title: CP011, 2 months, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: CP011_2m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)


title: 1022_BX15A-1

status: Public on Aug 21 2025

type: SRA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-29

library_source: transcriptomic

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM)

molecule: total RNA

organism: Homo sapiens

source_name: prostate

extract_protocol:
Total RNA was extracted from cells adhered to caps using the Qiagen RNeasy FFPE kit.
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit.

treatment_protocol: FFPE human prostate tissues were sectioned onto metal frame membrane slides, and regions of interest were excised onto caps using laser capture microdissection.

tag: gender

value: male

tag: case

tag: regionofinterest


title: NSC,Homo,2

city: Cincinnati

first: Jason

last: Tchieu

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw FASTQ files were quality checked using FastQC. Adapter sequences were trimmed using fastp with parameters "-q 20 -n7". Trimmed reads were then aligned to hg38 using HISAT2 with default parameters. The raw count files was generated using featureCounts in Subread with default parameters.
Genes with no raw counts in >= 75% samples were filtered out. Differential gene expression analysis was performed using "DESeq2" with p.adjust < 0.05 and fold change > 1.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: Human embryonic stem cells (hESCs) were maintained in Essential 8 medium in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen).
mRNA-Seq libraries (poly A enrichment) for hESCs were prepared using TruSeq Stranded mRNA library kit and sequenced at Roy J. Carver Biotechnology Center (CBC) at the University of Illinois at Urbana-Champaign (UIUC) for 150bp paired-end (PE) sequencing on an Illumina NovaSeq platform. mRNA-Seq libraries (poly A enrichment) for NSCs were prepared by Novogene for 150bp paired-end (PE) sequencing on an Illumina NovaSeq platform.

treatment_protocol: Cortical neural stem cells (NSCs) were directly differentiated from hESCs using dual-SMAD strategies for the first 8 days, and subsequently treated with FGF8 to pattern prefrontal cortical lineage until day 18. For overexpression studies, doxycycline treatment starts at d15 till d18.

tag: cell line

tag: cell type

value: cortical neural stem cells

tag: genotype

value: ZMYND11 -/-

tag: treatment

value: cortical differentiation


title: skin_TPC8TNFR1_1

city: Cologne

first: Gianmaria

last: Liccardi

address: Joseph Stelzmann strasse 52, Institute of Biochemistry

country: Germany

institute: Uniklinik, University of Cologne

description:
Library name: sample_7
excluded_from_analysis

data_processing:
Sequencing was then carried out on a NovaSeq 6000 platform, employing a single-read (SR) 1x100 bp sequencing strategy.
Assembly: genome mm10
Supplementary files format and content: raw counts after alignement

organism: Mus musculus

source_name: skin

extract_protocol:
RNA was extracted from skin tissue using the RNeasy Plus Mini Kit (74136, Qiagen). Skin was weighted at 30mg, snap frozen in liquid nitrogen and stored at -80°C before lysed. Skin tissues were lysed in lysis buffer (Buffer RLT + 40ul DTT 1M per ml + 0.5% Reagent DX) according to the kit’s manufacturer instructions in TissueLyser II (85300, Qiagen) using 7 mm stainless steel beads (69990, Qiagen). Extracted RNA was stored at -80°C.
Library preparation was performed using the Lexogen QuantSeq 3’ mRNA sequencing protocol.

tag: tissue

value: skin

tag: batch


title: 1022_BX19A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-33


title: CP016, 2 months, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

city: Miami

first: Akshay

last: Iyer

state: FL

institute: University of Miami

description:
Library name: CP016_2m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)

library_source: other

data_processing:
Cell Ranger v7 count and aggr funtions to aggregate reads across sequencing lanes. filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+FB/ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Blood

extract_protocol:
10x 5' V2.0 chemistry for cDNA amplification
Library preparation for gene expression profiling and V(D)J sequencing were carried out according to manufacturer’s instructions without modification (10x Genomics PN: 1000263, 1000286, 1000250, 1000215, 1000252,1000253, 1000190, 1000541)

value: Blood

value: PBMC

value: perinatal HIV (pHIV)


title: skin_non_disclosed_3

description:
Library name: sample_12
normalization_only


title: skin_not_discosed_1

description:
Library name: sample-11
normalization_only


title: 1022_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-28


title: skin_non_disclosed_2

description:
Library name: sample_11
normalization_only


title: NSC,Homo,1


title: skin_TPC8STING_3

description:
Library name: sample_6
excluded_from_analysis


title: NSC,Het4,4

value: ZMYND11 +/-


title: skin_TPC8TNFR1_3

description:
Library name: sample_9
yes


title: 1021_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-26


title: skin_TPC8STING_2

description:
Library name: sample_5
yes


title: NSC,Het4,3


title: 1021_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-27


title: NSC,Het4,2


title: 1022_BX18A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-30


title: NSC,Het4,1


title: skin_TPC8STING_1

description:
Library name: sample_4
yes


title: 1020_BX16A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-25


title: NSC,Het2,3


title: NSC,Het2,1


title: 1020_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-24


title: 1020_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-23


title: skin_TPC8_2

description:
Library name: sample_2
yes


title: 1020_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-22


title: NSC,WT,2

value: WT


title: NSC,WT,4


title: NSC,WT,3


title: NSC,WT,1


title: skin_TPC8_1

description:
Library name: sample_1
yes


title: 1019_BX17A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-21


title: NSC,mouse,IgG

library_source: genomic

data_processing:
CUT&RUN sequencing reads were quality checked using FastQC, and adapters were trimmed using fastp with parameters “-q 20 -n 7”. Reads were aligned to hg38 using bowtie2 with parameters “--very-sensitive--no-unal--no-mixed--no-discordant -I 10 -X 700”. Low quality (MAPQ<10) reads were discarded using Samtools view with parameters “-q 10”. Duplicated reads were discarded using Picard MarkDuplicates with parameters “REMOVE_DUPLICATES=true”. Only uniquely mapped reads were used for subsequent analysis after these filters. Bigwig files were generated using bamCompare in deepTools with parameters “--binSize 20--normalizeUsing RPKM”.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
Around half a million cells were harvested and bound to Concanavalin A beads. These cell-bound beads were incubated with antibodies overnight at 4°C and treated with pAG-MNase for 1 hour at 4°C. Calcium was added to start pAG-MNase digestion for 30 minutes and CUT&RUN fragments were released and purified by phenol-chloroform extraction. DNA concentration was measured by Quantus fluorometer.
CUT&RUN seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina and size selection was performed after PCR enrichment of adaptor-ligated library using MagBind Magnetic Beads. Libraries were sent to Novogene for premade libraries partial-lane sequencing aiming for 10-20million reads.

treatment_protocol: Cortical neural stem cells were directly differentiated from hESCs using dual-SMAD strategies for the first 8 days, and subsequently treated with FGF8 to pattern prefrontal cortical lineage until day 18. For overexpression studies, doxycycline treatment starts at d15 till d18.

tag: cut&run antibodies

value: Normal Mouse IgG (Millipore, 12-371)


title: NSC,FLAG,dox,FLAG,2

value: cortical differentiation, dox (200ng/ml) for 3 days

value: FLAG (Sigma-Aldrich, F1804)


title: TM3_Py_rep2

city: Zhenjiang

first: Jie

last: Yang

state: Jiangsu

address: 301 Xuefu Road

country: China

institute: Jiangsu University

description:
Library name: C_Py2
Column name in gene_count.xls: C_Py2

data_processing:
Raw data (raw reads) in fastq format were initially processed using fastp software. During this step, clean data (clean reads) were generated by removing reads containing adapters, reads with poly-N sequences, and low-quality reads. Additionally, the Q20, Q30, and GC content of the clean data were calculated. All downstream analyses were based on the high-quality clean data.
Reference genome and gene model annotation files were downloaded directly from the genome website. The index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome using the same version of Hisat2. We selected Hisat2 as the mapping tool because it can generate a splice junction database based on the gene model annotation file, providing better mapping results compared to other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene. The Fragments Per Kilobase of transcript sequence per Million base pairs sequenced (FPKM) for each gene was then calculated based on the gene length and the number of reads mapped to that gene. FPKM takes into account both the sequencing depth and the gene length, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (version 1.20.0). DESeq2 provides statistical routines for determining differential expression in digital gene expression data based on a model using the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg approach to control the false discovery rate (FDR). Genes with an adjusted P-value ≤ 0.05 were considered differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was performed using the clusterProfiler R package, with gene length bias correction applied. GO terms with a corrected P-value less than 0.05 were considered significantly enriched by differentially expressed genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of biological systems, such as the cell, organism, and ecosystem, from molecular-level information, especially large-scale datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). KEGG pathway enrichment analysis of differentially expressed genes was also conducted using the clusterProfiler R package.
Assembly: mm10
Supplementary files format and content: gene_count.xls – Excel file containing raw read counts for each gene, generated using featureCounts v1.5.0-p3.
Supplementary files format and content: gene_fpkm.xls – Excel file containing gene expression levels (FPKM), calculated based on gene length and read counts.

growth_protocol: The mouse Leydig cell line TM3 was purchased from Shanghai Yuchi Biotech Co., Ltd. (Catalog No. SC0443) and authenticated by STR species identification. Cells were cultured in DMEM (Gibco, 11995073) supplemented with 10% fetal bovine serum (Lonsera, S711-001S) and 1% penicillin-streptomycin (Servicebio, G4003) in a humidified incubator at 37°C with 5% CO₂. Medium was changed every 2–3 days. When cells reached ~80% confluence, they were dissociated with trypsin (Beyotime, C0201) and passaged at a ratio of 1:3.

extract_protocol:
RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA integrity was assessed with the RNA Nano 6000 Assay Kit on the Bioanalyzer 2100 system (Agilent, 5067-1511).Total RNA was used as input material for RNA sample preparation. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptors with hairpin loop structures were ligated for hybridization. To select cDNA fragments of 370–420 bp in length, the library fragments were purified using the AMPure XP system. PCR amplification was performed with Phusion High-Fidelity DNA Polymerase, Universal PCR primers, and Index (X) Primer. Finally, the PCR products were purified again using the AMPure XP system, and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: TM3 cells were exposed to 100 nM Pyrotinib (pyrrolo[2,3-d]pyrimidine-4,5-dione, supplied by Jiangsu Hengrui Medicine Co., Ltd.) for 48 hours, and 0.1‰ DMSO was used as a control.

value: Mouse leydig cells

tag: time

value: 48 hours

value: 100 nM Pyrotinib


title: TM3_Py_rep3

description:
Library name: C_Py3
Column name in gene_count.xls: C_Py3


title: NSC,FLAG,dox,FLAG,1


title: NSC,Het2,4


title: 1019_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-20


title: 1017_BX8A-4

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-30


title: TM3_Py_rep1

description:
Library name: C_Py1
Column name in gene_count.xls: C_Py1


title: NSC,FLAG,no,dox,ZM11

value: cortical differentiation, with no dox

value: ZMYND11 (Sigma-Aldrich, ABE1889)


title: NSC,FLAG,no,dox,FLAG

value: cortical neural stem cells


title: NSC,FLAG,dox,ZM11


title: NSC,Het2,2


title: 1017_BX8A-3

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-29

value: male


title: NSC,test,H3K36me3,Epi

value: cortical differentiation


title: TM3_DMSO_rep3

description:
Library name: C_NC3
Column name in gene_count.xls: C_NC3

value: 0.1‰ DMSO


title: skin_TPC8_3

description:
Library name: sample_3
excluded_from_analysis

value: skin


title: NSC,test,H3K36me3,Abcam


title: 1017_BX8A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-28


title: NSC,test,H3K36me3,AM

value: H3K36me3 (Active Motif, 61101)


title: NSC,test,H3K27me3

value: H3K27me3 (Cell Signaling Technology, 9733)


title: NSC,test,rabbit,IgG

value: Normal Rabbit IgG (Millipore, 12-370)


title: 1017_BX8A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-27


title: NSC,Homo,ZM11

value: ZMYND11 -/-


title: 1016_BX17A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-19


title: NSC,Het4,ZM11

value: ZMYND11 +/-


title: TM3_DMSO_rep1

description:
Library name: C_NC1
Column name in gene_count.xls: C_NC1


title: NSC,Het2,ZM11


title: Lung, rgPB2460S/NP163T infection, Rep3

city: Guangzhou

first: yuting

last: Ye

address: Guangzhou Dongfengxi road

institute: Guangzhou Medical University

description: Library name: ST_3

data_processing:
After obtaining raw data, paired-end reads were harvested and trimmed by trim-galore (version 0.6.10) to remove adaptor sequences and low-quality nucleotides.
High-quality reads were then aligned to ENSEMBL GRCm38 reference genome using HISAT2 (version 2.1.0) with default parameters
For RNA-seq, featureCounts (version 2.0.1) software was used to count reads mapped to RefSeq genes, and differential gene expression analysis was conducted using DESeq2 R package (version 1.38.3).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file represents counts

source_name: Lung

extract_protocol:
Total RNA was extracted using the Tissue RNA Purification Kit PLUS (EZBioscience).
RNA libraries for mRNA sequencing were prepared with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB), following the manufacturer's instructions.

treatment_protocol: Mice lungs intranasally infected with the recombinant influenza B viruses rgPB2460N/NP163I or rgPB2460S/NP163T were harvested at 5 dpi for RNA sequencing. Control mice were inoculated with 50 μl of PBS only.

value: Lung

value: rgPB2460S/NP163T infection


title: Lung, rgPB2460S/NP163T infection, Rep2

description: Library name: ST_2


title: 1016_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-18


title: NSC,rabbit,IgG

value: WT


title: NSC,WT,H3K36me3,2


title: NSC,WT,H3K36me3,1


title: 1014_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-17


title: Lung, rgPB2460N/NP163I infection, Rep2

description: Library name: NI_2

value: rgPB2460N/NP163I infection


title: spinal cord with sOrg_7wpi

city: Shanghai

first: Yanjing

last: Zhu

address: No.727 Zhongshan Road

institute: Tongji University

description: Library name: Sample 2

data_processing:
ST-Seq: The FASTQ files were processed using the 10x Genomics Space Ranger pipeline. Reads were aligned to the reference genome. The spaceranger count pipeline was used to perform alignment, tissue detection, fiducial alignment, and spatial barcode/UMI counting. This process generated a feature-spot barcode count matrix and determined the spatial location of each barcode on the tissue image
RNA-Seq: Raw FASTQ reads are checked for quality, adapter content, and other issues using FastQC. Low-quality bases and adapter sequences are removed to improve alignment accuracy. The cleaned reads are mapped to a reference genome using STAR. The number of reads mapping to each gene is counted from the BAM files using Stringtie, producing a the count matrix.
Assembly: mm10, hg38
Supplementary files format and content: Filtered Feature-Barcode Matrix: This contains the gene expression counts for tissue-associated spots.
Supplementary files format and content: Spatial Information Files: These files link the expression matrix to the spatial coordinates on the slide.
Supplementary files format and content: Histology Image: The tissue image used for spatial context.
Supplementary files format and content: Gene count matrix file: a csv-formatted file containing the number of sequencing reads that have been assigned to the human geneset for each of the samples.
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Spinal cord

extract_protocol:
ST-Seq: spinal cord samples were cryosectioned (10 m) and prepared for spatial transcriptomics using the 10x Genomics Visium platform. Sample quality (morphology & RNA integrity  RIN 7.9-8.8) was confirmed prior to analysis.      RNA-Seq: sOrg and enTsOrg  were sent to BGI for RNA-seq analysis. Total RNA was isolated, mRNA enriched, fragmented, and reverse transcribed into cDNA libraries using standard protocols. Untreated iPSCs served as a control.
ST-Seq: Each slide contained approximately 5,000 spots (55 m diameter, 100 m spacing) for capturing RNA. Permeation times were optimized for each group (6-18 min) using the Visium Tissue Optimization Kit. Libraries were generated with the Visium Spatial Gene Expression Kit and sequenced on an Illumina NextSeq.     RNA-Seq: sequencing was performed on a DNBSEQ system.

value: Spinal cord


title: 1012_BX6A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-15


title: Lung, rgPB2460S/NP163T infection, Rep1

description: Library name: ST_1


title: Lung, rgPB2460N/NP163I infection, Rep3

description: Library name: NI_3


title: Lung, rgPB2460N/NP163I infection, Rep1

description: Library name: NI_1


title: TM3_DMSO_rep2

description:
Library name: C_NC2
Column name in gene_count.xls: C_NC2

value: Mouse leydig cells

value: 48 hours


title: spinal cord with enTsOrg_7wpi

description: Library name: Sample 1


title: 1014_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-16


title: Basal_1

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

description: Library name: BaB1_S13

data_processing:
The quality of the samples was verified using FastQC v0.12.1 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v2.0.6 software and Gencode vM36 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: lymphocyte

growth_protocol: CD8+ T cells were purified from mouse splenocytes using the Miltenyi microbead negative selection kits and activated by plating them at 1x106 cells/mL in complete RPMI medium with anti-CD3/CD28 dynabeads at 1:2 beads: T cell ratio and 100 IU/mL IL-2. Activated T cells were incubated at 37C for 24 hours. Then , cells were retrovirally transduced  with a pRubiG vector to express antii mouse BCMA CART and SLC1A5 transporter. The infected cells were expanded for additional 3 days in  complete RPMI medium containing 100 UI/mL of IL-2 .

extract_protocol:
Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules in the total RNA.
The purified mRNA was fragmented and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. A second strand cDNA synthesis step removed the RNA template while incorporating dUTP in place of dTTP in order to preserve strand specificity. Next, double‐stranded cDNA was A‐tailed, then ligated to Illumina anchors bearing T‐overhangs. PCR‐amplification of the library allowed the barcoding of the samples with 10 bp dual indexes and the completion of Illumina sequences for cluster generation.

treatment_protocol: CD8 BCMA CART cells were  left untreated or activated in BCMA coated plates for 16h. After this incubation, total RNA was extracted and analyzed by RNAsec

value: lymphocyte

value: CD8 T lymphocyte

value: in vitro culture withouth antigen stimulation for 16h


title: 1012_BX4A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-14

value: male


title: NSC,WT,ZM11,1

value: cortical neural stem cells

value: cortical differentiation

value: ZMYND11 (Sigma-Aldrich, ABE1889)


title: Lung, PBS, Rep2

description: Library name: PBS_2

value: PBS inoculation


title: 1012_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-13


title: Basal_Slc1a5_3

description: Library name: BaA3_S18


title: Basal_3

description: Library name: BaB3_S15


title: Basal_Slc1a5_2

description: Library name: BaA2_S17


title: Lung, PBS, Rep1

description: Library name: PBS_1


title: RAW 264.7 cell, BPAP_rep3

first: Ze

last: Chen

state: -- Please Select --

address: 910 Hengshan Road

institute: International Peace Maternity and Child Health Hospital

description: Library name: Sample 6

data_processing:
Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000.
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina). The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization.
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Assembly: GRCm38
Supplementary files format and content: xls files include FPKM values and counts for each Sample

source_name: RAW 264.7 cell

growth_protocol: The RAW 264.7 cells were cultured in DMEM (Gibco, Thermo Fisher Scientific-CN),medium was routinely supplemented with 10% fetal bovine serum (Hyclone, Thermo Fisher

extract_protocol:
Total RNA from RAW 264.7 cells were extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's instructions.
RNA libraries  for RNA-seq were prepared according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ).

treatment_protocol: RAW 264.7 cells  were treated with BPAP.

value: RAW 264.7 cell

value: macrophage cells

value: BPAP


title: Basal_Slc1a5_1

description: Library name: BaA1_S16


title: Stimulated_3

description: Library name: AcB3_S21

value: In vitro stimulation with BCMA coated plates for 16h


title: 1011_BX4A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-12


title: Stimulated_2

description: Library name: AcB2_S20


title: Stimulated_1

description: Library name: AcB1_S19


title: NSC,WT,ZM11,2

value: WT


title: RAW 264.7 cell, BPAP_rep2

description: Library name: Sample 5


title: Stimulated_Slc1a5_3

description: Library name: AcA3_S24


title: Basal_2

description: Library name: BaB2_S14


title: 1006_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-9


title: RAW 264.7 cell, BPAP_rep1

description: Library name: Sample 4


title: Stimulated_Slc1a5_2

description: Library name: AcA2_S23


title: 1006_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-8


title: Stimulated_Slc1a5_1

description: Library name: AcA1_S22


title: C57BL6/J, 2

city: Barcelona

first: Ana

last: Hernández de Sande

address: C/ del Rosselló, 153

institute: IDIBAPS

description:
Library name: HL5
GEO_submission_counts_inVivo.csv

data_processing:
Quality control (QC) was performed using fastqc (version 0.11.9)
FastQ files were aligned using STAR (version 2.7.a) to GRCm39 with gencode annotation versus 30.
QoRTs (v1.3.6) was used for QC and for obtaining raw counts.
Normalization for subsequent analysis was performed using the edgeR package with the trimmed mean of M-values used for computing the scale factors
Assembly: GRCm39, Mus musculus
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Liver

growth_protocol: hydrodynamic tail vein delivery

extract_protocol:
RNA was extracted from excised HCC tumors using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions
Sequencing libraries were generated using 200 ng of total RNA with the Illumina TruSeq Stranded mRNA Prep Ligation kit (Illumina, Inc., San Diego, CA) following the manufacturer’s instructions. Each library was sequenced on an Illumina NextSeq2000 (Illumina, Inc.) in paired-end mode with a read length of 2×100 bp

treatment_protocol: Mice were randomized to receive vehicle control, E7386 (50 mg/kg), lenvatinib (10 mg/kg), and a combination of E7386 and lenvatinib

value: Liver

tag: strain

tag: mutations


title: 1006_BX5A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-10


title: C57BL6/J, 1

description:
Library name: HL4
GEO_submission_counts_inVivo.csv


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, E7386+Lenvatinib, 3

description:
Library name: REJA_238
GEO_submission_counts_inVivo.csv

source_name: Liver tumor

value: Liver tumor


title: 1001_BX7A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-7


title: RAW 264.7 cell, Control_rep2

description: Library name: Sample 2

value: DMSO


title: RAW 264.7 cell, Control_rep3

description: Library name: Sample 3


title: RAW 264.7 cell, Control_rep1

description: Library name: Sample 1


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, E7386+Lenvatinib, 1

description:
Library name: REJA_213
GEO_submission_counts_inVivo.csv


title: 1001_BX7A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-6


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, E7386, 1

description:
Library name: REJA_253
GEO_submission_counts_inVivo.csv


title: 1011_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-11


title: 1001_BX5A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-5


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, Lenvatinib, 1

description:
Library name: REJA_219
GEO_submission_counts_inVivo.csv

value: Lenvatinib


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, Lenvatinib, 3

description:
Library name: REJA_251
GEO_submission_counts_inVivo.csv


title: MIday14+T8Ab Rep2, MI study

city: Frederick

first: GuoJun

last: Yu

address: 560 CHANDLER STREET

department: Cell Biology

institute: National Institutes of Health

description: 10X Genomics, Chromium Next GEM Single Cell 5' reagent v2 dual index kits

library_source: transcriptomic single cell

data_processing:
The fastq files were aligned to the database of the mouse genome (refdata-gex-mm10-2020-A) using cellranger (v7.0.0, 10x Genomics) with the default parameters on the NIH HPC Biowulf cluster (http://hpc.nih.gov). The h5 files from the output folder were analyzed using the Seurat (v4.1.1) according to the manual. For each sample, the cutoff of the following parameters was set as: min.cells >= 10, min.features >= 250,  nCount_RNA >= 500, nFeature_RNA <= 10,000, and percent.mt <=10. After the above filter, the potential cell doublets were filtered out using DoubletFinder (v2.0.3). For the analysis of differentially expressed genes, the pseudo-bulk RNA-seq method with DESeq2 (v1.36.0) was adopted. The clusterProfiler (v4.4.4) was used for the GO enrichment analysis. The volcano plots and heatmap were plotted using ggplot2(v3.4.3) and ComplexHeatmap (v2.15.1), separately. For the RNA velocity analysis, velocyto (v0.17) and scvelo (v0.2.4) were used. CellChat (v1.6.1) was used for the analysis of cellular communication.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: H5 files contain all the reads number information for all the detected genes fromeach cell.

source_name: heart

extract_protocol:
Mice were anesthetized with 0.2 mL/10 g Avertin of body weight and the heart was perfused with sterile ice-cold PBS using a miniplus peristaltic pump (~1ml/heart/min, GILSON) for 10 min to clear red blood cells. Cardiac single cells were obtained using the Multi Tissue Dissociation Kit 2 (Cat# 130-110-203, Miltenyi Biotec) according to manufactures protocols. This kit removes most of the cardiomyocytes during the procedure and the cutoff of single cell viability from each sample was ~90%.
Libraries preparation and sequencing were performed at the Sequencing Facility, Frederick National Laboratory for Cancer Research. Briefly, ~16.5K cells were collected for each sample, and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and Chromium Next GEM Single Cell 5' reagent v2 dual index kits were used for the AngII/PE mouse model and the MI model, respectively.

tag: model

value: MI model

value: heart

value: purified single cells from mouse heart

value: Wild type C57BL/6-NCr


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, Lenvatinib, 2

description:
Library name: REJA_242
GEO_submission_counts_inVivo.csv


title: 1001_BX5A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-4

value: male


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, Vehicle, 2

description:
Library name: REJA_231
GEO_submission_counts_inVivo.csv

value: Vehicle


title: MIday14+T8Ab Rep1, MI study


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, Vehicle, 1

description:
Library name: REJA_216
GEO_submission_counts_inVivo.csv


title: MIday14+Saline Rep2, MI study


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, Vehicle, 3

description:
Library name: REJA_262
GEO_submission_counts_inVivo.csv


title: 1001_BX3A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-3


title: MIday14+Saline Rep1, MI study


title: Mouse intestine animal 3 plate 6

city: Munich

first: Christoph

last: Geisenberger

address: Thalkirchnerstr. 36

institute: Institute of Pathology

description: Library name: JvB-176-SI-mouse3-H3K27me3-scEpi2-seq-pl6

data_processing:
Demultiplexing of reads and extraction of single-cell barcodes
Adapter trimming with cutadapt
Mapping to mouse genome with bwa -mem algorithm
Custom bam tagging tool to add flags for data filtering
Extracting methylation state for each CpG covered in the data from sequencing reads with custom software and writing output to .tsv files
genome build/assembly: GRCm38
processed data files format and content: Data table containing library ID, cell ID, chromosome, genomic position, methylation state, cutsite motif
Library strategy: scEpi2-seq

source_name: Small intestine

growth_protocol: The mice that were used are of the Mus musculus C57BL/6 strain. Animals used in the experiments were between 8 and 22 weeks of age. Both male and female mice were used for the experiments. Mice were housed in open housing with 14:10 h light:dark cycle at 24 °C and 45–70% relative humidity with food and water ad libitum. Three individual mice were used, the proximal, middle and distal part of the intestines from a single individual was pooled following the generation of single cell suspension, fixation and CellTrace labeling (Invitrogen, according to manufacturer's protocol); randomization and blinding were not performed

extract_protocol: Custom library protocol. Briefly, cells were incubated with the antibodies listed above and a pA-MNase fusion protein. Next, individual cells were sorted into 384-well plate. Subsequently, MNase digestion was initiated through the addition of calcium. Next, MNase digestion was stopped and DNA released by Proteinase K digestion. DNA fragments were end-repaired by Klenow Large Fragment and PNK. Repaired ends were ligated to custom barcoded adapters containing a UMI, Illumina handle and T7 promoter. After IVT and PCR, sequencing libraries were assessed with Qubit and Bioanalyzer and normalized libraries loaded onto Illumina sequencer according to the manufacturers instructions.

value: Small intestine

value: Mouse intestinal cells


title: Mouse intestine animal 3 plate 7

description: Library name: JvB-176-SI-mouse3-H3K27me3-scEpi2-seq-pl7


title: MIday7+T8Ab Rep1, MI study


title: CEBPG_KD5

city: Malmo

first: Dmytro

last: Kryvokhyzha

address: Jan Waldenströms gata 35

department: Clinical Sciences

country: Sweden

institute: Lund University

data_processing:
QC with fastQC 0.10
reads counting with Salmon 1.5.0
Assembly: Rnor_6.0
Supplementary files format and content: raw counts for each sample in a tab-delimited file

organism: Rattus norvegicus

source_name: cell line

extract_protocol:
NucleoSpin RNA (Macherey Nagel, Prod# 740955.250)
Illumina truSeq stranded total RNA prep, LT Ribo zero

treatment_protocol: INS-1 cells were treated with negative control siRNA (NC2) and an siRNA for CEBPG.

value: cell line

value: pancreatic beta-cell line

value: Knockdown


title: MIday7+Saline Rep2, MI study


title: Mouse intestine animal 3 plate 3

description: Library name: JvB-176-SI-mouse3-H3K27me3-scEpi2-seq-pl3


title: MIday7+Saline Rep1, MI study


title: Mouse intestine animal 1 plate 8

description: Library name: JvB-176-SI-mouse1-H3K27me3-scEpi2-seq-pl8


title: CEBPG_KD3


title: 1001_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-1


title: Mouse intestine animal 2 plate 3

description: Library name: JvB-176-SI-mouse2-H3K27me3-scEpi2-seq-pl3


title: CEBPG_KD4


title: Mouse intestine animal 3 plate 2

description: Library name: JvB-176-SI-mouse3-H3K27me3-scEpi2-seq-pl2


title: 1001_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-2


title: Mouse intestine animal 1 plate 2

description: Library name: JvB-176-SI-mouse1-H3K27me3-scEpi2-seq-pl2


title: CEBPG_KD2


title: Sham Rep3, MI study

value: Sham


title: Mouse intestine animal 2 plate 2

description: Library name: JvB-176-SI-mouse2-H3K27me3-scEpi2-seq-pl2

value: WT


title: Sham Rep2, MI study

description: 10X Genomics, Chromium Next GEM Single Cell 5' reagent v2 dual index kits


title: Mouse intestine animal 1 plate 7

description: Library name: JvB-176-SI-mouse1-H3K27me3-scEpi2-seq-pl7


title: MIday7+T8Ab Rep2, MI study


title: Mouse intestine animal 3 plate 5

description: Library name: JvB-176-SI-mouse3-H3K27me3-scEpi2-seq-pl5


title: CEBPG_KD1


title: CEBPG_NC5

value: Control


title: Mouse intestine animal 2 plate 4

description: Library name: JvB-176-SI-mouse2-H3K27me3-scEpi2-seq-pl4


title: KPCYG12D_TMA_vehicle/panKRASi

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
library strategy: Spatial transcriptomics
The sequencing outputs for all Visium datasets were preprocessed using spaceranger-2.0.0 and mapped to the latest mouse reference genome and the filtered matrices were converted to Seurat objects in R and used for downstream analyses.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz : Filtered feature-barcode matrices from Space Ranger
Supplementary files format and content: spatial.tar.gz : processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format

source_name: Pancreas

extract_protocol:
Tissues were processed according to the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) protocol
Libraries were constructed according to the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) protocol

value: Pancreas

value: Vehicle/PanKRASi

tag: treatment duration

value: Treated for 14 days


title: Mouse intestine animal 1 plate 6

description: Library name: JvB-176-SI-mouse1-H3K27me3-scEpi2-seq-pl6


title: Cardiomyocytes, FA3ic, Healthy, 1

city: Fitzroy

first: Jarmon

last: Lees

state: VIC

address: 9 Princes Street, Fitzroy, Victoria, Australia

country: Australia

institute: St Vincent's Institute Of Medical Research

description:
Library name: Sample 16
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_10_S34

data_processing:
Reads were trimmed for adatoor sequence and quality (-q 20) using TrimGalore!
Read were mapped to a transcriptome index using Salmon, correcting for sequence and GC biases
Transcript counts were imported using tximeta
Assembly: GRCh38.93
Supplementary files format and content: tsv file of raw gene counts for each sample

growth_protocol: Patient iPSC-derived cardiomyocytes and isogenic control cardiomyocytes were differentiated over 19 days according to publsihed protocols (PMID: 39803589). On day 19, cardiomyocytes were plated on GFR-matrigel in RPMI medium + Ascorbic acid + B27-supplement for 48 hours, and then harvested for RNA.

extract_protocol:
Total RNA was extracted from cardiomyocytes derived from all three FRDA and isogenic control iPSC lines across three independent experiments using the Cytivia Mini RNA Extraction Kit (Cytivia, MA, USA), following the manufacturer’s instructions. Residual genomic DNA was removed by treatment with TURBO DNase (Thermo Fisher Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies), and all samples exhibited an RNA Integrity Number (RIN) of approx 10.
Library preparation was performed using 100 ng of input RNA per sample with the TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) as per manufacturer’s instruction.  The library was quantified using the Agilent Tapestation and the Qubit™ RNA assay kit for Qubit 2.0® Fluorometer (Life technologies).  Unique dual indexes (Illumina TruSeq RNA UD Indexes) were used to barcode individual libraries.  The indexed libraries were then prepared and diluted to 750pM for paired end (2x 101 base) sequencing on a NextSeq2000 instrument using the P3 200 cycle kit using v3 chemistry (Illumina, CA, USA) as per manufacturer’s instructions.

tag: patient

value: iPSC-cardiomyocytes

value: corrected


title: enTsOrg-sOrg_3w-ST-seq

description: Library name: Sample 3

source_name: Organoid

value: Organoid


title: Sham Rep1, MI study

value: MI model

value: heart

value: purified single cells from mouse heart

value: Wild type C57BL/6-NCr


title: Cardiomyocytes, FA3ic, Healthy, 3

description:
Library name: Sample 18
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_12_S36


title: Cardiomyocytes, FA3ic, Healthy, 2

description:
Library name: Sample 17
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_11_S35


title: AngII/PE+T8Ab Rep3, AngII/PE study

description: 10X Genomics, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: AngII/PE model


title: Cardiomyocytes, FA3, Disease, 3

description:
Library name: Sample 15
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_09_S33


title: Cardiomyocytes, FA3, Disease, 1

description:
Library name: Sample 13
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolB_c_07_S31


title: AngII/PE+T8Ab Rep2, AngII/PE study


title: Cardiomyocytes, FA2ic, Healthy, 3

description:
Library name: Sample 12
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_06_S30


title: Cardiomyocytes, FA2, Disease, 3

description:
Library name: Sample 9
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_03_S27


title: CEBPG_NC4

value: cell line


title: Cardiomyocytes, FA2ic, Healthy, 1

description:
Library name: Sample 10
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_04_S28


title: AngII/PE+Saline Rep2, AngII/PE study

value: AngII/PE+Saline


title: ZSF1ob14-22

city: Louisville

first: Andrew

middle: A.

last: Gibb

state: KY

address: 580 S Preston, Baxter II, 404C

institute: University of Louisville

description: Library name: Sample 18

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
High quality reads were mapped to rattus norvegicus whole genome using HISAT2 v2.1.0 and quantified using HTSeq v0.11.2
Differential expression was calculated using DESeq2 v1.22.2
Assembly: Rnor_6.0
Supplementary files format and content: tab delimited format contains fold change and FDR of differentially expressed genes between experimental and control groups

source_name: Heart Left Ventricle

extract_protocol:
Tissue was disrupted and total RNA isolated using Qiagen Rneasy kit according to manufacturer's instructions.
TrueSeq stranded mRNA library prep kit was used to enrich polyA mRNAs via poly-T based RNA purifications beads which were amplified using Hiseq rapid SR cluster kit and multiplexed and run using the HiSeq rapid SBS kit

value: Heart Left Ventricle

value: ZSF1 Obese

value: total RNA


title: AngII/PE+T8Ab Rep1, AngII/PE study


title: CEBPG_NC3

value: pancreatic beta-cell line

value: Control


title: CEBPG_NC2


title: Cardiomyocytes, FA1ic, Healthy, 3

description:
Library name: Sample 6
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_b_12_S24


title: Cardiomyocytes, FA2ic, Healthy, 2

description:
Library name: Sample 11
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_05_S29


title: AngII/PE+Saline Rep3, AngII/PE study


title: Cardiomyocytes, FA2, Disease, 1

description:
Library name: Sample 7
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_01_S25

value: WT


title: Cardiomyocytes, FA2, Disease, 2

description:
Library name: Sample 8
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolB_c_02_S26


title: Cardiomyocytes, FA3, Disease, 2

description:
Library name: Sample 14
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_c_08_S32


title: CEBPG_NC1


title: MYC-lucOS;CTNNB1 overexpression, C57BL6/J, E7386+Lenvatinib, 2

description:
Library name: REJA_228
GEO_submission_counts_inVivo.csv

value: Liver tumor


title: Saline+T8Ab Rep3, AngII/PE study


title: AngII/PE+Saline Rep1, AngII/PE study


title: ZSF1ob14-21

description: Library name: Sample 17


title: Cardiomyocytes, FA1, Disease, 2

description:
Library name: Sample 2
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_b_08_S20

value: iPSC-cardiomyocytes


title: Saline+T8Ab Rep2, AngII/PE study


title: Cardiomyocytes, FA1, Disease, 3

description:
Library name: Sample 3
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_b_09_S21


title: Cardiomyocytes, FA1ic, Healthy, 2

description:
Library name: Sample 5
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_b_11_S23

value: corrected


title: ZSF1ob14-20

description: Library name: Sample 16


title: ZSF1ob14-19

description: Library name: Sample 15


title: ZSF1ob14-18

description: Library name: Sample 14


title: Saline+T8Ab Rep1, AngII/PE study


title: Cardiomyocytes, FA1ic, Healthy, 1

description:
Library name: Sample 4
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_b_10_S22


title: SNU387, E7386-treated, 4

description:
Library name: X387_0_1uM_4_S68
GEO_submission_counts_inVitro.csv

data_processing:
Quality control (QC) was performed using fastqc (version 0.11.9)
Fastq files were aligned using STAR (version 2.7.6) to GRCh38
Raw gene counts were estimated using featureCounts (version 2.0.1)
Normalization for subsequent analysis was performed using the DESeq2 package with the relative log expression used for computing the scale factors
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: HCC cell lines were cultured in DMEM or RPMI (ThermoFisher, Waltham, MA) supplemented with 10% heat-inactivated FBS

extract_protocol:
RNA was extracted from seeded human HCC cell lines using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions
Sequencing libraries were generated using 200 ng of total RNA with the Illumina TruSeq Stranded mRNA Prep Ligation kit (Illumina, Inc., San Diego, CA) following the manufacturer’s instructions. Each library was sequenced on an Illumina NextSeq2000 (Illumina, Inc.) in paired-end mode with a read length of 2×50 bp

treatment_protocol: cells were treated for 24 hours with E7386 or DMSO at concentration of 0.1 μM.

value: TERT; TP53; NRAS

tag: passage

value: 8-10 passages


title: Cardiomyocytes, FA1, Disease, 1

description:
Library name: Sample 1
Column name in "Lees_FRDA_CM_RNAseq_GeneCounts_AllSamples.tsv": JL_poolC_b_07_S19


title: ZSF1ob14-17

description: Library name: Sample 13


title: Saline+Saline Rep2, AngII/PE study

description: 10X Genomics, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: heart

value: Saline+Saline


title: Mouse intestine animal 2 plate 7

description: Library name: JvB-176-SI-mouse2-H3K27me3-scEpi2-seq-pl7

value: Small intestine

value: Mouse intestinal cells


title: SNU387, E7386-treated, 1

description:
Library name: X387_0_1uM_1_S65
GEO_submission_counts_inVitro.csv


title: ZSF1lean14-38

description: Library name: Sample 12

value: ZSF1 Lean


title: SNU387, DMSO-treated, 3

description:
Library name: X387_DMSO_3_S63
GEO_submission_counts_inVitro.csv

value: DMSO


title: ZSF1lean14-37

description: Library name: Sample 11

value: Heart Left Ventricle


title: SNU387, DMSO-treated, 2

description:
Library name: X387_DMSO_2_S62
GEO_submission_counts_inVitro.csv


title: SNU387, DMSO-treated, 1

description:
Library name: X387_DMSO_1_S61
GEO_submission_counts_inVitro.csv


title: SNU387, DMSO-treated, 4

description:
Library name: X387_DMSO_4_S64
GEO_submission_counts_inVitro.csv


title: Saline+Saline Rep1, AngII/PE study

value: AngII/PE model

value: purified single cells from mouse heart

value: Wild type C57BL/6-NCr


title: Donor HSPC

city: Los Angeles

first: Apeksha

last: Singh

state: CA

address: 570 Boyer Hall

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
Demultiplexing, bardcode processing, feature counting, and aggregation performed with CellRanger (version 7.0; cellranger counts; --expect-cells=10000). Output from cellranger was loaded into Seurat (version 4.3.0) and cells with less than 200 features (min.features) or less than 2000 UMI (nCount_RNA) and features with less than 3 cells nonzero expression (min.cells) were filtered out.  Additionally, cells with more than 10% mitochondrial transcripts were removed.  Gene expression and hashtag counts were normalized using the “LogNormalize” and “CLR” methods respectively.  Next DoubletFinder (version 2.0.3) was used for doublet detection and exclusion.  The first 40 principal components (PCA calculated by Seurat using the scaled top 2000 variable features (method -“vst”) were used to identify the optimal pK parameter (paramSweep_v3).  A doublet rate of 5% was assumed as input for doubletFinder_v3 along with the identified pK parameter (0.001), and the suggested value of pN = 0.25 was used.  The normalized hashtag counts were used to demultiplex the cells from each recipient.  Cells identified as singlets from DoubletFinder were retained and then cells assigned doublet or negative from HTO demultiplexing were removed.  Next, a set of genes related to hematopoiesis were utilized for dimensionality reduction.  Normalized counts for these genes were scaled across all cells (deducted mean and divided by standard deviation) and input for principal component analysis.  Using the first 20 principal components, a k-nearest neighbors graph was constructed (k=15). To remove potential contaminating cells that were not LSK HSPCs, cells with likely zero Kit expression were removed.  More specifically, cells were only retained if they either had nonzero Kit expression or were assigned nonzero expression status through an iterative process that would include cells that had nonzero expression status in at least half of their neighbors.  This quality control resulted in 2757 cells from the wildtype recipient and 2769 cells from the IκB– recipient.
Assembly: mm10
Supplementary files format and content: tab separated value and matrix files

source_name: Bone Marrow

extract_protocol:
Bone marrow from the bilateral femur and tibia was collected; red blood cells were lysed and mature hematopoietic cells were depleted using magnetic bead-based lineage antibody cocktail.  Pre-selected cells were then flow sorted to collect CD45.1+/Lin-/Sca1+ cKithi (LSK) HSPCs. 30,000 cells were collected from each experimental condition, barcoded with TotalSeqB antibodies, and multiplexed for sequencing.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: Bone Marrow

value: LSK (Lin-Sca1+cKit+)


title: Hep3B, E7386-treated, 3

description:
Library name: X3B_0_1uM_3_S47
GEO_submission_counts_inVitro.csv

value: AXIN1; RB1


title: ZSF1lean14-36

description: Library name: Sample 10

value: total RNA


title: Hep3B, E7386-treated, 4

description:
Library name: X3B_0_1uM_4_S48
GEO_submission_counts_inVitro.csv


title: ZSF1lean14-35

description: Library name: Sample 9


title: E10.5forbrain_cKO_CUTTAG_IgG

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

data_processing:
The FASTQ data were trimmed by Trim Galore (v0.4.4_dev) and mapped to GRCh37 (hg19) or GCRm38 (mm10) using Bowtie2 (v2.3.4.1). PCR duplicates and mitochondrial DNA were removed, and bam files were generated by samtools (v1.8). Then peaks were called by macs2 (v2.1.2) (--broad for H3K27me3) and differential peaks were identified by R package DiffBind (v 2.10.0) with FDR < 0.05 and |FoldChange| > 2 or 1.5.
bed files were generated using macs2 (v2.1.2)
Assembly: mm10
Supplementary files format and content: narrowPeak, broadPeak
Library strategy: CUT&Tag

source_name: forebrain

extract_protocol:
Mouse brain tissues and human cortical organoids were digested with Papain to single cell, then about 5 x 104 cells and 0.5-1 μg antibodies or IgG were used for the downstream procedure with 12 cylcles during the final amplification PCR.
Cut&Tag-Seq was performed following manufacturer’s instructions (Vazyme, TD904).

tag: age

value: forebrain

value: Sox1 cre+/-; Chd7 f/f

tag: cut&tag antibody

value: IgG (CST 2729S)


title: Hep3B, E7386-treated, 2

description:
Library name: X3B_0_1uM_2_S46
GEO_submission_counts_inVitro.csv

value: 8-10 passages


title: Saline+Saline Rep3, AngII/PE study

value: heart

value: Saline+Saline


title: SNU387, E7386-treated, 3

description:
Library name: X387_0_1uM_3_S67
GEO_submission_counts_inVitro.csv

value: TERT; TP53; NRAS


title: ZSF1lean14-34

description: Library name: Sample 8

value: ZSF1 Lean


title: E10.5forbrain_con_CUTTAG_IgG

value: Chd7 +/f


title: Hep3B, E7386-treated, 1

description:
Library name: X3B_0_1uM_1_S45
GEO_submission_counts_inVitro.csv


title: Hep3B, DMSO-treated, 2

description:
Library name: X3B_DMSO_2_S42
GEO_submission_counts_inVitro.csv

value: DMSO


title: SNU387, E7386-treated, 2

description:
Library name: X387_0_1uM_2_S66
GEO_submission_counts_inVitro.csv


title: Hep3B, DMSO-treated, 1

description:
Library name: X3B_DMSO_1_S41
GEO_submission_counts_inVitro.csv


title: SNU398, E7386-treated, 4

description:
Library name: X398_0_1uM_4_S28
GEO_submission_counts_inVitro.csv

value: CTNNB1; TP53


title: Hep3B, DMSO-treated, 3

description:
Library name: X3B_DMSO_3_S43
GEO_submission_counts_inVitro.csv


title: E10.5forbrain_cKO_CUTTAG_H3K27me3_rep1


title: ZSF1lean14-33

description: Library name: Sample 7

value: Heart Left Ventricle


title: WKY14-7

description: Library name: Sample 6

value: WKY


title: SNU398, E7386-treated, 3

description:
Library name: X398_0_1uM_3_S27
GEO_submission_counts_inVitro.csv


title: SNU398, E7386-treated, 1

description:
Library name: X398_0_1uM_1_S25
GEO_submission_counts_inVitro.csv


title: SNU398, DMSO-treated, 4

description:
Library name: X398_DMSO_4_S24
GEO_submission_counts_inVitro.csv


title: E10.5forbrain_con_CUTTAG_H3K27me3_rep2


title: SNU398, E7386-treated, 2

description:
Library name: X398_0_1uM_2_S26
GEO_submission_counts_inVitro.csv


title: WKY14-5

description: Library name: Sample 4


title: E10.5forbrain_cKO_CUTTAG_H3K27me3_rep2


title: E10.5forbrain_con_CUTTAG_H3K27me3_rep1


title: WKY14-3

description: Library name: Sample 3


title: SNU398, DMSO-treated, 3

description:
Library name: X398_DMSO_3_S23
GEO_submission_counts_inVitro.csv


title: WKY14-6

description: Library name: Sample 5


title: E10.5forbrain_cKO_CUTTAG_H3K4me3_rep2


title: Hep3B, DMSO-treated, 4

description:
Library name: X3B_DMSO_4_S44
GEO_submission_counts_inVitro.csv


title: Huh7, E7386-treated, 4

description:
Library name: H7_0_1uM_4_S8
GEO_submission_counts_inVitro.csv

value: TERT; TP53; POLD3; KDR


title: WKY14-2

description: Library name: Sample 2


title: Huh7, E7386-treated, 2

description:
Library name: H7_0_1uM_2_S6
GEO_submission_counts_inVitro.csv


title: E10.5forbrain_cKO_CUTTAG_H3K4me3_rep1


title: Huh7, E7386-treated, 3

description:
Library name: H7_0_1uM_3_S7
GEO_submission_counts_inVitro.csv


title: WKY14-1

description: Library name: Sample 1


title: SNU398, DMSO-treated, 1

description:
Library name: X398_DMSO_1_S21
GEO_submission_counts_inVitro.csv


title: E10.5forbrain_con_CUTTAG_H3K4me3_rep1


title: E10.5forbrain_con_CUTTAG_H3K4me3_rep2


title: Huh7, E7386-treated, 1

description:
Library name: H7_0_1uM_1_S5
GEO_submission_counts_inVitro.csv


title: E10.5forebrain_cKO_RNA_rep2

data_processing:
Reads were aligned to the mm10 genome assembly using hisat2 and counted by featurecounts, DEGs were analyzed by DESeq2.
Assembly: mm10
Supplementary files format and content: featurecounts and DEGs generated by DESeq2

extract_protocol:
Tissues were dissolved in TRI reagent, mixed with chloroform, and centrifuged. The recovered supernatant was applied to RNeasy column to purify the RNA according to the manual.
One microgram total RNA was used for next generation sequencing library preparation according to the manufacturer’s protocol (VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina, Vazyme #NR605-01)


title: Huh7, DMSO-treated, 4

description:
Library name: H7_DMSO_4_S4
GEO_submission_counts_inVitro.csv


title: Huh7, DMSO-treated, 2

description:
Library name: H7_DMSO_2_S2
GEO_submission_counts_inVitro.csv


title: Huh7, DMSO-treated, 3

description:
Library name: H7_DMSO_3_S3
GEO_submission_counts_inVitro.csv


title: Huh7, DMSO-treated, 1

description:
Library name: H7_DMSO_1_S1
GEO_submission_counts_inVitro.csv


title: Treated 6c

city: Hyderabad

first: Rajagopal

last: Subramanyam

state: Telangana

address: School of Life Sciences Building UoH

department: Plant Sciences

country: India

institute: University of Hyderabad

description: Library name: 6c

data_processing:
After library preparation Illumina (Novaseq 6000) 150bp plateform was used for the sequencing. 60-80 million reads were generated for the earch sample.  The raw data quality was checked using FastQC and MultiQC software. The data was checked for base call quality distribution, % bases above Q30, %GC, and sequencing adapter contamination. All the samples have passed the QC threshold (Q30>85%).  The raw sequence reads were processed to remove adapter sequences and low quality bases using fastp v0.12.4 with default parameters. Reads shorter than 50 bp were removed from further analysis. From the quality trimmed data rRNA reads were removed using bbmap’s  v38.18 bbduk algorithm.
The pre-processed reads were mapped onto an indexed Cereibacter azotoformans str. KA25 (GCA_003050905) reference genome using Bowtie2 v2.4.5 aligner. On average 43.40% of the reads aligned onto the reference genome.
The gene level expression values were obtained from the Cereibacter azotoformans str.KA25 GCA_003050905)s read counts using feature Counts v2.0.0 software.
For differential expression analysis the samples were grouped as Control and Treated.
Differential expression analysis was carried out using the DESeq2 v1.34.1 package after normalizing the read counts (variance stabilized normalized counts). Genes with less than 5 reads in any of the samples were removed.  Genes with absolute log2 fold change ≥ 1 and adjusted p-value ≤ 0.05 were considered  significant.
Assembly: Rhodobacter azotoformans KA25
Supplementary files format and content: .csv

organism: Cereibacter alkalitolerans

source_name: Strain JA916T

growth_protocol: Bacteria were grown at 25 degree celcius (room temperature)

extract_protocol:
Samples were harvested after growth and freezed. RNA was extracted using STRN50-1KTspectrum TM Plant total RNA Kit. Further after verfying the RIN number samples were taken further.
Library construction was done using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.

treatment_protocol: Three light intensities of 30,250 and 500 micro moles photons/m2/s were used in neutral pH and high pH conditions.

value: Strain JA916T

value: Cereibacter alkalitolerans

value: Bacterial Cell

value: Wild type

value: Treated 4


title: Treated 6a

description: Library name: 6a

value: Treated 2


title: K562 H3K27me3 rep 2 plate 3

description: Library name: JvB-175-K562-H3K27me3-scepiseq-2Ox-pl1

data_processing:
Demultiplexing of reads and extraction of single-cell barcodes
Adapter trimming with cutadapt
Mapping to human genome with bwa -mem algorithm
Custom bam tagging tool to add flags for data filtering
Extracting methylation state for each CpG covered in the data from sequencing reads with custom software and writing output to .tsv files
genome build/assembly: GRCh38.p12 / Ensembl release 97 for Homo Sapiens
processed data files format and content: Data table containing library ID, cell ID, chromosome, genomic position, methylation state, cutsite motif
Library strategy: scEpi2-seq

growth_protocol: RPE-1 hTERT FUCCI cells were maintained in DMEM/F12, 10% FCS and 1% Pen-Strep. K562 cells were cultured in RPMI 1640 GlutaMAX medium, 5% FCS, non-essential amino acids and 1% Pen/Strep .

extract_protocol:
TrypLE digestion for RPE-1 hTERT FUCCI cells
Custom library protocol. Briefly, cells were incubated with the antibodies listed above and a pA-MNase fusion protein. Next, individual cells were sorted into 384-well plate. Subsequently, MNase digestion was initiated through the addition of calcium. Next, MNase digestion was stopped and DNA released by Proteinase K digestion. DNA fragments were end-repaired by Klenow Large Fragment and PNK. Repaired ends were ligated to custom barcoded adapters containing a UMI, Illumina handle and T7 promoter. After IVT and PCR, sequencing libraries were assessed with Qubit and Bioanalyzer and normalized libraries loaded onto Illumina sequencer according to the manufacturers instructions.

value: Bone Marrow

value: WT


title: Treated 6b

description: Library name: 6b

value: Treated 3


title: E10.5forebrain_cKO_RNA_rep1

value: forebrain

value: Sox1 cre+/-; Chd7 f/f


title: K562 H3K27me3 rep 2 plate 4

description: Library name: JvB-175-K562-H3K27me3-scepiseq-2Ox-pl2


title: E10.5forebrain_con_RNA_rep2

value: Chd7 +/f


title: SNU398, DMSO-treated, 2

description:
Library name: X398_DMSO_2_S22
GEO_submission_counts_inVitro.csv

value: 8-10 passages

value: DMSO


title: K562 H3K27me3 rep 2 plate 2

description: Library name: JvB-175-K562-H3K27me3-scepiseq-1Ox-pl2


title: Control 4c

description: Library name: 4c

value: Control 4


title: Control 4b

description: Library name: 4b

value: Control 3


title: E10.5forebrain_con_RNA_rep1


title: K562 H3K27me3 rep 2 plate 1

description: Library name: JvB-175-K562-H3K27me3-scepiseq-1Ox-pl1


title: LNCaP_FGC, steady state grown in RPMI1640 supplemented with 10%FBS and 1%Pen/Strep antibiotic.

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

description: Library name: LNCaP_FGC

data_processing:
CellRanger v6.0 used to generate matrix files
Downstream analysis was performed using Seurat V5.011.
Initial QC filtering removed cells with: num-ber genes < 200, number reads > upper outer fence, number reads > 10k, percent hemoglobin reads > 25, percent ribosomal reads > 50, percent mitochondrial reads > 15, quantiles of SCDS doublet score and number reads > 90% 12.
Seurat subset function was used to down-sample cell counts to be 1,850 and the scuttle package was used to down-sample to 19k average reads per cell for comparability between the lines13.
Each line was processed separately using the standard Seurat workflow with 3,000 variable genes and cluster resolution set to 0.5.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Prostate

growth_protocol: s grown in RPMI1640 supplemented with 10%FBS and 1%Pen/Strep antibiotic.

extract_protocol:
To collect single cell suspension, cells were trypsinized and washed once in PBS and re-suspended in cell culture media followed by haemocrytometer cell count to ensure cell viability above 70%.
The cell suspension were loaded into Chromium Next GEM Chip G (10x Genomics , PN#1000120) with 3′ v.3.1 beads (10x Genomics , PN#2000164) and partitioning oil.  Individual cells were barcoded using a 10× Chromium Controller (10x Genomics). RNA from the barcoded cells were subsequently reverse-transcribed and amplified with a Chromium Single Cell 3′ v3.1 Reagent Kit (10x Genomics, PN#1000123).  Libraries were subsequently constructed from 25% of amplified cDNA traces from pre-vious step with reagents from a Chromium Single Cell 3′ v3.1 Library Kit (10x Genomics, PN#1000190). The cDNA and library traces were quantitated and identified by Tapestation.  Sequencing were performed with an Illumina NextSeq 2000 P3.

treatment_protocol: Cells grown in steady state - no additional treatment.

value: Prostate

value: Grown in RPMI1640 supplemented with 10%FBS and 1%Pen/Strep antibiotic.  Otherwise no treatment.


title: LNCaP_C4-2B, steady state grown in RPMI1640 supplemented with 10%FBS and 1%Pen/Strep antibiotic.

description: Library name: LNCaP_C4-2B


title: LNCAP_FGC_2

description: Library name: LNCAP_FGC_2

data_processing:
Fastq files were aligned to human genome build hg38 using bowtie2 v2.4.2 8.
PCR duplicates were marked and removed using Picard MarkDuplicates v2.24.1 (https://broadinstitute.github.io/picard/).
Peaks were called using Genrich v0.6.1 in ATAC-Seq mode (https://github.com/jsh58/Genrich?tab=readme-ov-file#atacseq).
Called peaks had the ENCODE blacklisted regions removed.
Assembly: hg38
Supplementary files format and content: narrowPeak calls using Genrich

source_name: LNCaP-FGC

extract_protocol:
Nuclei Isolation and ATACseq: Cultured cells were freshly dissociated with TrypLE at 37℃ and washed with ice-cold PBS. Nuclei isolation and transposition was performed using the OMNI-ATACseq protocol (1) with some few adjustments 7. Briefly, 200, 000 cells were pelleted at 500 rcf for 5 minutes in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was carefully discarded in a 2-step method using a P1000 pipette followed by a P200 pipette. Pelleted cells were then resuspend-ed in 100 µL ice-cold lysis buffer comprising ATACseq resuspension buffer (A-RSB; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 in nuclease free H2O) supplemented with NP-40, tween-20 and digitonin at final concentrations of 0.1%, 0.1% and 0.01% respectively. After 3 minutes of lysis re-action on ice, 1ml of ice-cold wash buffer (A-RSB supplemented with tween-20; 0.1% final concen-tration) was added and the tubes inverted to mix. The nuclei were then pelleted by centrifugation, and suspension carefully discarded (as previously described). For transposition, nuclei were resus-pended in a 50 µL transposition mix (2x TD buffer, PBS, 0.01% digitonin, 0.1 % tween 20, nucle-ase-free H20 and TDE1Tn5 transposase enzyme). Transposition was performed at 37°C for 30 minutes in a thermomixer with shaking at 850 rpm. Transposed DNA was cleaned up using the MinElute® PCR purification kit.
Libraries were generated as previously described (2), double-sized selected using AMPure XP beads and eluted in EB buffer. For sequencing, 16 libraries were pooled together and sequenced pair-end in a NextSeq P3.

value: LNCaP-FGC

value: prostate tumor cell line


title: Control 4a

description: Library name: 4a

value: Strain JA916T

value: Cereibacter alkalitolerans

value: Bacterial Cell

value: Wild type

value: Control 2


title: shAR_pATK_2

description: Library name: shAR_pATK_2

source_name: LNCaP-shAR

value: LNCaP-shAR


title: shAR_pATK_1

description: Library name: shAR_pATK_1


title: Treated 3c

description: Library name: 3c

value: Treated 3


title: LNCAP_FGC_1

description: Library name: LNCAP_FGC_1


title: Treated 3a

description: Library name: 3a

value: Treated 1


title: C4_2-2

description: Library name: C4_2-2


title: Treated 3b

description: Library name: 3b

value: Treated 2


title: C4-2_1

description: Library name: C4-2_1


title: C4-2B_1

description: Library name: C4-2B_1


title: AR_909_3

description: Library name: AR_909_3


title: AR_909_4

description: Library name: AR_909_4


title: AR_907_1

description: Library name: AR_907_1


title: APIPC_2

description: Library name: APIPC_2

source_name: LNCaP-APIPC

value: LNCaP-APIPC


title: C4_1

description: Library name: C4_1


title: Control 1b

description: Library name: 1b


title: APIPC_1

description: Library name: APIPC_1


title: H1299, DMSO, 24hr, R3

city: LA JOLLA

first: Christopher

last: Parker

address: 10550 North Torrey Pines Road SR311E

institute: Scripps Research

description:
DMSO_R3_noninduced
6NOINDDMSO24HR_S21_R1_001

data_processing:
Raw data was converted to fastq files using the Element base2fastq script using default settings.
Assembly: StringTie
Supplementary files format and content: Tab-delimited text files including raw counts and DESeq2 normalized counts for each Sample.

growth_protocol: H1299 cells were cultured in complete RPMI supplemented with 10% FBS, 1% (v/v) penicillin/streptomycin, 2 mM glutamine, 10 mM HEPES, and 1 mM sodium pyruvate. Doxycycline-inducible wild-type or mutant p53-FKBP12F36V-HA H1299 cell lines were cultured in complete RPMI supplemented with 10% FBS, 1% (v/v) penicillin/streptomycin, 2 mM glutamine, 10 mM HEPES, 1 mM sodium pyruvate, 1 mL/mL Blasticidin and 50 mg/mL G418. Cells were cultured at 37℃ with 5% CO2.

extract_protocol:
RNA samples were extracted using Quick-RNA MiniPrep Kit (Zymo Research) following manufacturer’s recommended protocol.
Total RNA samples were prepared into RNAseq libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s recommended protocol.

treatment_protocol: Doxycycline-inducible wild-type p53-FKBP12F36V-HA H1299 cells were plated in 6-well plates 24 h before AceTAG treatment. Cells were treated with doxycycline following by AceTAG in complete RPMI (without Blasticidin and G418) when the cells were about 50-60% confluent.

value: Non-small cell lung cancer

value: wt

value: DMSO


title: C4-2B_2

description: Library name: C4-2B_2


title: Abl_3

description: Library name: Abl_3

source_name: LNCaP-Abl

value: LNCaP-Abl


title: AR_907_2

description: Library name: AR_907_2


title: Abl_1

description: Library name: Abl_1


title: Control 1c

description: Library name: 1c

value: Control 3


title: 95_2

description: Library name: 95_2


title: H1299, DMSO, 24hr, R2

description:
DMSO_R2_noninduced
6NOINDDMSO24HR_S20_R1_001


title: H1299, DMSO, 24hr, R1

description:
DMSO_R1_noninduced
6NOINDDMSO24HR_S19_R1_001


title: 42F_4

description: Library name: 42F_4


title: 42F_3

description: Library name: 42F_3


title: 42D_2

description: Library name: 42D_2


title: H1299, AceTAGPCAFGCN5-4, 24hr, R3

description:
AceTAG-PCAFGCN5_R3_noninduced
8NOINDPCAFGCN524HR_S27_R1_001


title: H1299, AceTAGPCAFGCN5-4, 24hr, R2

description:
AceTAG-PCAFGCN5_R2_noninduced
8NOINDPCAFGCN524HR_S26_R1_001


title: 42F_5

description: Library name: 42F_5


title: H1299, AceTAGPCAFGCN5-4, 24hr, R1

description:
AceTAG-PCAFGCN5_R1_noninduced
8NOINDPCAFGCN524HR_S25_R1_001


title: C4_2

description: Library name: C4_2


title: 42F_1

description: Library name: 42F_1


title: H1299, AceTAGp300CBP-1, 24hr, R3

description:
AceTAGp300CBP_R3_noninduced
7NOINDP300CBP24HR_S24_R1_001


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre;  AngII (3mg/kg/d, 14 days), biol rep 1

city: Ann Arbor

first: James

middle: P

last: Teuber

state: MI

address: 1150 W Medical Center Dr

department: Pharmacology

institute: University of Michigan

description:
Library name: F1_352M
F1_352M

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
HISAT2 (2.2.1) used to build the index of the reference genome, aligning paired-end clean reads to 3 the reference genome.
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene.
Prior to differential gene expression analysis, for each sequencing library, read counts were 4 adjusted using the edgeR R package (4.0.16) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: mm39
Supplementary files format and content: .txt files include raw counts and fpkm values per sample.

source_name: Mouse heart 8-10 weeks

extract_protocol:
RNA was extracted with the Qiagen RNeasy Mini Kit (Qiagen #74104).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. Library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Mouse heart 8-10 weeks

value: Ventricular tissue

value: Rac1 cKI/cKI; Myh6-Cre

value: AngII 3mg/kg/d

value: 14 days


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre;  AngII (3mg/kg/d, 14 days), biol rep 3

description:
Library name: F3_301F
F3_301F


title: 16D_4

description: Library name: 16D_4

value: prostate tumor cell line


title: 95_1

description: Library name: 95_1


title: Coc, Silveira, replicate 1, scRNAseq

city: Boston

first: Jatin

last: Vyas

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

description:
10x Genomics
hae_cocci_sim.rds

data_processing:
Demultiplexing the reads the create FASTQ files and alignment to human genom reference were performed using Cell Ranger (version 7.1.0, 10x Genomics) commands mkfastq and count, respectively.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics
Supplementary files format and content: Processed seurat objects

source_name: Lung

extract_protocol:
Cells were isolated from Transwell culturesTrypLE dissociation solution and washed to generate single-cell suspensions for loading onto the Chromium controller for droplet generation.
GEMs were generated and  libraries prepared using the Chromium Next GEM single cell 3’ V3.1 Reagent Kit  according to manufacturer protocols.

value: Lung

value: primary isolates

value: Human Airway Epithelial Cells

tag: infection

value: C. posadaii silveira


title: Mouse heart, Rac1 cKI/cKI; --; AngII (3mg/kg/d, 14 days) treated, biol rep 3

description:
Library name: E3_254F
E3_254F

value: Rac1 cKI/cKI; --


title: Mouse heart, Rac1 cKI/cKI; --; AngII (3mg/kg/d, 14 days) treated, biol rep 2

description:
Library name: E2_6M
E2_6M


title: ASP, B5233, replicate 1, scRNAseq

description:
10x Genomics
hae_af_sim.rds

tag: cell line

value: A. Fumigatus B5233


title: H1299, AceTAGp300CBP-1, 24hr, R1

description:
AceTAGp300CBP_R1_noninduced
7NOINDP300CBP24HR_S22_R1_001

tag: cell type

value: Non-small cell lung cancer


title: H1299, AceTAGp300CBP-1, 24hr, R2

description:
AceTAGp300CBP_R2_noninduced
7NOINDP300CBP24HR_S23_R1_001

tag: genotype

value: wt


title: MA36

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.10, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus.GRCm39.107  whole genome using star2.7.1a.  Counts were generated with the subread v2.0.6 and the featureCounts -p -t expm -g gene_id -a -o
Count matrixes were then analyzed using DESeq2 v1.28.1 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Assembly: Mus_musculus.GRCm39.107
Supplementary files format and content: csv file with normalized counts for each gene

extract_protocol:
Zymo Direct-Zol mini prep plus kit
Libraries were prepared for sequencing using standard Illumina protocols, and poly A selection

value: Kidney

tag: Sex

value: male

tag: treatment

value: inactive


title: COC, Mock, replicate 1, scRNAseq

description:
10x Genomics
hae_cocci_sim.rds

tag: tissue

value: Mock


title: p53-FKBP12F36V, H1299, DMSO, 24hr, R3

description:
DMSO_R3_induced
9INDDMSO24HR_S30_R1_001

source_name: p53-FKBP12F36V-induced H1299

value: p53-FKBP12F36V-induced H1299

value: DMSO


title: p53-FKBP12F36V, H1299, DMSO, 24hr, R2

description:
DMSO_R2_induced
9INDDMSO24HR_S29_R1_001


title: Control 1a

description: Library name: 1a

value: Strain JA916T

value: Cereibacter alkalitolerans

value: Bacterial Cell

value: Wild type

value: Control 1


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre;  AngII (3mg/kg/d, 14 days), biol rep 2

description:
Library name: F2_472M
F2_472M

value: Mouse heart 8-10 weeks

value: Ventricular tissue

value: Rac1 cKI/cKI; Myh6-Cre

value: AngII 3mg/kg/d

value: 14 days

tag: batch


title: MA35


title: Mouse heart, Rac1 cKI/cKI; --; AngII (3mg/kg/d, 14 days) treated, biol rep 1

description:
Library name: E1_355M
E1_355M

value: Rac1 cKI/cKI; --

tag: time


title: 42D_1

description: Library name: 42D_1

value: prostate tumor cell line


title: MA33

value: Kidney

value: male


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre;  AngII (3mg/kg/d, 3 days), biol rep 2

description:
Library name: D2_TLM
D2_TLM

value: 3 days


title: p53-FKBP12F36V, H1299, DMSO, 24hr, R1

description:
DMSO_R1_induced
9INDDMSO24HR_S28_R1_001

value: p53-FKBP12F36V-induced H1299

value: Non-small cell lung cancer

value: wt


title: 16D_3

description: Library name: 16D_3


title: p53-FKBP12F36V, H1299, AceTAGPCAFGCN5-4, 24hr, R3

description:
AceTAG-PCAFGCN5_R3_induced
11INDPCAFGCN524HR_S36_R1_001


title: 16D_1

description: Library name: 16D_1


title: MA31

value: inactive


title: MA30

value: active


title: MA34


title: p53-FKBP12F36V, H1299, AceTAGPCAFGCN5-4, 24hr, R2

description:
AceTAG-PCAFGCN5_R2_induced
11INDPCAFGCN524HR_S35_R1_001


title: Mouse heart, Rac1 cKI/cKI; --; AngII (3mg/kg/d, 3 days) treated, biol rep 3

description:
Library name: C3_203F
C3_203F


title: MA29


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre;  AngII (3mg/kg/d, 3 days), biol rep 3

description:
Library name: D3_199F
D3_199F


title: MA28


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre;  AngII (3mg/kg/d, 3 days), biol rep 1

description:
Library name: D1_TM
D1_TM


title: MA27


title: Mouse heart, Rac1 cKI/cKI; --; AngII (3mg/kg/d, 3 days) treated, biol rep 2

description:
Library name: C2_222M
C2_222M


title: MA26


title: ASP, Mock, replicate 1, scRNAseq

description:
10x Genomics
hae_af_sim.rds

value: Lung

value: primary isolates

value: Human Airway Epithelial Cells

value: Mock


title: MA25


title: MA32


title: FA36

value: female


title: p53-FKBP12F36V, H1299, AceTAGp300CBP-1, 24hr, R2

description:
AceTAGp300CBP_R2_induced
10INDP300CBP24HR_S32_R1_001


title: FA35