title: NH24_rep4

city: Baltimore

first: Michael

middle: R

last: Blatchley

state: MD

address: 3400 N Charles St

department: Biomedical Engineering

institute: Johns Hopkins University

data_processing:
RNA 100 base paired-end sequencing libraries were constructed from 24 samples of total RNA using the Illumina TruSeq Stranded mRNA kit following manufacturer’s protocol.
Following QC, the libraries were sequenced on the Illumina NovaSeq 6000 System using their S1 flow cell and base calling performed with RTA version 2.4.11.
Sequencing adapters were stripped with the bcl2fastq 2.17.1.14 program, which analysis provided 48 raw FASTQ files representing the 24 biological samples.
Using the CLCGenomicsServer 9.1.1 these reads were aligned to the NCBI April ’19 transcriptome, GRCh38.p13, of 54,136 transcripts.  The transcript identifiers were derived from these FPKM files’ “Name” column and were updated to current HGNC/NCBI nomenclature.
The raw data files’ FPKM values of 0.0 were treated as nulls and the remaining actual values transformed into log2 notation.  QC examination of the raw log2 signals in box plot and histogram showed technically consistent sequencing results across all 24 samples.  Principle component analysis figures showed clean separation of the biological classes.  Two samples, however, clustered unequivocally out of their expected classes and were therefore excluded from further analysis
The remaining 22 samples’ log2 signal values were quantile normalized together for further analysis.  The six biological classes’, three time points with and without hypoxia, underwent differential expression analysis with a two-tailed one way t-test ANOVA using the Partek GS 7.0 7.18.0723 platform
The results report transcripts’ differential expression in ratio, linear fold change, and log2 fold change notation, and their statistical significance in uncorrected p-values.  The original FPKM files’ ‘XLOC_###’ and gene annotations are retained as well as updated NCBI/HGNC gene nomenclature annotation
A standard deviation analysis was performed for each class-class comparison using only those transcripts that had: NCBI Entrez gene anotation, a mean FPKM log2 value > -0.8 in the higher-expressed assayed biological class.  On the order of 11K transcripts met these criteria for each cell-class comparison
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing Log2 quantile-normalized FPKM values for all samples

source_name: Endothelial colony forming cells

growth_protocol: All cells were cultured using standard, humidified cell culture incubators at 37 °C and 5% CO2, unless otherwise specified. Endothelial colony forming cells (ECFCs) (Yoder Lab, Indiana University School of Medicine) were cultured in EGM2 (Lonza) prepared according to the manufacturer’s instructions with an additional 10% Hyclone FBS, on standard tissue culture plates coated with type I collagen (Corning)

extract_protocol:
Cell medium was removed and 200 ul Trizol reagent was added atop the hydrogels and incubated at room temperature for 5 min. Hydrogels were then mixed using a P1000 pipette tip and transferred to a 1.5 mL microfuge tube containing an additional 300 ul Trizol reagent. Samples were then homogenized using a pellet pestle homogenizer (FisherBrand) for 1-2 min. Samples were then centrifuged at 12G for 10 min at 4°C. The supernatant was then transferred to a fresh 1.5 mL microfuge tube and stored at -80°C until ready for purification. Samples were thawed on ice prior to purification. RNA was purified using Direct-zol RNA Miniprep kits according to the manufacturer’s suggestion (Zymo Research; Irvine, CA), with a few minor exceptions and clarifications identified in the following text. All centrifugation steps were performed at 13G for 30 seconds at 4°C, unless another speed was specified. DNase I treatment was used. Samples were eluted in 15 μL DNase/RNase-free water. Following elution, the samples were reloaded and eluted a second time. Following purification, samples were stored at -80°C.
RNA-seq library for Illumina platform sequencing is prepared using Illumina TruSeq stranded total RNA Sample kit following manufacturer’s recommended procedure.

treatment_protocol: For all hydrogels, polymer solutions were dissolved in 1× DPBS (pH 7.4) and mixed with ECFC pellets to provide a cell suspension (4 million cells/mL), and then enzyme solution (laccase—100 U mL−1; mTG—0.6–2.4 U mL−1) was added at a volume ratio of 3:1 (polymer solution/enzyme solution) and gently mixed at 37 °C for a predetermined “preincubation time.” Preincubation times for each batch of polymer were based on the gelation time, as measured by the vial‐tilt method. On the basis of this gelation time, a preincubation time was calculated (gelation time minus 1 min) to prevent all cells from falling to the bottom of the hydrogel, thus ensuring a homogeneous distribution of cells in all conditions. Cells were cultured in hypoxic and non-hypoxic conditions for 40 mins, 10 hrs, or 24 hours, then RNA was collected for sequencing.

tag: cell type

value: Endothelial colony forming cells

value: Human umbilical cord blood

value: Non-hypoxia for 24 hours


title: 20_M_V_BLD

status: Public on Jun 04 2021

type: SRA

city: Austin

first: Laura

last: Ferguson

state: TX

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

country: USA

institute: Dell Medical School, University of Texas at Austin

library_source: transcriptomic

data_processing:
The reads were trimmed, de-duplicated, and quality filtered using custom Perl scripts from https://github.com/z0on/tag-based_RNAseq. The data were mapped to the GRCm38/mm10 Mus musculus reference transcriptome supplemented with the sequences of the ERCC spike-in control mRNAs using bowtie2. Then samtools and htseq-count were used to sort the mapped reads and convert mapped reads to counts. Read distributions were characterized using the read_distribution.py program from RSeQC package v2.6.2. The genome annotations for the analyses were taken from GENCODE using the main file containing comprehensive gene annotation on the reference chromosomes only. Raw counts were converted to log 2-counts per million (log-CPM) to account for library size differences and then transformed using the voom function from the limma package (version 3.42.2) to remove the heteroscedascity from the count data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.count.sorted.txt: Count files generated using htseq count (line of code used: for i in `ls -1 *.bam | sed 's/.bam//'`; do htseq-count -m intersection-nonempty -s yes -f bam -r pos -t gene $i.bam /stor/work/WCAAR/references/Mus_musculus/Bowtie2_ERCC_Gencode_Mmv24/ERCC.gencode.vM24.annotation.gtf > /stor/scratch/WCAAR/laura_scratch/tagseq/CIE_blood_brain/raw_files_brain_only/clean_fq_tagTrim/Bowtie2/Htseq_Bowtie2/$i.count.sorted.txt ;done).
Supplementary_files_format_and_content: voom_*.txt: Normalized data files generated using the voom function from the limma package in R which performs log2 counts per million (to correct for library size) then a "voom" transformation (to correct for heteroskedascity in the count data) (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937821/).

molecule: total RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
Total RNA was extracted from the whole blood samples using the Quick-RNA Whole Blood kit according to manufacturer instructions (Zymo, Irvine, CA, USA). Total RNA was extracted from the brain micropunches using the PureLink RNA Mini Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer instructions except that 2-mercaptoethanol was not added to the lysis buffer as this was found to reduce reads in downstream analyses during optimization tests. RNA purity, concentration, and integrity were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), Qubit 4 (Thermo Fisher Scientific, Waltham, MA, USA), and Tapestation 4150 (Agilent Technologies, Santa Clara, CA, USA). For quantitative assessment of RNA sequencing, External RNA Controls Consortium (ERCC) RNA Spike-In Mix 1 (Thermo Fisher) were added to samples. We submitted 300 ng total RNA/sample for brain samples and 2000 ng total RNA/sample for whole blood samples to the Genomic Sequencing and Analysis Facility at UT Austin for sequencing.
We surveyed gene expression using TagSeq by constructing libraries directed at the 3’ ends of mRNA according to established protocols [PMID: 27037501]. About 70% of mRNA from whole blood is globin mRNA, which limits the ability to detect other genes. Therefore, we depleted globin mRNA in the whole blood samples before library construction using the QIAseq Fast Select RNA removal kit (Qiagen, Germantown, MD, USA) according to manufacturer instructions. Before globin depletion, the blood samples were purified using an AMPure XP (Agencourt) bead clean-up as our optimization tests revealed this improved the blood library concentrations. Purified libraries were size-selected to obtain 350–550 bp target cDNA and pooled in equal proportions following relative quantification using a qPCR assay. Pooled sets of libraries were sequenced using an Illumina NovaSeq 6000 generating 1x100 bp single-end reads. Illumina adapters were removed, and lane pools were de-multiplexed according to the barcode assignments by the sequencing facility prior to return of raw data.

tag: strain

tag: tissue

value: BLD

tag: treatment

tag: Sex

value: Male


title: 20_M_V_HYP

source_name: Hypothalamus

value: HYP


title: CD3_Control_2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

molecule: polyA RNA

source_name: CD3+ TILs

extract_protocol:
10x Genomics
Single-cell RNA sequencing

treatment_protocol: (a) control mice that received PBS; (b) adjuvant control mice that received a STING agonist plusAddaVax; (c) KVax mice treated with KVax plus adjuvant; (d) CA170 treatment (10mg/kg in PBS) by oral gavage five times per week; and (e) combined treatment with KVax/adjuvant plus CA170. The experimental treatment scheme is shown in. Mice were administered one dose of the carcinogen vinyl carbamate30 (VC; Toronto Research Chemicals, Inc.) by i.p. injection (16 mg/kg in sterile saline). CA170 treatment was started one week after VC induction of lung adenocarcinoma. KVax was started two weeks after VC induction, followed by four more vaccinations at 2-week intervals, and additional boost vaccines every four weeks for the duration of the experiments.

value: A/J

tag: gender

value: female

value: Control

tag: infection

value: Carcinogen-induced lung tumor

value: lung tumor


title: 21_F_V_BLD

value: Female


title: BL1_IC096219

type: RNA

city: Tlalpan

first: Claudia

last: Rangel Escareño

state: CDMX

address: Periferico Sur

department: Departamento de Genómica Computacional

country: Mexico

institute: Instituto Nacional de Medicina Genómica

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III, Ductal, High grade

hyb_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (7G platform)

scan_protocol: Raw data were background-corrected using Robust Multiarray Average (RMA) and normalize using Quantile Normalization.

data_processing: RMA intensity values

label: biotin

organism: Homo sapiens

source_name: Triple Negative Breast Cancer Primary Tumor

label_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip HumanGene 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

growth_protocol: Paraffin sections were placed in sterile 1.5-ml microcentrifuge tubes, deparaffinized with 100% xylene, and washed twice in 100% ethanol. Deparaffinized tissue was digested with proteinase K at 56°C for 15 min and then incubated at 80°C for another 15 min to partially reverse the nucleic acids' crosslinking

extract_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100µl total RNA (Expression Analysis Technical Manual, 2003-2004 Affymetrix).

treatment_protocol: Total RNA and DNA were isolated from FFPE tissue sections using AllPrep DNA/RNA FFPE Kit by Qiagen

value: Stage III, Ductal, High grade

tag: genotype

value: Basal like 1

tag: age

value: 70 yrs


title: CD3_Control_1


title: NH24_rep3


title: NH24_rep2


title: Sample 4_Ppy-expressing cells: YFPpositive (5)

city: Geneva

first: Marta

last: Perez Frances

state: Geneva

address: 1, rue Michel-Servet

country: Switzerland

institute: University of Geneva

data_processing:
cDNA libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina) and sequenced on an Illumina HiSeq 2500 (for δ-cells) and HiSeq4000 platform (for γ-cells) with single-end 100-bp reads (for δ-cells) or pair-end 100bp reads (for γ-cells).
All sequencing data were uploaded to, and aligned on the Galaxy project against Ensembl reference genome GRCm38.p6 (release 100) using STAR version 2.7.2b in 2-pass mapping mode. Aligned data were counted using HTSeq version 0.9.1 in union mode.
Analyses were performed in a pair-wise manner between YFP-positive samples and alpha cell samples, YFP-positive samples and beta cell samples and YFP-positive samples and delta cell samples using DESeq2 version 1.28.1. For each pairwise comparison, genes were discarded if they had fewer than 5 counts per sample on average.
After calculating differential expression between groups, log2 fold changes were shrunken using the normal estimator. Genes were considered to be differentially expressed if the absolute shrunken log2 fold changes were equal to or above 1, and adjusted p-values were equal to or below 0.05.
Genome_build: Ensembl reference genome GRCm38.p6 (release 100) using STAR version 2.7.2b in 2-pass mapping mode
Supplementary_files_format_and_content: Tab-separated values files (.tsv) containing gene and sample names

source_name: Ppy-expressing cells: YFPpositive

extract_protocol:
Islet cells were obtained from two-month-old doxycycline-treated Ppy-rtTA;TetO-Cre;R26-YFP and Sst-Cre;R26-YFP mice FAC-sorted in a Moflo Astrios (Beckman Coutler) or BD FACS Aria II system. Total mRNA was extracted from sorted YFP+ from both mice models using the Qiagen RNeasy Micro Kit.
Libraries preparation, RNA-sequencing and quality controls were performed in the Genomics Core Facility of the University of Geneva. Reverse transcription and cDNA amplification were performed using the SMARTer Ultra Low RNA kit (Clontech). cDNA libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina) and sequenced on an Illumina HiSeq 2500 (for δ-cells) and HiSeq4000 platform (for γ-cells) with single-end 100-bp reads (for δ-cells) or pair-end 100bp reads (for γ-cells).

treatment_protocol: Doxycycline (1 mg/ml) was administered in the drinking water one moths prior to the sample extract in order to YFP-label Ppy-expressing ells

tag: strain background

value: Mixed

value: two-month-old

value: Endocrine pancreas - Islet of Langerhans

value: Pancreatic islet cells

tag: genotype/variation


title: 20_M_V_AMY

source_name: Amygdala

value: AMY


title: Sample 6_Ppy-expressing cells: YFPpositive (4)


title: Sample 10_Ppy-expressing cells: YFPpositive (3)


title: KO rep3 mLN [TCR-seq]

city: Vienna

first: Katharina

middle: A

last: Mayer

address: Lazarettgasse 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Library strategy: TCR-seq
UMI-based clustering and error correction with migec v.1.2.7
Alignment of V, D and J segments with mixcr v.2.1.11
Supplementary_files_format_and_content: *.txt: Tab-delimited text files, each raw corresponds to unique TCRbeta clonotype, one file per sample.

source_name: CD4+ T cell

extract_protocol: TCR cDNA library preparation was performed using TCR profiling Kit (MiLaboratory, Russia).

treatment_protocol: WT and KO T cells were transferred in to Rag KO recipients to induce T cell transfer colitis; donor T cells were isolated from spleen and mLN after 6 weeks.

value: KO (CD4-Cre PRKAA1fl/fl)

value: CD4+ T cell mLN


title: 18_M_V_PFC

source_name: Prefrontal cortex

value: PFC

value: Male


title: NH24_rep1

value: Endothelial colony forming cells

value: Human umbilical cord blood

value: Non-hypoxia for 24 hours


title: BL1_IC095605

value: 37 yrs


title: BSPCR_lib1_Col0_rep2

city: Los Angeles

first: Lucia

last: Ichino

state: CA

address: 610 Charles E Young Dr East

department: MCDB

institute: University of California, Los Angeles

description: PCR products from genomic DNA

library_source: genomic

data_processing:
Library strategy: BS-PCR
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown on soil in a greenhouse under long-day conditions (16h light / 8h dark).

extract_protocol:
DNA was extracted with DNeasy Plant Mini kit (Qiagen)
The DNA was bisulfite treated using the Epitect Bisulfite Conversion kit (QIAGEN). The conversion reaction in the thermocycler was performed twice to increase the efficiency. The converted DNA was amplified with the primers indicated in the manuscript of this study, using the Pfu Turbo Cx DNA polymerase (Agilent). Different PCR products for the same sample were pooled and purified with AMPure beads (Beckman Coulter). Libraries were generated using the Kapa HyperPrep DNA kit (KR0961) and the TruSeq DNA UD adapters (IDT for Illumina).

value: inflorescence

tag: ecotype

tag: genetic background

value: wild-type


title: KO rep3 spleen [TCR-seq]

value: CD4+ T cell spleen


title: BL1_IC090391

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage IV, Ductal, High grade

value: Stage IV, Ductal, High grade

value: Basal like 1

value: 40 yrs


title: KO rep2 spleen [TCR-seq]


title: 18_M_V_HYP

value: HYP


title: NH10_rep4

value: Non-hypoxia for 10 hours


title: 18_M_V_BLD

value: BLD


title: KO rep2 mLN [TCR-seq]

value: KO (CD4-Cre PRKAA1fl/fl)


title: Sample 14_Ppy-expressing cells: YFPpositive (1)

value: Mixed

value: two-month-old

value: Endocrine pancreas - Islet of Langerhans

value: Pancreatic islet cells


title: Sample 12_Ppy-expressing cells: YFPpositive (2)


title: NH10_rep3

value: Endothelial colony forming cells

value: Human umbilical cord blood


title: 18_M_V_AMY

value: AMY

value: Male


title: NH10_rep2


title: 16_M_V_PFC

value: PFC


title: KO rep1 mLN [TCR-seq]

value: CD4+ T cell mLN


title: 16_M_V_HYP


title: Non Ppy-expressing cells: YFPnegative2

data_processing:
Libraries were sequenced as 100bp paired-end reads on a HiSeq 40000 platform (Illumina). Demultiplex of barcodes was performed using Cell Ranger software pipeline (10x Genomics) using Ensembl mm10 build 84 reference genome with the addition of YFP and rtTA transgenic sequences.
Data were loaded as Seurat objects (v3.1.0) under R (version 3.6.1) in R Studio (version 1.0.153) using the Read10X function. Positive and negative fractions from each replicate were combined into a single sparse matrix before being used to generate a Seurat object, with min.features set to 500.
Cells were then filtered to contain at least 1000 UMIs and at most 7% mitochondrial genes. Data were normalized using the LogNormalize method, using 10’000 as scale factor. The top 1000 most variable genes were detected using the vst method after which all genes were scaled with use.umi set to TRUE, then principle component analysis was performed to find the first 40 PCs.
Data was integrated using Seurat FindIntegrationAnchors function, using 20 CC’s. The integrated object was scaled with use.umi set to FALSE, the first 50 PCs were calculated and tested using jackstraw (all 50 were significant).
Genome_build: mm10 build 84 reference genome with the addition of YFP and rtTA transgenic sequences
Supplementary_files_format_and_content: Sparse MatrixMarket files (.mtx) with separate tab-separated values files (.tsv) containing gene- and barcode names.

source_name: Pancreatic islet cells

extract_protocol:
Islet cells were obtained from two-month-old doxycycline-treated Ppy-rtTA; R26-YFP mice, FAC-sorted in a Moflo Astrios (Beckman Coutler) system. Sorted YFP+ and YFP- cells of Ppy-rtTA; R26-YFP were loaded separately for single-cell RNA-seq using the Chromium Controller (10x Genomics) following the Single Cell 3’ Library kit v2 manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mix background

value: two-month-old wild-type


title: KO rep1 spleen [TCR-seq]

value: CD4+ T cell spleen


title: NH10_rep1


title: NH30_rep4

value: Non-hypoxia for 40 minutes


title: 16_M_V_BLD


title: Non Ppy-expressing cells: YFPnegative


title: 16_M_V_AMY


title: NH30_rep3


title: Ppy-expressing cells: YFPpositive


title: WT rep4 mLN [TCR-seq]

value: WT (PRKAA1fl/fl)


title: WT rep3 spleen [TCR-seq]


title: WT rep4 spleen [TCR-seq]


title: NH30_rep2


title: 15_M_C_PFC


title: HiC-Hera_lat_HW-2

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

data_processing:
Library strategy: HiC-seq
Alignment to H. e. lativitta genome using juicer pipeline.
H. e. lativitta version 1: http://download.lepbase.org/v4/sequence/Heliconius_erato_lativitta_v1_-_scaffolds.fa.gz
Genome_build: Heliconius erato lativitta genome version 1
Supplementary_files_format_and_content: Juicer nodup file
The txt file is all of the called interactions between mate pair reads after alignment and filtering, and is the file we used for all of our analysis.

organism: Heliconius erato lativitta

source_name: Whole wing tissue

growth_protocol: Caterpillars and pupae were raised at ~27C until 3 days post pupation or ommochrome pigment deposition before sampling.

extract_protocol:
Nuclei extracted following Hi-C protocol
Libraries were prepared according to NEB instructions accompanying the NEBNext Ultra DNA Library Prep Kit

tag: developmental stage

value: Day 3 Post-Pupation


title: WT rep3 mLN [TCR-seq]


title: HiC-Hera_lat_FW-2


title: WT rep1 spleen [TCR-seq]


title: HiC-Hera_lat_HW-1


title: 15_M_C_HYP

value: HYP


title: 15_M_C_BLD

value: BLD


title: WT rep1 mLN [TCR-seq]


title: H24_rep4

value: Hypoxia for 24 hours


title: Ppy-expressing cells: YFPpositive2

value: Endocrine pancreas - Islet of Langerhans


title: H24_rep3


title: HiC-Hera_lat_FW-1


title: H24_rep2


title: ChIP_optix_Hera_lat_HW-2

data_processing:
Alignment to H. e. lativitta genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
H. e. lativitta version 1: http://download.lepbase.org/v4/sequence/Heliconius_erato_lativitta_v1_-_scaffolds.fa.gz
Genome_build: Heliconius erato lativitta genome version 1
Supplementary_files_format_and_content: FPKM normalizaed and input subtracted signal files were produced using Deeptools

extract_protocol:
Nuclei from whole wing tissue were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions accompanying the NEBNext Ultra DNA Library Prep Kit

tag: chip antibody

value: optix antibody


title: 15_M_C_AMY


title: HFrEF_12_LA

city: South San Francisco

first: Xin

last: Luo

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

data_processing:
RNA-Seq sequencing reads were aligned using OSA aligner embedded in the Omicsoft Array Suite (Omicsoft Inc., USA) based on human genome version GRCh38 and gene model GENCODE v24.
Quantification was performed to the gene level based on Omicsoft implementation of RSEM. Gene expression was quantile normalized by fragments per kilobase per million reads (FPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for every sample.
Matrix table with raw gene counts for every gene and every sample

source_name: Left Atrium

extract_protocol:
Frozen heart tissue samples were subjected to dry pulverization and RNA extraction was performed using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment (Qiagen) according to the manufacturer’s instructions.  Samples with ≥100 ng total RNA and RNA integrity numbers (RIN) ≥7 were used for sequencing.
After passing the QC, total RNA was used for cDNA library preparation using a modified protocol based on the Illumina Truseq RNA sample preparation kit and the published method for strand-specific RNA-Seq. cDNA libraries were sequenced by tthe HiSeq platform (Illumina).

value: Female

value: Heart

tag: tissue region

value: Left Atrium

tag: race

value: Caucasian

tag: disease state

value: HFrEF


title: HFrEF_11_LA

value: Male


title: ChIP_optix_Hera_lat_HW-1


title: HFrEF_10_LA


title: NH30_rep1

tag: cell type

value: Endothelial colony forming cells

value: Human umbilical cord blood


title: ChIP_optix_Hera_lat_FW-2


title: ChIP_optix_Hera_lat_FW-1


title: H10_rep3

tag: tissue

value: Hypoxia for 10 hours


title: 14_M_C_BLD

tag: strain

tag: treatment


title: H24_rep1


title: 14_M_C_AMY

value: AMY

tag: Sex


title: H10_rep2


title: H10_rep4


title: HFrEF_9_LA

tag: gender


title: 13_M_C_PFC

value: PFC


title: HFrEF_7_LA


title: ChIP_input_Hera_lat_HW-1

value: Day 3 Post-Pupation


title: ChIP_input_Hera_lat_HW-2


title: HFrEF_8_LA

value: Hispanic


title: 13_M_C_HYP

value: HYP


title: HFrEF_6_LA


title: H30_rep4

value: Hypoxia for 40 minutes


title: H10_rep1


title: 14_M_C_PFC


title: ChIP_input_Hera_lat_FW-1


title: 13_M_C_BLD

value: BLD


title: ChIP_input_Hera_lat_FW-2


title: H30_rep3


title: 14_M_C_HYP


title: HFrEF_5_LA


title: H30_rep2


title: 13_M_C_AMY


title: HFrEF_4_LA


title: HYR__f0eb5a__20201023_bst_S6

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Barcode reads (read 2) were trimmed using trimgalore (trim_galore -j 2 -o . $R1 $R2 --paired --gzip), corrected to a whitelist allowing 1 mismatch (custom seq script inVSN pipeline version 41df185308 [develop_atac]), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
Cell barcodes were written to the bam as a CB SAM tag using SAMtools and AWK (custom VSN pipeline version 41df185308 [develop_atac] script) (samtools view -h HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5.bwa.out.possorted.bam | mawk '/^@/ {print;next} {N=split($1,n,"_"); NN=split(n[1],nbc,"-"); ucorr_bc=""; corr_bc=""; if(NN==1){ # BioRad data with format {corrected_bc}_qname; corr_bc="CB:Z:" nbc[1];} if(NN==2){ucorr_bc="CR:Z:" nbc[1]; if(length(nbc[2])>0){corr_bc="
Reads were mapped to reference genomes using bwa-mem and duplicate-marked using samtools markdup by the VSN pipeline version 41df185308 [develop_atac] (bwa mem -t 8 genome.fa $R1.fq.gz $R2.fq.gz | samtools fixmate -@ 6 -m -u -O bam - - | samtools sort -@ 6 -u -O bam - | samtools markdup -@ 6 -f markdup.log - bwa.out.possorted.bam).
Fragments files were generated using Sinto (sinto fragments -b $bam -m 30 --barcodetag CB --use_chrom "(?i)^chr" --min_distance 10 --max_distance 5000 --chunksize 5000000 -p 2 -f $fragments.bed)
Per-cluster differentially accessible region were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='cell_type_finetuned', var_features=variable_regions, contrasts=None, adjpval_thr=0.05, log2fc_thr=np.log2(1.5), n_cpu=12)) and written to BED format using a custom python script.
Per-cluster coverage bigwigs were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (bw_paths, bed_paths = export_pseudobulk(input_data = cistopic '0.1.dev214+gc72ef83.d20210522'_obj.cell_data, variable = 'cell_type_finetuned', chromsizes = chromsizes, bed_path = bed_path, bigwig_path = bw_path, path_to_fragments = fragments_dict, n_cpu = nclusters, normalize_bigwig = True, remove_duplicates = True))
Aggregate genome coverage bigwigs were generated using DeepTools 3.5.0 (bamCoverage -b ${file} -o ${file%.bam}.RPGCnormalized.bw -bs 1 -p 4 --normalizeUsing RPGC  --effectiveGenomeSize 2913022398)
For HyDrop-RNA samples (prefix HYR):
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Reads were mapped  to reference genomes and expression matrices were generated using STAR version: 2.7.8a_2021-04-27 in STARsolo mode (STAR --runThreadN 6 --runMode alignReads --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --genomeDir "${star_reference_dir}" --readFilesIn "${fastq_R1_filename}" "${fastq_R2_filename}" --readFilesCommand 'gzip -c -d' --soloCBwhitelist "${whitelist_part1_filename}" "${whitelist_part2_filename}" "${whitelist_part3_filename}" --soloType CB_UMI_Complex --soloCBposition 0_0_0_9 0_20_0_29 0_40_0_49 --soloUMIposition 0_50_0_57 --sjdbGTFfile $sjdbgtf --soloCellFilter CellRanger2.2 2000 0.99 10 --soloCBmatchWLtype 1MM --outFilterMultimapNmax 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY --outFileNamePrefix ${bam_filename%bam} --outReadsUnmapped Fastx --quantMode GeneCounts --bamRemoveDuplicatesType UniqueIdentical --soloFeatures Gene GeneFull Velocyto)
For the optimisation samples (HYR__1ec4a0__20200929_Exo_S1 HYR__3ac717__20201006_non-exo_S2 HYR__70afb2__20201006_TSO-LNA_S3 HYR__c6c4b7__20201016_gtp_S4 HYR__d0a5b4__20201023_klenow_S5 HYR__f0eb5a__20201023_bst_S6), FASTQs were downsampled to match the reads per cell depth of the lowest sample and re-mapped using the same STAR parameters to generate the DOWNSAMPLED expression matrices.
Genome_build: For human samples: hg38, for mouse samples: mm10, for hybrid samples: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary_files_format_and_content: For HyDrop-ATAC samples (prefix HYA): standard tab-separated fragments files, tar archive with per-cluster differentially accessible region bed files, tar archive with per-cluster genome coverage bigwig
Supplementary_files_format_and_content: For HyDrop-RNA samples (prefix HYR): STARsolo gene expression matrix in MEX format

molecule: cytoplasmic RNA

organism:
Homo sapiens
Mus musculus

source_name: 50:50 mixture of human MM087 cells and mouse melanoma cells

growth_protocol: MM087 mouse melanoma cells were cultured in F-10 Nutrient mix supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. Mouse melanoma cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week.

extract_protocol: NOT PROVIDED; REQUESTED

tag: tissue/cell line

value: Human:melanoma cell line/mouse:melanoma cell line


title: 12_M_C_PFC


title: HFrEF_2_LA

tag: age


title: 12_M_C_HYP


title: HFrEF_3_LA

value: African-American


title: HYR__c6c4b7__20201016_gtp_S4


title: SOX10 mutant iPS cell-derived neurnal crest cells rep2

city: Changsha

first: Jian

last: Song

state: 湖南

address: 87 Xiangya Road

department: Department of Otorhinolaryngology

country: China

institute: Xiangya Hospital Central South University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iPS cell-derived neurnal crest cells

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #E7530L)) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPS cell-derived neurnal crest cells

tag: genotype

value: SOX10 mutant


title: SOX10 mutant iPS cell-derived neurnal crest cells rep1


title: HYR__3ac717__20201006_non-exo_S2


title: NF_10_LA

value: Female

value: Heart

value: Left Atrium

value: NF


title: 12_M_C_AMY

value: Male


title: SOX10 mutant iPS cell-derived neurnal crest cells rep3


title: HYR__70afb2__20201006_TSO-LNA_S3


title: wild type iPS cell-derived neurnal crest cells rep3

value: wild type


title: NF_8_LA


title: wild type iPS cell-derived neurnal crest cells rep2


title: 11_M_C_PFC


title: NF_7_LA


title: NF_9_LA

value: Caucasian


title: HYR__1ec4a0__20200929_Exo_S1


title: wild type iPS cell-derived neurnal crest cells rep1


title: 11_M_C_BLD


title: 11_M_C_AMY

value: AMY


title: H30_rep1

value: Endothelial colony forming cells

value: Human umbilical cord blood


title: NF_6_LA


title: SOX10 mutant iPS cell rep3

source_name: iPS cells

value: iPS cells


title: HFrEF_1_LA

value: HFrEF


title: HYR__d0a5b4__20201023_klenow_S5


title: NF_5_LA


title: 10_M_C_PFC

value: PFC


title: SOX10 mutant iPS cell rep2


title: HYA__932b0e__20210309_mouse_cortex_MCF-7_PC3_1-1_S2

description:
processed data file: HYA__932b0e__af8d60_MCF-7.bwa.out.possorted.GRCH38ONLY.RPGCnormalized.bw
processed data file: HYA__932b0e__af8d60_PC-3.bwa.out.possorted.GRCH38ONLY.RPGCnormalized.bw

source_name: 45:45:10 mixture of human MCF-7 cells, human PC-3 cells and mouse cortex nuclei

growth_protocol: MCF7 cells were cultured in RPMI1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and 10 ug/mL insulin and passaged twice per week. PC3 cells were cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin and passaged twice per week. Mouse melanoma cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. Female wild-type P56 BL/6 mice were kept according to standard animal husbandry practices were maintained in a specific pathogen-free facility under standard housing conditions with continuous access to food and water. Mice used in the study were 1–8-weeks old and were maintained on 14 h light, 10 h dark light cycle from 7 to 21 h.

extract_protocol:
Cells were washed in PBS and dissociated into single cell suspensions using 1.5 mL of 0.05% Trypsin. The single-cell suspension was centrifuged at 500 rcf for 5 min at 4°C and the resulting pellet was resuspended in PBS. This PBS wash was repeated once more. A pellet of 1 million dissociated cells or fewer was incubated on ice in 200 μL of ATAC Lysis Buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 uM Pitstop, 0.01% Digitonin) for 5 to 7 minutes. 1 mL of ATAC Nuclei Wash Buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm Flowmi strainer. 50 000 nuclei were resuspended in 50 μL of ATAC Reaction Mix (10% DMF, 10% Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/uL Tn5, 70 uM Pitstop, 0.1% Tween-20, 0.01% Digitonin) and incubated at 37 °C for 1 hour without shaking. 100 μL of 0.1% BSA in PBS was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes and resuspended in 40 μL of 0.1% BSA in PBS. Tagmented nuclei were added to 100 μL of PCR mix (1.3X Phusion HF Buffer, 15% Optiprep, 1.3 mM dNTPs, 39 mM DTT, 0.065 U/uL Phusion HF Polymerase, 0.065 U/uL Deep Vent Polymerase, 0.013 U/uL ET SSB). PCR mix was co-encapsulated with 35 μL of freshly thawed HyDrop-ATAC beads in RAN oil on the Onyx microfluidics platform. The resulting emulsion was collected in aliquots of 50 μL total volume and thermocycled according to the PCR1 program (72 °C 15 min., 98 °C 3 min., 13 PCR cycles of [98 °C 10 s, 63 °C 30 s, 72 °C 1 min.], followed by a final hold on 4 °C). 125 μL of recovery agent (20% PFO in HFE), 55 μL of GITC Buffer (5 M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4) and 5 μL of 1 M DTT was added to each separate aliquot of 50 μL thermocycled emulsion and incubated on ice for 5 minutes. 5 μL of Dynabeads was added to the aqueous phase and incubated for 10 minutes. Dynabeads were pelleted on a Nd magnet and washed twice with 80% EtOH. Elution was performed in 50 μL of EB-DTT-Tween (10 mM DTT, 0.1% Tween-20 in EB). A 1X Ampure bead purification was performed according to manufacturer’s recommendations. Elution was performed in 30 μL of EB-DTT (10 mM DTT in EB).
Eluted library was further amplified in 100 μL of PCR2 mix (1X KAPA HiFi, 1 uM index i7 primer, 1 uM index i5 primer). Final library was purified in a 0.4X-1.2X double-sided Ampure purification and eluted in 25 μL of EB-DTT (10 mM DTT in EB).

value: Human:breast cancer cell line/human:prostate cancer cell line/mouse:melanoma cell line


title: 12_M_C_BLD

value: BLD


title: NF_4_LA

value: African-American


title: 10_M_C_BLD


title: NF_2_LA

value: Hispanic


title: 10_M_C_HYP

value: HYP


title: 11_M_C_HYP


title: wild type iPS cell rep3


title: 22_Disseminated_DLBCL

city: Leiden

first: Ruben

last: de Groen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: See manufacturer's protocol for the NanoString nCounter Assay System

data_processing: Data was log2 transformed and standardized by geometric mean, followed by normalization with the housekeeping genes using the 'NanoStringNorm' package in R. Further analysis was additionally performed with R.

label: Fluorescent tag barcodes

extract_protocol: RNA was isolated from fresh frozen with TRIzol (Invitrogen) and Rneasy Mini Kit (Qiagen) and from deparaffinized 10 μm sections of FFPE tissues with the Tissue Preparation System (TPS) robot (Siemens Healthcare Diagnostics). RNA was quantifies with the Qubit RNA BR Assay kit with the Qubit Fluorometer (Invitrogen).

value: FFPE

tag: status after 5 years

value: Dead

tag: ann arbor stage

value: IV


title: NF_1_LA

value: Male

value: Heart

value: Left Atrium

value: NF


title: HYA__af8d60__20210309_mouse_cortex_MCF-7_PC3_1-2_S3


title: 34_Disseminated_DLBCL

scan_protocol: See manufacturer's protocol for the NanoString nCounter Assay System


title: wild type iPS cell rep2

value: wild type


title: 10_M_C_AMY

value: AMY


title: HFrEF_12_RA

source_name: Right Atrium

value: Female

value: Right Atrium

value: Caucasian


title: 13_PB_DLBCL

label_protocol: See manufacturer's protocol for the NanoString nCounter Assay System

value: Alive

value: IXE


title: 09_M_C_PFC

value: PFC


title: Healthy Control 5

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

data_processing:
Pre-processing of raw sequencing data was done using 10x genomics Cell Ranger pipeline with default settings (v6.0.1).
Raw data bcl files were first demultiplexed using Cellranger mkfastq.
Demultiplexed data was then processed using the Cellranger count.
The count output was loaded into R using the Seurat R v4.0.1 function Read10X.
Downstream processing (e.g. normalization, integration) and analysis were performed in R v4.0.5.
Genome_build: hg19-3.0.0
Supplementary_files_format_and_content: Output of Cell Ranger from the raw_feature_bc_matrix folder contain the UMI counts for cells in each sample.

source_name: mixture of whole blood myeloid-enriched and Ficoll-enriched peripheral blood mononuclear cells

extract_protocol: Cells were loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions. Libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed using XX library quantification assay. Sequencing was performed on Illumina NovaSeq or NextSeq.

value: circulating immune cells

tag: sepsis type

value: Healthy Control

tag: cci


title: HFrEF_11_RA

value: HFrEF


title: 51_Mix_NO_DLBCL

value: FFPE


title: 09_M_C_HYP

source_name: Hypothalamus

value: HYP


title: HFrEF_9_RA


title: 09_M_C_BLD

source_name: Blood

value: BLD

value: Male


title: Healthy Control 4


title: HYA__7d0f30__20210305_barnyard_MCF-7_MMel_1-1_S1

source_name: 50:50 mixture of human MCF-7 cells and mouse melanoma cells

growth_protocol: MCF7 cells were cultured in RPMI1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and 10 ug/mL insulin and passaged twice per week. Mouse melanoma cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week.

value: Human:breast cancer cell line/mouse:melanoma cell line

tag: developmental stage


title: HFrEF_10_RA

value: Heart

tag: tissue region


title: wild type iPS cell rep1

value: iPS cells

value: wild type


title: Healthy Control 3


title: 09_M_C_AMY

value: AMY


title: SOX10 mutant iPS cell rep1

value: SOX10 mutant


title: 33_Ext_NO_DLBCL

value: Female

value: Dead

value: IE


title: 08_M_C_PFC

value: PFC


title: Sepsis 4

value: circulating immune cells

value: Fungal

value: CCI


title: HFrEF_8_RA

value: Right Atrium

tag: race

value: Hispanic

value: HFrEF


title: 30_Mix_NO_DLBCL

value: FFPE

value: Alive

value: IV


title: 08_M_C_HYP

value: HYP

value: Male


title: 60_Ext_NO_DLBCL


title: HFrEF_7_RA

value: Heart

value: Caucasian

tag: disease state


title: Sepsis 3

tag: cell type

value: Bacterial


title: 08_M_C_BLD

tag: tissue

value: BLD


title: 08_M_C_AMY

tag: strain

value: AMY


title: 7_Polyostotic_DLBCL


title: HFrEF_5_RA


title: 71_Ext_NO_DLBCL

value: IE


title: MIBC_B371

first: Kenneth

middle: Howard

last: Gouin III

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description: Visium spatial transcriptomics of MIBC tissue

data_processing:
Samples were processed with SpaceRanger (10X genomics, v1.1.0) using the same pre-mrna reference as for the snSeq data analysis to improve consistency between the two datasets.
Genome_build: GRCh38
Supplementary_files_format_and_content: combined_visium.h5ad contains processed data for all spots passing QC filtering. These files contain raw counts for every gene in every spot as well as metadata such as sample identity. A1,B1,C1, and D1.jpg are the associated H&E images for each sample.

source_name: MIBC

extract_protocol:
Tissue optimization was performed on one representative MIBC sample from the cohort used in this study, and the optimal permeabilization time was determined to be 24 minutes. Then 4 samples were cryosectioned at 10mm and processed according to the 10x Visium protocol.
Libraries were constructed according to the 10x Visium library construction protocol and sequenced by Illumina to a sequencing saturation of approximately 90%.

value: muscle-invasive bladder cancer (MIBC)


title: 81_Mix_NO_DLBCL

value: Female

value: Dead


title: HFrEF_4_RA

value: Right Atrium


title: 07_M_C_HYP

tag: treatment


title: MIBC_B8


title: MIBC_B72


title: 07_M_C_PFC

value: PFC

tag: Sex


title: 52_Nod_NO_DLBCL

tag: gender

value: III


title: 47_Nod_NO_DLBCL

value: FFPE


title: HFrEF_2_RA

value: HFrEF


title: 77_Polyostotic_DLBCL

value: Alive

value: IV


title: MIBC_B1204


title: 07_M_C_BLD

value: Male


title: HFrEF_1_RA

value: Heart

value: African-American


title: NF_10_RA

value: NF


title: 06_M_C_PFC


title: 73_Mix_NO_DLBCL


title: HFrEF_6_RA

value: Caucasian


title: normalD: normal_sampleD

description: snSeq of histologically-normal bladder sample

data_processing:
Samples were processed with CellRanger (10X genomics, v3.0.2) using a pre-mrna reference based on the GRCh38-3.0.0 reference in a manner similar to a recent snSeq study42. Hashing libraries were aligned using the Cite-seq-count program (v1.4.3) with the cell barcodes from the CellRanger output as the barcode whitelist. The UMI counts from Cite-seq-count were then used for demultiplexing the MIBC samples using a combination of the Seurat HTOdemux function and a secondary custom script in MATLAB. The secondary script was used to recover nuclei that were identified as negative for all hashtags by the HTOdemux function, but actually passed the minimum number of counts identified by the HTOdemux function for one and only one hashtag. All nuclei that were determined to be doublets or that remained negative after the recovery step were then removed from subsequent analyses. Since the histologically-normal samples were not hashed, putative doublet nuclei were identified using Scrublet (v0.2.1)43 from the filtered feature barcode matrices produced by CellRanger. Scrublet was run using the 10% highest variable genes, identified using the Scanpy (scanpy.pp.highly_variable_genes function; scanpy v1.5.1)44, with an expected doublet rate of 10%. Nuclei were scored as candidate doublets by Scrublet and removed if their doublet score exceeded 0.25. Finally, for all samples, nuclei with more than 10% of their UMIs mapped to mitochondrial genes were removed, and the top and bottom 5% of nuclei based on number of unique genes and number of UMI were removed.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: MIBC_snSeq.h5ad and non_tumor_snSeq.h5ad contains processed data for all cells passing QC filtering from MIBC and normal bladder samples, respectively. These files contain raw counts for every gene in every cell as well as metadata associated with each cell (e.g. demultiplexed hashing sample identity). MIBC_HTO.h5ad contains UMI counts for every HTO for every cell from the cite-seq-count output. HTO_tags.csv contains the barcode associated with each HTO tag that was used. HTO_demultiplexing_table.csv contains the information for demultiplexing the HTO tags from each library into the individual samples.

extract_protocol:
Nuclei were isolated from fresh frozen muscle-invasive bladder cancer (MIBC) tumors using a method modified from a recent single-nuclei RNA-sequencing (snSeq) study41. The ST-SB buffer from that study was modified by removing Tween-20 and supplementing with 0.04U/L Protector RNase Inhibitor (Roche). Unless otherwise specified, all sample manipulation was performed on wet ice with wide-bore pipet tips (Rainin) and all centrifugations were performed with a swinging bucket rotor maintained at 4C for 5 minutes at 850x g. In brief, the frozen tissue was transferred onto a plate on dry ice and crushed into ≤ 1mm3 pieces. This was then transferred to a 2mL dounce homogenizer (Kimble, cat: 885300-0002) on wet ice containing 1mL of Nuclei EZ lysis buffer (Sigma, cat: NUC101). The tissue was then dounced approximately 20x with Pestle A followed by 20x with Pestle B. The lysis was then quenched by adding 1mL of ST-SB. The sample was filtered through a pre-wetted 30m filter (Miltenyi Biotec, cat: 130-041-407) into a 15mL conical tube. The homogenizer was rinsed 3x with 1mL of ST-SB and this was transferred through the same 30m filter into the 15mL conical tube. The sample was then centrifuged, the resulting supernatant removed, and the pellet resuspended with 500L of ST-SB. The sample was then passed through a pre-wetted 20m filter (Miltenyi Biotec, cat: 130-101-812) into a 1.5mL protein lo-bind microcentrifuge tube (Eppendorf, cat: 022431081) and centrifuged. At this point, Totalseq hashing antibodies (Biolegend, clone Mab414) were also centrifuged at 14,000xg for 10 minutes at 4C. The sample pellet was then resuspended in 100L of ST-SB and 10L of Human TruStain FcX block (Biolegend, cat: 422301) was added. The sample was pipet mixed and incubated at 4C for 5 minutes. Then 1.5g of the appropriate hashing antibody was added to the appropriate samples, pipet mixed, and incubated at 4C for 15 minutes. The samples were pipet mixed once halfway through this incubation. The samples were then washed 2x with 1mL of ST-SB, pooled appropriately, and filtered through another 30m and 20m filter. Nuclei concentration was quantified by mixing an aliquot of the sample with DAPI at a final concentration of 0.025 mg/mL in H2O.
Samples were finally processed according to 10x Genomics protocol for the 3’ v3.1 assay and were super-loaded to target of 20,000 nuclei recovery. We observed that nuclei yield less total cDNA than cells, therefore we increased the first cDNA amplification cycle number by 2. Hashing libraries were generated according to the Biolegend Totalseq protocol for the 3’ v3.1 assay. In total, 57 samples from 25 patients were processed. All samples were sequenced by the Cedars-Sinai Applied Genomics, Computation & Translational Core on a Novaseq to a sequencing saturation of approximately 60%.

value: normal bladder


title: normalC: normal_sampleC


title: 06_M_C_HYP

extract_protocol:
Total RNA was extracted from the whole blood samples using the Quick-RNA Whole Blood kit according to manufacturer instructions (Zymo, Irvine, CA, USA). Total RNA was extracted from the brain micropunches using the PureLink RNA Mini Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer instructions except that 2-mercaptoethanol was not added to the lysis buffer as this was found to reduce reads in downstream analyses during optimization tests. RNA purity, concentration, and integrity were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), Qubit 4 (Thermo Fisher Scientific, Waltham, MA, USA), and Tapestation 4150 (Agilent Technologies, Santa Clara, CA, USA). For quantitative assessment of RNA sequencing, External RNA Controls Consortium (ERCC) RNA Spike-In Mix 1 (Thermo Fisher) were added to samples. We submitted 300 ng total RNA/sample for brain samples and 2000 ng total RNA/sample for whole blood samples to the Genomic Sequencing and Analysis Facility at UT Austin for sequencing.
We surveyed gene expression using TagSeq by constructing libraries directed at the 3’ ends of mRNA according to established protocols [PMID: 27037501]. About 70% of mRNA from whole blood is globin mRNA, which limits the ability to detect other genes. Therefore, we depleted globin mRNA in the whole blood samples before library construction using the QIAseq Fast Select RNA removal kit (Qiagen, Germantown, MD, USA) according to manufacturer instructions. Before globin depletion, the blood samples were purified using an AMPure XP (Agencourt) bead clean-up as our optimization tests revealed this improved the blood library concentrations. Purified libraries were size-selected to obtain 350–550 bp target cDNA and pooled in equal proportions following relative quantification using a qPCR assay. Pooled sets of libraries were sequenced using an Illumina NovaSeq 6000 generating 1x100 bp single-end reads. Illumina adapters were removed, and lane pools were de-multiplexed according to the barcode assignments by the sequencing facility prior to return of raw data.

value: HYP


title: NF_9_RA


title: HFrEF_3_RA


title: 24_PB_DLBCL

value: IE


title: NF_8_RA

value: Hispanic


title: normalB: normal_sampleB


title: normalA: normal_sampleA


title: 06_M_C_AMY

source_name: Amygdala

value: AMY


title: NF_7_RA

value: Female

value: Right Atrium


title: 07_M_C_AMY


title: 79_Disseminated_DLBCL

value: IIIS


title: B8B-HTO: MIBC_rxn8B

description: snSeq of MIBC samples multiplexed with hashing antibodies

value: muscle-invasive bladder cancer (MIBC)


title: NF_4_RA


title: 05_M_V_PFC

value: PFC


title: 05_M_V_HYP


title: B8A-HTO: MIBC_rxn8A


title: NF_5_RA


title: B8B-GEX: MIBC_rxn8B


title: 69_PB_DLBCL

value: FFPE

value: Alive


title: 19_PB_DLBCL

value: Dead

value: IXE


title: NF_3_RA

value: Heart


title: 05_M_V_BLD

value: BLD

value: Male


title: B8A-GEX: MIBC_rxn8A


title: NF_2_RA

value: NF


title: 05_M_V_AMY


title: 10_PB_DLBCL


title: NF_1_RA

value: Caucasian


title: 35_PB_DLBCL

value: IE


title: 04_M_V_HYP

value: HYP


title: 11_PB_DLBCL

value: IIE


title: 04_M_V_PFC


title: B7A-HTO: MIBC_rxn7A


title: 12_PB_DLBCL


title: B7B-GEX: MIBC_rxn7B


title: 06_M_C_BLD


title: 37_Polyostotic_DLBCL

value: IV


title: 04_M_V_BLD


title: HFrEF_11_LV

source_name: Left Ventricle

value: Left Ventricle

value: HFrEF


title: HFrEF_10_LV


title: HFrEF_12_LV

value: Female


title: B6B-HTO: MIBC_rxn6B

value: muscle-invasive bladder cancer (MIBC)


title: 04_M_V_AMY

value: AMY


title: 48_PB_DLBCL

value: FFPE

value: Alive


title: 17_Polyostotic_DLBCL


title: 88_Mix_NO_DLBCL


title: 03_M_V_PFC

source_name: Prefrontal cortex

value: PFC


title: 83_Mix_NO_DLBCL


title: HFrEF_9_LV

value: Heart


title: B6B-GEX: MIBC_rxn6B


title: B7B-HTO: MIBC_rxn7B


title: 03_M_V_HYP


title: HFrEF_8_LV

value: Hispanic


title: 87_Ext_NO_DLBCL

value: Male


title: 03_M_V_BLD

value: BLD


title: HFrEF_7_LV

value: Caucasian


title: 68_PB_DLBCL

value: IE


title: B6A-GEX: MIBC_rxn6A


title: 03_M_V_AMY


title: HFrEF_6_LV


title: 9_PB_DLBCL


title: HFrEF_5_LV


title: B5B-HTO: MIBC_rxn5B


title: B7A-GEX: MIBC_rxn7A


title: B5B-GEX: MIBC_rxn5B


title: 02_M_V_PFC


title: B5A-HTO: MIBC_rxn5A


title: 91_PB_DLBCL


title: HFrEF_3_LV

value: African-American


title: B5A-GEX: MIBC_rxn5A


title: 31_PB_DLBCL

value: IIE


title: HFrEF_4_LV


title: 02_M_V_AMY


title: HFrEF_2_LV


title: 02_M_V_BLD


title: 01_M_V_PFC


title: B4-HTO: MIBC_rxn4


title: HFrEF_1_LV


title: B6A-HTO: MIBC_rxn6A


title: B4-GEX: MIBC_rxn4


title: 01_M_V_HYP

value: HYP


title: B3-HTO: MIBC_rxn3


title: NF_10_LV

value: Left Ventricle

value: NF


title: 01_M_V_BLD


title: B3-GEX: MIBC_rxn3


title: NF_9_LV


title: 02_M_V_HYP


title: 01_M_V_AMY


title: NF_8_LV


title: B2-HTO: MIBC_rxn2


title: NF_7_LV

value: Female


title: B2-GEX: MIBC_rxn2

value: muscle-invasive bladder cancer (MIBC)


title: NF_6_LV


title: Sample_1422-HS-26

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

institute: University of Michigan

description: HFD PN

data_processing:
Paired-end reads were aligned using Salmon v 1.3.0 to GRCm38.p6 with the parameters --validateMappings and --gcBias
Transcripts were merged into genes using tximeta and txiimport, then quantified using DESeq2 v1.28.1
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Salmon transcript quantification files, containing transcript id's (ENSEMBL), transcript length, reads, and transcripts per million

source_name: inguinal mammary gland

extract_protocol:
RNA extracted from whole mammary gland using Qiagen RNeasy Mini Kit
Followed manufacturers instructions forNEBNext®Ultra II Directional RNA Library Prep Kit for Illumina

value: postnatal day 16

tag: diet

value: HFD

value: Control


title: NF_5_LV

tag: age


title: Sample_1422-HS-22

description: Met PN

value: NCD

value: Metformin


title: B1-HTO: MIBC_rxn1


title: 65_PB_DLBCL

value: FFPE

value: Alive


title: B1-GEX: MIBC_rxn1


title: 102_PB_DLBCL


title: 84_Ext_NO_DLBCL

value: Male

value: IV


title: 43_Mix_NO_DLBCL


title: 94_PB_DLBCL

value: IE


title: 45_Mix_NO_DLBCL

value: II


title: 20_Disseminated_DLBCL

value: Dead


title: 55_Disseminated_DLBCL


title: 8_PB_DLBCL

value: IIE


title: 72_Disseminated_DLBCL


title: NF_4_LV

value: Heart

value: Left Ventricle

value: African-American


title: B1246-HTO: MIBC_rxn1246

value: muscle-invasive bladder cancer (MIBC)


title: 85_Nod_NO_DLBCL

value: Female

value: IIIA


title: Sample_1422-HS-20

description: HFD+Met PN

value: postnatal day 16

value: HFD


title: NF_2_LV

value: Hispanic

value: NF


title: NF_1_LV

value: Caucasian


title: Sample_1422-HS-19

description: HFD+Met PN

value: Metformin


title: URPL decidua single-cell RNA Seq

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: NO.3002 Sungang Road, Futian district

department: Institute of Translational Medicine

institute: Shenzhen Second People's Hospital

data_processing:
Cell Ranger 3.1.1 pipeline
Seurat R package v3
Genome_build: hg38/GRCH38
Supplementary_files_format_and_content: tsv/mtx

source_name: decidua

extract_protocol:
Decidual tissues were chopped using scalpels into approximately 0.5-mm^3 cubes and enzymatically digested with tumor dissociation kit (Miltenyi Biotec, 130-095-929) using GentleMACS Dissociator (Miltenyi Biotec, 130-093-235) following the manufacturer’s instructions. The supernatant was diluted with cold RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and then passed through a 40-μm cell sieve (Corning, 431750). The flow-through was centrifuged and cells were resuspended in 5ml of red blood cell lysis buffer (ThermoFisher, A1049201) for 5 min. The cells were then centrifuged and resuspended in cold RPMI-1640 medium supplemented with 10% FBS.
The 10x Genomics v2 libraries were prepared as per the manufacturer’s instructions. Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell on an Illumina NovaSeq 6000.
Single-cell RNA Seq

value: decidua

value: CD45+ cells

tag: phenotype

value: URPL pregnancy


title: Sample_1422-HS-23

description: HFD+Met PN


title: Sample_1422-HS-18

description: HFD PN

value: Control


title: 53_Mix_NO_DLBCL

value: Male

value: FFPE

tag: status after 5 years

value: Alive

value: IV


title: HFrEF_12_RV

source_name: Right Ventricle

value: Heart

value: Right Ventricle

value: HFrEF


title: Normal decidua single-cell RNA Seq

value: Normal pregnancy


title: Sample_1422-HS-17

description: HFD PN

value: postnatal day 16

value: HFD


title: Sample_1422-HS-10

description: HFD+Met PN


title: HFrEF_10_RV


title: HFrEF_8_RV

value: Female

value: Hispanic


title: Sample_1422-HS-14

description: Control PN

value: NCD


title: Sample_1422-HS-7

description: HFD PN


title: Sample_1422-HS-21

description: Met PN

value: Metformin


title: Sample_1422-HS-5

description: Met PN


title: HFrEF_9_RV

value: Caucasian


title: 89_Ext_NO_DLBCL

tag: ann arbor stage


title: HFrEF_11_RV


title: 16_Disseminated_DLBCL

value: Fresh Frozen


title: 40_PB_DLBCL

value: IE


title: 57_Disseminated_DLBCL

value: Male


title: B1246-GEX: MIBC_rxn1246

value: muscle-invasive bladder cancer (MIBC)


title: HFrEF_7_RV


title: Sample_1422-HS-4

description: Met PN


title: HFrEF_6_RV


title: 966-recurrence

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
human_cell_metadata.csv
human_raw_counts.csv.gz

data_processing:
Raw sequencing reads were demultiplexed, mapped to the human reference genome (build GRCh38) or mouse (mm10) as appropriate and gene-expression matrices were generated using CellRanger (version 3.0.1). The resulting count matrices were further filtered in Seurat 3.1.0 (https://satijalab.org/seurat/) to remove cell barcodes with less than 200 genes or 500 UMIs, more than 30% of UMIs derived from mitochondrial genes, or more than 40,000 UMIs.
Genome_build: GRCh38,mm10
Supplementary_files_format_and_content: UMI count matrices and associated cell-level metadata

source_name: Medulloblastoma tumor

extract_protocol:
Surgical material was collected at our institution at the time of surgery with consent (COMIRB 95-500). Samples were collected into PBS for subsequent scRNA-seq analysis and snap frozen for bulk-tumor methylome analysis. ScRNA-seq samples were rapidly dissociated into single cells using a mechanical process as described previously, viably cryopreserved and banked at <80oC for later use. (Reference Griesinger, A. M. et al. Characterization of distinct immunophenotypes across pediatric brain tumor types. J Immunol 191, 4880-4888, doi:10.4049/jimmunol.1301966 (2013).)
3' end 10x Genomics library prep (v2 and v3)

tag: tumor subgroup


title: 1433


title: 38_PB_DLBCL

value: Dead

value: IIE


title: HFrEF_5_RV

value: Heart


title: 1416

value: SHH


title: 54_PB_DLBCL

value: IXE


title: Sample_1422-HS-3

description: Control PN

value: Control


title: 56_Ext_NO_DLBCL

value: FFPE

value: Alive

value: IV


title: Sample_1422-HS-2

description: Control PN

value: postnatal day 16


title: HFrEF_3_RV

value: Right Ventricle

value: African-American

value: HFrEF


title: 80_Polyostotic_DLBCL

value: Female

value: Fresh Frozen


title: 59_Mix_NO_DLBCL

value: Male


title: mouse_ssh_model_3

description:
mouse_shh_model_cell_metadata.csv
mouse_shh_model_raw_counts.csv.gz

extract_protocol:
Tumor samples were dissociated using the Papain Dissociation System (Worthington Biochemical) as previous described (see reference). Briefly, tumor samples were incubated in papain at 37 °C for 15 min, then triturated and the suspended cells were spun through a density gradient of ovomucoid inhibitor. Pelleted cells were then resuspended in 2 ml of Bambanker media (fisher Scientific # NC9582225) and frozen at -80 degrees for storage prior to scRNA-seq analysis, (Ocasio J, Babcock B, Malawsky D, Weir SJ, Loo L, Simon JM, et al. scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy. Nat Commun. 2019;10(1):5829.)
3' end 10x Genomics library prep (v2 and v3)

tag: tumor model

value: SHH tumor model (Math1-Cre/SmoM2)


title: HFrEF_2_RV

value: Caucasian


title: Sample_1422-HS-1

description: Control PN

value: NCD


title: 1355


title: 1397


title: 70_Disseminated_DLBCL


title: HFrEF_1_RV

value: Heart


title: mouse_ssh_model_2


title: 6_PB_DLBCL

value: IIXE


title: NF_10_RV

value: NF


title: 1238


title: mouse_ssh_model_1


title: 1325

value: SHH


title: NF_9_RV


title: 25_Disseminated_DLBCL

value: Dead


title: NF_8_RV

value: Hispanic


title: 61_Disseminated_DLBCL

value: IV


title: mouse_Myc_DnTrp53

description:
mouse_myc_dnp53_model_cell_metadata.csv
mouse_myc_dnp53_model_raw_counts.csv.gz

extract_protocol:
Cerebellar stem/progenitor cells (Prominin1+ cells) were purified by fluorescence activated cell sorting (FACS) from the cerebella of postnatal day 5–7 (P5–P7) C57BL/6J pups as previously described (see references 1-3). To generate Myc-DnTrp53 or Myc-Gfi1 tumors, cells were infected with viruses produced from pMSCV-MycT58A-IRES-Luc and pMSCV-DNp53-IRES-GFP (for MP tumors) or pMSCV-GFI1-IRES-GFP (for MG tumors). After overnight infection, cells were washed and 10,000 cells were stereotaxically injected into the cerebellum of 6- to 8-week-old NSG mice. Animals were monitored weekly and euthanized when they showed signs of tumor. Tumors were then dissociated and resuspended in NeuroCult medium with proliferation supplement (STEMCELL Technologies) for scRNA sequencing analysis.    1. Pei, Y., et al. HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-Driven  Medulloblastoma. Cancer cell 29, 311-323 (2016).  2. Pei, Y., et al. An animal model of MYC-driven medulloblastoma. Cancer cell 21, 155-167  (2012).  3.Northcott, P.A., et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428-434 (2014).
3' end 10x Genomics library prep (v2 and v3)

value: GP3 tumor model (MYC + dnTrp53)


title: 18_Polyostotic_DLBCL

value: Alive


title: 1235


title: NF_7_RV

value: Right Ventricle

value: African-American


title: 1224


title: 1195


title: NF_6_RV

value: Female


title: 1177


title: 4_PB_DLBCL

value: Fresh Frozen

value: IXE


title: 27_PB_DLBCL


title: 93_PB_DLBCL

value: Male

value: IIE


title: NF_5_RV

value: Caucasian


title: 1167


title: Lps1

city: Hefei

first: zhi

last: zhang

state: Anhui

address: 443 Huangshan Road

department: School of Life Science

institute: University of Science and Technology of China

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and low quality reads.
These clean reads were then mapped to the reference genome sequence using Tophat 2.1. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
Gene expression levels were estimated by fragments per kilobase of transcript per million mapped reads (FPKM).
Differential gene expression analysis of two groups was performed using the DESeq R package (1.10.1).
Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the GOseq R packages based Wallenius non-central hyper-geometric distribution.
Genome_build: Ensemble: GRCm38_release95
Supplementary_files_format_and_content: Tab-delimited text files containing counts and normalized FPKM value of detected gene for each sample.

source_name: ACC tissue

growth_protocol: Mice were housed 4-5 per cage during a 12 hours’ light-dark cycle at a comfortable temperature (21 ± 3°C) with free access to water and food in clean environment.

extract_protocol:
Mice on P45 were anesthetized with isoflurane followed with pentobarbital (20 mg/kg, i.p.) and intracardially perfused with ice-cold PBS. Brain slices were sectioned and ACC samples were manually dissected using a syringe needle on ice. Total RNA was immediately extracted from ACC tissue of one mouse by using the RNAeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
A total of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were construced using NEBNext®UltraTM RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations

treatment_protocol: Animals were assigned to either treatment or control groups and were injected intraperitoneally (i.p.) on P14 with LPS (Sigma, L-2880, 50 μg/kg) or pyrogen-free saline using an 0.3-ml insulin syringe (BD Corporation).

value: ACC

value: LPS

tag: developmental stage

value: post natal day 45


title: Lps2


title: NF_4_RV

value: Heart

tag: tissue region

value: NF


title: EMseq_lambda_DNA

data_processing:
Library strategy: EM-seq
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

organism: Lambdavirus lambda

source_name: NEB Catalog # N3011

extract_protocol:
The DNA was purchased from NEB (N3011) and methylated in vitro with M.SssI (NEB Catalog # M0226). The reaction was set up according to NEB’s protocol for methylation of genomic DNA with their suggested adjustments to push methylation to completion (4 hours at  37°C).
The library was generated with NEBNext Enzymatic Methyl-seq (EM-seq) (NEB Catalog # E7120), following manufacturer’s instructions.

tag: ecotype

value: bacteriophage Lambda


title: 1155


title: 21_PB_DLBCL

value: Dead


title: 1130


title: mouse_Myc_Gfi1

description:
mouse_myc_gfi1_model_cell_metadata.csv
mouse_myc_gfi1_model_raw_counts.csv.gz

extract_protocol:
Cerebellar stem/progenitor cells (Prominin1+ cells) were purified by fluorescence activated cell sorting (FACS) from the cerebella of postnatal day 5–7 (P5–P7) C57BL/6J pups as previously described 1-3. To generate MP or MG tumors, cells were infected with viruses produced from pMSCV-MycT58A-IRES-Luc and pMSCV-DNp53-IRES-GFP (for MP tumors) or pMSCV-GFI1-IRES-GFP (for MG tumors). After overnight infection, cells were washed and 10,000 cells were stereotaxically injected into the cerebellum of 6- to 8-week-old NSG mice. Animals were monitored weekly and euthanized when they showed signs of tumor. Tumors were then dissociated and resuspended in NeuroCult medium with proliferation supplement (STEMCELL Technologies) for scRNA sequencing analysis.    1. Pei, Y., et al. HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-Driven  Medulloblastoma. Cancer cell 29, 311-323 (2016).  2. Pei, Y., et al. An animal model of MYC-driven medulloblastoma. Cancer cell 21, 155-167  (2012).  3.Northcott, P.A., et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428-434 (2014).
3' end 10x Genomics library prep (v2 and v3)

value: GP3 tumor model (MYC + Gfi1)


title: Saline3

value: Saline


title: RNAseq_polyA_lib7_mbd56_rep3

data_processing:
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep kit (Zymo, R2052) with in column DNAse I digestion
1 microgram of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.

tag: genetic background

value: mbd5 mbd6 T-DNA

value: unopened flower bud


title: NF_3_RV

extract_protocol:
Frozen heart tissue samples were subjected to dry pulverization and RNA extraction was performed using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment (Qiagen) according to the manufacturer’s instructions.  Samples with ≥100 ng total RNA and RNA integrity numbers (RIN) ≥7 were used for sequencing.
After passing the QC, total RNA was used for cDNA library preparation using a modified protocol based on the Illumina Truseq RNA sample preparation kit and the published method for strand-specific RNA-Seq. cDNA libraries were sequenced by tthe HiSeq platform (Illumina).

value: Female

value: Right Ventricle

tag: race

tag: disease state


title: 1128

value: WNT


title: RNAseq_polyA_lib7_mbd56_rep2

tag: tissue


title: Saline2

tag: strain

tag: treatment


title: NF_2_RV

tag: gender

value: Hispanic


title: Saline1


title: NF_1_RV

value: Male


title: DLBCL, methylSeq_4

city: St. Louis

first: Jerry

last: Fong

state: MO

address: 4565 McKinley Ave

institute: Washington University School of Medicine

description: bisulfite treated gDNA

data_processing:
Sequencing reads were demultiplexed with Illumina Software
Reads were aligned to hg19 using BISCUIT (v0.3.8) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Processed methylation data (bed) was generated with the BISCUIT (v0.3.8 pipeline, pileup and vcf2bed commands). Data was collapsed per strand, and only CpG methylation data was considered. Format is tab delimited chr, start, end, fractional methylation, coverage.

source_name: lymph node

extract_protocol: Genomic DNA was isolated from each sample using the Zymo Quick-DNA Miniprep kit. Agilent Sure-Select Methyl-Seq was then conducted. Briefly, gDNA was sheared using a Covaris instrument at the recommended settings to an expected fragment size 150-200bp, as confirmed by 2% agarose gel. Samples underwent end-repair, poly-A tailing, and ligation of methylated adapters to facilitate capture enrichment. DNA was resuspended in nuclease-free water as recommended and underwent vacuum-concentration to a volume of <5ul. This methylated-adapter ligated DNA was then allowed to hybridize to the capture regions as per manufacturer recommendations. Next, bisulfite conversion was conducted on the input DNA at 64°C for 2.5 hr using the EZ DNA Methylation-Gold kit (Zymo), After conversion, libraries were PCR amplified and then indexed using provided indices in the Agilent Methyl-Seq kit. Samples were sequenced with an Illumina Hi-Seq3000 (2x150 paired-end reads).

value: DLBCL

tag: disease status

value: Diagnosis

tag: subtype

value: GCB

tag: clinical flow

tag: ihc

tag: FISH

value: Igh-BCL2 +, loss of one copy of 8q24


title: U2OS_siSET8_H4_t16_ChIP-seq

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
ChIP-seq reads were aligned to the mm10 or hg19 genome assemblies using bowtie version 1.1.2 (PMID: 19261174) and the settings -m 1 -S
Mapped reads were sorted using samtools version 1.10 (PMID: 19505943).
Sorted mapped reads were imported into EaSeq version 1.111 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: mm10; hg19
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

source_name: U2OS osteosarcoma cell line

growth_protocol: Both U2OS and MEF cell lines were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% Penicillin–Streptomycin. MEF cells were in addition supplemented with non-essential amino acids.

extract_protocol:
Cells were formaldehyde fixed and lysed in ice-Cold IP buffer and sonicated to an average length of 300 to 1000 bp fragments using Bioruptor bath-based sonicator. After checking for fragment size 500 µg of chromatin lysate was pre-cleared with 40 µl of Protein-A sepharose beads (BSA blocked) for 1 h and incubated overnight at 4ºC on rotation with 5 µg of primary ChIP-grade antibody. Blocked Protein-A sepharose beads were then added next day to the chromatin and  incubated at 4ºC on rotation for 3-4 h. Samples were subsequently washed and DNA was decrosslinked overnight and purified using Qiagen PCR purification columns.
Chipped DNA was quantified using Qubit dsDNA HS kit. Libraries were prepared from 5 ng of Chipped DNA using NEBNext Ultra II library preparation kit according to manusfacturer's protocol.

treatment_protocol: U2OS and MEF cells were treated with either scramble siRNA sequence or siRNA against SET8 according to mansufacturer's protocol.

value: U2OS osteosarcoma cell line

tag: sirna

tag: chip antibody

value: H4:Millipore; 06-1304

tag: cell cycle stage


title: RNAseq_polyA_lib7_mbd56_rep1


title: 1070

tag: tumor subgroup


title: Lps3

value: ACC

value: LPS

tag: developmental stage

value: post natal day 45


title: RNAseq_polyA_lib7_mbd6_rep3

tag: ecotype

tag: genetic background


title: DLBCL, methylSeq_3

description: bisulfite treated gDNA

tag: disease state

value: Region A low SS:CD3:82%, CD19:15%; Region B high SS:CD19 7%

value: CD20+, CD10 +, PAX5 +, BCL2 +, BCL 6 WEAK,


title: U2OS_siCtrl_H4_t16_ChIP-seq

tag: tissue

value: siCtrl


title: 1028


title: U2OS_siSET8_H4K20me1_t16_ChIP-seq

value: H4K20me1:abcam, ab9051


title: DLBCL, methylSeq_2

description: bisulfite treated gDNA

value: Relapse


title: RNAseq_polyA_lib7_mbd6_rep2

value: unopened flower bud


title: U2OS_siCtrl_H4K20me1_t16_ChIP-seq


title: 1066


title: DLBCL, methylSeq_1

description: bisulfite treated gDNA

extract_protocol:
Genomic DNA was isolated from each sample using the Zymo Quick-DNA Miniprep kit. Agilent Sure-Select Methyl-Seq was then conducted.
Briefly, gDNA was sheared using a Covaris instrument at the recommended settings to an expected fragment size 150-200bp, as confirmed by 2% agarose gel. Samples underwent end-repair, poly-A tailing, and ligation of methylated adapters to facilitate capture enrichment. DNA was resuspended in nuclease-free water as recommended and underwent vacuum-concentration to a volume of <5ul. This methylated-adapter ligated DNA was then allowed to hybridize to the capture regions as per manufacturer recommendations. Next, bisulfite conversion was conducted on the input DNA at 64°C for 2.5 hr using the EZ DNA Methylation-Gold kit (Zymo), After conversion, libraries were PCR amplified and then indexed using provided indices in the Agilent Methyl-Seq kit. Samples were sequenced with an Illumina Hi-Seq3000 (2x150 paired-end reads).

value: nonGCB - recurrent

value: REGION A small cells:CD3:63%; CD19:37%; Region B large cells:CD3:37%, CD19:68%

value: CD20 +, PAX5 +, MUM-1 +, BCL6 weak in a subset; CD10 -

value: BCL2, MYC, BCL6 -


title: RNAseq_polyA_lib7_mbd6_rep1


title: Silique walls from Short silique D3

city: Wuhan

first: Quaid

last: Hussain

address: Oil Crops Research Institute of CAAS,  No.2 Xudong Second Road, Wuchang, Wuhan, 430062, Hubei China

department: Crop Breeding and Genetics

institute: Student

data_processing:
The library was constructed using the Illumina TruseqTM RNA sample prep Kit method
1. Library enrichment, PCR amplification of 15 cycles;  2. 2% agarose gum recovery target strip (Certified Low Range Ultra Agarose);  3. TBS380 (Picogreen) quantitative, mixed based on the data;  4. Bridge PCR amplification on cBot to generate clusters;  5. IlluminaHiseq sequencing
The results of quantitative expression are expressed in FPKM. FPKM can eliminate the influence of gene length and sequencing difference on the calculation of gene expression, and the calculated gene expression can be directly used to compare between different samples.
Genome_build: Expression difference analysis     Use software: edgeR (http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html)Or deseq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html)  The software used for differential expression is edgeR, which is calculated based on the gene read count data, which is based on the negative binomial distribution. Model: In this project, the screening criteria for significant differentially expressed genes were: FDR< 0.05 & |log2FC| >= 1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of genes for each sample

organism: Brassica napus

source_name: Silique wall

extract_protocol:
The siliques were taken and quickly frozen in liquid nitrogen to collect RNA. The RNA-seq libraries were prepared using the Illumina TrueSeq RNA Sample Preparation Kit (Illunima Inc., San Diego, USA). The final cDNA libraries were sequenced using the Illumina Hiseq platform, which generated the raw reads.  Prep Kit for Illumina® and 3ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Lines from Association population

value: Silique wall

value: 15 days after flowering


title: U2OS_siSET8_H4_t8_ChIP-seq

value: U2OS osteosarcoma cell line

value: H4:Millipore; 06-1304


title: 966


title: 1125


title: RNAseq_polyA_lib7_mbd5_rep3


title: Silique walls from Short silique D2


title: RNAseq_polyA_lib7_mbd5_rep1


title: 996


title: 945


title: Silique walls from Short silique D1


title: RNAseq_polyA_lib7_mbd5_rep2


title: U2OS_siSET8_H4K20me1_t8_ChIP-seq


title: Silique walls from Long silique C3


title: RNAseq_polyA_lib7_wt_rep3

value: wild-type


title: U2OS_siCtrl_H4_t8_ChIP-seq


title: RNAseq_polyA_lib7_wt_rep2


title: U2OS_siSET8_H4_t0_ChIP-seq


title: 925


title: Silique walls from Long silique C2


title: RNAseq_polyA_lib7_wt_rep1


title: U2OS_siCtrl_H4_t0_ChIP-seq


title: 898

value: SHH


title: U2OS_siSET8_H4K20me3_t0_ChIP-seq

value: H4K20me3:abcam, ab9053


title: Silique walls from Long silique C1


title: BSseq_lib1_mbd56_rep1

source_name: inflorescence

extract_protocol:
DNA was extracted with DNeasy Plant Mini kit (Qiagen)
200ng of DNA per sample were sheared with the Covaris S2 instrument to an average fragment size of 200bp (Duty Cycle = 10%, Intensity = 5, Cycles per Burst = 200, Treatment Time = 120 seconds). A-tailing and adapter ligation was performed with the Kapa Hyper Prep Kit (KR0961) using Illumina methylated adapters (TruSeq DNA Sgl index Set A or B). Bisulfite conversion of the DNA was carried on with the EpiTect Bisulfite Kit (Qiagen). The conversion reaction in the thermocycler was performed twice to increase the efficiency. The converted library was PCR amplified using myTaq HS mix (Bioline) with 12 PCR cycles, purified with Ampure XP beads (Beckman Coulter) and sequenced.

value: inflorescence

value: mbd5 mbd6


title: U2OS_siSET8_H4K20me1_t0_ChIP-seq

value: H4K20me1:abcam, ab9051


title: U2OS_siCtrl_H4K20me1_t8_ChIP-seq

value: siCtrl


title: U2OS_siCtrl_H4K20me3_t0_ChIP-seq


title: 934-repeat


title: 801


title: 753


title: 877


title: U2OS_siCtrl_H4K20me1_t0_ChIP-seq


title: 831


title: 934


title: extracellular vesicles from MCF7BoM2_2

city: Winston-Salem

first: Kounosuke

last: Watabe

state: NC

address: 1 Medical Center Blvd

institute: Wake Forest University School of Medicine

description: Bone metastatic cell line selected in vivo

hyb_protocol: Samples were heated to 99 °C for 5 min followed by heating at 45 °C for another 5 min. After that, hybridization was performed at 48 °C, 60 RPM for 16h on an Affymetrix® 450 Fluidics Station. The  Genechips were then washed and stained using the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing: Raw data was extracted using the  Affymetrix GeneChip® Command Console® Software (AGCC). Data analysis was performed using Affymetrix® Expression Console™ software.

source_name: human breast cancer cell line MCF7BoM2

label_protocol: Biotinylated RNA were prepared using the FlashTag™ Biotin RNA Labeling Kit.

growth_protocol: Cells were maintained at 37°C, 95% Air, 5% CO2,  with Eagle's Minimum Essential Medium (0.01 mg/ml human recombinant insulin and 10% fetal bovine serum).

extract_protocol: Total RNA was isolated by miRNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Cells were grown in extracellular vesicles-depleted media for 48 h before conditioned media were collected for extracellular vesicles purification.

value: Breast; Mammary gland

tag: cell line

value: Bone metastatic cell line derived from MCF7

tag: rna population

value: extracellular vesicle miRNA


title: BSseq_lib1_Col0_rep1


title: extracellular vesicles from MCF7_2

description: Parental cell line

source_name: human breast cancer cell line MCF7


title: extracellular vesicles from MCF7BoM2_1


title: extracellular vesicles from MCF7_1

description: Parental cell line


title: Nix-/-Bnip3-/- memory B cell replicate 1

status: Public on Jun 03 2021

city: Houston

first: Jin

last: Wang

address: 6670 Bertner Avenue

department: Immunobiology and Transplant Science

institute: Houston Methodist Research Institute

data_processing:
Illumina CASAVA software was used by Novogene Corp. for base calling
Sequenced reads were filtered to remove adaptor or low-complexity/low-quality sequences, then mapped to mm10 whole genome using STAR alignment tool by Novogene Corp.
Read counts and FPKM values for all genes and samples were calculated by Novogene Corp.
EdgeR software package in R (version 3.6.3) was used to determine differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for every gene and sample

source_name: Memory B cells

extract_protocol:
Splenocytes were isolated then stained with antibodies required for FACS. RNA from sorted cells was obtained using QIAseq FX Single Cell RNA Library Kit.
QIAseq FX Single Cell RNA Library Kit (QIAGEN) was used to extract RNA from ~1000 sorted NP-specific WT and DKO memory B cells and prepare cDNA libraries enriched for polyadenylated RNAs, according to manufacturer’s instructions. Library cleanup was performed using GeneRead Size Selection Kit (QIAGEN).

value: Spleen

tag: cell type

value: Memory B cell

tag: genotype/variation


title: Wild-type memory B cell replicate 3

value: wild type


title: Nix-/-Bnip3-/- memory B cell replicate 3


title: Wild-type memory B cell replicate 1


title: Nix-/-Bnip3-/- memory B cell replicate 2


title: Wild-type memory B cell replicate 2


title: BSseq_lib1_mbd56_rep2

first: Lucia

last: Ichino

institute: University of California, Los Angeles


title: BSseq_lib1_Col0_rep2


title: MEF +IdU Day2 Rep 2

city: San Francisco

first: Xinyue

last: Chen

state: California

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
For scRNA-seq, sequencing reads were aligned to mm10 reference genome using 10x Cell Ranger v2.
For mESC bulk RNA-seq, reads were aligned to an edited version of the mm10 reference genome containing the ERCC spike-in sequences using TopHat with default parameters. Transcript level quantification was performed using Cufflinks with default parameters.
For MEF bulk RNA-seq, sequencing reads were aligned to the mm10 reference genome using TopHat with default parameters. Transcript level quantification was performed using Cufflinks with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Qutifications generted from 10x Cell Ranger V2 for single-cell RNA-seq data
Supplementary_files_format_and_content: Matrix tables for every gene and every sample for bulk RNA-seq data

source_name: fibroblasts from embryos

growth_protocol: Mouse E14 embryonic stem cells (male) were cultured in feeder-free conditions on gelatin-coated plates with ESGRO-2i medium (Millipore, cat:SF016-200) at 37°C, 5% CO2, in humidified conditions.

extract_protocol:
For scRNA-seq, cells were trypsinized with TrypLE and spun down for 5 minutes at 200 x g. Single-cell suspensions were prepared in DPBS at a concentration of 83,000 cells/ml. Approximately 3000 cells from each sample were loaded into a chip and processed with the Chromium Single Cell Controller (10x Genomics).
For mESC bulk RNA-seq, cells were trypsinized with TrypLE and RNA was extracted using a RNeasy minikit (Qiagen) according to manufacturer’s instructions. ERCC spike-in RNA (2ml diluted at 1:100) was added to each RNA extraction (Ambion, cat:4456740).
For MEF bulk RNA-seq, RNA was extracted from frozen cell pellet using a RNeasy minikit (Qiagen) according to manufacturer’s instructions.
To generate single-cell gel beads in emulsion (GEMs), samples were assigned unique indexes using Single Cell 3’ Library and Gel Bead Kit V2 (10x Genomics, cat:120237). Sequencing was performed on an Illumina for 10x libraries.
For bulk RNA-seq, cDNA libraries were prepared with an NEBNext Ultra II RNA Library Prep kit (NEB, cat:E7770S) and sequenced with an Illumina HiSeq4000.

treatment_protocol: Cells were treated with indicated concentrations of IdU or an equivalent volume of DMSO control.

value: mouse embryonic fibroblasts

tag: treatment

value: 4uM IdU

value: 1ug/ml doxycycline for reprogramming


title: MEF +DMSO Day5 Rep 1

value: DMSO control


title: MEF +DMSO Day2 Rep 2


title: MEF +DMSO Day5 Rep 2


title: mESC +10uM IdU Bulk Rep 2

source_name: embryonic stem cells

value: mouse embryonic stem cells

value: 10uM IdU


title: mESC +DMSO Bulk Rep 1


title: mESC +5uM IdU Bulk Rep 2

value: 5uM IdU


title: mESC +10uM IdU Bulk Rep 1


title: mESC +5uM IdU Bulk Rep 3


title: mESC +10uM IdU Bulk Rep 3


title: mESC +5uM IdU Bulk Rep 1


title: mESC +DMSO Bulk Rep 3


title: MEF +IdU Day5 Rep 2

value: 4uM IdU for 2 days


title: scRNA-seq mESC +IdU


title: 5xFAD+T+Ts+_Contralateral

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

description:
Heterozygous F+/T+ offspring of the cross of hemizygous 5xFAD mice overexpressing mutant human APP695 carrying EOFAD mutations K670N/M671L (Swedish), I716V (Florida), V717I (London) and mutant human PS1 harboring 2 EOFAD mutations (M146L and L286V) driven by the thymocyte differentiation antigen 1 (ThyI) promoter (F+ mice), and hemizygous Tau P301S transgenic mice (PS19), expressing human Tau-P301S (1N4R) driven by the mouse prion protein promoter (T+ mice).
metadata_Merge_WT_5xFAD_5xFADTTsIpsilateral_5xFADTTsContralateral.csv

data_processing:
Raw data bcl files were first demultiplexed using Cellranger mkfastq
Demultiplexed data was then processed using the Cellranger count pipeline
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) for each sample and annotation metadata with information per cell

source_name: CD45+ cells

extract_protocol:
Processing and tissue-collection of whole brain was performed as previously described (Van Hove et al., 2019, doi: https://doi.org/10.1038/s41593-019-0393-4; Shemer et al., 2020, doi: https://doi.org/10.1016/j.immuni.2020.09.018, Kim et al., 2021, doi: https://doi.org/10.1016/j.immuni.2020.11.007). From these tissue samples, CD45+ FACS sorted immune cells were loaded on a Chromium Chip B (10x Genomics, No.1000074), or Chip G (10x Genomics, No. 2000177) on a GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). GEMs  were prepared using the GemCode Single Cell 3’ Gel Bead according to the manufacturer’s instructions. Briefly, GEM reverse-transcription incubation was performed in a 96-deep-well reaction module at 53°C for 45 min, 85°C for 5 min and ending at 4°C. Next, GEMs were broken and complementary DNA (cDNA) was cleaned up with DynaBeads MyOne Silane Beads (10x Genomics, No. 2000048) and SPRIselect Reagent Kit (Beckman Coulter, No. B23318). Full-length, barcoded cDNA was PCR amplified with a 96-deep-well reaction module at 98°C for 3 min, eleven cycles at 98°C for 15 s, 63°C for 20 s and 72°C for 1 min, followed by one cycle at 72°C for 1 min and ending at 4°C.
Following cleaning up with the SPRIselect Reagent Kit and enzymatic fragmentation, library construction to generate Illumina-ready sequencing libraries was performed using the Library Kit (v3 and v3.1, 10xGenomics, No. 1000075) and the Chromium i7 Multiplex Kit (10x Genomics, No. 120262), according to the manufacturer's instructions. R1 (read 1 primer), P5, P7, i7 sample index and R2 (read 2 primer sequence) were added via end-repair, A-tailing, adapter ligation, post-ligation SPRIselect cleanup/size selection and sample index PCR. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent).

treatment_protocol: Seven-month-old mice, 4 mice per condition (4 WT control mice (F-/T-), 4 5xFAD mice (F+/T-) and 4 Tau-seeded 5xFAD/PS19 Tau transgenic mice (F+/T+) 3 months post injection), were sacrificed for brain isolation and single-cell processing. For single cell experiments related to PLX3397 treatment, 2 mice per condition were used (2 tau-seeded 5xFAD/PS19 tau transgenic mice (F+/T+) which received PLX3397 chow 1.5 months after tau-seeding for 1.5 months, and 2 tau-seeded 5xFAD/PS19 tau transgenic mice (F+/T+) which received control chow 1.5 months after tau-seeding for 1.5 months).

tag: genotype

value: 5xFADxPS19 heterozygous (F+/T+) transgenic

value: whole brain CD45+ cells


title: 5xFAD T+ Ts PLX treatment

description:
Heterozygous F+/T+ offspring of the cross of hemizygous 5xFAD mice overexpressing mutant human APP695 carrying EOFAD mutations K670N/M671L (Swedish), I716V (Florida), V717I (London) and mutant human PS1 harboring 2 EOFAD mutations (M146L and L286V) driven by the thymocyte differentiation antigen 1 (ThyI) promoter (F+ mice), and hemizygous Tau P301S transgenic mice (PS19), expressing human Tau-P301S (1N4R) driven by the mouse prion protein promoter (T+ mice).
metadata_Merge_5xFADTTsPLX_5xFADTTsCTRL.csv


title: 5xFAD+T+Ts+_Ipsilateral


title: 5xFAD+ T- Ts-

description:
5xFAD transgenic offspring (F+) of the cross of hemizygous 5xFAD mice overexpressing mutant human APP695 carrying EOFAD mutations K670N/M671L (Swedish), I716V (Florida), V717I (London) and mutant human PS1 harboring 2 EOFAD mutations (M146L and L286V) driven by the thymocyte differentiation antigen 1 (ThyI) promoter (F+ mice), and hemizygous Tau P301S transgenic mice (PS19), expressing human Tau-P301S (1N4R) driven by the mouse prion protein promoter (T+ mice).
metadata_Merge_WT_5xFAD_5xFADTTsIpsilateral_5xFADTTsContralateral.csv

value: 5xFAD hemizygous (F+) transgenic


title: WT 5xFAD-T-Ts-

description:
Non-transgenic (WT) offspring of the cross of hemizygous 5xFAD mice overexpressing mutant human APP695 carrying EOFAD mutations K670N/M671L (Swedish), I716V (Florida), V717I (London) and mutant human PS1 harboring 2 EOFAD mutations (M146L and L286V) driven by the thymocyte differentiation antigen 1 (ThyI) promoter (F+ mice), and hemizygous Tau P301S transgenic mice (PS19), expressing human Tau-P301S (1N4R) driven by the mouse prion protein promoter (T+ mice).
metadata_Merge_WT_5xFAD_5xFADTTsIpsilateral_5xFADTTsContralateral.csv

value: WT non-transgenic


title: MEF +IdU Day2 Rep 1


title: mESC +DMSO Bulk Rep 2


title: MEF +DMSO Day2 Rep 1


title: scRNA-seq mESC +DMSO


title: MEF +IdU Day5 Rep 1