQC and multiQC
reads were aligned to the mouse Ensembl GRCh38.76 primary assembly using STAR v2.5.3a in a two-passing mode to generate a gene count matrix
Genome_build: mouse Ensembl GRCh38.76
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: lung tissue

extract_protocol:
Snip from lower inferior lobe was taken and RNA was extracted from murine lung tissue preserved in trizol by bead beating (tissuelyserII, Qiagen), followed by a phenol-chloroform extraction and RNA Isolation Kit (Qiagen). RNA quality was assessed using Agilent Tape station.
Ribosomal RNA was depleted using the rRNA depletion kit (NEB E6310). Following rRNA  2 depletion cDNA libraries were prepared using the NEB ultra-directional library preparation kit  3 2.0 (NEB E7760) and indexed using the NEBNext Multiplex Oligos for Illumina (NEB E7335, E7500).
Libraries were diluted and pooled. 15 libraries were sequenced on the Illumina Nextseq 500 using a 150 high output kit (400 Million 8 reads, 2x75bp paired end, 150 cycles)

value: Tg(K18-hACE2) 2Prlmn

value: uninfected

tag: disease state

value: Covid19 uninfected


title: 293T_KuDNA-PKcs+/- + siControl_rep1

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A16


title: 20L004204: Het_H3_ChIP_Rep1

description: 8 weeks animals under normal diet


title: CM_13: uninfected rep 3


title: SAM24329685 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: 293T_Ku80+/- + siKu80_rep3

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A15

value: human embryionic kidney cells

value: treated with 50 nM siKu80 for 72 hours


title: CM_12: uninfected rep 2


title: 293T_Ku80+/- + siKu80_rep2

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A14


title: SAM24329697 CD4 aE+ CD4 AphaE_positive


title: 20L004202: WT_H3_ChIP_Rep1

description: 8 weeks animals under normal diet


title: 293T_Ku80+/- + siKu80_rep1

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A13


title: 20L004201: Het_Mof_ChIP_Rep2

description: 8 weeks animals under normal diet

value: Mof heterozygous

value: MOF (abcam #ab200660)


title: CM_11: uninfected rep 1


title: SAM24329743 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: 293T_Ku80+/- + siControl_rep3

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A12


title: CM_10: Covid 19 infected treated with anti-IL13- rep 5

value: Covid19 infected


title: SAM24329599 CD4 aE+ CD4 AphaE_positive


title: CM_15: uninfected rep 5


title: SAM24329601 CD4 aE+ CD4 AphaE_positive


title: 293T_KuDNA-PKcs+/- + siControl_rep2

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A17


title: 20L004199: WT_Mof_ChIP_Rep2

description: 8 weeks animals under normal diet

value: Visceral white adipocyte


title: SAM24329910 CD8 aE+ CD8 AphaE_positive


title: 20L004200: Het_Mof_ChIP_Rep1

description: 8 weeks animals under normal diet


title: SAM24329787 CD4 aE+ CD4 AphaE_positive


title: CM_09: Covid 19 infected treated with anti-IL13- rep 4


title: 293T_Ku80+/- + siControl_rep2

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A11


title: CM_08: Covid 19 infected treated with anti-IL13- rep 3


title: SAM24329616 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: 20L004198: WT_Mof_ChIP_Rep1

description: 8 weeks animals under normal diet


title: CM_07: Covid 19 infected treated with anti-IL13- rep 2


title: 293T_Ku70+/- + siKu70_rep3

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A9

value: treated with 50 nM siKu70 for 72 hours


title: 20L004203: WT_H3_ChIP_Rep2

description: 8 weeks animals under normal diet

value: wild type


title: SAM24329761 CD4 aE- CD4 AphaE_negative


title: HFD_het2

data_processing:
Reads for mouse bulk RNA-seq datasets were mapped with following the default SnakePipes parameters of  bulk RNAseq pipeline (Bhardwaj et al. 2019). In brief, STAR software alignment against mouse genome version GRCm38. The total number of sequenced reads averaged 15 million pairs of which mean alignment of 65 % of the reads were uniquely mapped. Reads were counted with featureCounts (subread-1.5.0-p1). Differential expression analysis was performed with DESEQ2 (v1.26). Multi-FASTA QC statistics indicated data were of high quality and sequencing depth was sufficient to test for differential expression between conditions. Differential genes were called with an FDR threshold of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts

molecule: polyA RNA

source_name: WAT

growth_protocol: Tissue was extract directly from the animals

extract_protocol:
 WAT was weighed and an equal amount of tissue was used to extract mRNA from  WAT. For RNA extraction from various sources were lysed directly in TRIZOL and samples were homogenized using an electric tissue homogenizer. Then, samples were incubated with 95% EtOH and transferred into mini-kit RNA extraction Zymo kit (R1054) and pure total RNA was extracted according to the manufacturer’s instructions. RNA concentrations were quantified on a Qubit 2.0 Fluorometer (Life Technology) and quality for deep sequencing checked by Fragment analyzer.
After quality control was then used to generate libraries using Illumina TruSeq RNA Sample Prep v2 (RS-122-2001). The manufacturer’s recommendations were followed and the libraries were sequenced on an Illumina NovaSeq6000 sequencer. All sequence data were performed in 3 biological replicates for SD group and duplicates for HFD group. The reads were conducted at 2 x 100 bp length.

treatment_protocol: Animals was kept in standart diet (SD) or high fat diet (HFD)

tag: diet

value: high fat diet


title: Rami_KO_EAE1_S4

value: Ingunial Lymph node

value: 10 weeks

value: Imp2 Konckout

value: EAE


title: 293T_Ku70+/- + siKu70_rep2

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A8


title: CM_06: Covid 19 infected treated with anti-IL13- rep 1

value: Tg(K18-hACE2) 2Prlmn


title: HFD_het1


title: SAM24329755 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: 293T_Ku70+/- + siKu70_rep1

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A7

value: human embryionic kidney cells


title: HCT116p53-/- cells, 8h Isoginkgetin 2 (transcript-level)

type: RNA

city: Ottawa

first: Bruce

last: McKay

state: Ontario

address: 1125 Colonel By Dr, Ottawa

department: Biology

country: Canada

institute: Carleton University

hyb_protocol: Samples were hybridized to Affymetrix Human Transcriptome 2.0 oligonucleotide microarrays and scanned at the Affymetrix Core Facility, Stemcore Laboratories, Ottawa Hospital Research Institute.

scan_protocol: Hybridized microarrays were scanned according to the manufacturer's instructions (Affymetrix)

data_processing: Data was analyzed using the Transcriptome Analysis Console (TAC) 4.0 software.

label: biotin

source_name: Cell culture

label_protocol: Single-stranded cDNA was generated with the WT cDNA Synthesis Kit (Affymetrix), fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix) at the Affymetrix Core Facility, Stemcore Labs, Ottawa Hospital Research Institute.

growth_protocol: HCT116 cells and the p53 null subline (provided by Dr. Bert Vogelstein: Science 282, 1497 – 1501) were grown in McCoys media (Hyclone, San Angelo) supplemented with a 12% mixture of Newborn to Fetal Calf Serum (3:1 ratio) (Gibco, ThermoFisher Scientific, Ottawa), and antibiotic (90 units/ml penicillin, 90 ug/ml streptomycin, Hyclone).

extract_protocol: Total RNA was collected using the QIAGEN RNeasy mini kit according to the manufacturers instractions.

treatment_protocol: Cells were seeded at 1.0 x 10^6 cells per 10 cm dish at least 24 hours before treatment. Cells were left untreated or they exposed to 30 µM IGG or an equivalent volume of DMSO in growth media for 8 hours.

value: Isoginkgetin


title: CM_05: Covid 19 infected treated with IgG-rep 5

value: IgG


title: SAM24329590 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: 293T_Ku70+/- + siControl_rep3

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A6

value: treated with 50 nM siControl for 72 hours


title: SAM24329719 CD8 aE- CD8 AphaE_negative


title: HFD_control1


title: HFD_control2


title: CM_04: Covid 19 infected treated with IgG-rep 4

value: Covid19 infected


title: SD_het3

value: Mof heterozygous

value: standart diet


title: 293T_Ku70+/- + siControl_rep2

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A5


title: CM_03: Covid 19 infected treated with IgG-rep 3


title: HCT116p53-/- cells, 8h DMSO 1 (transcript-level)

value: DMSO


title: SD_het1


title: 293T_Ku70+/- + siControl_rep1

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A4


title: CM_02: Covid 19 infected treated with IgG-rep 2


title: 293T_Ku80+/- + siControl_rep1

description:
293T_Ku70+/- were obtained from 293T cell by CRIPR-Cas9 mediated knock-in of epitope tag for selecetion of modified cells (detailed description at E. Knyazhanskaya et al., Retrovirology, 2019)
A10


title: SAM24329668 CD4 aE- CD4 AphaE_negative


title: SD_het2


title: HCT116p53-/- cells, 8h untreated 2 (transcript-level)

value: untreated


title: CM_01: Covid 19 infected treated with IgG-rep 1


title: HCT116p53-/- cells, 8h untreated 1 (transcript-level)


title: 293T + siControl_rep3


title: SAM24329912 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: SD_control1

value: wild type


title: 293T + siControl_rep2


title: SAM24329873 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: SAM24329819 CD8 aE+ CD8 AphaE_positive


title: SAM24329679 CD4 aE- CD4 AphaE_negative


title: HCT116 cells, 8h Isoginkgetin 2 (transcript-level)


title: SAM24329624 CD8 aE- CD8 AphaE_negative


title: SAM24329814 CD8 aE+ CD8 AphaE_positive


title: SAM24329691 CD4 aE+ CD4 AphaE_positive


title: 293T + siControl_rep1


title: Late follicular phase - participant 22

city: Stirling

first: Colin

middle: N

last: Moran

address: Univeristy of Stirling

country: United Kingdom

institute: University of Stirling

description: Adipose tissue miRNA expression from the late follicular phase

hyb_protocol: Hybridisation cocktails were prepared using the GeneChip hybridisation kit (ThermoFisher Scientific, UK, cat no. 900720). Biotin labelled samples were hybridised overnight onto GeneChip miRNA 4.0 arrays (ThermoFisher Scientific, UK, cat no. 902413) according to manufacturer’s instructions. Arrays were washed and stained using the GeneChip wash and stain kit (ThermoFisher, UK, cat no. 902413) and the Affymetrix fluidics station 450, as per manufacturer’s instructions.

scan_protocol: GeneChips were scanned by the Affymetrix scanner 3000 7G.

data_processing: Microarray signal intensities were normalised using the variance stabilisation normalisation 2 (VSN2) algorithm and probe level summarisation conducted using robust multi-chip analysis (RMA).

label: Biotin

source_name: Human adipose tissue- late follcular phase

label_protocol: 100 ng RNA were labelled using the Flashtag Biotin HSR labelling kit according to manufacturers instructions

extract_protocol: Total RNA was isolated from 30-100 mg homogenised adipose tissue in a combined protocol using TRIzol reagent (ThermoFisher Scientific, UK, cat no. 15596026) and miRNeasy mini lipid kit (Qiagen, Germany, cat no. 217004), as previously described by Cirera et al. 2013 (doi:10.1186/1756-0500-6-472).

treatment_protocol: Immediately following the biposy, adipose tissue samples were placed into an RNA-free 1.5 ml microcentrifuge tube containing 5-10 x tissue volume RNAlater (ThermoFisher, UK, cat no. AM7020), flash frozen in liquid nitrogen and stored at -80 ¬oC until analysis.

value: Subcutaneous adipose

tag: bmi

tag: menstrual cycle phase

value: Late Follicular

tag: menstrual cycle day


title: Mid luteal phase - participant 22

description: Adipose tissue miRNA expression from the mid luteal phase

source_name: Human adipose tissue- mid luteal phase

tag: tissue

value: Mid Luteal


title: HCT116p53-/- cells, 8h DMSO 2 (transcript-level)


title: Post ovulatory phase - participant 22

description: Adipose tissue miRNA expression from the post ovulatory phase

source_name: Human adipose tissue- post ovulatory phase

tag: age

value: Post ovulatory


title: HCT116 cells, 8h untreated 1 (transcript-level)


title: HCT116 cells, 8h Isoginkgetin 1 (transcript-level)


title: HCT116 cells, 8h untreated 2 (transcript-level)


title: Early follicular phase - participant 22

description: Adipose tissue miRNA expression from the early follicular phase

source_name: Human adipose tissue- early follicular phase

value: Early Follicular


title: SAM24329583 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: Mid luteal phase - participant 21


title: SAM24329816 CD8 aE+ CD8 AphaE_positive


title: SAM24329578 CD4 aE- CD4 AphaE_negative


title: SAM24329654 CD8 aE+ CD8 AphaE_positive


title: Early follicular phase - participant 21


title: SAM24329648 CD8 aE+ CD8 AphaE_positive


title: HCT116p53-/- cells, 8h Isoginkgetin 1 (transcript-level)

value: Isoginkgetin


title: Mid luteal phase - participant 17


title: GEX HI 2

city: Gothenburg

first: Xiaoyang

address: Medicinaregatan 11

department: Physiology

country: Sweden

institute: University of Gothenburg

description: HI 2

data_processing:
Genome_build: mouse reference genome: mm10_withIgTCRgenes
Genome_build: V(D)J reference: vdj_GRCm38_alts_ensembl
alignment: CellRanger 2.2.0
main software: Seurat 3.027
general filtering: cells with between 200 and 6000 expressed genes and with mitochondrial counts below 7% were kept for downstream analysis
normalization: data were normalized with a scale factor of 10,000 and were log transformed before identify-ing the 2,000 most highly variable genes
scaling: all genes were scaled using the default settings in Seurat (including cell cycle bias) before performing the principal component analysis
Supplementary_files_format_and_content: for all GEX amples, barcodes.tsv, genes.tsv and matrix.mtx are provided; for V(D)J enrichment analysis, the filtered_contig_annotations file is provided
Supplementary_files_format_and_content: MTX files: The top three lines of this file are header lines. The third line contains the total number of rows in all the three files in this folder (genes.tsv, barcodes.tsv, matrix.mtx).  The next lines (line number 4 onwards) have three columns:   - The first column refers to the "gene id" index.   - The second column refers to "cell id" index.

source_name: brain meninges

extract_protocol:
Used 10x Genomics kits - GEX 5' Library & Gel Bead Kit (PN-1000014) and 5’ Library & Gel Bead Kit + Single Cell V(D)J Enrichment Kit (Mouse T cells and B cells)
Manufacturer's instructions
droplet scRNA-seq (10x Genomics)

tag: strain

value: postnatal day 4 - 6h after HI

tag: pooling

value: 12 mice, 6 males and 6 females


title: GEX Naïve 2

description: Naïve 2

value: postnatal day 4


title: Late follicular phase - participant 21


title: SAM24329886 CD8 aE- CD8 AphaE_negative

source_name: RNA from human intestinal biopsy


title: SAM24329764 CD4 aE- CD4 AphaE_negative


title: SAM24329862 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: SAM24329823 CD8 aE+ CD8 AphaE_positive


title: Post ovulatory phase - participant 15


title: Late follicular phase - participant 17


title: Early follicular phase - participant 17


title: GEX HI 1

description: HI 1


title: Mid luteal phase - participant 15


title: SAM24329806 CD8 aE- CD8 AphaE_negative


title: HCT116 cells, 8h DMSO 1 (transcript-level)

tag: cell line


title: GEX Naïve 1

description: Naïve 1


title: SAM24329689 CD4 aE+ CD4 AphaE_positive


title: SAM24329663 CD4 aE- CD4 AphaE_negative


title: A549-ACE2 RPB1 SARS-CoV-2 rep3 ChIP-Seq

city: HOUSTON

first: Ruoyu

state: Texas

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome build: hg19

growth_protocol: Human lung adenocarcinoma cells A549 expressing human ACE2 (A549-ACE2, #NR53821) was acquired from BEI Resources, Manassas, VA). They were maintained in DMEM/F-12 (1:1, Corning) medium supplemented with 10% FBS (GeneDepot) and blasticidin (100uM).

extract_protocol:
Lysates were clarified from sonicated nuclei and biotin-labelled DNA were isolated with C1 beads
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol: SARS-CoV-2 isolate USA-WA1/2020 (NR-52281; BEI Resources, Manassas, VA) was employed to infect human A549-ACE2 cells (NR53821; Bei Resources, Manassas, VA). For viral infections, serum/antibiotics-free Eagle’s MEM medium supplemented with 1mM HEPES was used. Briefly, cells grown in 10-cm culture dishes at about 70-80% confluency were washed with the serum free medium, viral inoculum was added at 0.1 MOI for 1 hr. After that, non-adsorbed viral particles were gently aspirated out and the monolayers were replenished with 10% FBS containing MEM supplemented with 1mM HEPES. Infected cells were incubated at 37°C with 5% CO2 for 6hr or 24hr post-infection for experiments.

tag: cell type

value: epithelial cell

value: SARS-CoV-2 isolate USA-WA1/2020

value: RPB1 N terminus, Cell Signaling Technology, #14958S, Lot4


title: A549-ACE2 RPB1 Mock rep3 ChIP-Seq

value: mock

tag: chip antibody


title: Early follicular phase - participant 15


title: SAM24329896 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: HCT116 cells, 8h DMSO 2 (transcript-level)

value: DMSO


title: SAM24329747 CD8 aE+ CD8 AphaE_positive


title: SAM24329768 CD4 aE- CD4 AphaE_negative


title: Mid luteal phase - participant 14

value: Subcutaneous adipose


title: A549-ACE2 H3K9me3 SARS-CoV-2 rep2 ChIP-Seq


title: A549-ACE2 H3K9me3 Mock rep2 ChIP-Seq


title: Post ovulatory phase - participant 14


title: SAM24329911 CD8 aE+ CD8 AphaE_positive


title: A549-ACE2 H3K4me3 SARS-CoV-2 rep2 ChIP-Seq


title: SAM24329757 CD4 aE- CD4 AphaE_negative


title: SD_control3

tag: genotype

value: wild type

value: standart diet


title: A549-ACE2 H3K4me3 Mock rep2 ChIP-Seq


title: SAM24329686 CD4 aE+ CD4 AphaE_positive


title: Early follicular phase - participant 14


title: A549-ACE2 RPB1 SARS-CoV-2 rep2 spiChIP-Seq


title: Post ovulatory phase - participant 12

value: Post ovulatory


title: NR8383 - Pass Nu 200 - rep3

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

description: Gene expression in NR8383 cells after 200 passages

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA were fragmented at 60°C for 30 min in a reaction volume of 25 µL following the manufacturer’s instructions. 25 µL of 2x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Rat GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent).

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 074036_D_F_20150914) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

organism: Rattus norvegicus

source_name: NR8383_Passage Number 200

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: NR8383 cell line were established from normal rat by lung lavage and was obtained from American Type Culture Collection (ATCC® CRL-2192™, Manassas, VA, USA). Cells, with a 50% adherent and 50% floating cell phenotype, were grown in DMEM medium supplemented with 15 % of heat-inactivated fetal bovine serum, 2 mM of L-glutamine, as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma Aldrich). Cells were incubated at 37°C in an atmosphere composed of 95 % air, 5 % CO2 and medium are changed every 2-3 days.

extract_protocol: The quality of the RNA extracted by RNA-Solv Reagent (Omega Bio-tek, USA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 7.5, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: Cells were seeded in 25 cm2 flasks at a density of 3 x 105 cells / mL for 48 h. Cells were at two different passage numbers 20 and 200 in four biological replicates.

tag: tissue origin

value: lung

value: alveolar macrophage cell line

tag: passage number

value: high (passage 200)


title: SAM24329820 CD8 aE+ CD8 AphaE_positive


title: NR8383 - Pass Nu 200 - rep4


title: SAM24329876 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: Late follicular phase - participant 12

value: Late Follicular


title: NR8383 - Pass Nu 200 - rep1


title: A549-ACE2 RPB1 Mock rep2 spiChIP-Seq

tag: treatment


title: NR8383 - Pass Nu 20 - rep4

description: Gene expression in NR8383 cells after 20 passages

source_name: NR8383_Passage Number 20

value: low (passage 20)


title: A549-ACE2 RAD21 SARS-CoV-2 rep2 spiChIP-Seq


title: SAM24329874 CD8 aE- CD8 AphaE_negative


title: A549-ACE2 RAD21 Mock rep2 spiChIP-Seq


title: Late follicular phase - participant 14


title: Early follicular phase - participant 12

value: Early Follicular


title: SAM24329644 CD8 aE+ CD8 AphaE_positive


title: Post ovulatory phase - participant 11


title: Late follicular phase - participant 15


title: SAM24329795 CD8 aE- CD8 AphaE_negative


title: Mid luteal phase - participant 11

value: Mid Luteal


title: A549-ACE2 H3K27me3 Mock rep2 spiChIP-Seq

value: epithelial cell

value: H3K27me3 (Cell Signaling Technology, #9733S, Lot19)


title: NR8383 - Pass Nu 20 - rep3


title: ISO-12-EI

city: Oslo

first: Ibrahim

last: Akkouh

address: Kirkeveien 166

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

data_processing:
Raw sequencing reads were quality assessed with FastQC and Trimmomatic V0.32 using default parameters
Sequencing reads were separated according to their species of origin using the in silico RNA-seq read sorting tool Sargasso using the "best" option
Reads were mapped to the human reference genome (hg38) with Sargasso, which internally uses STAR alignment tool
To quantify gene expression levels, reads mapped by Sargasso were summarized at the gene level using featureCounts (ref ) guided by ENSEMBL annotations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts every sample and for genes passing the filtering threshold

source_name: iPSC neurons

growth_protocol: iPSCs were plated in E8 flex supplemented with doxycycline (4 µg/ml), Revitacell (1:100,) and Forskolin (10 µM). At day 1 cultures were switched to DMEM/F12 containing Forskolin, N2 (1:100), non-essential amino acids (1:100), primocin (0.1 µg/ml), NT3 (10 ng/ml), BDNF (10 ng/ml), and doxycycline (4µg/ml). To support neuronal maturation, freshly prepared rat astrocytes were added to the culture in a 1:1 ratio at day 2. At day 3 the medium was changed to Neurobasal medium supplemented with Forskolin (10 µM), B-27, glutaMAX, primocin (0.1 µg/ml), NT3 (10 ng/ml), BDNF (10 ng/ml), and doxycycline (4 µg/ml). To remove the proliferating cells from the culture, cytosine-b-D-arabinofuranoside (Ara-C; 2 µM) was added to the medium at day 3. From day 6 onwards half of the medium was refreshed three times a week. From day 10 onwards, the medium was additionally supplemented with 2.5% FBS to support astrocyte viability. After day 13, Forskolin and doxycycline were removed from the medium. Cultures were kept at least until DIV49.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA isolation kit (Machery Nagel, 740955.250) according to the manufacturer's instructions
Libraries were prepared with the TruSeq Stranded mRNA kit from Illumina

value: Excitatory and inhibitory hiPSC neurons

tag: condition

tag: source

value: Healthy male, 30 years old


title: SAM24329611 CD4 aE+ CD4 AphaE_positive

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were based on Refseq canonical transcript alignments to GRCh38. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

extract_protocol: Single T cells were sorted into individual wells of 96 well plates. SMART-seq v4 kit was used to generate cDNA from the sorted cells. Samples were assessed by PicoGreen assay at this point, and only wells with detectable DNA were included in the library preparation. Libraries were prepared with the Nextera kits using 1ng of cDNA per cell, according to manufacturer's specifications. Samples in each plate were uniquely barcoded, and pooled. Each plate was pooled individually. Pooled libraries were QC'd by Bioanalyzer and Qubit. Pooled libraries were then sequenced on one lane of an Illumina HiSeq4000 (Illumina) to generating an average of ~260M of paired end 75 base pair reads per pool.

value: CD4 aE+


title: ISO-11-EI


title: NR8383 - Pass Nu 200 - rep2


title: Early follicular phase - participant 11

value: Subcutaneous adipose


title: Late follicular phase - participant 11


title: NR8383 - Pass Nu 20 - rep2


title: ISO-10-EI


title: A549-ACE2 H3K27ac SARS-CoV-2 rep2 spiChIP-Seq

value: SARS-CoV-2 isolate USA-WA1/2020


title: SAM24329576 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: CTRL-09-EI

value: Wildtype


title: A549-ACE2 H3K27ac Mock rep2 spiChIP-Seq

value: mock


title: SAM24329615 CD8 aE- CD8 AphaE_negative


title: A549-ACE2 H3K27me3 SARS-CoV-2 rep2 spiChIP-Seq


title: Mid luteal phase - participant 2


title: CTRL-07-EI


title: A549-ACE2 H3K9me3 SARS-CoV-2 rep1 spiChIP-Seq


title: A549-ACE2 H3K9me3 Mock rep1 spiChIP-Seq


title: Late follicular phase - participant 2


title: SAM24329640 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: Post ovulatory phase - participant 2

value: Post ovulatory


title: cwo5073 mutant ZT22 rep2

city: College Station

first: Paul

last: Hardin

address: 3258 TAMU Dept of Biology Buttler Hall room 100H

institute: Texas A&M University

data_processing:
Basecalls performed using RTA v2 software
Reads were mapped to the Drosophila melanogaster genome (dm6 – UCSC) with STAR aligner version 2.6.1d using the following parameters STAR --runThreadN 16
mapped reads were assembled and expression levels were quantified using Strigtie v1.3.5 following parameters described in Pertea et al., Nature Protocols. 2016. Ballgown input table files were generated in StringTie using -B option
A Python script (prepDE.py) was used to extract the read count information from the GTF files generated previously with StringTie. This matrix with read count values for all genes was used to estimate differential expression across all time points using DesSeq2
In parallel, to estimate rhythmicity of genes, the Ballgown object was filtered to remove low expressed genes (using a variance filter to remove transcripts with a variance across all samples less than one, as described in Pertea et al 2016) and as a result a matrix of 8489 genes was created with normalized FPKM values using the function gexp.
This matrix with FKPM was used to estimate significant rhythms using the programs RAIN and MetaCycle and and only genes with an adjusted p-value ≤ 0.05 and fold-change ≥ 1.3 were considered rhythmic.
Genome_build: Drosophila melanogaster genome (dm6 – UCSC)
Supplementary_files_format_and_content: Matrix table with read count values for genes combined for all samples that was used to estimate differential expression with DESeq2.
Supplementary_files_format_and_content: Matrix table with gene-level expression values (FPKM) combined for all samples that was used to evaluate rhythmic expression with RAIN and MetaCycle.
Supplementary_files_format_and_content: Ballgown input tables (from t_data CTAB file but saved here as a txt file) for each sample and replicate, with transcript-level expression values (FPKM).

organism: Drosophila melanogaster

source_name: Heads

growth_protocol: Flies were reared on standard cornmeal/agar medium supplemented with yeast and kept in 12 hr light/12 hr dark (LD) cycles at 25oC.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen), treated with a TURBO™ DNase (Thermo Fisher Scientific), precipitated and purified with Lithium Chloride (Thermo Fisher Scientific) following the manufacture’s instructions.
1.0 μg of total RNA was used to isolate mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), which was used for RNA library construction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs). The resulting cDNA products were then used as template for PCR amplification for 12 cycles following the PCR conditions in the manufacturer’s instructions, and after purification the eluted DNA fragments were sent for sequencing. RNA (cDNA) libraries were mixed and multiplexed at the same equimolar concentrations and sequenced using Illumina Next Seq 500 system using 75bp single end reads

treatment_protocol: Flies were entrained  under a condition of 12 hr light/12 hr dark (LD) cycles at 25oC for 3 days prior the collection at ZT2 and ZT14 on the fourth day.

value: mutant

value: cwo5073 mutant strain


title: ISO-05-E

value: Excitatory hiPSC neurons


title: A549-ACE2 H3K27me3  SARS-CoV-2 rep1 spiChIP-Seq


title: cwo5073 mutant ZT18 rep2


title: SAM24329598 CD4 aE+ CD4 AphaE_positive

first: Jason

institute: Genentech, Inc.


title: A549-ACE2 H3K27me3 Mock rep1 spiChIP-Seq


title: NR8383 - Pass Nu 20 - rep1

value: lung

value: alveolar macrophage cell line

value: low (passage 20)


title: ISO-06-E


title: ISO-04-E


title: Early follicular phase - participant 2

value: Early Follicular


title: SAM24329678 CD4 aE- CD4 AphaE_negative


title: A549-ACE2 H3K4me3 SARS-CoV-2 rep1 spiChIP-Seq

value: epithelial cell


title: SAM24329592 CD4 aE+ CD4 AphaE_positive


title: CTRL-08-EI

value: Excitatory and inhibitory hiPSC neurons

value: Healthy male, 30 years old


title: A549-ACE2 H3K4me3 Mock rep1 spiChIP-Seq


title: CTRL-03-E


title: CTRL-02-E


title: cwo5073 mutant ZT10 rep2


title: SAM24329859 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: SAM24329674 CD4 aE- CD4 AphaE_negative


title: CTRL-01-E


title: A549-ACE2 H3K27ac  Mock rep1 spiChIP-Seq


title: A549-ACE2 H3K27ac SARS-CoV-2 rep1 spiChIP-Seq

value: SARS-CoV-2 isolate USA-WA1/2020


title: SD_control2

value: wild type

tag: diet

value: standart diet


title: cwo5073 mutant ZT2 rep2


title: SAM24329865 CD4 aE+ CD4 AphaE_positive


title: cwo5073 mutant ZT14 rep2


title: SAM24329635 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: A549-ACE2 SMC3 SARS-CoV-2 rep1 spiChIP-Seq

value: SMC3 (Abcam, Ab9263, Lot:GR466-7)


title: SAM24329789 CD4 aE+ CD4 AphaE_positive


title: cwo5073 mutant ZT18 rep1


title: KO_2 (RGCC KO) RNAseq

city: Shanghai

first: Guang

last: He

state: China

address: 1954 Huashan Rd, Shanghai Jiao Tong University

institute: Bio-X Center

data_processing:
Quality control：Raw data (raw reads) of fastq format were firstly processed through in-house   perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome： Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b)   (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files (xlsx) containing the differential expression analysis (standard DESeq2 output)

source_name: human induced pluripotent stem cells

growth_protocol: Human ESCs were differentiated to 2D NSCs by Dual-SMAD methods

extract_protocol:
RNA was isolated from individual organoids using RNeasy Micro Kit (QIAGEN, cat. #74004) according to the manufacturers instructions.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: gene aberrations

value: RGCC Knockout

tag: days in culture

value: 12 days

value: 2D NSCs


title: KO_3 (RGCC KO) RNAseq


title: A549-ACE2 SMC3  Mock rep1 spiChIP-Seq

value: mock


title: KO_1 (RGCC KO) RNAseq


title: A549-ACE2 RAD21 SARS-CoV-2 rep1 spiChIP-Seq


title: A549-ACE2 RAD21 Mock rep1 spiChIP-Seq


title: SAM24329634 CD8 aE- CD8 AphaE_negative

city: South San Francisco

address: 1 DNA Way


title: cwo5073 mutant ZT10 rep1

value: mutant

value: cwo5073 mutant strain


title: cwo5073 mutant ZT6 rep2


title: SAM24329781 CD4 aE+ CD4 AphaE_positive


title: H9_4 (WT) RNAseq


title: A549-ACE2 CTCF  SARS-CoV-2 rep1 spiChIP-Seq

value: CTCF (Millipore, 07-729)


title: cwo5073 mutant ZT6 rep1


title: SAM24329617 CD8 aE- CD8 AphaE_negative


title: cwo5073 mutant ZT2 rep1


title: A549-ACE2 CTCF Mock rep1 spiChIP-Seq


title: SAM24329749 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: cwo5073 mutant ZT22 rep1


title: H9_2 (WT) RNAseq


title: KO_4 (RGCC KO) RNAseq


title: SAM24329664 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: A549-ACE2 RPB1 SARS-CoV-2 rep1 spiChIP-Seq

value: epithelial cell

value: RPB1 N terminus, Cell Signaling Technology, #14958S, Lot4


title: wild type (cwo5073 control) ZT22 rep2

value: wild-type

value: w1118 strain


title: cwo5073 mutant ZT14 rep1


title: A549-ACE2 SARS-CoV-2 rep2 Hi-C

data_processing:
Hi-C reads were primarily pocessed using HiC-Pro (v.2.11.0) with minor modifications. The Hi-C validPairs files were converted into cool/mcool format for further visualiztion purpose
Genome build: hg19

value: SARS-CoV-2 isolate USA-WA1/2020


title: A549-ACE2 RPB1 Mock rep1 spiChIP-Seq


title: wild type (cwo5073 control) ZT14 rep2


title: SAM24329877 CD8 aE- CD8 AphaE_negative


title: SAM24329671 CD4 aE- CD4 AphaE_negative


title: A549-ACE2 Mock rep2 Hi-C


title: wild type (cwo5073 control) ZT10 rep2


title: SAM24329770 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: wild type (cwo5073 control) ZT6 rep2


title: SAM24329610 CD4 aE+ CD4 AphaE_positive


title: H9_3 (WT) RNAseq


title: A549-ACE2 Mock rep1 Hi-C


title: SAM24360357

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
Gene models were based on GENCODE basic (v.27)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include mRNA_umi raw count values for each Sample

source_name: Sorted CD45+ cells from colonic biopsy

extract_protocol:
Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v3 following manufacturer’s guide (10x Genomics). The cell density and viability of single-cell suspension were determined by Vi-CELL XR cell counter (Beckman Coulter). All of the processed samples had a very high percentage of viable cells. The cell density was used to infer the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~6,000 cells per sample.
cDNAs and libraries were prepared following the manufacturer's user guide (10x Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems). Each library was sequenced in one lane of HiSeq4000 (Illumina) following the manufacturer's sequencing specification (10x Genomics).
scRNA-seq

treatment_protocol: Tissues were digested into single cell suspension and sorted by FACS into 3 populations: CD45+Epcam-, CD45-Epcam+, and CD45-Epcam-. Sort time was capped at 2 hours.

value: Sorted CD45+ cells from colonic biopsy

value: Healthy


title: wild type (cwo5073 control) ZT2 rep2


title: SJTUBio-X23_3 (RGCC KO) RNAseq

growth_protocol: Human ESCs were differentiated to 3D brain tissue according to the original cerebral organoid protocol (Lancaster et al. Nature 2013)

value: RGCC Knockout

value: 45 days

value: cerebral organoid


title: wild type (cwo5073 control) ZT22 rep1


title: wild type (cwo5073 control) ZT18 rep2


title: SJTUBio-X23_2 (RGCC KO) RNAseq


title: SJTUBio-X23_1 (RGCC KO) RNAseq


title: H9_1 (WT) RNAseq

value: 12 days

value: 2D NSCs


title: wild type (cwo5073 control) ZT18 rep1


title: SAM24360351


title: SAM24329909 CD8 aE+ CD8 AphaE_positive


title: 115b

city: Blacksburg

first: RODERICK

middle: V.

last: JENSEN

address: Life Sciences 1, Room 119

institute: Department of Biological Sciences at Virginia Tech

data_processing:
The Illumina paired-end fastq files for the three replicate samples for each of the two strains were aligned to the annotated PAO1 reference genome (NC_002561) using the Geneious 11 software (Biomatters, Ltd) with the default “low sensitivity” setting, allowing 10% mismatch.
The read counts aligning to each of the annotated PAO1genes were normalized using the Geneious software to compute the transcripts per million (TPM) expression levels.
Genome_build: NC_002561
Supplementary_files_format_and_content: Tab-delimited files contain the TPM normalized  gene expression values for each of the annotated genes in the PAO1 reference genome.
Supplementary_files_format_and_content: The TPM_Matrix Table is a Tab-delimited file containing the TPM normalized  gene expression values for each of the annotated genes in the PAO1 reference genomea for every sample along with  gene names and descriptions.

organism: Pseudomonas aeruginosa

source_name: Bacterial Culture

growth_protocol: A single colony from CMC-115 and CMC-097 strain was inoculated in Lysogeny broth (LB) and incubated at 37◦C at 200 revolutions per minute (rpm) for 18 h, after which they were diluted 1:100 in 50 ml fresh LB medium in three replicates.

extract_protocol:
Total RNA was isolated using the RiboPure Bacterial (RNAwiz) kit (Ambion) and the contaminating DNA was removed with the DNA-free kit (Ambion) following the manufacturer’s specification. Sequencing libraries for the RNA-Seq were constructed following the instruction of the Illumina TrueSeq RNA sample preparation by the manufacturer.
Sequencing libraries for the RNA-Seq were constructed following the instruction of the Illumina TrueSeq RNA sample preparation by the manufacturer.

treatment_protocol: 10 ml of each bacterial sample from each replicate was collected at early stationary growth phase of 5-hour

value: clincal isolate

tag: disease state

value: acute infection


title: 115c


title: wild type (cwo5073 control) ZT14 rep1


title: SJTUBio-XH9_3 (WT) RNAseq

tag: tissue


title: SAM24360348


title: 115a


title: wild type (cwo5073 control) ZT10 rep1


title: SAM24354443


title: 97c2

value: chronic infection


title: SJTUBio-XH9_2 (WT) RNAseq


title: SAM24354440


title: A549-ACE2 SARS-CoV-2 rep1 Hi-C


title: 97b


title: DRG only rep2

status: Public on Jul 22 2021

city: medford

first: Thanh

middle: Thien

last: Le

state: MASSACHUSETTS

address: 20 sawyer avenue

department: Biomedical Engineering

institute: Tufts University

data_processing:
Base calling was done with Illumina Casava by Tufts Genomic Core
Adapter sequence was trimmed using Trimmomatic, and alligned to both human (hg38) and mouse (mm10) genome with STAR 2.7.3a
Both mapped files were input into S3 Species specific sequencing algorithm to separate human and mouse reads
Differential gene expression analysis was performed using EdgeR package in R, genes with <1 cpm were filtered, and a fold change threshold of 1.2 was used.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: text files containing raw counts and differentially expressed genes

source_name: Dorsal root ganglia

growth_protocol: DRGs were dissected, isolated into single cell and seeded on PDL/laminin coated glass bottom wells. Media used: Neurobasal, 2% B27, 1% Glutamax, 1% Antibiotic-Antimycotic, 25ng/ml NGF, 10ng/ml GDNF

extract_protocol:
Lysates were prepared using Quick-RNA miniprep kit (R1057, Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA)

treatment_protocol: MDA-MB-231-GFP cells were added on D3 of DRG seeding. Control 231 cells were seeded on PDL/laminin coated glass bottom wells. Same neuronal media was used

value: SW-F

tag: age

value: 7 weeks

value: Dorsal root ganglia

value: untreated


title: DRG only rep1

tag: strain


title: SAM24360354

last: Hackney


title: wild type (cwo5073 control) ZT2 rep1

value: wild-type

value: w1118 strain


title: WT_S_H2AP_INP

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

data_processing:
Sequenced paired-end reads subjected to quality control pipeline using the FASTQ Toolkit V.1.0.0 software (Illumina) and then mapped to the Saccharomyces cerevisiae reference genome sacCer3 using the Rsubread V 2.0.1 software package with unique=TRUE parameter.  Coverage profiling was performed using bamCoverage from deepTools and RPKM normalisation method was applied. In order to compare properly the samples treated or not with RNH1, we applied a scale factor to RNH-treated samples based on the ratio between the uniquely mapped reads and the total reads of each sample.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in YPAD media at 30ºC with shaking to mid-log phase. Cultures were synchronized at G1 with α-factor and collected for G1 experiments. S phase experiments were collected after G1 release, when the cultures reached S mid-log phase.

extract_protocol:
Cells were collected, crosslinked with formaldehyde and lysed with glass beads in lysis buffer with protease inhibitors. Then chromatin was sonicated.
ThruPLEX DNA-Seq 6S (12rxn)

treatment_protocol: cell cultures were treated with Auxin 1 mM and α-factor simultaneously. After G1 release, auxin 1 mM was added again to the media.

tag: strain background


title: sen1_S_H2AP_INP

value: YMK612 MATa ura3-3::ADH1-AtTIR1-9myc (URA3) RAD5 bar1{delta} sen1::sen1-aid (hphB)


title: hpr1_S_H2AP_INP

value: YMK612 MATa ura3-3::ADH1-AtTIR1-9myc (URA3) RAD5 bar1-delta hpr1::hpr1-aid (hphB)


title: sen1_S_H2AP_IP

extract_protocol:
Cells were collected, crosslinked with formaldehyde and lysed with glass beads in lysis buffer with protease inhibitors. Then chromatin was sonicated and immunoprecipitated with H2AP specific antibody.
ThruPLEX DNA-Seq 6S (12rxn)


title: WT_S_H2AP_IP


title: hpr1_S_H2AP_IP


title: control1 [N2-C1]

city: shanghai

first: shuang

last: yuan

email: frosty52@163.com, frosty52@126.com

address: No.910, Hengshan Road

institute: The international peace maternity and child health hospital

data_processing:
library strategy: circRNA-seq
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: Ishikawa Cell_control

extract_protocol:
RNA extraction protocol
library construction protocol

tag: cell line

value: Ishikawa Cell

value: none; control


title: control2 [N2-C2]


title: control3 [N2-C3]


title: treat2 [N2-M2]

source_name: Ishikawa Cell_treat

value: MPA


title: wild type (cwo5073 control) ZT6 rep1


title: DRG only rep3


title: 97a

tag: cell type


title: SJTUBio-XH9_1 (WT) RNAseq

value: 45 days

value: cerebral organoid


title: treat1 [N2-M1]


title: 905

city: WEST HOLLYWOOD

first: Moray

last: Campbell

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Sequenced on HiSeq 4000; bcl2fastq v2.19.1.403 base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Rsubread align function
Read counts for each transcript were obtained using featureCounts (Liao 2014).
Raw count data were directly analyzed for differential gene expression by using the edgeR  (Robinson 2010).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow: AML

extract_protocol:
Bone marrow was harvested and enriched for AML using MACS (Milteny Biotec) separation of human CD45+ cells. RNA was harvested using Trizol reagent. Illumina NEBNext Ultra II Directional RNA Library Prep Kit (Cat# E7765) was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment cohort

value: Gilteritinib 30mg/kg


title: 921


title: 924


title: 904


title: 926


title: 903


title: 911


title: 912


title: 923


title: 925


title: 914


title: treat3 [N2-M3]


title: 917


title: 908


title: 907


title: 910

value: Vehicle


title: 906


title: 909


title: 915


title: 922


title: 927


title: 916


title: 901


title: 918


title: 679


title: 668


title: 675


title: 661


title: 680


title: 656


title: 662


title: 678


title: 674


title: 669


title: 667


title: 654


title: 658


title: 666


title: 659


title: 660


title: 655


title: 671


title: 913


title: 653


title: 652


title: 665


title: 676


title: trd_16

city: Philadelphia

middle: T

last: Ranum

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

institute: The Children's Hospital of Philadelphia

data_processing:
Read Alignment with STAR_2.6.0c
Custom splicing analysis pipeline written in R
Genome_build: GRCh38
Supplementary_files_format_and_content: STAR generated tab delimited splice junction counts files "_SJ_out.tab"

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies) according to the manufacturer’s protocol, with the exception of 1 µL Glycoblue (Life Technologies) in addition to the aqueous phase on the isopropanol precipitation step and a single wash with cold 70% ethanol.
Illumina TruSeq Stranded Total RNA kit with Ribozero gold ribosomal delpletion

value: human cell line

value: 25nM LMI070


title: trd_14


title: trd_15


title: ctrl_10

value: DMSO


title: trd_13


title: ctrl_12


title: ctrl_9


title: ctrl_11


title: HeLa control DMSO - Input DNA replicate 2

city: Barcelona

first: Maria

middle: Pia

last: Cosma

address: Dr Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Centre for Genomic Regulation

data_processing:
Illumina RTA 1.18.66.3 software was used for basecalling.
ChIP-seq reads were filtered for low quality ones using fastp version 0.20.0 with default parameters
Filtered reads aligned to the GRCh38 genome assembly using STAR version 2.5.2a with the following parameters: --alignIntronMax 1 --outFilterMultimapNmax 1
Resulting bam files were filtered for duplicated reads using Picard tools version 2.6.0 and merged using samtools version 1.10
Peaks were called using MACS version 3.0.0a5 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig file of treatment pileup signal normalized to input
Supplementary_files_format_and_content: Peaks text file

source_name: HeLa

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Thermo Fisher Scientific, #41965039) supplemented with 10% Fetal Bovine Serum (FBS, Thermo Fisher Scientific, #10270106), 1% Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 1% GlutaMAX (Thermo Fisher Scientific, #35050038).

extract_protocol:
Nuclear chromatin extracts were prepared from 1% formaldehyde crosslinked HeLa cells and Histone-DNA complexes were immunoprecipitated with H3K4me2 antibody. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared using the NEBNext Ultra DNA Library Prep for Illumina kit (#E7370) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with DMSO 1:1000 (control, mock treatment) for 5h.

value: HeLa

tag: chip antibody


title: HeLa control DMSO - Input DNA replicate 1


title: HeLa control DMSO - H3K4me2 -replicate 2

value: H3K4me2 (Millipore, #07-030)


title: HeLa control DMSO - H3K4me2 -replicate 1


title: 657


title: OlaR SUM1315 25 uM olaparib  rep3

city: Detroit

first: Malathy

middle: P

last: Shekhar

state: MI

address: 421 East Canfield Avenue

department: Oncology

institute: Wayne State University

data_processing:
Data were demultiplexed using Illumina's CASAVA 1.8.2 software.
After quality was assessed using FastQC, reads were aligned to the human reference genome using STAR before tabulation using htseq-count.
RNA-seq data were analyzed using the R/Bioconductor package edgeR.
Read counts within and between samples were normalized using the trimmed mean of M-values (TMM) method.
Genome_build: hg38
Supplementary_files_format_and_content: Parental_OlaR TNBC_.csv contains counts and differential expressions between isogenic parental and olaparib resistant MDA-MB-468 and SUM1315 cells treated with olaprib, cisplatin or combinations.

source_name: TNBC BRCA1 mutant

growth_protocol: Parental MDA-MB-468 and SUM1315 cells were cultured in DMEM/F12 supplemented with 5% fetal bovine serum. OlaR (OR) MDA-MB-468 and SUM1315 cells were maintained in same media supplemented with 15 or 25 mM olaparib, respectively.

extract_protocol:
Total RNA was isolated from cell lines using RNA later followed by purification with RNeasy mini kit (Qiagen) using the manufacturer’s recommended in-solution DNase digestion.
RNA-seq libraries were prepared using Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina) from 200 ng of DNAse I treated total RNA. Libraries were quantified using Qubit 2.0 dsDNA HS kit and the size distribution determined on a Fragment Analyzer.

treatment_protocol: Parental MDA-MB-468 cells were treated overnight with 3 mM olaparib, 1 or 2.5 mM cisplatin, or a combination of 3 mM olaparib and 1 or 2.5 mM cisplatin. Parental SUM1315 cells were treated overnight with 8  mM olaparib, 2 or 4 mM cisplatin, or a combination of 8  mM olaparib and 2 or 4 mM cisplatin. OlaR MDA-MB-468 cells maintained in 15 mM olaparib were treated with 1 or 2.5 mM cisplatin. OlaR SUM1315 cells were maintained in 25 mM olaparib were treated with 2 or 4 mM cisplatin.


title: OlaR SUM1315 25 uM olaparib + 4 uM cisplatin  rep2


title: OlaR SUM1315 25 uM olaparib + 2 uM cisplatin  rep2


title: OlaR SUM1315 25 uM olaparib + 2 uM cisplatin  rep1


title: OlaR SUM1315 25 uM olaparib  rep2


title: olaparib+ 4 uM cisplatin SUM1315 rep3


title: OlaR SUM1315 25 uM olaparib + 2 uM cisplatin  rep3


title: olaparib+ 4 uM cisplatin SUM1315 rep2


title: OlaR SUM1315 25 uM olaparib  rep1


title: olaparib+2 uM cisplatin SUM1315 rep3


title: olaparib+2 uM cisplatin SUM1315 rep2


title: OlaR SUM1315 25 uM olaparib + 4 uM cisplatin  rep1


title: olaparib+ 4 uM cisplatin SUM1315 rep1


title: olaparib+2 uM cisplatin SUM1315 rep1


title: 4 uM cisplatin SUM1315 rep3


title: 4 uM cisplatin SUM1315 rep2


title: OlaR SUM1315 25 uM olaparib + 4 uM cisplatin  rep3


title: 4 uM cisplatin SUM1315 rep1


title: 2 uM cisplatin SUM1315 rep2


title: Meth replicate 3

city: Porto

first: Teresa

last: Canedo

address: R. Alfredo Allen 208

country: Portugal

data_processing:
Thermo Fisher Torrent Suite V5.12 used for basecalling
Thermo Fisher Torrent Suite V5.12 used for alignment
Thermo Fisher ampliSeqRNA V5.12 in Torrent Suite V5.12 used for reads counting and normalization
Genome_build: AmpliSeq_Mouse_Transcriptome_v1_designed

source_name: Microglial cells

extract_protocol:
Brains from PBS-perfused mice were collected and microglial cells (Cd11b+, CD45low, and CD206-) were sorted on the FACS ARIA (BD Immunocytometry Systems). Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's instructions.
Ion Torrent sequencing libraries were prepared according to AmpliSeq™ Transcriptome Mouse Gene Expression Kit protocol following manufacturer's instructions. Briefly, 1 ng of total RNA was reverse transcribed, the resulting cDNA was amplified for 16 cycles by adding PCR Master Mix and the AmpliSeq Mouse transcriptome gene expression primer pool. Amplicons were digested with the proprietary FuPa enzyme, then barcoded adapters were ligated onto the target amplicons. The library amplicons were bound to magnetic beads, and residual reaction components were washed off. Libraries were amplified, re-purified and individually quantified using Agilent TapeStation High Sensitivity tape. Individual libraries were diluted to a 50 pM concentration and pooled equally. Emulsion PCR, templating and 550 chip loading was performed with an Ion Chef Instrument (Thermo-Fisher). Sequencing was performed on an Ion S5XL™ sequencer (Thermo-Fisher).

value: Adult

value: Microglial cells

value: 4x 5mg/kg Meth, 2h apart


title: 2 uM cisplatin SUM1315 rep3


title: Meth replicate 2


title: 2 uM cisplatin SUM1315 rep1


title: olaparib SUM1315 rep3


title: Meth replicate 1


title: olaparib SUM1315 rep1


title: Control SUM1315 rep3


title: olaparib SUM1315 rep2


title: Control SUM1315 rep2


title: OlaR MDA-MB-468 15 uM olaparib + 2.5 uM cisplatin  rep3

source_name: TNBC BRCA1 wild type


title: 231 + DRG rep1

value: SW-F

value: 7 weeks

value: Dorsal root ganglia

value: co-cultured with DRG


title: Saline replicate 3

value: 4xSaline, 2h apart


title: 231 + DRG rep3


title: Saline replicate 2


title: Saline replicate 1


title: 231 + DRG rep2


title: Control SUM1315 rep1


title: OlaR MDA-MB-468 15 uM olaparib + 2.5 uM cisplatin  rep1


title: 231 + conditioned media rep3

value: cultured in DRG conditioned media


title: OlaR MDA-MB-468 15 uM olaparib + 1 uM cisplatin  rep3


title: 231 + conditioned media rep2


title: 231 + conditioned media rep1


title: 231 only rep3

value: untreated


title: SAM24329613 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: OlaR MDA-MB-468 15 uM olaparib + 1 uM cisplatin  rep2


title: OlaR MDA-MB-468 15 uM olaparib  rep2


title: OlaR MDA-MB-468 15 uM olaparib + 1 uM cisplatin  rep1


title: Mother

city: Houston

first: Christopher

last: Grochowski

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0)

data_processing: Agilent Feature Extraction Software (version 12.0) was used for background subtraction and normalization.

source_name: Whole Blood Extracted Genomic DNA

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: gender

value: Female

value: peripheral blood

tag: affected status

value: Unaffected

tag: neurological phenotype

tag: structural abnormalities

tag: muscle phenotype

tag: skin/hair abnormalities

source_name: Reference Sample BAB3778

tag: sample type

value: Reference Sample


title: olaparib+ 2.5 uM cisplatin MDA-MB-468 rep3


title: Proband

value: Affected

value: Developmental Delay

value: Facial Dymorphism

value: Hypotonia

value: Hirsutism/Hypertrichosis


title: Father

value: Male

source_name: Reference Sample BAB5319


title: olaparib+ 2.5 uM cisplatin MDA-MB-468 rep2


title: olaparib+1 uM cisplatin MDA-MB-468 rep3


title: 231 only rep1

tag: treatment


title: olaparib+1 uM cisplatin MDA-MB-468 rep2


title: olaparib+ 2.5 uM cisplatin MDA-MB-468 rep1


title: OlaR MDA-MB-468 15 uM olaparib  rep1


title: VZ-B-3

city: Kunming

first: Decai

last: Xiang

address: Qinglongshan

institute: Yunnan Animal Science and Veterinary Institute

data_processing:
These embryos were transferred into cell lysis buffer, immediately frozen in LN2 and stored at −80 °C. The full-length cDNA was generated with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA. USA) following manufacturer’s instructions.
Briefly, first-strand cDNA was synthesized using 3’ SMART-Seq CDS Primer II A and SMART-Seq v4 Oligonucleotide, following by cDNA amplification through LD-PCR. Then the amplified cDNA was purified by immobilization on AMPure XP beads and validated using the Agilent High Sensitivity DNA Kit on an Agilent 2100 bioanalyzer (Agilent Technologies, CA, USA).
Library preparation was generated from an equal amount of cDNA samples using the Illumina Nextera XT DNA Sample Preparation Kit (Illumina, San Diego, CA, USA), and library quality was assessed in an Agilent 2100 bioanalyzer.
RNA-Seq was conducted on the Illumina Novaseq™ 6000 platform (Illumina, San Diego, CA, USA) in the 150 bp paired-end configuration by LC-Bio Sciences (Hangzhou, China).
Firstly, the reads that contained adaptor contamination, low quality bases and undetermined bases were removed by Cutadapt (https://code.google.com/p/cutadapt/). Then FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to verify sequence quality. The clean reads were mapped to the genome data of Sus scrofa with Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and Hisat2 (https://daehwankimlab.github.io/hisat2/), and mapped reads of each sample were subsequently assembled using StringTie (http://ccb.jhu.edu/software/stringtie/). Finally, all transcriptomes were merged to reconstruct a comprehensive transcriptome using a Perl script.
Supplementary_files_format_and_content: excel,expression profiles

organism: Sus scrofa

source_name: blastocyst derived from vitrified porcine cloned zygotes

growth_protocol: Reconstructed cloned embryos were washed three times in PZM-3 and then cultured in the same medium under conditions described above.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: The cloned embryos of each stage during preimplantation development were collected at the following time points after chemical activation: 24 h for 2-cells (4 per pool), 48 h for 4-cells (2 per pool), and 144 h for blastocysts (1 per pool).

value: zygotes


title: VZ-B-2


title: VZ-B-1


title: olaparib+1 uM cisplatin MDA-MB-468 rep1


title: 2.5 uM cisplatin MDA-MB-468 rep3


title: OlaR MDA-MB-468 15 uM olaparib + 2.5 uM cisplatin  rep2


title: FZ-B-3

source_name: blastocyst derived from fresh porcine cloned zygotes


title: VZ-4C-2

source_name: 4-cells derived from vitrified porcine cloned zygotes


title: FZ-B-2


title: VZ-4C-1


title: 2.5 uM cisplatin MDA-MB-468 rep2


title: FZ-B-1


title: ΔMx1Adam10ffRag2KO CD45-positive cells, scRNA-seq

city: Bethesda

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

data_processing:
Post-processing and quality control were performed using the 10x Cell Ranger pipelines (v2.2.0 for main figure datasets, v3.0.2 for supplementary figure datasets, 10x Genomics). Reads were aligned to mouse reference genome (mm10) using a STAR aligner to produce the digital gene expression matrix (10x Genomics Cell Ranger).
Genome_build: mm10
Supplementary_files_format_and_content: Mx1Cre-Adam10ffRag2KO_filtered_feature_bc_matrix.h5

source_name: skin

extract_protocol:
Droplet-based scRNA-seq captures were performed with 10x Chromium (10x Genomics) in accordance with the manufacturer protocol.
cDNA libraries were prepared following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit ( v3 Chemistry).
Single-cell RNA-seq

treatment_protocol: CD45+ immune cells were sorted from ADAM10ΔMx1 Rag2–/– mice 30 days post-induction with poly(I:C). Whole skin cell suspensions were sorted for viable cells based on SYTOXTMRed dead cell stain. Cells were further sorted for CD45+ cells.

value: CD45-positive cells

value: skin

tag: genotype

value: Mx1-Cre x Adam10f/f Rag2KO

value: poly(I:C) injection

tag: time

value: Day 30 post-injection


title: VZ-4C-3


title: mpkCCD dDAVP 24h replicate 3

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 (M22) using salmon (0.14.10).
Genome_build: GRCm38.p6 (M22)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse cortical collecting duct cell line

growth_protocol: mpkCCD cells were grown on a permeable filter membrane for 6 days in the complete medium and maintained in the minimum medium for 24 hours before dDAVP treatment.

extract_protocol:
Cells were lyzed in Trizol. Total RNA was extracted using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
cDNAs were synthesized from total RNA using SMART-Seq HT kit (Takara Bio). cDNA libraries were prepared for sequencing using a Nextera DNA library preparation protocol.

treatment_protocol: Vasopressin analog dDAVP (0.1 M) or vehicle was treated at the basolateral side (a bottom chamber) and then cells were incubated for appropriate time according to the time points.

tag: tissue

value: kidney

tag: age

value: passage 10-11

value: wild type

value: dDAVP


title: 2.5 uM cisplatin MDA-MB-468 rep1


title: OlaR MDA-MB-468 15 uM olaparib  rep3


title: 231 only rep2

tag: strain

value: untreated


title: mpkCCD dDAVP 24h replicate 1

value: mouse cortical collecting duct cell line


title: mpkCCD vehicle 24h replicate 3

value: Vehicle


title: mpkCCD dDAVP 24h replicate 2


title: FZ-4C-2

source_name: 4-cells derived from fresh porcine cloned zygotes


title: 1 uM cisplatin MDA-MB-468 rep3

tag: cell line


title: FZ-4C-3


title: mpkCCD vehicle 24h replicate 2

tag: cell type


title: VZ-2C-3

source_name: 2-cells derived from vitrified porcine cloned zygotes


title: 1 uM cisplatin MDA-MB-468 rep2


title: mpkCCD vehicle 24h replicate 1


title: FZ-4C-1


title: mpkCCD vehicle 12h replicate 3


title: mpkCCD dDAVP 12h replicate 1


title: olaparib MDA-MB-468 rep3


title: mpkCCD dDAVP 6h replicate 3


title: VZ-2C-2


title: mpkCCD vehicle 12h replicate 2


title: FZ-2C-3

source_name: 2-cells derived from fresh porcine cloned zygotes


title: mpkCCD dDAVP 12h replicate 3


title: mpkCCD dDAVP 6h replicate 1


title: 1 uM cisplatin MDA-MB-468 rep1


title: mpkCCD dDAVP 12h replicate 2


title: VZ-2C-1


title: mpkCCD vehicle 12h replicate 1


title: olaparib MDA-MB-468 rep2


title: FZ-2C-1


title: Control MDA-MB-468 rep2


title: mpkCCD dDAVP 6h replicate 2


title: Control MDA-MB-468 rep1


title: mpkCCD vehicle 3h replicate 1


title: FZ-2C-2


title: Control MDA-MB-468 rep3


title: mpkCCD vehicle 6h replicate 3


title: mpkCCD vehicle 6h replicate 2