title: Heart, Chow_3

city: Boston

first: Haobo

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw sequeence image files from the sequencer were converted to the fastq format and checked for quality: per base sequence quality, the per base sequence content, per base N content, sequence length distribution, adapter and k-mer content and sequence duplication levels are collected for each sequencing run using fastqc.
fastqs are then aligned to the mouse reference genome (mm10) using STAR46 aligner.
Alignment statistics such as average red length, percentage of uniquely mapped reads, percentage of multi-mapped reads and number of splice junctions are collated. Only reads that are uniquely mapped will be considered for read annotation to gene features. Reads are annotated with the ENSEMBL 75 gene transfer format (gtf) file using Salmon.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole heart tissue

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries. Libraries were made with the RiboZero kit followed by the NEB RNA lib kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole heart tissue

value: Chow

tag: time

value: 26 weeks


title: lacrimal gland, NOD, 12 weeks, rep2

status: Public on Dec 25 2025

type: SRA

city: Beijing

first: Siyuan

last: Li

address: No. 1 Dongjiaominxiang, Dongcheng District

country: China

institute: Beijing Tongren Hospital

description:
Library name: Sample 8
N12_2

library_source: transcriptomic

data_processing:
Image processing and base recognition were performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Assembly: GRCm38
Supplementary files format and content: The Express file format is xlsx, which analyses the expression of gene and transcript in the lacrimal gland of mice.

molecule: total RNA

organism: Mus musculus

source_name: lacrimal gland

extract_protocol:
RNA was harvested using Trizol reagent and  1-2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Roche) following manufacturer's protocols.

tag: tissue

value: lacrimal gland


title: Heart, Chow_2

country: USA

tag: genotype

tag: treatment


title: lacrimal gland, NOD, 12 weeks, rep3

description:
Library name: Sample 9
N12_3


title: CPV96-1

city: suzhou

first: Xiaolong

last: Hu

state: jiangju

address: renai road

institute: soochow university

description:
Library name: Wcpv961
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).

library_source: genomic

data_processing:
To assess quality of constructed library, initial quantification was conducted using Qubit 2.0 with the dilution of 1 ng/μL. The insert size distribution was verified through Agilent 2100 Bioanalyzer analysis.
Assembly: silkDB3.0 (https://silkdb.bioinfotoolkits.net /main/species-info/-1)
Supplementary files format and content: bw files include CG, CHG and CHH levels for each Sample

molecule: genomic DNA

organism: Bombyx mori

source_name: midgut

extract_protocol:
The genomic DNA was extracted by phenol-chloroform method and validated by agarose gels for degradation and contamination.
The genomic DNA was fragmented into 200-300 bp with Covaris S220 (30s/30s for 10 times). These short sequences were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research, USA) to turn unmethylated cytosine(C) into Uridine(U) and remain methylated cytosine(C) unchanged. DNA libraries were constructed through Adaptase-mediated adapter ligation to single-stranded DNA (ssDNA) fragments, followed by PCR amplification. The WGBS were performed by Illumina HiSeq (Novogene, China).

value: midgut


title: CPV96-2

description:
Library name: Wcpv962
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).


title: Heart, Chow_1


title: K562_imatinib_resistant cells transfected with PLAG1 KD shRNA

type: genomic

city: Kharghar

first: Rukmini

last: Govekar

state: Maharashtra

address: Sector 22, Utsav Chowk-CISF Rd, Owe camp

department: Cancer Research Institute

country: India

institute: Advanced centre for Treatment, Research and Education in Cancer

description: DNA from PLAG1 KD cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC v2.0 BeadChip(Illumina) using standard illumina protocol

scan_protocol: Array was imaged using illumina iScan system

data_processing: Illumina GenomeStudiov2011 software

label: Cy3 and Cy6

organism: Homo sapiens

label_protocol: standard illumina protocol

extract_protocol: genomic DNA was extracted from PLAG1 VC and KD cells resistant to imatinib using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, USA, #80224), according to the manufacturer’s protocol.

tag: cell line

tag: cell type

value: Erythroid cells

value: IM treated

value: Imatinib resistant cells transfected with PLAG1 KD vector


title: Donor1_10x

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

description: All raw files are associated with one sample.

data_processing:
Analysis up to counting UMIs per cell per gene (DigitalExpression) was done following the Drop-seq_tools protocol (v1.12 of the software, https://github.com/broadinstitute/Drop-seq/releases).
STAR (v2.5.2a) was used to align. For human, we use hg19 with Gencode v18 annotation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_raw_counts.txt: Matrix tables with raw gene counts for every gene.

molecule: polyA RNA

source_name: RPE

extract_protocol:
Donor eyes were dissected and RPE cells were dissociated using 0.25% Trypsin-EDTA solution. RNA Sample preparation procedures were carried out according to the official Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: population

value: Caucasian

value: retinal pigment epithelium

tag: age

tag: Sex

value: female

value: untreated


title: lacrimal gland, NOD, 12 weeks, rep1

description:
Library name: Sample 7
N12_1


title: GUT96-1

description:
Library name: Wgut961
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).


title: K562_imatinib_resistant cells transfected_VC shRNA

description: DNA from PLAG1 VC cells

label: Cy3 and Cy5

value: WT

value: Imatinib resistant cells transfected with control vector


title: Heart, HFD+STZ_1

value: HFD+STZ


title: lacrimal gland, ESS, rep3

description:
Library name: Sample 6
ESS3


title: Heart, HFD+STZ+AAV METTL3_4

value: HFD+STZ+AAV METTL3


title: KU812_imatinib_resistant_cells

description: DNA from KU812 imatinib resistant cells

label: biotin

extract_protocol: genomic DNA was extracted from K562 and KU812 cells sensitive and resistant ti imatinib using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, USA, #80224), according to the manufacturer’s protocol.

value: Basophilic cells

value: Imatinib resistant


title: CPV48-1

description:
Library name: Wcpv481
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).


title: lacrimal gland, ESS, rep2

description:
Library name: Sample 5
ESS2


title: Heart, HFD+STZ+AAV METTL3_3

value: Whole heart tissue


title: KU812_imatinib_sensitive_cells

description: DNA from KU812 imatinib sensitive cells

value: Imatinib sensitive


title: GUT48-2

description:
Library name: Wgut482
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).


title: lacrimal gland, ESS, rep1

description:
Library name: Sample 4
ESS1

value: lacrimal gland


title: Heart, HFD+STZ+AAV METTL3_2

value: 26 weeks


title: K562_imatinib_sensitive_cells

description: DNA from K562 imatinib sensitive cells

value: Erythroid cells


title: lacrimal gland, control, rep3

description:
Library name: Sample 3
Ctrl3


title: K562_imatinib_resistant_cells

description: DNA from K562 imatinib resistant cells

value: IM treated


title: GUT48-1

description:
Library name: Wgut481
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).

value: midgut


title: lacrimal gland, control, rep2

description:
Library name: Sample 2
Ctrl2


title: CD8,WT,infected,spleen

city: Xiamen City

first: GUO

last: FU

address: No. 4221, Xiang'an South Road, Xiang'an District, Xiamen, Fujian Province

institute: Xiamen University

description:
Library name: day5_spleen_WT
BGI C4 single-cell RNA-seq

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (version 3.0.2) with default parameters for alignment, UMI quantification, and generation of the gene expression matrix.
Assembly: mm10 (Mouse Genome, GRCm38)
Supplementary files format and content: Processed files: Gene expression matrix in Matrix Market Exchange format (.mtx),Cell barcodes: barcodes.tsv ,Gene annotations: genes.tsv

source_name: spleen

extract_protocol:
Single-cell suspensions were prepared from harvested lung and spleen tissues. Samples were processed using mechanical dissociation and enzymatic digestion to ensure viable single-cell isolation. Dead cells and debris were removed using density gradient centrifugation.
Single-cell RNA-seq libraries were constructed using the BGI C4 single-cell sequencing platform. The libraries were generated following the C4 protocol, which uses droplet-based single-cell capture, UMI barcoding, and cDNA synthesis. Libraries were then sequenced on the BGI DNBSEQ-G400 instrument.

value: spleen

value: 6-8 weeks old

value: CD8+ T cells

value: male

value: LCMV-clone 13

value: 5 days


title: GUT96-2

description:
Library name: Wgut962
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).


title: P09_LM

city: Shanghai

first: Xuege

last: Wang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

description:
Library name: Sample 24
BD Rhapsody

data_processing:
For RNA seq, paired-end reads were aligned to the mouse (GRCm38) reference genome with HISAT2
For scRNA seq, libraries were mapped with Cellranger (version 4.0.0), clustered with Seurat (version 4.3.0).
For stereo seq, sequences were aligned to mouse (GRCm38) reference genome using STAR and down processed with Stereo-Seq Analysis Workflow (SAW).
Assembly: mm10 and hg38
Supplementary files format and content: matrix, bam

source_name: liver metastases

growth_protocol: For liver metastases sequence, AKP cells were intrasplenically injected to C57BL/6 mice.

extract_protocol:
For mRNA sequence, RNA was extracted from Kupffer cells of AKP liver metastases before and after chemotherapy using Trizol (Invitrogen) and reverse transcribed into cDNA using the HiScript II Q RT SuperMix kit (Vazyme).
For RNA seq, libraries were prepared according to the illumina standard instructions. For scRNA seq, libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v2. For spatial transcriptomics,  libraries were prepared using the Stereo-seq Transcriptomics Set for Chip-on-a-slide (STOmics).

treatment_protocol: treatment with FOLFOX regimen

value: liver metastases


title: Heart, HFD+STZ_3

value: HFD+STZ


title: P10_LM

description:
Library name: Sample 25
BD Rhapsody


title: Heart, HFD+STZ_4


title: CD8,WT,infected,lung

description:
Library name: day5_lung_WT
BGI C4 single-cell RNA-seq

source_name: lung

value: lung


title: lacrimal gland, control, rep1

description:
Library name: Sample 1
Ctrl1


title: CPV48-2

description:
Library name: Wcpv482
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).


title: P08_LM

description:
Library name: Sample 23
BD Rhapsody


title: ID1OE_KC_ATAC

description: Library name: Sample 9

data_processing:
For cut&tag seq and atac seq, paired-end reads were mapped to the mouse (GRCm38) reference genome using the Bowtie2 aligner (version 2.5.4)
Peaks were called with MACS2
Assembly: mm10
Supplementary files format and content: bigwig

source_name: kupffer cells

growth_protocol: For cut&tag seq of WT_KC_ATAC and ID1OE_KC_ATAC samples, kupffer cells were cocultured with 5-FU pre-treated AKP for 4 days.

extract_protocol:
Cells were isolated via flow cytometry, fixed and nuclei extraced according to standard protocol of CUT&Tag Assay Kit (Vazyme, TD503)
DNA libraries were prepared using the TruePrep Index Kit v2 (Vazyme, TD503

value: kupffer cells

value: ID1 overexpression


title: WT_KC_ATAC

description: Library name: Sample 8

value: WT

value: cocultured with 5-FU pre-treated AKP for 4 days


title: Heart, HFD+STZ+AAV METTL3_1

value: Whole heart tissue

value: HFD+STZ+AAV METTL3

value: 26 weeks


title: Donor4_ICELL8

description: Individual fastq files for each cell.

value: Caucasian

value: retinal pigment epithelium

value: female

value: untreated


title: CD8,KO,infected,lung

description:
Library name: day5_lung_KO
BGI C4 single-cell RNA-seq

value: 6-8 weeks old

value: CD8+ T cells

value: male


title: P07_LM

description:
Library name: Sample 22
BD Rhapsody

value: liver metastases


title: RL_LM_Stereo-seq

description:
Library name: Sample 31
Stereo-seq

data_processing:
For RNA seq, paired-end reads were aligned to the mouse (GRCm38) reference genome with HISAT2
For scRNA seq, libraries were mapped with Cellranger (version 4.0.0), clustered with Seurat (version 4.3.0).
For stereo seq, sequences were aligned to mouse (GRCm38) reference genome using STAR and down processed with Stereo-Seq Analysis Workflow (SAW).
Assembly: mm10 and hg38
Supplementary files format and content: matrix, bam
Library strategy: Spatial Transcriptomics

value: FOLFOX regimen for 15 days


title: Donor3_ICELL8

description: Individual fastq files for each cell.


title: RS_LM_Stereo-seq

description:
Library name: Sample 30
Stereo-seq

value: FOLFOX regimen for 5 days


title: P06_LM

description:
Library name: Sample 21
BD Rhapsody


title: Donor2_ICELL8

description: Individual fastq files for each cell.

value: African-American


title: KC2_ATAC

description: Library name: Sample 6

value: kupffer cells


title: LEPR+KC_ATAC

description: Library name: Sample 7


title: P05_LM

description:
Library name: Sample 20
BD Rhapsody


title: Heart, HFD+STZ_2

value: HFD+STZ


title: CD8,KO,infected,spleen

description:
Library name: day5_spleen_KO
BGI C4 single-cell RNA-seq

value: spleen

value: LCMV-clone 13

value: 5 days


title: KC1_ATAC

description: Library name: Sample 5


title: P04_LM

description:
Library name: Sample 19
BD Rhapsody


title: WT_LM

description:
Library name: Sample 29, WT
10x Genomics
WT&DTR_LM_matrix.mtx.gz
WT&DTR_LM_barcodes.tsv.gz
WT&DTR_LM_features.tsv.gz

value: LRDTR and LRKC-DTR mice


title: LEPR+ KC_PU1_cuttag

description: Library name: Sample 4

data_processing:
For cut&tag seq and atac seq, paired-end reads were mapped to the mouse (GRCm38) reference genome using the Bowtie2 aligner (version 2.5.4)
Peaks were called with MACS2
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag


title: DTR_LM

description:
Library name: Sample 29, DTR
10x Genomics
WT&DTR_LM_matrix.mtx.gz
WT&DTR_LM_barcodes.tsv.gz
WT&DTR_LM_features.tsv.gz


title: HLCZ01 cells without HBV infection, repeat_1

city: Jinan

first: Yang

last: Sun

state: Shandong

address: No.44 Wenhua West Road

department: Immunology

institute: Shandong University

description: Library name: Sample_3

data_processing:
Sequencing raw reads were preprocessed by filtering out sequencing adapters, short-fragment reads and other low-quality reads. We used HISAT2 to map the cleaned reads to the human GRCh38 reference genome. After genome mapping, Read Count for each gene was counted by HTSeq, and fragments per kilobase million mapped reads (FKPM) were calculated to represent the expression level of genes in each sample. DEseq2 package was used for differential expression analysis. Differentially expressed lncRNAs between the two groups were identified through fold change and adjusted P values (q value).
Assembly: GRCh38
Supplementary files format and content: csv files include FPKM value for each sample.
Supplementary files format and content: csv files include FPKM value for each sample.

source_name: HCC

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen), and 1μg total RNA was used for the construction of sequencing libraries.
3 μg RNA per sample was used as the initial material for the RNA sample preparations. Ribosomal RNA was removed using the Epicentre Ribo-Zero Gold Kits (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA). RNA concentration of the library was measured using Qubit RNA Assay Kit in Qubit 2.0 to quantify and then dilute to 1 ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using Taqman fluorescence probe of AB Step One Plus Real-Time PCR system. Clustering was generated by cBot cluster generation system and then was sequenced on an Illumina platform.

value: HCC

value: HCC-derived cell line


title: HLCZ01 cells without HBV infection, repeat_2

description: Library name: Sample_4


title: RL_LM

description:
Library name: Sample 28
10x Genomics


title: KC1_PU1_cuttag

description: Library name: Sample 3


title: P02_LM

description:
Library name: Sample 17
BD Rhapsody


title: P03_LM

description:
Library name: Sample 18
BD Rhapsody


title: HBV-infected HLCZ01 cells, repeat_1

description: Library name: Sample_1


title: RS_LM

description:
Library name: Sample 27
10x Genomics


title: P01_LM

description:
Library name: Sample 16
BD Rhapsody


title: NT_LM

description:
Library name: Sample 26
10x Genomics

value: isotype control


title: WTKC_PU1_cuttag

description: Library name: Sample 1

value: WT


title: Parp7 siRNA2 CEBPb Replicate 1

status: Public on Dec 24 2025

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The CUT&RUN reads were aligned to the mm10 mouse reference genome using Bowtie2.
Mapped reads were sorted and captured in bam files and converted to bed files for further downstream analysis of peak calling . Bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: mm10
Supplementary files format and content: BigWig - Browser Tracks for visualization on UCSC geneome browser
Library strategy: CUT&RUN

growth_protocol: The cells were transfected with siRNAs targeting Parp7 or a universal control 48hrs before the addition of the differentiation cocktail. The cells were then differentiated for 24hrs before collection as described below.

extract_protocol:
3T3-L1 cells were cultured and treated as described above in 15 cm diameter plates.  The cells were transfected with siRNAs targeting Parp7 or a universal control 48hrs before the addition of the differentiation cocktail. The cells were then differentiated for 24hrs
Cells were harvested by trypsinization and counted using the BioRad TC20 automated cell counter. 100,000 cells were collected and pelleted by centrifugation. Cut & Run was preformed using the Epicypher kit (CUTANA ChIC / CUT&RUN Kit) according to manufacturer protocol. In short, the cells were bound to beads, permeabilized using 0.1% digitonin and incubated with 0.5µg antibodies. n= 2 biological replicates.


title: Parp7 siRNA2 CEBPb Replicate 1 Additional Reads


title: Parp7 siRNA1 CEBPb Replicate 1 Additional Reads


title: Parp7 siRNA1 CEBPb Replicate 2


title: Control siRNA CEBPb Replicate 2


title: Control siRNA CEBPb Replicate 1


title: Parp7 siRNA1 CEBPb Replicate 1


title: Control siRNA CEBPb Replicate 1 Additional Reads


title: Control siRNA CEBPb Replicate 2 Additional Reads


title: Parp7 siRNA1 CEBPb Replicate 2 Additional Reads


title: Parp7 siRNA1 IgG Replicate 2


title: Parp7 siRNA2 IgG Replicate 2


title: Parp7 siRNA2 IgG Replicate 1


title: Control SiRNA IgG Replicate 2 Additional Reads


title: Parp7 siRNA1 IgG Replicate 1 Additional Reads


title: HBV-infected HLCZ01 cells, repeat_2

description: Library name: Sample_2


title: Parp7 siRNA2 IgG Replicate 1 Additional Reads


title: Parp7 siRNA2 IgG Replicate 2 Additional Reads


title: Control SiRNA IgG Replicate 1 Additional Reads


title: Parp7 siRNA1 IgG Replicate 1


title: ID1KOKC_PU1_cuttag

description: Library name: Sample 2


title: Control SiRNA IgG Replicate 2


title: Control SiRNA IgG Replicate 1


title: Parp7 siRNA2 CEBPb Replicate 2


title: Parp7 siRNA2 CEBPb Replicate 2 Additional Reads


title: Parp7 siRNA2 2 day Replicate 3

data_processing:
The RNA-seq reads were aligned to the mm10 human reference genome using TopHat.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: mm10
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on UCSC geneome browser

extract_protocol:
3T3-L1 cells were grown and differentiated, in a 6-well plate, as mentioned above and were transfected with siRNAs targeting Parp7 using the Lipofectamine 3000 Reagent (Invitrogen, L3000015). The cells were collected, and total RNA was isolated using the Direct-zol RNA MiniPrep Plus (ZYMO Research) according to the manufacturer’s instructions.
The RNA obtained above was used to generate strand-specific RNA-seq libraries. Briefly, the libraries were prepared using the the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs #E7760S) with the NEBNext Poly(A) mRNA magnetic Isolation Module (New England Biolabs #E7490S) for mouse SVF samples and 3T3-L1 cells. Specifically, 0.6µM adapter was used for its ligation and final mRNA library was amplified with 14 x PCR cycles and sequenced on an illumina NEXTseq2000 system by paired-end 50bp using NEXTseq 2000 P3-100cycle sequencing kit (20040559). n= 4 biological replicates.


title: Parp7 siRNA2 2 day Replicate 2

growth_protocol: 3T3-L1 cells were grown and differentiated, in a 6-well plate, as mentioned above and were transfected with siRNAs targeting Parp7 using the Lipofectamine 3000 Reagent (Invitrogen, L3000015). The cells were collected, and total RNA was isolated using the Direct-zol RNA MiniPrep Plus (ZYMO Research) according to the manufacturer’s instructions


title: Parp7 siRNA1 2 day Replicate 4


title: Parp7 siRNA2 2 day Replicate 1


title: Parp7 siRNA1 2 day Replicate 2


title: Parp7 siRNA1 2 day Replicate 1


title: Control siRNA 2 day Replicate 4


title: Control siRNA 2 day Replicate 1


title: Parp7 siRNA2 0 day Replicate 3


title: Control siRNA 2 day Replicate 2


title: Parp7 siRNA2 0 day Replicate 4


title: Control siRNA 2 day Replicate 3


title: Parp7 siRNA2 0 day Replicate 2


title: Parp7 siRNA1 0 day Replicate 3


title: Parp7 siRNA2 0 day Replicate 1


title: Parp7 siRNA1 0 day Replicate 2


title: Parp7 siRNA1 0 day Replicate 1


title: Control siRNA 0 day Replicate 3


title: MG132 Treatment Replicate 3

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for later Metagene and read-density analyses by using the BEDTools software package  (Quinlan et al, 2010).
Assembly: mm10
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

growth_protocol: 3T3-L1 cells were cultured and treated as described above in 15 cm diameter plates.  The cells were treated with vehicle control DMSO, MG132, or RBN2397. The cells were then differentiated for 8hrs before collection

extract_protocol:
The samples were used in immunoprecipitation reactions with antibodies against PARP7 (in-house N-term antibody) or rabbit IgG (as a control) with incubation overnight at 4 °C with gently mixing. The next day, Protein A Dynabeads were washed 3 times, they were then added to each IP sample and were left to rotate at 4°C for 3 hours. The samples were then washed 2 times  with each of the following buffers (1) RIPA 0 Buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, and 1x complete protease inhibitor cocktail), (2) RIPA 0.3 Buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.3 M NaCl, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, and 1x complete protease inhibitor cocktail), (3) LiCl Wash Buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, and 1x complete protease inhibitor cocktail), and (4) 1x Tris-EDTA (TE). The immunoprecipitated genomic DNA was eluted in SDS Elution Buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCL pH 7.9) and was decrosslinked at 65°C overnight. Supernatant was then collected and was digested with proteinase K and RNase A to remove protein and RNA, respectively. ChIP DNA was then recovered using Qiagen PCR Purification Kit (Cat. No. 28104)and was eluted in DEPC- treated, nuclease-free water.
ChIP-seq libraries were generated from three biological replicates for each condition. A total of 10 ng for PARP7 ChIPed DNA, or equivalent amounts input DNA, were used to generate libraries for sequencing. ChIP-seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs #E7645) and sequenced on an Illumina NextSeq2000 system by paired end 50bp using NEXTseq 2000 P3-100cycle sequencing kit (20040559). n= 3 biological replicates. Publicly available data from GSE27826 was used for some analysis{Siersbaek, 2011 #131}.

treatment_protocol: The cells were differentiated for 8hrs before collection. At the time of differentiation the cells were treated with vehicle control DMSO, MG132, or RBN2397.


title: RBN2397 Treatment Replicate 2


title: Control siRNA 0 day Replicate 2


title: RBN2397 Treatment Replicate 3


title: Control siRNA 0 day Replicate 4


title: MG132 Treatment Replicate 2


title: Parp7 siRNA2 2 day Replicate 4


title: Control siRNA 0 day Replicate 1


title: MG132 Treatment Replicate 1


title: Vehicle Treatment Replicate 3


title: Vehicle Treatment Replicate 1

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO


title: RBN2397 Treatment Replicate 1


title: Vehicle Treatment Replicate 2


title: Input RBN2397 Treatment


title: Parp7 siRNA1 2 day Replicate 3


title: Input MG132 Treatment


title: Parp7 siRNA 2 Replicate 2

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using theusing BWAKit ver.0.7.15.
The aligned reads were then subjected to a quality score check, assessed for unique alignments using Picard tools (ver. 2.10.3, http://broadinstitute.github.io/picard/) and only the reads with a score over 10 were used for further analysis. The uniquely mapped reads were normalized for read depth across all samples and converted to bigWig files using the writeWiggle function from the groHMM {Chae, 2015 #147} package in R and visualized on the UCSC genome browser.
Assembly: mm10
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

growth_protocol: 3T3-L1 cells (Green and Kehinde, 1975) cells were obtained from the American Type Cell Culture (ATCC, CL-173 and CRL-1658, respectively) and were mycoplasma-free. They were maintained in DMEM (Cellgro, 10-017-CM) supplemented with 10% fetal bovine serum (Atlanta Biologicals, S11550) and 1% penicillin/streptomycin. For the induction of adipogenesis, the 3T3-L1 cells were grown to confluence and then cultured for 2 more days under contact inhibition. The cells were then treated for 2 days with an MDI adipogenic cocktail containing 0.25 mM IBMX, 1 μM dexamethasone, and 10 μg/ml insulin. Subsequently, the cells were cultured in medium containing 10 μg/ml insulin for the indicated times before collection.

extract_protocol:
3T3-L1 cells were cultured and treated as described above in 15 cm diameter plates.  The cells were transfected with siRNAs targeting Parp7 or a universal control 24hrs before the addition of the differentiation cocktail. The cells were then differentiated for 24hrs
Cells were harvested by trypsinization and counted using the BioRad TC20 automated cell counter. 50,000 cells were collected and pelleted by centrifugation. Samples were then resuspended in buffer containing 10mM Tris-HCL pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 3 min. Nuclei were then washed twice with buffer containing 10mM Tris-HCL pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20. Nuclei were pelleted by spinning at 500g for 10 min at 4°C in a fixed angle centrifuge. Pellets were then resuspended in transposition mixture containing 20mM Tris-HCL pH 7.6, 10mM MgCl2, 20% DMF, 0.01% Digitonin, 0.1% Tween-20, and 100 nM recombinant Tn5 transposase. After pipetting up and down 6 times, mixture was incubated at 37°C for 30 mins with 1000 RPM mixing using the Eppendorf Thermomixer C. Resulting tagmented DNA was purified using Qiagen PCR CleanUp columns and was eluted with elution buffer. Samples were then combined with 2X NEBNext High-Fidelity Master Mix (NEB cat#M0541L), Nextera i7 and i5 indexed primers, and amplified by PCR: 1) 72C 5Min, 2) 98°C 30Sec, 3) 98°C 10Sec, 4) 63°C 10Sec. PCR steps 3-4 were repeated 8 times. Adaptor contamination was removed from libraries using 1.3X volume AMPure beads and eluted in 10mM Tris-HCL (pH 8). n= 2 biological replicates

treatment_protocol: The cells were transfected with siRNAs targeting Parp7 or a universal control 24hrs before the addition of the differentiation cocktail. The cells were then differentiated for 24hrs before collection.


title: Input Vehicle Treatment


title: Parp7 siRNA 2 Replicate 1


title: Parp7 siRNA 1 Replicate 2


title: Parp7 siRNA1 0 day Replicate 4


title: Parp7 siRNA 1 Replicate 1


title: GM14297, technical replicate1

city: Tallahassee

first: Shahin

last: Behrouz Sharif

state: Florida

address: 319 Stadium Dr.

department: Biological Sciences

institute: Florida State University

description: Library name: GM14297_rep1

data_processing:
reads were aligned with HISAT2 v.2.1.0 (https://github.com/DaehwanKimLab/hisat2) to GENCODE GRCh38. Low‑quality reads (<10) and PCR duplicates were removed. Read summarization to genomic features was performed with featureCounts v2.0.3
Assembly: hg38
Supplementary files format and content: txt file including the raw counts of aligned reads (output of featureCounts)

source_name: Human B-cell

extract_protocol:
Total nuclear RNA was isolated from biological and technical replicates using the NucleoSpin RNA Plus Mini kit with on‑column DNase treatment (Macherey‑Nagel, 740984). Polyadenylated RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).
Libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7765). Almost 2ug of mRNA was used for library preparation. No size selection was performed during library preparation.

value: Human B-cell


title: GM14295, technical replicate1

description: Library name: GM14295_rep1


title: GM14295, technical replicate2

description: Library name: GM14295_rep2


title: GM14295, technical replicate3

description: Library name: GM14295_rep3


title: Wild-type HCT116, replicate1, IgG

description: Library name: HCT116_rep1_INPUT

data_processing:
Raw FASTQ files were trimmed with Trimmomatic-0.39 to remove adapters and low‑quality bases. CUT&RUN sequencing reads were aligned to the GENCODE GRCh38 reference genome using Bowtie2 v2.3.5.1. Alignments were processed with SAMtools v1.10; reads with mapping quality <10 and PCR duplicates were removed. Library complexity and coverage were assessed, and replicate concordance was evaluated by Spearman correlation and principal component analysis (PCA). Peaks were called with MACS3 v3.0.0b1 using broad peaks for histone post‑translational modifications and narrow peaks for chromatin remodelers and enzymes; a common INPUT control was used for all samples and a q‑value threshold of 0.01 was applied. BedGraph files were generated for genome browser visualization and heatmap production using deepTools v3.5.1.
Assembly: hg38
Supplementary files format and content: bigwig, macs3 peak-caller bedgraph output
Library strategy: CUT&Run

extract_protocol:
For each reaction,  approximately 2.5×105 intact cells were crosslinked with 0.1% formaldehyde for 2 minutes and quenched with 125 mM glycine (pH 2.0). Cells were immobilized on Concanavalin A‑coated magnetic beads (BioMag® Plus Concanavalin A, Polysciences Inc. #86057), washed in Wash Buffer containing 0.1% Triton X‑100, and incubated with primary antibody or normal rabbit IgG overnight at 4°C. pAG‑MNase was added to bind chromatin‑associated antibody. MNase was then activated to cleave and release DNA fragments.
DNA fragments were prepared for sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7103) based on the manufacturers recomandation. 15 cycles of PCR were used to amplify the libraries .

value: Human epithelial


title: GM14296, technical replicate1

description: Library name: GM14296_rep1


title: GM14297, technical replicate2

description: Library name: GM14297_rep2


title: GM14297_technical replicate3

description: Library name: GM14297_rep3


title: HCT116_WSTF_knock-out, replicate1, H4K12ac

description: Library name: HCT116_WSTFKO_rep1_H4K12ac


title: GM14296, technical replicate2

description: Library name: GM14296_rep2


title: HCT116_WSTF_knock-out, replicate2, H4K12ac

description: Library name: HCT116_WSTFKO_rep2_H4K12ac


title: GM14296, technical replicate3

description: Library name: GM14296_rep3


title: HCT116_WSTF_knock-out, replicate1, H4K20me1

description: Library name: HCT116_WSTFKO_rep1_H4K20me1


title: HCT116_WSTF_knock-out, replicate2, H4K20me1

description: Library name: HCT116_WSTFKO_rep2_H4K20me1


title: HCT116_WSTF_knock-out, replicate2, H4K5ac

description: Library name: HCT116_WSTFKO_rep2_H4K5ac


title: HCT116_WSTF_knock-out, replicate1, H4K5ac

description: Library name: HCT116_WSTFKO_rep1_H4K5ac


title: HCT116_WSTF_knock-out, replicate1, H3K36me2

description: Library name: HCT116_WSTFKO_rep1_H3K36me2


title: HCT116_WSTF_knock-out, replicate1, H4K8ac

description: Library name: HCT116_WSTFKO_rep1_H4K8ac


title: HCT116_WSTF_knock-out, replicate2, H3K36me2

description: Library name: HCT116_WSTFKO_rep2_H3K36me2


title: HCT116_WSTF_knock-out, replicate2, H3K27ac

description: Library name: HCT116_WSTFKO_rep2_H3K27ac


title: HCT116_WSTF_knock-out, replicate1, H3K27me3

description: Library name: HCT116_WSTFKO_rep1_H3K27me3


title: HCT116_WSTF_knock-out, replicate2, H3K27me3

description: Library name: HCT116_WSTFKO_rep2_H3K27me3


title: HCT116_WSTF_knock-out, replicate2, H3K9ac

description: Library name: HCT116_WSTFKO_rep2_H3K9ac


title: HCT116_WSTF_knock-out, replicate2, H3K14ac

description: Library name: HCT116_WSTFKO_rep2_H3K14ac


title: HCT116_WSTF_knock-out, replicate1, H3K14ac

description: Library name: HCT116_WSTFKO_rep1_H3K14ac


title: SAS cells, siNAT10, bio rep 2

city: Nanjing

first: Junguo

address: No.321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

description:
Library name: Sample 4
KO_2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: SAS cells

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent (ThermoFisher, cat. no. 15596026) following the manufacturer's recommended protocol.
For library preparation, the total RNA was used as input for RNA sequencing library preparation utilizing the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan, China), according to the manufacturer's instructions.

value: SAS cells

value: Cancer cells

value: NAT11 knockdown

value: total RNA

tag: batch

value: paired-end


title: SAS cells, siControl, bio rep 2

description:
Library name: Sample 2
NC_2


title: HCT116_WSTF_knock-out, replicate1, H3K4me3

description: Library name: HCT116_WSTFKO_rep1_H3K4me3


title: SAS cells, siNAT10, bio rep 1

description:
Library name: Sample 3
KO_1

value: NAT10 knockdown


title: HCT116_WSTF_knock-out, replicate2, H3K9me3

description: Library name: HCT116_WSTFKO_rep2_H3K9me3


title: HCT116_WSTFKO, bio-rep2, technical replicate3

description: Library name: HCT116_WSTFKO_rep6

source_name: Human epithelial


title: SAS cells, siControl, bio rep 1

description:
Library name: Sample 1
NC_1


title: HCT116_WSTF_knock-out, replicate2, H3K4me3

description: Library name: HCT116_WSTFKO_rep2_H3K4me3


title: Control siRNA Replicate 1


title: HCT116_WSTFKO, bio-rep2, technical replicate1

description: Library name: HCT116_WSTFKO_rep4


title: HCT116_WSTF_knock-out, replicate2, H4K8ac

description: Library name: HCT116_WSTFKO_rep2_H4K8ac


title: HCT116_WSTFKO, bio-rep2, technical replicate2

description: Library name: HCT116_WSTFKO_rep5


title: HCT116_WSTFKO, bio-rep1, technical replicate3

description: Library name: HCT116_WSTFKO_rep3


title: HCT116_WSTF_knock-out, replicate1, H3K4me2

description: Library name: HCT116_WSTFKO_rep1_H3K4me2


title: HCT116_WSTF_knock-out, replicate2, H3K4me1

description: Library name: HCT116_WSTFKO_rep2_H3K4me1


title: HCT116_WSTF_knock-out, replicate1, H3K4me1

description: Library name: HCT116_WSTFKO_rep1_H3K4me1


title: HCT116_WSTF_knock-out, replicate1, H3K9ac

description: Library name: HCT116_WSTFKO_rep1_H3K9ac


title: HCT116_WSTF_knock-out, replicate1, H3K27ac

description: Library name: HCT116_WSTFKO_rep1_H3K27ac


title: HCT116_WSTF_knock-out, replicate2, H3K4me2

description: Library name: HCT116_WSTFKO_rep2_H3K4me2


title: Control siRNA Replicate 2

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: HCT116_WSTFKO, bio-rep1, technical replicate2

description: Library name: HCT116_WSTFKO_rep2


title: Wild-type HCT116, technical replicate3

description: Library name: HCT116_rep3


title: HCT116_WSTF_knock-out, replicate1, H2AK119ub

description: Library name: HCT116_WSTFKO_rep1_H2AK119ub


title: Wild-type HCT116, technical replicate1

description: Library name: HCT116_rep1


title: HCT116_WSTF_knock-out, replicate2, SNF2H

description: Library name: HCT116_WSTFKO_rep2_SNF2H


title: HCT116_WSTF_knock-out, replicate1, SNF2H

description: Library name: HCT116_WSTFKO_rep1_SNF2H


title: Wild-type HCT116, technical replicate2

description: Library name: HCT116_rep2


title: HCT116_WSTF_knock-out, replicate1, H3K9me3

description: Library name: HCT116_WSTFKO_rep1_H3K9me3


title: HCT116_WSTF_knock-out, replicate1, LaminB

description: Library name: HCT116_WSTFKO_rep1_LaminB


title: HCT116_WSTF_knock-out, replicate2, EZH2

description: Library name: HCT116_WSTFKO_rep2_EZH2


title: HCT116_WSTFKO, bio-rep1, technical replicate1

description: Library name: HCT116_WSTFKO_rep1


title: HCT116_WSTF_knock-out, replicate2, LaminB

description: Library name: HCT116_WSTFKO_rep2_LaminB


title: HCT116_WSTF_knock-out, replicate1, EZH2

description: Library name: HCT116_WSTFKO_rep1_EZH2


title: HCT116_WSTF_knock-out, replicate1, CBX4

description: Library name: HCT116_WSTFKO_rep1_CBX4


title: HCT116_WSTF_knock-out, replicate2,CBX4

description: Library name: HCT116_WSTFKO_rep2_CBX4


title: HCT116_WSTF_knock-out, replicate2, CBP

description: Library name: HCT116_WSTFKO_rep2_CBP


title: HCT116_WSTF_knock-out, replicate2, ASH2L

description: Library name: HCT116_WSTFKO_rep2_ASH2L


title: HCT116_WSTF_knock-out, replicate1, ASH2L

description: Library name: HCT116_WSTFKO_rep1_ASH2L


title: S2-007_n3

city: Yonago

first: Hirotoshi

last: Mochida

state: Tottori

address: 86 Nishi-cho

department: Pathology

country: Japan

institute: Faculty of Medicine, Tottori University

description: Library name: Sample 3

data_processing:
Adapter trimming and quality trimming were performed using trimmomatic (ver. 0.39).
Cleaned RNA-seq reads were aligned to the GRCh38.p14 genome assembly using BWA (ver. 0.7.17).
Calculating mapping statistics from BAM file were performed using SAMtools (ver. 1.12).
The analysis data of mapping statistics of transcript IDs was compiled for each gene using gene IDs.
Nromalization using the Trimmed Mean of M-values (TMM) method for comparing the expression levels of each genes was performed using edgeR (ver. 3.16.5). Normalization; ( Read of the gene/total reads of  sample)x(total reads of the sample with the least total reads)
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts, normalized total counts, and TMM values for each sample

source_name: Pancreas

growth_protocol: S2-007, S2-020, and S2-028 cells were seeded at a density of 3.6 × 10^5 in 6-well plates, and maintained in DMEM supplemented with 10% inactivated fetal bovine serum.

extract_protocol:
Total RNA from S2-007, S2-020, and S2-028 cells were recovered using RNeasy Mini Kit according to the manufacturer’s instructions.
To purify the strand-specific mRNA library, the mRNA was reverse transcribed into cDNA using random primers, and then the synthesized double-strand cDNA was fragmented, and the cDNA was subsequently ligated adapters. Transcriptome sequencing in strand-specific mRNA-seq library was performed using illumine NovaSeq 6000 Sequencing System.

value: Pancreas

value: Adenocarcinoma


title: S2-007_n1

description: Library name: Sample 1


title: S2-007_n2

description: Library name: Sample 2


title: S2-020_n3

description: Library name: Sample 6


title: S2-028_n3

description: Library name: Sample 9


title: S2-028_n1

description: Library name: Sample 7


title: S2-020_n1

description: Library name: Sample 4


title: HCT116_WSTF_knock-out, replicate1, CBP

description: Library name: HCT116_WSTFKO_rep1_CBP


title: S2-028_n2

description: Library name: Sample 8


title: S2-020_n2

description: Library name: Sample 5


title: Wild-type HCT116, replicate4, WSTF

description: Library name: HCT116_rep4_WSTF


title: Wild-type HCT116, replicate5, WSTF

description: Library name: HCT116_rep5_WSTF


title: SLE, Donor AB4887, Non Lesional

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

description:
Library name: Sample 34
10x Genomics

data_processing:
The 10x Cellranger software v6.0.1 was used to process data including gene quantification, quality control, and read alignment.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Upper-thigh Skin

extract_protocol:
Skin biopsies were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 40μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 40μM mesh. Epidermal and dermal cells were combined in 1:1 ratio.
The 10x Chromium system with chemistry v3 was used by the University of Michigan Advanced Genomics Core to generate libraries, which were subsequently sequenced on the Illumina NovaSeq 6000 platform, generating 150-base pair paired-end reads.

value: Upper-thigh Skin


title: SLE, Donor AB4887, Lesional

description:
Library name: Sample 33
10x Genomics

source_name: Skin

value: Skin


title: Wild-type HCT116, replicate2, WSTF

description: Library name: HCT116_rep2_WSTF


title: SLE, Donor AB4801, Lesional

description:
Library name: Sample 31
10x Genomics


title: SLE, Donor AB4022, Non Lesional

description:
Library name: Sample 30
10x Genomics


title: SLE, Donor AB4022, Lesional

description:
Library name: Sample 29
10x Genomics


title: Wild-type HCT116, replicate2, H4K20me1

description: Library name: HCT116_rep2_H4K20me1


title: Wild-type HCT116, replicate1, WSTF

description: Library name: HCT116_rep1_WSTF


title: Wild-type HCT116, replicate1, H4K20me1

description: Library name: HCT116_rep1_H4K20me1


title: SLE, Donor AB4016, Lesional

description:
Library name: Sample 27
10x Genomics


title: Wild-type HCT116, replicate2, H4K12ac

description: Library name: HCT116_rep2_H4K12ac


title: Wild-type HCT116, replicate1, H4K12ac

description: Library name: HCT116_rep1_H4K12ac


title: SLE, Donor AB3149, Non Lesional

description:
Library name: Sample 26
10x Genomics


title: SLE, Donor AB4801, Non Lesional

description:
Library name: Sample 32
10x Genomics


title: Wild-type HCT116, replicate2, H4K5ac

description: Library name: HCT116_rep2_H4K5ac


title: HCT116_WSTF_knock-out, replicate2, H2AK119ub

description: Library name: HCT116_WSTFKO_rep2_H2AK119ub


title: DM, Donor MW288, Non Lesional

description:
Library name: Sample 24
10x Genomics


title: Wild-type HCT116, replicate1, H4K5ac

description: Library name: HCT116_rep1_H4K5ac


title: Wild-type HCT116, replicate2, H3K36me2

description: Library name: HCT116_rep2_H3K36me2


title: DM, Donor AB4685, Non Lesional

description:
Library name: Sample 20
10x Genomics


title: Wild-type HCT116, replicate2, H3K27ac

description: Library name: HCT116_rep2_H3K27ac


title: Wild-type HCT116, replicate1, H3K36me2

description: Library name: HCT116_rep1_H3K36me2


title: C2C12 cells,znf143_knockdown,rep2,myogenic_induction

city: GuangZhou

first: Xingan

last: Zhao

state: GuangDong

address: 1023-1063 shatai South Road

department: School of Basic Medical Sciences

institute: Southern Medical University

description:
Library name: C2C12siIN2
Column name in salmon_tximport_counts_matrix.txt:C2C12si2IN

data_processing:
Raw Data Quality Control and Filtering: Raw sequencing reads were preprocessed using the fastp tool (Version: 1.0.1). Adapter sequences were automatically detected and trimmed (--detect_adapter_for_pe). Low-quality bases were trimmed from both the front (--cut_front) and tail (--cut_tail) of reads using a sliding window approach (--cut_window_size 4, --cut_mean_quality 20). Further filtering was applied: reads were discarded if the percentage of bases with quality score below 20 (--qualified_quality_phred 20) exceeded 40% (--unqualified_percent_limit 40), or if the read length was less than 30 bp (--length_required 30). Additionally, poly-G (--trim_poly_g) and poly-X (--trim_poly_x) sequences were trimmed. Clean reads were output as *_clean_1.fq.gz and *_clean_2.fq.gz.
Reference Genome and Transcriptome Preparation: The reference genome for Mouse (Build: GRCm39) and corresponding GTF annotation file (Version: gencode.vM38.basic.annotation.gtf) were obtained from GENCODE. A STAR genome index was generated using the STAR aligner (Version: 2.7.11b) in genomeGenerate mode, using the genome FASTA and GTF files, with the parameter --sjdbOverhang 149. A reference transcriptome FASTA file was extracted from the genome FASTA (GRCm39.primary_assembly.genome.fa) and GTF files using gffread. A transcript-to-gene (tx2gene) mapping file was created by parsing the GTF file using awk to link transcript_id to gene_id.
Sequence Alignment and Transcriptome Mapping: Clean reads were mapped to the reference genome using STAR (Version: 2.7.11b) with the following key parameters: --outFilterMultimapNmax 20, --outFilterMismatchNoverReadLmax 0.04, and standard splicing junction parameters. The output was unsorted BAM files (--outSAMtype BAM Unsorted). Importantly, the option --quantMode TranscriptomeSAM was used to generate an additional BAM file (*_Aligned.toTranscriptome.out.bam) containing reads mapped to the transcriptome, which serves as input for the next step.
Transcript Quantification and Gene-level Count Matrix Generation: Transcript abundance was quantified using the quasi-mapping approach implemented in Salmon (Version: v1.10.3) in alignment mode, taking the transcriptome-aligned BAM files as input (-a). Sequence-specific and GC-content biases were corrected using the --seqBias and --gcBias flags. Finally, the estimated counts from Salmon's output were imported into R (using the tximport package) and summarized from the transcript level to the gene level using the custom tx2gene mapping file. The resulting raw (unnormalized) gene-level count matrix was exported as a tab-delimited file, where row names are ENSEMBL gene IDs and column names are the unique Library Names for each sample.
Assembly: GRCm39
Supplementary files format and content: This file contains raw read count data (i.e., unnormalized estimated counts) quantified directly from the RNA-seq FastQ files using the Salmon quantification tool (version 1.10.3).
Supplementary files format and content: The matrix's first column serves as the row names and contains the ENSEMBL gene/transcript identifiers. The first row contains the column headers, starting with the identifier column followed by the unique Library Name for each sample (e.g., C2C12con1, C2C12con1IN, etc.).
Supplementary files format and content: The counts represent the estimated number of reads mapped to each gene/transcript. No further normalization or filtering has been applied to this raw count matrix.

source_name: skeletal muscle

growth_protocol: C2C12 mouse myoblasts were cultured in Growth Medium (GM) consisting of Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained in a humidified incubator at 37°C with 5% CO2. For maintenance, cells were passaged at 60-70% confluence using 0.25% trypsin-EDTA to prevent premature spontaneous differentiation.

extract_protocol:
Total RNA was extracted from C2C12 cells using TRIzol reagent (Invitrogen/Servicebio) according to the manufacturer's instructions. Cells were lysed directly in the culture dish by adding 1 mL of TRIzol and homogenized by pipetting. After addition of chloroform, the mixture was centrifuged to separate the aqueous phase containing RNA. RNA was then precipitated with isopropanol, washed with 75% ethanol, and finally dissolved in RNase-free water. RNA concentration and purity (A260/280 and A260/230 ratios) were measured using a NanoDrop spectrophotometer. RNA integrity was further assessed by agarose gel electrophoresis or an Agilent 2100 Bioanalyzer to ensure suitability for downstream sequencing.
Sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s instructions for non-strand-specific library preparation. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed using divalent cations under elevated temperature. First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The double-stranded cDNA fragments were then subjected to end-repair, A-tailing, and ligation with NEBNext Adaptors. To select cDNA fragments of approximately 250~300 bp, the library fragments were purified with the AMPure XP system (Beckman Coulter). PCR amplification was performed using Phusion High-Fidelity DNA polymerase and universal/index primers. Finally, PCR products were purified, and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For Zfp143 knockdown, C2C12 myoblasts were transfected with siRNA targeting Zfp143 (si-Zfp143) or a non-targeting control siRNA (si-Control) using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions. 24 hours post-transfection, cells were harvested for proliferation analysis or switched to Differentiation Medium (DM). DM consisted of DMEM supplemented with 1% horse serum (HS) to induce myogenic differentiation. Medium was refreshed every 24 hours, and cells were harvested at day 5 of differentiation.

value: skeletal muscle

value: myoblasts

value: ZNF143 knockdown

value: myogenic induction


title: Wild-type HCT116, replicate1, H3K27ac

description: Library name: HCT116_rep1_H3K27ac


title: Wild-type HCT116, replicate2, H3K27me3

description: Library name: HCT116_rep2_H3K27me3


title: SLE, Donor AB4016, Non Lesional

description:
Library name: Sample 28
10x Genomics


title: SLE, Donor AB3149, Lesional

description:
Library name: Sample 25
10x Genomics


title: Wild-type HCT116, replicate3, WSTF

description: Library name: HCT116_rep3_WSTF


title: Wild-type HCT116, replicate1, H3K27me3

description: Library name: HCT116_rep1_H3K27me3


title: Wild-type HCT116, replicate1, H3K14ac

description: Library name: HCT116_rep1_H3K14ac


title: DM, Donor AB496, Lesional

description:
Library name: Sample 21
10x Genomics


title: DM, Donor AB4547, Lesional

description:
Library name: Sample 17
10x Genomics


title: C2C12 cells,control,rep3,myogenic_induction

description:
Library name: C2C12conIN3
Column name in salmon_tximport_counts_matrix.txt:C2C12con3IN

value: WT


title: DM, Donor AB496, Non Lesional

description:
Library name: Sample 22
10x Genomics


title: Wild-type HCT116, replicate1, H4K8ac

description: Library name: HCT116_rep1_H4K8ac


title: DM, Donor AB4312, Non Lesional

description:
Library name: Sample 16
10x Genomics


title: DM, Donor MW288, Lesional

description:
Library name: Sample 23
10x Genomics


title: C2C12 cells,control,rep2,myogenic_induction

description:
Library name: C2C12conIN2
Column name in salmon_tximport_counts_matrix.txt:C2C12con2IN


title: Wild-type HCT116, replicate2, H4K8ac

description: Library name: HCT116_rep2_H4K8ac


title: C2C12 cells,znf143_knockdown,rep3,myogenic_induction

description:
Library name: C2C12siIN3
Column name in salmon_tximport_counts_matrix.txt:C2C12si3IN


title: Wild-type HCT116, replicate2, H3K9me3

description: Library name: HCT116_rep2_H3K9me3


title: Wild-type HCT116, replicate1, H3K9ac

description: Library name: HCT116_rep1_H3K9ac


title: DM, Donor AB4685, Lesional

description:
Library name: Sample 19
10x Genomics


title: C2C12 cells,znf143_knockdown,rep3,control

description:
Library name: C2C12si3
Column name in salmon_tximport_counts_matrix.txt:C2C12si3

value: control


title: DM, Donor AB4312, Lesional

description:
Library name: Sample 15
10x Genomics


title: Wild-type HCT116, replicate1, H3K4me3

description: Library name: HCT116_rep1_H3K4me3

value: Human epithelial


title: DM, Donor AB4547, Non Lesional

description:
Library name: Sample 18
10x Genomics


title: Wild-type HCT116, replicate2, H3K4me2

description: Library name: HCT116_rep2_H3K4me2


title: Wild-type HCT116, replicate1, H3K9me3

description: Library name: HCT116_rep1_H3K9me3


title: C2C12 cells,znf143_knockdown,rep1,myogenic_induction

description:
Library name: C2C12siIN1
Column name in salmon_tximport_counts_matrix.txt:C2C12si1IN


title: C2C12 cells,control,rep1,myogenic_induction

description:
Library name: C2C12conIN1
Column name in salmon_tximport_counts_matrix.txt:C2C12con1IN


title: Wild-type HCT116, replicate2, H3K4me1

description: Library name: HCT116_rep2_H3K4me1


title: Wild-type HCT116, replicate2, H3K4me3

description: Library name: HCT116_rep2_H3K4me3


title: DM, Donor AB4267, Non Lesional

description:
Library name: Sample 14
10x Genomics


title: Wild-type HCT116, replicate2, H3K14ac

description: Library name: HCT116_rep2_H3K14ac


title: C2C12 cells,znf143_knockdown,rep2,control

description:
Library name: C2C12si2
Column name in salmon_tximport_counts_matrix.txt:C2C12si2


title: Wild-type HCT116, replicate1, H3K4me2

description: Library name: HCT116_rep1_H3K4me2


title: DM, Donor AB4267, Lesional

description:
Library name: Sample 13
10x Genomics


title: Wild-type HCT116, replicate2, H2AK119ub

description: Library name: HCT116_rep2_H2AK119ub


title: Wild-type HCT116, replicate1, H3K4me1

description: Library name: HCT116_rep1_H3K4me1


title: DM, Donor AB3970, Non Lesional

description:
Library name: Sample 12
10x Genomics


title: Wild-type HCT116, replicate2, H3K9ac

description: Library name: HCT116_rep2_H3K9ac


title: C2C12 cells,znf143_knockdown,rep1,control

description:
Library name: C2C12si1
Column name in salmon_tximport_counts_matrix.txt:C2C12si1


title: C2C12 cells,control,rep3,control

description:
Library name: C2C12con3
Column name in salmon_tximport_counts_matrix.txt:C2C12con3


title: Wild-type HCT116, replicate1, H2AK119ub

description: Library name: HCT116_rep1_H2AK119ub


title: Wild-type HCT116, replicate2, SNF2H

description: Library name: HCT116_rep2_SNF2H


title: C2C12 cells,control,rep2,control

description:
Library name: C2C12con2
Column name in salmon_tximport_counts_matrix.txt:C2C12con2


title: Wild-type HCT116, replicate2, LaminB

description: Library name: HCT116_rep2_LaminB


title: Wild-type HCT116, replicate1, SNF2H

description: Library name: HCT116_rep1_SNF2H


title: DM, Donor AB3970, Lesional

description:
Library name: Sample 11
10x Genomics


title: C2C12 cells,control,rep1,control

description:
Library name: C2C12con1
Column name in salmon_tximport_counts_matrix.txt:C2C12con1


title: DM, Donor AB3121, Lesional

description:
Library name: Sample 9
10x Genomics


title: DM, Donor AB3121, Non Lesional

description:
Library name: Sample 10
10x Genomics


title: Wild-type HCT116, replicate1, LaminB

description: Library name: HCT116_rep1_LaminB


title: Wild-type HCT116, replicate1, EZH2

description: Library name: HCT116_rep1_EZH2


title: Wild-type HCT116, replicate2, EZH2

description: Library name: HCT116_rep2_EZH2


title: CTL, Donor AR021

description:
Library name: Sample 7
10x Genomics


title: Wild-type HCT116, replicate2,CBX4

description: Library name: HCT116_rep2_CBX4


title: Wild-type HCT116, replicate1, CBX4

description: Library name: HCT116_rep1_CBX4


title: Arm2,gouprC2,HOPE+NMP,48h

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

description:
Library name: Sample36
name for fastq files: P15

data_processing:
Study Arm 1: Bulk RNA-seq raw fastq files were first subjected to quality control using FastQCa (v0.12.1) to identify potential issues such as contamination and adapter sequences. After trimming low-quality sequences, FastQC was rerun on the cleaned reads to ensure that all major quality issues were resolved. Study Arm 2: Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Study Arm 1: The sequencing reads were then aligned to the Sus scrofa reference genome (Sscrofa11.1) using HISAT2 (v2.2.1). Study Arm 2: The trimmed reads were mapped to the Sus Scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Study Arm 1: Gene expression levels were quantified with featureCounts (v2.0.6), and differential expression analysis was conducted using DESeq2. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. Study Arm 2: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the geneid feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Assembly: Study Arm 1: The sequencing reads were then aligned to the Sus scrofa reference genome (Sscrofa11.1) using HISAT2 (v2.2.1). Study Arm 2: The trimmed reads were mapped to the Sus Scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: csv file for normalized data for Arm1 and Arm2

organism: Sus scrofa

source_name: Myocardium

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (Qiagen) as per manufacturer guidelines. RNA purity was assessed on a NanoDrop spectrophotometer. Study Arm 1: RNA concentration was measured on a Qubit 2.0 fluorometer (Invitrogen). RNA integrity was assessed on an Agilent Bioanalyzer 2100 using a Nano 6000 assay kit (Agilent Technologies); samples with RIN > 6 were used for library preparation. A total amount of > 600 ng RNA per sample was used as input material for the RNA sample preparations. Study Arm 2: RNA samples were quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA inputs were normalized to 100ng.
Study Arm 1: Sequencing libraries were generated using Illumina TruSeq Stranded mRNA kit and modified the protocol by replacing the Illumina TruSeq PCR reaction with KAPA HiFi HotStart Ready Mix for the final PCR step to ensure compatibility with the 2x75bp paired-end sequencing on the Aviti Element. Study Arm 2: ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software.

treatment_protocol: Myocardial biopsies were collected at the end of experiment, flash-frozen in liquid nitrogen and stored at -80°C.

value: Myocardium

value: Cardiomyocytes

tag: experimental treatment

value: HOPE+NMP

tag: experimental time


title: CTL, Donor AR019

description:
Library name: Sample 6
10x Genomics


title: Arm2,gouprD,SCS+NMP,24h

description:
Library name: Sample37
name for fastq files: P23

value: SCS+NMP


title: Arm2,gouprB1,HOPE+NMP,24h

description:
Library name: Sample33
name for fastq files: P12


title: Wild-type HCT116, replicate2, CBP

description: Library name: HCT116_rep2_CBP


title: CTL, Donor AR017

description:
Library name: Sample 5
10x Genomics


title: CTL, Donor AR016

description:
Library name: Sample 4
10x Genomics


title: Wild-type HCT116, replicate2, ASH2L

description: Library name: HCT116_rep2_ASH2L


title: CTL, Donor AR015

description:
Library name: Sample 3
10x Genomics


title: Arm2,gouprA2,HOPE+NMP,3h

description:
Library name: Sample32
name for fastq files: P22


title: Arm2,gouprB2,HOPE+NMP,24h

description:
Library name: Sample34
name for fastq files: P14


title: Wild-type HCT116, replicate1, CBP

description: Library name: HCT116_rep1_CBP


title: CTL, Donor AR022

description:
Library name: Sample 8
10x Genomics


title: Wild-type HCT116, replicate1, ASH2L

description: Library name: HCT116_rep1_ASH2L


title: Arm2,gouprA1,HOPE+NMP,3h

description:
Library name: Sample31
name for fastq files: P11


title: CTL, Donor AR012

description:
Library name: Sample 2
10x Genomics


title: Arm2,gouprC1,HOPE+NMP,48h

description:
Library name: Sample35
name for fastq files: P13


title: CTL, Donor AR010

description:
Library name: Sample 1
10x Genomics


title: NPS_treated CAF3

first: wang

last: zaozao

state: Beijing

address: No. 52 Fucheng Rd., Haidian District

department: Key Laboratory of Carcinogenesis and Translational Research

institute: Peking University Cancer Hospital & Institute

description:
Library name: sample6
DN70-3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples
Assembly: GRCh38.p13
Supplementary files format and content: Supplementary_files_format_and_content:fpkm.xls

source_name: Colorectal cancer

growth_protocol: CAFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Hyclone) in humidified atmosphere with 5% CO2 at 37°.

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions.The sequencing library of each sample of RNA was prepared according to the protocol provided by the manufacture.
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

value: Colorectal cancer

value: Missing

value: CAFs

value: NPs


title: 5ff

city: beijing

first: huiyang

last: Jia

address: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Library name: Sample 4

data_processing:
The library was enriched by PCR and, for sequencing on the DNBSEQ-T7 platform, the double-stranded cDNA was thermally denatured to single-stranded DNA and circularized with a specific oligonucleotide to generate a single-stranded circular library. Libraries that passed quality control on a Qubit 3.0 fluorometer and an Agilent 2100 Bioanalyzer were subjected to high-throughput sequencing using a PE150 strategy.
We processed the raw 150-bp paired-end Illumina reads using CASAVA to generate FASTQ files, then removed adapter-contaminated reads, reads containing undetermined bases (N), and low-quality reads in which bases with Qphred ≤ 20 accounted for more than 50% of the read length; Q30 scores and GC content were calculated and all downstream analyses were based on these high-quality clean reads. Clean reads were aligned to the reference genome using HISAT2 (v2.0.5) with the corresponding gene model annotation, and gene expression levels were quantified as FPKM, taking both gene length and sequencing depth into account. Differential expression between sample groups was assessed with DESeq2 (or DESeq when biological replicates were not available) using a negative binomial model and Benjamini–Hochberg correction, designating genes with adjusted P ≤ 0.05 as differentially expressed. Differentially expressed genes were then subjected to GO and KEGG pathway enrichment analysis using the clusterProfiler package, and terms/pathways with P < 0.05 were considered significantly enriched.
Assembly: Mus_musculus.NCBI.GRCm39
Supplementary files format and content: excel file(xlsx)
Supplementary files format and content: xlsx

source_name: Microglia

extract_protocol:
Total RNA was extracted using the TRIzol method
After quality assessment, poly(A)+^++ mRNA was enriched from total RNA using Oligo(dT) magnetic beads and fragmented with Fragmentation Buffer. First- and second-strand cDNA were synthesized from the fragmented mRNA, and the resulting double-stranded cDNA was purified, end repaired, A-tailed, ligated to sequencing adapters, and size-selected to obtain ~350 bp fragments.

value: Microglia


title: 2ff

description: Library name: Sample 3


title: CEL-3

city: Tianjin

first: Rong

last: Fu

address: xinxing street

institute: Tianjin Medical University General Hospital

description: Library name: Sample 12

data_processing:
The library was sequenced using next-generation high-throughput double-end sequencing, with 150 bp paired-end reads (Pair end 150 bp, PE150).
Assembly: hg38
Supplementary files format and content: The analysis included an assessment of the sequencing data quality, a comparison with reference sequences, and a differential gene function analysis.

source_name: cell line

extract_protocol:
Total RNA was extracted from the samples, the integrity of the extracted RNA was determined using agarose gel electrophoresis, and RNA concentration was determined using NanoDrop.
Oligo-dT magnetic beads were used to isolate mRNA from total RNA, and the captured mRNA was fragmented. The first and second strands of cDNA were synthesised using RT, and end repair was performed with the addition of an A base at the 3' end. Subsequently, the ligation product was purified, and PCR amplification was performed. The sequencing library was purified using magnetic beads. The library concentration was detected using a Qubit instrument, while the fragment length was determined using an Agilent fragment analyser.

value: cell line

value: human mononuclear

value: lps with treatment

value: LPS, ATP, CsA, Eltrombopag, Luspatercept


title: 3ko

description: Library name: Sample 2


title: CEL-2

description: Library name: Sample 11


title: NPS_treated CAF2

description:
Library name: sample5
DN70-2


title: CEL-1

description: Library name: Sample 10


title: 1ko

description: Library name: Sample 1


title: NPS_treated CAF1

description:
Library name: sample4
DN70-1


title: LP-1_S.A. pH6.8_rep1

type: RNA

city: Zhunan Town

first: Wun-Shaing

middle: Wayne

last: Chang

state: Miaoli County

address: No. 35, Keyan Road

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description: Human MM LP-1 cells cultured in Acidic buffered medium at pHe 6.8 for 2-3 weeks, biological rep1

hyb_protocol: cDNA was hybridized to Applied Biosystems GeneChip Human Transcriptome Array 2.0 according to the manufacturer’s instructions

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw array intensity data were pre-processed using the robust multiarray averaging (RMA) algorithm for background adjustment, probe set signal summarization, and quantile normalization with Transcriptome Analysis Console (TAC) v4.0.3.14 software.

source_name: Human MM LP-1 cells, Acidic medium, 2-3 weeks

label_protocol: RNA was amplified (in vitro transcription) and generate biotin labeled Single-stranded cDNA according to manufacturer's instructions.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 15% FBS, 23.8 mM NaHCO3, 2 mM GlutaMAX, and 10 000 U/mL penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol: RNA was extracted using RNeasy mini kit (QIAGEN, Hilden, Germany) according to manufacturer's instructions.

value: Multiple myeloma (MM)

tag: medium

value: Acidic medium

tag: phe

value: pHe 6.8


title: LP-1_L.A. pH6.8_rep1

description: Human MM LP-1 cells cultured in Acidic buffered medium at pHe 6.8 for 8-10 weeks, biological rep1

source_name: Human MM LP-1 cells, Acidic medium, 9 months


title: LP-1_Ctrl pH7.4_rep2

description: Human MM LP-1 cells cultured in Ctrl medium at pHe 7.4, biological rep2

source_name: Human MM LP-1 cells, Ctrl medium,  9 months

value: Ctrl medium

value: pHe 7.4


title: NC_treated CAF3

city: Beijing

description:
Library name: sample3
RD-3

value: Reference


title: CE-2

description: Library name: Sample 8

value: LPS, ATP, CsA, Eltrombopag


title: LP-1_Ctrl pH7.4_rep1

description: Human MM LP-1 cells cultured in Ctrl medium at pHe 7.4, biological rep1


title: ChIP_homecage_input

city: Iowa City

first: Snehajyoti

last: Chatterjee

state: IA

address: 169 Newton Road

department: Neuroscience & Pharmacology

institute: University of Iowa

description: Library name: ChIP_homecage_input

data_processing:
ChIP-Seq reads were trimmed from both 5' and 3' ends using Trimmomatic paired end mode until the final base had a quality score > 30, discarding reads with < 23 bp.
ChIP-Seq trimmed reads were aligned were aligned to mm10 reference genome using bwa aligner.
Broad peaks were first called with ‘MACS2’ using thresholds to capture histone mark enrichment compared against the background input samples.
Differential histone crotonylation between learning and homecage control was assessed using 'MAnorm' algorithm using the MACS2 peaks.
To focus on regulatory elements, significantly differential peaks were filtered to retain only those located within ±2,000 bp of gene promoters (defined relative to the annotated TSS).
Assembly: mm10
Supplementary files format and content: broadpeak normalized to input samples

source_name: Dorsal hippocampus

extract_protocol:
Freshly dissected hippocampal tissue (~20 mg) was crosslinked in 1% formaldehyde for 10 min at room temperature.Chromatin was sonicated for 10 cycles using a Diagenode Bioruptor Pico to generate DNA fragments of 200–500 bp.
ChIP-Seq libraries were prepared using KAPA library preparation kit. Indexed libraries were pooled and sequenced in illumina Novaseq6000.

value: Dorsal hippocampus

tag: condition

value: Homecage

tag: chip-antibody


title: CE-1

description: Library name: Sample 7


title: ChIP_learning_input

description: Library name: ChIP_learning_input

value: Learning


title: NC_treated CAF2

description:
Library name: sample2
RD-2

value: Colorectal cancer

value: Missing

value: CAFs


title: 293-NTCP CCT251545 1

city: Heidelberg

first: Angga

last: Prawira

address: Im Neuenheimer Feld 344

department: Molecular Virology

country: Germany

institute: University Hospital Heidelberg

description: CCT251545, biological rep 1

hyb_protocol: hybridisation was done according to manufacturer's instructions

scan_protocol: Cartridges were scanned with GeneChip Scanner 3000 7G System (cartridge) and GeneTitan Multi-channel

data_processing: Data were processed in R/Bioconductor using the robust multiarray analysis (RMA)  of affy library

source_name: 293-NTCP cells treated with 50 nM CCT251545

label_protocol: no labeling of RNA performed

growth_protocol: Cells were cultivated in DMEM+10% FCS+PenStrep at 5% CO2, 90% humidity and 37C temperature

extract_protocol: RNA was extracted using the Macherey-Nagel NucleoSpin RNA isolation kit according to manufacturer's instructions

treatment_protocol: Cells were treated in the corresponding concentrations in the normal growth medium.

value: human embryonic kidney cells


title: 293-NTCP CCT251545 2

description: CCT251545, biological rep 2


title: LP-1_L.A. pH6.8_rep2

description: Human MM LP-1 cells cultured in Acidic buffered medium at pHe 6.8 for 8-10 weeks, biological rep2


title: 293-NTCP MSC2530818 2

description: MSC2530818, biological rep 2

source_name: 293-NTCP cells treated with 500 nM MSC2530818


title: ChIP_learning_Kcr

description: Library name: ChIP_learning_Kcr

value: Pan-Kcr PTM BIO, #PTM-501


title: LP-1_S.A. pH6.8_rep2

description: Human MM LP-1 cells cultured in Acidic buffered medium at pHe 6.8 for 2-3 weeks, biological rep2


title: CEL

description: Library name: CEL

source_name: peripheral blood

growth_protocol: Peripheral blood samples (3–4 mL) were collected in ethylenediaminetetraacetic acid (EDTA)-coated vacutainer tubes (BD Biosciences) and gently inverted 4–6 times to ensure anticoagulant mixing. The samples were immediately transported to the laboratory at a controlled temperature (4–8°C) and processed within 2 h to preserve cell viability.

value: peripheral blood

value: female

value: Mononuclear cells

value: treatment

value: with Luspatercept


title: 293-NTCP SEL120 2

description: SEL120, biological rep 2

source_name: 293-NTCP cells treated with 2 µM SEL120


title: LPS-2

description: Library name: Sample 5

value: cell line

value: human mononuclear

value: lps

value: LPS, ATP


title: 293-NTCP MSC2530818 1

description: MSC2530818, biological rep 1


title: 293-NTCP SEL120 1

description: SEL120, biological rep 1


title: 293-NTCP untreated 2

description: Untreated, biological rep 2

source_name: 293-NTCP cells untreated


title: LPS-1

description: Library name: Sample 4


title: NC_treated CAF1

description:
Library name: sample1
RD-1

value: Reference


title: Control2

city: Suzhou

first: Rui

middle: xing

last: Hou

state: Jiangsu

address: No.5, Tayun Road, Wuzhong District

department: Key Laboratory of Hand Surgery

institute: Suzhou Ruihua Orthopedic Hospital

description: Library name: sample_Control2

data_processing:
Quality control：The raw sequencing data, in the form of fastq files, underwent initial processing using in-house Perl scripts. During this step, clean data (clean reads) were generated by filtering out reads containing adapters, poly-N sequences, and low-quality reads from the raw data. Concurrently, the Q20, Q30, and GC content of the clean data were calculated. All subsequent analyses were based on these high-quality clean data.
Reads mapping to the reference genome：The reference genome and gene model annotation files were directly downloaded from the genome website. The index of the reference genome was constructed using Hisat2 v2.0.5. Subsequently, the paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Hisat2 was chosen as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, thereby achieving a more accurate mapping result compared to other non-splice mapping tools.
Quantification of gene expression level：featureCounts v1.5.0-p3 was used to count reads mapped to each gene. Then, FPKM values were calculated based on gene length and read counts. FPKM, which stands for Fragments Per Kilobase of transcript sequence per Millions of base pairs sequenced, normalizes gene expression levels by accounting for sequencing depth and gene length. This widely-used method enables accurate comparisons across samples.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: skin epidermal stem cells

growth_protocol: Epidermal stem cells (EpSCs) were isolated from mouse skin and cultured in EpiLife™ medium (containing HKGS additives).

extract_protocol:
Total RNA was extracted from EpSCs using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared by Shanghai Genechem Co., Ltd (Shanghai, China).

treatment_protocol: EpSCs were treated with  30 μg/mL ALP or 0.06% DMSO for 48 h.

tag: strain

value: skin epidermal stem cells


title: Control1

description: Library name: sample_Control1

tag: time


title: LPS-3

description: Library name: Sample 6

tag: tissue


title: Ascaris suum, testis, Hi-C

city: Knoxville

first: Jianbin

state: TN

address: 1311 Cumberland Avenue, Ken and Blaire Mossman Building Rm 309

institute: The University of Tennessee

description: Library name: As_testis_Hi-C_rep1

data_processing:
Paired-end Hi-C reads are mapped and analyzed with HiC-Pro.  A shell script was used to convert the allValidPairs file to a .hic file.
Assembly: AG.v50.fa
Supplementary files format and content: .hic

organism: Ascaris suum

source_name: testis

extract_protocol:
Adult Ascaris tissues were frozen at -80°C and ground to a fine powder using a mortar and pestle with liquid nitrogen. Embryos and larvae were fixed in formaldehyde then run through a metal dounce to break them open.
Hi-C was performed using the Arima-HiC 2.0 kit according to the manufacturer’s protocol (Arima, #A410110).

value: testis


title: SphkMx1_H_44116

city: PARIS

first: Ilaria

last: Del Gaudio

address: 56 Rue Leblanc

country: France

institute: Paris Cardiovascular research center_ InsermU970

description: Library name: Sample 10

data_processing:
reads were trimmed from adapters using Fastp 0.20.1 (Chen et al., 2018) then mapped to the Mus musculus GRCm39 genome assembly from Ensembl using STAR 2.7.8a
FeatureCounts 2.0.1 (Liao et al., 2014) was used to produce the count matrix, assigning reads to features using corresponding annotation v109 from Ensembl with strand-specificity information
Assembly: GRCm39 genome assembly
Supplementary files format and content: cvs file with raw_counts for each sample

source_name: heart

extract_protocol:
Total RNA was isolated from cardiac tissue using TRIzol Reagent and RNeasy mini kits (QIAGEN) following the manufacturer’s protocol
Libraries were built using a Illumina Stranded mRNA library Preparation Kit (Illumina, USA) following the manufacturer’s protocol

value: heart

value: male

tag: genotype


title: 293-NTCP untreated 1

description: Untreated, biological rep 1


title: ChIP_homecage_Kcr

description: Library name: ChIP_homecage_Kcr

value: Dorsal hippocampus

value: Homecage


title: NC-3

description: Library name: Sample 3

value: nc

tag: treatment


title: SphkMx1_H_44029

description: Library name: Sample 9


title: ALP1

description: Library name: sample_ALP1

value: 30 μg/mL ALP


title: SphkMx1_H_38503

description: Library name: Sample 8


title: ALP2

description: Library name: sample_ALP2


title: NC-1

description: Library name: Sample 1

tag: cell line


title: NC-2

description: Library name: Sample 2

tag: cell type


title: Ascaris suum, L1 larvae, Hi-C

description: Library name: As_L1_Hi-C_rep1

source_name: L1 larvae

value: L1 larvae


title: Ascaris suum, 32-64-cell embryos, Hi-C

description: Library name: As_32-64-cell_Hi-C_rep1

source_name: 32-64-cell embryo

value: 32-64-cell embryo


title: CE-3

description: Library name: Sample 9

value: lps with treatment

value: LPS, ATP, CsA, Eltrombopag


title: TASL-WT-4 B cells, CpG 24h

city: Oxford

first: Julia

last: Johnstone

address: Kennedy Institute of Rheumatology, Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description: Library name: Sample 8

data_processing:
Salmon
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: csv file containing raw counts per million in each sample

source_name: spleen

extract_protocol:
RNA extracted using RNeasy mini plus kit (Qiagen)
Library construction performed by Genewiz (Azenta), using Poly(A) selection method

treatment_protocol: B cells were isolated from murine splenocytes by MACS, then plated in RPMI (containing 10% FBS, 20mM 2-mercaptoethanol, 1mM glutamine, 0.01% sodium pyruvate, 10mM HEPES buffer, and penicillin and streptomycin) and stimulated with 100nm CpG-B (ODN1826) for 24h

value: spleen

value: B cells

value: WT

value: 100nm CpG 24h


title: SphkMx1_H_38369

description: Library name: Sample 6


title: Arabidopsis, ssrp1

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

description: Library name: 12DAG_ssrp1,FLEP-Seq2

library_source: other

data_processing:
Raw fast5 files were basecalled using Guppy (v4.0.11) with the ‘dna_r9.4.1_450bps_hac.cfg’ high-accuracy model. The resulting FASTQ reads were aligned to the ARAPROT11 reference genome using minimap2 with the parameters -ax splice --secondary=no. Adapter identification and read information extraction were performed using the official FLEP-seq pipeline (https://github.com/ZhaiLab-SUSTech/FLEPSeq). The 3' ends of full-length elongating reads were used to determine the genomic position of RNA Polymerase II. For gene-level analysis of Pol II distribution, only genes covered by more than 10 uniquely mapped, full-length elongating reads were included.
Assembly: ARAPROT 11
Supplementary files format and content: This file provides a complete annotation of a single long-read generated by FLEP-seq, including its genomic alignment, exon–intron structure, intron retention events, and its positions relative to the annotated mRNA. It also includes Nanopore-specific poly(A) tail signals and adapter/primer detection results, allowing assessment of transcript processing and read integrity.

molecule: other

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Plants were grown on GM in a growth chamber under long-day conditions supplemented with 1% sucrose under long-day photoperiod and ~21°C. Seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
Nuclear isolation was performed based on a previously published protocol. Approximately 1 g of 12-day-old Arabidopsis thaliana seedlings were ground to a fine powder in liquid nitrogen. The powder was resuspended in ice-cold Honda buffer (0.44 M sucrose, 1.25% (w/v) Ficoll, 2.5% (w/v) dextran T40, 20 mM HEPES-KOH pH 7.4, 10 mM MgCl₂, 0.5% (v/v) Triton X-100, 1 mM DTT, 1× protease inhibitor cocktail, 100 ng/μL tRNA) and washed twice by centrifugation at 3,500 × g for 5 min at 4 °C. Total RNA was subsequently extracted from the isolated nuclei using the RNAprep Pure Plant Plus Kit (DP441; Tiangen). RNA concentration was measured using a NanoDrop spectrophotometer, and samples were stored at -80 °C until further use.
FLEP-seq2 libraries were constructed starting from 1 μg of nuclear RNA per sample. First, ribosomal RNA (rRNA) was depleted using pan-plant riboPOOL probes targeting Pan-plant. The rRNA-depleted RNA was then ligated to a 3’ linker (S1315S, NEB). The ligated RNA was purified using the RNA Clean & Concentrator-5 kit (R1013, ZYMO). Reverse transcription was performed using a custom cDNA RT primer and a Strand-Switching Primer with Maxima H Minus Reverse Transcriptase (EP0752; Thermo). The thermal cycling conditions were: 42 °C for 90 min, followed by 10 cycles of 50 °C for 2 min and 42 °C for 2 min, with a final enzyme inactivation step at 85 °C for 5 min. The resulting cDNA was amplified by PCR using unique barcode primers from the PCR Barcoding Kit (SQK-PCB109; Oxford Nanopore Technologies). Following amplification, residual primers were removed by treating the library with 1 μL of Exonuclease I (M0293; NEB) at 37 °C for 15 min. The final library was purified using a 0.8× volume of AMPure XP beads (Beckman). Libraries were loaded onto a FLO-MIN106 (R9.4.1) flow cell and sequenced on a MinION Mk1B instrument for 72 hours.

value: 12DAG seedling


title: Ascaris suum, 4-8-cell embryos, Hi-C

last: Wang

description: Library name: As_4-8-cell_Hi-C_rep1

source_name: 4-8-cell embryo

value: 4-8-cell embryo


title: SphkMx1_H_38407

description: Library name: Sample 7


title: TASL-WT-3 B cells, CpG 24h

description: Library name: Sample 7


title: Ascaris suum, 2-4-cell embryos, Hi-C

description: Library name: As_2-4-cell_Hi-C_rep1

source_name: 2-4-cell embryo

value: 2-4-cell embryo


title: CE

description: Library name: CE

value: peripheral blood

value: female

value: Mononuclear cells

value: treatment

value: without Luspatercept


title: Ascaris suum, ovary, Hi-C

description: Library name: As_ovary_Hi-C_rep1

source_name: ovary

value: ovary


title: Arabidopsis, Columbia

description: Library name: 12DAG_Columbia,FLEP-Seq2


title: TASL-WT-1 B cells, CpG 24h

description: Library name: Sample 5


title: Sphk_cont_H_38991

description: Library name: Sample 4

value: heart

value: male


title: Arabidopsis, spt16

description: Library name: 12DAG_spt16,FLEP-Seq2


title: TASL-KO-2 B cells, CpG 24h

description: Library name: Sample 2

value: Tasl knockout


title: Sphk_cont_H_44033

description: Library name: Sample 5


title: TASL-WT-2 B cells, CpG 24h

description: Library name: Sample 6


title: TASL-KO-3 B cells, CpG 24h

description: Library name: Sample 3


title: Ascaris suum, 1-cell embryos, Hi-C

description: Library name: As_1-cell_Hi-C_rep1

source_name: 1-cell embryo

value: 1-cell embryo


title: TASL-KO-4 B cells, CpG 24h

description: Library name: Sample 4

value: spleen


title: P12 whole molar

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v2.0 using default settings.
Secondary analysis was performed using Loupe Cell Browser v5 (10x Genomics, San Francisco, CA, USA). Clusters were defined by k-means clustering based on the PCA of the transcriptomic signature.
Assembly: Custom mm10 including common mouse transgenes
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Molar

extract_protocol:
Molars were dissected with sharp tweezers from seven littermates of P7 Krt14-RFP mice. Single cell dissociation was essentially performed as previously described (Li et al. 2015). Briefly, dissected incisors were incubated in 4 mg/ml Dispase II (Roche) for 14 min at 37°C. Then incisors were placed in cold DMEM/F12 and dental epithelium and mesenchyme were separated under microscope. The tissues are then placed in Accutase (Sigma) for 30min at 37°C. After pipetting up and down using 1000 μm tips, single cell suspension was further produced through a 70 μm sterile cell strainer. The cells were resuspended with 0.04% BSA containing cold PBS.
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) and library preparation was performed according to the manufacturer’s instructions for the 10X Chromium Next GEM Single Cell Library kit v2 (10X Genomics). Libraries were then pooled and sequenced on 4 lanes on a NextSeq500 sequencer (Illumina) using 10X Genomics recommended reads configuration.

value: Molar


title: Arm1,Pig#4,HOPE, 48h

description:
Library name: Sample29
name for fastq files: GC24

source_name: Myocardium

value: Myocardium

value: Cardiomyocytes

value: HOPE


title: Arm1,Pig#6,HOPE, 48h

description:
Library name: Sample30
name for fastq files: GC29


title: Sphk_cont_H_38406

description: Library name: Sample 1


title: TASL-KO-1 B cells, CpG 24h

description: Library name: Sample 1

value: B cells

value: 100nm CpG 24h


title: Sphk_cont_H_38504

description: Library name: Sample 2


title: Arm1,Pig#6,HOPE, 24h

description:
Library name: Sample27
name for fastq files: GC28


title: Arm1,Pig#2,HOPE, 48h

description:
Library name: Sample28
name for fastq files: GC19


title: Sphk_cont_H_38910

description: Library name: Sample 3


title: BC-TuX-4IC-MFAP2_OE_replcate 3

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

department: Medicine

institute: Tulane University

description: Library name: Sample 6

data_processing:
Kallisto was used to map short sequencing reads to the reference genome.
Assembly: Reads were aligned to the human genome with cDNA sequences corresponding to Ensembl genes, excluding ncRNA genes.
Supplementary files format and content: Data files represent relative gene abundance as TMPs. Format excel.

source_name: Cell line

growth_protocol: The metaplastic TNBC cell line TU-BcX-4IC and non-metaplastic TNBC cell line MDA-MB-231 (ATCC, Manassas, VA, USA) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Waltham, MA, USA) supplemented with 10% HyClone Cosmic Calf Serum (Cytiva), 1% minimal essential amino acids (Gibco, Waltham, MA), 1% non-essential amino acids (Gibco, Waltham, MA, USA), 1% antibiotic/anti-mycotic (Gibco, Waltham, MA, USA) and insulin (Gibco, Waltham, MA, USA) under mycoplasma-free conditions at 37 °C and 5% v/v CO2. Cells were seeded in T25 flasks and collected at 80% confluence for RNA extraction.

extract_protocol:
Total RNA was extracted from the cell lines using Quick RNA Miniprep Kit from Zymo Research (Irvine, CA, USA) and sent to Azenta (TU-BcX-4IC) (Burlington, MA, USA)  for RNA sequencing.
The RNA sequencing workflow after RNA isolation included initial PolyA selection: based mRNA enrichment, mRNA fragmentation, and random priming with subsequent first- and second-strand complementary DMA (cDNA) synthesis. Afterward, end-repair 5’ phosphorylation and nucleotide (dA)-tailing were performed. Last, adaptor ligation, polymerase chain reaction (PCR), and Illumina NovaSeq technology-based sequencing with 2 150-base pair (bp) read length were carried out.

treatment_protocol: No treatments were used in this study

value: Cell line

value: breast cancer cell line

value: WT