title: HeLa_4sU_siWdr82_rep3

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

description: HeLa siWdr82 rep 3

data_processing:
After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), strand specific single end reads (76 bp) were aligned using TopHat v2.1.0 1 (PMID:23618408), allowing up to two mismatches and using the option --b2-very- sensitive --library-type fr-firststrand. Indels due to sequencing errors were identified using Bowtie2 v 2.2.6 (PMID: 19261174). Reads originating from the two strands were separated according to the XS:A:+/XS:A:-flag provided by TopHat2 (PMID:23618408).
SICER v2 (PMID: 24743992) was used to detect the extra-genic transcripts regulated in cells depleted of individual factors. The entire genome was partitioned into blocks of non-overlapping 500 bp windows with a gap size <1000 nt. An effective genome fraction of 1, a fragment size of 0 and a False Discovery Rate (FDR) cut-off <0.01 were used.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM containing 10% South American origin Foetal Bovine Serum, 1% L-Glutamax solution and 1% Penicillin/Streptomycin solution.

extract_protocol:
Total RNA was extracted using Trizol (Thermofisher, cat 15596026) and nascent 4sU-labelled RNA was then extracted as described (Austenaa et al. 2015, PMID 26593720)
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 100-300 ng of nascent 4sU-labelled RNA, without ribosomal depletion.

treatment_protocol: 4-thio-uridine was added to the medium at a final concentration of 300 uM for 45 min before harvesting the cells.

value: HeLa

value: human cervix, epitheloid carcinoma

tag: treatment


title: HeLa_4sU_siZc3h4_rep3

status: Public on Feb 01 2021

type: SRA

description: HeLa siZc3h4 rep 3

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: NCI-H1299 cells, Pooled input

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

country: Japan

institute: Tokyo Medical University

library_source: genomic

data_processing:
Sequence Analysis: The 75-nt single-end (SE75) sequence reads generated by Illumina  sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm (“bwa  aln/samse” with default settings). Alignment information for each read is stored in the BAM format.  Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map  uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR  duplicates”) are removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected  library. To identify the density of fragments (extended tags) along the genome, the genome is  divided into 32-nt bins and the number of fragments in each bin is determined. This information  (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in  genome browsers (see Section VI.). bigWig files also provide the peak metrics in the Active Motif  analysis program described below.
Peak Finding: The generic term “Interval” is used to describe genomic regions with local  enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end  coordinate. The two main peak callers used at Active Motif are MACS/MACS2 (Zhang et al.,  Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).  MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often  containing a consensus DNA sequence) as well as many active histone marks and methyl-C  enriched regions, while SICER is used to study proteins that bind to extended regions in the  genome (such as repressive histone marks or RNA polymerase II). Both methods look for  3 of 8  Active Motif, Inc. • 1914 Palomar Oaks Way, Suite 150 • Carlsbad, CA 92008 • toll free 877.222.9543 • fax 760.431.1351  www.activemotif.com  significant enrichments in the ChIP/IP data file when compared to the Input data file or relative to  neighboring background regions.
Standard Normalization: In the default analysis, the tag number of all samples (within a  comparison group) is reduced by random sampling to the number of tags present in the smallest  sample. This normalization method works well for most assays where the majority of tags map to  background (i.e. non-peak) regions, and it can detect site-specific as well as global differences in  target enrichments between samples.
Spike-in Adjustment: If spike-in of Drosophila chromatin was performed, the number of test tags  are adjusted (again by down-sampling) by a factor that would result in the same number of spikein  Drosophila tags for each sample. Spike-in adjustment can be useful for rare assays where  standard normalization does not result in the expected global differences in enrichments  between test samples. (This normalization method is not available for MethylPath.)
Supplementary_files_format_and_content: BW

molecule: genomic DNA

growth_protocol: RPMI-1640 supplemented with 10% fetal calf serum, penicillin (100 units/ml), and streptomycin (100 μg/ml)

extract_protocol:
ActiveMotif
ActiveMotif

treatment_protocol: miR-34a was transfected into cells using the Lipofectamine RNAiMAX transfection reagent (Life Technologies, Gaithersburg, MD, USA) with a final RNA concentration of 25 nmol/l.

value: carcinoma; non-small cell lung cancer

tag: chip antibody


title: NCI-H1299 cells, miR-34a-treated

value: Total RNA Pol II antibody AbFlex®, Active Motif, Cat#91151, lot#24317002, 5ul


title: NCI-H1299 cells, untreated


title: D12_1: PRDM15 Exon gRNA2 rep2

city: Boston

first: Nina

last: Mann

state: MA

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

data_processing:
Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75 bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities
Sequenced reads were mapped to the GRCh38 with NCBI Ensembl IDs using STAR aligner (R software)
edgeR (R software) was used to generate TMM-normalized counts per million (CPM)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with normalized counts per million (CPM) for every gene and every sample

source_name: Immortalized human podocytes

growth_protocol: Immortalized human podocytes were cultured at 33degC in RPMI media with added penicillin/streptomycin (1%) and insulin, transferrin, and selenium (1%), and 10% fetal bovine serum

extract_protocol:
RNA was extracted from cultured podocytes using the Qiagen Rneasy Mini Kit per the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Immortalized human podocytes

tag: genotype/variation

value: PRDM15 knock-out


title: D12_1: PRDM15 Exon gRNA2 rep1


title: HeLa_4sU_siCtl_rep3

description: HeLa siCtl rep 3

value: siCtl


title: A6_3: Control gRNA rep3

value: Control


title: A6_2: Control gRNA rep2


title: d25_R541C_3_RNAseq

city: Philadelphia

first: Parisha

last: Shah

state: PA

address: 3400 Civic Ctr. Blvd

department: Medicine, Cell and Developmental Biology, Cardiovascular Institute

institute: University of Pennsylvania Perelman School of Medicine

description:
mRNA
Control_vs_R541C.DEG_output.txt
RNAseq.log2cpmmatrix.filtered.txt
RNAseq.log2cpmmatrix.unfiltered.txt

data_processing:
ChIP-seq data processing: Raw reads were trimmed with Trimmomatic v0.32 and then aligned to hg19 genome using bwa (Version 0.7.17) aln with parameters ‘bwa aln -q 5 -l 32 -k 2’. Bwa samse was then used to convert to sam format. Sam files were then filtered using samtools(version 1.7) view with ‘-F 1804 -q 30’ parameters, sorted and converted to bam format. PCR duplicates were removed using Picardtools MarkDuplicates command with ‘VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true’ parameters.
ChIPseq bigWig generation: Merged bam files were input intoDeeptools(version 3.1.1) bamCoverage with ‘--normalizeUsing RPGC -bs 1 -e 200’ and hg19 blacklist. Resulting bigWig tracks where then input into Deeptools bigWigCompare with parameters ‘--normalizeUsing RPGC -bs 10 -e 200 --operation subtract’ and hg19 blacklist, to create input normalized bigWig coverage tracks for each treatment.
LAD and KDD calling: LADs and KDDs were called using EDD  (version 1.1.18) with paired merged CHiP and Input bam files, parameters ‘-bin-size auto -g 4 --fdr 0.05’, modified parameter config file ‘required_fraction_of_informative_bins = 0.98’ and hg19 blacklist.
Differential peak calling:Peaks for differential binding analysis were called using Epic2 (version 0.0.16) with paired replicate CHiP and Input bam files, and parameters ‘-fs 200 -bin 600 -g 4 -fdr 0.05’. Resulting peak files, along with paired replicate Chip and Input bam files, were input into DiffBind for differential binding analysis using fdr <0.1 as significance threshold.
RNAseq data processing:Raw reads were trimmed with Trimmomatic v0.32 and then aligned to hg19 genome using STAR(version 2.6.0c) ’ and then filtered using samtools view with ‘-F 4 -q 10’ parameters. Rsubread featureCounts quantified the number of reads per feature of Ensembl hg19 gene annotation file. For differential gene expression analysis, genes with <1 count per million (CPM) in less than 25% of samples were removed from differential expression analysis. For analyses using all genes, no cpm filter was applied.  EdgeR’s calcNormFactors was used to calculate library size normalization factors. Limma voom function was used to log2 transform and quantile normalize the CPM matrix. For differential expression analysis, Limma lmFit, contrast.fit and eBayes functions were used to fit the linear model, compute coefficients and standard error, and then perform differential expression calculation with Benjamini–Hochberg multiple correction adjusted P-values (Benjamini and Hochberg, 1995). Cutoffs of FDR≤0.05 and log2 fold change ≥1.5 or ≤−1.5 were used for differentially upregulated or downregulated genes.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed, csv

source_name: iPSC-derived Cardiac Myocytes

growth_protocol: Cells were grown under feeder-free conditions on Geltrex (Life Technologies)-coated plates in chemically defined StemMACS IPS-Brew XF medium (Miltenyi Biotec) supplemented with 1% penicillin/streptomycin and 5 μg/mL Plasmocin (InvivoGen). Medium was changed every 24 hours. At 80-90% confluence, cells were dissociated with Accutase and split at a 1:8 ratio to create frozen stocks and working stocks that were maintained in culture.

extract_protocol:
RNA: iPSC-CMs, -heps, and -adips were isolated at indicated times, scraped from plates with 1xPBS, and centrifuged at 1500g for 5 minutes at room temperature. After discarding supernatant, cell pellets were flash frozen in dry ice and stored at -80C until processing. RNA was isolated using QIAGEN RNeasy total RNA extraction kit (QIAGEN). RNA quality was analyzed by BioAnalyzer; samples with RIN scores >8 were chose for further processing.     ChIP: Control or LMNA T10I iPSC-derived cardiac myocyctes or hepatocytes were crosslinked in culture by addition of methanol-free formaldehyde (ThermoFisher; final 1% v/v) and incubated at room temperature for 10 minutes with gentle rotation. Crosslinking was quenched by addition of glycine (final 125mM) and incubated at room temperature for 5 minutes with gentle rotation. Media was discarded and replaced with PBS; cells were scraped and transferred to conical tubes and pelleted by centrifugation (250xg, 5 minutes at room temperature). Supernatant was removed, and pellets were flash frozen on dry ice and stored at -80C.    Six hours before lysing cells, 30uL protein G magnetic beads (per ChIP sample) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250uL blocking buffer and 2ug antibody (Lamin B1: ab16048 [Abcam]; H3K9me2: ab1220 [Abcam]) and rotated at 4C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP‐40, 0.25% Triton X‐100, and protease inhibitors), and rotated at 4C for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris‐HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris‐HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na‐Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris) Samples were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50uL blocking buffer and added to 500ug input protein for overnight incubation with rotation at 4C. 50ug lysate was aliquoted and stored at -20C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES‐KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP‐40, 0.7% Na‐Deoxycholate) with 2-minute incubation at room temperature with rotation for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes with rotation at room temperature before final resuspension in 210uL elution buffer (50mM Tris‐HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65C for 30 minutes. 200uL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65C with agitation for a minimum of 12 hours, but not more than 18 hours. 200uL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were RNaseA treated (final 0.2mg/mL RNase; 37C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich for poly-A tailed RNA molecules. RNA-seq library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).     ChIP and input DNA was quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB).
ChIP and RNA samples were indexed for multiplex sequencing. Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems). Libraries were sequenced on the Illumina NextSeq500 platform (vII; 75bp single end sequencing; Illumina).

treatment_protocol: Undifferentiated iPSCs were detached by a 4-min incubation with Accutase (STEMCELL Technologies) and seeded onto Geltrex (Life Technologies)-coated plates at a density of 200,000 cells/cm2. To induce cardiac differentiation, we replaced iPSC medium with RPMI/B27-insulin (RPMI-1640 with 2% B-27 Supplement Minus Insulin; Thermo Fisher Scientific) medium supplemented with recombinant human/mouse/rat activin A (100 ng/mL; R&D Systems) for 18 hours, followed by recombinant human BMP-4 (5 ng/mL; R&D Systems) and CHIR 99021 (1 nM, Tocris) for 2 days. The medium was then exchanged for RPMI/B27–insulin with Xav (1 nM, Tocris) for another 2 days. The medium was then replaced with RPMI/B27–insulin without supplementary cytokines for three more days. RPMI-B27 (with insulin) was added every 2 to 3 days thereafter. Widespread spontaneous beating activity was typically observed 10 days after addition of activin A. For hepatic differentiation, cells were incubated in definitive endoderm media with recommended supplements (Stem Cell Technologies) for 4 days in ambient O2 and 5% CO2, yielding homogeneous monolayer of definitive endoderm cells. At day 5, cells were incubated with recombinant human BMP-4 (20ng/mL; Peprotech) and recombinant human FGF basic (10ng/mL; R&D Systems) for 5 days in RPMI-B27 (with insulin) in 5% O2 and 5% CO2, yielding hepatic progenitor cells. At day 10, cells were incubated in RPMI-B-27 (with insulin) supplemented with recombinant human HGF (20ng/mL; PeproTech) for 5 days at 5% O2 and 5% CO2, yielding immature HLCs. Finally, at d15, cells were incubated with HCM Hepatocyte Culture Medium (Lonza) without EGF and supplemented with recombinant human oncostatin M (20ng/mL; R&D Systems) for 7 days in ambient O2 and 5% CO2, yielding mature HLCs, which were collected at day 23. For adipogenic differentiation, iPSCs were induced for mesoderm in STEMdiff Mesoderm Induction Medium (Stem Cell Technologies) for 4 days.  On day 5, cells were incubated with Mesencult-ACF Plus medium (Stem Cell Technologies) to induce mesenchymal stem cell (MSC) formation. Media was refreshed daily from day 5 to day 12. Starting on day 12 and every 3 days thereafter until day 30, cells were passaged at 1:2 or 1:3 ratio in the same media and assayed at each passage for MSC surface markers CD105, CD73, CD90, CD146 and PDGFR by flow cytometry. At day 30, when the cells were 95% positive for the MSC markers, they were then plated in Mesencult-ACF attachment substrate (Stem Cell Technologies)-coated plated for adipogenic conversion. The following day, cells were incubated for 2 days in Mesencult ACF Plus media supplemented with human IL-4 (10nM) and the TGFBinhibitor SB431542 to obtain adipogenic precursors. Cells were then induced for adipogenesis for 3 days in EGM-2 media without FGF basic (Lonza) supplemented with adipogenic induction cocktail (0.5mM IBMX, 5uM dexamethasone, 125uM indomethacin, 2nM T3, 170nM insulin, 1uM rosiglitazone, and 5uM SB31542). Finally, cells were maintained in EGM-2 without FGF basic supplemented with only insulin, T3, rosiglitazone and SB431542 until adipogenesis is complete. Beige adipocytes were harvested on day 14-20 from plating for subsequent experiments.

tag: time point

value: day 25

tag: strain

value: DiPS 1016 SevA LMNA R541C

value: mRNA

tag: replicate


title: d25_R541C_2_RNAseq


title: d25_R541C_1_RNAseq


title: ChIP-seq_MOLM-13_H3K4me3_rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
ChIP-seq raw reads were aligned to the hg38 genome assembly using Bowtie2 with the default parameters
Bigwig files were generated by deepTools  bamCoverage with the parameters  of  --normalizeUsing RPGC --extendReads 200
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file

growth_protocol: Human leukemia cells MOLM-13 were cultured in RPMI-1640 medium containing 10% FBS and 1% penicillin/streptomycin. Cultures were incubated at 37°C in 5% CO2.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 1-10 ng of ChIP DNA was processed for library generation using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s protocol (New England Biolabs).

value: human myeloid leukemia cell line


title: R541C_d23HEP_LB1_2_Redo

description:
ChIP DNA
R541C_LB_Hep.RPGC.inputsubtract.bigWig
R541C_LB_CM_peaks.clipped.bed

source_name: iPSC derived Hepatocytes

value: day 23

value: LB1 (abcam, ab16048)


title: R541C_d25_Input_3_Redo

description:
ChIP DNA
R541C_H3K9me2_CM.RPGC.inputsubtract.bigWig
R541C_LB_CM.RPGC.inputsubtract.bigWig

value: Input


title: ChIP-seq_MOLM-13_H3K4me3_rep1


title: d25_R541C_4_RNAseq


title: R541C_d25_Input_3

description:
genomic DNA
R541C_H3K9me2_CM.RPGC.inputsubtract.bigWig
R541C_LB_CM.RPGC.inputsubtract.bigWig


title: R541C_d25_K9me2_3

description:
ChIP DNA
R541C_H3K9me2_CM.RPGC.inputsubtract.bigWig
R541C_H3K9me2_CM_peaks.clipped.bed

value: H3K9me2 (abcam, ab1220)


title: D12_1: PRDM15 Exon gRNA2 rep3


title: C7_1: PRDM15 Exon gRNA1 rep1


title: C7_1: PRDM15 Exon gRNA1 rep2


title: C7_1: PRDM15 Exon gRNA1 rep3


title: A6_1: Control gRNA rep1


title: R541C_d23HEP_K9me2_2

description:
ChIP DNA
R541C_H3K9me2_Hep.RPGC.inputsubtract.bigWig
R541C_H3K9me2_Hep_peaks.clipped.bed


title: R541C_d23HEP_Input_2

description:
genomic DNA
R541C_H3K9me2_Hep.RPGC.inputsubtract.bigWig
R541C_LB_Hep.RPGC.inputsubtract.bigWig


title: R541C_d23HEP_K9me2_1


title: R541C_d23HEP_Input_1


title: R541C_d23HEP_LB1_2

description:
ChIP DNA
R541C_LB_Hep.RPGC.inputsubtract.bigWig
R541C_LB_Hep_peaks.clipped.bed


title: R541C_d23HEP_LB1_1


title: R541C_d25_LB1_3

description:
ChIP DNA
R541C_LB_CM.RPGC.inputsubtract.bigWig
R541C_LB_CM_peaks.clipped.bed


title: T10I_d25ADIP_LB1_1

description:
ChIP DNA
T10I_LB_Adip.RPGC.inputsubtract.bigWig
T10I_LB_Adip_peaks.clipped.bed

source_name: iPSC derived Adipocytes

value: DiPS 1016 SevA LMNA T10I


title: R541C_d25ADIP_K9me2_2

description:
ChIP DNA
R541C_H3K9me2_Adip.RPGC.inputsubtract.bigWig
R541C_H3K9me2_Adip_peaks.clipped.bed


title: R541C_d25ADIP_Input_2

description:
genomic DNA
R541C_H3K9me2_Adip.RPGC.inputsubtract.bigWig
R541C_LB_Adip.RPGC.inputsubtract.bigWig


title: T10I_d25ADIP_K9me2_1

description:
ChIP DNA
T10I_H3K9me2_Adip.RPGC.inputsubtract.bigWig
T10I_H3K9me2_Adip_peaks.clipped.bed


title: Ctrl_d25ADIP_K9me2_1

description:
ChIP DNA
Ctrl_H3K9me2_Adip.RPGC.inputsubtract.bigWig
Ctrl_H3K9me2_Adip_peaks.clipped.bed

value: DiPS 1016 SevA


title: Ctrl_d25ADIP_Input_1

description:
genomic DNA
Ctrl_H3K9me2_Adip.RPGC.inputsubtract.bigWig
Ctrl_LB_Adip.RPGC.inputsubtract.bigWig


title: Ctrl_d25ADIP_LB1_2

description:
ChIP DNA
Ctrl_LB_Adip.RPGC.inputsubtract.bigWig
Ctrl_LB_Adip_peaks.clipped.bed


title: Ctrl_d25ADIP_K9me2_2


title: Ctrl_d25ADIP_LB1_1


title: R541C_d45_Input_2

value: day 45


title: T10I_d25ADIP_Input_1

description:
genomic DNA
T10I_H3K9me2_Adip.RPGC.inputsubtract.bigWig
T10I_LB_Adip.RPGC.inputsubtract.bigWig


title: T10I_d25ADIP_LB1_2


title: T10I_d25ADIP_Input_2


title: T10I_d25ADIP_K9me2_2


title: R541C_d25ADIP_LB1_1

description:
ChIP DNA
R541C_LB_Adip.RPGC.inputsubtract.bigWig
R541C_LB_Adip_peaks.clipped.bed


title: R541C_d25ADIP_K9me2_1


title: R541C_d25ADIP_Input_1


title: R541C_d25ADIP_LB1_2


title: R541C_d45_K9me2_2


title: R541C_d45_LB1_2


title: R541C_d45_K9me2_1


title: input DNA

city: Bethesda

first: Lorinc

last: Pongor

state: MD

address: 37 Convent Dr,

department: DTB

institute: NIH

data_processing:
Bam files were used for peak calling, using IgG as controls. Peak calling was performed using MACS2.0 through the Genomatix genome analyzer suite. Settings: band width = 300, model fold = [5, 50], qvalue cutoff = 1.00e-02, Range for calculating regional lambda is: 1000 bps and 10000 bps, Broad region calling on
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of  ChipSeq

source_name: Breast cancer cell line MCF7

growth_protocol: MCF7 cells were grown in complete medium according to the instructions from ATCC.

extract_protocol:
Formaldehyde crosslinked MCF7 cells were lysed by sonication and RECQ1-DNA or ERalpha-DNA complexes were isolated using antibody against RECQ1, ERalpha or IgG control. ChIP-IT high sensitivity kit (Active Motif) was used for the extraction and ChIP process.
Immunoprecipitated DNA and input DNA were made into the sequencing libraries using TruSeq ChIP Sample Preparation kit (Illumina), which were then sequenced in single-end 75-bp sequencing using a NextSeq 500 system (Illumina).

tag: passages

value: ATCC


title: ER alpha_ChIPSeq-rep 2

description: MCF7_ER_2_vs_MCF7_IgG_2_MACS2_broadpks.bed


title: R541C_d45_LB1_1


title: IgG_ChIPSeq-rep 1

description: MCF7_ER_1_vs_MCF7_IgG_1_MACS2_broadpks.bed


title: R541C_d45_Input_1

description:
genomic DNA
R541C_H3K9me2_CM.RPGC.inputsubtract.bigWig
R541C_LB_CM.RPGC.inputsubtract.bigWig


title: Ctrl_d25ADIP_Input_2


title: ER alpha_ChIPSeq-rep 1


title: RECQ1_ChIPSeq-rep 1

description: MCF7_RecQ1_1_vs_MCF7_IgG_1_MACS2_brdpks.bed


title: d25_T10I_4_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-306_S5

data_processing:
ChIP-seq data processing: Raw reads were trimmed with Trimmomatic v0.32 and then aligned to hg19 genome using bwa (Version 0.7.17) aln with parameters ‘bwa aln -q 5 -l 32 -k 2’. Bwa samse was then used to convert to sam format. Sam files were then filtered using samtools(version 1.7) view with ‘-F 1804 -q 30’ parameters, sorted and converted to bam format. PCR duplicates were removed using Picardtools MarkDuplicates command with ‘VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true’ parameters.
ChIPseq bigWig generation: Merged bam files were input intoDeeptools(version 3.1.1) bamCoverage with ‘--normalizeUsing RPGC -bs 1 -e 200’ and hg19 blacklist. Resulting bigWig tracks where then input into Deeptools bigWigCompare with parameters ‘--normalizeUsing RPGC -bs 10 -e 200 --operation subtract’ and hg19 blacklist, to create input normalized bigWig coverage tracks for each treatment.
LAD and KDD calling: LADs and KDDs were called using EDD  (version 1.1.18) with paired merged CHiP and Input bam files, parameters ‘-bin-size auto -g 4 --fdr 0.05’, modified parameter config file ‘required_fraction_of_informative_bins = 0.98’ and hg19 blacklist.
Differential peak calling:Peaks for differential binding analysis were called using Epic2 (version 0.0.16) with paired replicate CHiP and Input bam files, and parameters ‘-fs 200 -bin 600 -g 4 -fdr 0.05’. Resulting peak files, along with paired replicate Chip and Input bam files, were input into DiffBind for differential binding analysis using fdr <0.1 as significance threshold.
RNAseq data processing: Raw reads were trimmed with Trimmomatic v0.32 and then aligned to hg19 genome using STAR(version 2.6.0c) ’ and then filtered using samtools view with ‘-F 4 -q 10’ parameters. Rsubread featureCounts quantified the number of reads per feature of Ensembl hg19 gene annotation file. For differential gene expression analysis, genes with <1 count per million (CPM) in less than 25% of samples were removed from differential expression analysis. For analyses using all genes, no cpm filter was applied.  EdgeR’s calcNormFactors was used to calculate library size normalization factors. Limma voom function was used to log2 transform and quantile normalize the CPM matrix. For differential expression analysis, Limma lmFit, contrast.fit and eBayes functions were used to fit the linear model, compute coefficients and standard error, and then perform differential expression calculation with Benjamini–Hochberg multiple correction adjusted P-values (Benjamini and Hochberg, 1995). Cutoffs of FDR≤0.05 and log2 fold change ≥1.5 or ≤−1.5 were used for differentially upregulated or downregulated genes.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed, csv

growth_protocol: Cells were grown under feeder-free conditions on Geltrex (Life Technologies)-coated plates in chemically defined StemMACS IPS-Brew XF medium (Miltenyi Biotec) supplemented with 1% penicillin/streptomycin and 5 µg/mL Plasmocin (InvivoGen). Medium was changed every 24 hours. At 80-90% confluence, cells were dissociated with Accutase and split at a 1:8 ratio to create frozen stocks and working stocks that were maintained in culture.

extract_protocol:
RNA: iPSC-CMs, -heps, and -adips were isolated at indicated times, scraped from plates with 1xPBS, and centrifuged at 1500g for 5 minutes at room temperature. After discarding supernatant, cell pellets were flash frozen in dry ice and stored at -80C until processing. RNA was isolated using QIAGEN RNeasy total RNA extraction kit (QIAGEN). RNA quality was analyzed by BioAnalyzer; samples with RIN scores >8 were chose for further processing.     ChIP: Control or LMNA T10I iPSC-derived cardiac myocyctes or hepatocytes were crosslinked in culture by addition of methanol-free formaldehyde (ThermoFisher; final 1% v/v) and incubated at room temperature for 10 minutes with gentle rotation. Crosslinking was quenched by addition of glycine (final 125mM) and incubated at room temperature for 5 minutes with gentle rotation. Media was discarded and replaced with PBS; cells were scraped and transferred to conical tubes and pelleted by centrifugation (250xg, 5 minutes at room temperature). Supernatant was removed, and pellets were flash frozen on dry ice and stored at -80C.    Six hours before lysing cells, 30uL protein G magnetic beads (per ChIP sample) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250uL blocking buffer and 2ug antibody (Lamin B1: ab16048 [Abcam]; H3K9me2: ab1220 [Abcam]) and rotated at 4C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP‐40, 0.25% Triton X‐100, and protease inhibitors), and rotated at 4C for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris‐HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris‐HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na‐Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris) Samples were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50uL blocking buffer and added to 500ug input protein for overnight incubation with rotation at 4C. 50ug lysate was aliquoted and stored at -20C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES‐KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP‐40, 0.7% Na‐Deoxycholate) with 2-minute incubation at room temperature with rotation for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes with rotation at room temperature before final resuspension in 210uL elution buffer (50mM Tris‐HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65C for 30 minutes. 200uL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65C with agitation for a minimum of 12 hours, but not more than 18 hours. 200uL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were RNaseA treated (final 0.2mg/mL RNase; 37C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich for poly-A tailed RNA molecules. RNA-seq library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).     ChIP and input DNA was quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB).
Six hours before lysing cells, 30uL protein G magnetic beads (per ChIP sample) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250uL blocking buffer and 2ug antibody (Lamin B1: ab16048 [Abcam]; H3K9me2: ab1220 [Abcam]) and rotated at 4C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP‐40, 0.25% Triton X‐100, and protease inhibitors), and rotated at 4C for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris‐HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris‐HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na‐Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris) Samples were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50uL blocking buffer and added to 500ug input protein for overnight incubation with rotation at 4C. 50ug lysate was aliquoted and stored at -20C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES‐KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP‐40, 0.7% Na‐Deoxycholate) with 2-minute incubation at room temperature with rotation for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes with rotation at room temperature before final resuspension in 210uL elution buffer (50mM Tris‐HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65C for 30 minutes. 200uL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65C with agitation for a minimum of 12 hours, but not more than 18 hours. 200uL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were RNaseA treated (final 0.2mg/mL RNase; 37C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich for poly-A tailed RNA molecules. RNA-seq library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).
ChIP and input DNA was quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB).
ChIP and RNA samples were indexed for multiplex sequencing. Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems). Libraries were sequenced on the Illumina NextSeq500 platform (vII; 75bp single end sequencing; Illumina).

treatment_protocol: Undifferentiated iPSCs were detached by a 4-min incubation with Accutase (STEMCELL Technologies) and seeded onto Geltrex (Life Technologies)-coated plates at a density of 200,000 cells/cm2. To induce cardiac differentiation, we replaced iPSC medium with RPMI/B27-insulin (RPMI-1640 with 2% B-27 Supplement Minus Insulin; Thermo Fisher Scientific) medium supplemented with recombinant human/mouse/rat activin A (100 ng/mL; R&D Systems) for 18 hours, followed by recombinant human BMP-4 (5 ng/mL; R&D Systems) and CHIR 99021 (1 nM, Tocris) for 2 days. The medium was then exchanged for RPMI/B27–insulin with Xav (1 nM, Tocris) for another 2 days. The medium was then replaced with RPMI/B27–insulin without supplementary cytokines for three more days. RPMI-B27 (with insulin) was added every 2 to 3 days thereafter. Widespread spontaneous beating activity was typically observed 10 days after addition of activin A. For hepatic differentiation, cells were incubated in definitive endoderm media with recommended supplements (Stem Cell Technologies) for 4 days in ambient O2 and 5% CO2, yielding homogeneous monolayer of definitive endoderm cells. At day 5, cells were incubated with recombinant human BMP-4 (20ng/mL; Peprotech) and recombinant human FGF basic (10ng/mL; R&D Systems) for 5 days in RPMI-B27 (with insulin) in 5% O2 and 5% CO2, yielding hepatic progenitor cells. At day 10, cells were incubated in RPMI-B-27 (with insulin) supplemented with recombinant human HGF (20ng/mL; PeproTech) for 5 days at 5% O2 and 5% CO2, yielding immature HLCs. Finally, at d15, cells were incubated with HCM Hepatocyte Culture Medium (Lonza) without EGF and supplemented with recombinant human oncostatin M (20ng/mL; R&D Systems) for 7 days in ambient O2 and 5% CO2, yielding mature HLCs, which were collected at day 23. For adipogenic differentiation, iPSCs were induced for mesoderm in STEMdiff Mesoderm Induction Medium (Stem Cell Technologies) for 4 days.  On day 5, cells were incubated with Mesencult-ACF Plus medium (Stem Cell Technologies) to induce mesenchymal stem cell (MSC) formation. Media was refreshed daily from day 5 to day 12. Starting on day 12 and every 3 days thereafter until day 30, cells were passaged at 1:2 or 1:3 ratio in the same media and assayed at each passage for MSC surface markers CD105, CD73, CD90, CD146 and PDGFR? by flow cytometry. At day 30, when the cells were 95% positive for the MSC markers, they were then plated in Mesencult-ACF attachment substrate (Stem Cell Technologies)-coated plated for adipogenic conversion. The following day, cells were incubated for 2 days in Mesencult ACF Plus media supplemented with human IL-4 (10nM) and the TGFB?inhibitor SB431542 to obtain adipogenic precursors. Cells were then induced for adipogenesis for 3 days in EGM-2 media without FGF basic (Lonza) supplemented with adipogenic induction cocktail (0.5mM IBMX, 5uM dexamethasone, 125uM indomethacin, 2nM T3, 170nM insulin, 1uM rosiglitazone, and 5uM SB31542). Finally, cells were maintained in EGM-2 without FGF basic supplemented with only insulin, T3, rosiglitazone and SB431542 until adipogenesis is complete. Beige adipocytes were harvested on day 14-20 from plating for subsequent experiments.

value: iPSC-derived Cardiac Myocytes


title: d25_T10I_3_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-305_S3


title: d25_T10I_2_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-304_S4


title: d25_T10I_1_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-303_S14


title: d25_control_4_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-302_S9


title: d25_control_1_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-299_S6


title: T10I_d23HEP_H3K9me2_2

description:
T10I_H3K9me2_Hep_d23.bigwig
T10I_H3K9me2_Hep_d23_peaks.clipped.bed
Library_376_S1

value: iPSC derived Hepatocytes


title: d25_control_3_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-301_S16


title: T10I_d23HEP_Input_2

description:
T10I_LB_Hep_d23.bigwig
T10I_H3K9me2_Hep_d23.bigwig
Library_377_S9


title: d25_control_2_RNAseq

description:
differential_expression_output.csv
log2cpm_expression_matrix.csv
raw_count_matrix.csv
Library-300_S12


title: Ctrl_d23HEP_LB1_2

description:
Ctrl_LB_Hep_d23.bigwig
Control_LB_Hep_d23_peaks.clipped.bed
Library_369_S11


title: T10I_d23HEP_H3K9me2_1

description:
T10I_H3K9me2_Hep_d23.bigwig
T10I_H3K9me2_Hep_d23_peaks.clipped.bed
Library_373_S13


title: T10I_d23HEP_Input_1

description:
T10I_LB_Hep_d23.bigwig
T10I_H3K9me2_Hep_d23.bigwig
Library_374_S2


title: T10I_d23HEP_LB1_2

description:
T10I_LB_Hep_d23.bigwig
T10I_LB_Hep_d23_peaks.clipped.bed
Library_375_S12


title: T10I_d23HEP_LB1_1

description:
T10I_LB_Hep_d23.bigwig
T10I_LB_Hep_d23_peaks.clipped.bed
Library_372_S14


title: Ctrl_d23HEP_Input_2

description:
Ctrl_H3K9me2_Hep_d23.bigwig
Ctrl_LB_Hep_d23.bigwig
Library_371_S6


title: Ctrl_d23HEP_H3K9me2_2

description:
Ctrl_H3K9me2_Hep_d23.bigwig
Control_H3K9me2_Hep_d23_peaks.clipped.bed
Library_370_S10


title: IgG_ChIPSeq-rep 2


title: Ctrl_d23HEP_Input_1

description:
Ctrl_H3K9me2_Hep_d23.bigwig
Ctrl_LB_Hep_d23.bigwig
Library_368_S3


title: RECQ1_ChIPSeq-rep 2

description: MCF7_RecQ1_2_vs_MCF7_IgG_2_MACS2_brdpks.bed


title: Ctrl_d23HEP_LB1_1

description:
Ctrl_LB_Hep_d23.bigwig
Control_LB_Hep_d23_peaks.clipped.bed
Library_366_S5


title: Ctrl_d23HEP_H3K9me2_1

description:
Ctrl_H3K9me2_Hep_d23.bigwig
Control_H3K9me2_Hep_d23_peaks.clipped.bed
Library_367_S4


title: T10I_d45_K9me2_4

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_H3K9me2_peaks.clipped.bed
Library_281_S1


title: T10I_d45_Input_4

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_LB.bigWig
Library_282_S8


title: Ctrl_d45_Input_3

description:
d45_control_H3K9me2.bigWig
d45_control_LB.bigWig
Library_273_S10


title: T10I_d45_K9me2_3

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_H3K9me2_peaks.clipped.bed
Library_278_S3


title: Ctrl_d45_LB1_4

description:
d45_control_LB.bigWig
d45_control_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_274_S5


title: Ctrl_d45_K9me2_3

description:
d45_control_H3K9me2.bigWig
d45_control_H3K9me2_peaks.clipped.bed
Library_272_S11


title: Ctrl_d45_LB1_3

description:
d45_control_LB.bigWig
d45_control_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_271_S6


title: Ctrl_d45_Input_4

description:
d45_control_H3K9me2.bigWig
d45_control_LB.bigWig
Library_276_S16


title: T10I_d45_K9me2_2

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_H3K9me2_peaks.clipped.bed
Library_198_S11


title: T10I_d45_Input_3

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_LB.bigWig
Library_279_S19


title: T10I_d45_LB1_2

description:
d45_T10I_LB.bigWig
d45_T10I_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_199_S9


title: T10I_d45_K9me2_1

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_H3K9me2_peaks.clipped.bed
Library_195_S10


title: T10I_d25_Input_4

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_LB.bigWig
Library_270_S7


title: T10I_d45_LB1_3

description:
d45_T10I_LB.bigWig
d45_T10I_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_277_S9


title: T10I_d45_LB1_4

description:
d45_T10I_LB.bigWig
d45_T10I_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_280_S2


title: T10I_d45_Input_1

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_LB.bigWig
Library_197_S1


title: Ctrl_d45_K9me2_4

description:
d45_control_H3K9me2.bigWig
d45_control_H3K9me2_peaks.clipped.bed
Library_275_S4


title: T10I_d45_LB1_1

description:
d45_T10I_LB.bigWig
d45_T10I_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_196_S4


title: Ctrl_d45_Input_2

description:
d45_control_H3K9me2.bigWig
d45_control_LB.bigWig
Library_194_S2


title: T10I_d25_K9me2_4

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_H3K9me2_peaks.clipped.bed
Library_269_S17


title: T10I_d25_Input_3

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_LB.bigWig
Library_267_S13


title: T10I_d25_LB1_4

description:
d25_T10I_LB.bigWig
d25_T10I_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_268_S12


title: Ctrl_d45_LB1_2

description:
d45_control_LB.bigWig
d45_control_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_193_S8


title: Ctrl_d45_K9me2_1

description:
d45_control_H3K9me2.bigWig
d45_control_H3K9me2_peaks.clipped.bed
Library_189_S12


title: T10I_d45_Input_2

description:
d45_T10I_H3K9me2.bigWig
d45_T10I_LB.bigWig
Library_200_S7


title: Ctrl_d45_Input_1

description:
d45_control_H3K9me2.bigWig
d45_control_LB.bigWig
Library_191_S6


title: Ctrl_d45_LB1_1

description:
d45_control_LB.bigWig
d45_control_LB_peaks.clipped.bed
d45_LB_lost_peaks.bed
d45_LB_gained_peaks.bed
Library_190_S3


title: T10I_d25_K9me2_3

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_H3K9me2_peaks.clipped.bed
Library_266_S20


title: T10I_d25_LB1_3

description:
d25_T10I_LB.bigWig
d25_T10I_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_265_S21


title: T10I_d25_LB1_2

description:
d25_T10I_LB.bigWig
d25_T10I_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_211_S6


title: T10I_d25_Input_2

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_LB.bigWig
Library_212_S1


title: Ctrl_d45_K9me2_2

description:
d45_control_H3K9me2.bigWig
d45_control_H3K9me2_peaks.clipped.bed
Library_192_S5


title: T10I_d25_Input_1

description:
d25_T10I_LB.bigWig
d25_T10I_LB_peaks.clipped.bed
Library_209_S10


title: T10I_d25_K9me2_2

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_H3K9me2_peaks.clipped.bed
Library_210_S7


title: T10I_d25_LB1_1

description:
d25_T10I_LB.bigWig
d25_T10I_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_208_S2


title: Ctrl_d25_Input_3

description:
d25_control_H3K9me2.bigWig
d25_control_LB.bigWig
Library_261_S22


title: Ctrl_d25_K9me2_4

description:
d25_control_H3K9me2.bigWig
d25_control_H3K9me2_peaks.clipped.bed
Library_263_S15


title: Ctrl_d25_K9me2_1

description:
d25_control_H3K9me2.bigWig
d25_control_H3K9me2_peaks.clipped.bed
Library_201_S4


title: Ctrl_d25_LB1_4

description:
d25_control_LB.bigWig
d25_control_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_262_S18


title: Ctrl_d25_Input_2

description:
d25_control_H3K9me2.bigWig
d25_control_LB.bigWig
Library_206_S14


title: T10I_d25_K9me2_1

description:
d25_T10I_H3K9me2.bigWig
d25_T10I_H3K9me2_peaks.clipped.bed
Library_207_S5


title: Ctrl_d25_LB1_3

description:
d25_control_LB.bigWig
d25_control_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_259_S24


title: Ctrl_d25_K9me2_3

description:
d25_control_H3K9me2.bigWig
d25_control_H3K9me2_peaks.clipped.bed
Library_260_S23


title: Ctrl_d25_K9me2_2

description:
d25_control_H3K9me2.bigWig
d25_control_H3K9me2_peaks.clipped.bed
Library_204_S12


title: Ctrl_d25_LB1_1

description:
d25_control_LB.bigWig
d25_control_LB_peaks.clipped.bed
d25_LB_lost_peaks.bed
d25_LB_gained_peaks.bed
Library_202_S8


title: Ctrl_d25_Input_1

description:
d25_control_H3K9me2.bigWig
d25_control_LB.bigWig
Library_203_S11


title: 2_PD_RNASeq: 18381

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

data_processing:
TrimGalore (v0.4.4) was applied to remove low quality bases and for adapter trimming
 STAR (v2.5.3a) was used to index Ensembl GRCh37 p13 primary assembly genome with the Gencode v19 primary assembly annotation. STAR (v2.5.3a) was then used for read alignment to the genome
 Expected gene-level counts were obtained after processing of raw RNA-seq reads with RSEM
The edgeR package was used to read the counts of all samples and transform them into count per million values (CPM). Only the genes having more than 1 CPM in 80% of samples were retained. Next, transcript per million (TPM) estimates were loaded from RSEM output and only genes previously selected were retained. TPM was used for subsequent model fitting following the same procedure as for padlock bisulfite sequencing with the following exceptions. Genes falling into the group of 10% least variable genes were removed.
Using Voom, TPM count data were transformed to log2-counts per million (logCPM) and adjusted for mean-variance relationshipResulting matrix was used to calculate surrogate value vectors and perform linear model fitting
Genome_build: hg19
Supplementary_files_format_and_content: Each .results.txt file contain the following information in order: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Appendix

extract_protocol:
Total RNA was isolated from appendix tissue of PD patients and controls. Frozen appendix tissue (~20 mg) was homogenized using a Covaris cryoPREP pulverizer, and then in 1 mL of Trizol (Life Technologies) with a ceramic bead-based homogenizer (Precellys, Bertin Instruments). Total RNA was isolated according to the Trizol manufacturer’s instructions, treated with RNase-free DNase I (Qiagen) at room temperature for 30 min, followed by clean-up with the RNeasy Mini Kit (Qiagen). RNA yield was quantified using a NanoDrop ND-1000 (Thermo Fisher Scientific) and RNA integrity was verified with an Agilent Bioanalyzer 2100 system (Agilent Technologies).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA stranded mRNA-seq kit (v5.17) Libraries were prepared by the Van Andel Genomics Core from 300 ng of total RNA using the using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16; for PD vs control appendix) or KAPA stranded mRNA-seq kit (v5.17; for aging appendix) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex dual adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp.), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 101 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S1 100 cycle kit (Illumina Inc.)

tag: tissue

value: Appendix

tag: age

tag: Sex

value: M

tag: pmi

tag: rin

tag: batch

tag: dignosis

tag: aginganalysis

value: Yes

tag: pdvscontrolanalysis

value: No

tag: sampleID


title: 2_PD_RNASeq: 17720

value: F

value: Control


title: 2_PD_RNASeq: 32422


title: 2_PD_RNASeq: 171099


title: 2_PD_RNASeq: 17973


title: 2_PD_RNASeq: 17849


title: 2_PD_RNASeq: 17832


title: 2_PD_RNASeq: 17903


title: 2_PD_RNASeq: 171010


title: 2_PD_RNASeq: 32388


title: 2_PD_RNASeq: 17949


title: 2_PD_RNASeq: 17411


title: 2_PD_RNASeq: 17710


title: Ctrl_d25_Input_4

description:
d25_control_H3K9me2.bigWig
d25_control_LB.bigWig
Library_264_S14

value: day 25

tag: cell type


title: 2_PD_RNASeq: 17978


title: 2_PD_RNASeq: 17331


title: 2_PD_RNASeq: 17277


title: 2_PD_RNASeq: 17265


title: 2_PD_RNASeq: 17048


title: 2_PD_RNASeq: 17047


title: 2_PD_RNASeq: 16741


title: 2_PD_RNASeq: 16666


title: 2_PD_RNASeq: 16814


title: 2_PD_RNASeq: 16475


title: 2_PD_RNASeq: 17029


title: 2_PD_RNASeq: 16577


title: 2_PD_RNASeq: 15515


title: 2_PD_RNASeq: 16490


title: 2_PD_RNASeq: 16697


title: 2_PD_RNASeq: 3551


title: 2_PD_RNASeq: 3554

value: PD


title: 2_PD_RNASeq: 3557


title: 2_PD_RNASeq: 3525


title: 2_PD_RNASeq: 3548


title: 2_PD_RNASeq: 3547


title: 2_PD_RNASeq: 3512


title: 2_PD_RNASeq: 3518


title: 2_PD_RNASeq: 9387


title: 2_PD_RNASeq: 3469


title: 2_PD_RNASeq: 3511


title: 2_PD_RNASeq: 3508


title: 2_PD_RNASeq: 6755


title: 2_PD_RNASeq: 3461


title: 2_PD_RNASeq: 3455


title: 2_PD_RNASeq: 3454


title: 2_PD_RNASeq: 3453


title: 2_PD_RNASeq: 16629


title: 2_PD_RNASeq: 3441


title: hUC.MSC7

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

data_processing:
Reads were mapped to a human genome (hg19) by using hisat2(v2.1). Gene counts were estimated by HTSeq (0.11).
Genome_build: hg19

source_name: human umbilical MSCs

growth_protocol: MSCs were isolated from different human umbilical cords samples. The MSCs were cultured in α-MEM supplemented with 5% UltraGRO™(Helios).

extract_protocol:
Total RNA was extracted from cultured cells using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs were plated into 10cm dish at a density of 7*10^5, then stimulated with TNF-α and IFN-γ(10ng/ml) for 12 hours. Washed the MSCs with PBS, and exchang fresh medium for another 24 hours.

tag: condition

value: blank


title: 2_PD_RNASeq: 3452


title: hUC.MSC9


title: 2_PD_RNASeq: 3389


title: 2_PD_RNASeq: 3446


title: 2_PD_RNASeq: 3371


title: hUC.MSC4


title: hUC.MSC5


title: hUC.MSC6


title: hUC.MSC3


title: hUC.MSC31


title: 2_PD_RNASeq: 3363


title: 2_PD_RNASeq: 3362


title: hUC.MSC32


title: hUC.MSC30


title: 2_PD_RNASeq: 3369


title: 2_PD_RNASeq: 3366


title: 2_PD_RNASeq: 3360


title: 2_PD_RNASeq: 3361


title: hUC.MSC28


title: hUC.MSC29


title: hUC.MSC26


title: HeLa_polyA_siZc3h4_rep2

description: polyA-RNAseq HeLa siZc3h4 rep 2

data_processing:
Strand specific paired end reads (76nt) were trimmed for removing the adapter sequence and discarding low quality bases using Trimmomatic v0.27 with PE option (PMID:24695404)
Read quality was then checked for each sample using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were then aligned with TopHat2 v2.1.0 (–very-sensitive --library-type fr-firststrand -r 200 --segment-length 35  --microexon-search --no-mixed --no-discordant -g 1 --coverage-search) (PMID:23618408). Indels due to sequencing errors were identifies using Bowtie2 v.2.6 (PMID: 19261174).
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)

source_name: polyA-RNAseq HeLa siZc3h4 rep 2

growth_protocol: HeLa cells were cultured in DMEM containing 10% South American FBS, 1% L-Glutamax solution and 1% Pen/Strep solution.

extract_protocol:
Total RNA was extracted using the Zymo kit with on-column DNAse digestion.
After oligodT-based selection of polyadenylated transcripts from 3-5 ug total RNA, library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007).

treatment_protocol: Cells were untreaded.

tag: cell line

value: HeLa

value: human cervix, epitheloid carcinoma

tag: treatment


title: hUC.MSC25

tag: strain


title: HeLa_polyA_siWdr82_rep2

description: polyA-RNAseq HeLa siWdr82 rep 2

source_name: polyA-RNAseq HeLa siWdr82 rep 2


title: hUC.MSC27


title: hUC.MSC8


title: HeLa_polyA_siZc3h4_rep1

description: polyA-RNAseq HeLa siZc3h4 rep 1

source_name: polyA-RNAseq HeLa siZc3h4 rep 1


title: hUC.MSC23


title: hUC.MSC24


title: HeLa_polyA_siCtl_rep2

description: polyA-RNAseq HeLa siCtl rep 2

source_name: polyA-RNAseq HeLa siCtl rep 2

value: siCtl


title: 2_PD_RNASeq: 3370


title: hUC.MSC22


title: HeLa_polyA_siCtl_rep1

description: polyA-RNAseq HeLa siCtl rep 1

source_name: polyA-RNAseq HeLa siCtl rep 1


title: hUC.MSC21


title: hUC.MSC20


title: HeLa_4sU_siWdr82_rep2

description: 4sU-RNAseq HeLa siWdr82 rep 2

source_name: 4sU-RNAseq HeLa siWdr82 rep 2

extract_protocol:
Total RNA was extracted using Trizol whereafter nascent 4sU-labelled RNA was extracted as described (Austenaa et al. 2015 )
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 100-300 ng of nascent 4sU-labelled RNA, without ribosomal depletion.

treatment_protocol: 4-thio-uridine was added to the medium at a final concentration of … for 45 min before harvesting the cells.


title: hUC.MSC19


title: hUC.MSC18


title: HeLa_4sU_siCtl_rep2

description: 4sU-RNAseq HeLa siCtl rep 2

source_name: 4sU-RNAseq HeLa siCtl rep 2


title: HeLa_4sU_siWdr82_rep1

description: 4sU-RNAseq HeLa siWdr82 rep 1

source_name: 4sU-RNAseq HeLa siWdr82 rep 1


title: hUC.MSC16


title: HeLa_4sU_siCtl_rep1

description: 4sU-RNAseq HeLa siCtl rep 1

source_name: 4sU-RNAseq HeLa siCtl rep 1


title: hUC.MSC14


title: 104_13_IPS_nodox_2

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

department: Hematology/Oncology

data_processing:
RNA-seq reads were trimmed for adaptor sequence using Trimmomatic and aligned to the human genome hg38 using Bowtie/Tophat
Counts were generated using featureCounts
Normalization was performed with DESeq2
Classification of samples was performed using CellNet
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated text file containing gene expression counts

source_name: HSPCs

extract_protocol:
Total RNA was extracted using the qiagen RNA-easy micro kit.
Libraries were prepared with the SMART-Seq v4 Ultra low Input RNA kit.


title: hUC.MSC13


title: 104_13_IPS_dox_2

value: dox


title: 104_13_IPS_nodox


title: 104_13_IPS_dox


title: hUC.MSC12


title: HeLa_polyA_siWdr82_rep1

description: polyA-RNAseq HeLa siWdr82 rep 1

source_name: polyA-RNAseq HeLa siWdr82 rep 1


title: 106_IPS_nodox


title: 106_IPS_dox


title: hUC.MSC10


title: hUC.MSC11


title: HeLa_4sU_siZc3h4_rep2

description: 4sU-RNAseq HeLa siZc3h4 rep 2

source_name: 4sU-RNAseq HeLa siZc3h4 rep 2


title: hUC.MSC1


title: hUC.MSC2


title: HeLa_4sU_siZc3h4_rep1

description: 4sU-RNAseq HeLa siZc3h4 rep 1

source_name: 4sU-RNAseq HeLa siZc3h4 rep 1


title: MSC3-2IF-2


title: H8-1001000354-AB-1

city: Stanford

first: Gerlinde

last: Wernig

state: CA

address: 265 Campus Drive

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description: Single cell from HSC

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: CD34+ CD38- CD90+ CD45RA- HSC

growth_protocol: Human bone marrows were obtained from Stanford Medical Center with informed consent, according to Institutional Review Board (IRB)-approved protocols (Stanford IRB 39881). CD34+ progenitors from each sample were isolated by Ficoll separation and CD34+ progenitors were isolated by a positive selection using an immunomagnetic cell sorting system (AutoMacs; Miltenyi Biotec,Bergisch Gladbach, Germany). 56,000 cells were incubated in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin, in the presence SCF 20 ng/ml and different diabodies at 100 nM for 12 days, with change medium every other day, and addition of new cytokines 3 times per day. After 12 days, cells were pelleted and resuspended in PBS 2% FCS. Fc block was performed for 20 min and the mononuclear cells were stained with directly conjugated anti-mouse CD34, CD38, CD45RA, CD90 and HSC were isolated as DAPI-CD34+CD38-CD45RA-CD90+ cells on a BD FACS ARIA sorter.

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cells cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturers instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

treatment_protocol: CD34+ Bone Marrow derived cells were culture in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin for 12 days. In all conditions 20 ng/ml SCF was added. Additional conditions receive 100 nM of TPO or different agonist or antagonist, with or without 14 µg/ml of TPO blocking antibody. Media was changed every other day and cytokines were added 3 times per day.

value: HSC

value: AB

tag: days in culture

tag: date sequencing


title: H9-1001000353-AK111_AB-1

description: Single cell from HSC


title: hUC.MSC17


title: MSC3-blank-3


title: MSC3-blank-2


title: H6-1001000354-AB-1

description: Single cell from HSC


title: H7-1001000353-AK111_AB-1

description: Single cell from HSC


title: MSC2-2IF-3


title: hUC.MSC15


title: H6-1001000353-AK111_AB-1

description: Single cell from HSC


title: MSC2-2IF-2


title: H5-1001000353-AK111_AB-1

description: Single cell from HSC


title: H5-1001000354-AB-1

description: Single cell from HSC


title: MSC2-2IF-1


title: H4-1001000353-AK111_AB-1

description: Single cell from HSC


title: 2_PD_RNASeq: 3374

tag: tissue


title: H3-1001000354-AB-1

description: Single cell from HSC


title: MSC3-2IF-3


title: H3-1001000353-AK111_AB-1

description: Single cell from HSC


title: H8-1001000353-AK111_AB-1

description: Single cell from HSC


title: MSC2-blank-3


title: H2-1001000353-AK111_AB-1

description: Single cell from HSC


title: MSC2-blank-1


title: H11-1001000354-AB-1

description: Single cell from HSC


title: MSC1-2IF-3


title: H1-1001000353-AK111_AB-1

description: Single cell from HSC


title: G9-1001000354-AB-1

description: Single cell from HSC


title: G9-1001000353-AK111_AB-1

description: Single cell from HSC


title: MSC3-blank-1


title: MSC1-2IF-2


title: MSC1-2IF-1


title: MSC1-blank3


title: MSC1-blank2


title: G8-1001000354-AB-1

description: Single cell from HSC


title: MSC3-2IF-1


title: G7-1001000354-AB-1

description: Single cell from HSC


title: G8-1001000353-AK111_AB-1

description: Single cell from HSC


title: MSC1-blank1


title: MSC2-blank-2


title: G5-1001000354-AB-1

description: Single cell from HSC


title: G4-1001000353-AK111_AB-1

description: Single cell from HSC


title: G6-1001000354-AB-1

description: Single cell from HSC


title: G4-1001000354-AB-1

description: Single cell from HSC


title: G7-1001000353-AK111_AB-1

description: Single cell from HSC


title: G3-1001000354-AB-1

description: Single cell from HSC


title: 284_T5710_HC_cMo

city: La Jolla

first: Ferhat

last: Ay

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
Bulk_Human_RawCounts.txt
Bulk_Human_TPM.txt

data_processing:
Bulk RNA-seq data (FASTQ files) were mapped against the hg38 genome (GRCh38.p7) reference using TopHat (Trapnell et al. 2009); v2.0.9 (--max-multihits 1 --microexon-search --bowtie1) with FastQC (v0.11.2), and Samtools v0.1.19.0 (Li et al. 2009).
Trimmomatic (v0.36) was used to remove adapters (Bolger et al. 2014).
HTSeq-count with -m union -s no -t exon -i gene_name parameters (part of the HTSeq framework, version v0.7.1 (Anders et al. 2015)) was used for calculating read counts.
Genome_build: hg38
Supplementary_files_format_and_content: Bulk_Human_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Bulk_Human_TPM.txt contains Transcript per Million normalized counts

molecule: polyA RNA

source_name: PBMCs

growth_protocol: Cell types were isolated from blood samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
Total RNA was isolated from sorted cell populations using miRNAeasy Micro kit (Qiagen, USA) and quantified. 3ng of total RNA was used to generate cDNA following the Smart-seq2 protocol. cDNA was purified using AMPure XP beads (0.8x, Beckman Coulter).
Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)
1ng of cDNA from each sample was used to generate a sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). The libraries were pooled and sequenced on a HiSeq2500 (Illumina) to obtain 50-bp single end reads. Both full-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included after each step to eliminate samples with low quality from downstream process. A detailed protocol has been previously published (Rosales et al. 2018).
Libraries were sequenced on a HiSeq2500 Illumina to obtain a minimum of 10 million 50-bp single-end reads (HiSeq SR Cluster Kit v4 cBot, HiSeq SBS Kit v4).

tag: disease state

value: healthy control

tag: cell type surface markers

value: cMo

tag: ifn status

value: HC

tag: patientuid

tag: patientid

tag: visit number

tag: gender

value: Female

tag: age

tag: race

value: White

tag: ethnicity

value: Non Hispanic


title: 281_T5466_HC_cMo

tag: cell type

value: Other, multiple

value: Hispanic


title: 288_T4631_HC_cMo

value: Black


title: 286_T5695re_HC_cMo


title: 282_T5755_HC_cMo

value: Asian


title: 285_T5257_HC_cMo


title: 287_T5246_HC_cMo


title: G2-1001000353-AK111_AB-1

description: Single cell from HSC


title: G3-1001000353-AK111_AB-1

description: Single cell from HSC


title: 280_T5777_HC_cMo


title: G11-1001000354-AB-1

description: Single cell from HSC


title: 278_T5695_HC_cMo


title: 279_T5375_HC_cMo

value: not listed


title: G10-1001000354-AB-1

description: Single cell from HSC


title: 276_T5502_HC_cMo


title: 277_T5599_HC_cMo


title: F9-1001000354-AB-1

description: Single cell from HSC


title: F8-1001000354-AB-1

description: Single cell from HSC


title: G1-1001000353-AK111_AB-1

description: Single cell from HSC


title: 275_L0088fresh_HC_cMo

value: Not available


title: G6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 283_T5790_HC_cMo


title: 274_L10014fresh_HC_cMo


title: 273_L0140_HC_cMo


title: F8-1001000353-AK111_AB-1

description: Single cell from HSC


title: F7-1001000353-AK111_AB-1

description: Single cell from HSC


title: 272_L0088_HC_cMo


title: 271_L0038_HC_cMo


title: F7-1001000354-AB-1

description: Single cell from HSC


title: F6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 269_L0142_HC_cMo


title: 270_L0150_HC_cMo


title: F3-1001000354-AB-1

description: Single cell from HSC


title: 266_T5210_HC_cMo


title: 267_T5863_HC_cMo


title: F11-1001000354-AB-1

description: Single cell from HSC


title: F4-1001000354-AB-1

description: Single cell from HSC


title: 265_T4867_HC_cMo


title: 264_T5663_HC_cMo


title: E9-1001000354-AB-1

description: Single cell from HSC


title: E8-1001000354-AB-1

description: Single cell from HSC


title: F10-1001000354-AB-1

description: Single cell from HSC


title: E6-1001000354-AB-1

description: Single cell from HSC


title: 261_S1078a_IFNneg_cMo

value: systemic lupus erythematosus (SLE)

value: IFNneg

value: Non-Hispanic/Latino


title: 262_S1064b_IFNneg_cMo


title: 260_S1064a_IFNneg_cMo


title: E5-1001000354-AB-1

description: Single cell from HSC

value: HSC


title: 259_S1063a_IFNneg_cMo

value: Other, Pacific Islander


title: E4-1001000354-AB-1

description: Single cell from HSC

value: AB


title: E11-1001000354-AB-1

description: Single cell from HSC


title: F6-1001000354-AB-1

description: Single cell from HSC


title: 257_S1031c_IFNneg_cMo

value: cMo


title: 268_L0147_HC_cMo

value: healthy control

value: HC


title: F5-1001000354-AB-1

description: Single cell from HSC


title: D9-1001000354-AB-1

description: Single cell from HSC


title: E10-1001000354-AB-1

description: Single cell from HSC


title: 263_T4918_HC_cMo

value: Female

value: White


title: 256_S1044c_IFNneg_cMo


title: 254_S1046b_IFNneg_cMo


title: E7-1001000354-AB-1

description: Single cell from HSC


title: 253_S1067c_IFNneg_cMo


title: D6-1001000354-AB-1

description: Single cell from HSC


title: D5-1001000354-AB-1

description: Single cell from HSC


title: 255_S2011c_IFNneg_cMo


title: D4-1001000354-AB-1

description: Single cell from HSC


title: 252_S1057d_IFNneg_cMo


title: 250_S1027c_IFNneg_cMo


title: 249_S1069a_IFNneg_cMo


title: D3-1001000354-AB-1

description: Single cell from HSC


title: 258_S1031d_IFNneg_cMo


title: 248_S1058a_IFNneg_cMo


title: D11-1001000354-AB-1

description: Single cell from HSC


title: D7-1001000354-AB-1

description: Single cell from HSC


title: C9-1001000354-AB-1

description: Single cell from HSC


title: D10-1001000354-AB-1

description: Single cell from HSC


title: C8-1001000354-AB-1

description: Single cell from HSC


title: 247_S2015a_IFNneg_cMo

value: Hispanic/Latino


title: 246_S2011d_IFNneg_cMo


title: 245_S2001e_IFNneg_cMo


title: C7-1001000354-AB-1

description: Single cell from HSC


title: D8-1001000354-AB-1

description: Single cell from HSC


title: 244_S2016a_IFNneg_cMo


title: C6-1001000354-AB-1

description: Single cell from HSC


title: 243_S1023c_IFNneg_cMo


title: C5-1001000354-AB-1

description: Single cell from HSC


title: 242_S2013a_IFNneg_cMo


title: C4-1001000354-AB-1

description: Single cell from HSC


title: 241_S1053c_IFNneg_cMo


title: 251_S1059a_IFNneg_cMo


title: 240_S1053b_IFNneg_cMo


title: 239_S3009a_IFNneg_cMo


title: C10-1001000354-AB-1

description: Single cell from HSC


title: B9-1001000354-AB-1

description: Single cell from HSC


title: 238_S1071b_IFNneg_cMo


title: B8-1001000354-AB-1

description: Single cell from HSC


title: 235_S1061a_IFNneg_cMo


title: 237_S1053d_IFNneg_cMo


title: B7-1001000354-AB-1

description: Single cell from HSC


title: 236_S2019a_IFNneg_cMo

value: Other


title: 234_S1056a_IFNneg_cMo


title: B5-1001000354-AB-1

description: Single cell from HSC


title: 233_S1053a_IFNneg_cMo


title: B11-1001000354-AB-1

description: Single cell from HSC


title: B3-1001000354-AB-1

description: Single cell from HSC


title: 231_S1087a_IFNneg_cMo


title: 232_S1071a_IFNneg_cMo


title: 230_S1023d_IFNneg_cMo


title: B10-1001000354-AB-1

description: Single cell from HSC


title: A8-1001000354-AB-1

description: Single cell from HSC


title: 229_S1018c_IFNneg_cMo


title: A9-1001000354-AB-1

description: Single cell from HSC


title: 228_S1045d_IFNneg_cMo

value: Black


title: C11-1001000354-AB-1

description: Single cell from HSC


title: C3-1001000354-AB-1

description: Single cell from HSC


title: A6-1001000354-AB-1

description: Single cell from HSC


title: 226_S1061c_IFNneg_cMo

value: Asian


title: A7-1001000354-AB-1

description: Single cell from HSC


title: 227_S1067b_IFNneg_cMo


title: A4-1001000354-AB-1

description: Single cell from HSC


title: A5-1001000354-AB-1

description: Single cell from HSC


title: 224_S1061b_IFNneg_cMo


title: A3-1001000354-AB-1

description: Single cell from HSC


title: 223_S1067a_IFNneg_cMo


title: B6-1001000354-AB-1

description: Single cell from HSC


title: 222_S1057b_IFNneg_cMo


title: A10-1001000354-AB-1

description: Single cell from HSC


title: 221_S1027b_IFNneg_cMo


title: H4-1001000354-AB-1

description: Single cell from HSC


title: H10-1001000357-TPO_AB-1

description: Single cell from HSC


title: 220_S1085a_IFNneg_cMo


title: B11-1001000358-AK111-1

description: Single cell from HSC


title: 219_S3006a_IFNneg_cMo


title: A11-1001000358-AK111-1

description: Single cell from HSC


title: D2-1001000359-AK113_AB-1

description: Single cell from HSC


title: 218_S1068a_IFNneg_cMo


title: 217_S1062a_IFNneg_cMo


title: D5-1001000353-AK111_AB-1

description: Single cell from HSC


title: 225_S1057c_IFNneg_cMo


title: 214_S1054b_IFNneg_cMo


title: 216_S1088a_IFNneg_cMo


title: E11-1001000358-AK111-1

description: Single cell from HSC


title: 215_S1086a_IFNneg_cMo


title: B4-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: 212_S1018b_IFNneg_cMo


title: A1-1001000359-AK113_AB-1

description: Single cell from HSC


title: D4-1001000361-SCF-1

description: Single cell from HSC


title: B12-1001000358-AK111-1

description: Single cell from HSC


title: A2-1001000354-AB-1

description: Single cell from HSC


title: 209_S2014a_IFNneg_cMo


title: 211_S1054a_IFNneg_cMo


title: 210_S1024d_IFNneg_cMo


title: G12-1001000358-AK111-1

description: Single cell from HSC


title: 207_S1075a_IFNpos_cMo

value: IFNpos


title: 208_S1020c_IFNpos_cMo

value: systemic lupus erythematosus (SLE)


title: 213_S1059b_IFNneg_cMo

value: IFNneg


title: C5-1001000353-AK111_AB-1

description: Single cell from HSC


title: G11-1001000360-AK119-1

description: Single cell from HSC


title: A4-1001000361-SCF-1

description: Single cell from HSC


title: E1-1001000359-AK113_AB-1

description: Single cell from HSC


title: 206_S1074a_IFNpos_cMo

value: Non-Hispanic/Latino


title: 204_S1079a_IFNpos_cMo


title: F3-1001000360-AK119-1

description: Single cell from HSC

value: HSC


title: 205_S1073a_IFNpos_cMo


title: 203_S1060b_IFNpos_cMo


title: C1-1001000359-AK113_AB-1

description: Single cell from HSC


title: B1-1001000359-AK113_AB-1

description: Single cell from HSC


title: C5-1001000361-SCF-1

description: Single cell from HSC


title: E12-1001000358-AK111-1

description: Single cell from HSC


title: B2-1001000359-AK113_AB-1

description: Single cell from HSC


title: 202_S1072a_IFNpos_cMo


title: 199_S2017a_IFNpos_cMo


title: 201_S1060a_IFNpos_cMo


title: D1-1001000359-AK113_AB-1

description: Single cell from HSC


title: F2-1001000360-AK119-1

description: Single cell from HSC


title: 198_S1084a_IFNpos_cMo


title: 197_S1052b_IFNpos_cMo


title: D11-1001000358-AK111-1

description: Single cell from HSC


title: A6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 196_S1076a_IFNpos_cMo


title: C4-1001000361-SCF-1

description: Single cell from HSC


title: H11-1001000357-TPO_AB-1

description: Single cell from HSC


title: 194_S3005a_IFNpos_cMo

value: Pacific Islander


title: C11-1001000358-AK111-1

description: Single cell from HSC


title: 193_S1065b_IFNpos_cMo


title: 192_S1022c_IFNpos_cMo


title: C12-1001000358-AK111-1

description: Single cell from HSC


title: 195_S2010b_IFNpos_cMo


title: 189_S1081a_IFNpos_cMo


title: 190_S3007a_IFNpos_cMo


title: 191_S1077a_IFNpos_cMo


title: H3-1001000359-AK113_AB-1

description: Single cell from HSC


title: G10-1001000360-AK119-1

description: Single cell from HSC


title: F6-1001000361-SCF-1

description: Single cell from HSC


title: 200_S1070a_IFNpos_cMo


title: 188_S3003a_IFNpos_cMo


title: 187_S1083a_IFNpos_cMo


title: E2-1001000359-AK113_AB-1

description: Single cell from HSC


title: G1-1001000359-AK113_AB-1

description: Single cell from HSC


title: 185_S1065c_IFNpos_cMo


title: 186_S2018a_IFNpos_cMo

value: not listed


title: A5-1001000353-AK111_AB-1

description: Single cell from HSC


title: 184_S3002a_IFNpos_cMo

value: cMo

value: Male


title: D5-1001000360-AK119-1

description: Single cell from HSC


title: F12-1001000358-AK111-1

description: Single cell from HSC


title: 183_S1057a_IFNpos_cMo


title: D5-1001000361-SCF-1

description: Single cell from HSC


title: D12-1001000358-AK111-1

description: Single cell from HSC


title: A5-1001000360-AK119-1

description: Single cell from HSC


title: 181_S1065a_IFNpos_cMo


title: A12-1001000358-AK111-1

description: Single cell from HSC


title: 182_S3010a_IFNpos_cMo


title: 180_S1083b_IFNpos_cMo


title: 179_S3011a_IFNpos_cMo


title: B5-1001000361-SCF-1

description: Single cell from HSC


title: F2-1001000359-AK113_AB-1

description: Single cell from HSC


title: F5-1001000361-SCF-1

description: Single cell from HSC


title: 178_S3008a_IFNpos_cMo


title: 177_S1082a_IFNpos_cMo


title: F11-1001000358-AK111-1

description: Single cell from HSC


title: 176_S1055c_IFNpos_cMo


title: 174_S1055a_IFNpos_cMo


title: A7-1001000360-AK119-1

description: Single cell from HSC


title: A5-1001000361-SCF-1

description: Single cell from HSC


title: G2-1001000359-AK113_AB-1

description: Single cell from HSC


title: 175_S1055b_IFNpos_cMo


title: 173_S1055f_IFNpos_cMo


title: 172_S1055e_IFNpos_cMo


title: 171_S1055d_IFNpos_cMo


title: G11-1001000358-AK111-1

description: Single cell from HSC


title: 169_S3011a_IFNpos_pDC

value: pDC


title: 170_S3004a_IFNpos_cMo

value: Female


title: C2-1001000359-AK113_AB-1

description: Single cell from HSC


title: E5-1001000353-AK111_AB-1

description: Single cell from HSC


title: H1-1001000359-AK113_AB-1

description: Single cell from HSC


title: 168_S3010a_IFNpos_pDC

value: White


title: B11-1001000360-AK119-1

description: Single cell from HSC


title: 167_S3008a_IFNpos_pDC

value: Hispanic/Latino


title: D6-1001000360-AK119-1

description: Single cell from HSC


title: B5-1001000353-AK111_AB-1

description: Single cell from HSC


title: 166_S3007a_IFNpos_pDC


title: 165_S3005a_IFNpos_pDC


title: E5-1001000361-SCF-1

description: Single cell from HSC


title: 164_S3004a_IFNpos_pDC


title: F1-1001000359-AK113_AB-1

description: Single cell from HSC


title: 162_S1084a_IFNpos_pDC


title: 163_S3003a_IFNpos_pDC


title: B9-1001000360-AK119-1

description: Single cell from HSC


title: 161_S1083a_IFNpos_pDC


title: B6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 160_S1079a_IFNpos_pDC


title: A1-1001000358-AK111-1

description: Single cell from HSC


title: E4-1001000361-SCF-1

description: Single cell from HSC


title: 158_S3009a_IFNneg_pDC


title: E6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 157_S2014a_IFNneg_pDC


title: D6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 156_S2013a_IFNneg_pDC


title: B1-1001000358-AK111-1

description: Single cell from HSC


title: 155_S1088a_IFNneg_pDC


title: D1-1001000358-AK111-1

description: Single cell from HSC


title: 154_S1087a_IFNneg_pDC


title: E1-1001000358-AK111-1

description: Single cell from HSC


title: 152_S1085a_IFNneg_pDC


title: 151_S1078a_IFNneg_pDC


title: H1-1001000358-AK111-1

description: Single cell from HSC


title: A2-1001000359-AK113_AB-1

description: Single cell from HSC


title: G1-1001000358-AK111-1

description: Single cell from HSC


title: 148_S1064a_IFNneg_pDC


title: C6-1001000353-AK111_AB-1

description: Single cell from HSC


title: 159_S1073a_IFNpos_pDC


title: F5-1001000360-AK119-1

description: Single cell from HSC


title: 149_S1067a_IFNneg_pDC


title: A9-1001000360-AK119-1

description: Single cell from HSC


title: C1-1001000358-AK111-1

description: Single cell from HSC


title: 145_T5695re_HC_pDC

value: healthy control

value: HC

value: Hispanic


title: 144_T5663_HC_pDC

value: Non Hispanic


title: B6-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: H1-1001000360-AK119-1

description: Single cell from HSC


title: 153_S1086a_IFNneg_pDC

value: systemic lupus erythematosus (SLE)


title: B12-1001000360-AK119-1

description: Single cell from HSC


title: 147_T5695_HC_pDC


title: F1-1001000358-AK111-1

description: Single cell from HSC


title: 143_T5599_HC_pDC


title: 141_T5466_HC_pDC

value: Other, multiple


title: 150_S1069a_IFNneg_pDC

value: IFNneg

value: Non-Hispanic/Latino


title: 142_T5502_HC_pDC


title: C6-1001000361-SCF-1

description: Single cell from HSC

value: HSC


title: 140_T4631_HC_pDC

value: Black


title: B3-1001000359-AK113_AB-1

description: Single cell from HSC


title: C3-1001000359-AK113_AB-1

description: Single cell from HSC


title: A3-1001000359-AK113_AB-1

description: Single cell from HSC


title: D7-1001000360-AK119-1

description: Single cell from HSC


title: 138_L0088fresh_HC_pDC

value: not listed

value: Not available


title: 139_L0140_HC_pDC

value: pDC


title: 146_T5777_HC_pDC

value: Female


title: D3-1001000359-AK113_AB-1

description: Single cell from HSC


title: 136_S3011a_IFNpos_cDC

value: cDC

value: IFNpos

value: White


title: E3-1001000359-AK113_AB-1

description: Single cell from HSC


title: F3-1001000359-AK113_AB-1

description: Single cell from HSC


title: 137_L0038_HC_pDC

value: healthy control

value: HC


title: 135_S3008a_IFNpos_cDC

value: Male

value: Hispanic/Latino


title: A6-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: 134_S3005a_IFNpos_cDC

value: systemic lupus erythematosus (SLE)

value: Asian

value: Pacific Islander


title: 133_S3004a_IFNpos_cDC


title: 132_S3003a_IFNpos_cDC

value: Non-Hispanic/Latino


title: 131_S1083a_IFNpos_cDC


title: 130_S1079a_IFNpos_cDC


title: 129_S1075a_IFNpos_cDC


title: 128_S1073a_IFNpos_cDC


title: E6-1001000361-SCF-1

description: Single cell from HSC

value: HSC


title: G3-1001000359-AK113_AB-1

description: Single cell from HSC


title: A7-1001000353-AK111_AB-1

description: Single cell from HSC


title: B7-1001000353-AK111_AB-1

description: Single cell from HSC


title: 125_S2013a_IFNneg_cDC

value: IFNneg

value: not listed


title: D7-1001000353-AK111_AB-1

description: Single cell from HSC


title: C7-1001000353-AK111_AB-1

description: Single cell from HSC


title: D6-1001000361-SCF-1

description: Single cell from HSC


title: 126_S2016a_IFNneg_cDC


title: 127_S3009a_IFNneg_cDC


title: F7-1001000361-SCF-1

description: Single cell from HSC


title: 123_S1087a_IFNneg_cDC


title: C2-1001000358-AK111-1

description: Single cell from HSC


title: 124_S1088a_IFNneg_cDC


title: H4-1001000359-AK113_AB-1

description: Single cell from HSC


title: 122_S1086a_IFNneg_cDC


title: B2-1001000358-AK111-1

description: Single cell from HSC


title: 121_S1085a_IFNneg_cDC


title: D2-1001000358-AK111-1

description: Single cell from HSC


title: A2-1001000358-AK111-1

description: Single cell from HSC


title: F2-1001000358-AK111-1

description: Single cell from HSC


title: 119_S1069a_IFNneg_cDC


title: E7-1001000353-AK111_AB-1

description: Single cell from HSC


title: A10-1001000360-AK119-1

description: Single cell from HSC


title: 118_S1067a_IFNneg_cDC


title: G2-1001000358-AK111-1

description: Single cell from HSC


title: H3-1001000358-AK111-1

description: Single cell from HSC


title: 116_T5695_HC_cDC

value: Hispanic


title: 114_T5695re_HC_cDC

value: Female


title: 115_T5777_HC_cDC

value: cDC

value: Black

value: Non Hispanic


title: F7-1001000360-AK119-1

description: Single cell from HSC


title: 117_S1064a_IFNneg_cDC

value: White


title: H2-1001000360-AK119-1

description: Single cell from HSC


title: D8-1001000360-AK119-1

description: Single cell from HSC


title: C3-1001000360-AK119-1

description: Single cell from HSC


title: 113_T5663_HC_cDC

value: healthy control

value: HC


title: 111_T5502_HC_cDC


title: E2-1001000358-AK111-1

description: Single cell from HSC


title: 112_T5599_HC_cDC


title: B7-1001000361-SCF-1

description: Single cell from HSC


title: 108_T4631_HC_cDC


title: A7-1001000361-SCF-1

description: Single cell from HSC


title: 107_L0140_HC_cDC

value: Not available


title: 110_T5466_HC_cDC

value: Other, multiple


title: 105_L0038_HC_cDC


title: 109_T5210_HC_cDC


title: C7-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: E4-1001000359-AK113_AB-1

description: Single cell from HSC


title: B4-1001000359-AK113_AB-1

description: Single cell from HSC


title: 106_L0088fresh_HC_cDC


title: D4-1001000359-AK113_AB-1

description: Single cell from HSC


title: F4-1001000359-AK113_AB-1

description: Single cell from HSC


title: 103_S3010a_IFNpos_PMN

value: systemic lupus erythematosus (SLE)

value: dextran density gradient

value: PMN

value: IFNpos


title: C4-1001000359-AK113_AB-1

description: Single cell from HSC

value: HSC


title: 102_S3008a_IFNpos_PMN

value: Male

value: Hispanic/Latino


title: 100_S3005a_IFNpos_PMN

value: Female

value: Asian

value: Pacific Islander


title: 099_S3004a_IFNpos_PMN


title: F8-1001000361-SCF-1

description: Single cell from HSC


title: D7-1001000361-SCF-1

description: Single cell from HSC


title: A8-1001000353-AK111_AB-1

description: Single cell from HSC


title: 098_S3003a_IFNpos_PMN

value: Non-Hispanic/Latino


title: B8-1001000353-AK111_AB-1

description: Single cell from HSC


title: A4-1001000359-AK113_AB-1

description: Single cell from HSC


title: 101_S3007a_IFNpos_PMN

value: White


title: 096_S1083a_IFNpos_PMN


title: 095_S1079a_IFNpos_PMN


title: D8-1001000353-AK111_AB-1

description: Single cell from HSC


title: 104_S3011a_IFNpos_PMN


title: 093_S1073a_IFNpos_PMN


title: A3-1001000358-AK111-1

description: Single cell from HSC


title: 094_S1075a_IFNpos_PMN


title: B3-1001000358-AK111-1

description: Single cell from HSC


title: 092_S3009a_IFNneg_PMN

value: IFNneg


title: G4-1001000359-AK113_AB-1

description: Single cell from HSC


title: 091_S2016a_IFNneg_PMN


title: E8-1001000353-AK111_AB-1

description: Single cell from HSC


title: H5-1001000359-AK113_AB-1

description: Single cell from HSC


title: 097_S1084a_IFNpos_PMN


title: 089_S2013a_IFNneg_PMN

value: not listed


title: E3-1001000358-AK111-1

description: Single cell from HSC


title: 088_S1088a_IFNneg_PMN


title: D3-1001000358-AK111-1

description: Single cell from HSC


title: E7-1001000361-SCF-1

description: Single cell from HSC


title: C3-1001000358-AK111-1

description: Single cell from HSC


title: F3-1001000358-AK111-1

description: Single cell from HSC


title: C8-1001000353-AK111_AB-1

description: Single cell from HSC


title: H4-1001000358-AK111-1

description: Single cell from HSC


title: 086_S1086a_IFNneg_PMN


title: 087_S1087a_IFNneg_PMN


title: 085_S1085a_IFNneg_PMN


title: A11-1001000360-AK119-1

description: Single cell from HSC


title: G3-1001000358-AK111-1

description: Single cell from HSC


title: 083_S1069a_IFNneg_PMN


title: D9-1001000360-AK119-1

description: Single cell from HSC


title: 084_S1078a_IFNneg_PMN


title: C4-1001000360-AK119-1

description: Single cell from HSC


title: 082_S1067a_IFNneg_PMN


title: 081_S1064a_IFNneg_PMN


title: F11-1001000360-AK119-1

description: Single cell from HSC


title: A8-1001000361-SCF-1

description: Single cell from HSC


title: 080_T5695_HC_PMN

value: healthy control

value: HC

value: Hispanic


title: H5-1001000360-AK119-1

description: Single cell from HSC


title: 090_S2014a_IFNneg_PMN

value: systemic lupus erythematosus (SLE)


title: 078_T5695re_HC_PMN

value: dextran density gradient


title: A5-1001000359-AK113_AB-1

description: Single cell from HSC


title: B5-1001000359-AK113_AB-1

description: Single cell from HSC


title: A10-1001000353-AK111_AB-1

description: Single cell from HSC


title: C10-1001000353-AK111_AB-1

description: Single cell from HSC


title: 076_T5599_HC_PMN

value: PMN


title: 077_T5663_HC_PMN

value: Non Hispanic


title: 075_T5502_HC_PMN


title: B10-1001000353-AK111_AB-1

description: Single cell from HSC

value: HSC


title: A5-1001000358-AK111-1

description: Single cell from HSC


title: 071_L0140_HC_PMN

value: Not available


title: 074_T5466_HC_PMN

value: Other, multiple


title: D10-1001000353-AK111_AB-1

description: Single cell from HSC


title: B5-1001000358-AK111-1

description: Single cell from HSC


title: 069_L0038_HC_PMN

value: Female


title: E10-1001000353-AK111_AB-1

description: Single cell from HSC


title: 072_T4631_HC_PMN

value: Black


title: 079_T5777_HC_PMN


title: B8-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: C5-1001000358-AK111-1

description: Single cell from HSC


title: 068_S3011a_IFNpos_B

value: CD19+, TCRa/b-

value: B cells

value: IFNpos

value: Hispanic/Latino


title: H6-1001000358-AK111-1

description: Single cell from HSC


title: D5-1001000358-AK111-1

description: Single cell from HSC


title: F5-1001000358-AK111-1

description: Single cell from HSC


title: 067_S3010a_IFNpos_B

value: White

value: Non-Hispanic/Latino


title: 065_S3007a_IFNpos_B


title: 066_S3008a_IFNpos_B

value: Male


title: G5-1001000358-AK111-1

description: Single cell from HSC


title: 064_S3005a_IFNpos_B

value: systemic lupus erythematosus (SLE)

value: Asian

value: Pacific Islander


title: 073_T5210_HC_PMN

value: healthy control

value: dextran density gradient

value: PMN

value: HC

value: Non Hispanic


title: 063_S3004a_IFNpos_B

value: Female


title: D12-1001000360-AK119-1

description: Single cell from HSC

value: HSC


title: 062_S3003a_IFNpos_B

value: CD19+, TCRa/b-


title: 061_S1083a_IFNpos_B

value: B cells


title: G2-1001000360-AK119-1

description: Single cell from HSC


title: B1-1001000360-AK119-1

description: Single cell from HSC


title: 059_S1075a_IFNpos_B

value: IFNpos


title: 058_S3009a_IFNneg_B

value: IFNneg


title: A7-1001000359-AK113_AB-1

description: Single cell from HSC


title: C10-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: 060_S1079a_IFNpos_B

value: White

value: Hispanic/Latino


title: 070_L0088fresh_HC_PMN

value: not listed

value: Not available


title: A10-1001000361-SCF-1

description: Single cell from HSC


title: B10-1001000361-SCF-1

description: Single cell from HSC


title: 057_S2016a_IFNneg_B

value: systemic lupus erythematosus (SLE)


title: 053_S1087a_IFNneg_B

value: Non-Hispanic/Latino


title: 055_S2013a_IFNneg_B


title: 056_S2014a_IFNneg_B


title: D7-1001000359-AK113_AB-1

description: Single cell from HSC


title: E7-1001000359-AK113_AB-1

description: Single cell from HSC


title: B7-1001000359-AK113_AB-1

description: Single cell from HSC


title: H8-1001000359-AK113_AB-1

description: Single cell from HSC


title: C6-1001000360-AK119-1

description: Single cell from HSC


title: 054_S1088a_IFNneg_B


title: 050_S1069a_IFNneg_B


title: 049_S1064a_IFNneg_B


title: 051_S1078a_IFNneg_B


title: C7-1001000359-AK113_AB-1

description: Single cell from HSC


title: 052_S1085a_IFNneg_B


title: F7-1001000359-AK113_AB-1

description: Single cell from HSC


title: 048_T5695_HC_B

value: healthy control

value: Hispanic


title: E11-1001000361-SCF-1

description: Single cell from HSC


title: 047_T5777_HC_B

value: HC

value: Black


title: G7-1001000359-AK113_AB-1

description: Single cell from HSC


title: D10-1001000361-SCF-1

description: Single cell from HSC


title: F11-1001000361-SCF-1

description: Single cell from HSC


title: H9-1001000360-AK119-1

description: Single cell from HSC


title: 045_T5663_HC_B

value: Female

value: Non Hispanic


title: A11-1001000353-AK111_AB-1

description: Single cell from HSC

value: HSC


title: 043_T5502_HC_B

value: CD19+, TCRa/b-

value: B cells


title: 044_T5599_HC_B


title: D11-1001000353-AK111_AB-1

description: Single cell from HSC


title: B11-1001000353-AK111_AB-1

description: Single cell from HSC


title: C11-1001000353-AK111_AB-1

description: Single cell from HSC


title: 042_T5466_HC_B

value: Other, multiple


title: 041_T5210_HC_B


title: A6-1001000358-AK111-1

description: Single cell from HSC


title: 040_T4631_HC_B


title: 039_L0140_HC_B


title: E11-1001000353-AK111_AB-1

description: Single cell from HSC


title: B6-1001000358-AK111-1

description: Single cell from HSC


title: 038_L0088fresh_HC_B


title: 120_S1078a_IFNneg_cDC

value: cDC

value: IFNneg


title: 037_L0038_HC_B


title: D6-1001000358-AK111-1

description: Single cell from HSC


title: C6-1001000358-AK111-1

description: Single cell from HSC


title: E6-1001000358-AK111-1

description: Single cell from HSC


title: 036_S3011a_IFNpos_T

value: T cells

value: IFNpos

value: White

value: Hispanic/Latino


title: 033_S3007a_IFNpos_T

value: systemic lupus erythematosus (SLE)


title: 035_S3010a_IFNpos_T

value: Non-Hispanic/Latino


title: 046_T5695re_HC_B

value: healthy control

value: Hispanic


title: G6-1001000358-AK111-1

description: Single cell from HSC


title: F6-1001000358-AK111-1

description: Single cell from HSC


title: B2-1001000360-AK119-1

description: Single cell from HSC


title: 034_S3008a_IFNpos_T

value: Male


title: 032_S3005a_IFNpos_T

value: Female

value: Asian

value: Pacific Islander


title: 030_S3003a_IFNpos_T


title: H7-1001000358-AK111-1

description: Single cell from HSC

value: HSC


title: E1-1001000360-AK119-1

description: Single cell from HSC


title: C8-1001000360-AK119-1

description: Single cell from HSC


title: A11-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: H10-1001000360-AK119-1

description: Single cell from HSC


title: 029_S1084a_IFNpos_T


title: 028_S1083a_IFNpos_T


title: G5-1001000360-AK119-1

description: Single cell from HSC


title: 027_S1079a_IFNpos_T


title: B11-1001000361-SCF-1

description: Single cell from HSC


title: 026_S1075a_IFNpos_T


title: B8-1001000359-AK113_AB-1

description: Single cell from HSC


title: 024_S3009a_IFNneg_T


title: 025_S1073a_IFNpos_T


title: C11-1001000361-SCF-1

description: Single cell from HSC


title: 023_S2016a_IFNneg_T


title: E8-1001000359-AK113_AB-1

description: Single cell from HSC


title: 022_S2014a_IFNneg_T


title: 020_S1088a_IFNneg_T


title: D8-1001000359-AK113_AB-1

description: Single cell from HSC


title: 021_S2013a_IFNneg_T

value: not listed


title: C8-1001000359-AK113_AB-1

description: Single cell from HSC


title: G8-1001000359-AK113_AB-1

description: Single cell from HSC


title: 019_S1087a_IFNneg_T


title: 017_S1085a_IFNneg_T


title: 018_S1086a_IFNneg_T


title: A8-1001000359-AK113_AB-1

description: Single cell from HSC


title: 031_S3004a_IFNpos_T


title: H9-1001000359-AK113_AB-1

description: Single cell from HSC


title: 015_S1069a_IFNneg_T


title: F8-1001000359-AK113_AB-1

description: Single cell from HSC


title: D11-1001000361-SCF-1

description: Single cell from HSC


title: 016_S1078a_IFNneg_T


title: E12-1001000361-SCF-1

description: Single cell from HSC


title: 013_S1064a_IFNneg_T


title: 014_S1067a_IFNneg_T


title: C12-1001000353-AK111_AB-1

description: Single cell from HSC


title: 012_T5695_HC_T

value: HC


title: A12-1001000353-AK111_AB-1

description: Single cell from HSC


title: 011_T5777_HC_T

value: Black

value: Non Hispanic


title: D12-1001000353-AK111_AB-1

description: Single cell from HSC


title: 010_T5695re_HC_T

value: T cells


title: B12-1001000353-AK111_AB-1

description: Single cell from HSC


title: 009_T5663_HC_T

value: White


title: A7-1001000358-AK111-1

description: Single cell from HSC


title: 008_T5599_HC_T


title: 007_T5502_HC_T


title: G7-1001000358-AK111-1

description: Single cell from HSC


title: E12-1001000353-AK111_AB-1

description: Single cell from HSC


title: E7-1001000358-AK111-1

description: Single cell from HSC


title: 003_L0140_HC_T

value: Not available


title: 002_L0088fresh_HC_T


title: B7-1001000358-AK111-1

description: Single cell from HSC


title: 006_T5466_HC_T

value: Other, multiple


title: D7-1001000358-AK111-1

description: Single cell from HSC


title: B5-1001000360-AK119-1

description: Single cell from HSC


title: 005_T5210_HC_T


title: Ro75 in M199 rep 3

city: Providence

first: Alper

last: Uzun

state: RI

address: 200 Chestnut St.

department: Pediatrics

institute: Women and Infants Hospital of Rhode Island

description: Adhesive isolate  Ro75 grown in adhesion inducing medium: M199 at 37 degrees C

data_processing:
Raw sequence quality control and trimming was performed with FastQC v0.11.5 and Skewer v0.2.1
Reads were simultaneously aligned to the CDC317 C. parapsilosis reference genome and quantified using Salmon v1.0.0 in mapping-based mode
Gene-level expression values in quant files were imported into DESeq2 v1.18.1 R package using the tximport v1.6.0 R package
DESeq2 v1.18.1 R package was used to run differential expression analysis
Genome_build: CDC317
Supplementary_files_format_and_content: Salmon quant files containing gene level expression counts which have been corrected for gc content and sequence-specific random hexamer priming biases

organism: Candida parapsilosis

source_name: Liquid Culture

growth_protocol: Isolates were confirmed as C. parapsilosis sensu stricto using PCR probes specific to the ITS1 region. Yeast were grown overnight in YPD medium (1% yeast extract, 2% peptone, 2% dextrose) with vigorous agitation at 37°C. Stationary phase cultures were washed with sterile water, and resuspended in fresh YPD medium, tissue culture medium M199 (BioWhittaker/Lonza #BW12-117Q) or pooled human blood plasma (sodium heparin anticoagulated) at 3 x 106 / ml, and further incubated at 37°C for 3 hours without shaking. Under these growth conditions, filaments (hyphae or pseudohyphae) were not observed. Parallel samples were tested in adhesion assays to confirm the adhesive phenotype, or yeast were centrifuged, and pellets flash frozen in liquid N2, and stored at -80° C for later RNA extraction for RNA seq or qPCR validation.

extract_protocol:
Total RNA was extracted from each and purified using RiboPure Yeast extraction kit (Ambion/Life Technologies). RNA integrity was assessed using agarose gels and Agilent Bioanalyzer.
RNA-seq library preparation and sequencing of extracted total RNA was performed following ribosomal RNA depletion using paired end reads (Illumina HiSeq2000), 2x150 bp, from all samples.

tag: growth medium


title: 001_L0038_HC_T


title: F7-1001000358-AK111-1

description: Single cell from HSC

tag: treatment


title: H8-1001000358-AK111-1

description: Single cell from HSC


title: Ro75 in Plasma rep 1

description: Adhesive isolate  Ro75 grown in adhesion inducing medium: Plasma at 37 degrees C

value: Plasma

tag: strain


title: Ro75 in M199 rep 2


title: Ro75 in Plasma rep 3


title: E9-1001000360-AK119-1

description: Single cell from HSC

tag: days in culture


title: G6-1001000360-AK119-1

description: Single cell from HSC

tag: date sequencing


title: B12-1001000361-SCF-1

description: Single cell from HSC


title: A12-1001000361-SCF-1

description: Single cell from HSC


title: Ro75 in Plasma rep 2


title: Ro75 in YPD rep 2

description: Adhesive isolate  Ro75 grown in adhesion supressing medium: YPD at 37 degrees C

value: YPD


title: H11-1001000360-AK119-1

description: Single cell from HSC