title: 24-month doxycycline treated tTAxAPP, ID45

value: Doxycycline


title: Whole heart tissue, mG4H-ON, rep 1 [Bisulfite-Seq]

status: Public on Mar 11 2026

type: SRA

city: Birmingham

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

country: USA

institute: University of Alabama at Birmingham

library_source: genomic

data_processing:
Fastq files generated from RRBS were checked for quality using FastQC (v0.11.9). In this step, Con-ON sample failed to meet the quality needed for downstream analysis, hence, excluded from rest of the analysis.
Prior to alignment to the reference mouse genome, each sequence in the raw FASTQ files was trimmed on base call quality and sequencing adapter contamination using the Trim Galore! wrapper tool. Reads shorter than 20 base pairs were removed from the FASTQ files.
Trimmed reads were aligned to the reference genome using the Bismark, which then generated methylation coverage files.
From these coverage files, differentially methylated CpG (DMC) sites were detected via methylKit (v1.16.1)
Assembly: mm39
Supplementary files format and content: excel file include beta values for all samples

molecule: genomic DNA

organism: Mus musculus

source_name: Whole heart tissue

extract_protocol:
Whole hearts were excised and were snap frozen in liquid nitrogen and stored at - 80 °C until subjected to further analysis.
DNA was isolated using Qiagen DNeasy DNA isolation and purification kit following the manufacturer’s guidelines. DNA was subsequently sent to Zymo Research for bisulfite conversion, library preparation, and reduced representation bisulfite sequencing (RRBS).
RRBS was performed via Zymo’s Methyl-MidiSeq protocol.

tag: tissue

value: Whole heart tissue

tag: genotype

tag: treatment

value: 2 weeks DOX to induce glucose delivery (ON)


title: C798CBm_ATAC

city: New Haven

first: Yuting

last: Liu

state: CT

address: 333 Cedar Street

institute: YALE UNIVERSITY

description: Library name: C798CBm_ATAC_MAH

library_source: genomic single cell

data_processing:
Raw base call files were converted to FASTQ format and processed using Cell Ranger ARC (v2.0.1, 10x Genomics). Reads were aligned to species-specific reference genomes. Gene expression matrices and chromatin accessibility peak counts were generated using default Cell Ranger ARC parameters. Nuclei were filtered based on quality control thresholds including UMI counts, feature counts, mitochondrial gene percentage (>5%), total ATAC fragment counts (<1,000), and transcription start site enrichment score (<4). Downstream clustering and cell type annotation were performed using Seurat (v4.0.6).
Assembly: human, GRCh38; chimpanzees, panTro5;rhesus macaque, rheMac10; marmoset, calJac4
Supplementary files format and content: cellranger output: feature_bc_matrix.h5
Supplementary files format and content: cellranger output: atac_fragments.tsv.gz

organism: Callithrix jacchus

source_name: cerebellum

extract_protocol:
Frozen cerebellar cortex tissue was homogenized and nuclei were isolated using detergent-based resuspension buffers containing NaCl, MgCl₂, Tris-HCl, NP-40, Tween-20, digitonin, protease inhibitors, DTT, BSA, and RNase inhibitor. Nuclei were filtered through 70 µm strainers, centrifuged at 500 × g at 4°C, and resuspended in nuclei buffer supplemented with DTT and RNase inhibitor. Nuclei concentration was adjusted to 4.5 × 10⁶ nuclei/mL prior to microfluidic capture.
Single-nucleus RNA and chromatin accessibility libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC and Gene Expression kit (10x Genomics, PN-1000283) according to the manufacturer’s instructions. Approximately 10,000 nuclei were targeted per sample using the Chromium microfluidic system with Multiome Gel Bead Kit A and Multiome GEM Kit A. RNA and ATAC libraries were generated in parallel from the same nuclei preparation.

value: cerebellum

tag: developmental stage

value: adult

tag: library type

value: ATAC


title: C797CBm_RNA

description: Library name: C797CBm_GEX_MAH

library_source: transcriptomic single cell

molecule: nuclear RNA

value: mRNA


title: 18-month placebo treated tTAxAPP, ID164

city: Bonn

first: Kan

last: Xie

address: Venusberg-Campus 1/99

department: Translational Gerontology

country: Germany

institute: German Center for Neurodegenerative Diseases

library_source: transcriptomic

data_processing:
align with mm10 using STAR 2.4.0
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains normalized counts for individual biological replicates.

molecule: total RNA

source_name: Brain

extract_protocol:
RNA was isolated in a two-stepped protocol using peqGold TriFast and RNeasy Mini Kit.
Library preparation was completed using the TruSeq RNA Library Prep Kit following the manufacturer´s instructions.

treatment_protocol: Doxycycline was administered by adding 200 mg/kg doxycycline to chow.

value: Brain

tag: age

tag: Sex

value: female

value: Camk2a-tTA x tetO-APPSwInd

value: Placebo


title: 24-month placebo treated tTAxAPP, ID43


title: C796CBm_ATAC

description: Library name: C796CBm_ATAC_MAH


title: Barcode Association Sequencing

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: Barcode Association Sequencing

library_source: other

data_processing:
DNA and RNA Counts as well as DNA and RNA annotations were generated using the MPRAflow count utility as specified in Gordon et al. 2020 using the --mpranalyze flag
Barcode association dictionary and design file with illegal characters removed were generated using the MPRAflow association utility as specified in Gordon et al. 2020
Assembly: hg38
Supplementary files format and content: DNA and RNA counts are total barcode counts in csv format
Supplementary files format and content: DNA and RNA annotations are label files for use with mpranalyze in tsv format
Supplementary files format and content: Design File contains MPRA sequences and lables for input into MPRAflow's association utility in fasta format
Supplementary files format and content: Barcode association dictionary is used for MPRAflow's count utility and is a python pickle file

molecule: other

organism: Homo sapiens

source_name: NEB 10-beta electrocompetent cells

extract_protocol:
Qiagen Allprep RNA/DNA mini kit for MPRA output sequencing, Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

tag: cell line

value: NEB 10-beta electrocompetent cells

tag: cell type

value: not applicable


title: C797CBm_ATAC

description: Library name: C797CBm_ATAC_MAH


title: HEK293FT, RNA, Replicate 1

description:
Library name: HEK_MPRA1_RNA
label in metadata files is RNA_Neurons_1

value: human embryonic kidney cells


title: C796CBm_RNA

description: Library name: C796CBm_GEX_MAH


title: 18-month doxycycline treated tTAxAPP, ID196


title: HEK293FT, DNA, Replicate 1

description:
Library name: HEK_MPRA1_DNA
label in metadata files is DNA_Neurons_1


title: Neurons, RNA, Replicate 1

description:
Library name: Neuron_MPRA1_RNA
label in metadata files is RNA_Neurons_1

value: Neurons


title: Neurons, DNA, Replicate 1

description:
Library name: Neuron_MPRA1_DNA
label in metadata files is DNA_Neurons_1


title: 8693-JF-6

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 8693-JF-6

data_processing:
“BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCh38
Supplementary files format and content: cellranger output format

source_name: skin

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722286172/support-documents/CG000331_Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_RevF.pdf

value: skin

value: Nonles

value: baseline


title: sgSEPHS2_3

city: shenzhen

first: yihuizhi

last: zhang

state: guangdong

address: 1088 Xueyuan Avenue, Nanshan District

department: School of Medicine

country: China

institute: Southern University of Science and Technology

description: Library name: Sample 6

data_processing:
Raw sequencing FASTQ files were quality controlled using FASTQC (v0.12.1) to evaluate read quality and adapter contamination. Clean reads were aligned to the human reference genome GRCh38 using HISAT2 (v2.2.1). The resulting alignment files were processed with SAMtools (v1.21) to generate coordinate-sorted and indexed BAM files. Gene-level read counts were quantified using featureCounts (v2.0.6) from the Subread package, based on the UCSC GRCh38 known gene annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files contained raw read counts, with genes as rows and samples as columns.

extract_protocol:
RNA was extracted by using the RNA-easy Isolation Reagent(Vazyme, Cat#R701-01, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: melanoma


title: sgSEPHS2_1

description: Library name: Sample 4


title: sgCTRL_3

description: Library name: Sample 3


title: sgSEPHS2_2

description: Library name: Sample 5


title: sgCTRL_2

description: Library name: Sample 2


title: sgCTRL_1

description: Library name: Sample 1


title: HNE_sg4long_1

city: Baltimore

first: Garry

middle: R

last: Cutting

state: MD

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins School of Medicine

description:
Library name: Sample 3
10X Genomics

data_processing:
Sequencing was performed by the Johns Hopkins GRCF via paired-end sequencing 2x100 cycles using a NovaSeq 6000 Illumina sequencing machine.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: nasal epithelial cells

growth_protocol: After electroporation, cells were plated onto human collagen type IV (Sigma, no. C6745-1ML) coated snapwell filters (Costar, catalog no. 3801) in a 6-well plate seeded with irradiated mouse fibroblast cells (3T3). Two electroporation reactions were added to each filter. Fluorescence microscopy was performed 24 hrs post-electroporation to validate successful transfection of the GFP control. Cells were allowed to recover from electroporation in medium containing ROCK inhibitor until confluency was reached (~5–10 days), at which point cells were moved to differentiation medium (no ROCK inhibitor). The next day, apical medium was removed, starting air-liquid-interface (ALI) culture. Cells were maintained on ALI culture for 21 days before short circuit measurements and collection of gDNA and RNA.

extract_protocol:
Fully differentiated HNEs were incubated in accutase/trypsin solution at 37ºC for 7 minutes then resuspended. Cells were centrifuged, washed and re-suspended in PBS, with a portion stained with a viability dye for scRNASeq library prep.
Library preparation was performed in the Cutting lab using 10X Genomics v.3.1 30 Library Preparation chemistry with a dual indexing system.

treatment_protocol: Base editor and sgRNA were delivered to non-differentiated primary cells via electroporation. Base editor mRNA was at a concentration of 2 μg/μL and synthetic sgRNA (IDT) was at a concentration of 100 μM. Editor and sgRNA were combined in a 3:1 volume ratio and a total of 1 μL of RNA was used for each electroporation reaction. In the no sgRNA control, synthetic sgRNA was substituted with equivalent volume of DEP-C H2O and for GFP control eGFP mRNA with unmodified bases and CleanCap was used (TriLink Biotechnologies, catalog no. L-7601). Electroporation was performed using the Neon Transfection System (Invitrogen) with 10μL Neon tips (Invitrogen, catalog no. MPK1025). Each electroporation reaction consisted of 1.5x105 undifferentiated primary cells resuspended in 9 μL of buffer R (Invitrogen, catalog no. MPK1025) and combined with 1 μL of nucleic acid mix.

value: nasal epithelial cells

value: epithelial


title: HNE_sg5long_2

description:
Library name: Sample 6
10X Genomics


title: HNE_unedited_2

description:
Library name: Sample 2
10X Genomics

value: unedited


title: HNE_sg5long_1

description:
Library name: Sample 5
10X Genomics


title: HNE_sg4long_2

description:
Library name: Sample 4
10X Genomics


title: HNE_unedited_1

description:
Library name: Sample 1
10X Genomics


title: Control_3

city: Nanchang

first: fengfen

last: guo

address: No.17 Yongwaizheng Street, Donghu District

department: Department of Orthopedics

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: Control_3
control

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell culture

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: 143B cells were seeded in a 6-well plate at 5×10^5 cells/well and cultured at 37°C and 5% CO2 for 24 hours. Randomly set 3 wells as the Control group and continue culturing for 24 hours to collect, labeled control-1, control-2, and control-3. The remaining 3 wells are the Celastrol group. Add Celastrol and continue culturing for 24 hours to collect, labeled cel-1, cel-2, and cel-3.

value: cell culture

value: control


title: Cel_2

description:
Library name: Cel_2
Add Celastrol

value: Add Celastrol


title: Cel_3

description:
Library name: Cel_3
Add Celastrol


title: Control_2

description:
Library name: Control_2
control


title: Cel_1

description:
Library name: Cel_1
Add Celastrol


title: RNA-seq of peripheral blood in HTRA5-associated cerebral small vessel disease

city: Shanxi

first: Shina

last: Song

address: Jiefangnan 85 Road

institute: The First Hospital of Shanxi Medical University

description: Library name: sample5

data_processing:
Reference genome index was constructed using HISAT2 v2.0.5, and paired-end clean reads were aligned to the reference genome. Feature Counts (1.5.0-p3) was used to count the reads mapped to each gene, and the gene expression levels were quantified by Fragments Per Kilobase of transcript per Million mapped reads (FPKM). After the image data generated by the high-throughput sequencer was processed for base calling using CASAVA software, it was converted into sequence data (reads). To ensure the quality and reliability of data analysis, raw data was filtered, including removing reads with adapter sequences, reads containing ambiguous base information, and low-quality reads (the number of bases with Qphred ≤ 5 accounting for more than 50% of the entire read length).
Assembly: hg38
Supplementary files format and content: TXT file including Reads count for each sample.

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted by the chloroform method.
Total RNA was used as the starting material for library construction. After enrichment of the extracted total RNA, the poly-A–tailed mRNA was randomly fragmented by adding buffer. Using the fragmented mRNA as template and random oligonucleotides as primers, the first-strand cDNA was synthesized, followed by the second-strand cDNA synthesis with dNTPs. The purified double-stranded cDNA was subjected to end repair, A-tailing and ligation of sequencing adapters, followed by PCR amplification and purification of PCR products, and the sequencing library was finally constructed.

value: Peripheral blood

tag: group

value: healthy control


title: RNA-seq of peripheral blood in HTRA7-associated cerebral small vessel disease

description: Library name: sample7


title: RNA-seq of peripheral blood in HTRA2-associated cerebral small vessel disease

description: Library name: sample2


title: RNA-seq of peripheral blood in HTRA3-associated cerebral small vessel disease

description: Library name: sample3


title: RNA-seq of peripheral blood in HTRA6-associated cerebral small vessel disease

description: Library name: sample6


title: RNA-seq of peripheral blood in HTRA1-associated cerebral small vessel disease

description: Library name: sample1


title: Sample_02-TCR

city: Houston

first: Peixin

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description: Library name: Sample_02-TCR

data_processing:
Raw data were processed through CellRanger 4.0.0 pipeline for demultiplexing, alignment, barcode processing, and CDR3 α/β sequence assembly of clonotypes.
Assembly: GRCh38
Supplementary files format and content: Tab-Separated values files and matrix files.

source_name: FOXM1 antigen reactive HLA-A*23:01 T cells, expanded

extract_protocol:
Expanded antigen-reactive T cells were sorted using live/dead dye, T cells markers, and tetramers and resuspended in PBS before library preparation.
Expanded, reactive antigen-specific T cells were processed using 10x Genomics Single Cell 5’ Gene Expression and V(D)J profiling kit and sequenced using Illumina NovaSeq 6000 at Advanced Technology Genomics Core of UT MD Anderson Cancer Center.

value: PBMC

value: T Cells


title: Sample_03-5GE

description: Library name: Sample_03-5GE

source_name: FOXM1 antigen reactive HLA-A*24:02 T cells, expanded


title: Sample_03-TCR

description: Library name: Sample_03-TCR


title: RNA-seq of peripheral blood in HTRA8-associated cerebral small vessel disease

description: Library name: sample8


title: Sample_01-TCR

description: Library name: Sample_01-TCR

source_name: FOXM1 antigen reactive HLA-A*02:01 T cells, expanded


title: Control_1

description:
Library name: Control_1
control


title: ZWCT1860

city: Rochester

first: Zhiquan

last: Wang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description:
Library name: ZWCT1860
Group=CLL6; treatment=IgM; batch=batch2; genome=hg38; paired-end RNA-seq.

data_processing:
Reads were aligned using Star1. Transcript abundance files were then used in the DESeq2 R package, which was used for all downstream differential expression analysis and generation of volcano plots. Differentially expressed genes between samples from healthy individuals and CLL patients were compared with a cutoff of fold change > 2, FDR <0.05.
Assembly: hg38
Supplementary files format and content: CLL_NX5948_DESeq2_De_Means_and_NormalisedCount2.STAR.txt

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: CLL B cells were cultured in AIM V medium with NX-NX-5948 (MedChemExpress) (1nM) or DMSO for 6 hours. Then, the anti-IgM (10 mg/ml) or vehicle control was added to the culture for another 18 hours before the cells were harvested.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Kit (Zymo Research).
Library preparation and sequencing were performed using the NovaSeq 6000 platform, paired-end 150 bp by Novogene

value: peripheral blood

value: CLL B cell

value: IgM


title: ZWCT1861

description:
Library name: ZWCT1861
Group=CLL6; treatment=NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: Sample_02-5GE

description: Library name: Sample_02-5GE


title: ZWCT1856

description:
Library name: ZWCT1856
Group=CLL5; treatment=IgM; batch=batch2; genome=hg38; paired-end RNA-seq.


title: RNA-seq of peripheral blood in HTRA4-associated cerebral small vessel disease

description: Library name: sample4


title: ZWCT1853

description:
Library name: ZWCT1853
Group=CLL2.1; treatment=NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1857

description:
Library name: ZWCT1857
Group=CLL5; treatment=NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1859

description:
Library name: ZWCT1859
Group=CLL6; treatment=DMSO; batch=batch2; genome=hg38; paired-end RNA-seq.

value: DMSO


title: ZWCT1854

description:
Library name: ZWCT1854
Group=CLL2.1; treatment=IgM_NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1848

description:
Library name: ZWCT1848
Group=CLL1.1; treatment=IgM; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1851

description:
Library name: ZWCT1851
Group=CLL2.1; treatment=DMSO; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1852

description:
Library name: ZWCT1852
Group=CLL2.1; treatment=IgM; batch=batch2; genome=hg38; paired-end RNA-seq.


title: Sample_01-5GE

description: Library name: Sample_01-5GE


title: ZWCT1862

description:
Library name: ZWCT1862
Group=CLL6; treatment=IgM_NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1850

description:
Library name: ZWCT1850
Group=CLL1.1; treatment=IgM_NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1847

description:
Library name: ZWCT1847
Group=CLL1.1; treatment=DMSO; batch=batch2; genome=hg38; paired-end RNA-seq.


title: ZWCT1849

description:
Library name: ZWCT1849
Group=CLL1.1; treatment=NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: WL4

description:
Library name: WL4
Group=CLL4; treatment=IgM_NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: LG4

description:
Library name: LG4
Group=CLL3; treatment=IgM_NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: WL1

description:
Library name: WL1
Group=CLL4; treatment=DMSO; batch=batch1; genome=hg38; paired-end RNA-seq.


title: WL2

description:
Library name: WL2
Group=CLL4; treatment=IgM; batch=batch1; genome=hg38; paired-end RNA-seq.


title: WL3

description:
Library name: WL3
Group=CLL4; treatment=NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: ZWCT1858

description:
Library name: ZWCT1858
Group=CLL5; treatment=IgM_NX5948; batch=batch2; genome=hg38; paired-end RNA-seq.


title: LG2

description:
Library name: LG2
Group=CLL3; treatment=IgM; batch=batch1; genome=hg38; paired-end RNA-seq.


title: LG3

description:
Library name: LG3
Group=CLL3; treatment=NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: ZWCT1855

description:
Library name: ZWCT1855
Group=CLL5; treatment=DMSO; batch=batch2; genome=hg38; paired-end RNA-seq.


title: LG1

description:
Library name: LG1
Group=CLL3; treatment=DMSO; batch=batch1; genome=hg38; paired-end RNA-seq.


title: MP4

description:
Library name: MP4
Group=CLL2; treatment=IgM_NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: MP3

description:
Library name: MP3
Group=CLL2; treatment=NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: MP1

description:
Library name: MP1
Group=CLL2; treatment=DMSO; batch=batch1; genome=hg38; paired-end RNA-seq.


title: MP2

description:
Library name: MP2
Group=CLL2; treatment=IgM; batch=batch1; genome=hg38; paired-end RNA-seq.


title: AB2

description:
Library name: AB2
Group=CLL1; treatment=IgM; batch=batch1; genome=hg38; paired-end RNA-seq.


title: AB1

description:
Library name: AB1
Group=CLL1; treatment=DMSO; batch=batch1; genome=hg38; paired-end RNA-seq.


title: GM12878 cells, pH 6.8 with PARP1 inhibitor, replicate 3

city: Thuwal

first: Mo

last: Li

address: King Abdullah University Of Science And Technology

country: Saudi Arabia

description: Library name: Sample12

data_processing:
Gene expression was quantified at the gene level. Fragments per kilobase of transcript per million mapped reads (FPKM) values were used for quantifying gene expression levels.
Assembly: GRCh38
Supplementary files format and content: The processed RNA-seq data are provided as tab-delimited text files (.xls) containing gene-level expression quantification. Columns B–M correspond to individual samples. Rows represent genes, annotated by information including gene identifier and gene symbol. Columns report normalized expression values calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Expression values were derived from aligned RNA-seq reads using a standard RNA-seq quantification pipeline, with normalization accounting for gene length and sequencing depth.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit (cat#74106).
The RNA samples with RIN > 7.0 are outsourced to Novogene and X Genomics for directional library preparation and sequencing.

value: lymphoblastoid cell

value: wild type

value: pH 6.8 with PARP1 inhibitor

tag: batch


title: GM12878 cells, pH 6.8 with PARP1 inhibitor, replicate 1

institute: King Abdullah University Of Science And Technology

description: Library name: Sample10


title: GM12878 cells, pH 7.4, replicate 1

description: Library name: Sample4


title: AB3

description:
Library name: AB3
Group=CLL1; treatment=NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: GM12878 cells, pH 6.8 with NMN, replicate 2

description: Library name: Sample8

value: pH 6.8 with NMN


title: AB4

description:
Library name: AB4
Group=CLL1; treatment=IgM_NX5948; batch=batch1; genome=hg38; paired-end RNA-seq.


title: GM12878 cells, pH 6.8 with PARP1 inhibitor, replicate 2

description: Library name: Sample11


title: HT29, HPLM

city: Chicago

first: Zongjie

state: Illinois

address: 400 N Aberdeen St., STE800

department: Biohub Chicago

institute: Biohub

description: Library name: Sample 4

data_processing:
Raw sequencing reads were preprocessed with Trimmomatic (v0.36) for adapter trimming and quality filtering and subsequently aligned to the Homo sapiens GRCh38 reference genome using the STAR aligner (v2.5.2b). Gene expression quantification was performed using the Subread package (v1.5.2) to calculate unique gene hit counts. Differentially expressed genes (DEGs) were identified with DESeq2, applying a significan ce threshold of adjusted p-value < 0.05 and an absolute log2 fold change (FC) >1.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: csv files include TPM and DEG

growth_protocol: Grow in HPLM or RPMI-1640 supplied with 10% FBS and 1% P/S.

extract_protocol:
Qiagen QIAcube Connect with Rneasy Mini Kits and QIAshredder columns
Illumina TruSeq RNA Library Prep Kit v2

value: Epithelial cancer cells

value: WT

value: Culture in HPLM


title: GM12878 cells, pH 6.8 with NMN, replicate 3

description: Library name: Sample9


title: GM12878 cells, pH 6.8 with NMN, replicate 1

description: Library name: Sample7


title: GM12878 cells, pH 7.4, replicate 3

description: Library name: Sample6


title: GM12878 cells, pH 6.8, replicate 1

description: Library name: Sample1


title: HT29, RPMI

description: Library name: Sample 3

value: Culture in RPMI-1640


title: H441, HPLM

description: Library name: Sample 2


title: GM12878 cells, pH 7.4, replicate 2

description: Library name: Sample5


title: GM12878 cells, pH 6.8, replicate 2

description: Library name: Sample2


title: H441, RPMI

description: Library name: Sample 1


title: Merlin KO RPE1 starved replicate 3 DMSO

city: New York

first: Tobias

last: Meyer

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

description:
Library name: R3_KO_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_KO_SM

data_processing:
Raw reads were mapped to GRCh38 using HISAT2 and assigned to genomic features using featureCounts using standard paramters
Differential expression analysis and normalization were performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples (by column)
Supplementary files format and content: comma separated values file includes normalized counts for all samples (by column)

source_name: retinal pigmented epithelial cells

growth_protocol: Wildype (WT), doxycycline-inducible YAP5SA, and Merlin knockout (Merlin KO) retinal pigmented epithelial cells (RPE1) were plated at 38,000 cells/well in a 96-well plate in 1.0% FBS in DMEM/F12 media. After ~2h adherence time, cells were arrested in 0.1% or 1.0% FBS containing CDK4/6 inhibitor (palbociclib, SelleckChem, 1 µM) for 28h in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested by RNeasy Mini kit and QIAshredder (Qiagen), pooling 6 technical replicate wells per condition.
RNA libraries were prepared using Illumina Stranded mRNA library prep kit with polyA capture according to manufacturer instructions by the Weill Cornell Genomics Core Facility.

treatment_protocol:
YAP activation was induced in starved (0.1% serum) and serum (1.0%) CDK4/6 inhibitor-arrested conditions by either 1) chemical inhibition of LATS1/2 kinases (TRULI, courtesy of the laboratory of James Hudspeth, 5 µM) for 0 (DMSO), 3, or 6h in WT cells; or 2) doxycycline-induced YAP5SA expression (0.5 µg/mL, Sigma-Aldrich) for 0 (DMSO) 6, 12, 24, or 36h. Merlin knockout cells were treated with DMSO in starvation and serum CDK4/6 inhibitor-arrested conditions.
Two DMSO controls were included for the YAP5SA time course treatments, one matched for 6-12h DOX, the other matched for 24-36h DOX.

value: retinal pigmented epithelial cells

value: Merlin KO

tag: drug time

tag: media

value: serum


title: Merlin KO RPE1 serum replicate 1 DMSO

description:
Library name: R1_KO_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_KO_GM

value: starvation


title: Merlin KO RPE1 serum replicate 3 DMSO

description:
Library name: R3_KO_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_KO_GM


title: Merlin KO RPE1 starved replicate 2 DMSO

description:
Library name: R2_KO_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_KO_SM


title: Merlin KO RPE1 starved replicate 1 DMSO

description:
Library name: R1_KO_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_KO_SM


title: Merlin KO RPE1 serum replicate 2 DMSO

description:
Library name: R2_KO_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_KO_GM


title: CA-YAP RPE1 serum replicate 3 DOX 36h

description:
Library name: R3_P36_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P36_GM

value: Doxycycline (DOX)


title: GM12878 cells, pH 6.8, replicate 3

description: Library name: Sample3


title: CA-YAP RPE1 serum replicate 3 DMSO 24h

description:
Library name: R3_P64_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P64_GM


title: CA-YAP RPE1 serum replicate 3 DOX 12h

description:
Library name: R3_P12_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P12_GM


title: CA-YAP RPE1 serum replicate 3 DMSO

description:
Library name: R3_P0_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P0_GM


title: CA-YAP RPE1 serum replicate 3 DOX 6h

description:
Library name: R3_P6_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P6_GM


title: CA-YAP RPE1 serum replicate 3 DOX 24h

description:
Library name: R3_P24_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P24_GM


title: CA-YAP RPE1 starved replicate 3 DOX 36h

description:
Library name: R3_P36_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P36_SM


title: CA-YAP RPE1 starved replicate 3 DMSO 24h

description:
Library name: R3_P64_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P64_SM


title: CA-YAP RPE1 starved replicate 3 DOX 24h

description:
Library name: R3_P24_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P24_SM


title: CA-YAP RPE1 serum replicate 2 DOX 24h

description:
Library name: R2_P24_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P24_GM


title: CA-YAP RPE1 serum replicate 2 DOX 36h

description:
Library name: R2_P36_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P36_GM


title: CA-YAP RPE1 starved replicate 3 DMSO

description:
Library name: R3_P0_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P0_SM


title: CA-YAP RPE1 serum replicate 2 DOX 12h

description:
Library name: R2_P12_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P12_GM


title: CA-YAP RPE1 serum replicate 2 DMSO 24h

description:
Library name: R2_P64_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P64_GM


title: CA-YAP RPE1 serum replicate 2 DOX 6h

description:
Library name: R2_P6_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P6_GM


title: CA-YAP RPE1 serum replicate 2 DMSO

description:
Library name: R2_P0_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P0_GM


title: CA-YAP RPE1 starved replicate 2 DMSO 24h

description:
Library name: R2_P64_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P64_SM


title: CA-YAP RPE1 starved replicate 2 DOX 12h

description:
Library name: R2_P12_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P12_SM


title: CA-YAP RPE1 serum replicate 1 DOX 36h

description:
Library name: R1_P36_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P36_GM


title: CA-YAP RPE1 starved replicate 2 DOX 6h

description:
Library name: R2_P6_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P6_SM


title: CA-YAP RPE1 starved replicate 2 DOX 36h

description:
Library name: R2_P36_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P36_SM


title: CA-YAP RPE1 serum replicate 1 DOX 24h

description:
Library name: R1_P24_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P24_GM


title: CA-YAP RPE1 starved replicate 3 DOX 12h

description:
Library name: R3_P12_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P12_SM


title: CA-YAP RPE1 starved replicate 2 DOX 24h

description:
Library name: R2_P24_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P24_SM


title: CA-YAP RPE1 starved replicate 3 DOX 6h

description:
Library name: R3_P6_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_P6_SM


title: CA-YAP RPE1 serum replicate 1 DMSO 24h

description:
Library name: R1_P64_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P64_GM


title: CA-YAP RPE1 serum replicate 1 DOX 12h

description:
Library name: R1_P12_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P12_GM


title: CA-YAP RPE1 starved replicate 2 DMSO

description:
Library name: R2_P0_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_P0_SM


title: CA-YAP RPE1 serum replicate 1 DMSO

description:
Library name: R1_P0_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P0_GM


title: CA-YAP RPE1 starved replicate 1 DOX 6h

description:
Library name: R1_P6_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P6_SM


title: CA-YAP RPE1 starved replicate 1 DOX 24h

description:
Library name: R1_P24_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P24_SM


title: CA-YAP RPE1 serum replicate 1 DOX 6h

description:
Library name: R1_P6_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P6_GM


title: CA-YAP RPE1 starved replicate 1 DMSO 24h

description:
Library name: R1_P64_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P64_SM


title: CA-YAP RPE1 starved replicate 1 DMSO

description:
Library name: R1_P0_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P0_SM


title: CA-YAP RPE1 starved replicate 1 DOX 12h

description:
Library name: R1_P12_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P12_SM


title: WT RPE1 serum replicate 3 LATSi 6h

description:
Library name: R3_W6_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W6_GM

value: LATS inhibitor


title: CA-YAP RPE1 starved replicate 1 DOX 36h

description:
Library name: R1_P36_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_P36_SM


title: WT RPE1 starved replicate 3 LATSi 6h

description:
Library name: R3_W6_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W6_SM


title: WT RPE1 serum replicate 3 DMSO

description:
Library name: R3_W0_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W0_GM


title: WT RPE1 serum replicate 3 LATSi 1h

description:
Library name: R3_W1_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W1_GM


title: WT RPE1 serum replicate 2 DMSO

description:
Library name: R2_W0_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W0_GM


title: WT RPE1 starved replicate 3 DMSO

description:
Library name: R3_W0_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W0_SM


title: WT RPE1 serum replicate 2 LATSi 1h

description:
Library name: R2_W1_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W1_GM


title: WT RPE1 serum replicate 2 LATSi 3h

description:
Library name: R2_W3_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W3_GM


title: WT RPE1 starved replicate 2 LATSi 6h

description:
Library name: R2_W6_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W6_SM


title: WT RPE1 starved replicate 2 LATSi 3h

description:
Library name: R2_W3_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W3_SM


title: WT RPE1 serum replicate 1 LATSi 6h

description:
Library name: R1_W6_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W6_GM


title: WT RPE1 starved replicate 3 LATSi 3h

description:
Library name: R3_W3_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W3_SM


title: WT RPE1 serum replicate 2 LATSi 6h

description:
Library name: R2_W6_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W6_GM


title: WT RPE1 serum replicate 3 LATSi 3h

description:
Library name: R3_W3_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R3_W3_GM


title: WT RPE1 serum replicate 1 DMSO

description:
Library name: R1_W0_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W0_GM


title: WT RPE1 serum replicate 1 LATSi 3h

description:
Library name: R1_W3_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W3_GM


title: WT RPE1 starved replicate 2 DMSO

description:
Library name: R2_W0_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R2_W0_SM


title: WT RPE1 starved replicate 1 LATSi 3h

description:
Library name: R1_W3_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W3_SM


title: PC3TWPlusCAY_2

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description: Library name: X7122.PC3TWPlus_7122.PC3

data_processing:
Barcoded libraries were multiplexed at equimolar concentrations and sequenced with 76 bp single reads on a NovaSeq 6000
Data was demultiplezed using Illumina's CASAVA 1.8.2 software and reads were aligned to the human genome
RNA-seq reads were aligned to the [species] reference genome using STAR v2.7.5a with standard parameters. Gene-level counts were generated with htseq-count (HTSeq v0.11) using union mode
Assembly: Ilumina/NGS
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample

source_name: Prostate

growth_protocol: ARCaP(M) cells were mainained in RPM1 supplemented with 5% fetal bovine serum (FBS) and PC3 cells were mainted in DMEM supplemented with 10% FBS. Both cells cells were in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2000 ng of total RNA was used for sequencing.
RNA libraries for RNA-seq were preapred using Lexogen's QuantSeq 3'mRNA-seq Library Prep Kit (FWD for Illumina)

treatment_protocol: ARCaP(M) and PC3 cells were treated with 0.1% DMSO or 1uM of CAY10566 24 hours after plating and treated for a total of 48 hours.

value: Prostate

value: Human Prostate Cancer Cells


title: WT RPE1 serum replicate 1 LATSi 1h

description:
Library name: R1_W1_GM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W1_GM


title: PC3PlusCAY_3

description: Library name: X7822.PC3PlusCAY.10566_7822.PC3


title: PC3PlusCAY_2

description: Library name: X7122.PC3PlusCAY.10566_7122.PC3


title: PC3TWPlusCAY_1

description: Library name: X3722.PC3TWPlus_3722.PC3


title: WT RPE1 starved replicate 1 DMSO

description:
Library name: R1_W0_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W0_SM

value: DMSO


title: PC3 TW_3

description: Library name: X7822.PC3TWS66_7822.PC3

value: 0.1% DMSO


title: PC3PlusCAY_1

description: Library name: X3722.PC3PlusCAY.10566_3722.PC3


title: PC3 TW_2

description: Library name: X7122.PC3TWS58_7122.PC3


title: PC3 TW_1

description: Library name: X3722.PC3TWS50_3722.PC3


title: PC3_3

description: Library name: X7822.PC3S64R1_7822.PC3


title: WT RPE1 starved replicate 1 LATSi 6h

description:
Library name: R1_W6_SM
Column name in normalizedCounts_20220813 and 20220415-21_rawCountscombMulti: R1_W6_SM


title: PC3TWPlusCAY_3

description: Library name: X7822.PC3TWPlus_7822.PC3


title: PC3_1

description: Library name: X3722.PC3S48R1_3722.PC3


title: PC3_2

description: Library name: X7122.PC3S56R1_7122.PC3


title: ARCaPTWPlusCAY_3

description: Library name: X7822.ARCAPTWPlus_7822.ARCAP

value: ARCaP(M)


title: ARCaPPlusCAY_3

description: Library name: X7822.ARCAPPlusCAY.10566_7822.ARCAP


title: ARCaPPlusCAY_1

description: Library name: X121918.ARCaPPlusCAY.10566_121918.ARCaP


title: ARCaPTWPlusCAY_1

description: Library name: X121918.ARCaPTWPlus_121918.ARCaP


title: ARCaP TW_1

description: Library name: X121918.ARCaPTWS54_121918.ARCaP


title: ARCaP TW_3

description: Library name: X7822.ARCAPTWS70_7822.ARCAP


title: ARCaP TW_2

description: Library name: X7122.ARCAPTWS62_7122.ARCAP


title: ARCaP _2

description: Library name: X7122.ARCAPS60R1_7122.ARCAP


title: PBMC, 1 month after start of chemoradiation, patient 11

city: Besançon

first: Olivier

last: Adotévi

state: Franche-Comté

address: 8 rue du Dr JFX Girod

department: Oncology

country: France

institute: Université de Franche-Comté

description:
Library name: 001-070-LT V2
70_V2_S32

data_processing:
Bulk RNA-Seq reads were aligned using STAR v2.7.9a to GENCODE Human Release 39 (GRCh38.p13) and read counts matrix produced with FeatureCounts v2.0.1, both with default parameters. The Bioconductor RNA-seq workflow was followed to detect differential expression genes with DESEQ2 v1.34.0. A total of 19,258 coding genes filtered with *biomaRt* v2.5.3 were analyzed for transcript abundance and poorly expressed genes were eliminated based on the criteria of a maximum read count > 10 for all samples;
Data visualization was achieved in R v4.1.1 with the *ComplexHeatmap* package v2.11.1 and the *EnhancedVolcanoPlot* v1.12 using DESeq 2’s regularized-logarithm transformation (rlog) of the count data. Genes were considered as differentially expressed genes (DEG) if they achieved a false discovery rate of 5% or less and a log2 fold change of 0.5 (-0.5 < log2Foldchange > 0.5). Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler (v4.0)
Xcell was used with the 64 immune and stroma cell types of signature to perform cell type enrichment from expression data.
TCRs were extracted from RNA-seq data and processed using the tool MIXCR v3.0.13 with the default parameter “analyze shotgun”.
Assembly: GRCh38.p13
Supplementary files format and content: txt

source_name: PBMC

extract_protocol:
3 to 5 million PBMC per sample were thawed and RNA was extracted using the Maxwell® CSC RNA Blood Kit (Cat. No. 1S1410, Promega, France) according to the supplier's recommendations and then isolated on columns. Quantification was performed using NanoDrop (ThermoFisher), and quality control confirmed a RNA Integrity Score (RIN) greater than 7 for all samples required for sequencing.
Library preparation and sequencing benefited from the equipment and services of the iGenSeq core facility at the ICM. Libraries were generated from total RNA using the TruSeq Stranded mRNA LT Kit (Cat. No. RS-122-2101, Illumina). The quality and quantity of the final libraries were assessed using the TapeStation system (Agilent Technologies, Inc.) and the QuantiFluor dsDNA system (Promega Corp.). Paired-end sequencing (2 × 150 bp) was performed on the NovaSeq6000 (Illumina) using the NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles).

value: PBMC

value: chemoradiation


title: ARCaPPlusCAY_2

description: Library name: X7122.ARCAPPlusCAY.10566_7122.ARCAP


title: PBMC, 3 month after start of chemoradiation, patient 11

description:
Library name: 001-070-LT V3
70_V3_S33


title: PBMC, 3 month after start of chemoradiation, patient 10

description:
Library name: 001-069-LG V3
69_V3_S30


title: PBMC, 1 month after start of chemoradiation, patient 10

description:
Library name: 001-069-LG V2
69_V2_S29


title: PBMC, baseline, patient 11

description:
Library name: 001-070-LT V1
70_V1_S31

value: No treatment


title: PBMC, 3 month after start of chemoradiation, patient 9

description:
Library name: 002-054-VJ V3
54_V3_S15


title: ARCaPTWPlusCAY_2

description: Library name: X7122.ARCAPTWPlus_7122.ARCAP


title: PBMC, baseline, patient 10

description:
Library name: 001-069-LG V1
69_V1_S28


title: ARCaP _1

description: Library name: X121918.ARCaPS52R1_121918.ARCaP


title: PBMC, 3 month after start of chemoradiation, patient 8

description:
Library name: 001-047-BG V3
47_V3_S18


title: PBMC, 1 month after start of chemoradiation, patient 8

description:
Library name: 001-047-BG V2
47_V2_S17


title: PBMC, 1 month after start of chemoradiation, patient 7

description:
Library name: 002-043-IB V2
43_V2_S20


title: PBMC, baseline, patient 9

description:
Library name: 002-054-VJ V1
54_V1_S13


title: PBMC, baseline, patient 8

description:
Library name: 001-047-BG V1
47_V1_S16


title: PBMC, 3 month after start of chemoradiation, patient 6

description:
Library name: 002-041-GD V3
41_V3_S6


title: PBMC, baseline, patient 7

description:
Library name: 002-043-IB V1
43_V1_S19


title: PBMC, baseline, patient 6

description:
Library name: 002-041-GD V1
41_V1_S4


title: ARCaP _3

description: Library name: X7822.ARCAPS68R1_7822.ARCAP


title: PBMC, baseline, patient 5

description:
Library name: 002-035-MF V1
35_V1_S1


title: PBMC, 1 month after start of chemoradiation, patient 9

description:
Library name: 002-054-VJ V2
54_V2_S14


title: PBMC, 3 month after start of chemoradiation, patient 7

description:
Library name: 002-043-IB V3
43_V3_S21


title: PBMC, 1 month after start of chemoradiation, patient 5

description:
Library name: 002-035-MF V2
35_V2_S2


title: PBMC, 3 month after start of chemoradiation, patient 5

description:
Library name: 002-035-MF V3
35_V3_S3


title: PBMC, 1 month after start of chemoradiation, patient 6

description:
Library name: 002-041-GD V2
41_V2_S5


title: PBMC, 1 month after start of chemoradiation, patient 4

description:
Library name: 002-034-VA V2
34_V2_S8


title: PBMC, baseline, patient 4

description:
Library name: 002-034-VA V1
34_V1_S7


title: PBMC, 3 month after start of chemoradiation, patient 2

description:
Library name: 004-022-LG V3
22_V3_S27


title: PBMC, baseline, patient 2

description:
Library name: 004-022-LG V1
22_V1_S25


title: PBMC, 3 month after start of chemoradiation, patient 4

description:
Library name: 002-034-VA V3
34_V3_S9


title: PBMC, 1 month after start of chemoradiation, patient 3

description:
Library name: 001-031-BJ V2
31_V2_S11


title: PBMC, baseline, patient 3

description:
Library name: 001-031-BJ V1
31_V1_S10


title: PBMC, 1 month after start of chemoradiation, patient 2

description:
Library name: 004-022-LG V2
22_V2_S26


title: PBMC, 1 month after start of chemoradiation, patient 1

description:
Library name: 002-020-ID V2
20_V2_S23


title: PBMC, 3 month after start of chemoradiation, patient 1

description:
Library name: 002-020-ID V3
20_V3_S24


title: PBMC, baseline, patient 1

description:
Library name: 002-020-ID V1
20_V1_S22


title: Whole Human saphenous vein, Day 7, patient #3

city: Augusta

first: David

middle: S

last: Kim

state: GA

department: Vascular Biology Center

institute: Augusta University

description:
Library name: 3D7_GEX_GTTACTAGAT-ATGATCAGTC
FFPE Spatial transcriptome sequencing

data_processing:
BCL Convert v4.0 (Illumina) was used to generate de-multiplexed FASTQ files.
FASTQ files were processed using 10x Genomics Space Ranger (v2.0). Tissue detection and fiducial alignment were performed using spaceranger mkfastq and spaceranger count.
Reads were aligned to the human reference genome GRCh38 using Space Ranger default parameters.
Spatial barcode matrices, high-resolution tissue images, low-resolution images, scalefactor JSON files, and tissue position lists were generated using Space Ranger.
Assembly: Hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue with detected spots
Supplementary files format and content: scalefactors_json.json: scalefactors in JSON format
Supplementary files format and content: tissue_hires_image.png: high-resolution tissue image
Supplementary files format and content: tissue_lowres_image.png: low-resolution tissue image
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Human saphenous vein

growth_protocol: Human saphenous vein (SV) segments were collected from patients undergoing coronary artery bypass grafting. Explants were immediately transported in sterile PBS on ice before processing.

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) human saphenous vein tissues were sectioned at 5 µm thickness using a microtome. Sections were mounted onto 10x Genomics Visium Spatial Gene Expression FFPE slides, baked, deparaffinized, and H&E-stained according to the manufacturer’s Visium FFPE Tissue Preparation Guide. Slide brightfield images were acquired prior to probe hybridization and library construction.
Spatial transcriptomics libraries were prepared using the 10x Genomics Visium Spatial Gene Expression FFPE kit according to the manufacturer’s instructions. Following probe hybridization, ligation, reverse transcription, and cDNA amplification, libraries were indexed and pooled. The pooled libraries were sequenced as 28×91 bp paired-end reads on an Illumina NovaSeq system following the Visium FFPE recommended workflow.

treatment_protocol: SV segments were cultured ex vivo in RPMI 1640 supplemented with 30% fetal bovine serum for 7 days (Day 7). Paired Day 0 tissue from each donor served as baseline controls. No additional pharmacologic treatments were applied.

value: Human saphenous vein

value: Neointima proliferation

tag: time

value: Day 7


title: Whole Human saphenous vein, Day 0, patient #3

description:
Library name: 3D0_GEX_ACCCGCTCGA-TACGGGTGAC
FFPE Spatial transcriptome sequencing

value: Day 0


title: E150009308_L01_UC3DDP-2

city: Chongqing

first: Weiyang

last: He

state: chongqing

address: No.1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

description: Library name: Sampie 5

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for lowcomplexity or lowquality sequence
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

source_name: bladder

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. lllumina TruSeq RNA Sample Prep Kit (Cat#FC-122-10）
RNA libraries were prepared for sequencing using standard lllumina protocols

value: bladder

value: Spontaneously Immortalized


title: E150009308_L01_UC3DDP-3

description: Library name: Sampie 6


title: E150009308_L01_UC3-2

description: Library name: Sampie 2


title: Whole Human saphenous vein, Day 0, patient #2

description:
Library name: 2D0_GEX_AAACAGGAGA-CAAGGGCCGA
FFPE Spatial transcriptome sequencing


title: E150009308_L01_UC3DDP-1

description: Library name: Sampie 4


title: Whole Human saphenous vein, Day 7, patient #1

description:
Library name: 1D7_GEX_CTGAAGTTGC-GCTTAAGATC
FFPE Spatial transcriptome sequencing


title: E150009308_L01_UC3-3

description: Library name: Sampie 3


title: T24DDP_1

description: Library name: Sampie 4


title: T24_3

description: Library name: Sampie 3


title: T24DDP_2

description: Library name: Sampie 5


title: E150009308_L01_UC3-1

description: Library name: Sampie 1


title: PBMC, 3 month after start of chemoradiation, patient 3

description:
Library name: 001-031-BJ V3
31_V3_S12


title: T24DDP_3

description: Library name: Sampie 6


title: T24_2

description: Library name: Sampie 2


title: CGND-HRA-03003

first: Hemali

last: Phatnani

address: 101 Avenue of the Americas

institute: New York Genome Center

description: Library name: CGND-HRA-03003

data_processing:
Raw sequencing files was demultiplexed with bcl2fastq
Samples were uniformly processed using RAPiD-nf, an efficient RNA-Seq processing pipeline implemented in the NextFlow framework(Di Tommaso et al. 2017). Following adapter trimming with Trimmomatic (version 0.36)(Bolduc, n.d.), all samples were aligned to the hg38 build (GRCh38.primary_assembly) of the human reference genome using STAR (2.7.2a)(Dobin et al. 2013), with indexes created from GENCODE, version 30(Harrow et al. 2012). Gene expression was quantified using RSEM (1.3.1)(B. Li and Dewey 2011). Quality control was performed using SAMtools(H. Li et al. 2009) and Picard, and the results were collated using MultiQC(Ewels et al. 2016).
Assembly: hg38
Supplementary files format and content: csv files contatining count and tpm data

extract_protocol:
Total RNA extraction from fresh frozen tissue or cells – starting material is homogenized in TRIzol reagent using a series of needles for trituration. The homogenized sample undergoes phase separation with the addition of chloroform,  the upper aqueous phase of the mixture then follows the RNeasy Mini procedure (Qiagen, 74106). A series of washes will purify the final eluted total RNA. The RNeasy Mini portion of the protocol is processed on the QIAcube Connect automated platform (Qiagen, 9002864) for higher throughput.
RNA sequencing libraries are prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche 07962304001) in accordance with the manufacturer’s instructions. Samples are normalized to 500ng and undergo rRNA depletion through oligo hybridization and RNase H treatment. DNase treatment removes DNA oligos. Samples are fragmented to 350bp inserts and undergo cDNA generation. Samples undergo A-tailing and are ligated to Illumina sequencing adapters and amplified. Final libraries are quantified using the Qubit Fluorometer (Life Technologies) or Spectramax M2 (Molecular Devices) and Fragment Analyzer (Agilent). Libraries are sequenced on an Illumina sequencer.

value: CTL

tag: subject id

tag: gender

value: male


title: CGND-HRA-02990

description: Library name: CGND-HRA-02990

value: female


title: CGND-HRA-02983

description: Library name: CGND-HRA-02983


title: T24_1

description: Library name: Sampie 1


title: Whole Human saphenous vein, Day 7, patient #2

description:
Library name: 2D7_GEX_GCTACCCGGT-TCCATTACAT
FFPE Spatial transcriptome sequencing


title: CGND-HRA-02994

description: Library name: CGND-HRA-02994


title: CGND-HRA-02984

description: Library name: CGND-HRA-02984

value: ALS


title: Whole Human saphenous vein, Day 0, patient #1

description:
Library name: 1D0_GEX_GCGAGTTTGG-GTACGGGTGC
FFPE Spatial transcriptome sequencing


title: CGND-HRA-02989

description: Library name: CGND-HRA-02989


title: CGND-HRA-02981

description: Library name: CGND-HRA-02981


title: CGND-HRA-02982

description: Library name: CGND-HRA-02982


title: CGND-HRA-02980

description: Library name: CGND-HRA-02980


title: CGND-HRA-02974

description: Library name: CGND-HRA-02974


title: CGND-HRA-02965

description: Library name: CGND-HRA-02965


title: CGND-HRA-02968

description: Library name: CGND-HRA-02968


title: CGND-HRA-02971

description: Library name: CGND-HRA-02971


title: CGND-HRA-02958

description: Library name: CGND-HRA-02958


title: E18 Prx1cre; Gata4 F/D, CKO; Biol rep 3

city: La Jolla

last: McCulley

state: CA

address: 9300 Campus Point Dr, MC 7774

institute: University of California, San Diego

description:
Library name: Sample 6
Column name in GEO_Gata4_rawcounts.xlsx: CKO3 (4723-3)

data_processing:
STAR v2.7.10a software for alignment to mouse reference genome
FeatureCounts (v2.0.1) was used for read counting
DESeq2 (1.36.0) for differential gene expression analysis
Assembly: Genome assembly GRCm38, mm10
Supplementary files format and content: Excel file with raw counts for each sample

source_name: bulk lung

extract_protocol:
RNA was harvested from total lung cells of E18 lungs using the Qiagen Rneasy Plus Mini Kit. Minimum 0.8 mg of RNA utilized for construction of RNA sequencing libraries.
Library preparation by Illumina Stranded mRNA Prep following manufacturer's protocols.

treatment_protocol: Induction of Prx1cre conditional deletion of Gata4 in the embryonic lateral plate mesoderm through breeding of Gata4(fl/fl) with Gata4(delta/+);Prx1Cre mice.

value: bulk lung

value: total lung cells

value: conditional knockout


title: CGND-HRA-02963

description: Library name: CGND-HRA-02963


title: E18 Prx1cre; Gata4 F/D, CKO; Biol rep 2

description:
Library name: Sample 5
Column name in GEO_Gata4_rawcounts.xlsx: CKO2 (4723-6)


title: CGND-HRA-02962

description: Library name: CGND-HRA-02962


title: CGND-HRA-02960

description: Library name: CGND-HRA-02960


title: CGND-HRA-02957

description: Library name: CGND-HRA-02957


title: CGND-HRA-1957-1

description: Library name: CGND-HRA-1957-1


title: CGND-HRA-03140

description: Library name: CGND-HRA-03140


title: E18 Prx1cre; Gata4 F/D, CKO; Biol rep 1

description:
Library name: Sample 4
Column name in GEO_Gata4_rawcounts.xlsx: CKO1 (4229-2)


title: XE 2-4, mouse embryonic stem cells, RNA-seq, technical replicate2

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
Library name: XERep2
5XERep2

data_processing:
Single-end reads were aligned to a diploid B6×D2 hybrid transcriptome constructed from Ensembl release 78 strain-specific genome reconstructions (R78-REL1505) using bowtie (v1.0.0) with parameters --best -a --strata -v 3 -m 100. Alignments were processed with EMASE model 4 to generate per-gene expected read counts each allele. B6/(B6+D2) allele ratios were calculated per gene from transcript-per-million estimates. To identify genes where EMASE reliably distinguishes alleles, parental B6 and D2 samples served as truth sets; genes were retained where mean B6 parental ratio exceeded 0.8 and mean D2 parental ratio fell below 0.4, yielding 2,863 informative genes genome-wide (42 within the Chr13 congenic interval). For gene expression analysis in congenic and parental strains, EMASE total expected counts were TMM-normalized and log2-transformed downstream differential analysis using edgeR (version 3.34.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were grown in DMEM high glucose base medium supplemented with 15% fetal bovine serum, 1X Pen/Strep, 2 mM GlutaMAX, 1 mM sodium pyruvate, 0.1 mM MEM NEAA, 0.1 mM 2-Mercaptoethanol, 103 IU LIF, 1 μM PD0325901, and 3 μM CHIR99021

extract_protocol:
RNA-seq experiments performed with B6, D2, B6-13D2, and D2-13B6 used three independent cultures from the same cell line for each strain. For each library, 1 million cells were collected, and RNA was isolated using the NucleoMag RNA Kit (Machery-Nagel) and the KingFisher Flex purification system (ThermoFisher). RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape (Agilent Technologies).
Libraries were constructed using the mRNA Library Prep Kit (Watchmaker) and assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively. Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq X Plus to a read depth of about 40 million reads per sample.

tag: strain

value: mouse embryonic stem cells


title: CGND-HRA-1927-1

description: Library name: CGND-HRA-1927-1

tag: tissue


title: E18 Prx1cre; Gata4 F/+, Control; Biol rep 3

description:
Library name: Sample 3
Column name in GEO_Gata4_rawcounts.xlsx: CONT3 (4503-6)

tag: genotype

value: control


title: XE 2-4, mouse embryonic stem cells, RNA-seq, technical replicate3

description:
Library name: XERep3
5XERep3


title: CGND-HRA-1930-1

description: Library name: CGND-HRA-1930-1


title: CGND-HRA-02976

description: Library name: CGND-HRA-02976


title: QJ 6-1, mouse embryonic stem cells, RNA-seq, technical replicate2

description:
Library name: QJRep2
5QJRep2


title: CGND-HRA-03127

description: Library name: CGND-HRA-03127


title: QJ 6-1, mouse embryonic stem cells, RNA-seq, technical replicate3

description:
Library name: QJRep3
5QJRep3


title: XE 2-4, mouse embryonic stem cells, RNA-seq, technical replicate1

description:
Library name: XERep1
5XERep1


title: CGND-HRA-02961

description: Library name: CGND-HRA-02961


title: E18 Prx1cre; Gata4 F/+, Control; Biol rep 2

description:
Library name: Sample 2
Column name in GEO_Gata4_rawcounts.xlsx: CONT2 (4229-7)


title: CGND-HRA-02956

description: Library name: CGND-HRA-02956


title: CGND-HRA-03139

description: Library name: CGND-HRA-03139


title: CGND-HRA-1941-1

description: Library name: CGND-HRA-1941-1


title: CGND-HRA-03107

description: Library name: CGND-HRA-03107


title: Embryonic day 18 (E18) Prx1Cre; Gata4 F/+, Control; Biol rep 1

description:
Library name: Sample 1
Column name in GEO_Gata4_rawcounts.xlsx: CONT1 (4229-6)


title: QJ 6-1, mouse embryonic stem cells, RNA-seq, technical replicate1

description:
Library name: QJRep1
5QJRep1


title: D2 2-9, mouse embryonic stem cells, RNA-seq, technical replicate3

description: Library name: D2Rep3


title: CGND-HRA-03062

description: Library name: CGND-HRA-03062


title: D2 2-9, mouse embryonic stem cells, RNA-seq, technical replicate1

description: Library name: D2Rep1


title: D2 2-9, mouse embryonic stem cells, RNA-seq, technical replicate2

description: Library name: D2Rep2


title: B6 4-1, mouse embryonic stem cells, RNA-seq, technical replicate3

description: Library name: B6Rep3


title: CGND-HRA-03061

description: Library name: CGND-HRA-03061


title: CGND-HRA-03057

description: Library name: CGND-HRA-03057

source_name: Cerebellum

value: Cerebellum


title: B6 5-1, mouse embryonic stem cells, RNA-seq, technical replicate1

description: Library name: B6Rep1


title: CGND-HRA-03060

description: Library name: CGND-HRA-03060


title: CGND-HRA-03059

description: Library name: CGND-HRA-03059


title: CGND-HRA-03056

description: Library name: CGND-HRA-03056


title: CGND-HRA-03063

description: Library name: CGND-HRA-03063


title: KO-P>A,rep2,Day 0,Cut&Tag Brg1

city: Guangzhou

first: Li

last: Chen

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: Library name: KO-P_A,rep2,Day 0,Cut_Tag Brg1

data_processing:
Sequencing reads were aligned to the mm39 mouse reference genome using Bowtie2, with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Sambamba was used for sorting and duplicate removal with the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate.
Reads mapped to mitochondrial DNA or unassigned sequences were discarded.
Alignment BAM files were converted into bigWig format using deepTools, with RPKM normalization.
Assembly: mm39
Supplementary files format and content: Bigwig
Library strategy: CUT&Tag

growth_protocol: Immortalized brown preadipocytes line-LGT cells were maintained in complete DMEM/F12 medium (Gibco™, C11330500BT) supplemented with 10% FBS and 1% P/S. All these cells were grown at a humidified atmosphere at 37°C with 5% CO₂.

extract_protocol:
A total of 2 × 10⁵ LGT preadipocytes or differentiated adipocytes were processed using the NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit for Illumina (Novoprotein Scientific, Cat# N259-YH01-01A), following the manufacturer’s protocol.
The library preparations were sequenced on Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: For LGT differentiation, LGT cells were cultured to 100% confluence and subsequently induced with differentiation medium which contains 20 nM insulin (Sigma, I9278), 1 nM triiodothyronine (T3; Sigma, T2877), 1 μM dexamethasone (Sigma, D4902), 500 μM 3-isobutyl-1-methylxanthine (IBMX; Sigma, I5879), 125 μM indomethacin (Sigma, I7378), and 1 μM rosiglitazone (Selleck, S2556) for 48 hours. The differentiation medium was then replaced with maintenance medium containing 20 nM insulin and 1 nM T3 for an additional 5 days.

value: KO-P>A

tag: treatment

value: preadipocyte differentiation


title: CGND-HRA-03058

description: Library name: CGND-HRA-03058


title: KO-P>A,rep2,Day0,Cut&Tag Chd4

description: Library name: KO-P_A,rep2,Day0,Cut_Tag Chd4

source_name: Immortalized brown preadipocytes line-LGT cells


title: KO-P>A,rep1,Day0,Cut&Tag Chd4

description: Library name: KO-P_A,rep1,Day0,Cut_Tag Chd4

value: Immortalized brown preadipocytes line-LGT cells


title: KO-EBF2,rep2,Day0,Cut&Tag Chd4

description: Library name: KO-EBF2,rep2,Day0,Cut_Tag Chd4


title: KO-P>A,rep1,Day 0,Cut&Tag Brg1

description: Library name: KO-P_A,rep1,Day 0,Cut_Tag Brg1


title: KO-EV,rep2,Day0,Cut&Tag Chd4

description: Library name: KO-EV,rep2,Day0,Cut_Tag Chd4

value: KO-EV


title: CGND-HRA-03121

description: Library name: CGND-HRA-03121


title: KO-EV,rep1,Day0,Cut&Tag Chd4

description: Library name: KO-EV,rep1,Day0,Cut_Tag Chd4


title: CGND-HRA-03053

description: Library name: CGND-HRA-03053


title: CGND-HRA-03055

description: Library name: CGND-HRA-03055


title: B6 5-1, mouse embryonic stem cells, RNA-seq, technical replicate2

description: Library name: B6Rep2


title: CGND-HRA-03050

description: Library name: CGND-HRA-03050


title: CGND-HRA-03049

description: Library name: CGND-HRA-03049


title: KO-EBF2,rep1,Day 0,Cut&Tag Brg1

description: Library name: KO-EBF2,rep1,Day 0,Cut_Tag Brg1


title: CGND-HRA-03052

description: Library name: CGND-HRA-03052


title: KO-EBF2,rep1,Day0,Cut&Tag Chd4

description: Library name: KO-EBF2,rep1,Day0,Cut_Tag Chd4


title: KO-EBF2,rep2,Day 0,Cut&Tag Brg1

description: Library name: KO-EBF2,rep2,Day 0,Cut_Tag Brg1


title: CGND-HRA-03054

description: Library name: CGND-HRA-03054


title: CGND-HRA-03048

description: Library name: CGND-HRA-03048


title: AtT-20 cells, P-3

city: Wuhan

first: Qian

address: No. 1095, Jiefang Avenue, Wuhan City, Hubei Province

institute: Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology

description: Library name: Sample12

data_processing:
Raw paired-end fastq reads were filtered by Fastp discard the adapters and low quality bases[1]. The clean reads obtained were then aligned to the mm10 mouse genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol extraction kit (cat. no. DP424, TIANGEN), yielding > 2 μg of total RNA per sample.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) following manufacturer’s recommendations.

value: Pituitary adenoma cell

value: P300 overexpression


title: AtT-20 cells, NC-3

description: Library name: Sample9

value: WT


title: CGND-HRA-03047

description: Library name: CGND-HRA-03047


title: AtT-20 cells, P-2

description: Library name: Sample11


title: CGND-HRA-03043

description: Library name: CGND-HRA-03043


title: AtT-20 cells, NC-1

description: Library name: Sample7


title: CGND-HRA-03046

description: Library name: CGND-HRA-03046


title: AtT-20 cells, L-1

description: Library name: Sample4


title: AtT-20 cells, NC-2

description: Library name: Sample8


title: CGND-HRA-03045

description: Library name: CGND-HRA-03045


title: CGND-HRA-03051

description: Library name: CGND-HRA-03051


title: CGND-HRA-03044

description: Library name: CGND-HRA-03044


title: AtT-20 cells, P-1

description: Library name: Sample10


title: AtT-20 cells, L-3

description: Library name: Sample6


title: AtT-20 cells, L-2

description: Library name: Sample5


title: CGND-HRA-03039

description: Library name: CGND-HRA-03039


title: CGND-HRA-03040

description: Library name: CGND-HRA-03040


title: CGND-HRA-03038

description: Library name: CGND-HRA-03038


title: CGND-HRA-03041

description: Library name: CGND-HRA-03041


title: AtT20, p300 overexpression, treated with BRC, H3K18la (ChIP)

description: Library name: OE-p300+BRC, ChIP

data_processing:
For data analysis, raw reads were filtered using fastp to obtain clean reads, which were aligned to the mm10 genome using Bowtie2. High-quality alignment results were selected using SAMtools. Peaks were called using MACS2 with default parameters (p-adjust < 0.05), and genes associated with peaks were annotated using HOMER.
Assembly: mm10
Supplementary files format and content: txt file includes peaks for each Sample
Library strategy: CUT&Tag

source_name: cell line

extract_protocol:
Cell samples were washed twice with wash buffer containing 20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM Spermidine, and protease inhibitors (cat. no. G2007, Servicebio).
For tissue samples, cell nuclei were isolated using lysis buffer containing 0.1% Triton X-100. 10 μL of Concanavalin A-coated magnetic beads (cat. no. 14203D, Thermo Fisher) were added to each sample and incubated at room temperature for 10 min. Bead-bound cells were immunoprecipitated with specific antibodies, followed by secondary antibodies to enhance binding sites. After washing, cells were treated with PAG-Tn5 transposase complex to obtain DNA fragments, which were amplified by 15 cycles of PCR to construct libraries. Libraries were sequenced on the Illumina NovaSeq Xplus platform (cat. no. FC-410-1001, Illumina) with paired-end 150 bp reads

value: cell line


title: CGND-HRA-03035

description: Library name: CGND-HRA-03035


title: CD90.2, Flex, T3

city: Singapore

first: Amit

last: Singhal

address: 8A Biomedical Grove, Immunos #05-13

department: A*STAR Infectious Diseases Labs (ID Labs)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description:
Library name: Flex_T3
10x Genomics Flex Gene Expression

data_processing:
Raw Flex scRNA-seq reads in FASTQ format were aligned to the mouse reference genome (mm10) using Cell Ranger multi (v7.1.0).
Assembly: mm10
Supplementary files format and content: Hierarchical data format 5

source_name: Lung

extract_protocol:
CD90.2 T cells from infected and uninfected WT and Nur77-KO mice were sorted and fixed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).
Four T cell samples were multiplexed in one reaction by hybridizing four differently barcoded mouse transcriptome probe sets from the Chromium Fixed RNA Kit (10x Genomics). For each pool of four samples, 20,000 cells were targeted for capture on the Chromium iX instrument, followed by library generation following the manufacturer's protocol for 10x Genomics Flex Gene Expression.

value: Lung

value: T cells

value: WT and Nur77-KO

value: infected and uninfected


title: AtT-20 cells, B-2

description: Library name: Sample2


title: CGND-HRA-03037

description: Library name: CGND-HRA-03037

value: ALS

value: female


title: CGND-HRA-03042

description: Library name: CGND-HRA-03042


title: AtT-20 cells, B-1

description: Library name: Sample1


title: AtT20, p300 overexpression treated with BRC, IgG

description: Library name: OE-p300+BRC, IgG


title: CD90.2, Flex, T4

description:
Library name: Flex_T4
10x Genomics Flex Gene Expression


title: AtT-20 cells, B-3

description: Library name: Sample3


title: CGND-HRA-03036

description: Library name: CGND-HRA-03036


title: Treg group 9 day aftre TAC surgery, #3

city: Suita

first: Takura

last: Taguchi

state: Osaka

address: 2-15, Yamadaoka

country: Japan

institute: Department of Cardiovascular Surgery, The University of Osaka Graduate School of Medicine

description: Library name: Treg9D 3

data_processing:
Adapter trimming and quality filtering were performed using Trimmomatic v0.39 with default parameters. Filtered reads were mapped to the mouse reference genome (GRCm38) using HISAT2 v2.1.0. Gene-level read counts were calculated using featureCounts v2.0.6. Differential gene expression analysis was conducted using Cuffdiff v2.2.1.
Assembly: GRCm38
Supplementary files format and content: raw_count data

source_name: left ventricular

extract_protocol:
The myocardial tissue was sacrificed and the left ventricle was cut into small pieces, immediately sealed in a polypropylene tube containing RNA later, and stored at -80°C.
Total RNA was extracted from frozen myocardial tissue samples using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany), and RNA quality was assessed by Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA sequencing libraries were constructed using the TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) and subjected to a paired-end 101bp sequencing run on the NovaSeq X plus (Illumina).

value: left ventricular

value: cardiomyocytes and other cells


title: CGND-HRA-03031

description: Library name: CGND-HRA-03031

value: Cerebellum

value: male


title: CGND-HRA-03033

description: Library name: CGND-HRA-03033


title: CGND-HRA-03032

description: Library name: CGND-HRA-03032


title: CGND-HRA-03034

description: Library name: CGND-HRA-03034


title: Treg group 9 day aftre TAC surgery, #2

description: Library name: Treg9D 2


title: AtT20 treated with BRC, IgG

description: Library name: Vec+BRC, IgG


title: Control group 9 day aftre TAC surgery, #3

description: Library name: Cont9D 3


title: CGND-HRA-03028

description: Library name: CGND-HRA-03028


title: CGND-HRA-03029

description: Library name: CGND-HRA-03029


title: CGND-HRA-03030

description: Library name: CGND-HRA-03030


title: AtT20 treated with BRC, H3K18la (ChIP)

description: Library name: Vec+BRC, ChIP


title: Treg group 9 day aftre TAC surgery, #1

description: Library name: Treg9D 1


title: CGND-HRA-03027

description: Library name: CGND-HRA-03027


title: CGND-HRA-03026

description: Library name: CGND-HRA-03026


title: Control group 9 day aftre TAC surgery, #2

description: Library name: Cont9D 2


title: CGND-HRA-03023

description: Library name: CGND-HRA-03023


title: KO-P>A,rep6,Day 7,RNA

description:
Library name: post-KO-P2A-6
column name in raw count file: post-KO-P>A-6
raw_count-2.csv

data_processing:
For RNA-seq data analysis, transcript quantification was performed using Salmon (v1.2.28) with a pre-built mm39 mouse genome index. Transcript-to-gene mapping was based on Ensembl release 104 genome annotations.  For ATAC-seq data analysis, all sequencing reads were aligned to the mm39 mouse genome assembly using Bowtie2 (v2.5.4) with the following parameters: -p 20 --very-sensitive -k 10. Duplicate reads were removed using Sambamba (v1.0.1) based on the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Alignment BAM files were converted into read coverage files (bigWig format) using deepTools (v3.5.5) with RPKM normalization.  For CUT&Tag and data analysis, Sequencing reads were aligned to the mm39 mouse reference genome using Bowtie2, with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Sambamba was used for sorting and duplicate removal with the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Reads mapped to mitochondrial DNA or unassigned sequences were discarded. Alignment BAM files were converted into bigWig format using deepTools, with RPKM normalization.
Assembly: mm39
Supplementary files format and content: Bigwig, CSV file(raw count for each smaple in RNAseq)

extract_protocol:
Total RNA from cells were extracted using RN28-EASYspin Plus RNA Mini Kit (Aidlab, RN2801) according to manufacturer’s protocol.
RNA libraries were constructed with Fast RNA-seq Lib Prep Kit V2 (Cat. No. RK2030) and sequenced using Illumina Novaseq X PLUS.  ATAC-seq libraries were generated using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat# TD711-02) following the manufacturer’s instructions and the protocol as previously described (Buenrostro et al., 2013). Briefly, 50,000 cells were washed twice with cold PBS and pelleted by centrifugation at 300 × g for 5 minutes at 4°C. Cells were then resuspended in 50 μL of ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.2% IGEPAL CA-630) and incubated on ice for 15 minutes to release nuclei. Nuclei were pelleted by centrifugation at 300 × g for 10 minutes at 4°C. Tagmentation and library construction were performed using the TruePrep™ DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD501–503). Libraries were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified for quality control. Sequencing was performed on the Illumina NovaSeq X PLUS platform.  A total of 2 × 10⁵ LGT preadipocytes or differentiated adipocytes were processed using the NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit for Illumina (Novoprotein Scientific, Cat# N259-YH01-01A), following the manufacturer’s protocol. The library preparations were sequenced on Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: EBF2 CTD

value: Day 7

value: preadipocyte differentiation


title: CGND-HRA-03021

description: Library name: CGND-HRA-03021


title: KO-P>A,rep5,Day 7,RNA

description:
Library name: post-KO-P2A-5
column name in raw count file: post-KO-P>A-5
raw_count-2.csv

value: Immortalized brown preadipocytes line-LGT cells


title: CGND-HRA-03020

description: Library name: CGND-HRA-03020


title: CGND-HRA-03025

description: Library name: CGND-HRA-03025


title: CGND-HRA-03017

description: Library name: CGND-HRA-03017


title: CGND-HRA-03024

description: Library name: CGND-HRA-03024


title: CGND-HRA-03009

description: Library name: CGND-HRA-03009

value: CTL


title: CGND-HRA-03018

description: Library name: CGND-HRA-03018


title: KO-MED1,rep5,Day 7,RNA

description:
Library name: post-KO-MED1-5
column name in raw count file: post-KO-MED1-5
raw_count-2.csv


title: KO-IDR,rep5,Day 7,RNA

description:
Library name: post-KO-IDR-5
column name in raw count file: post-KO-IDR-5
raw_count-2.csv


title: KO-IDR,rep6,Day 7,RNA

description:
Library name: post-KO-IDR-6
column name in raw count file: post-KO-IDR-6
raw_count-2.csv


title: KO-MED1,rep4,Day 7,RNA

description:
Library name: post-KO-MED1-4
column name in raw count file: post-KO-MED1-4
raw_count-2.csv


title: CGND-HRA-03022

description: Library name: CGND-HRA-03022


title: CGND-HRA-03019

description: Library name: CGND-HRA-03019


title: KO-P>A,rep4,Day 7,RNA

description:
Library name: post-KO-P2A-4
column name in raw count file: post-KO-P>A-4
raw_count-2.csv


title: KO-FUS,rep6,Day 7,RNA

description:
Library name: post-KO-FUS-6
column name in raw count file: post-KO-FUS-6
raw_count-2.csv


title: Control group 9 day aftre TAC surgery, #1

description: Library name: Cont9D 1


title: KO-IDR,rep4,Day 7,RNA

description:
Library name: post-KO-IDR-4
column name in raw count file: post-KO-IDR-4
raw_count-2.csv


title: CGND-HRA-03016

description: Library name: CGND-HRA-03016


title: CGND-HRA-03008

description: Library name: CGND-HRA-03008


title: KO-FUS,rep5,Day 7,RNA

description:
Library name: post-KO-FUS-5
column name in raw count file: post-KO-FUS-5
raw_count-2.csv


title: KO-EV,rep6,Day 7,RNA

description:
Library name: post-KO-EV-6
column name in raw count file: post-KO-EV-6
raw_count-2.csv


title: CGND-HRA-03007

description: Library name: CGND-HRA-03007


title: KO-MED1,rep6,Day 7,RNA

description:
Library name: post-KO-MED1-6
column name in raw count file: post-KO-MED1-6
raw_count-2.csv


title: CGND-HRA-03004

description: Library name: CGND-HRA-03004


title: CGND-HRA-03005

description: Library name: CGND-HRA-03005


title: KO-EV,rep4,Day 7,RNA

description:
Library name: post-KO-EV-4
column name in raw count file: post-KO-EV-4
raw_count-2.csv


title: KO-EV,rep3,Day 7,RNA

description:
Library name: post-KO-EV-3
column name in raw count file: post-KO-EV-3
raw_count-1.csv


title: CGND-HRA-03006

description: Library name: CGND-HRA-03006


title: CGND-HRA-03002

description: Library name: CGND-HRA-03002


title: CGND-HRA-02992

description: Library name: CGND-HRA-02992


title: KO-FUS,rep4,Day 7,RNA

description:
Library name: post-KO-FUS-4
column name in raw count file: post-KO-FUS-4
raw_count-2.csv


title: KO-EV,rep2,Day 7,RNA

description:
Library name: post-KO-EV-2
column name in raw count file: post-KO-EV-2
raw_count-1.csv


title: KO-EV,rep1,Day 7,RNA

description:
Library name: post-KO-EV-1
column name in raw count file: post-KO-EV-1
raw_count-1.csv


title: KO-EBF2,rep6,Day 7,RNA

description:
Library name: post-KO-EBF2-6
column name in raw count file: post-KO-EBF2-6
raw_count-2.csv


title: CGND-HRA-02973

description: Library name: CGND-HRA-02973


title: CGND-HRA-02972

description: Library name: CGND-HRA-02972


title: KO-EBF2,rep4,Day 7,RNA

description:
Library name: post-KO-EBF2-4
column name in raw count file: post-KO-EBF2-4
raw_count-2.csv


title: KO-EV,rep5,Day 7,RNA

description:
Library name: post-KO-EV-5
column name in raw count file: post-KO-EV-5
raw_count-2.csv


title: CGND-HRA-02985

description: Library name: CGND-HRA-02985


title: CGND-HRA-02969

description: Library name: CGND-HRA-02969


title: KO-EBF2,rep3,Day 7,RNA

description:
Library name: post-KO-EBF2-3
column name in raw count file: post-KO-EBF2-3
raw_count-1.csv


title: KO-EBF2,rep5,Day 7,RNA

description:
Library name: post-KO-EBF2-5
column name in raw count file: post-KO-EBF2-5
raw_count-2.csv


title: KO-EBF2,rep1,Day 7,RNA

description:
Library name: post-KO-EBF2-1
column name in raw count file: post-KO-EBF2-1
raw_count-1.csv


title: CGND-HRA-02927

description: Library name: CGND-HRA-02927


title: KO-EBF2,rep2,Day 7,RNA

description:
Library name: post-KO-EBF2-2
column name in raw count file: post-KO-EBF2-2
raw_count-1.csv


title: KO-CTD,rep3,Day 7,RNA

description:
Library name: post-KO-CTD-3
column name in raw count file: post-KO-CTD-3
raw_count-1.csv


title: CGND-HRA-02959

description: Library name: CGND-HRA-02959


title: CGND-HRA-02932

description: Library name: CGND-HRA-02932


title: CGND-HRA-02912

description: Library name: CGND-HRA-02912


title: KO-CTD,rep2,Day 7,RNA

description:
Library name: post-KO-CTD-2
column name in raw count file: post-KO-CTD-2
raw_count-1.csv


title: CGND-HRA-02914

description: Library name: CGND-HRA-02914


title: KO-P>A,Day 0,Cut&Tag Zfp423

description: Library name: pre-Zfp423-KO-P2A

data_processing:
For RNA-seq data analysis, transcript quantification was performed using Salmon (v1.2.28) with a pre-built mm39 mouse genome index. Transcript-to-gene mapping was based on Ensembl release 104 genome annotations.  For ATAC-seq data analysis, all sequencing reads were aligned to the mm39 mouse genome assembly using Bowtie2 (v2.5.4) with the following parameters: -p 20 --very-sensitive -k 10. Duplicate reads were removed using Sambamba (v1.0.1) based on the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Alignment BAM files were converted into read coverage files (bigWig format) using deepTools (v3.5.5) with RPKM normalization.  For CUT&Tag and data analysis, Sequencing reads were aligned to the mm39 mouse reference genome using Bowtie2, with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Sambamba was used for sorting and duplicate removal with the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Reads mapped to mitochondrial DNA or unassigned sequences were discarded. Alignment BAM files were converted into bigWig format using deepTools, with RPKM normalization.
Assembly: mm39
Supplementary files format and content: Bigwig, CSV file(raw count for each smaple in RNAseq)
Library strategy: CUT&Tag

value: Day 0


title: CGND-HRA-02909

description: Library name: CGND-HRA-02909


title: KO-EV,Day 0,Cut&Tag Zfp423

description: Library name: pre-Zfp423-KO-EV


title: W82 leaf ChIP-seq anti-FLAG, rep1

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

description: Library name: GmJMJ20-ChIP-seq-IP-rep1

data_processing:
Paired reads were trimmed by cutadapt v4.2 and then mapped to the Arabidopsis genome Wm82.a2 using Bowtie2 v2.4.5 with default parameters.
Peak calling was performed by Genrich with parameters "-r -a 200 -p 0.01".
Assembly: Wm82.a2.v1
Supplementary files format and content: bigWig files describing genome coverage of mapped reads

organism: Glycine max

source_name: 14-day-old leaf

growth_protocol: 12 hr light/12 hr dark, 25˚C

extract_protocol:
DNA was extracted from 14-day-old leaves following ChIP assay.
DNA  was subjected to ChIP-seq library construction with VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme #ND607) and VAHTS Multiplex Oligos Set 4/5 for Illumina (Vazyme #N321)

value: 14-day-old leaf

value: somatic cells


title: W82 leaf ChIP-seq anti-FLAG, rep2

description: Library name: GmJMJ20-ChIP-seq-IP-rep2


title: lux1lux2 leaf RNA-seq, rep2

description: Library name: lux1lux2 RNAseq R2

data_processing:
Paired reads were trimmed by cutadapt v4.2 and then mapped to the soybean genome Wm82.a2 using STAR v2.7.10b with parameters "--alignIntronMax 5000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Assembly: Wm82.a2.v1
Supplementary files format and content: Tab-delimited txt files containing gene accession, raw read counts, and gene length.

source_name: Leaf

extract_protocol:
Total RNA was isolated from 17-day-old leaves using RN38 Reagent (Aidlab Biotechnologies Co.,Ltd) according to the manufacturer’s instructions. 4 ug of DNase-treated total RNA was used for the construction of sequencing libraries.
Polyadenylated RNA isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) was subjected to RNA-seq library construction with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L).

value: Leaf


title: KO-EBF2,Day 0,Cut&Tag Zfp423

description: Library name: pre-Zfp423-KO-EBF2


title: CGND-HRA-02904

description: Library name: CGND-HRA-02904


title: CGND-HRA-02915

description: Library name: CGND-HRA-02915


title: CGND-HRA-02902

description: Library name: CGND-HRA-02902


title: KO-CTD,rep1,Day 7,RNA

description:
Library name: post-KO-CTD-1
column name in raw count file: post-KO-CTD-1
raw_count-1.csv


title: W82 leaf ChIP-seq input_rep2

description: Library name: GmJMJ20-ChIP-seq-input-rep2


title: KO-CTD,Day 0,Cut&Tag Zfp423

description: Library name: pre-Zfp423-KO-CTD


title: CGND-HRA-02899

description: Library name: CGND-HRA-02899


title: gmjmj1920-2 leaf RNA-seq, rep1

description: Library name: jmj1920 RNAseq R1


title: W82 leaf RNA-seq, rep2

description: Library name: W82 RNAseq R2


title: gmjmj1920-2 leaf RNA-seq, rep2

description: Library name: jmj1920 RNAseq R2


title: KO-P>A,Day 0,Cut&Tag Pprag

description: Library name: pre-Pprag-KO-P2A


title: lux1lux2 leaf RNA-seq, rep1

description: Library name: lux1lux2 RNAseq R1


title: KO-EV,Day 0,Cut&Tag Pprag

description: Library name: pre-Pprag-KO-EV


title: W82 leaf ChIP-seq input_rep1

description: Library name: GmJMJ20-ChIP-seq-input-rep1


title: W82 leaf ChIP-seq anti-LUX, rep2

description: Library name: LUX-ChIP-seq-IP-rep2

source_name: 17-day-old leaf

extract_protocol:
DNA was extracted from 17-day-old leaves following ChIP assay.
DNA  was subjected to ChIP-seq library construction with VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme #ND607) and VAHTS Multiplex Oligos Set 4/5 for Illumina (Vazyme #N321)

value: 17-day-old leaf


title: W82 leaf ChIP-seq input, rep2

description: Library name: LUX-ChIP-seq-input-rep2


title: KO-EBF2,Day 0,Cut&Tag Pprag

description: Library name: pre-Pprag-KO-EBF2


title: W82 leaf RNA-seq, rep1

description: Library name: W82 RNAseq R1


title: W82 leaf ChIP-seq anti-LUX, rep1

description: Library name: LUX-ChIP-seq-IP-rep1


title: CGND-HRA-02886

description: Library name: CGND-HRA-02886


title: CGND-HRA-02896

description: Library name: CGND-HRA-02896


title: W82 leaf ChIP-seq input, rep1

description: Library name: LUX-ChIP-seq-input-rep1


title: KO-CTD,Day 0,Cut&Tag Pprag

description: Library name: pre-Pprag-KO-CTD


title: Healthy C75Bd

city: Philadelphia

first: Nezar

last: Al-hebshi

state: PA

address: 3223 N Broad Street, Office L213

institute: Temple University

description:
Library name: Strain C75Bd
C75

data_processing:
Novogene pipeline for analysis of prokaryote RNA-seq data
Assembly: NCTC10562
Supplementary files format and content: fpkm normalized gene counts for each sample

organism: Fusobacterium polymorphum

source_name: Strain C75Bd

extract_protocol:
Pelleted cells were processed for total RNA extraction using the PureLink™ RNA Mini Kit (Thermo Fisher Scientific, USA) according to the bacterial RNA workflow
Novogene pipeline for directional library preparation from prokaryote RNA seq

value: Strain C75Bd

tag: source subject_status

value: Healthy control


title: CGND-HRA-02884

description: Library name: CGND-HRA-02884

value: ALS

value: female


title: WT_1_MG1655

city: Seattle

first: Monica

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

description: Library name: MG1655 isolate #1, in exponential phase (KL3243)

data_processing:
Paired-end sequencing reads were aligned to E. coli NC_000913.3 with bowtie2 using default parameters.
The read coverage was mapped by assigning each mapped base a value of 1/N where N equals the length of the read and normalizing by the total number of reads per million across both forward and reverse strands.
Assembly: NC_000913.3
Supplementary files format and content: Wiggle files first column containing chromosome positions and second column containing the normalized fraction of reads mapped to the position in reads per million. Two files are provided, for reads mapped to the forward and reverse strand.

organism: Escherichia coli

growth_protocol: Strains were grown overnight in LB at 37°C with shaking and back-diluted in the morning to an OD600 0.05. After outgrowth, cells were harvested at OD600 0.5 into 5% acid phenol in ethanol.

extract_protocol:
RNA was purified using a phenol/chloroform extraction method.
rRNA was depleted using Qiagen Fastselect and sequencing libraries were generated using a NEB Ultra II Directional RNA library kit.

treatment_protocol: No treatment


title: CGND-HRA-02889

description: Library name: CGND-HRA-02889


title: CGND-HRA-02883

description: Library name: CGND-HRA-02883


title: KO-P>A,rep1,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-P2A-1


title: ∆sbmC_isolate2

description: Library name: MG1655 sbmC::FRT-Kan-FRT isolate #2, in exponential phase (KL3241)


title: CGND-HRA-02872

description: Library name: CGND-HRA-02872


title: KO-P>A,rep2,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-P2A-2


title: CGND-HRA-02880

description: Library name: CGND-HRA-02880


title: ∆sbmC_isolate1

description: Library name: MG1655 sbmC::FRT-Kan-FRT isolate #1, in exponential phase (KL3241)


title: Healthy C55Bd

description:
Library name: Strain C55Bd
C55

source_name: Strain C55Bd

value: Strain C55Bd


title: KO-FUS,rep2,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-FUS-2


title: Healthy C65Bd

description:
Library name: Strain C65Bd
C65

source_name: Strain C65Bd

value: Strain C65Bd


title: Healthy C48Bd

description:
Library name: Strain C48Bd
C48

source_name: Strain C48Bd

value: Strain C48Bd


title: CGND-HRA-02871

description: Library name: CGND-HRA-02871

value: male


title: KO-FUS,rep1,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-FUS-1

value: EBF2 CTD


title: Mild dysplasia 60A2

description:
Library name: Strain 60A2
A60

source_name: Strain 60A2

value: Strain 60A2

value: Mild dysplasia


title: Severe dysplasia 43A3

description:
Library name: Strain 43A3
A43

source_name: Strain 43A3

value: Strain 43A3

value: Severe dysplasia


title: Severe dysplasia 41A

description:
Library name: Strain 41A
A41

source_name: Strain 41A

value: Strain 41A


title: Healthy C44Ad

description:
Library name: Strain C44Ad
C44

source_name: Strain C44Ad

value: Strain C44Ad


title: Moderate dysplasia 40A2

description:
Library name: Strain 40A2
A40

source_name: Strain 40A2

value: Strain 40A2

value: Moderate dysplasia


title: CGND-HRA-02848

description: Library name: CGND-HRA-02848

source_name: Hippocampus

value: Hippocampus


title: KO-EV,rep2,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-EV-2

source_name: Immortalized brown preadipocytes line-LGT cells

value: Day 0

value: preadipocyte differentiation


title: Mild dysplasia 199A2d

description:
Library name: Strain 199A2d
A199

source_name: Strain 199A2d

value: Strain 199A2d


title: KO-EV,rep1,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-EV-1

value: Immortalized brown preadipocytes line-LGT cells


title: CGND-HRA-02847

description: Library name: CGND-HRA-02847

value: ALS


title: Severe dysplasia 141A

description:
Library name: Strain 141A
A141

source_name: Strain 141A

value: Strain 141A