title: StageI_Day2-0618

status: Public on Feb 09 2022

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
The clean single-cell RNA-seq reads were mapped to human reference genome hg19 using Cell Ranger v3.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: .tar.gz files containing cellranger output

source_name: human somatic cells during chemical reprogramming stage I day 2

growth_protocol: Human CiPS cells and hES cells (H1) were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) and human adult skin fibroblasts (hASFs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Using single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, cells at different time points throughout chemical reprogramming process were harvested and resuspended at 1 x 106 cells per milliliter in 1 x PBS with 0.04% BSA. About 1 x 104 cells were added to each channel, and the target cell will be recovered was estimated to be about 5 x 103 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min, and hold at 4 ℃. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.

tag: cell line


title: 12C

status: Public on Feb 16 2022

type: SRA

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

country: USA

institute: OUHSC

library_source: transcriptomic

data_processing:
trimomatic
gSNAP
cufflinks
R programming environment (ver 4.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files

molecule: total RNA

organism: Homo sapiens

source_name: vastus lateralis skeletal muscle biopsy

growth_protocol: Randomized cross-over treatment design of individuals who were seditary, had small bouts, or one continuous bout of moderate intensity walking

extract_protocol:
RNA was isolated using Trizol from Ambion according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
NuGEN universal Plus mRNA SEQ protocol part no. 9133

treatment_protocol: Interventions were given for 4-days and vastus lateralis skeltal muscle was biopsied

tag: tissue

value: vastus lateralis skeletal muscle biopsy

tag: treatment

value: MICRO

tag: treatment id

value: C


title: 12A

value: SED

value: A


title: StageI_Day0.5-0618

country: China

molecule: polyA RNA

source_name: human somatic cells during chemical reprogramming stage I day 0.5


title: StageI_Day0-0618

source_name: human somatic cells during chemical reprogramming stage I day 0


title: 8A


title: 17B

value: ONE

value: B


title: TrifKO_Vehicle_rep2

status: Public on Feb 08 2022

city: Seattle

first: Eva

middle: Kristine

last: Nichols

state: Washington

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Sample 7_EN08

data_processing:
Sequencing results from libraries were directly used as input to the 10X Cell Ranger software (v3.0.2 operated in cluster mode) in order to generate a barcodes, features, and matrix files in addition to base metrics of the run.
Filtered barcodes, features, and matrix files from 10x Cell Ranger were imported to Seurat (version 2.1.4) to create a gene-by-cell Seurat Object. Seurat was used for downstream quality-control and analysis within RStudio (version 1.1.463). Only cells with a minimum of 200 features were present for downstream steps. The treatment, batch, percent mitochondrial genes,  and percent ribosomal genes were added to the metadata of every cell. Next, each Seurat object was filtered such that only cells contening equal to or more than 500 features (but less than 6500) and equal to or less than 15% mitochondrial genes per cell were included for downstream analysis. The data was then log-normalized using the NormalizeData Seurat function. Next, 2000 variable features were selected using the FindVariableFeatures Seurat function (via vst selection method). These variable features were used as input later for principle component analysis.
Cell sex was assigned on the basis of sex gene expression after merging datasets using the merge function of Seurat. Briefly, the lists of all genes from the Y and X mouse chromosomes were extracted from Ensembl's biomaRt using the "ENSEMBL_MART_MOUSE" mart and the "mmusculus_gene_ensembl" dataset. The merged object data was rthen normalized and scaled on features found only on the Y- and X-chromosomes. These sex gene lists were used to find all Y and X genes expressed in the dataset. Only 8 total Y-chromosome features were found. Meanwhile, Xist was chosen as the representative X-chromosome gene. Density histograms of gene expression were constructed for all 8 Y-chromosome genes and Xist; cutoff values were determined at the first minimum. For any cell that has expression of any Y-chromosome gene above the cutoff, and below the cutoff of Xist, were counted as male. Conversely, any cells with Xist expression above its cutoff, and below that of all Y-chromosome genes, were counted as female. Any cells that did not fall in these categories were deemed indeterminate and removed from teh study; all remaining cells had sex assigned to the metadata.
Any additional low-quality cells, such as doublets remaining after filtering, were identified and removed using the DoubletFinder tool (version 2.0.3). We then used Seurat's CellCycleScoring function to infer the cell cycle phase of every cell and added cell cycle phase to the metadata. The Scater package (version 1.14.6) was used to further assess dataset quality.
After each replicate has undergone the above steps, replicates underwent batch-correction following Seurat's FindIntegrationAnchors and IntegrateData functions using 40 dimensions and normalized using the log normalization method. The integrated dataset was then scaled using Seurat's ScaleData function; here, the mitochondrial genes, RNA counts, and cell cycle scores were regressed out. All variable features were also scaled.
Seurat's ElbowPlot function was used to infer how many useful principal components to include for downstream analysis. We chose to include 15 principal components to reduce the dimensionality of the dataset via Seurat's RunPCA function on the integrated assay. Next, RunUMAP, FindNeighbors, and FindClusters Seurat functions were used to cluster the data. Using the Clustree tool allowed us to infer an appropriate clustering resolution of 0.4 to proceed. The top marker genes (positive and negative) defining the clusters were found using Seurat's FindAllMarkers function (with parameters min.pct and thresh.use at 0.25).
Assembly: mm10
Supplementary files format and content: For each replicate, the 10X Cell Ranger filtered barcodes, features, and matrix is provided.

organism: Mus musculus

source_name: Fetal mouse brain

growth_protocol: All mice were maintained in specific pathogen-free conditions in the Li Ka Shing animal facility at the University of California, Berkeley. A 12-hour light/dark cycle was maintained, and food and water were accessed ad libitum. C57BL6/J wild-type mice were obtained from Jackson Laboratory, and Trif(-/-) KO mice were originally provided by Gregory Barton. Mice underwent timed breeding; presence of vaginal plug indicated embryonic day (E)0.5.

extract_protocol:
24 hours after treatment, dams were sacrificed and embryonic day (E)13.5 embryos were collected. Fetal brains were dissected, minced, triturated, and digested in order to obtain a single-cell suspension. Embryo tails were taken for SRY genotyping. Whenever possible, equal number of male and female brain suspensions were pooled before myeloid cell staining. Cells were stained using Cd11b and Cd45.2 antibodies. Cd11b and Cd45.2 double positive cells were sorted and concentrated prior to maximally loading onto the 10X Chromium Single Cell 3' Regent Kit chip (v3 chemistry).
Libraries were prepared according to 10X Chromium Single Cell 3' Reagent Kit (v3 chemistry) vendor specifications at the Functional Genomics Lab at the University of California, Berkeley. Each library corresponds to a replicate with a unique set of 4 barcodes. N=2 independent biological replicates per genotype per treatment are included in the study (8 total libraries).
Four single-cell RNA-sequencing libraries corresponding to genotype were pooled (N=2 treatment replicates) for sequencing on one S4 lane of the NovaSeq 6000 platform (2 lanes total) at the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley and the University of California, San Francisco Center for Advanced Technology. There are 12 raw fastq files for Samples 1 through 4 (WT libraries) and 48 raw fastq files for Samples 5 through 8 (Trif KO libraries) due to different de-multiplexing strategies at the aforementioned sequencing facilities.

treatment_protocol: On embryonic day (E)12.5, dams were given a single dose of either Poly(I:C) TLR3 agonist (2 mg/kg; Sigma-Aldrich, cat. no. P9582) or PBS saline Vehicle control intraperitoneally.

tag: developmental stage

tag: cell type

value: Myeloid

value: Brain

tag: strain

tag: genotype

value: Trif KO

value: Vehicle

tag: sorting antibodies

value: CD11b-PE-Cy7 (eBioscience, cat. no. 25-0112-81), CD45.2-PE (Invitrogen, cat. no. 12-0454-83)


title: 28C


title: cbf1Δ, S phase (t=40 min), HybCap, Rep 2

status: Public on Feb 07 2022

first: Glennis

middle: Amelia

last: Logsdon

state: WA

description:
SBY4958 (cbf1Δ), t=40, HybCap, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv

data_processing:
Library strategy: Iso-Seq
All CCS reads were demultiplexed and trimmed to remove the adapter with Lima v1.10.0 (https://lima.how/) and the following parameters: --isoseq --dump-clips. The resulting reads were tagged for deduplication and trimmed to remove the linker and UMI with the isoseq3 v3.2.2 (https://github.com/PacificBiosciences/IsoSeq) tag step and the following parameters: --design T-17B-7U. Full-length non-chimeric (FLNC) reads were extracted with the isoseq3 v3.2.2 refine step and the following parameters: --min-polya-length 10 –require-polya. The resulting FLNC reads were deduplicated with the isoseq3 v3.2.2 dedup step and the following parameters: --max-tag-mismatches 0 --max-tag-shift 0.
The FLNC, deduplicated reads were mapped to the April 2011 sacCer3 yeast reference genome via Minimap2 v2.17-r941 (Li, 2018) with the following parameters: -ax splice -t {threads} -G2k -uf -C5 {ref.fasta } {input.fastq}. SAM files were filtered using SAMtools (Li et al., 2009) with FLAG score 2308 to prevent multi-mapping of reads.
Genome_build: April 2011 sacCer3 assembly of the S. cerevisiae genome from Saccharomyces Genome Database (GCA_000146055.2).
Supplementary_files_format_and_content: bw

organism: Saccharomyces cerevisiae

growth_protocol: All strains were grown in yeast peptone dextrose (YPD)-rich media

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher, #15596) following the manufacturer’s instructions. Briefly, frozen cell pellets were resuspended in TRIzol and lysed using glass beads and a bead beater (Biospec products). RNA was extracted twice with chloroform, precipitated with isopropanol, washed twice with 75% ethanol and resuspended in H2O. RNA was stored at -80°C. Cell cycle progression was monitored by RT-PCR analysis, as described below, of HTA1 (histone H2A) and SWI5 genes whose expression peaks in S phase and G2/M respectively (data not shown). RNAs from t=0 min (G1 phase) and t=40 min (S phase) were selected for further polyadenylated tail enrichment and sequencing.  Polyadenylated (poly(A)) RNA was enriched using Oligo d(T)25 Magnetic Beads (NEB, #S1419S) following the manufacturer’s instructions, using ~150 μg of purified total RNA.  Poly(A)-enriched RNA was treated with DNase I to remove any contaminating DNA using the RNA Clean & Concentrator kit (Zymo, #R1014) according to the manufacturer’s instructions. RNA was ligated to the universal miRNA cloning linker (NEB, #S1315S) by combining 100 ng of poly(A)-enriched RNA with 1 μM universal miRNA cloning linker, 1X T4 RNA ligase buffer, 20% PEG 8000, 100 U T4 RNA ligase 2 (truncated KQ) (NEB, #M0373S), and 10 U SUPERase-In RNase inhibitor (ThermoFisher Scientific, #AM2694) in a 20 μL  volume and incubating at 25°C for 2 hr in a thermocycler. The linker-ligated RNA was purified using the RNA Clean & Concentrator kit (Zymo, #R1014) and eluted in 15 μL RNase/DNase-free water. The RNA was reverse-transcribed into cDNA using the SMARTer PCR cDNA Synthesis Kit (Clontech, #634925) with modifications to the manufacturer’s protocol. Briefly, 10-50 ng of RNA was mixed with 1 mM dNTP mix and 1 μM of the following oligo: 5’- AAGCAGTGGTATCAACGCAGAGTNNNNNNATTGATGGTGCCTACAG-3', where N is either an A, C, G, or T, and the string of Ns creates a unique molecular identifier (UMI) that serves as a barcode for each cDNA molecule. This mixture was heated at 65°C for 2 min on a thermocycler and then combined with a pre-heated mixture of 1x First-Strand Buffer, 10 μM DTT, 1.2 μM Clontech SMARTer IIA template-switch oligo, 5 U SUPERase-In RNase inhibitor, and 100 U Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific, #EP0751). This 10 μL mixture was incubated at 50°C for 1 hr, 45°C for 30 min, and 85°C for 5 min before being cooled on ice. The resulting cDNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB, #T1030S) and amplified via PCR with 1x KAPA HiFi HotStart ReadyMix (Roche, #KR0370) and 1 μM of the following oligo: 5’-AAGCAGTGGTATCAACGCAGAGT-3’ for 12 PCR cycles. The amplified DNA was purified with the QIAquick PCR Purification Kit (Qiagen, #28104) and eluted in 30 μL Elution Buffer.  To capture centromeric cDNA molecules, the xGen Hybridization and Wash Kit (IDT, # 1080577) was used with some modifications to the manufacturer’s protocol. Briefly, 500 ng-1 μg of cDNA was lyophilized with 6 μM 5’ blocking oligo (Clontech SMARTer IIA template-switch oligo), 6 μM 3’ blocking oligo (Pacbio 3' blocker-16bpBC), and 1 μg salmon sperm (Invitrogen, #15-632-011) using a SpeedVac system. The lyophilized DNA was resuspended in 17 μL hybridization mastermix consisting of 8.5 μL xGen 2X Hybrization Buffer, 2.7 μL xGen Hybridization Buffer Enhancer, 1.8 μL water, and 4 μL of 0.75 μM biotinylated probes. The solution was heated at 80°C for 5 min, incubated at 95°C for 1 min, and then incubated at 65°C for 2-4 hours. Washed streptavidin beads (Invitrogen, #65306) were added to the mixture and incubated at 65°C for 45 min. The beads were washed with a series of heated and room temperature washes according to the manufacturer’s protocol. The remaining DNA on the beads were amplified via PCR with 1x KAPA HiFi HotStart ReadyMix (Roche, #KR0370) and 1 μM of the following oligo: 5’-AAGCAGTGGTATCAACGCAGAGT-3’ for 15 PCR cycles according to the manufacturer’s instructions. The resulting DNA was purified and checked via Agilent’s BioAnalyzer System to ensure successful amplification.
Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, #100-938-900) according to the manufacturer’s protocol. Briefly, 250 ng of DNA was damage-repaired by mixing it with 7 μL DNA prep buffer, 0.6 μL NAD, and 2 μL DNA Damage Repair Mix v2. This reaction was incubated at 37°C for 30 min before proceeding to the end-repair step. For the end-repair step, 3 μL End Prep Mix was added to the reaction and incubated at 20°C for 30 min, followed by a second incubation at 65°C for 30 min. The reaction was then mixed with 3 μL barcoded overhang adapter, 30 μL Ligation Mix, 1 μL Ligation Enhancer, and 1 μL Ligation Additive to ligate the barcoded adapter. This reaction was incubated at 20°C for 1 hr. The SMRTbell libraries were cleaned up with ProNex beads (Promega, #NG2001), pooled, and sequenced on a SMRT Cell 8M on the Pacific Biosciences Sequel II in CCS mode with the following parameters: --noPolish –minLength 10 –minPasses=3).

treatment_protocol: Cells were treated with 1 ug/mL ⍺-factor pheromone for ~3 hours, washed twice with an equivalent volume of YPD, and released into medium lacking the ⍺-factor pheromone. Cells collected just after ⍺-factor release form the G1 fraction (t=0 min). Cells collected 40 mins after ⍺-factor release form the S fraction (t=40 min).

value: Treated with 1 ug/mL alpha-factor for 3 hr, released for 40 min


title: WT_PIC_rep2

description: Sample 4_EN05

value: WT


title: cbf1Δ, G1 phase (t=0 min), HybCap, Rep 1

description:
SBY4958 (cbf1Δ), t=0, HybCap, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv

value: Treated with 1 ug/mL alpha-factor for 3 hr to arrest in G1 phase


title: TrifKO_PIC_rep1

description: Sample 6_EN07


title: TrifKO_PIC_rep2

description: Sample 8_EN09


title: WT_PIC_rep1

description: Sample 2_EN03


title: cbf1Δ, G1 phase (t=0 min), Input, Rep 2

description:
SBY4958 (cbf1Δ), t=0, Input, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: cbf1Δ, S phase (t=40 min), Input, Rep 2

description:
SBY4958 (cbf1Δ), t=40, Input, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: WT_Vehicle_rep1

description: Sample 1_EN02


title: Wild-type, S phase (t=40 min), HybCap, Rep 2

description:
SBY3 (WT), t=40, HybCap, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: cbf1Δ, G1 phase (t=0 min), HybCap, Rep 2

description:
SBY4958 (cbf1Δ), t=0, HybCap, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: Wild-type, S phase (t=40 min), HybCap, Rep 1

description:
SBY3 (WT), t=40, HybCap, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: LIB046510_TRA00182899_S17_quant

status: Public on Jan 31 2022

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
RNA-seq fastq reads were aligned to the hg38 genome and quantified using Salmon 1.4.0 with default settings.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count matrix in csv

source_name: CD14+ cells cocultured with stromal cells

growth_protocol: Primary liver stromal cells were seeded onto 96 well flat bottom plates (VWR) at a density of 10,000 cells/well in ALPHA-MEM complete. Frozen PBMCs were thawed into R10 media and CD14+ cells were isolated immediately using CD14 MACS positive isolation kit (Milteyni). CD14+ cells were resuspended in ALPHA MEM complete media and plated on the adherent stromal cells at a density of 100,000 cells/well. Cells were cocultured for 24, 48, and 72 hour timepoints. To harvest the CD14+ cells, gentle mechanical pipetting of the supernatant released the CD14+ cells from the stromal layer and the stromal cells remained adherent to the plastic. Harvested CD14+ cells were transferred to a V-Bottom plate (VWR) for cellular staining and analysis.

extract_protocol:
Prior to plating, the freshly isolated CD14+ cells were pelleted and lysed, and RNA isolation was performed using the Qiagen RNEasy Mini Kit. Likewise, RNA was isolated from liver stromal cell lines, previously plated at 10,000 cells per well 24hrs prior. This was performed following two rinses by gently- pipetted 200 uL volumes of sterile, room temperature PBS (Life Technologies).
CD14+ cells were then plated alone, with stromal cell coculture, or in the presence of 500 pg/mL recombinant human IL6 (R&D Systems). Following 72 hours in culture, monocytes from each condition were harvested by pipetting and pelleted by centrifugation at 1000 RPM for 10 minutes. Stromal cell cultures adherent in the plate were rinsed twice with 200 uL volumes of sterile, room temperature PBS (Life Technologies). CD14+ Monocytes were re-purified using the CD14 MACS positive isolation kit (Milteyni) to minimize stromal cell contamination. RNA was prepared using the Qiagen RNEasy Mini Kit, according to manufacturer’s instructions. Conditioned supernatant was pooled for each condition and frozen in sterile eppendorf tubes at -20°C prior to CBA analysis. Aliquots of RNA preparations were analyzed for quality and concentration at the Biopolymers facility at Harvard Medical School using the Agilent Bioanalyzer.

value: CD14+ cells from PBMCs

tag: condition

value: Coculture

tag: hours

value: 72 hr

tag: donor cd14


title: Wild-type, G1 phase (t=0 min), HybCap, Rep 2

description:
SBY3 (WT), t=0, HybCap, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: cbf1Δ, S phase (t=40 min), Input, Rep 1

description:
SBY4958 (cbf1Δ), t=40, Input, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: WT_Vehicle_rep2

description: Sample 3_EN04


title: Wild-type, S phase (t=40 min), Input, Rep 2

description:
SBY3 (WT), t=40, Input, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: cbf1Δ, S phase (t=40 min), HybCap, Rep 1

description:
SBY4958 (cbf1Δ), t=40, HybCap, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: cbf1Δ, G1 phase (t=0 min), Input, Rep 1

description:
SBY4958 (cbf1Δ), t=0, Input, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: Wild-type, S phase (t=40 min), Input, Rep 1

description:
SBY3 (WT), t=40, Input, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: TrifKO_Vehicle_rep1

description: Sample 5_EN06


title: Wild-type, G1 phase (t=0 min), HybCap, Rep 1

description:
SBY3 (WT), t=0, HybCap, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: LIB046510_TRA00182897_S16_quant


title: LIB046510_TRA00182885_S14_quant

source_name: stromal cells  cocultured

value: stromal cells from liver


title: Wild-type, G1 phase (t=0 min), Input, Rep 2

description:
SBY3 (WT), t=0, Input, Rep 2
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: LIB046510_TRA00182895_S15_quant


title: LIB046510_TRA00182867_S9_quant

source_name: CD14+ cells  with IL-6


title: LIB046510_TRA00182881_S12_quant


title: LIB046510_TRA00182869_S10_quant


title: LIB046510_TRA00182861_S8_quant

source_name: CD14+ cells  alone

value: Culture Alone


title: LIB046510_TRA00182851_S5_quant

source_name: stromal cells alone

value: N


title: Wild-type, G1 phase (t=0 min), Input, Rep 1

description:
SBY3 (WT), t=0, Input, Rep 1
all_reads.entireCDEcounts.summary.tsv
all_reads.50bpcounts.right.summary.tsv
all_reads.50bpcounts.left.summary.tsv
all_reads.1bpcounts.summary.tsv
all_reads.50bp_meanreadlength.right.allsummary.tsv
all_reads.50bp_meanreadlength.left.allsummary.tsv
all_reads.1bp_meanreadlength.allsummary.tsv
all_reads.100bpcounts.divergent.left.summary.tsv
all_reads.100bpcounts.divergent.right.summary.tsv


title: LIB046510_TRA00182901_S18_quant


title: LIB046510_TRA00182883_S13_quant


title: LIB046510_TRA00182879_S11_quant


title: LIB046510_TRA00182853_S6_quant


title: LIB046510_TRA00182859_S7_quant


title: LIB046509_TRA00182898_S17_quant


title: LIB046510_TRA00182835_S1_quant

value: 0 hr


title: LIB046509_TRA00182896_S16_quant


title: LIB046509_TRA00182900_S18_quant


title: LIB046510_TRA00182839_S3_quant


title: LIB046510_TRA00182837_S2_quant


title: LIB046509_TRA00182894_S15_quant


title: LIB046509_TRA00182884_S14_quant


title: LIB046509_TRA00182882_S13_quant


title: LIB046509_TRA00182878_S11_quant


title: LIB046510_TRA00182841_S4_quant


title: LIB046509_TRA00182880_S12_quant


title: LIB046509_TRA00182868_S10_quant


title: LIB046509_TRA00182860_S8_quant


title: LIB046509_TRA00182850_S5_quant


title: LIB046509_TRA00182852_S6_quant


title: LIB046509_TRA00182858_S7_quant


title: LIB046509_TRA00182836_S2_quant


title: LIB046509_TRA00182834_S1_quant


title: LIB046509_TRA00182838_S3_quant


title: LIB046508_TRA00186676_S19_quant


title: LIB046508_TRA00182891_S17_quant


title: LIB046509_TRA00182840_S4_quant


title: LIB046508_TRA00182889_S16_quant


title: LIB046508_TRA00182893_S18_quant


title: LIB046508_TRA00182875_S13_quant


title: LIB046508_TRA00182887_S15_quant


title: LIB046508_TRA00182871_S11_quant


title: LIB046508_TRA00182873_S12_quant


title: LIB046508_TRA00182877_S14_quant


title: LIB046508_TRA00182865_S10_quant


title: LIB046508_TRA00182857_S8_quant


title: LIB046508_TRA00182863_S9_quant


title: LIB046508_TRA00182849_S6_quant


title: LIB046508_TRA00182855_S7_quant


title: LIB046508_TRA00182843_S3_quant


title: LIB046508_TRA00182845_S4_quant


title: LIB046508_TRA00182847_S5_quant


title: LIB046508_TRA00182833_S2_quant


title: LIB046507_TRA00182890_S17_quant


title: LIB046508_TRA00182831_S1_quant


title: LIB046507_TRA00182892_S18_quant


title: 28A

value: vastus lateralis skeletal muscle biopsy

value: SED

value: A


title: LIB046507_TRA00182886_S15_quant


title: LIB046507_TRA00182888_S16_quant


title: LIB046507_TRA00182876_S14_quant


title: LIB046507_TRA00182872_S12_quant


title: LIB046507_TRA00182862_S9_quant


title: LIB046507_TRA00182854_S7_quant


title: LIB046507_TRA00182870_S11_quant


title: LIB046507_TRA00182864_S10_quant


title: LIB046507_TRA00182846_S5_quant


title: LIB046507_TRA00182844_S4_quant


title: LIB046507_TRA00182830_S1_quant


title: LIB046507_TRA00182832_S2_quant


title: liver, S20

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.0). Human genome hg38 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 600.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count matrix in csv

source_name: liver

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Tissue was placed in PBS on ice and transported from the hospital directly to the laboratory for immediate tissue dissociation. To enable paired histological assessment, a section of the sample was fixed in 10% Neutral Buffered Formalin (VWR) for 24 hours and then placed into 70% ethanol for long term storage before paraffin embedding and staining. For human liver scRNA-seq, liver tissue was mechanically dissociated with scissors and placed into a digestion buffer of 15mL PBS +/+ (Invitrogen), DNAse I (250mg/l, Akron Biotech), and Collagenase (500 mg/l, Worthington Biochemical) at 37 °C for 20 minutes with one agitation halfway through digestion. Samples were strained through a 250um metal strainer. Cells were centrifuged (450 x g for 5 minutes; cell were washed twice with 10mL PBS -/- (Invitrogen).  Red blood cell lysis was performed (Gibco ACK Lysing Buffer), followed by centrifugation (450 x g, 5 minutes), and resuspension in stromal growth media (ALPHA MEM  + L-Glutamine, -Deoxyribo, -Ribonucleodite (Life Technologies, Cat #12561072), 30% heat inactivated fetal bovine serum (Sigma), 1 % penicillin (100 U ),streptomycin (100ug/mL) (Invitrogen). Cells were passed through 70um filter. Single cell suspensions were used for primary cell line development and scRNA-seq analysis.

tag: patient id

tag: steatosis score

tag: ballooning score

tag: lobular inflammation

value: Y

value: liver


title: liver, S22


title: liver, S16


title: liver, S23


title: LIB046507_TRA00182874_S13_quant


title: liver, S21


title: liver, S17


title: liver, S14


title: LIB046507_TRA00182856_S8_quant


title: liver, S13


title: liver, S15


title: liver, S9


title: liver, S12


title: liver, S6


title: LIB046507_TRA00182842_S3_quant


title: liver, S11


title: liver, S10


title: liver, S8


title: liver, S5


title: liver, S7


title: LIB046507_TRA00182848_S6_quant


title: liver, S18


title: liver, S3


title: wt-rep #3

status: Public on Jan 13 2022

city: Rehovot

first: Eitan

last: Reuveny

state: Please Select

address: Dept. Biomolecular Sciences, 234 Hertzl St.

country: Israel

institute: Weizmann Inst. of Science

data_processing:
Sequenced reads were mapped to the Mus musculus genome version GRCm38, using TopHat v2.0.10.
Genes were identified using a gtf obtained from Ensembl release 82. Per gene, reads were counted using HTSeq.
Normalization of read counts and P-values for differentially expressed genes were computed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: DE2output

source_name: Embryonic fibroblasts

growth_protocol: E14.5 embryos were dissected, and their trunks were extracted into cold PBS. Trunks were finely minced using a razor until they were pipettable. Cells were suspended in 3ml trypsin-EDTA 0.05%, at 37C for 10 min. Cells were flushed through 21g (3ml) syringe three times, and double serum levels blocked trypsin. Next, cells were centrifuged at 1800rpm for 5 min, and the pellet re-suspended in 8ml of MEF media, containing 10% fetal calf serum, 2% Penstrep, 1% L-glutamine, and 1% sodium pyruvate. Cells from each embryo were plated on a 100mm dish coated with 0.1% gelatin. Cells were split 1:4 and frozen when they reached confluence.

extract_protocol:
Total RNA was extracted from the indicated cell cultures using the RNeasy kit (QIAGEN). Then, RNA integrity was evaluated on Bioanalyzer (Agilent 2100 Bioanalyzer), requiring a minimal RNA integrity number (RIN) of 8.5.
Libraries were prepared according to Illumina’s instructions accompanying the TruSeq RNA Sample Preparation Kit v2 (cat # RS-122–2001).

tag: strain background

tag: genotype/variation

value: wild type

value: Embryonic fibroblasts


title: liver, S2

tag: tissue


title: liver, S4


title: 30A

tag: treatment


title: liver, S19


title: liver, S1


title: wt- rep #1


title: StageI_Day1-0618

source_name: human somatic cells during chemical reprogramming stage I day 1

tag: cell line


title: wt- rep #2


title: Pt8-1Lin-

status: Public on Nov 09 2021

city: Albuquerque

first: DARIO

last: MARCHETTI

state: NM

address: 915 Camino de Salud

department: Internal Medicine

institute: UNM Health Sciences Center

description: bulk RNAseq sample

data_processing:
Sequencing was performed using the Ion Proton S5/XL systems (Life Technologies) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center
Sequences were aligned using tmap (v5.10.11) to a BED file containing non-overlapping exons from UCSC genome hg38. Exon counts were calculated using HTseq (v0.11.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCount file

source_name: Patient clinical blood sample Pt8-1Lin-

extract_protocol:
RBC lysis, stain with antibodies to CD45, CD34, CD73, CD90, CD105, CD235 and DAPI.  FACS sorting sends DAPI+ and CD235+ to Waste , Lin+ fraction contains cells positive for all other antibodies, while Lineage negative fraction would contain cells not tagged by these antibodies.  Total RNA was extracted from fractions using microRNA kit (Qiagen #74004)
Ribosomal RNA was removed using the RiboGone Kit, followed by cDNA synthesis using the SMARTer Universal Low Input RNA Kit for Sequencing (Takara Bio). Libraries were prepared using the Ion Plus Fragment Library Kit

tag: disease state

value: metastatic breast cancer

value: ER+/ PR-/Her2neu-

tag: tissue type

value: blood


title: Pt8-2Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt8-2Lin+


title: Pt14Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt14Lin+


title: Pt8-1Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt8-1Lin+


title: Pt21Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt21Lin-

value: ER-/ PR-/Her2neu-


title: Pt13Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt13Lin+

value: ER+/ PR-/Her2neu+


title: Pt8-2Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt8-2Lin-


title: Pt18Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt18Lin+

value: ER-/ PR-/Her2neu+


title: Pt13Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt13Lin-


title: Pt19Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt19Lin-


title: Pt14Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt14Lin-


title: Pt19Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt19Lin+


title: Pt18Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt18Lin-


title: Pt16Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt16Lin+


title: Pt12Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt12Lin+


title: Pt16Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt16Lin-


title: Pt12Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt12Lin-


title: Pt20Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt20Lin+


title: Pt20Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt20Lin-


title: sample 6, healthy control 6

status: Public on Dec 14 2021

type: RNA

city: Rostock

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a healthy individual

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: healthy control

tag: therapy

tag: Sex

value: male

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: Pt11Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt11Lin+

tag: genotype

value: ER+/ PR+/Her2neu-


title: Pt11Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt11Lin-


title: sample 1, healthy control 1


title: sample 2, healthy control 2

value: female


title: Pt17Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt17Lin+


title: sample 8, healthy control 8


title: Pt17Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt17Lin-


title: sample 10, healthy control 10


title: Pt10Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt10Lin+


title: Pt15Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt15Lin-


title: Pt10Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt10Lin-


title: Pt9Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt9Lin-


title: sample 9, healthy control 9


title: sample 12, healthy control 12


title: sample 4, healthy control 4


title: Pt15Lin+

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt15Lin+


title: sample 5, healthy control 5


title: Pt7Lin-

description: bulk RNAseq sample

source_name: Patient clinical blood sample Pt7Lin-

value: ER+/ PR+/Her2neu+


title: sample 11, healthy control 11


title: SF6420 (snATAC)

status: Public on Oct 20 2021

city: San Francisco

first: Aaron

last: Diaz

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

library_source: genomic

data_processing:
We used CellRanger (version 3.0.2) to pre-process the sc/snRNA-seq data from the 10X Genomics platform.
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
The output matrix of CellRanger was further filtered for quality based on two criteria: 1) number of fragments > 1000; 2) fragments in promoter ratio > 0.2.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Filtered peak matrix (.mtx)  files.  Bed files, peaks (TSV).

molecule: genomic DNA

source_name: Brain

growth_protocol: All surgical procedures were conducted according to our Institutional Animal Care and Use Committee and NIH ethical guidelines. ATRX-KO and wildtype SB28 cells expressing IDH1R132H and a luciferase reporter were used to establish intracranial tumors in C57BL/6j mice, using 6 mice per cohort. Animals were anesthetized using isoflurane, each surgical procedure was performed after placing the animal in a stereotactic frame.  An aliquot of 5 × 104 SB28 cells was injected into the right parietal region of the brain. The injection site was 2 mm to the right of the central suture and 0.5 mm anterior to the lambda junction; depth of injection was 2-3 mm. The rate of injection was 1 l/min.

extract_protocol:
Tissue processing, tagmentation, nuclei capture and library prep was performed by the 10X Genomics platform.
Single-cell/nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol.
Sequencing was performed according to 10X Genomics recommended protocols on an Illumina NovaSeq 6000.

treatment_protocol: Following euthanasia, mice were perfused with PBS, tumor tissue was harvested and snap frozen.

tag: age

value: M

value: Oligodendroglioma (WHO gr. 2)


title: SF7003 (snATAC)


title: SF4007 (snATAC)

value: F


title: SF6244 (snATAC)

value: Astrocytoma  Anaplastic (WHO gr. 3)


title: SF4454 (snATAC)

value: Astrocytoma (WHO gr. 2)


title: sample 3, healthy control 3


title: sample 7, healthy control 7


title: SF7233 (snATAC)


title: SF12038 (snATAC)

value: Diffuse Astrocytoma  IDH-mutant


title: SF11310 (snATAC)

value: Oligodendroglioma  IDH-mutant  1p19q codeleted


title: SF11940 (snATAC)

value: Anaplastic Astrocytoma  IDH-mutant


title: SF10922 (snATAC)


title: SF10619 (snATAC)


title: SF10328 (snATAC)

value: Unknown


title: IDH1R132H+/ATRX-intact (snATAC-seq)

growth_protocol: All surgical procedures were conducted according to our Institutional Animal Care and Use Committee and NIH ethical guidelines. ATRX-KO and wildtype SB28 cells expressing IDH1R132H and a luciferase reporter were used to establish intracranial tumors in C57BL/6j mice, using 6 mice per cohort. Animals were anesthetized using isoflurane, each surgical procedure was performed after placing the animal in a stereotactic frame.  An aliquot of 5 × 104 SB28 cells was injected into the right parietal region of the brain. The injection site was 2 mm to the right of the central suture and 0.5 mm anterior to the lambda junction; depth of injection was 2-3 mm. The rate of injection was 1 ul/min.

value: Male


title: PBMC 1

status: Public on Oct 18 2021

description: Ion S5XL buik RNAseq sample

source_name: donated anonymous normal blood sample#1

growth_protocol: none, clinical samples

treatment_protocol: none, clinical samples

value: normal

value: unknown

value: blood


title: SF12374 (snATAC)


title: Pt6Lin+

description: Ion S5XL buik RNAseq sample

source_name: Patient clinical blood sample Pt6Lin+

value: metastatic breast cancer

value: ER+/ PR-/Her2neu -


title: IDH1R132H+/ATRX-KO (snATAC-seq)

extract_protocol:
Tissue processing, tagmentation, nuclei capture and library prep was performed by the 10X Genomics platform. Single-cell/nucleus capture, reverse transcription, cell lysis, and library preparation were performed per the manufacturer’s protocol.
Sequencing was performed according to 10X Genomics recommended protocols on an Illumina NovaSeq 6000.


title: PBMC 2

description: Ion S5XL buik RNAseq sample

source_name: donated anonymous normal blood sample#2


title: SF10086 (snATAC)

value: Oligodendroglioma  Anaplastic (WHO gr. 3)


title: Pt6Lin-

description: Ion S5XL buik RNAseq sample

source_name: Patient clinical blood sample Pt6Lin-

value: ER+/ PR+/Her2neu -


title: Pt3 Lin+

description: 10x Genomics single cell RNA seq sample

data_processing:
Supplementary_files_format_and_content: CellRanger output files
Illumina NovaSEQ 6000 at University of Colorado Anschutz Medical Campus Genomics Shared Resource Cancer Center, demultiplexed with bcl2fastq v2.20.0.422 with “--barcode-mismatches” set to 1
Aligned and counted with CellRanger v3.1.1
Genome_build: GRCh38

source_name: Patient clinical blood sample #3

extract_protocol:
RBC lysis, stain with antibodies to CD45, CD34, CD73, CD90, CD105, CD235 and DAPI.  FACS sorting sends DAPI+ and CD235+ to Waste , Lin+ fraction contains cells positive for all other antibodies, while Lineage negative fraction would contain cells not tagged by these antibodies.
Cell concentrations and viability were determined using the Cell Countess II FL (ThermoFisher) prior to calculating cell counts and loading the suspension into the Next GEM Chip G and Chromium Controller (10x Genomics) per the manufacturer’s protocol for GEM formation. The 10x Chromium Next GEM 3’ protocol was used to create 3’ libraries; briefly, cells were lysed and barcoded within each GEM prior to first strand cDNA synthesis, also within each GEM. After GEM’s are broken, cells are pooled prior to library completion as described in the manufacture’s protocol. Library quality was assess after cDNA synthesis and after completion on the BioAnalyzer using a DNA High Sensitivity Chip (Agilent). Prior to sequencing, Agilent Tape Station 4200 and Invitrogen Qubit 4.0 reagents were used determine final library concentrations prior to dilution, normalization and pooling at 4nM. qPCR was used to determine cluster efficiency.

value: ER+/ PR+/Her2neu +

value: CD45+ (Lineage positive)  WBC


title: Pt1 Lin-

description: 10x Genomics single cell RNA seq sample

source_name: Patient clinical blood sample #1

value: ER-/ PR-/Her2neu -

value: CD45- (Lineage Negative)  WBC


title: 38x_2

status: Public on Sep 20 2021

city: Shenyang City, Liaoning Province

first: XinDi

last: Gao

state: Liaoning

address: 89, North WenHua Road

institute: Northeastern university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Bowtie 2 suite (version 4.1.2)
Genome_build: Cryptococcus neoformans var. grubii H99 .
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample.

organism: Cryptococcus neoformans H99

source_name: Fungal cells

growth_protocol: WT and hsf3∆ strains were inoculated into 50 ml of YPD broth and cultured overnight at 30°C in a shaking incubator. Cells were subcultured in 100 ml fresh YPD broth at OD600=0.2 until the OD600 reached 0.6 to 0.8 at 30°C or 40°C, respectively. Three independent cultures for each strain were prepared. Every culture was washed three times with PBS and placed in a liquid nitrogen tank for RNA-seq.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), and the concentration, quality and integrity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the preparations of RNA sample.
Sequencing libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

tag: condition

value: grown at logarithmic phase in 100ml YPD broth at 40°C


title: Pt3 Lin-

description: 10x Genomics single cell RNA seq sample


title: Pt4Lin+

description: Ion S5XL buik RNAseq sample

source_name: Patient clinical blood sample Pt4Lin+


title: Pt2 Lin+

description: 10x Genomics single cell RNA seq sample

source_name: Patient clinical blood sample #2


title: Pt4Lin-

description: Ion S5XL buik RNAseq sample

source_name: Patient clinical blood sample Pt4Lin-


title: Pt2 Lin-

description: 10x Genomics single cell RNA seq sample


title: 38x_1


title: 38H_1

value: wild type


title: 38H_3


title: SF10207 (snATAC)

value: M


title: 38H_2


title: 38x_3


title: 30x_3

value: grown at logarithmic phase in 100ml YPD broth at 30°C


title: Pt1 Lin+

description: 10x Genomics single cell RNA seq sample


title: Pt5Lin-

description: Ion S5XL buik RNAseq sample

source_name: Patient clinical blood sample Pt5Lin-


title: SF10679 (snATAC)


title: 30x_2


title: 30x_1


title: 30H_3


title: 30H_2


title: TX1.ChIP.rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Bowtie 2 suite (version 4.1.2)
Genome_build: Cryptococcus neoformans var. grubii H99 .
Supplementary_files_format_and_content: tab-delimited text files include the start and end site of indicated chromosome and fold_enrichment for each Sample.

growth_protocol: Hsf1-Flag-tagged and Hsf3-Flag-tagged cells were inoculated into YPD broth overnight at 30°C in a shaking incubator and then subcultured in 100 ml fresh YPD broth at OD600=0.2 until the OD600 reached 0.8 at 40°C. Three independent cultures for each strain were prepared. Every culture was extracted as the Chip protocol.

extract_protocol:
Cells were poured into 200 ml conical flasks containing 1.39 ml of 37% formaldehyde up to the 50 ml mark and incubated with gentle rocking for 15 min at room temperature, after which 2.7 ml of 2.5M glycine was added to stop the crosslinking and cells were mixed for 5 min. Cells were harvested at 3000 rpm for 5min at 4 °C, washed twice with ice-cold PBS containing 125mM glycine. Chromatin was extracted as described previously(Li et al., 2019).
The ChIP-seq library was generated using the MicroPlex Library Preparation Kit v2 (Diagenode, Liège, Belgium) according to the manufacturer’s instructions. The ChIP DNA libraries were sequenced using an Illumina Hiseq-PE150 Platform.

value: grown at logarithmic phase in 50ml YPD broth at 40°C


title: 30H_1


title: TX1.Input


title: TF1.ChIP.rep3


title: TX1.ChIP.rep1


title: TF1.ChIP.rep2


title: Pt5Lin+

description: Ion S5XL buik RNAseq sample

source_name: Patient clinical blood sample Pt5Lin+


title: TF1.Input


title: BMM8-Benign

status: Public on Aug 29 2021

description: Bone marrow samples from patients undergoing hip replacement surgery (Benign) served as a non-malignant comparator group

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 600.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: count matrix in csv

source_name: bone marrow_benign

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Dissociation of tissues into single cells: All samples were collected in Media 199 supplemented with 2% (v/v) FBS. Single cell suspensions of the tumors were obtained by cutting the tumor in to small pieces (1mm3) followed by enzymatic dissociation for 45 minutes at 37°C with shaking at 120 rpm using Collagenase I, Collagenase II, Collagenase III, Collagenase IV (all at a concentration of 1 mg/ml) and Dispase (2mg/ml) in the presence of RNase inhibitors (RNasin (Promega) and RNase OUT (Invitrogen)). Erythrocytes were subsequently removed by ACK Lysing buffer (Quality Biological) and cells resuspended in Media 199 supplemented with 2% (v/v) FBS for further analysis.

tag: subject id

tag: subject status

value: bone marrow


title: BMM5-Benign

value: patients undergoing hip replacement surgery

tag: tissue


title: BMM9-Benign


title: BMM3-Benign


title: BMET8-Distal

source_name: bone marrow_Distal

value: prostate cancer patient

value: GnRH agonist, abiraterone (9 mo; ongoing PSA response)

value: liquid bone marrow from a vertebral body distant from the tumor site (Distal)


title: BMM2-Benign


title: BMM4-Benign


title: BMET7-Distal

value: 35 mo

value: GnRH agonist (ongoing PSA response)


title: BMET8-Involved

source_name: bone marrow_Involved

value: liquid bone marrow at the site of the metastasis (Involved)


title: BMET8-Tumor

source_name: bone marrow_Tumor

value: solid metastatic tissue (Tumor fraction)


title: BMET7-Tumor


title: BMET6-Involved

value: 47 mo

value: GnRH agonist, abiraterone (17 mo), docetaxel (4 cycles)


title: BMET6-Tumor


title: BMET3-Distal

value: 1 mo


title: TX1.ChIP.rep2


title: BMET3-Involved


title: BMET5-Involved

value: 10 mo

value: GnRH agonist, abiraterone (3 months)


title: BMET5-Distal


title: BMET5-Tumor


title: BMET3-Tumor


title: BMET2-Involved

value: 2 days

value: 2 days bicalutamide (antiandrogen; newly-initiated therapy)


title: TF1.ChIP.rep1

value: grown at logarithmic phase in 50ml YPD broth at 40°C


title: BMET2-Distal

value: bone marrow


title: BMET11-Distal

value: 19 mo

value: GnRH agonist, docetaxel (6 cycles), abiraterone (5 mo), radium-223, pembrolizumab (deficient mismatch repair by IHC)


title: BMET2-Tumor

value: prostate cancer patient


title: BMM6-Benign

value: patients undergoing hip replacement surgery


title: BMET11-Involved


title: BMET1-Involved

value: 57 mo

value: GnRH agonist, abiraterone (9 months), docetaxel (5 cycles)


title: BMET1-Tumor


title: BMET1-Distal

value: liquid bone marrow from a vertebral body distant from the tumor site (Distal)


title: BMET6-Distal


title: ARPE-19_MNase_batch1

status: Public on Jun 08 2021

city: Shanghai

first: Jianing

last: Wang

address: Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
MNase-seq data were mapped using bowtie2 to hg38 genome and the midpoint of fragments with lengths between 120~180 bp were smoothed before position calling. From the smoothed data we detect the local maxima, then counted the number of reads within 30bp of each side of the local maximum. The p-value was the calculated based on Poisson distribution. The p-value was then adjusted using BH method, and the peaks with p ＜0.001 were selected as peak calling results.
We take the midpoint of the sequenced fragment as the center position of the nucleosome, and obtain the position of the nucleosome occupancy at different positions in the genome.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: ARPE-19_inter_120_180_peak_2_hg38.bed: Tab-delimited text file includes chromosome position of each nucleosome peak calling.
Supplementary_files_format_and_content: bedgraph file includes chromosome position of nucleosome occupancy score.

source_name: ARPE-19 cell line

growth_protocol: The cells were cultured with DMEM/F-12 medium (Biological Industries, Israel) containing 20% fetal bovine serum (Gibco BRL/Invitrogen, Carlsbad, CA, USA), 100μg/ml streptomycin, and 100IU/ml penicillin, and incubated with 37℃ and 5% CO2.

extract_protocol:
ARPE-19 cells in interphase were lysed in 0.1% NP-40 buffer and then incubated with Micrococcal Nuclease (NEB, San Diego, California, USA) at 37℃ for 5 min to digest the mono-nucleosomes (Pajoro, A et al. 2018). Then DNA was incubated with RNase A for 1h at 37℃, and further with 1% SDS, proteinase K (Thermo Scientific, Waltham, Massachusetts, USA) for 2 hours at 55℃. After phenol-chloroform extraction and ethanol precipitation, the DNA was separated by 1.5% agarose gel electrophoresis and the 150bp DNA fragments were recovered by gel extraction kit (Axygen Scientific Inc, USA).
The library was generated via the NEB Next Ultra II DNA library Prep kit for Illumina. The quality of library was assessed by Agilent 2100 Bioanalyzer system.

tag: cell line

tag: cell type

value: Epithelial Cells

tag: treatment

value: Normal culture

tag: cell cycle

value: Interphase


title: Veh2

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

country: Canada

institute: University of Manitoba

description:
BleoVSVehicle_Gene_differential_expression
BleoVSVehicle_Known_lncRNA_differential_expression
BleoVSVehicle_Novel_lncRNA_differential_expression

data_processing:
All bioinformatic analysis was carried out by an independent company, LC Sciences. Briefly, Cutadapt (v1.10) and perl scripts used to filter adapter contamination and undetermined bases
FastQC (v0.10.1) used to quality check sequences
BowTie2 and HISAT (v2.0.4) used to map sequences to hg38
Mapped reads assembled for each sample with StringTie (v1.3)
Comprehensive transcriptome built with perl scripts and gffcompare, StringTie and edgeR used to estimate transcript expression levels
LncRNAs identified based on filtering transcripts overlapping with known mRNAs and transcripts <200 bps. CPC and CNCI used to predict coding potential, with CPC score <-1 and CNCI score <0 removed. Remaining transcripts were considered lncRNAs. Differential expression performed using StringTie and edgeR to calculate FPKM
Genome_build: GRCh38.p12 (ENSEMBL v96) and lncRNA (v27)
Supplementary_files_format_and_content: Normalized gene and lncRNA expression levels (FPKM) from edgeR

source_name: Pancreatic Islets of Langerhans_Veh

growth_protocol: Human islets were rested in culture for 24 h prior treatments

extract_protocol:
Total RNA was extracted with TRIzol-based kit and DNAse I treated
Illumina TruSeq libaries done by LC Sciences

treatment_protocol: After resting, islets wered culture in vehicle (DMSO) or 50 uM bleomycin in normal human islet media (RPMI1640, 10% FBS, 5.5 mM glucose, 1Xantibiotic-antimycotic) for 48 h. Islets were transferred to fresh media for 4 days of culture prior to harvest

tag: individual

value: donor 1

value: Pancreatic Islets of Langerhans

value: vehicle (DMSO) for 48 h

value: Adult

value: Female

tag: disease state

value: Non-diabetic


title: BMET11-Tumor

value: bone marrow

tag: tissue type

value: solid metastatic tissue (Tumor fraction)


title: Bleo1

source_name: Pancreatic Islets of Langerhans_Bleo

value: 50 uM bleomycin for 48 h

tag: Sex


title: 14489X11 BP TX 2

status: Public on Apr 27 2021

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

description: 14489X11_170906_D00550_0459_ACB5JLANXX_3

data_processing:
For bulk RNA-Seq, mouse GRCm38 reference genome and gene feature files were downloaded from Ensembl release 90.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Transcript abundance was quantified using Salmon v0.9.1 with transcriptome from Gencode release 26.
Differentially expressed genes were identified using a 10% false discovery rate with DESeq2.
For scRNA-seq, fastq files were demultiplexed with cellranger mkfastq version 3.1.0 from 10x Genomics to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to combined refdata-cellranger-mm10-3.0.0 and tdTomato reference.
Barcodes and UMIs were counted using cellranger count version 3.1.0 with expected-cells=6000
Genome_build: mm10
Supplementary_files_format_and_content: For bulk RNA-Seq, tab-delimited file with Salmon quasi-mapped counts.  For scRNA-seq, filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: BP_MAPK inhibitor treated

extract_protocol:
For bulk RNAseq, FACS-sorted cells were pelleted and total RNA was isolated using the Animal Tissue RNA Purification Kit (Norgen Biotek) following manufacturer’s instructions. For scRNA-seq, FACS-sorted cells were resuspended in PBS and mixed with 10X Gel Beads and reverse transcription reagents in order to form Gel Beads-in-emulsion (GEMs) according to 10X Genomics instructions.
For bulk RNAseq, Illumina TruSeq Stranded mRNA Library Preparation Kit with polyA selection. Subsequently, HiSeq 50 Cycle Single-Read Sequencing v4 was performed. For scRNA-seq, 10X Genomics Single Cell 3’ Gene Expression Library Prep v3. Subsequently, NovaSeq 2 x 150 bp Sequencing-100M read-pairs per sample was performed.

treatment_protocol: Control and drug treatments performed in vivo

tag: strain background

value: mixed C57BL/6J x 129SvJ

tag: genotype/variation

value: 1 week on MAPK-inhibitor chow

value: lung adenocarcinoma

tag: tumor stage

value: 7 weeks post-initiation

value: FACS sorted tdTomato+ lung tumor cells

tag: seq type

value: bulk RNAseq


title: 14489X9 BPN C 4

source_name: BPN control

value: 1 week on control chow


title: Bleo2

tag: age


title: BMET10-Tumor

value: prostate cancer patient

value: 74 mo

value: GnRH agonist, abiraterone (39 mo), radium-223


title: 14489X16 BPN TX 3

description: 14489X16_170906_D00550_0459_ACB5JLANXX_3

source_name: BPN_MAPK inhibitor treated


title: 14489X14 BPN TX 1

description: 14489X14_170906_D00550_0459_ACB5JLANXX_3


title: BMET10-Involved

value: liquid bone marrow at the site of the metastasis (Involved)


title: ARPE-19_MNase_batch2

value: Epithelial Cells

value: Normal culture

value: Interphase


title: 14489X8 BPN C 3


title: Veh1

value: donor 1

value: Pancreatic Islets of Langerhans

value: vehicle (DMSO) for 48 h

value: Adult

value: Female

value: Non-diabetic


title: 14489X7 BPN C 2

value: mixed C57BL/6J x 129SvJ

value: lung adenocarcinoma

value: 7 weeks post-initiation


title: 14489X10 BP TX 1

description: 14489X10_170906_D00550_0459_ACB5JLANXX_3

value: 1 week on MAPK-inhibitor chow

value: FACS sorted tdTomato+ lung tumor cells

value: bulk RNAseq


title: 14489X2 BP C 2

source_name: BP control

value: 1 week on control chow


title: 14489X15 BPN TX 2

description: 14489X15_170906_D00550_0459_ACB5JLANXX_3


title: 14489X18 BPN TX 5

description: 14489X18_170906_D00550_0459_ACB5JLANXX_3


title: Veh3


title: Bleo3

value: 50 uM bleomycin for 48 h


title: 14489X1 BP C 1


title: 16286X1_191025 BP/BPN TX

description: 16286X1_191025_A00421_0123_BHL3FVDMXX_S2_L002

source_name: BPBPN_MAPK inhibitor treated

value: single-cell RNAseq


title: 16285X1_190830 BP/BPN C

description: 16285X1_190830_A00421_0104_BHNKCCDSXX_S7_L003

source_name: BP/BPN control


title: 14489X5 BP C 5


title: mCK-hLPL_REL_rep_5

status: Public on Mar 24 2021

data_processing:
R programming environment (ver 4.0.1)
BBDuk (ver 38.86; trim reads)
Salmon (ver 0.14.2; mapping and quantification of raw counts)
DESeq2 (ver 1.28.1;data set analysis)
Genome_build: mm10; Mus_musculus.GRCm38.79
Supplementary_files_format_and_content: excel spreadsheet

source_name: Gastrocnemius

extract_protocol:
RNA was isolated using Rneasy kit from Qiagen according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
NuGEN universal Plus mRNA SEQ protocol part no. 9133

treatment_protocol: Gastrocnemius was removed during weight loss maintenance or after 24 hours of refeeding and immediately flash frozen.

tag: strain

value: FVB

value: First day of weight regain

tag: genotype

value: mCK-hLPL


title: 16286X1_190830 BP/BPN TX

description: 16286X1_190830_A00421_0104_BHNKCCDSXX_S8_L003


title: mCK-hLPL_REL_rep_4


title: 14489X12 BP TX 3

description: 14489X12_170906_D00550_0459_ACB5JLANXX_3


title: WT_REL_rep_3

value: WT


title: 16285X1_191025 BP/BPN C

description: 16285X1_191025_A00421_0123_BHL3FVDMXX_S1_L002


title: 14489X3 BP C 3


title: 14489X17 BPN TX 4

description: 14489X17_170906_D00550_0459_ACB5JLANXX_3


title: mCK-hLPL_WLM_rep_5

value: Weight loss maintenance


title: 14489X4 BP C 4


title: mCK-hLPL_REL_rep_1


title: mCK-hLPL_WLM_rep_3


title: 14489X6 BPN C 1


title: mCK-hLPL_REL_rep_3


title: SF4794 (snATAC)

source_name: Brain

value: M

value: Oligodendroglioma (WHO gr. 2)


title: WT_REL_rep_4


title: mCK-hLPL_REL_rep_2


title: mCK-hLPL_WLM_rep_1


title: WT_WLM_rep_4


title: WT_WLM_rep_3


title: WT_WLM_rep_1


title: WT_WLM_rep_5


title: WT_REL_rep_1


title: mCK-hLPL_WLM_rep_4


title: White_1

status: Public on Feb 01 2021

city: xuzhou

first: chenxu

last: zhao

state: jiangsu

address: No.101, Shanghai road,  Tongshan District

institute: jiangsu normal university

data_processing:
Clean data for each sample were obtained from the raw data using Trimmomatic (version 0. 39) with default parameters.
The obtained clean data were mapped to the C. maxima genome (v1.0) (doi:10.1038/ng.3839) using STAR (version 2.7.1a) under the 2-pass mapping mode.
The read counts mapped to each gene were calculated using featureCounts (v2.0.1), and the FPKM values for each gene were obtained using RSEM (v1.3.1). A gene was considered expressed if its average expression level in FPKM is lower than 1.
DEseq2 package was employed to perform DEG analysis between white- and red-sarcocarp pomelo.
genome build: C. maxima genome reported in article (doi:10.1038/ng.3839) was used as reference genome.https://www.citrusgenomedb.org/organism/5947
processed data files format and content: All_results.White_Red.combined_FPKM.annotation.txt showed the results of gene expression level and gene annotation, DEG.White_Red.combined_FPKM.annotation.txt showed expression and annotation of differentially expressed genes, sequencing_and_mapping_summary.xls was statistics of sequencing.

organism: Citrus maxima

source_name: pomelo (Citrus maxima (Burm.) Osbeck)

extract_protocol:
For transcriptomic analysis of pomelo fruits, total RNA was extracted with RNAprep pure plant plus kit (Tiangen, Beijing, China). The extracted total RNA was checked on Nano Photometer® spectrophotometer (IMPLEN, CA, USA) and Agilent 2100 bio analyzer (Agilent Technologies, CA, USA) to analyze the purity and quality of RNA, respectively. The degree of stability of RNA was measured by running the RNA on 1% agarose gel electrophoresis.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: pulp

tag: developmental stage

value: fructescence

value: White pulp


title: FCtx_S794_snATACseq

status: Public on Jan 29 2021

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: 35 Convent Drive

department: National Institute on Aging

institute: National Institutes of Health

description: snATACseq_Sample 4

data_processing:
10x Genomics cellranger-atac count algorithm (v1.2.0) was used to align fastqs and count reads mapping to the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Per barcode singlecell.csv file (CSV), fragment file (TSV), and barcode-feature count matrix (HDF5).

source_name: frozen frontal cortex tissue

extract_protocol:
Nuclei were extracted from frozen tissue by ultracentrifugation using the Nuclei PURE Prep nuclei isolation kit from Sigma Aldrich.
Libraries were constructed according to the Chromium Single Cell ATAC Reagent Kits User Guide (v1 Chemistry) from 10x Genomics.

tag: rs76904798 genotype

value: CC

tag: tissue

value: frontal cortex

tag: differentiation protocol


title: FCtx_S5079_snATACseq

description: snATACseq_Sample 3

value: TT

tag: cell line


title: WT_REL_rep_2

tag: treatment


title: White_3


title: 14687X4 ES1661P2

status: Public on Jan 14 2021

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

source_name: pancreas

extract_protocol:
miRNAeasy kit (Qiagen)
TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina)

value: mixed 129/B6

value: Hnf4a F/F


title: White_2


title: FCtx_S1274_snATACseq

description: snATACseq_Sample 2


title: 14687X2 ES4085P

value: Hnf4a +/+


title: mCK-hLPL_WLM_rep_2


title: FCtx_S1230_snATACseq

description: snATACseq_Sample 1


title: 14687X1 HC1033P


title: Red_1

data_processing:
Clean data for each sample were obtained from the raw data using Trimmomatic (version 0. 39) with default parameters.
The obtained clean data were mapped to the C. maxima genome (v1.0) (doi:10.1038/ng.3839) using STAR (version 2.7.1a) under the 2-pass mapping mode.
The read counts mapped to each gene were calculated using featureCounts (v2.0.1), and the FPKM values for each gene were obtained using RSEM (v1.3.1). A gene was considered expressed if its average expression level in FPKM is lower than 1.
DEseq2 package was employed to perform DEG analysis between white- and red-sarcocarp pomelo.
genome build: C. maxima genome reported in article (doi:10.1038/ng.3839) was used as reference genome. https://www.citrusgenomedb.org/organism/5947
processed data files format and content: All_results.White_Red.combined_FPKM.annotation.txt showed the results of gene expression level and gene annotation, DEG.White_Red.combined_FPKM.annotation.txt showed expression and annotation of differentially expressed genes, sequencing_and_mapping_summary.xls was statistics of sequencing.

source_name: pomelo (Citrus maxima Merr. var. Tubtim Siam)

value: Red pulp


title: WT_WLM_rep_2

value: FVB


title: 14687X3 ES4289P


title: 14687X5 ES1638P2


title: Red_2


title: 14687X6 ES1283P2


title: 15783X6 HC800-A8-1-DOX rep2

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in Dox condition
15783X6

growth_protocol: Cells were grown in DMEM + 10% FBS and treated with 1mg/ml of doxycycline or vehicle for 7 days.

extract_protocol:
TRIzol extraction followed by PureLink RNA Mini Kit purification
TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina)

tag: hnf4a status

value: Positive

tag: agent

value: DOX


title: 15783X4 HC569-A8-18-DOX rep2

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in Dox condition
15783X4


title: 14224X1 ES912P


title: 15783X5 HC800-A8-1-Control rep2

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in control condition
15783X5

value: Negative

value: Control


title: 15783X3 HC569-A8-18-DOX rep1

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in Dox condition
15783X3


title: 14224X4 HC377P1


title: 15783X1 HC569-A8-18-Control rep1

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in control condition
15783X1


title: 15145X8 HC800-A8-1-DOX rep1

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in Dox condition
15145X8


title: 15783X2 HC569-A8-18-Control rep2

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in control condition
15783X2


title: Red_3


title: 15143X6 SC1853-4-OH-Tam

description:
3D cultures derived from murine pancreas. 4-OH-Tamoxifen treated culture
15143X6

growth_protocol: Organoids were cultured in 50% L-WRN conditioned media and treated for 72hs with 4-OH-Tamoxifen or vehicle to delete Hnf4a

value: 4-OH-Tamoxifen treated culture


title: 14224X6 2264PN


title: 14224X5 2256PN


title: 15143X1 SC1640-control

description:
3D cultures derived from murine pancreas. Control condition
15143X1

value: Control condition


title: 14224X3 HC494P


title: B(HT-2)

status: Public on Dec 05 2020

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

description: G14 CUT&Tag (High)

data_processing:
Library strategy: CUT&Tag
cutadapt (v1.9.2) software was used for adaptor-trimming and low quality reads removing to get clean reads. Then clean reads were aligned to reference genome  (UCSC galGal6) using bowtie2 software  (v2.2.4) with default parameters. Peak calling was performed with MACS software (v1.4.3).
Genome_build: galGal6
Supplementary_files_format_and_content: bed peaks

organism: Gallus gallus

source_name: broiler liver

extract_protocol: Not provided

treatment_protocol: high temperature treatment

tag: treatment type

value: high temperature

value: liver


title: 15143X5 SC1853-control

description:
3D cultures derived from murine pancreas. Control condition
15143X5


title: 15145X7 HC800-A8-1-Control rep1

description:
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in control condition
15145X7


title: 14224X2 HC673P


title: B(HT-4)

description: G16 CUT&Tag (High)


title: 15143X3 SC1693-control

description:
3D cultures derived from murine pancreas. Control condition
15143X3


title: B(HT-1)

description: G13 CUT&Tag (High)


title: B(HT-3)

description: G15 CUT&Tag (High)


title: A(PT-1)

description: G1 CUT&Tag (Normal)

value: phloretin treatment


title: HC5

status: Public on Nov 16 2020

city: Guangzhou

first: Yuming

last: Luo

state: Guangdong

address: 107 Yanjiang West Avenue,Yuexiu district

department: General Surgery

institute: Sun yat-sen Memorial Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Anders S, et al., Bioinformatics 2015, 31(2):166-169 and Robinson MD, et al. Genome Biol 2010, 11(3):R25. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: urinary exosomes

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
Urine samples were collected from patients with bladder cancer and healthy volunteers and followed by 2,000g centrifugation for 10 min and 10,000g centrifugation for 30min at 4℃ to obtain the supernatant. Subsequently, the supernatant was centrifuged at 120,000g for 70min and washed again in PBS at 120,000g for 70min to obtain extracellular vesicles.
The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions.

tag: disease state

value: healthy

value: urinary exosomes


title: HC2


title: 15143X7 SC1956-control

description:
3D cultures derived from murine pancreas. Control condition
15143X7


title: 15143X4 SC1693-4-OH-Tam

description:
3D cultures derived from murine pancreas. 4-OH-Tamoxifen treated culture
15143X4


title: 15143X8 SC1956-4-OH-Tam

description:
3D cultures derived from murine pancreas. 4-OH-Tamoxifen treated culture
15143X8


title: A(PT-2)

description: G2 CUT&Tag (Normal)


title: A(PT-3)

description: G3 CUT&Tag (Normal)


title: 15143X2 SC1640-4-OH-Tam

description:
3D cultures derived from murine pancreas. 4-OH-Tamoxifen treated culture
15143X2


title: CA2

value: bladder cancer


title: HC4


title: A(PT-4)

description: G4 CUT&Tag (Normal)


title: CA4


title: HC3


title: CHO47

status: Public on Nov 12 2020

description:
single cell RNAseq
processed data file: matrix.mtx
processed data file: features.tsv
processed data file: barcodes.tsv

data_processing:
10x Genomics CellRanger Count function was used on primary FastQ files for initial QC and reads alignment.
CellRanger Aggregate function was applied to coalesce outputs from the Count Function as a single output.
Seurat version 3.0.1 was used for filtering, normalization, scaling, and analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix, features, and barcode files.

source_name: Fresh whole milk

growth_protocol: Mid-feed milk samples were collected from fasting women in the morning and transported to the laboratory.

extract_protocol:
Cryopreserved mammary epithelial cells isolated from whole milk were flow-sorted for viability and input directly to 10x Genomics cell capture.
10x Genomics 3prime V3.

treatment_protocol: Cells were pelleted, washed, and cryopreserved in FBS + 10% DMSO. After thawing at 37°C, permeable cells were removed after staining with a fixable permeability dye.

tag: cell type

value: Mammary epithelial cells from fresh whole milk

tag: time point

value: 2 weeks postpartum


title: eclip_hela_igg_IP_r1

status: Public on Aug 21 2020

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

data_processing:
Data was processed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810
https://github.com/YeoLab/eclip
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files, strand specific  bed files: clipper v1.1 output (col1: chrom, col2: chromStart, col3: chromEnd, col4: -log10 pvalue, col5: log2 fold enrichment above input, col6: strand)) contains clusters of Ints11 binding.

growth_protocol: HeLa cells were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS.

extract_protocol:
eCLIP was performed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810
libraries were prepared as described in Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810
In brief, 2 x 107 cells were crosslinked by UV-C irradiation (254 nm, 400 mJ/cm2) and lysed on ice followed by sonication. Antibodies were incubated with Dynabeads™ M-280 Sheep Anti-Rabbit IgG (Invitrogen, 11204D) for 1 hour. After limiting RNase I (Ambion) digest in presence of DNase, the lysate was subjected to immunoprecipitation at 4˚C for 16 hours. In the following, 2% of the lysate was removed for size-matched input control. IP efficiency and specificity were verified by immunoblot using 20% of the IP material. Co-immunoprecipitated RNA was dephosphorylated, followed by 3’RNA adapter ligation using T4 RNA Ligase (NEB). Input and IgG controls and INTS11-RNA complexes were run on a NuPAGETM 4-12% Bis-Tris Gel, transferred to nitrocellulose and cut from the membrane between 65-145kDa. Protein-bound RNA was released from the membrane by Urea/ Proteinase K digest, followed by acid Phenol/ Chloroform/ Isoamyl alcohol RNA extraction and purification using RNA Clean & Concentrator (Zymo Research). After reverse transcription (AffinityScript reverse transcriptase, Agilent), RNA was treated with exonuclease (ExoSAP-IT, Affymetrix) and removed by combined NaOH/ HCl treatment. A 3’Linker was ligated to the cDNA, and the resulting library was PCR amplified using Q5 Polymerase (NEB), purified and size selected for sequencing. Single-end (SE100) sequencing was performed to an average of 40 million reads per sample using Illumina HiSeq 3000 sequencer.

value: HeLa

value: cervical adenocarcinoma

tag: cell source

tag: chip antibody

value: rabbit IgG (Invitrogen, 02-6102, LOT# R1238244)


title: CA5


title: eclip_hela_ints11_abcam_IP_r2

value: INTS11 (Sigma prestige, HPA029025, LOT# A107128)


title: control_269

status: Public on Jul 01 2020

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

data_processing:
base-calling done by Real-Time Analysis software v3.3.3
fastq file demultiplexing done by bcl2fastq2 Conversion Software v2.20.0.422
genome indexing, pseudoalignments, and counts quantification done by kallisto v0.45.0
Genome_build: GENCODE GRCh38 v27
Supplementary_files_format_and_content: CSV matrix containing all quantified counts

source_name: Human lung

extract_protocol:
Lung tissue was collected from all participants as either a surgical lung biopsy or at the time of lung transplantation. RNA and DNA were isolated from tissues using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA), according to manufacturer’ s protocol.
To establish RNA library, we used  TruSeq Stranded mRNA Library Prep Kit (San Diego, CA) accoridng to maunfacture`s protocol

value: lung tissue

tag: Sex

value: female

tag: age

tag: diagnosis

value: control

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: biopsy

tag: psl

value: UNKNOWN

tag: is

value: NO

tag: batch

tag: lane

tag: plate

tag: institution

value: LTRC


title: control_263

tag: tissue

value: yes


title: CHO52

first: Michael

last: Rudolph

institute: OUHSC


title: CAL27_scRNA_xenograft

status: Public on Jun 22 2020

city: New York

first: Andrew

last: Ji

state: NY

address: 1428 Madison Ave.

institute: Icahn School of Medicine at Mount Sinai

description:
CAL27_counts.txt.gz includes human reads.
XG_TME_counts.txt.gz includes murine reads

data_processing:
For patient tissue, raw sequencing data was processed with the cellranger pipeline (version 2.1.0, 10X Genomics) and mapped to the hg19 reference genome to generate matrices of gene counts by cell barcodes
For xenograft tumors, raw sequencing data was processed with the cellranger pipeline (version 2.1.0, 10X Genomics) and mapped to the combined hg19 and mm10 reference genomes to generate matrices of gene counts by cell barcodes
Genome_build: hg19 for patients, hg19/mm10 combined reference for xenograft tumors
Supplementary_files_format_and_content: Tab-delimited text files containing genes by barcode counts matrices

source_name: Xenograft tumor

growth_protocol: Cutaneous SCCs and patient-matched normal adjacent skin samples were collected under a protocol approved by the Institutional Review Board at Stanford University Medical Center (Protocol #21750). Individuals donating fresh surgical tissue provided informed consent. All diagnoses were verified by histological review.

extract_protocol:
Fresh tumor specimens (patient or xenograft) and normal skin (patient only) were minced with a scalpel in serum-free DMEM (Gibco) with DNAse I (0.2 mg/mL, Worthington, Inc., Columbus, OH) to pieces <1 mm3 and placed in 5mL of 0.25% trypsin-EDTA (Gibco) at 37C for 30 minutes with trituration with a wide-bore pipet tip every 10 minutes. For normal skin, subcutaneous fat was removed with surgical scissors prior to mincing and trypsin-EDTA incubation. After 30 minutes, trypsin-EDTA was quenched with DMEM supplemented with 10% FBS and cells were filtered through a 70mm filter (BD Falcon). Dissociated cells were pelleted and washed once with cold serum-free DMEM with DNase I and were immediately cryopreserved in 90% SCC-13 media with 10% DMSO (Sigma-Aldrich). All steps other than trypsin incubation were completed at 4°C or on ice. For patients 3 and 8, samples were incubated in 0.25% trypsin-EDTA and type I collagenase 5mg/mL (Gibco) for 30 minutes (instead of trypsin-EDTA 0.25% alone for other patients), which led to recovery of higher numbers of T cells in normal skin samples from these patients. We did not observe major differences in downstream processing of cells recovered from collagenase dissociation. On the day of scRNA-seq droplet capture, cells were thawed in at least 5X dilution volume of SCC-13 media to wash off residual DMSO in cryopreservation media. Cells were pelleted and resuspended in cold phosphate buffered saline (PBS) (Gibco) with 2% FBS and 2mM EDTA (Invitrogen, Carlsbad, CA). Cells were stained with propidium iodide (Sigma-Aldrich) prior to sorting on a BD FACS Aria II. For patients 1 and 8, cells were stained with anti-CD45 antibody conjugated to V450 (clone HI30, 560367, BD Biosciences) to separate immune cells from non-immune cells. For patient 1, only CD45-negative cells were sequenced while for patient 8, both CD45+ and CD45- fractions were sequenced, neither of which affected downstream data processing. Sorted cells were pelleted and resuspended in PBS with 2% FBS and 2mM EDTA prior to scRNA-seq droplet capture
10X Genomics Chromium 3' v2 kit according to manufacturer's protocol

value: Xenograft tumor

tag: cell line

tag: strain

value: SCID Hairless Outbred


title: P10_normal_scRNA

source_name: Skin

value: Normal Skin


title: eclip_hela_igg_IP_r2

value: HeLa

tag: cell type


title: control_834

value: GT

value: explant

value: other


title: P8_normal_scRNA_2


title: CA1

tag: disease state

value: bladder cancer

value: urinary exosomes


title: CAL27_vitro_scRNA

extract_protocol:
Fresh tumor specimens (patient or xenograft) and normal skin (patient only) were minced with a scalpel in serum-free DMEM (Gibco) with DNAse I (0.2 mg/mL, Worthington, Inc., Columbus, OH) to pieces <1 mm3 and placed in 5mL of 0.25% trypsin-EDTA (Gibco) at 37C for 30 minutes with trituration with a wide-bore pipet tip every 10 minutes. For normal skin, subcutaneous fat was removed with surgical scissors prior to mincing and trypsin-EDTA incubation. After 30 minutes, trypsin-EDTA was quenched with DMEM supplemented with 10% FBS and cells were filtered through a 70mm filter (BD Falcon). Dissociated cells were pelleted and washed once with cold serum-free DMEM with DNase I and were immediately cryopreserved in 90% SCC-13 media with 10% DMSO (Sigma-Aldrich). All steps other than trypsin incubation were completed at 4°C or on ice. For patients 3 and 8, samples were incubated in 0.25% trypsin-EDTA and type I collagenase 5mg/mL (Gibco) for 30 minutes (instead of trypsin-EDTA 0.25% alone for other patients), which led to recovery of higher numbers of T cells in normal skin samples from these patients. We did not observe major differences in downstream processing of cells recovered from collagenase dissociation. On the day of scRNA-seq droplet capture, cells were thawed in at least 5X dilution volume of SCC-13 media to wash off residual DMSO in cryopreservation media. Cells were pelleted and resuspended in cold phosphate buffered saline (PBS) (Gibco) with 2% FBS and 2mM EDTA (Invitrogen, Carlsbad, CA). Cells were stained with propidium iodide (Sigma-Aldrich) prior to sorting on a BD FACS Aria II. For patients 1 and 8, cells were stained with anti-CD45 antibody conjugated to V450 (clone HI30, 560367, BD Biosciences) to separate immune cells from non-immune cells. For patient 1, only CD45-negative cells were sequenced while for patient 8, both CD45+ and CD45- fractions were sequenced, neither of which affected downstream data processing. Sorted cells were pelleted and resuspended in PBS with 2% FBS and 2mM EDTA prior to scRNA-seq droplet capture. CAL27 cells were cultured in DMEM + 10% FBS, tyrpsinized with 0.05% tyrpsin-EDTA and washed twice with FBS prior to capture and library prep with the 10X Chromium 3' v3 kit per manufacturer's protocol.
10X Genomics Chromium 3' v2 kit according to manufacturer's protocol for patient tissue and xenograft tumors; Chromium 3' v3 kit for CAL27 in vitro cells


title: eclip_hela_ints11_abcam_input_r2

value: cervical adenocarcinoma

tag: cell source


title: SCC13_scRNA_xenograft

description:
SCC13_counts.txt.gz includes human reads.
XG_TME_counts.txt.gz includes murine reads


title: eclip_hela_ints11_sigma_IP_r1

tag: chip antibody


title: P8_normal_scRNA_1


title: eclip_hela_ints11_sigma_input_r1


title: HC1

value: healthy


title: P10_cSCC_scRNA

value: cSCC


title: P6_cSCC_scRNA


title: CA3


title: P5_cSCC_scRNA


title: P9_cSCC_scRNA


title: P4_cSCC_scRNA


title: P4_normal_scRNA


title: P9_normal_scRNA


title: P8_cSCC_scRNA_2


title: P3_cSCC_1_scRNA


title: P8_cSCC_scRNA_1


title: P2_cSCC_scRNA


title: P7_cSCC_scRNA


title: P5_normal_scRNA


title: A431_murine_scRNA


title: P1_normal_scRNA_2


title: P1_cSCC_scRNA_2


title: P7_normal_scRNA


title: P1_cSCC_scRNA_1


title: P1_normal_scRNA_1


title: P9_cSCC_WES

data_processing:
Library strategy: DNA-seq
Raw reads were aligned to hg19 using BWA with default parameters and duplicate reads were removed, resulting in a mean sequencing depth of 158x for on-target regions. The resulting aligned reads were processed using GATK 4.1.0.0 and Mutect2 variant calling for tumor-normal matched pairs, mostly following parameters from the GATK 4 documentation (https://software.broadinstitute.org/gatk/documentation). Mutect2 was run using a panel of normals derived from our cohort and the HapMap 3.3 allele frequencies as a germline resource. The resulting VCF files were filtered using FilterMutectCalls and FilterByOrientationBias and finally annotated using Funcotator, all within GATK tools.
Genome_build: hg19
Supplementary_files_format_and_content: All mutations passing filter for tumor vs. normal comparison are listed as rows of the table, the following columns: gene name, mutation type, mutation code, original base, and mutated base.

growth_protocol: Cutaneous SCCs and patient-matched normal adjacent skin samples were collected under a protocol approved by the Institutional Review Board at Stanford University Medical Center (Protocol #21750). Individuals donating fresh surgical tissue provided informed consent. All diagnoses were verified by histological review. For tumors of adequate size, small fragments of each tumor were snap frozen in optical cutting tissue (OCT) compound (Fisher Healthcare) and/or fixed in 10% formalin (Sigma-Aldrich).

extract_protocol:
Approximately 10-12 8mm sections of fresh-frozen tissue in OCT were dissolved in PBS to remove OCT. The tissue was pelleted and used as input for the DNeasy Blood and Tissue Kit (Qiagen) to extract genomic DNA.
The Agilent V6 whole exome capture kit (60 Mbp) was used and the resulting libraries were sequenced on the BGISEQ-500 instrument using paired-end 100bp reads to achieve approximately 100x coverage for each tumor sample and 50x coverage for each normal skin sample.


title: P8_normal_WES


title: P10_cSCC_WES


title: P6_normal_scRNA


title: P8_cSCC_WES


title: P3_cSCC_scRNA_2


title: P6_normal_WES


title: P10_normal_WES