title: snRNA-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 4, Replicate 2

city: Philadelphia

first: Sheridan

middle: Hope

last: Littleton

state: PA

address: 3615 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
.fastq files were generated with Cell Ranger ARC version 2.0.2 -mkfastq
.fastq files were aligned to GRCh38 and cells were called using Cell Ranger ARC version 2.0.2 with parameters -count --min-atac-count=2000 --min-gex-count=1000
Cells underwent quality control with SoupX version 1.6.2, Scrublet version 0.2.3 and Seurat version 4.3.0
Samples were integrated with SCTransform version 0.3.5 and then Harmony version 0.1.1 was used for batch correction
Assembly: GRCh38
Supplementary files format and content: barcode.tsv contains 10X barcodes used to identify cells, features.tsv contains Ensembl IDs and gene symbols, matrix.tx contains read counts for all cells

molecule: nuclear RNA

source_name: Hypothalamic cells

extract_protocol:
Nuclei were isolated from each sample following 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression protocols
Libraries were prepared following the 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression workflow, according to manufacturer's instructions.

value: Hypothalamic cells

tag: genetic modification

value: Female


title: NS+ esophageal tumor 14

status: Public on Mar 29 2024

type: RNA

city: Hyderabad

first: Murali

middle: Dharan

last: Bashyam

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description: NS+ esophageal squamous cell carcinoma 14

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization

molecule: total RNA

organism: Homo sapiens

source_name: Surgically resected esophagus

label_protocol: 2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled RNA from 11 cell lines (Bashyam et al., 2005) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Sex

value: M

tag: age

tag: tissue

value: Esophageal Squamous Cell Carcinoma

tag: Stage

tag: grade

value: I

tag: p53 status

value: nuclear-stabilized p53 (NS+)

source_name: pooled 11 cell line

tag: sample type

value: Universal reference RNA


title: CCA147, YF-17D vaccination, day 28, rep 1

type: SRA

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

country: France

institute: Sanofi

library_source: transcriptomic

data_processing:
A read quality check was performed on raw data in FASTQ format using FastQC (v0.11.2).
Reads were imported and then processed in OmicSoft Array Studio software (v9.0.6.38-v9.0.8.28).
The raw data QC wizard of Array Studio was executed on the reads to assess the read quality.
The reads were aligned with OmicsSoft Aligner (OSA4; (53)) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations, including a first step of read trim per quality score (minimum of 2).
Samples (CCB102J-21, CCA100J1, CCB102J1, CCA100J14, CCA100J-21, CA100J7, CCA100J3, CCB102J3, CCA100J28) that did not meet quality criteria based on the minimal number of reads sequenced underwent a second run, and files were merged after read alignment, i.e. at the BAM file level.
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations (In Array Studio, “Naïve” means that no EM algorithm was used to handle ambiguous reads). Multiple mapping reads and first-read-forward-strand reads were discarded from the analysis (i.e. “Exclude multi-reads” option selected, “Count First-Read-Forward-Strand reads” option unselected).
Assembly: Cyno.WashU2013
Supplementary files format and content: raw_counts.txt raw counts per sample and gene (WashUGene20140620 gene annotations)
Supplementary files format and content: Count_Annotation.txt (annotation file from OmicSoft, https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA46N0000008OqZSAU&categoryName=OmicSoft_Suite)

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Whole blood

extract_protocol:
Whole blood from cynomolgus macaques was collected in PAXgene tubes (BD762165 –Ozyme), and stored according to the manufacturer's protocol. RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation. The RNA quantity, purity and quality were checked on the Labchip (Caliper) and the Nanodrop Spectrophotometer (Thermo Scientific).
Extracted RNA samples with an A260/A280 ratio ~2, a RIN>8 and a minimal concentration of 70ng/µL of RNA were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. The quantity, purity and quality of the RNA depleted of globin mRNA was reassessed as already described before library preparation for sequencing. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300ng of RNA according to manufacturer’s instructions. The quality, length distribution and quantity of the resulting libraries were analyzed with the Qubit 3.0 Fluorometer (Life Technologies) and the Labchip (Caliper). Libraries were pooled at equimolar amounts and sequenced by single reads of 75bp on high-output flowcell (Illumina – FC-404-2005) using the Nextseq500 sequencer (Illumina) in a batch of 10 samples per flowcell with the specification to achieve 30 million reads per sample. On run completion, libraries were demultiplexed, adapters trimmed and FASTQ files generated.

treatment_protocol: Live, attenuated YF-17D-204 vaccine (monodose Stamaril®, Sanofi)

value: Whole blood

tag: animal id

tag: treatment

value: YF-17D Vaccination

tag: time

value: day 28

value: male


title: NS+ esophageal tumor 13

description: NS+ esophageal squamous cell carcinoma 13


title: snRNA-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 4, Replicate 1

country: USA

library_source: transcriptomic single cell

tag: cell type


title: NS- esophageal tumor 9

description: NS- esophageal squamous cell carcinoma 9

value: II

value: unstable p53 (NS-)


title: NS+ esophageal tumor 10

description: NS+ esophageal squamous cell carcinoma 10

value: F


title: CCA147, YF-17D vaccination, day -21, rep 1

value: day -21


title: Trim28_Heavy_rep12

type: genomic

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged on the iScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v.2011.1 and SeSAMe
single_signal_supp.txt = Unmethylated and methylated signal intensities
processed_matrix.txt = Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: genomic DNA from lungs

label_protocol: Standard Illumina Infinium HD Assay Methylation Protocol document #15019519 v01

growth_protocol: Curls from FFPE healthy tissues

extract_protocol: We used the Quick-DNA/RNA™ FFPE Kit (Zymo) for DNA extraction

treatment_protocol: Deparaffinization according to Quick-DNA/RNA™ FFPE Kit (Zymo)

value: lungs

tag: batch


title: snRNA-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 2, Replicate 1


title: VFDM_V_1

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the mouse genome mm10 with STAR (version 2.7.10a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10), filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”) and reducing the minimum of read mapping length to 0.4 (outFilterScoreMinOverLread=0.4 and outFilterMatchNminOverLread=0.4) . The mm10 genome reference was supplemented with CreERT2, induceable Homo_sapiens_JAK2_V617F construct and pEGFP sequences.
All subsequent analyses were performed using the R software (version 4.3.0) and Bioconductor 3.18 packages. The featureCounts function from the Bioconductor Rsubread package (version 2.0.6) was used to count the number of reads overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model
Assembly: mm10
Supplementary files format and content: gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq raw read counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: column 1. = gene Ensembl ID, column 2.-32.= read counts per gene and sample. Counts on the CreERT2, pEGFP and Homo_sapiens_JAK2_V617F construct (exons 3 to 12 and exons 13 to 25 separately) are listed at the end of the file

source_name: Bone marrow

growth_protocol: Mice were kept in the animal facility of the University of Basel according to the swiss animal welfare regulations. Bone marrow cells were isolated and sorted immediately after sacrifice.

extract_protocol:
PicoPure RNA isolation kit (ThermoFisher) was used to extract RNA. Cells were directly sorted into the extraction buffer provided with the kit, and the isolation was performed according to the manual.
Stranded RNA-seq libraries were prepared using the kit Takara SMART-Seq Stranded

treatment_protocol: Mice were treated for 8 weeks with pegylated-interferon-alpha (25 ug/kg SC weekly), 5-Azacytidine (2 mg/kg, IP QD) or the combination of both drugs (same dose as treatments alone).

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

tag: genotype

value: Vehicle (V)


title: NS- esophageal tumor 12

description: NS- esophageal squamous cell carcinoma 12

value: M


title: snRNA-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 1, Replicate 1

value: Hypothalamic cells

value: Female


title: CCA147, YF-17D vaccination, day 7, rep 1

value: day 7


title: VFDM_V_2

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: CCA147, YF-17D vaccination, day 14, rep 1

value: day 14


title: CCA147, YF-17D vaccination, day 1, rep 1

value: Whole blood

value: day 1


title: snRNA-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 3, Replicate 1


title: VF_COMBO_3

description: SclCre;FF1;GFP (VF)

value: SclCre;FF1;GFP (VF)

value: pegylated-interferon-alpha + 5-Azacytidine (IFN+Aza)


title: NS- esophageal tumor 7

description: NS- esophageal squamous cell carcinoma 7

value: Esophageal Squamous Cell Carcinoma

value: II

value: Universal reference RNA


title: VFDM_V_3

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: NS- esophageal tumor 5

description: NS- esophageal squamous cell carcinoma 5

value: F

value: I

value: unstable p53 (NS-)


title: snRNA-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 1, Replicate 3


title: CCB112, YF-17D vaccination, day 3, rep 1

value: YF-17D Vaccination

value: day 3

value: male


title: VF_COMBO_2

description: SclCre;FF1;GFP (VF)

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)


title: VF_COMBO_1

description: SclCre;FF1;GFP (VF)


title: CCB112, YF-17D vaccination, day -21, rep 1

value: day -21


title: CCB112, YF-17D vaccination, day 1, rep 1


title: snRNA-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 1, Replicate 2

value: Hypothalamic cells

value: Female


title: snRNA-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 1, Replicate 1


title: NS- esophageal tumor 8

description: NS- esophageal squamous cell carcinoma 8

value: M


title: VF_COMBO_4

description: SclCre;FF1;GFP (VF)

value: SclCre;FF1;GFP (VF)


title: VF_AZA_4

description: SclCre;FF1;GFP (VF)

value: 5-Azacytidine (Aza)


title: CCB106, YF-17D vaccination, day 7, rep 1

value: Whole blood

value: day 7


title: VF_AZA_3

description: SclCre;FF1;GFP (VF)


title: CCB106, YF-17D vaccination, day 3, rep 1


title: snATAC-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 4, Replicate 2

library_source: genomic

data_processing:
.fastq files were generated with Cell Ranger ARC version 2.0.2 -mkfastq
.fastq files were aligned to GRCh38 and cells were called using Cell Ranger ARC version 2.0.2 with parameters -count --min-atac-count=2000 --min-gex-count=1000
Cells underwent quality control with SoupX version 1.6.2, Scrublet version 0.2.3 and Seurat version 4.3.0
Samples were integrated with SCTransform version 0.3.5 and then Harmony version 0.1.1 was used for batch correction
Assembly: GRCh38
Supplementary files format and content: barcode.tsv contains 10X barcodes used to identify cells, features.tsv contains peak location, matrix.tx contains read counts for all cells


title: NS- esophageal tumor 1

description: NS- esophageal squamous cell carcinoma 1

value: Esophageal Squamous Cell Carcinoma

value: Universal reference RNA


title: NS- esophageal tumor 6

description: NS- esophageal squamous cell carcinoma 6

value: I


title: snATAC-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 2, Replicate 1


title: NS- esophageal tumor 3

description: NS- esophageal squamous cell carcinoma 3

value: F

value: unstable p53 (NS-)


title: VF_AZA_2

description: SclCre;FF1;GFP (VF)


title: VF_AZA_1

description: SclCre;FF1;GFP (VF)


title: CCB106, YF-17D vaccination, day 28, rep 1

value: YF-17D Vaccination

value: day 28


title: NS- esophageal tumor 2

description: NS- esophageal squamous cell carcinoma 2


title: snATAC-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 1, Replicate 1


title: CCB106, YF-17D vaccination, day -21, rep 1

value: male


title: WT_IEL

city: Aurora

first: Kristine

middle: A

last: Kuhn

state: Colorado

address: 1775 Aurora Ct. Mail Stop B115

department: Medicine

institute: University of Colorado School of Medicine

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.4.0.38

label: biotin

label_protocol: standard affymetrix protocol

extract_protocol: RNA extraction was done using Trizol.

tag: strain

value: 8-10 week

value: intraepithelial lymphocyte (IEL)


title: Recolonized

source_name: Recolonized


title: FT43_ldcA_24h

city: Madison

first: Joseph

last: Dillard

state: WI

institute: University of Wisconsin-Madison

description:
biological replicate of sample 15
24h_genes_TPM_table.txt

data_processing:
Sequencing reads were trimmed to remove sequencing adaptors and low quality bases using Skewer
After trimmming, reads were aligned to the annotated human reference genome using the alignment tool STAR(v2.4.0j for 6h samples, v2.4.2a for 24h samples)
Quantification of expression for each gene was calculated by RSEM (v1.2.16 for 6h samples, v.1.2.22 for 24h samples)
The expected read counts were used to determine differential gene expression using EBSeq (v1.1.5)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Fallopian tube

growth_protocol: Fallopian tube samples were cultured  in Eagles Minimal Essential Medium (MEM) (Cellgro) buffered with 1M HEPES to pH 7.4 and penicillin-streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
Stranded cDNA libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit (Illumina).

value: Fallopian tube

tag: donor number

value: ldcA mutant supernatant

value: 24 hour


title: snATAC-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 3, Replicate 1

value: Hypothalamic cells

value: Female


title: FT43_WT_24h

description:
biological replicate of sample 14
24h_genes_TPM_table.txt

value: WT supernatant


title: NS- esophageal tumor 4

description: NS- esophageal squamous cell carcinoma 4


title: VF_IFN_4

description: SclCre;FF1;GFP (VF)

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

value: SclCre;FF1;GFP (VF)

value: pegylated-interferon-alpha (IFN)


title: VF_IFN_3

description: SclCre;FF1;GFP (VF)


title: CCB106, YF-17D vaccination, day 1, rep 1

value: Whole blood

value: day 1


title: snATAC-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 4, Replicate 1


title: VF_IFN_2

description: SclCre;FF1;GFP (VF)


title: FT43_mock_24h

description:
biological replicate of sample 13
24h_genes_TPM_table.txt

value: mock


title: snATAC-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 1, Replicate 2


title: snATAC-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 1, Replicate 3


title: CCB105, YF-17D vaccination, day 3, rep 1

value: YF-17D Vaccination

value: day 3


title: CCB105, YF-17D vaccination, day 7, rep 1

value: day 7

value: male


title: FT40_ldcA_24h

value: Fallopian tube


title: VF_IFN_1

description: SclCre;FF1;GFP (VF)


title: VF_V_4

description: SclCre;FF1;GFP (VF)

value: Vehicle (V)


title: FT40_mock_24h

value: 24 hour


title: HiC Primary Astrocyte, Replicate 2

data_processing:
bcl2fastq2 version 2.20 was used to generate FASTQ files
Reads were processed using the HiCUP pipeline version 0.7.4 and aligned to GRCh38 with bowtie2 version 2.2.6
Alignment files were processed with pairtools version 0.3.0 and indexed and compressed with pairix version 0.3.7
Alignment files were converted to .cool by cooler version 0.8.11 and normalized with the ICE method
Significant intra-chromosomal interaction loops from merged replicates were called with Mustache version 1.0.1 and Fit-Hi-C2 version 2.0.7
Assembly: GRCh38
Supplementary files format and content: bigbed file includes significant intra-chromosal interaction loops

source_name: Lonza NHA

extract_protocol:
Cells were fixed with formaldehyde, then chromatin was digested with multiple restriction enzymes, and DNA was sheared and then size-selected for 200-600 bp fragments
Libraries were prepared using the Arima-HiC, Swift Accel-NGS 2S Plus DNA, and Swift 2S Indexing kit, according to manufacturer's instructions.

tag: cell line

value: Lonza NHA


title: CCB105, YF-17D vaccination, day 28, rep 1

value: day 28


title: LP

source_name: LP

value: 8-10 week

value: lamina propria

value: T cells


title: VF_V_3

description: SclCre;FF1;GFP (VF)

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

value: SclCre;FF1;GFP (VF)


title: CCB106, YF-17D vaccination, day 14, rep 1

value: Whole blood

value: day 14


title: SI_IEL

value: small intestine epithelium

value: intraepithelial lymphocyte (IEL)


title: HiC Primary Astrocyte, Replicate 1


title: CCB105, YF-17D vaccination, day -21, rep 1

value: YF-17D Vaccination

value: day -21


title: FT37_ldcA_24h

value: Fallopian tube

value: ldcA mutant supernatant


title: VF_V_2

description: SclCre;FF1;GFP (VF)

value: Vehicle (V)


title: ATAC-Seq Primary Astrocyte, Replicate 3

description: Primary Astrocyte, Replicate 3

data_processing:
bcl2fastq2 version 2.20
Reads were aligned to GRCh38 with bowtie2 version 2.2.6
Duplicate reads were removed using Picard version 2.7.1 and SAMtools version 1.7
Narrow peaks were called independently for each replicate using MACS2 version 2.1.1
Peaks called in at least 2 replicates were used to generate a consensus set of peaks
Signal peaks were normalized with csaw version 1.32.0
Peaks with counts per million > 1 were used to test for differential accessibility is ESCs due to rs7132908 genotype with edgeR version 3.40.2
Assembly: GRCh38
Supplementary files format and content: bigwig files include peak data merged for each experimental condition

extract_protocol:
Nuclei were isolated from each cell type and transposed using the Illumina Tagment DNA TDE1 Enzyme and Buffer kit, according to manufacturer's instructions
Libraries were prepared using the Nextera DNA CD Indexes kit, according to manufacturer's instructions.

value: Lonza NHA


title: CCB105, YF-17D vaccination, day 14, rep 1

value: male


title: FT37_WT_24h

value: WT supernatant

value: 24 hour


title: FT37_mock_24h

value: mock


title: CCB105, YF-17D vaccination, day 1, rep 1

value: day 1


title: VF_V_1

description: SclCre;FF1;GFP (VF)

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)


title: CCB102, YF-17D vaccination, day 7, rep 1

value: Whole blood

value: day 7


title: wildtype mTECs, Ribo, replicate novaseq C, ALID03

city: San Francisco

first: Semil

last: Choksi

email: semilc@gmail.com, semil.choksi@ucsf.edu

state: CA

address: 555 Mission Bay Blvd. South

institute: UCSF

description:
10x Genomics
RiboC_barcodes.tsv.gz
RiboC_features.tsv.gz
RiboC_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: counts and metadata for integrated dataset

source_name: mouse tracheal epithelial cells cultured at air-liquid interface

growth_protocol: Mouse tracheal epithelial cells (mTECs) were purified and cultured as previously described (You and Brody, 2013).

extract_protocol:
To generate single-cell suspensions for mTEC scRNA-seq, mTECs derived from wild-type Bl6  mice  Cells were cultured for six days submerged before initiating air/liquid interface. Ribociclib, resuspended in DMSO, was added to a final concentration of 10 uM in mTEC NS media at 1 day post air/liquid interface. Cells were collected at 3 days post air/liquid interface for scRNA-seq analysis.. Collection involved washing mTECs with PBS three times both apically and basally, incubating in 0.05% Trypsin-EDTA in Cell Dissociation Buffer (Gibco, Cat #13151014) added both apically and basally at 37°C for 15 min, gentle trituration, and inactivating trypsin in mTEC Basic with 2% Nu-Serum (Corning, Cat #355100). Additional 0.05% Trypsin-EDTA in Cell Dissociation Buffer was added to the apical surface and incubated at 37°C for 5 min. Cells were washed and resuspended in 0.04% BSA in PBS at 1000 cells/uL.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, 16,000 mTECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: wild-type

value: 10 uM Ribo


title: snATAC-Seq Hypothalamic Cells, rs7132908 GG, Differentiation 1, Replicate 1

value: Hypothalamic cells

value: Female


title: FT24_ldcA_24h

value: Fallopian tube


title: ATAC-Seq Primary Astrocyte, Replicate 1

description: Primary Astrocyte, Replicate 1


title: wildtype mTECs, Ribo, replicate novaseq B, ALID03

description:
10x Genomics
RiboB_barcodes.tsv.gz
RiboB_features.tsv.gz
RiboB_matrix.mtx.gz

value: mouse tracheal epithelial cells cultured at air-liquid interface


title: FT40_WT_24h


title: ATAC-Seq H9 ESC, rs7132908 AA Clone 10.1

description: H9 ESC, rs7132908 AA Clone 10.1

value: Embryonic stem cell

tag: genetic modification


title: CCB102, YF-17D vaccination, day 28, rep 1

value: YF-17D Vaccination

value: day 28

tag: Sex


title: FT24_mock_24h


title: wildtype mTECs, Ribo, replicate novaseq A, ALID03

description:
10x Genomics
RiboA_barcodes.tsv.gz
RiboA_features.tsv.gz
RiboA_matrix.mtx.gz


title: ATAC-Seq H9 ESC, rs7132908 AA Clone 9.1

description: H9 ESC, rs7132908 AA Clone 9.1


title: FT33_ldcA_6h

description:
biological replicate of sample 3
6h_genes_TPM_table.txt

value: ldcA mutant supernatant

value: 6 hour


title: CCB102, YF-17D vaccination, day 14, rep 1

value: day 14

value: male


title: wildtype mTECs, DMSO, replicate novaseq C, ALID03

description:
10x Genomics
DMSOC_barcodes.tsv.gz
DMSOC_features.tsv.gz
DMSOC_matrix.mtx.gz

value: DMSO


title: CCL052, YF-17D vaccination, day 28, rep 1


title: wildtype mTECs, DMSO, replicate novaseq B, ALID03

description:
10x Genomics
DMSOB_barcodes.tsv.gz
DMSOB_features.tsv.gz
DMSOB_matrix.mtx.gz


title: ATAC-Seq H9 ESC, rs7132908 AA Clone 2.1

description: H9 ESC, rs7132908 AA Clone 2.1


title: CCL052, YF-17D vaccination, day 7, rep 1


title: FT33_WT_6h

description:
biological replicate of sample 2
6h_genes_TPM_table.txt

value: WT supernatant


title: ATAC-Seq H9 ESC, rs7132908 GG, Replicate 3

description: H9 ESC, rs7132908 GG, Replicate 3


title: ATAC-Seq Primary Astrocyte, Replicate 2

description: Primary Astrocyte, Replicate 2

value: Lonza NHA


title: ATAC-Seq H9 ESC, rs7132908 GG, Replicate 2

description: H9 ESC, rs7132908 GG, Replicate 2


title: CCB072, YF-17D vaccination, day 7, rep 1

value: Whole blood

value: day 7


title: FT33_mock_6h

description:
biological replicate of sample 1
6h_genes_TPM_table.txt

value: mock


title: CCL052, YF-17D vaccination, day 14, rep 1


title: ATAC-Seq H9 ESC, rs7132908 GG, Replicate 1

description: H9 ESC, rs7132908 GG, Replicate 1


title: FT24_WT_24h

value: 24 hour


title: wildtype mTECs, ALID36

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: counts and metadata for integrated dataset

extract_protocol:
For the transcriptional time course, cells were collected on day one, three, nine, and thirty-six at air/liquid interface. Collection involved washing mTECs with PBS three times both apically and basally, incubating in 0.05% Trypsin-EDTA in Cell Dissociation Buffer (Gibco, Cat #13151014) added both apically and basally at 37°C for 15 min, gentle trituration, and inactivating trypsin in mTEC Basic with 2% Nu-Serum (Corning, Cat #355100). Additional 0.05% Trypsin-EDTA in Cell Dissociation Buffer was added to the apical surface and incubated at 37°C for 5 min. Cells were washed and resuspended in 0.04% BSA in PBS at 1000 cells/L.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, 10,000 (ALID01) or 25,000 (ALID03, ALID09, ALID36)  mTECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: 9 days


title: wildtype mTECs, DMSO, replicate novaseq A, ALID03

description:
10x Genomics
DMSOA_barcodes.tsv.gz
DMSOA_features.tsv.gz
DMSOA_matrix.mtx.gz

value: wild-type


title: NS+ esophageal tumor 16

description: NS+ esophageal squamous cell carcinoma 16

value: F

tag: age

value: Esophageal Squamous Cell Carcinoma

value: II

value: nuclear-stabilized p53 (NS+)

value: Universal reference RNA


title: CCB072, YF-17D vaccination, day 3, rep 1

tag: tissue

value: YF-17D Vaccination

value: day 3


title: FT32_WT_6h

value: Fallopian tube

value: 6 hour


title: FT32_ldcA_6h

value: ldcA mutant supernatant


title: wildtype mTECs, ALID09

description: 10x Genomics

value: mouse tracheal epithelial cells cultured at air-liquid interface

value: 6 days


title: Primary Astrocyte, Replicate 3

data_processing:
bcl2fastq2 version 2.20
Reads were aligned to GRCh38 with STAR version 2.7.9a (primary astrocytes) and Kallisto version 0.48.0 (all other samples)
Abundance data was annotated with GENCODE v40 annotation data (primary astrocytes) and Ensembl human gene annotation data version 86 (all other samples)
Gene-level counts per million were calculated using htseq-count (primary astrocytes) and edgeR versions 3.38.4 and 3.40.2 (all other samples)
Genes with less than 1 cpm in the smallest number of replicates per analysis were removed and samples within each analysis were normalized with the trimmed mean of M values method
Assembly: GRCh38
Supplementary files format and content: comma-separated values and text files include raw counts for each sample

extract_protocol:
Total RNA was extracted from the embryonic stem cells, derived hypothalamic neural progenitors and primary astrocytes with the Zymo Direct-zol RNA miniprep kit. Total RNA was extracted from hypothalamus tissue with the Zymo Quick-DNA/RNA Miniprep Plus kit.
Libraries were prepared using the QIAseq FastSelect RNA Removal kit, NEBNext Ultra II Directional RNA Library Prep for Illumina kit, and NEBNext Oligos for Illumina (Dual Index Primers Set 1), according to manufacturer's instructions.

value: Lonza NHA


title: CCB072, YF-17D vaccination, day 28, rep 1

value: Whole blood

value: day 28

value: male


title: Primary Astrocyte, Replicate 2


title: wildtype mTECs, ALID03

description: 10x Genomics, included as GSM6620452 in series GSE215046

value: 3 days


title: FT32_mock_6h

value: mock


title: CCB072, YF-17D vaccination, day -21, rep 1

value: day -21


title: wildtype mTECs, ALID01,replicate 4

description: 10x Genomics

value: 1 day


title: CCB072, YF-17D vaccination, day 14, rep 1

value: day 14


title: Primary Astrocyte, Replicate 1


title: Hypothalamus Tissue, Donor 6032, Replicate 3

description:
6032C
Hypothalamus_RawCounts.csv

data_processing:
bcl2fastq2 version 2.20
Reads were aligned to GRCh38 with Kallisto version 0.48.0
Abundance data was annotated with Ensembl human gene annotation data version 86
Gene-level counts per million were calculated using edgeR versions 3.38.4 and 3.40.2
Genes with less than 1 cpm in the smallest number of replicates per analysis were removed and samples within each analysis were normalized with the trimmed mean of M values method
Assembly: GRCh38
Supplementary files format and content: comma-separated values files includes raw counts for each sample

source_name: Hypothalamus

extract_protocol:
Total RNA was extracted from the embryonic stem cells and derived hypothalamic neural progenitors with the Zymo Direct-zol RNA miniprep kit. Total RNA was extracted from hypothalamus tissue with the Zymo Quick-DNA/RNA Miniprep Plus kit.
Libraries were prepared using the QIAseq FastSelect RNA Removal kit, NEBNext Ultra II Directional RNA Library Prep for Illumina kit, and NEBNext Oligos for Illumina (Dual Index Primers Set 1), according to manufacturer's instructions.

value: Hypothalamus

tag: individual

value: Donor 6032

value: Male

tag: developmental stage

value: pediatric


title: wildtype mTECs, ALID01,replicate 3

description: 10x Genomics


title: CCB072, YF-17D vaccination, day 1, rep 1

value: YF-17D Vaccination

value: day 1


title: FT30_ldcA_6h

value: Fallopian tube

value: ldcA mutant supernatant

value: 6 hour


title: FT30_mock_6h


title: wildtype mTECs, ALID01,replicate 2

description: 10x Genomics

value: mouse tracheal epithelial cells cultured at air-liquid interface


title: wildtype mTECs, ALID01,replicate 1

description: 10x Genomics


title: FT30_WT_6h

value: WT supernatant


title: Hypothalamus Tissue, Donor 6032, Replicate 1

description:
6032A
Hypothalamus_RawCounts.csv


title: Hypothalamus Tissue, Donor 6032, Replicate 2

description:
6032B
Hypothalamus_RawCounts.csv


title: FT28_ldcA_6h


title: CCL052, YF-17D vaccination, day -21, rep 1

value: Whole blood

value: male


title: FT28_WT_6h


title: Hypothalamus Tissue, Donor 5976, Replicate 2

description:
5976B
Hypothalamus_RawCounts.csv

value: Donor 5976

value: Female


title: homozygous E2f7 knockout mTECs, replicate B, ALID07

description: 10x Genomics

extract_protocol:
To generate single-cell suspensions for mTEC scRNA-seq, mTECs derived from E2f7-/- and littermate control wild-type mice  were cultured and differentiated. E2f7+/+ and E2f7-/- mTECs were collected on day seven at air/liquid interface. Collection involved washing mTECs with PBS three times both apically and basally, incubating in 0.05% Trypsin-EDTA in Cell Dissociation Buffer (Gibco, Cat #13151014) added both apically and basally at 37°C for 15 min, gentle trituration, and inactivating trypsin in mTEC Basic with 2% Nu-Serum (Corning, Cat #355100). Additional 0.05% Trypsin-EDTA in Cell Dissociation Buffer was added to the apical surface and incubated at 37°C for 5 min. Cells were washed and resuspended in 0.04% BSA in PBS at 1000 cells/uL.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, 16,000 mTECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: homozygous E2f7 knockout mTECs, replicate A, ALID07

description: 10x Genomics


title: FT28_mock_6h

value: mock


title: Hypothalamus Tissue, Donor 5976, Replicate 1

description:
5976A
Hypothalamus_RawCounts.csv


title: CCC047, YF-17D vaccination, day 7, rep 1

value: day 7


title: A375- MSCV-YAP-S127A,S381A-IRES-Hygro, rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
aa_2
Skin

data_processing:
Sequencing run with HiSeq Control Software (HCS) version 1.5.15.1 and Real Time Analysis (RTA) version 1.13.48.
Fastq sequences prepared with bcl2fastq version 2.15.0.
RNA-Seq reads were aligned to the hg19 human assembly with a UCSC known genes version 2012 using bowtie2 version 2.0.0-beta6 and tophat version 2.0.4 and gene summary was prepared with cufflinks version 2.0.2.
Assembly: hg19 with UCSC known genes version 2012 annotation.
Supplementary files format and content: jlamar_l2fpkm.txt is a tab-delimited text file of log 2 FPKM.

growth_protocol: Cells were cultured on plastic at 37 °C, 5% CO2 in DMEM+ 10% fetal bovine serum & 2 mM L-glutamine.

extract_protocol:
TRIzol extraction using manufacturer's protocol.
cDNA was prepared with Illumina TruSeq chemistry and libraries were prepared using SPRIworks (Beckman Coulter).

value: Malignant melanoma epithelial

value: hypotriploid with a modal number of 62 chromosomes

tag: condition


title: CCL052, YF-17D vaccination, day 1, rep 1


title: CCC047, YF-17D vaccination, day 3, rep 1

value: day 3


title: wildtype mTECs, replicate B, ALID07

description: 10x Genomics


title: Hypothalamus Tissue, Donor 5309, Replicate 3

description:
5309C
Hypothalamus_RawCounts.csv

value: Hypothalamus

value: Donor 5309

value: pediatric


title: A375- MSCV-YAP-S127A,S381A-IRES-Hygro, rep2

description:
aa_1
Skin


title: Hypothalamus Tissue, Donor 5309, Replicate 2

description:
5309B
Hypothalamus_RawCounts.csv


title: DM_IFN, HTO

description:
TotalSeqB 2, 3, 4
10x Single Cell 3' V3
hto.txt.gz
counts_HTO.txt.gz

library_source: other

data_processing:
cDNA reads were aligned to ‘mm10’ genome using Ensembl 102 gene models including the sequence of human JAK2 gene and CreERT2 using the STARsolo tool (v2.7.9a) with default parameter values except the following parameters: soloUMIlen=12, soloBarcodeReadLength=0, clipAdapterType=CellRanger4, outFilterType=BySJout, outFilterMultimapNmax=10, outSAMmultNmax=1, soloType=CB_UMI_Simple, outFilterScoreMin=30, soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts, soloUMIfiltering=MultiGeneUMI_CR, soloUMIdedup=1MM_CR, soloCellFilter=None.
HTO libraries were also processed using the STARsolo tool with default parameters except  soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts, soloUMIfiltering= MultiGeneUMI_CR, soloUMIdedup=1MM_CR, soloCellFilter=None, clipAdapterType=False, soloType=CB_UMI_Simple, soloBarcodeReadLength=0, soloUMIlen=12, clip5pNbases=10, clip3pNbases=65.
Further analysis steps were performed using R (v4.2.0). Cells were considered as high-quality if they got a confident assignment of an HTO reported by the function ‘hashedDrops’ and had at least 2000 counts, which is the threshold derived from the distribution of UMI counts across cells. Based on the expression of the proliferation marker Mki67, around 380 cells were progressing in the cell cycle and removed from the further analysis forming the final data set of 41187 cells.
Multiple Bioconductor (v3.15) packages including DropletUtils (v1.16.0), scDblFinder (v1.10.0), scran (v1.24.1), scater (v1.24.0), scuttle (1.6.2) and batchelor (v1.12.3) were applied for the further analysis of the data set mostly following the steps of the workflow presented at https://bioconductor.org/books/release/OSCA/. Raw counts were normalized by deconvolution (Lun, Bach, and Marioni 2016). The function ‘computeDoubletDensity’ did not point at any group of cells, which could be potential doublets, confirming the efficiency of removing doublets while demultiplexing samples. The normalized gene expression of remaining cells was used to construct a shared nearest-neighbour (SNN) graph (k=10) (Xu and Su 2015), which nodes, i.e. cells, were clustered by ‘cluster_louvain’ method from the R igraph package (Blondel et al. 2008).
A t-SNE dimensionality reduction was used for visualizing single cells on two dimensions. T-SNE coordinates were calculated using the ‘runTSNE’ function from the scater package and default parameters. For the visualization of cells based on the gene expression, coordinates of principal components and most variable genes were used as the input. To get most variable genes the function ‘getTopHVGs’ was applied with parameters fdr.threshold=0.01 and var.threshold=0.1.
Assembly: mm10 with added Jak2-V617F sequence
Supplementary files format and content: Tab-separated values files: hto.txt.gz with HTO sequences, counts_cDNA.tsv.gz with cDNA read counts, counts_HTO.tsv.gz with HTO read counts, CreERT2_hsa_JAK2_201_sequence_V617F.fa.gz and CreERT2_hsa_JAK2_201_sequence_V617F.gtf.gz with the human sequence of JAK2 and CreERT2, tsne_hto_clusters.tsv.gz with t-sne coordinates, sample demultiplexing and cluster assignment.

molecule: protein

extract_protocol:
LT-HSCs (Lineage-, c-Kit+, Sca-1+, CD150+, CD48-) were FACS-sorted (100 nozzle, 4°C sample and collection, into PBS/3%FBS) from bone marrow of mice treated with pegylated IFN alpha (25µg/kg, s.c. in 100µl) for 24 hours or vehicle (saline) and used for downstream single-cell RNAseq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The polyA RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: LT-HSC (LSK; CD48-; CD150+)

value: Bone marrow

value: 8-10 weeks old

value: IFNa


title: DM_V, HTO

value: Vehicle


title: CCL052, YF-17D vaccination, day 3, rep 1

value: Whole blood

value: YF-17D Vaccination


title: CCC047, YF-17D vaccination, day 28, rep 1

value: day 28

value: male


title: A375- MSCV-YAP-S127A,S381A-IRES-Hygro, rep1

description:
aa_0
Skin


title: Hypothalamus Tissue, Donor 5309, Replicate 1

description:
5309A
Hypothalamus_RawCounts.csv

value: Female


title: wildtype mTECs, replicate A, ALID07

description: 10x Genomics

value: mouse tracheal epithelial cells cultured at air-liquid interface


title: Hypothalamus Tissue, Donor 5976, Replicate 3

description:
5976C
Hypothalamus_RawCounts.csv

value: Donor 5976


title: CCC047, YF-17D vaccination, day -21, rep 1

value: day -21


title: Hypothalamus Tissue, Donor 1674, Replicate 3

description:
1674C
Hypothalamus_RawCounts.csv

value: Donor 1674

value: Male


title: A375- MSCV-YAP-S94A,S127A-IRES-Hygro, rep2

description:
s94a_1
Skin

value: Malignant melanoma epithelial

value: hypotriploid with a modal number of 62 chromosomes


title: CCC047, YF-17D vaccination, day 14, rep 1

value: day 14


title: CCC047, YF-17D vaccination, day 1, rep 1

value: day 1


title: A375- MSCV-YAP-S94A,S127A-IRES-Hygro, rep3

description:
s94a_2
Skin


title: WT_V, HTO

value: LT-HSC (LSK; CD48-; CD150+)

value: Bone marrow

value: Wild type

value: 8-10 weeks old


title: A375- MSCV-YAP-S94A,S127A-IRES-Hygro, rep1

description:
s94a_0
Skin


title: VFDM_V, HTO

value: Vehicle


title: CCC046, YF-17D vaccination, day 7, rep 1

value: Whole blood

value: YF-17D Vaccination

value: day 7


title: Hypothalamus Tissue, Donor 1674, Replicate 1

description:
1674A
Hypothalamus_RawCounts.csv

value: Hypothalamus

value: pediatric


title: WT_IFN, HTO

value: IFNa


title: CCC046, YF-17D vaccination, day 3, rep 1

value: day 3

value: male


title: Hypothalamic Neural Progenitor, rs7132908 AA, Differentiation 2, Replicate 3

description:
AA6c
HP_RawCounts.csv

source_name: Hypothalamic neural progenitor

value: Hypothalamic neural progenitor

value: Female


title: VF_IFN, HTO


title: CCC046, YF-17D vaccination, day 28, rep 1

value: day 28


title: VF_V, HTO


title: CCC046, YF-17D vaccination, day -21, rep 1

value: day -21


title: A375- MSCV-IRES-Hygro (Control), rep3

description:
ctrl_2
Skin

value: Malignant melanoma epithelial

value: hypotriploid with a modal number of 62 chromosomes

value: empty vector control


title: A375- MSCV-YAP-S127A-IRES-Hygro, rep1

description:
yap_0
Skin


title: Hypothalamic Neural Progenitor, rs7132908 AA, Differentiation 2, Replicate 1

description:
AA6a
HP_RawCounts.csv


title: Hypothalamic Neural Progenitor, rs7132908 AA, Differentiation 2, Replicate 2

description:
AA6b
HP_RawCounts.csv


title: WT_IFN, cDNA

description:
10x Single Cell 3' V3
counts_cDNA.txt.gz

value: LT-HSC (LSK; CD48-; CD150+)

value: Bone marrow

value: Wild type

value: 8-10 weeks old


title: Hypothalamus Tissue, Donor 1674, Replicate 2

description:
1674B
Hypothalamus_RawCounts.csv

value: Donor 1674

value: Male


title: CCC046, YF-17D vaccination, day 14, rep 1

value: Whole blood

value: YF-17D Vaccination

value: day 14


title: Hypothalamic Neural Progenitor, rs7132908 AA, Differentiation 1, Replicate 3

description:
AA4c
HP_RawCounts.csv


title: VFDM_IFN, HTO

value: IFNa


title: Hypothalamic Neural Progenitor, rs7132908 AA, Differentiation 1, Replicate 1

description:
AA4a
HP_RawCounts.csv

value: Hypothalamic neural progenitor


title: CCA034, YF-17D vaccination, day 7, rep 1

value: day 7

value: male


title: A375- MSCV-IRES-Hygro (Control), rep2

description:
ctrl_1
Skin


title: CCC046, YF-17D vaccination, day 1, rep 1

value: day 1


title: A375- MSCV-IRES-Hygro (Control), rep1

description:
ctrl_0
Skin

value: Malignant melanoma epithelial


title: VFDM_IFN, cDNA

description:
10x Single Cell 3' V3
CreERT2_hsa_JAK2_201_sequence_V617F.gtf.gz
CreERT2_hsa_JAK2_201_sequence_V617F.fa.gz
counts_cDNA.txt.gz


title: A375- MSCV-YAP-S127A-IRES-Hygro, rep3

description:
yap_2
Skin

value: hypotriploid with a modal number of 62 chromosomes


title: Hypothalamic Neural Progenitor, rs7132908 GG, Differentiation 2, Replicate 3

description:
GG6c
HP_RawCounts.csv

value: control

value: Female


title: VF_IFN, cDNA

value: LT-HSC (LSK; CD48-; CD150+)

value: Bone marrow


title: Parental MKN-28/74

city: Suwon

first: Jae-Il

last: Choi

address: 164, World cup-ro, Yeongtong-gu

department: Pathology

country: South Korea

institute: Ajou University School of Medicine

description: Bulk RNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Gastric cancer cell

growth_protocol: All cell lines were grown in RPMI-1640, medium containing 10% fetal bovine serum, and 1% penicillin/streptomycin at 37℃ in humidified, 5% CO2 atmosphere.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: For generation of ECF resistant gastric cancer cell line (ECF-R MKN-28/74), we were treated with the IC50 concentration of ECF, which varied by cell line. After 72 hr, the media were changed to drug free media, and we performed sub-culturing twice. Subsequently, each cell line was exposed to the appropriate IC70 and IC80 concentrations, and then we repeated those procedures. To prevent reversion to the chemo-sensitive equilibrium, we treated the gastric cancer cell lines with the appropriate IC80 concentration of ECF every 2 weeks. All experiments were performed after sub-culturing twice.

value: Parental gastric cancer cell


title: ECF-R MKN-28/74

description: Bulk RNA-seq

value: ECF-resistant (ECF-R) gastric cancer cell


title: A375- MSCV-YAP-S127A-IRES-Hygro, rep2

description:
yap_1
Skin


title: CCA034, YF-17D vaccination, day 28, rep 1

value: day 28


title: CCA034, YF-17D vaccination, day 14, rep 1

value: Whole blood


title: Hypothalamic Neural Progenitor, rs7132908 GG, Differentiation 2, Replicate 2

description:
GG6b
HP_RawCounts.csv


title: NLS-GFP, control for E2F7-GFP 1, GFP antibody, replicate 1, CUT&RUN

data_processing:
FASTQs were trimmed using trimmomatic with a second trimming step to remove any remaining read-through adaptors (CUT&RUNtools)
Reads were aligned with bowtie2 (Langmead B. 22388286) using parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Samples were filtered for reads under 120bp and duplicates were marked, but not removed, with picard MarkDuplicates.
MACS2 was used to call peaks using parameters --keep-dup all -q 0.05. The paired NLS-GFP sample was utilized as a control in the MACS2 callpeaks command.
Assembly: mm10
Supplementary files format and content: Bigwigs for individual replicates
Supplementary files format and content: MACS2 narrow peak files for each E2F7-GFP replicate with NLS-GFP control.
Library strategy: CUT&RUN

source_name: trachea

extract_protocol:
CUT&RUN was performed as described (Meers et al., 2019; Peter J. Skene and Henikoff, 2017), with protocol and buffers detailed in Protocol 2: High Ca2+/low salt (https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3). Briefly, E2F7-GFP- or NLS-GFP-transduced mTECs were dissociated in 0.05% trypsin-EDTA in Cell Dissociation Buffer for 15 min at 37°C. Cells were collected in mTEC Basic medium   with 2% Nu-Serum, washed twice in 5 mL of CUT&RUN Wash Buffer, and resuspended in CUT&RUN Wash Buffer. One million cells of each sample were aliquoted in 1.5 mL Eppendorf tubes and brought up to a volume of 1 mL with CUT&RUN Wash Buffer. Cells were incubated with 10 L activated wheat germ agglutinin  beads (Bangs Laboratories, Cat #BP530) at room temperature for 10 minutes with gentle rocking. Cells were combined and incubated overnight with anti-GFP (Abcam, Cat #ab290) diluted 1:100 in 0.05% digitonin in CUT&RUN Wash Buffer.  Following two washes in CUT&RUN Wash Buffer, samples were incubated for 1 hour at room temperature in 1:100 rabbit anti-guinea pig IgG in 0.05% digitonin in CUT&RUN Wash Buffer. Samples were incubated with Protein A/G-MNase fusion protein (Addgene, Cat #123461) at 700 ng/mL for 1 hour at 4°C. Following two washes in 0.05% digitonin in CUT&RUN Wash Buffer and one wash in CUT&RUN Low-Salt Rinse Buffer, samples were digested for 10 min at 0°C in cold CUT&RUN Incubation Buffer. DNA fragments were released by incubation at 37°C for 30 min and then collected by phenol-chloroform extraction. Library preparation was performed with the Next Ultra II DNA Library Prep Kit for Illumina (NEB, Cat #E7645S) using 25 L of CUT&RUN DNA as input, as detailed by N. Liu (https://www.protocols.io/view/library-prep-for-cut-amp-run-with-nebnext-ultra-ii-kxygxm7pkl8j/v2). Adaptors were diluted 1:15 in adaptor dilution buffer. High sensitivity D5000 ScreenTape reagents (Agilent, Cat #5067-5593) and the Tapestation 4200 (Agilent) were used to assess library quality and pool libraries for sequencing. Sequencing was done using the NextSeq 550 (Illumina).
Library preparation was performed with the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, Cat #E7645S) using 25 uL of CUT&RUN DNA as input, as detailed by N. Liu (https://www.protocols.io/view/library-prep-for-cut-amp-run-with-nebnext-ultra-ii-kxygxm7pkl8j/v2)

treatment_protocol: mTECs were plated in 6.5 mm transwells and transduced with 1-15 ul of lentivirus in mTEC Plus medium supplemented with 50 nM retinoic acid and 10 uM ROCK inhibitor, as modified from a previously transduction protocol (Horani et al., 2013). Basal media was changed 24 hours after transduction and apical media was changed 48 hours after transduction. Media in both chambers was changed at 72 hours post transduction and mTECs were differentiated

value: trachea

tag: cut&run antibody

value: GFP (Abcam, ab290)

value: NLS-GFP lentivrial transduction


title: Hypothalamic Neural Progenitor, rs7132908 GG, Differentiation 1, Replicate 3

description:
GG4c
HP_RawCounts.csv

value: Hypothalamic neural progenitor


title: VFDM_V, cDNA

value: 8-10 weeks old

value: Vehicle


title: NLS-GFP, control for E2F7-GFP 2, GFP antibody, replicate 2, CUT&RUN


title: Hypothalamic Neural Progenitor, rs7132908 GG, Differentiation 2, Replicate 1

description:
GG6a
HP_RawCounts.csv


title: WT_V, cDNA

value: Wild type


title: Hypothalamic Neural Progenitor, rs7132908 AA, Differentiation 1, Replicate 2

description:
AA4b
HP_RawCounts.csv


title: DM_V, cDNA


title: DM_IFN, cDNA

value: IFNa


title: E2F7-GFP, GFP antibody, replicate 2, CUT&RUN

value: E2F7-GFP lentivrial transduction


title: Hypothalamic Neural Progenitor, rs7132908 GG, Differentiation 1, Replicate 2

description:
GG4b
HP_RawCounts.csv

value: control


title: CCC021, YF-17D vaccination, day 28, rep 1

tag: animal id

value: YF-17D Vaccination

value: male


title: VF_V, cDNA

value: LT-HSC (LSK; CD48-; CD150+)

value: Bone marrow

tag: treatment


title: longissimus dorsi, jm5

city: Zhengzhou

first: Geyang

last: Zhang

state: Henan

address: 116 Huayuan Road, Jinshui District

department: Animal husbandry institute

country: China

institute: Henan Academy of Agricultural Sciences

data_processing:
Quality control.Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads mapping to the reference genome.Reads mapping to the reference genome.
Quantification of gene expression level.HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Differential expression analysis.(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1).
Assembly: Bos taurus UMD3.1.1
Supplementary files format and content: 1ab-delimited text file includes FPKM values for each Sample

organism: Bos taurus

source_name: longissimus dorsi

extract_protocol:
RNA was harvested using TRNzol Universal Reagent+small(DP424+RK177-A).A total amount of 3 µg RNA per sample was used as input material for the RNA  sample preparations.
RNA  libraries for RNA-seq were prepared using  NEBNext® UltraTM  RNA Library Prep Kit following manufacturer’s protocols.

value: longissimus dorsi

tag: breed

value: Jiaxian Red


title: Mouse 1608-control ASO

city: Ottawa

first: Katey

last: Rayner

state: ON

address: 40 Ruskin Street, Room H-4211A

country: Canada

institute: University of Ottawa Heart Institute

data_processing:
The FASTQ files from the sequencing run were generated by BaseSpace and downloaded using the basespace-cli
Reads were trimmed for quality and adapters using fastp 0.20.1
The trimmed files were then analyzed using salmon v1.3.0 mapping to GENCODE mouse vM25 transcripts
Assembly: vM25
Supplementary files format and content: Comma-separated values, Raw gene counts for each sample
Supplementary files format and content: Comma-separated values, DESeq2 table

source_name: Spleen

extract_protocol:
RNA was extracted using Direct-zol RNA Miniprep Kit (Zymo Research).
Library preparation was performed using the NEBNext Ultra II mRNA directional kit (New England BioLabs)

value: Spleen

tag: cell type

value: Endothelial

value: 8 weeks ASO and high cholesterol diet


title: Mouse 1607-MLKL ASO

value: Mlkl KD


title: CCC021, YF-17D vaccination, day 7, rep 1

data_processing:
A read quality check was performed on raw data in FASTQ format using FastQC (v0.11.2).
Reads were imported and then processed in OmicSoft Array Studio software (v9.0.6.38-v9.0.8.28).
The raw data QC wizard of Array Studio was executed on the reads to assess the read quality.
The reads were aligned with OmicsSoft Aligner (OSA4; (53)) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations, including a first step of read trim per quality score (minimum of 2).
Samples (CCB102J-21, CCA100J1, CCB102J1, CCA100J14, CCA100J-21, CA100J7, CCA100J3, CCB102J3, CCA100J28) that did not meet quality criteria based on the minimal number of reads sequenced underwent a second run, and files were merged after read alignment, i.e. at the BAM file level.
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations (In Array Studio, “Naïve” means that no EM algorithm was used to handle ambiguous reads). Multiple mapping reads and first-read-forward-strand reads were discarded from the analysis (i.e. “Exclude multi-reads” option selected, “Count First-Read-Forward-Strand reads” option unselected).
Assembly: Cyno.WashU2013
Supplementary files format and content: raw_counts.txt raw counts per sample and gene (WashUGene20140620 gene annotations)
Supplementary files format and content: Count_Annotation.txt (annotation file from OmicSoft, https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA46N0000008OqZSAU&categoryName=OmicSoft_Suite)

extract_protocol:
Whole blood from cynomolgus macaques was collected in PAXgene tubes (BD762165 –Ozyme), and stored according to the manufacturer's protocol. RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation. The RNA quantity, purity and quality were checked on the Labchip (Caliper) and the Nanodrop Spectrophotometer (Thermo Scientific).
Extracted RNA samples with an A260/A280 ratio ~2, a RIN>8 and a minimal concentration of 70ng/µL of RNA were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. The quantity, purity and quality of the RNA depleted of globin mRNA was reassessed as already described before library preparation for sequencing. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300ng of RNA according to manufacturer’s instructions. The quality, length distribution and quantity of the resulting libraries were analyzed with the Qubit 3.0 Fluorometer (Life Technologies) and the Labchip (Caliper). Libraries were pooled at equimolar amounts and sequenced by single reads of 75bp on high-output flowcell (Illumina – FC-404-2005) using the Nextseq500 sequencer (Illumina) in a batch of 10 samples per flowcell with the specification to achieve 30 million reads per sample. On run completion, libraries were demultiplexed, adapters trimmed and FASTQ files generated.

value: Whole blood

tag: time

value: day 7


title: Hypothalamic Neural Progenitor, rs7132908 GG, Differentiation 1, Replicate 1

description:
GG4a
HP_RawCounts.csv

value: Hypothalamic neural progenitor

value: Female


title: longissimus dorsi, jm4


title: CCC021, YF-17D vaccination, day 14, rep 1

value: day 14


title: CCC021, YF-17D vaccination, day 1, rep 1

value: day 1


title: H9 ESC, rs7132908 AA Clone 9.1

description:
AA9
H9_ESC_RawCounts.csv

value: Embryonic stem cell


title: CCC021, YF-17D vaccination, day -21, rep 1

value: YF-17D Vaccination

value: day -21


title: E2F7-GFP, GFP antibody, replicate 1, CUT&RUN

value: trachea

value: GFP (Abcam, ab290)

value: E2F7-GFP lentivrial transduction


title: H9 ESC, rs7132908 AA Clone 10.1

description:
A10
H9_ESC_RawCounts.csv


title: CCC021, YF-17D vaccination, day 3, rep 1

value: day 3

value: male


title: H9 ESC, rs7132908 AA Clone 2.1

description:
AA2
H9_ESC_RawCounts.csv


title: longissimus dorsi, jm3

value: longissimus dorsi

value: Jiaxian Red


title: Mouse 1603-MLKL ASO

value: Spleen

value: Endothelial

tag: genotype

value: Mlkl KD

value: 8 weeks ASO and high cholesterol diet


title: CCA034, YF-17D vaccination, day 3, rep 1

value: Whole blood


title: H9 ESC, rs7132908 GG, Replicate 2

description:
GG3
H9_ESC_RawCounts.csv

value: control

value: Female


title: longissimus dorsi, jm2


title: Mouse 1604-MLKL ASO


title: H9 ESC, rs7132908 GG, Replicate 1

description:
GG1
H9_ESC_RawCounts.csv

value: Embryonic stem cell


title: CCA034, YF-17D vaccination, day 1, rep 1

value: YF-17D Vaccination

value: day 1


title: Mouse 1601-control ASO


title: RNAseq reporter Pro-135-tga

status: Public on Mar 28 2024

city: Dresden

first: Agnes

last: Toth-Petroczy

address: Pfotenhauerstrasse 108

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description: targeted sequencing of mScarlet amplicon with added premature STOP codon

data_processing:
Base calling from the raw data from the sequencer PacBio Sequel 2 was done with consensus calling ccs (https://github.com/PacificBiosciences/ccs, version 6.4.0).
Reads were demultiplexed with lima (https://github.com/PacificBiosciences/barcoding, version 2.7.1).
Remaining PacBio adapters were removed with blast searches.
The long PacBio reads were mapped to the mScarlet plasmid with BWA v0.7.17-r1198. Importantly, the referene sequence for each sample includes (if any) the added pre-mature STOP codon.
Unmapped reads were removed from the resulting BAM files and the resulting BAM files were sorted by coordinate with Samtools v1.15.1

organism: Escherichia coli str. K-12 substr. MG1655

source_name: K-12 substr. MG1655

growth_protocol: Single-colony E. coli LB-cultures were grown at 37°C until an absorbance of 0.4 at 600nm. Then, they were grown at 18℃ until an absorbance of 0.6 (~2h), protein expression was induced by addition of anhydrotetracycline to a final concentration of 400 µg/L, and cells were grown overnight at 18 °C.

extract_protocol:
Total RNA of the samples was extracted according to manufacturing specifications (RNeasy Protect Bacteria Mini Kit Qiagen kit)
300 ng of total RNA per sample was mixed with 50 ng of random hexamers and dNTPs and hybridized at 65°C for 5 minutes. cDNA was reversely transcribed making use of the Thermo Fisher Superscript IV transcriptase according to the manufacturer’s instructions. Then, mScarlet was specifically amplified from the resulting cDNA with forward primer 5’ AGTTATTTTACCACTCCCTATCAGT 3’ and reverse primer 5’ AGTAGCGGTAAACGGCAGAC 3’ resulting in an amplified PCR fragment of 948 bps. The NEB Q5® High-Fidelity DNA polymerase was used according to the manufacturer’s instructions. PCR conditions were as such, an initial denaturation step for 30 sec at 98°C, 30 cycles of 10 sec denaturation at 98°C followed by annealing at 67°C for 30 sec and extension at 72°C for 30 sec. A final extension step was done for 2 min at 72°C. Primer and dNTPs have been removed with 1x volume AMPure bead purification. Amplified mScarlet fragments were finally quantified with the Thermo Fisher Qubit high sensitivity DNA quantification system. 1 ng of the amplified mScarlet fragments were analyzed on the Agilent Fragment Analyzer system making use of the NGS high sensitivity kit

tag: strain

value: K-12 substr. MG1655


title: RNAseq reporter wt-mScarlet

description: targeted sequencing of WT mScarlet amplicon without premature STOP codons

value: wt-mScarlet


title: RNAseq reporter Pro-056-tga


title: RNAseq reporter Pro-135-tag


title: longissimus dorsi, jm1


title: RNAseq reporter Pro-056-tag


title: RNAseq reporter Met-190-tga


title: RNAseq reporter Asp-155-tga


title: RNAseq reporter Pro-056-taa


title: RNAseq reporter Glu-145-tga


title: Mouse 1602-control ASO


title: RNAseq reporter Ala-105-tga


title: RNAseq reporter Glu-145-tag


title: CCA034, YF-17D vaccination, day -21, rep 1

value: day -21


title: RNAseq reporter Ala-105-taa


title: RNAseq reporter Ala-105-tag


title: Soft biol rep 1

city: Cincinnati

first: Claire

last: Chougnet

state: OH

address: 240 Albert Sabin Way

department: Immunobiology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1. The trimmed reads were aligned to the reference human genome version hg38 with the program STAR v2.6.1e. Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8. Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database. Read counting was done with the program featureCounts v1.6.2 from the Rsubread package. Raw counts were normalized as transcripts per million (TPM).
Assembly: Hg38
Supplementary files format and content: tab delimited file containing raw counts for all samples
Supplementary files format and content: tab delimited files containing transcript per million (tpm) values for each sample

growth_protocol: Cal27 spheroids were cultured in soft (3 mg/mL Matrigel) and stiff (12 mg/mL Matrigel) using the liquid overlay technique.

extract_protocol:
Cal27 spheroids were harvested upon 14 days of culture using the cell recovery solution. Harvested gels were held on ice and repeatedly vortex for complete disintegration of the Matrigel matrix. The resulting suspension was centrifuged and resuspended in RNAlater stabilization solution. Total RNA was isolated using mirVana miRNA Isolation kit from spheroid samples.
The quality of total RNA was QC analyzed by Bioanalyzer. To enrich polyA RNA for library preparation, NEBNext Poly(A) mRNA Magnetic Isolation Module was used with 500 ng good quality total RNA as input. Next, NEBNext Ultra II Directional RNA Library Prep kit was used for library preparation under PCR cycle number 10. After library QC and Qubit quantification, the normalized libraries were sequenced using NextSeq 2000 Sequencer under the setting of PE 2x61 bp to generate an average of 59.7M reads.

treatment_protocol: Soft (3 mg/mL Matrigel) or Stiff (12 mg/mL Matrigel) conditions.

value: Squamous epithelial

value: Day 14

value: Soft ECM


title: Stiff biol rep 2

value: Stiff ECM


title: Stiff biol rep 3


title: Input replicate 1

city: Belfast

first: Guilherme

last: Costa

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University of Belfast

data_processing:
Pre-alignment QC with FastQC
Alignment with Star. The reference genome build for this study is: Release 33 from GRCh38.p13 build.
Count assignment with HTSeq –count
Supplementary files format and content: tab-delimited .txt files include htseq gene counts
Supplementary files format and content: tab delimited .csv file include normalised counts for each sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs; PromoCell) were routinely cultured on gelatine coated dishes in complete ECGM2 (PromoCell) containing 50 μg/ml gentamycin (Merck) and 50 ng/ml amphotericin (Merck).

extract_protocol:
Cells were lysed in IP lysis buffer (Thermofisher Scientific), lysates prcessed through AKAP12 immunoprecipitation and RNA extracted with Trizol
Libraries were generated using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to the manufacturer’s protocol.

value: HUVECs

value: WT


title: Soft biol rep 3


title: Input replicate 2


title: AKAP12 UV RIP replicate 3


title: Soft biol rep 2


title: Input replicate 3


title: STA - Health - Colon 10X Visium

city: London

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

institute: King's College London

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data processed with SpaceRanger to generate fastQ files
Sequences aligned to hg38 genome for gene expression count in Space Ranger
Gene expression matrices output by SpaceRanger
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered expression matrix
Supplementary files format and content: raw_feature_bc_matrix.h5: raw expression matrix
Supplementary files format and content: aligned_fiducials.jpg: aligment of fiducials on edge of image
Supplementary files format and content: detected_tissue_image.jpg: spots detected as being on tissue
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of positions of spots on tissue
Library strategy: Spatial Transcriptomics

source_name: FFPE block STA

extract_protocol:
6x6mm2 sections from FFPE blocks were cut at 5mm and placed on the Visium slide inside fiducial frames
Human whole transcriptome probes (v1 chemistry), consisting of a pair of specific probes for ~18,000 genes, were added to each section for hybridizing to their target genes. Hybridized and ligated probes were released from the tissue sections and captured on the spatially barcoded oligonucleotides on the capture areas. Sequencing libraries were generated from the probes and sequenced on the NextSeq 2000

value: Colon

tag: disease state

value: healthy


title: STB - Health - Colon 10X Visium

description: FFPE Spatial transcriptome sequencing

source_name: FFPE block STB


title: AKAP12 UV RIP replicate 1


title: AKAP12 UV RIP replicate 2


title: Mouse GL261-GSC glioblastoma TMZ 7d rep3

city: Salamanca

first: Arantxa

last: Tabernero

address: Pintor Fernando Gallego 1

department: INCyL

country: Spain

institute: Universidad de Salamanca

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software
Assembly: mm10
Supplementary files format and content: 10xnuclei_annotated.h5ad: annotated file in h5ad format

source_name: Brain

growth_protocol: GL261-GSCs were intracranially injected into the brains of C57BL/6 mice

extract_protocol:
Brains were fresh-frozen and nuclei were obtained from tissue blocks
Single nuclei were processed using the 10x Multiome ATAC + Gene Expression kit according to manufacturer's instructions

treatment_protocol: 100 μM Tat-Cx43266-283 or 250 μM TMZ were intracranially injected in 1 μl of physiological saline together with the cells. For 28-day experiments, 4 nmol/g Tat-Cx43266–283 or 10 nmol/g TMZ were intraperitonially injected twice per week, starting on day 8 and until the end of the experiment. An equivalent amount of saline was injected to control mice.

value: Brain

tag: time point

value: TMZ


title: Mouse GL261-GSC glioblastoma TMZ 7d rep2


title: Mouse GL261-GSC glioblastoma peptide 7d rep3

value: Peptide


title: Mouse GL261-GSC glioblastoma peptide 7d rep2


title: Mouse GL261-GSC glioblastoma TMZ 7d rep1


title: Mouse GL261-GSC glioblastoma peptide 7d rep1


title: Stiff biol rep 1

tag: cell line


title: Mouse GL261-GSC glioblastoma control 7d rep1

value: Control


title: Mouse GL261-GSC glioblastoma control 7d rep2


title: N_6

city: Fort Collins

first: Dylan

middle: T

last: Ammons

state: CO

address: 200 W Lake St

department: Clinical Sciences

institute: Colorado State University

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counting was completed using Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: canFam3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Canis lupus familiaris

source_name: Osteosarcoma

extract_protocol:
Between 3 and 5 tumor biopsies were collected from the amputated limb, washed with phosphate buffered saline (PBS), minced using a scalpel, and digested with collagenase type II (250 U/mL) in Hanks' Balanced Salt Solution (HBSS) for 45 minutes at 37˚C with agitation (Thermo Fisher Scientific Inc.). Samples were passed through a 70-µm cell strainer, washed with PBS, then centrifuged for 5 minutes at 400 rcf. To enrich for live cells, samples were pooled into 4-mL HBSS layered onto 3-mL Ficoll Paque (Cytiva; Marlborough, MA), and centrifuged for 30 minutes at 400 rcf with acceleration at 9 and brake at 0. Following density centrifugation, the cell interface layer was collected, washed one time with PBS, and resuspended in 10-mL of Ammonium-Chloride-Potassium lysis buffer for 3-7 minutes at room temperature. To remove small debris and platelets, a final wash at 100 rcf for 15 minutes was completed. The sample was then prepared to be run on a Chomium iX instument by resusspending in 0.04% molecular grade BSA. The instumnet was loaded to target 5,000 cells per sample.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol, 10x Genomics). Briefly, a Chromium iX instrument was used to pass cells and oligonucleotide coated gel beads at a limiting dilution to obtain a coupling of cells and beads in a 1:1 ratio. The cell-bead pair was then passed from an aqueous phase to an oil phase to form an emulsion. Within the emulsions, cells were lysed, and the oligonucleotide sequences on the gel beads pull down message RNA and other RNA molecules that have long adenosine stretches with an oligo-d(T) pull down. After hybridization, reverse transcription is completed to generate a cDNA library with each transcript now associated with a unique cell barcode and an Illumina R1 primer sequence.  Once cells were barcoded and unique molecular identifiers (UMIs) added, a standard Illumina library preparation kit was completed with SPRIselect used for fragment size selection. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Osteosarcoma

value: Wt


title: N_4

description: 10x Genomics


title: N2_2

description: 10x Genomics


title: N_3

description: 10x Genomics


title: N1_1

description: 10x Genomics


title: N_5

description: 10x Genomics


title: N1_2

description: 10x Genomics


title: N2_1

description: 10x Genomics


title: AC16 Clone 8B9, Rep1

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
Reads were aligned with HISAT2 v2.1.0 using the downstream transcriptome assembly option and the RF paired-end stranded option. An artificial chromosome was added to the GRCh38 release 99 reference genome containing open reading frames of the integrated pSLIK CVB3 A67G plasmid: positive and negative strand “genes” for CVB3, neomycin resistance gene, reverse tetracycline-controlled transactivator (rtTa), hygromycin resistance gene, and ampicillin resistance gene. SV40 genes (small t [exon 1 and 2], large T [exon 1 and 2], agnoprotein, VP1, and VP2) were also included in the artificial chromosome because SV40 was involved in creating the AC16 cell line. Transcripts were assembled and counted with Stringtie v2.1.0, restricting assembly to the reference genome and associated artificial chromosome. The prepDE.py3 script provided by Stringtie was used to extract count information for downstream differential expression.
Assembly: GRCh38 + SV40 + CVB3
Supplementary files format and content: Tab separated matrix containing raw output counts from the Stringtie prepDE.py script.

growth_protocol: iPSCs: iCell Cardiomyocytes² Maintenance Medium as recommended by the manufacturer and plated in iCell Cardiomyocytes² Plating Medium for two days (asynchronous beating) or four days (synchronous beating). AC16 cells: DMEM/F12 medium (Gibco Cat#11330-032) + 12.5% fetal bovine serum + 1% pen/strep + 10 mg/ml blasticidin (AC16-CAR only) + 100 µg/ml hygromycin (AC16 CVB3+ clones only) + 2 µg/ml puromycin (IkBa-SR, MKK6-EE, and IKK2-EE only).

extract_protocol:
iPSCs, AC16-CAR cells, and unperturbed AC16 clones: lysed with buffer RLT and mRNA extracted with the RNeasy Mini Kit. Perturbed AC16 clones: lysed with buffer RLT and mRNA extracted with the RNeasy Plus Mini Kit.
iPSCs, AC16-CAR cells, and unperturbed AC16 clones: prepared with the TruSeq stranded mRNA library prep kit. Perturbed AC16 clones: strand-specific sequencing libraries, after poly(A) pulldown, were prepared by Novogene.

treatment_protocol: iPSCs and AC16-CAR cells: infected with wildype CVB3 (MOI 10 for 8 hours) or encapsidation-deficient CVB3 (VP4 A67G - MOI of 3 for 16 hours). All AC16 cells: terminally quiesced by shSV40 lentivirus and serum withdrawal. AC16 CVB3+ clones: stably transfected with encapsidation-deficient pSLIK CVB3 (VP4 A67G) and clonally isolated. Perturbed AC16 clones: transduced with retrovirus encoding pBABE FLAG-IKK2-EE puro, pBABE 3xHA-MKK6-EE puro, pBABE IκBα-SR puro, or empty pBABE puro then selected with 2 µg/ml puromycin for 3 days, and replated at equivalent cell density. Transduced AC16 clones were treated with 5 µM BIRB796 or 0.05% DMSO while undergoing the quiescence protocol.

tag: modifications

value: CVB3+ Clone 8B9


title: AC16 Clone 7G5, Rep1

value: CVB3+ Clone 7G5


title: AC16 Clone 7F4, Rep2

value: CVB3+ Clone 7F4


title: AC16 Clone 7E7, Rep1

value: CVB3+ Clone 7E7


title: AC16 Clone 7E11, Rep2

value: CVB3+ Clone 7E11


title: AC16 Clone 8B9, Rep2


title: AC16 Clone 7F4, Rep1


title: AC16 Clone 7G5, Rep2


title: AC16 Clone 9B4, Rep1

value: CVB3+ Clone 9B4


title: AC16 Clone 7E11, Rep1


title: AC16 Clone 7C2, Rep1

value: CVB3+ Clone 7C2


title: AC16 Clone 7E7, Rep2


title: AC16 Clone 6E8, Rep2

value: CVB3+ Clone 6E8


title: AC16 Clone 7C2, Rep2


title: AC16 Clone 6E8, Rep1


title: AC16 Clone 4B8, Rep2

value: CVB3+ Clone 4B8


title: AC16 Clone 5C2, Rep1

value: CVB3+ Clone 5C2


title: AC16 Clone 9B4, Rep2


title: AC16 Clone 4B8, Rep1


title: AC16 Clone 5C2, Rep2


title: AC16 Clone 1C2, Rep2

value: CVB3+ Clone 1C2


title: BJ1, CTCF ChIP

city: Gif-sur-Yvette

first: Benoit

last: Moindrot

address: 1, avenue de la terrasse

institute: Institute for Integrative Biology of the Cell

data_processing:
For Allele-specific analysis: Reads were aligned with bowtie2 on an mm10 N-masked genome in which SNPs differing between JF1 and C57BL/6J genomes were replaced by an N, the list of SNP being been obtained from the Mouse Genomes Project (release #1807). SNPsplit tool (Krurger et al. 2016; PMID: 27429743) was used to allocate reads to their respective allele and bedgraph for uniquely mapped and paired reads were generated using bedtools for each allele. Bedgraphs were scaled to a total of 10 million uniquely mapped and paired reads on both JF1 and C57BL/6J allele. A bedgraph has also been generated with unassigned reads (and scaled to a total of 10 million uniquely mapped and paired reads)
For non-allelic analysis (total): Reads were aligned with bowtie2 on mm10 genomes. The corresponding bedgraph was generated using bedtools (scaled to a total of 10 million uniquely mapped and paired reads).
Assembly: mm10
Supplementary files format and content: Enrichment score in bedgraph format (mm10)
Supplementary files format and content: A bedgraph for each allele (JF1 and Bl6). A bedgraph for unassigned reads (not overlapping known SNPs). A bedgraph for total reads (non-allelic)

source_name: mouse embyronic stem cells

growth_protocol: ESGRO Complete PLUS Clonal Grade Medium (Merck)

extract_protocol:
BJ1 and JB1 ESCs for ChIP-seq experiment were fixed for 5 min in 2% formaldehyde at room temperature while tumbling. A 15 million cell pellet was sequentially lysed in the following 3 buffers: 5mL Buffer 1 (10% Glycerol, 50 mM Tris pH7.5, 140 mM NaCl, 1 mM EDTA, 0.5% NP40, 0.25% Triton X100, 0.33X protease inhibitors (Roche)) for 10 min on ice; 5mL Buffer 2 (10 mM Tris pH7.5, 0.2 M NaCl, 1 mM EDTA, 0.33X Protease inhibitors (Roche)) for 10 min on ice; 1mL Buffer 3 (100 mM NaCl, 10 mM Tris pH7.5, 1 mM EDTA, 0.25% SDS, 0.1% Sodium Deoxycholate, 1X Protease inhibitor (Roche)) for 10 min on ice. The chromatin was then sheared for 15 min using a Covaris S220 device (Peak power: 140W; Duty Factor: 20%; Cycle/Burst: 200), clarified by centrifugation, quantified and stored at -80°C.  For CTCF ChIP-seq experiment, 10 µg sonicated chromatin was diluted in the following buffer (16 mM Tris pH8, 1 mM EDTA, 167 mM NaCl, 1.1% Triton X100, 0.01% SDS, 1X Protease inhibitor (Roche)) to a total volume of 1mL and was precipitated with 5 µg CTCF antibody (Millipore # 07-729) overnight. After recovering the antibody-bound chromatin with Salmon Sperm DNA/Protein A agarose beads (Millipore #16-157), beads were sequentially washed in Low Salt Wash buffer (20 mM Tris pH8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X100, 0.1% SDS), High Salt Wash buffer (20 mM Tris pH8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X100, 0.1% SDS), LiCl Wash buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.26 M LiCl, 1% NP-40, 1% Na Deoxycholate) and twice in TE buffer (10 mM Tris pH7.5, 1 mM EDTA). Chromatin was then eluted in 1% SDS, 0.1 mM NaHCO3 and decrosslinked over-night.
ChIP-seq libraries were prepared on purified DNA using the NEB Ultra II DNA library prep kit following manufacturer’s instructions

value: mouse embyronic stem cells

value: BJ1 (C57BL/6J x JF1)

value: C57BL/6J x JF1

tag: chip antibody

value: CTCF (Millipore; ref:07-729)


title: BJ1, Input

tag: tissue

value: none (Input)


title: AC16 Clone 2E3, Rep1

value: CVB3+ Clone 2E3


title: AC16-CAR, CVB3 A67G, Rep1

value: CAR overexpression

value: CVB3 A67G


title: iPSC, Day4, CVB3 A67G, Rep2

source_name: iPSC-derived cardiomyocytes

value: iPSC-derived cardiomyocytes

value: 4 days of differentiation


title: AC16 Clone 1C2, Rep1


title: iPSC, Day4, CVB3 A67G, Rep1


title: iPSC, Day4, CVB3, Rep2

value: Wildtype CVB3


title: zebrafish_14dpi_rep3

city: SALT LAKE CITY

first: Clayton

last: Carey

state: UT

address: 1390 President's Circle

department: Biology

institute: University of Utah

description: 10X Genomics

data_processing:
Single-cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings, using GRCz11 v4.3.2 reference (Lawson et al., 2020) for zebrafish read alignments and ASM223467v1 for Medaka.
Assembly: GRCz11, ASM223467v1
Supplementary files format and content: Tab separated values files and matrix files

organism: Danio rerio

source_name: Heart Ventricle

growth_protocol: Wild-type Tübingen zebrafish and CAB medaka, aged 6-18 months unless otherwise stated, were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee (IACUC no. 20-07013) of the University of Utah’s animal care and use program.

extract_protocol:
To prepare cells for scRNA-seq, adult fish were euthanized by immersion in ice-cold water. After dissection and removal of hearts, the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH (Millipore Sigma cat# 5401089001) in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. After complete digestion, the reaction was quenched with ice-cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice-cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample.
Libraries wer constructed according to the manufacturer's protocol (10X chromium controller)

treatment_protocol: Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously (González-Rosa et al., 2011). Briefly, 0.02% and 0.04% Tricaine (MS-222) was used to anesthetize zebrafish and medaka, respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wire(González-Rosa and Mercader, 2012). After submersion in liquid nitrogen for at least 2 minutes, the probe was placed in contact with the ventricle apex for exactly 23 seconds. After injury, fish were placed back into freshwater tanks to recover, then transferred back into the fish facility for monitoring.

value: Heart Ventricle

value: 14 days post-injury


title: AC16-CAR, CVB3, Rep2


title: zebrafish_3dpi_rep3

description: 10X Genomics

value: 3 days post-injury


title: zebrafish_14dpi_rep6

description: 10X Genomics


title: AC16-CAR, CVB3, Rep1


title: iPSC, Day4, CVB3, Rep1


title: zebrafish_14dpi_rep1

description: 10X Genomics


title: zebrafish_14dpi_rep5

description: 10X Genomics


title: zebrafish_14dpi_rep4

description: 10X Genomics


title: AC16 Clone 2E3, Rep2


title: JB1, Input

value: JB1 (JF1 x C57BL/6J)

value: JF1 x C57BL/6J


title: zebrafish_3dpi_rep2

description: 10X Genomics


title: iPSC, Day4, Uninfected, Rep1


title: iPSC, Day2, CVB3 A67G, Rep2

value: 2 days of differentiation


title: zebrafish_3dpi_rep1

description: 10X Genomics


title: zebrafish_uninjured_rep4

description: 10X Genomics

value: Uninjured


title: iPSC, Day4, Uninfected, Rep2


title: zebrafish_uninjured_rep3

description: 10X Genomics


title: AC16-CAR, CVB3 A67G, Rep2


title: zebrafish_uninjured_rep2

description: 10X Genomics


title: zebrafish_14dpi_rep2

description: 10X Genomics


title: JB1, CTCF ChIP

value: mouse embyronic stem cells


title: iPSC, Day2, CVB3, Rep1


title: zebrafish_uninjured_rep1

description: 10X Genomics


title: Os_mRNA_DRS_CK

city: Shanghai

first: Xiang

last: Yu

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: Oryza sativa seedlings

data_processing:
The fast5 files containing raw electric signals were basecalled using Guppy(v6.1.5 with options ‘--recursive --fast5_out --config rna_r9.4.1_70bps_hac.cfg’)
Multi-fast5 files were converted to single-fast5 files using ont_fast5_api(v4.0.0)
Basecalled sequences were corrected according to reference and aligned to corresponding raw electric signals using tombo resquiggle(v1.5.1 with options ‘--overwrite --basecall-group Basecall_1D_000 --fit-global-scale --include-event-stdev’).
Raw current signals were normalized by median and median absolute deviation.
Then, mean, standard deviation, median, signal length and base quality were extracted as features for each event. 5-mer sequence was also considered as one event-level feature in this work and was embedded to vectors.
Assembly: Osativa_323_v7.0
Supplementary files format and content: txt files, count

organism: Oryza sativa

source_name: seedlings

growth_protocol: Oryza sativa plants were grown under 16h light 8h dark days, and seedlings were harvested at 2 weeks of age

extract_protocol:
Seedlings tissue was ground with a mortar and pestle. RNA was extracted with RNA isolator (Vazyme, R401-01-AA, China), and treated with RNase-free DNase I (NEB, M0303S, USA) at 37°C for 15 minutes to remove residual DNA.
Sequencing libraries were prepared according to the ONT’s SQK-RNA002 protocol.

treatment_protocol: Oryza sativa plants were cultrued on MS medium plus 100 mM NaCl

value: seedlings

tag: cultivar

value: DongJing

value: Control


title: iPSC, Day2, Uninfected, Rep2


title: iPSC, Day2, CVB3, Rep2


title: after NTD [DK22190_08]

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

description:
DK22190_08
3' RNA-seq

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw counts for each sample.
Supplementary files format and content: xlsx files include RPM values for each sample.

source_name: PBMC

extract_protocol:
RNA was harvested using ISOGEN reagent (Life Technologies, Carlsbad, CA, USA).
Purified total RNA (200 ng) was used for RNA library preparation, according to the instructions of the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.

tag: disease

value: Idiopathic Pulmonary Fibrosis

value: PBMC

tag: age

tag: Sex

value: Male

tag: race

value: Asian

value: NTD


title: Os_mRNA_DRS_NaCl

description: Oryza sativa seedlings

tag: treatment

value: 100mM NaCl


title: IVET_DRS_m5C

description: In vitro transcripts from Oryza sativa cDNA library

source_name: leaf and inflorescence

value: leaf and inflorescence


title: iPSC, Day2, Uninfected, Rep1

value: iPSC-derived cardiomyocytes


title: IVET_DRS_m1A


title: synthetic_DRS_m5C

description: In vitro transcripts from synthetic sequences

organism: synthetic construct


title: IVET_DRS_m6A


title: medaka_3dpi_rep3

description: 10X Genomics

organism: Oryzias latipes

value: Heart Ventricle

value: 3 days post-injury


title: iPSC, Day2, CVB3 A67G, Rep1

value: CVB3 A67G


title: Human H1 DNA SPRITE 11

city: Pasadena

first: Mitchell

last: Guttman

address: 1200 E. California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

description: H1 human embryonic stem cells Replicate 11

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and assessed with Fastqc v0.11.9. Subsequently, the DPM (GATCGGAAGAG) and RPM (ATCAGCACTTA) sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1 along with the 3’ end DPM sequences that result from short reads being read through into the barcode. The additional trimming helps improve read mapping in the end-to-end alignment mode. The SPRITE barcodes of trimmed reads are identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with an RPM or a DPM barcode are split into two separate files, to process RNA and DNA reads individually downstream, respectively.
RNA reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping --sp 1000,1000. Unmapped and reads with a low MapQ score (samtools view -bq 20) were filtered out for downstream realignment. Mapped reads were annotated for gene exons and introns with the featureCounts tool from the subread package v1.6.4 using Ensembl GRCm38 v95 gene model annotation and the Repeat and Transposable element annotation from the Hammel lab. Filtered reads were subsequently realigned to our custom collection of repeat sequences using Bowtie v2.3.5, only keeping mapped and primary alignment reads. For the H1 dataset, hg38 genome annotation was used.
DNA reads were aligned to GRCm38.p6 using Bowtie2 v2.3.5, filtering out unmapped and reads with a low MapQ score (samtools view -bq 20). Data generated in F1 hybrid cells (pSM33: C57BL/6 × 129SV-Jae or pSM44: 129 × castaneous) were assigned the allele of origin using SNPsplit v0.3.4. RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0. For the H1 dataset, hg38 genome assembly was used.
RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Assembly: mm10 and hg38
Supplementary files format and content: Each cluster occupies one line of the .clusters text file. A cluster corresponds to all reads with a shared series of tags and is identified by the barcode name and genomic alignments of contained reads.
Supplementary files format and content: Config files contain the SPRITE tag sequence strings and sample identifiers which were embedded in the DPM tag.

source_name: H1 hESC

growth_protocol: MM14 mouse skeletal myoblasts were passaged at 50-60% confluency every 1-2 days using the Wold lab protocol: (https://www.encodeproject.org/documents/a5f5c35a-cdda-4a45-9742-22e69ff50c9c/@@download/attachment/C2C12_Wold_protocol.pdf). Undifferentiated myoblasts grow in growth medium (20% fetal bovine serum). H1 hESC cells were maintained on matrigel matrix (Corning, 354277) in feeder free media using mTeSR1 (Stemcell Tech, 85850). Every 4-5 days cells were passaged using ReLeSR reagent (Stemcell tech, 05872).

extract_protocol:
SPRITE crosslinking, lysis, and DNA fragmentation.
SPRITE library construction as previously described in Quinodoz et al 2022 and Quinodoz et al 2021.

treatment_protocol: Myogenic differentiation was initiated upon reaching confluence by switching MM14 cells to medium containing 2% horse serum supplemented with insulin. Differentiation was performed for 60 hours by rinsing fully confluent cells once with PBS and adding 25mL of low-serum differentiation medium. Fresh differentiation medium was changed every 24 hours up to the 48h timepoint and 12 hours afterward were crosslinked using SPRITE crosslinking procedures.

value: H1 hESC

value: H1 human embryonic stem cells


title: Human H1 DNA SPRITE 10

description: H1 human embryonic stem cells Replicate 10


title: medaka_14dpi_rep1

description: 10X Genomics

value: 14 days post-injury


title: after NTD [DK22190_06]

description:
DK22190_06
3' RNA-seq


title: synthetic_DRS_unmodified

source_name: In vitro transcripts from synthetic sequences


title: medaka_3dpi_rep2

description: 10X Genomics


title: medaka_uninjured_rep4

description: 10X Genomics

value: Uninjured


title: Human H1 DNA SPRITE 8

description: H1 human embryonic stem cells Replicate 8


title: Human H1 DNA SPRITE 9

description: H1 human embryonic stem cells Replicate 9


title: Human H1 DNA SPRITE 12

description: H1 human embryonic stem cells Replicate 12


title: medaka_uninjured_rep3

description: 10X Genomics


title: after NTD [DK21068_05]

description:
DK21068_05
3' RNA-seq


title: medaka_14dpi_rep2

description: 10X Genomics


title: after PFD [DK22190_04]

description:
DK22190_04
3' RNA-seq

value: PFD


title: medaka_3dpi_rep1

description: 10X Genomics


title: IVET_DRS_unmodified


title: medaka_uninjured_rep2

description: 10X Genomics


title: Human H1 DNA SPRITE 6

description: H1 human embryonic stem cells Replicate 6


title: PDGFRα+ cells, H3K4me3 C&R, biol rep2

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

data_processing:
Paired-end reads were trimmed with Trim Galore and mapped to mm10 using Bowtie2 (v2.4.5) with the following options: --no-mixed --no-discordant. Multi or no mate reads were removed with samtools (v1.10) view (-q 4 -F 0x2).
To identify AR peaks across samples, BAM files were merged across biological replicates (n = 2) to call peaks with MACS2 (v2.2.7.1) (-q 0.05). H3K4me3 peaks were called on individual BAM files using MACS2 (-q 0.0001).
Merged BAM files for AR and IgG were used for downstream analysis (2 merged BAM files for AR and 1 merged BAM file for IgG).
Motif enrichment analysis of AR peaks was performed with HOMER (v4.11) findMotifs with -size 200 -mask options and AR peaks were annotated to mm10 genes using annotatePeaks (-size 200 -mask) from MACS2 summit files.
To generate bigwig files, merged (AR or IgG) or individual (H3K4me3) BAM files were converted to CPM-normalized bigwig files using deepTools (v3.5.1) bamCoverage (--binSize 100 --normalizeUsing CPM).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Hindlimb muscles

extract_protocol:
The nuclei were prepared with ChIC/CUT&RUN Assay Kit (Active Motif, Cat# 53180) following the manufacturer’s protocol.
The library was prepared using NEBNext Ultra II for DNA Library Preparation for Illumina (New England Biolabs, Cat# E7645L) with some modifications according to the Active Motif's instruction.

treatment_protocol: To induce AR signaling, dihydrotestosterone (DHT, 2.5 mg/mouse), dissolved in absolute ethanol and diluted in 0.3% w/v hydroxypropyl cellulose in PBS, was injected subcutaneously at 2 hours before sampling.

value: Hindlimb muscles

tag: cut&run antibody

value: H3K4me3 (Active Motif, Cat# 39916)

value: mesenchymal progenitors

value: DHT for 2h


title: after PFD [DK21068_07]

description:
DK21068_07
3' RNA-seq

value: Idiopathic Pulmonary Fibrosis

value: PBMC

value: Male

value: Asian


title: medaka_uninjured_rep1

description: 10X Genomics


title: after PFD [DK22190_02]

description:
DK22190_02
3' RNA-seq


title: PDGFRα+ cells, AR C&R, biol rep4

value: AR (Abcam, Cat# ab108341)

tag: cell type


title: IPF (before NTD) [DK22190_07]

description:
DK22190_07
3' RNA-seq


title: PDGFRα+ cells, IgG C&R, biol rep2

value: IgG (Active Motif, part of Cat# 53180)


title: PDGFRα+ cells, H3K4me3 C&R, biol rep1


title: Human H1 DNA SPRITE 4

description: H1 human embryonic stem cells Replicate 4


title: IPF (before NTD) [DK22190_05]

description:
DK22190_05
3' RNA-seq


title: Human H1 DNA SPRITE 3

description: H1 human embryonic stem cells Replicate 3


title: IPF (before NTD) [DK21068_01]

description:
DK21068_01
3' RNA-seq


title: PDGFRα+ cells, IgG C&R, biol rep1


title: PDGFRα+ cells, AR C&R, biol rep2


title: GL261-GSCs-rep3

data_processing:
Sequences were aligned to the mm10 genome using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: SmartSeq_processed.h5ad

growth_protocol: Single-cell RNA-sequencing (scRNA-Seq) of GL261 and GL261-GSCs

extract_protocol:
Fresh frozen brains were OCT embedded and 10 μm sections were cut with cryostat
Preparation of lysis plates, FACS sorting, cDNA synthesis using the Smart-Seq2 protocol (Picelli, et al. 2013; Darmanis, et al. 2015), library preparation using an in-house version of Tn5 (Picelli, et al. 2014; Hennig, et al. 2018), library pooling and quality control, and sequencing.

value: Brain


title: Human H1 DNA SPRITE 7

description: H1 human embryonic stem cells Replicate 7


title: PDGFRα+ cells, AR C&R, biol rep1


title: Human H1 DNA SPRITE 2

description: H1 human embryonic stem cells Replicate 2


title: IPF (before PFD) [DK22190_03]

description:
DK22190_03
3' RNA-seq


title: GL261-GSCs-rep4


title: GL261-GSCs-rep2


title: Human H1 DNA SPRITE 5

description: H1 human embryonic stem cells Replicate 5