title: PC3_ONC212_N3

description: Library name: PC3_ONC212_replicate_2

value: Prostate cancer cells


title: Liver_MD_5

status: Public on Apr 27 2026

type: SRA

city: Oklahoma City

first: Tae

middle: Gyu

last: Oh

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Oncology Science

country: USA

institute: University of Oklahoma Health Science Center

description:
Library name: S47
column name in MP_raw_counts_gene_level.csv: MD_5_S47

library_source: transcriptomic

data_processing:
Samples were normalized and pooled onto a 150 paired end run on Illumina's NextSeq 2000 Platform to obtain 15M reads per sample at the OUHSC's Genomics Core. Raw RNA-seq reads were preprocessed for quality control using fastp (v0.23.4) with adapter trimming, poly-G, and poly-X removal. Following QC, filtered paired-end RNA-seq reads were quantified using Salmon (v1.10.3) with selective alignment mode enabled (--validateMapping), allowing more accurate mapping of reads to the GRCm39 transcriptome from the GENCODE. Library type was automatically detected (-l A), and sequence bias correction (--seqBias) and variational Bayesian optimization (--useVBOpt) were applied. Resulting quantification files (quant.sf) were collected for downstream analysis. Gene-level abundance estimates were imported into R using the tximport package, using a transcript-to-gene mapping file. Differential expression analysis was performed using DESeq2.
Assembly: GRCm39 M35
Supplementary files format and content: Raw counts

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted from four randomly selected (using Randomice tool) snap-frozen mouse liver tissues (~ 50 mg) using Trizol. Overall quality of RNA was verified using Agilent’s 2100 Bioanalyzer (Agilent)
Standard RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit (New England Biolabs, Ipswich, MA) followed directly by IDT’s XGen Broad Range RNA Library Prep Kit (Integrated DNA technologies, Coralville, IA) and the established protocols. The library construction was done using 500 ng of RNA. Each of the libraries was indexed during library construction to multiplex the sequencing. Libraries were quantified using Invitrogen’s Qubit 4 fluorometer (Thermofisher Scientific) and checked for size and quality using Agilent’s 2100 Bioanalyzer (Agilent).

tag: tissue

value: Liver

tag: cell type

tag: genotype

value: WT

tag: treatment

value: MASH Diet

tag: batch


title: MDA-MB-231 cells, TRIM27-KO, siPARP1, CTD, rep2, batch3

city: Zhengzhou City

first: Leixi

last: Cao

address: Zhengzhou University People's Hospital, Fengchan Road Subdistrict, Jinshui District, Zhengzhou City, Henan Province

country: China

institute: Zhengzhou University People's Hospital, Translational Medicine Research Center

description:
Library name: WRJ-H28
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

library_source: genomic

data_processing:
Raw sequencing reads were generated by Frasergen on the MGISEQ-2000 platform. 1. Quality control: Raw reads were filtered to remove low-quality sequences, adapter sequences, and short reads using fastp. 2. Alignment: Clean reads were aligned to the human reference genome GRCh38/hg38 using Bowtie2 with default parameters. 3. Filtering: Mapped reads were filtered to remove duplicates, low-quality alignments (MAPQ < 30), and mitochondrial reads using SAMtools. 4. Signal track generation: Filtered bam files were used to generate normalized BigWig (.bw) signal tracks using bamCoverage (deepTools), with reads per kilobase per million mapped reads (RPKM) normalization for visualization. 5. IgG control tracks were generated using the same pipeline for all experimental groups. 6. Peak calling was performed using MACS2 with default parameters, and peak files are provided as supplementary processed data.
Assembly: GRCh38
Supplementary files format and content: Normalized BigWig (.bw) files for CUT&Tag signal visualization. Tracks show genome-wide read coverage for target proteins and IgG controls aligned to GRCh38.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 wild-type and TRIM27 knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained in a humidified atmosphere of 5% CO2 at 37℃

extract_protocol:
Genomic chromatin was extracted from intact MDA-MB-231 human breast cancer cells using native nuclear isolation conditions suitable for CUT&Tag. No cross-linking (fixation) was performed. Crude nuclei were isolated gently and used directly for the CUT&Tag reaction without further fragmentation, in accordance with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) protocol.
Libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following the manufacturer’s instructions. Briefly, intact nuclei were isolated and incubated with primary antibodies targeting TRIM27, CTD, p-CTD-S2, or IgG control. Protein A/G-tn5 transposase was then added to bind the antibodies and fragment chromatin. Library fragments were enriched by PCR amplification and purified using magnetic beads. Final libraries were quantified and subjected to high-throughput sequencing on the MGISEQ-2000 platform.

treatment_protocol: For Olaparib treatment, cells were seeded at a density of 2×10⁵ cells per well in 6-well plates and allowed to adhere overnight. The next day, medium was replaced with fresh medium containing 2 μM Olaparib (or an equivalent volume of vehicle control, DMSO), and cells were incubated for 24 hours prior to RNA extraction. For PARP1 knockdown, cells were transfected with 100 pM PARP1-specific siRNA (or non-targeting control siRNA) using Lipofectamine RNAiMAX reagent, following the manufacturer's instructions. After 48 hours of incubation, cells were harvested for RNA isolation.

value: Breast; Mammary gland

tag: cell line

value: epithelial cell

value: TRIM27 Knockout (TRIM27-KO)

value: siPARP1, 48h

tag: cut&tag antibody

value: CTD (Cell Signaling Technology, 2629)


title: MDA-MB-231 cells, p-CTD-S5, rep1, batch2

description: Library name: pCTD_S5_1

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: Breast cancer cell, epithelial cell


title: Liver_MD_2

description:
Library name: S44
column name in MP_raw_counts_gene_level.csv: MD_2_S44


title: Liver_CD_MP_1

description:
Library name: S48
column name in MP_raw_counts_gene_level.csv: CD_MP_1_S48

value: Chow Diet + Microplastics


title: PC3_ONC206_N4

city: Beirut

first: AUB

last: Submission

address: Bliss street

country: Lebanon

institute: American University of Beirut

description: Library name: PC3_ONC206_replicate_2

data_processing:
Quality check was done using Fastqc
Alignment step was performed using HISAT2
FeatureCounts was used to generate the count matrix
DESeq2 was used to perform differential expression
Assembly: Hg38
Supplementary files format and content: Count matrix in tab-separated format

growth_protocol: PC3 and DU145 human prostate cancer cell lines were cultured in RPMI 1640 medium, supplemented with 10% fetal bovine serum, 1% penicillin–streptomycin, and Plasmocin® prophylactic. Cultures were maintained at 37 °C in a humidified atmosphere containing 5% CO2 and were routinely confirmed to be mycoplasma-free.

extract_protocol:
Total RNA was extracted from PC3 and DU145 cells using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA library.

treatment_protocol: Approximately 50% confluent PC3 and DU145 cells were treated with either ONC206 at 0.5 µM or ONC212 at 0.1 µM for 48 hours. Vehicle control samples were treated with DMSO matched to the corresponding treatment conditions.


title: Liver_MD_3

description:
Library name: S45
column name in MP_raw_counts_gene_level.csv: MD_3_S45


title: PC3_ONC212_N2

description: Library name: PC3_ONC212_replicate_1


title: MDA-MB-231 cells, TRIM27-WT, siPARP1, CTD, rep1, batch3

description:
Library name: WRJ-H25
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: TRIM27 Wild-type (TRIM27-WT)


title: PC3_CN_Ve_N4

description: Library name: PC3_control_replicate_3

value: Untreated


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-A08

city: Washington

first: Christopher

last: Albanese

address: 3800 Reservoir Road NW

institute: Georgetown university

description:
Library name: DSP-1001660022855-A-A08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

data_processing:
Raw FASTQ files were processed using the NanoString GeoMx DSP analysis pipeline. Sequencing reads were demultiplexed and aligned to probe sequences to generate digital count matrices for each ROI/AOI. Quality control was performed using NanoString GeoMx DSP QC metrics, including sequencing saturation, alignment rate, and negative control probe assessment. Data were normalized using upper quartile (Q3) normalization to account for technical variability across ROIs. Downstream analyses were performed using normalized counts
Assembly: mm10
Supplementary files format and content: Processed gene expression count matrix from NanoString GeoMx DSP WTA platform for mouse brain ROIs.
Library strategy: Spatial Transcriptomics

source_name: Hippocampus

extract_protocol:
Tissue sections were processed directly for NanoString GeoMx DSP analysis, where RNA targets were hybridized in situ with oligonucleotide probes. Regions of interest (ROIs/AOIs) were selected, and target-specific oligonucleotide tags were released via UV photocleavage for downstream quantification.”
Tissue sections were processed using the NanoString GeoMx DSP RNA assay according to the manufacturer’s slide preparation protocol. After ROI/AOI selection and UV-photocleavage of oligo tags, NGS libraries were generated following the NanoString GeoMx DSP NGS readout/library preparation workflow and sequenced on an Illumina Novaseq 6000 platform.

treatment_protocol: Treatments were administered via intraperitoneal injection in fractionated doses, twice weekly over a two-week period with one of the following regimens: (1) doxorubicin (3 mg/kg/week, Abcam, Waltham, MA) plus docetaxel (10 mg/kg/week, Abcam), referred to as DD; (2) doxorubicin (3 mg/kg/week) plus cyclophosphamide (40 mg/kg/week, Abcam), referred to as DC, or (3) vehicle control (V; 50% Dimethyl Sulfoxide (Fisher Scientific, Pittsburgh, PA):50% Phosphate Buffered Saline (PBS, Fisher Scientific).

value: Hippocampus

value: veh


title: APOE4_DD_Cortex_DSP-1001660022855-A-A10

description:
Library name: DSP-1001660022855-A-A10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

source_name: Cortex

value: Cortex

value: DD


title: MDA-MB-231 cells, TRIM27-KO, Olaparib, CTD, rep2, batch3

description:
Library name: WRJ-H16
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: Olaparib, 24h


title: Atad2 sample 4 C2C12 cells, ATAD2 shRNA (ATAD2-shRNA)

city: Montreal

first: Sabah

last: Hussain

address: 1001 Bd Décarie

country: Canada

institute: McGill University Health Centre

description: Library name: Sample 8

data_processing:
Base calling was performed using RTA v3.
Samples were demultiplexed and FASTQ files were generated using bcl2fastq2 v2.20.
Aligned reads were sorted and indexed using SAMtools v1.1
Counts were normalized internally by DESeq2 using variance-stabilizing transformation.
Gene-level read counts were quantified using HTSeq-count v0.13.5. Genes with adjusted p-value < 0.05 and |log2 fold change| > 1 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: Processed result files include normalized expression values and differential expression analysis tables with gene identifiers, log2 fold changes, adjusted p-values, and significance annotations.

source_name: Skeletal Muscle

extract_protocol:
Forty-eight hours after transfection, cells were lysed with QIAzol® and total RNA was extracted using the PureLink RNA Mini Kit.
Library preparation and RNA sequencing were performed at the McGill University Genome Centre. cDNA synthesis was carried out using the NEBNext RNA First Strand Synthesis Module and the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England BioLabs). Subsequent library preparation steps were completed using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit, and fragment size distribution was assessed using a LabChip GX instrument. Libraries were normalized, pooled, denatured in 0.05 N NaOH, neutralized using HT1 buffer, and loaded at 225 pM onto an Illumina NovaSeq S4 lane using the Xp workflow. A 1% PhiX control library was included.

value: Skeletal Muscle

value: myoblasts

value: ATAD2 shRNA


title: MDA-MB-231 cells, TRIM27-KO, Olaparib, CTD, rep1, batch3

description:
Library name: WRJ-H15
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: Breast; Mammary gland


title: Liver_CD_3

description:
Library name: S41
column name in MP_raw_counts_gene_level.csv: CD_3_S41

value: Liver

value: WT

value: Chow Diet


title: APOE4_veh_Cortex_DSP-1001660022855-A-A03

description:
Library name: DSP-1001660022855-A-A03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: MDA-MB-231 cells, TRIM27-WT, siPARP1, CTD, rep2, batch3

description:
Library name: WRJ-H26
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: epithelial cell

value: siPARP1, 48h

value: CTD (Cell Signaling Technology, 2629)


title: PC3_ONC206_N2

description: Library name: PC3_ONC206_replicate_1

value: Prostate cancer cells


title: APOE4_veh_Cortex_DSP-1001660022855-A-A02

description:
Library name: DSP-1001660022855-A-A02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: PC3_CN_Ve_N3

description: Library name: PC3_control_replicate_2

value: Untreated


title: Liver_CD_4

description:
Library name: S42
column name in MP_raw_counts_gene_level.csv: CD_4_S42


title: PC3_CN_Ve_N2

description: Library name: PC3_control_replicate_1


title: Liver_MD_1

description:
Library name: S43
column name in MP_raw_counts_gene_level.csv: MD_1_S43

value: MASH Diet


title: PDX53_CD9_Pos_Rep2

city: Marseille

first: Dominique

last: Payet Bornet

address: 27bd Lei Roure

country: France

institute: CRCM

description:
Library name: Sample12
column name in counts and norm_cpm_counts =  PDX53_9Pos_Rep2

data_processing:
Fastq were processed using nfcore RNAseq pipeline v3.21.0 with STAR RSEM as aligner with default parameters
Assembly: GRCh38
Supplementary files format and content: counts.txt : tab delimited text including raw counts
Supplementary files format and content: norm_cpm_counts.csv : tab delimited csv including normalized CPM counts from edgeR object

molecule: polyA RNA

source_name: Patient-Derived Xenograft

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen)
Libraries were prepared using the Illumina Stranded mRNA Prep, ligation kit, according to the manufacturer’s protocol

value: Patient-Derived Xenograft

value: Thymocyte


title: MDA-MB-231 cells, TRIM27-WT, Olaparib, CTD, rep2, batch3

description:
Library name: WRJ-H14
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: TRIM27 Wild-type (TRIM27-WT)


title: Control sample 4 C2C12 cells, non-targeting shRNA

description: Library name: Sample 4

value: non-targeting shRNA


title: Atad2 sample 3 C2C12 cells, ATAD2 shRNA (ATAD2-shRNA)

description: Library name: Sample 7

value: Skeletal Muscle


title: Atad2 sample 2 C2C12 cells, ATAD2 shRNA (ATAD2-shRNA)

description: Library name: Sample 6

value: myoblasts


title: PDX52_CD9_Pos_Rep2

description:
Library name: Sample10
column name in counts and norm_cpm_counts =  PDX52_9Pos_Rep2


title: Liver_CD_2

description:
Library name: S40
column name in MP_raw_counts_gene_level.csv: CD_2_S40


title: MDA-MB-231 cells, TRIM27-WT, Olaparib, CTD, rep1, batch3

description:
Library name: WRJ-H13
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: Olaparib, 24h


title: PDX53_CD9_Neg_Rep2

description:
Library name: Sample11
column name in counts and norm_cpm_counts =  PDX53_9Neg_Rep2


title: MDA-MB-231 cells, TRIM27-KO, p-CTD-S2, rep1, batch3

description:
Library name: WRJ-H7
Normalized BigWig files for CUT&Tag (p-CTD-S2) in MDA-MB-231 cells

value: Breast; Mammary gland

value: TRIM27 Knockout (TRIM27-KO)

value: p-CTD-S2 (Cell Signaling Technology, 13499)


title: Liver_CD_1

description:
Library name: S39
column name in MP_raw_counts_gene_level.csv: CD_1_S39

value: Liver

value: WT

value: Chow Diet


title: MDA-MB-231 cells, TRIM27-KO, p-CTD-S2, rep2, batch3

description:
Library name: WRJ-H8
Normalized BigWig files for CUT&Tag (p-CTD-S2) in MDA-MB-231 cells

value: epithelial cell


title: Atad2 sample 1 C2C12 cells, ATAD2 shRNA (ATAD2-shRNA)

description: Library name: Sample 5

value: ATAD2 shRNA


title: 50093, C118F, DMSO

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

description: Library name: 50093_C118F.DMSO

data_processing:
nextflow RNAseq pipeline (https://github.com/uschwartz/RNAseq_NAC, v2.1)
Sequence reads were trimmed for adapter sequences using Trim Galore (v0.6.7)
Reads were mapped to the reference genome (GRCm39) and corresponding gene annotation (Ensembl version 110) using the Spliced Transcripts Alignment to a Reference (STAR) software (version v2.7.8a)(Dobin et al., 2013). The following options were used to optimize the alignment process: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --alignIntronMin 10, --alignIntronMax 1000000, --outFilterMismatchNoverReadLmax 0.04, --runThreadN 12, --outSAMtype BAM SortedByCoordinate, --outSAMmultNmax 1, and --outMultimapperOrder Random
The level of PCR duplication was assessed using Picard MarkDuplicates (v2.21.8) (Broad Institute, 2019), and dupRadar (version v1.15.0) (Sayols et al., 2016).
Gene expression quantification was carried out using featureCounts (v1.6.3) (Liao et al., 2014).
Assembly: GRCm39
Supplementary files format and content: tab delimited text file includes TPM values of each sample

source_name: kidney

extract_protocol:
Both kidneys together with neighboring stretches of the abdominal aorta were removed and perfused with suspensions of tosylactivated magnetic dynabeads® in 1x HBSS pH 7.5. Podocytes were isolated. After the final digest, cell suspensions were passed through a 40 μm cell strainer and subjected to FACS.  Podocytes were collected in RNAlater® and then processed using the RNeasy Plus Micro kit (Qiagen).
Library preparation was carried out as described in the SMART-Seq-mRNA LP User Manual (Takara Bio, Inc., CA, USA)

treatment_protocol: Podocyte-specific inactivation of the Lmx1b gene was achieved through the administration of 2 mg/ml of doxycycline to the drinking water for a total of seven days.  A stock solution of bortezomib was prepared at a concentration of 1 µg/µl in DMSO, the required amounts for injections were combined with a volume of 1x PBS corresponding to 1% of the body weight.  Beginning with the administration of doxycycline, 0.3 μg of bortezomib per g body weight was injected intraperitoneally every other day, the solvent DMSO served as a negative control. Spot urine was collected from the mice on day 7 before they were subjected to perfusion fixation under general anesthesia with xylamine/kethamine.

value: kidney

value: podocytes

value: DMSO


title: MDA-MB-231 cells, TRIM27-WT, p-CTD-S2, rep1, batch3

description:
Library name: WRJ-H5
Normalized BigWig files for CUT&Tag (p-CTD-S2) in MDA-MB-231 cells


title: 50096, C118F, Btz

description: Library name: 50096_C118F.Btz

value: Btz


title: MDA-MB-231 cells, TRIM27-WT, p-CTD-S2, rep2, batch3

description:
Library name: WRJ-H6
Normalized BigWig files for CUT&Tag (p-CTD-S2) in MDA-MB-231 cells

value: TRIM27 Wild-type (TRIM27-WT)


title: 50095, C118F, Btz

description: Library name: 50095_C118F.Btz


title: Control sample 3 C2C12 cells, non-targeting shRNA

description: Library name: Sample 3

value: non-targeting shRNA


title: 50091, C118F, Btz

description: Library name: 50091_C118F.Btz


title: Control sample 2 C2C12 cells, non-targeting shRNA

description: Library name: Sample 2

value: Skeletal Muscle


title: Jurkat_CD9_Pos_Rep2

description:
Library name: Sample8
column name in counts and norm_cpm_counts =  jkt_9Pos_Rep2

source_name: Jurkat

value: Jurkat

value: Thymocyte


title: PDX52_CD9_Neg_Rep2

description:
Library name: Sample9
column name in counts and norm_cpm_counts=  PDX52_9Neg_Rep2

value: Patient-Derived Xenograft


title: Jurkat_CD9_Neg_Rep2

description:
Library name: Sample7
column name in counts and norm_cpm_counts =  jkt_9Neg_Rep2


title: Control sample 1 C2C12 cells, non-targeting shRNA

description: Library name: Sample 1

value: myoblasts


title: MDA-MB-231 cells, TRIM27-KO, CTD, rep2, batch3

description:
Library name: WRJ-H4
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: Breast; Mammary gland

value: TRIM27 Knockout (TRIM27-KO)

value: CTD (Cell Signaling Technology, 2629)


title: spleen, Control, long-term,6

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

description: Library name: SL_48

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

source_name: spleen

extract_protocol:
Tissues were collected and immediately submerged in stayRNA™ (A&A Biotechnology) reagent. After 24 of cooling (4C), tissues were frozen at -80C until the time of RNA isolation. For RNA isolation, tissue scrapes (10-20 mg) were homogenized and used for RNA isolation with AllPrep DNA/RNA (Qiagen) kit. Following isolation, RNA was controlled for quality with the TapeStation4150 system and quantified.
Libraries were prepared using QuantSeq 3’mRNA-Seq (FWD) V2  (Lexogen) following standard protocol.

treatment_protocol: The experiment was conducted on C57BL/6J laboratory mice strain (n=48), divided into subgroups receiving CBD at doses of 0.2, 10, or 20 mg/kg of body weight, and a control group receiving placebo, administered for 2 (short-term) or 28 (long-term) days. CBD was administered once a day via intraperitoneal injection. RNA-Seq analysis of the spleen was conducted to identify transcriptomic alternations induced by CBD treatment in this organ.

value: spleen

tag: strain

value: Control, long-term


title: MDA-MB-231 cells, TRIM27-KO, CTD, rep1, batch3

description:
Library name: WRJ-H3
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: epithelial cell


title: 48975, H77L, DMSO

description: Library name: 48975_H77L.DMSO

value: kidney


title: PDX53_CD9_Neg_Rep1

description:
Library name: Sample5
column name in counts and norm_cpm_counts = PDX53_9Neg_Rep1


title: PDX52_CD9_Pos_Rep1

description:
Library name: Sample4
column name in counts and norm_cpm_counts = PDX52_9Pos_Rep1


title: MDA-MB-231 cells, TRIM27-WT, CTD, rep1, batch3

description:
Library name: WRJ-H1_S14_L004
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells


title: PDX52_CD9_Neg_Rep1

description:
Library name: Sample3
column name in counts and norm_cpm_counts= PDX52_9Neg_Rep1


title: 46302, WT, DMSO

description: Library name: 46302_WT.DMSO

value: podocytes

value: WT


title: spleen, Control, long-term,3

description: Library name: SL_45


title: spleen, Control, long-term,4

description: Library name: SL_46


title: 48986, WT, Btz

description: Library name: 48986_WT.Btz

value: Btz


title: MDA-MB-231 cells, TRIM27-WT, CTD, rep2, batch3

description:
Library name: WRJ-H2
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: TRIM27 Wild-type (TRIM27-WT)


title: spleen, Control, long-term,5

description: Library name: SL_47


title: Jurkat_CD9_Pos_Rep1

description:
Library name: Sample2
column name in counts and norm_cpm_counts = jkt_9Pos_Rep1


title: PDX53_CD9_Pos_Rep1

description:
Library name: Sample6
column name in counts and norm_cpm_counts = PDX53_9Pos_Rep1


title: 49335, C118F, DMSO

description: Library name: 49335_C118F.DMSO

value: DMSO


title: MDA-MB-231 cells, TRIM27-KO, CTD, rep3, batch2

description:
Library name: KO-C3_L3_Q0061W0150
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells


title: 46381, C118F, DMSO

description: Library name: 46381_C118F.DMSO


title: spleen, Control, long-term,1

description: Library name: SL_43


title: Jurkat_CD9_Neg_Rep1

description:
Library name: Sample1
column name in counts and norm_cpm_counts = jkt_9Neg_Rep1


title: 47993, H77L, Btz

description: Library name: 47993_H77L.Btz


title: spleen, Control, long-term,2

description: Library name: SL_44


title: MDA-MB-231 cells, TRIM27-WT, CTD, rep3, batch2

description:
Library name: WT-C3_L3_Q0058W0150
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells


title: Breast cell line beta clone

city: Kingston

first: Simone

last: Badal

address: Mona, Kingston 7

department: Department of Basic Medical Sciences

country: Jamaica

institute: University of the West Indies

description: Library name: Beta-p50_RNA

data_processing:
Standard RNA-seq analysis pipeline including quality control with FastQC, trimming with Trimmomatic, alignment with STAR, gene quantification with featureCounts
Assembly: GRCh38
Supplementary files format and content: CSV with raw count data for each sample
Supplementary files format and content: fastq files with the sequenced data

source_name: Breast

growth_protocol: Biospecimens from ultrasound-guided biopsies were collected from each patient and then transported on ice in DMEM supplemented with 5% FBS , 1% penicillin/streptomycin , and 1% amphotericin B, and processed within 6 hours of collection

extract_protocol:
RNA from the cell lines was extracted using a RNeasy Mini Kit (Qiagen 74104). The RNA samples were submitted to PSOMAGEN for bulk RNA sequencing. The next-generation sequencing (NGS) library was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit
NGS library preparation was performed using a modified protocol with the Illumina Nextera DNA Flex Library Preparation Kit (Illumina 20060059) with standard Illumina format adapter sequences

value: Breast

value: TNBC breast cancer cell lines

value: DMEM, hydrocortisone, FBS


title: MDA-MB-231 cells, TRIM27-KO, CTD, rep2, batch2

description:
Library name: KO-C2_L3_Q0060W0150
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells


title: MDA-MB-231 cells, TRIM27-KO, CTD, rep1, batch2

description:
Library name: KO-C1_L1_Q0059W0150
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells


title: 47592, H77L, DMSO

description: Library name: 47592_H77L.DMSO


title: 46621, H77L, DMSO

description: Library name: 46621_H77L.DMSO


title: spleen, 20CBD, long-term,6

description: Library name: SL_42

value: 20CBD, long-term


title: spleen, 20CBD, long-term,5

description: Library name: SL_41


title: Breast cell line alpha clone

description: Library name: Alpha-p49_RNA


title: spleen, 20CBD, long-term,4

description: Library name: SL_40


title: 47991, H77L, Btz

description: Library name: 47991_H77L.Btz


title: spleen, 20CBD, long-term,3

description: Library name: SL_39


title: E. faecalis and C. albicans  co-biofilm 48h in urine 3

city: South Bend

first: Ellsa

last: Wongso

address: 809 Lindenwood Dr S

institute: University of Notre Dame

description: Library name: EF-CA3

data_processing:
Sequence reads were trimmed for adapter sequence/low quality sequence using Trimmomatic on UseGalaxy (E. faecalis and E. coli) and by GeneWiz for C. albicans
HISAT2 and htseq-count were used to mapped reads to reference genome. Deseq2 was used to normalized and analyzed counts
Assembly: GCF_000013265.1 (E. coli UTI89), GCF_000172575.2 (E. faecalis OG1RF), GCF_000182965.3 (C. albicans SC5314)
Supplementary files format and content: tab delimited text files includes raw counts for each file provided by GeneWiz

organism:
Enterococcus faecalis
Candida albicans

source_name: bacteria, fungi

growth_protocol: Bacteria and/or fungi were grown in human sterilized urine in a fibrinogen-coated flasks for 48 hours at 37℃

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep kit from Zymo Research. 500 ng of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by GeneWiz

value: OG1RF, SC5314

value: bacteria, fungi

value: urine 48h


title: 48813, H77L, DMSO

description: Library name: 48813_H77L.DMSO


title: MDA-MB-231 cells, TRIM27-WT, CTD, rep1, batch2

description:
Library name: WT-C1_L3_Q0056W0150
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

value: Breast; Mammary gland

value: CTD (Cell Signaling Technology, 2629)


title: spleen, 20CBD, long-term,2

description: Library name: SL_38

value: spleen


title: E. faecalis and C. albicans  co-biofilm 48h in urine 2

description: Library name: EF-CA2


title: spleen, 20CBD, long-term,1

description: Library name: SL_37


title: 47615, C118F, Btz

description: Library name: 47615_C118F.Btz


title: E. faecalis and C. albicans  co-biofilm 48h in urine 1

description: Library name: EF-CA1


title: MDA-MB-231 cells, TRIM27-KO, TRIM27, rep3, batch2

description:
Library name: KO-T3_L1_Q0058W0179
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells

value: epithelial cell

value: TRIM27 Knockout (TRIM27-KO)

value: TRIM27 (Proteintech, 12205-1-AP)


title: MDA-MB-231 cells, TRIM27-WT, CTD, rep2, batch2

description:
Library name: WT-C2_L3_Q0057W0150
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells


title: 47063, WT, DMSO

description: Library name: 47063_WT.DMSO

value: kidney

value: podocytes

value: WT


title: spleen, 10CBD, long-term,6

description: Library name: SL_36

value: 10CBD, long-term


title: MDA-MB-231 cells, TRIM27-KO, TRIM27, rep1, batch2

description:
Library name: KO-T1_L1_Q0056W0179
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells


title: spl9ko_Cu_excess_Rep2

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

description: Library name: Sample24

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files including FPKM for each sample.

organism: Oryza sativa Indica Group

source_name: Genotype: Rice, Indica, Pusa Basmati1 (PB1)

growth_protocol: The plants were grown in a growth chamber at 24°C/70% RH with a 16-h–8-h light–dark cycle for hardening before transferring to a greenhouse maintained at 28°C with a natural day–night cycle.

extract_protocol:
Total RNA was isolated from 21 day whole seedlings. RNA was extracted using TRIzol method.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: All samples were handled in the same manner.

value: 21 day whole seedlings


title: spl9ko_Cu_sufficient_Rep2

description: Library name: Sample22


title: 47221, WT, Btz

description: Library name: 47221_WT.Btz

value: Btz


title: MDA-MB-231 cells, TRIM27-WT, TRIM27, rep4, batch2

description:
Library name: WT-T4_L1_Q0059W0178
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells

value: TRIM27 Wild-type (TRIM27-WT)


title: spleen, 10CBD, long-term,3

description: Library name: SL_33


title: MDA-MB-231 cells, TRIM27-KO, TRIM27, rep4, batch2

description:
Library name: KO-T4_L1_Q0059W0179
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells


title: 46622, WT, DMSO

description: Library name: 46622_WT.DMSO

value: DMSO


title: MDA-MB-231 cells, TRIM27-WT, TRIM27, rep3, batch2

description:
Library name: WT-T3_L1_Q0058W0178
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells


title: MDA-MB-231 cells, TRIM27-KO, TRIM27, rep2, batch2

description:
Library name: KO-T2_L1_Q0057W0179
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells


title: Original breast tissue

description: Library name: OG-P63_RNA

value: Breast

value: TNBC breast cancer cell lines

value: DMEM, hydrocortisone, FBS


title: spl9ko_Cu_excess_Rep1

description: Library name: Sample23


title: spleen, 10CBD, long-term,4

description: Library name: SL_34


title: 47067, H77L, Btz

description: Library name: 47067_H77L.Btz


title: spl9ko_Cu_sufficient_Rep1

description: Library name: Sample21


title: spleen, 10CBD, long-term,2

description: Library name: SL_32


title: MDA-MB-231 cells, TRIM27-WT, TRIM27, rep2, batch2

description:
Library name: WT-T2
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells

value: Breast; Mammary gland


title: spleen, 10CBD, long-term,1

description: Library name: SL_31


title: 48638, H77L, Btz

description: Library name: 48638_H77L.Btz


title: MDA-MB-231 cells, TRIM27-WT, TRIM27, rep1, batch2

description:
Library name: WT-T1_L1_Q0056W0178
Normalized BigWig files for CUT&Tag (TRIM27) in MDA-MB-231 cells


title: 46301, C118F, DMSO

description: Library name: 46301_C118F.DMSO


title: spl9ko_Cu_deficient_Rep1

description: Library name: Sample19


title: spl9ko_Cu_deficient_Rep2

description: Library name: Sample20


title: 46731, WT, Btz

description: Library name: 46731_WT.Btz


title: MDA-MB-231 cells, TRIM27-WT, IgG, rep1, batch1

description:
Library name: IgG-2_S42_L002
Normalized BigWig files for CUT&Tag (IgG) in MDA-MB-231 cells

value: IgG (abcam, ab172730)


title: s288_ki_w_1y: Liver 1-year old +/+

type: genomic

city: Edinburgh

first: Dan

last: Sarni

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Infinium® Mouse Methylation BeadChip performed according to manufacturer instructions by Edinburgh ECRF

scan_protocol: Prepared arrays were scanned on Illumina iScan

data_processing:
Raw idat files were processed to beta and detection p-values using the Bioconducter package minfi (v1.50.0) using single-sample normal exponential out of band (ss noob) background correction and dye bias normalization annotations (IlluminaMouseMethylationanno.12.v1.mm10). Probes overlapping known SNPs (MAF>1% and within 5 bp of the probe’s CpG target, based on https://github.com/zhou-lab/InfiniumManifestAnnotator), located on sex chromosomes, or with detection p-value > 0.01 were excluded.
Normalized mean Beta and detection p-value.

label: Cy3 and Cy5

label_protocol: Bisulphite conversion was done using EZ-96 DNA Methylation kit from Zymo using the protocol adjustments recommended for preparing samples for Illumina Methylation  - protocol appendix points 1 and 6

extract_protocol: Genomic DNA was extracted using Dneasy Blood and Tissue Kit (QIAGEN).

value: Dnmt3a +/+

value: liver


title: SPL9OE_Cu_excess_Rep2

description: Library name: Sample18


title: spleen, 0.2CBD, long-term,4

description: Library name: SL_28

value: spleen

value: 0.2CBD, long-term


title: 46402, WT, DMSO

description: Library name: 46402_WT.DMSO

value: kidney


title: SPL9OE_Cu_excess_Rep1

description: Library name: Sample17


title: 46403, WT, DMSO

description: Library name: 46403_WT.DMSO

value: podocytes


title: k431_li_m_1y: Liver 1-year old W326R/+

value: Dnmt3a W326R/+


title: spleen, 0.2CBD, long-term,3

description: Library name: SL_27


title: 47222, H77L, Btz

description: Library name: 47222_H77L.Btz


title: 47157, WT, Btz

description: Library name: 47157_WT.Btz

value: WT


title: spleen, 0.2CBD, long-term,5

description: Library name: SL_29


title: k429_li_m_1y: Liver 1-year old W326R/+


title: SPL9OE_Cu_sufficient_Rep2

description: Library name: Sample16

value: 21 day whole seedlings


title: SPL9OE_Cu_sufficient_Rep1

description: Library name: Sample15


title: spleen, Control, short-term,6

description: Library name: SL_24

value: Control, short-term


title: k428_li_m_1y: Liver 1-year old W326R/+


title: spleen, Control, short-term,5

description: Library name: SL_23


title: k430_li_w_1y: Liver 1-year old +/+


title: spleen, 0.2CBD, long-term,2

description: Library name: SL_26


title: 47155, WT, DMSO

description: Library name: 47155_WT.DMSO


title: SPL9OE_Cu_deficient_Rep2

description: Library name: Sample14


title: k427_li_w_1y: Liver 1-year old +/+


title: SPL9OE_Cu_deficient_Rep1

description: Library name: Sample13


title: 48814, H77L, DMSO

description: Library name: 48814_H77L.DMSO


title: PB1_Cu_excess_Rep2

description: Library name: Sample12


title: spleen, Control, short-term,4

description: Library name: SL_22


title: spleen, Control, short-term,3

description: Library name: SL_21


title: 46732, H77L, DMSO

description: Library name: 46732_H77L.DMSO


title: spleen, Control, short-term,2

description: Library name: SL_20


title: k542_li_m_3m: Liver 3-month old W326R/+


title: 46587, WT, Btz

description: Library name: 46587_WT.Btz

value: Btz


title: PB1_Cu_excess_Rep1

description: Library name: Sample11


title: k543_li_m_3m: Liver 3-month old W326R/+


title: spleen, 20CBD, short-term,6

description: Library name: SL_18

value: 20CBD, short-term


title: 47614, C118F, Btz

description: Library name: 47614_C118F.Btz


title: PB1_Cu_sufficient_Rep2

description: Library name: Sample10


title: spleen, 20CBD, short-term,5

description: Library name: SL_17


title: spleen, 20CBD, short-term,4

description: Library name: SL_16


title: k536_li_w_3m: Liver 3-month old +/+


title: k535_li_w_3m: Liver 3-month old +/+


title: PB1_Cu_sufficient_Rep1

description: Library name: Sample9


title: k541_li_m_3m: Liver 3-month old W326R/+


title: spleen, 20CBD, short-term,2

description: Library name: SL_14


title: 47672, C118F, DMSO

description: Library name: 47672_C118F.DMSO

value: DMSO


title: 47151, C118F, DMSO

description: Library name: 47151_C118F.DMSO


title: PB1_Cu_deficient_Rep1

description: Library name: Sample7


title: 48982, H77L, Btz

description: Library name: 48982_H77L.Btz


title: PB1_Cu_deficient_Rep2

description: Library name: Sample8


title: spleen, 20CBD, short-term,3

description: Library name: SL_15


title: 46588, WT, Btz

description: Library name: 46588_WT.Btz


title: k529_li_w_23d: Liver 23-day old +/+


title: k528_li_w_23d: Liver 23-day old +/+


title: k534_li_w_3m: Liver 3-month old +/+


title: Onivara_Cu_excess_Rep2

description: Library name: Sample6


title: Onivara_Cu_sufficient_Rep2

description: Library name: Sample4


title: IP_ints11chIP_biorep2

city: Oxford

first: Luke

last: Slade

address: Sherrington Rd, Oxford

department: Biochemistry

institute: University of Oxford

description:
Library name: IP-ints11chIP-rep2
Condition represented by column: ChIP_peak generated from MACS2 merge of replicates 1 & 2

data_processing:
Raw paired-end FASTQ files from multiple lanes were concatenated per sample. Reads were quality-controlled and trimmed using fastp with a minimum read length of 30 bp and automatic paired-end adapter detection
Trimmed reads were aligned to the C. elegans genome using STAR with the following parameters: --alignIntronMin 10 --alignIntronMax 5000 --alignMatesGapMax 10000. Aligned BAMs were sorted and indexed using samtools
Uniquely mapped reads were extracted using samtools view -q 255
bigwig files were generated using bamCoverage (deepTools) at 1 bp resolution
Assembly: WBCel235 v113
Supplementary files format and content: INTS11_narrowpeaks.txt: MACS2 outputs using --q 0.01, --extsize 250, and --keep-dup auto using combined bam inputs. ChIP_peaks represent the confident peaks across both replicates

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Day 1 adults were collected for ChIP-seq. The JCP643 ints-11(jcp31)[ints-11::3xFLAG])) strain was used for ChIP-seq and Anti-FLAG M2 Magnetic Beads (Merck, M8823) were used for immuno-precipitations. C. elegans (~10,000 per plate, amounting to ~400,000 per condition per replicate) were grown at 20 degrees on 150mm petri plates seeded with 3mL of concentrated OP50 bacteria. Samples were disrupted in a freezer mill (SPEX SamplePrep) in liquid nitrogen to generate 5mL of lysed worm powder per replicate. Lysed worm powder was then cross-linked in warm PBS supplemented with formaldehyde (1.1% final) and PMSF (1% final) in a total volume of 40mL. Tubes were placed on a rotator at room temperature for 10-minutes, and then quenched with glycine to a final concentration of 125mM. Cross-linked samples were then washed with 10mL of ice-cold PBS supplemented with protease inhibitors for a total of three washes with centrifugation at 4000g and 4°C. Pellets were resuspended in ice-cold B-ChIP-L0 buffer for chromatin shearing.
NEBNext Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: No treatment, INTS-11 immuno-precipitation of day 1 adult animals harbouring endogenous INTS11::3XFLAG tag

value: whole animal

value: wild-type (with INTS11 3XFLAG tag)

tag: chip antibody

value: Millipore, Anti-FLAG (M8823)

tag: time


title: Onivara_Cu_excess_Rep1

description: Library name: Sample5


title: IP_ints11chIP_biorep1

description:
Library name: IP-ints11chIP-rep1
Condition represented by column: ChIP_peak generated from MACS2 merge of replicates 1 & 2

growth_protocol: (~10,000 per plate, amounting to ~400,000 per condition per replicate) were grown at 20 degrees on 150mm petri plates seeded with 3mL of concentrated OP50 bacteria.


title: spleen, 20CBD, short-term,1

description: Library name: SL_13


title: k526_li_m_23d: Liver 23-day old W326R/+


title: input_ints11chIP_biorep2

description: Library name: input-ints11chIP-rep2


title: k520_li_w_23d: Liver 23-day old +/+


title: Onivara_Cu_sufficient_Rep1

description: Library name: Sample3


title: spleen, 10CBD, short-term,5

description: Library name: SL_11

value: 10CBD, short-term


title: k519_li_m_23d: Liver 23-day old W326R/+


title: spleen, 10CBD, short-term,4

description: Library name: SL_10


title: input_ints11chIP_biorep1

description: Library name: input-ints11chIP-rep1


title: Onivara_Cu_deficient_Rep2

description: Library name: Sample2


title: spleen, 10CBD, short-term,3

description: Library name: SL_9


title: spleen, 10CBD, short-term,6

description: Library name: SL_12


title: WT4DF_li_w_4d: Liver 4-day old +/+

value: Dnmt3a +/+


title: spleen, 10CBD, short-term,2

description: Library name: SL_8


title: k518_li_m_23d: Liver 23-day old W326R/+

value: liver


title: INPUT_Rep2

description: Library name: Sample 8

data_processing:
Adaptor trimming by cutadapt.
The reads obtained were trimmed using cutadapt and aligned to IRGSP1 rice genome with parameters -q -v 1 -k 1 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 5bp bin size.
Assembly: Oryza sativa japonica Nipponbare genome – IRGSP1
Supplementary files format and content: The coverage files of the ChIP-seq alignments were provided in bigwig format.

source_name: Genotype: Rice, Indica, Pusa Basmati 1 (PB1)

extract_protocol:
Sheared chromatin from 21 day old seedlings of 3XFlag:SPL9OE (T2 generation) were grown in appropriate copper concentrations and immunoprecipitated with Anti-FLAG M2 Magnetic Beads-M8823. Washes, elution, de-crosslinking and DNA.  purification was done as described. The purified DNA was taken for library preparation. .
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: Seedling tissues were handled in the same manner.


title: spleen, 10CBD, short-term,1

description: Library name: SL_7

value: spleen


title: mut16-D10-ints11-biorep1

description:
Library name: mut16-ints11-rep1
Column name in raw_feature_counts_MUT16_all.txt & Deseq_normalised_counts_MUT16.xlxs: mut16_ints11_rep1

data_processing:
Sequencing reads were quality filtered and adapter-trimmed using fastp (minimum length 30 bp, automatic adapter detection).
Trimmed reads were aligned to a concatenated C. elegans and S. pombe genome using STAR
Library size normalisation was used for final datasets
Gene-level counts were generated using Featurecounts
Strand-specific normalized coverage tracks (bigWig) were generated using deepTools bamCoverage.
Assembly: WBCel235 v113
Supplementary files format and content: raw_feature_counts_ageing_all.txt: featurecounts for all samples on rows 39-42 in samples section
Supplementary files format and content: raw_feature_counts_MUT16_all.txt: featurecounts for all samples on rows 43-46 in samples section
Supplementary files format and content: Deseq_normalised_counts.csv: log2 fold-change and adj. P-values for main analysis of samples in rows 39-42 in samples section
Supplementary files format and content: Deseq_normalised_counts_MUT16.xlsx: log2 fold-change and adj. P-values for main analysis of samples in rows 43-46 in samples section

growth_protocol: C. elegans were grown on standard NGM plates seeded with OP50 from eggs to L4 larval stage. At L4, animals were shifted to RNAi NGM plates seeded with either control (empty vector; L4440) or ints-11 dsRNA bacteria. Transferred every 2-days onto fresh plates.

extract_protocol:
For collections, samples were manually picked from plates with platinum wire onto unseeded NGM plates for 15-minutes to reduce bacterial contamination. Samples were then washed from plates and cleaned five times in 1mL of M9 buffer by gravity flotation. Supernatants were removed to a final volume of 30 uL and 500 uL of TriZol reagent was added before snap freezing in liquid nitrogen. Samples were stored at -70 degrees until further processing for RNA extraction. Total RNA was extracted using the TRIzol method. Approximately 70 worms collected in 500uL of TRIzol were freeze/thawed five times with vortexing. Phase separating tubes were utilised to obtain aqueous phases, precipitated with isopropanol overnight and cleaned up/washed with 75% ethanol and air dried. DNAse treatment of ~500ng per sample that contained a 5% spike-in of Schizosaccharomyces pombe RNA (final data were not spike-in normalised, see methods manuscript for details). Ribodepletion was performed using siTOOLS depletion kit for C. elegans.
All samples were checked pre- and post-ribodepletion for integraity and rRNA depletion sufficiency. RNA was normalised using Qubit high sensitivity for library preparation (~300ng). Libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: RNAi plates contained Carbenicillin (100ug/mL) and IPTG (1mM) for dsRNA induction. Empty vector vs ints-11 RNAi

value: ints11 RNAi


title: mut16-D10-ints11-biorep2

description:
Library name: mut16-ints11-rep2
Column name in raw_feature_counts_MUT16_all.txt & Deseq_normalised_counts_MUT16.xlsx: mut16_ints11_rep2


title: INPUT_Rep1

description: Library name: Sample 7


title: mut16-D10-ev-biorep2

description:
Library name: mut16-ev-rep2
Column name in raw_feature_counts_MUT16_all.txt & Deseq_normalised_counts_MUT16.xlsx: mut16_ev_rep2

value: empty vector RNAi


title: spleen, 0.2CBD, short-term,6

description: Library name: SL_6

value: 0.2CBD, short-term


title: k502_5_li_m_4d: Liver 4-day old W326R/+

value: Dnmt3a W326R/+


title: Onivara_Cu_deficient_Rep1

description: Library name: Sample1


title: k502_4_li_w_4d: Liver 4-day old +/+


title: spleen, 0.2CBD, short-term,5

description: Library name: SL_5


title: SPL9OE_Cu_excess_Rep1

description: Library name: Sample 5


title: k502_3_li_m_4d: Liver 4-day old W326R/+


title: INTS11-D10-biorep2

description:
Library name: INTS11-D10-rep2
Column name in raw_feature_counts_ageing_all.txt & Deseq_normalised_counts.csv: ints11_rep2

value: wild type


title: mut16-D10-ev-biorep1

description:
Library name: mut16-ev-rep1
Column name in raw_feature_counts_MUT16_all.txt & Deseq_normalised_counts_MUT16.xlsx: mut16_ev_rep1


title: spleen, 0.2CBD, short-term,4

description: Library name: SL_4


title: SPL9OE_Cu_excess_Rep2

description: Library name: Sample 6

value: 21 day whole seedlings


title: k502_2_li_w_4d: Liver 4-day old +/+


title: spleen, 0.2CBD, short-term,3

description: Library name: SL_3


title: INTS11-D10-biorep1

description:
Library name: INTS11-D10-rep1
Column name in raw_feature_counts_ageing_all.txt & Deseq_normalised_counts.csv: ints11_rep1


title: spleen, 0.2CBD, short-term,2

description: Library name: SL_2


title: SPL9OE_Cu_deficient_Rep2

description: Library name: Sample 2


title: EV-D10-biorep2

description:
Library name: EV-D10-rep2
Column name in raw_feature_counts_ageing_all.txt & Deseq_normalised_counts.csv: ev_rep2


title: k502_1_li_m_4d: Liver 4-day old W326R/+


title: SPL9OE_Cu_sufficient_Rep1

description: Library name: Sample 3


title: s288_in_w_1y: Intestine 1-year old +/+

value: intestine


title: INTS11-D2-biorep2

description:
Library name: INTS11-D2-rep2
Used for genome coverage tracks only, strand-specific bigwigs added


title: k430_in_w_1y: Intestine 1-year old +/+


title: SPL9OE_Cu_deficient_Rep1

description: Library name: Sample 1


title: ATAC-seq Apc flox;Lef1 del biol rep 3

city: Helsinki

first: Marika

last: Lassila

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Library name: Sample 8

data_processing:
Cutadapt version 1.18  in Trim Galore version 0.6.5 , with default parameters, was used for quality and adaptor trimming. Trimmed reads were aligned to the mm10 reference genome using Bowtie 2 version 2.3.5. Reads with a mapping quality below 20 were filtered out, mitochondrial reads were counted, and PCR duplicates were removed using Samtools version 1.9. MACS2 version 2.1.4 was used for peak calling. We created fixed-width peaks ranging 250bp from the peak summit called with MACS2 callpeak command with parameters ‘--shiff 75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01’. Differential accessibility between groups was calculated using DESeq2 version 1.32.0 with default settings and Wald statistics. To obtain the number of Tn5 insertions, the properly paired paired-end read alignments were corrected for the Tn5 offset (‘+’ stranded +4 bp, ‘−’ stranded −5 bp) (68). Tn5 insertions were counted at non-overlapping peaks, with the peak with the highest peak score kept in the analysis, for all peaks present in at least two samples. Differentially accessible regions (DARs) were defined with a BH-adjusted p-value <0.05. The closest gene for each DAR was annotated using HOMER annotatePeaks.pl against the mm10 RefSeq database. Enrichment of transcription factor (TF) motifs to DARs was calculated separately for more accessible (log2 Fold Change > 0) and less accessible (log2 Fold Change < 0) regions using Simple Enrichment Analysis (sea) in MEME-Suite with default settings.
Assembly: mm10
Supplementary files format and content: bed

source_name: Tumor tissue isolated from small intestinal tumors of Apc flox mice

extract_protocol:
Small intestines of Apcfl/fl mice were cut open, washed with PBS, and incubated in 10 mM EDTA in a shaker at 37°C for 10 min. Tissues were washed twice with PBS, and the cells were scraped off with a coverslip. The cells were then centrifuged at 1500 RPM for 5 min, followed by incubation with a digestion mix composed of HBSS with Mg2+ and Ca2+ (Gibco, #14025-050) and supplemented with 1 mg/ml of collagenase type I (Gibco,#17100-017), collagenase type IV (1 mg/ml) (Gibco #17104-019), 4 mg/ml of Dispase II (Sigma Aldrich, #04942078001), and 1 µl/ml of DNase1 (Thermo Fisher Scientific, #EN0521) for 30-40 min at 37°C. After this, DMEM was added, and the cell suspension was filtered through 70 µm and twice through a 40 µm filter and centrifuged for 10 min at 150 RCF. TdTomato+ cells from the mice were sorted using BD Influx (BD Biosciences).
To induce the library complexity transposition was performed for 50000 nuclei per sample in triplicates totaling 150000 nuclei. After transposition DNA fragments for each sample were pooled and purified by using Zymo DNA Clean and Concentrator-5 kit. Libraries were amplified by PCR and quantified, and the quality was measured by qPCR and TapeStation 2200.

value: Tumor cells

value: Lgr5-CreERT2; Apc fl/fl; Lef1


title: H146, 2.5 µM Valemetostat, Day9, Rep2, microC

city: Milwaukee

first: Huizi

last: Chen

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Department of Medicine

institute: Medical College of Wisconsin

description: Library name: H146_val9d_rep2 (microC)

data_processing:
Paired-end FASTQ files were aligned to hg38 using BWA-MEM, valid ligation events were extracted using pairtools, and the sparse chromatin interaction matrices were generated using cooler using 1000bp bin size.
Assembly: hg38
Supplementary files format and content: Pair files containing valid ligation events.
Supplementary files format and content: Cool files representing the chromatin contact matrices at a 1000‑bp bin resolution.

source_name: Lung

growth_protocol: NCI-H146 cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5%CO2 at 37C.

extract_protocol:
The Micro‑C assay was performed using the Dovetail Micro‑C Kit according to the manufacturer’s instructions. Briefly, cells were crosslinked with disuccinimidyl glutarate (DSG) and formaldehyde, and the crosslinked chromatin was digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed and the chromatin digested fragments were bound to Chromatin Capture Beads. Later, the digested fragments were end-polished, and subjected to bridge ligation and intra-aggregate proximity ligation. Following ligation, crosslinks were reversed, proteins were degraded, and the DNA was purified.
Purified DNA was used to prepare the sequencing library by end repair, adapter ligation, and DNA purification. Briefly, biotin-containing ligation products were captured using streptavidin beads, followed by index PCR amplification and size selection to generate the final sequencing-ready Micro‑C library. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end reads.

treatment_protocol: NCI-H146 cells were treated with 2.5 µM of valemetostat for 9 days. Drug was replenished every 3rd day.

value: Lung

value: SCLC

value: 2.5 µM Valemetostat, 9 days


title: ATAC-seq Apc flox;Lef1 del biol rep 4

description: Library name: Sample 9

value: Tumor tissue isolated from small intestinal tumors of Apc flox mice


title: INTS11-D2-biorep1

description:
Library name: INTS11-D2-rep1
Used for genome coverage tracks only, strand-specific bigwigs added

value: whole animal


title: SPL9OE_Cu_sufficient_Rep2

description: Library name: Sample 4


title: k431_in_m_1y: Intestine 1-year old W326R/+


title: ATAC-seq Apc flox;Lef1 del biol rep 2

description: Library name: Sample 7


title: EV-D2-biorep1

description:
Library name: EV-D2-rep1
Used for genome coverage tracks only, strand-specific bigwigs added


title: H146, Vehicle, Day9, Rep2, microC

description: Library name: H146_ctrl_rep2 (microC)

value: DMSO vehicle, 9 days


title: H146, 2.5 µM Valemetostat, Day9, Rep1, microC

description: Library name: H146_val9d_rep1 (microC)


title: ATAC-seq Apc flox;Lef1 del biol rep 1

description: Library name: Sample 6


title: ATAC-seq Apc flox ctrl biol rep 5

description:
Library name: Sample 5
Processed data file not provided.

value: Lgr5-CreERT2; Apc fl/fl


title: EV-D10-biorep1

description:
Library name: EV-D10-rep1
Column name in raw_feature_counts_ageing_all.txt & Deseq_normalised_counts.csv: ev_rep1


title: CW-2

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
FASTQ files were pre-filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Fastp
Transcript-level mapping and gene-level quantification were conducted using Salmon aligner (version 1.10.3)
Gene-level quantification and annotation were done using Tximeta Bioconductor utility
Normalization and Differential expression analyses were done in DESeq2  Bioconductor utility.
Assembly: GRCr8/GCF_036323735.1
Supplementary files format and content: tab-delimited text file includes Salmon aligner quantification.
Supplementary files format and content: Columns: Name - This is the name of the target transcript provided in the input transcript database (FASTA file). Length -the length of the target transcript in nucleotides. EffectiveLength -the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias. TPM -salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads -salmon’s estimate of the number of reads mapping to each transcript that was quantified.

organism: Rattus norvegicus

source_name: Embryonic BD1X rat heart tissue

growth_protocol: H9c2 cells were maintained in DMEM supplimented with 10% FBS Aand antibiotics 1% in humified atomospheres with 5% CO2 at 37 C

extract_protocol:
Total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen)
High-throughput sequencing was conducted at the IGM Genomics Center (UCSD, La Jolla, CA, USA) on Illumina NovaSeq X Plus. RNA-seq data (58.8-107 million reads/sample) were saved in FASTQ format

treatment_protocol: Cells were pre-treated with ESW and CW at the dilutions 10^-2 for 72 hours. Control cells were maintained with normal growth media. Media replaced every 24 hours with freshy diluted sample

value: Embryonic BD1X rat heart tissue

value: Myoblast

value: WT

value: Control water


title: k429_in_m_1y: Intestine 1-year old W326R/+

value: Dnmt3a W326R/+


title: H146, Vehicle, Day9, Rep1, microC

description: Library name: H146_ctrl_rep1 (microC)


title: CW-3


title: K600_in_w_3m: Intestine 3-month old +/+

value: Dnmt3a +/+


title: ATAC-seq Apc flox ctrl biol rep 4

description: Library name: Sample 4


title: CW-1


title: k427_in_w_1y: Intestine 1-year old +/+


title: ESW-3

value: Eneried structured water


title: k428_in_m_1y: Intestine 1-year old W326R/+

value: intestine


title: ATAC-seq Apc flox ctrl biol rep 3

description: Library name: Sample 3

value: Tumor cells


title: K592_in_w_3m: Intestine 3-month old +/+


title: ATAC-seq Apc flox ctrl biol rep 2

description: Library name: Sample 2


title: H146, 2.5 µM Valemetostat, Day9, Rep3, RNA-seq

description:
Library name: H146_val9d_rep3 (RNA-seq)
Column name in H146_STAR_salmon_gene_counts.tsv: Val9d_Rep3

data_processing:
Raw sequencing reads were trimmed with Trim Galore. Reads were aligned to the human reference genome hg38 using STAR with GENCODE v43 annotation. The transcript abundance was quantified using Salmon.
Assembly: hg38
Supplementary files format and content: H146_STAR_salmon_gene_counts.tsv is a tab-delimited gene-level count matrix generated from Salmon.

growth_protocol: H146 cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5%CO2 at 37C.

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Plus Mini Kit as per manufacturere's recommendation.
Libraries were prepared using the Illumina Stranded Total RNA Library Prep kit with 500 ng of input RNA and sequenced as 100 bp paired-end reads on the Illumina NovaSeq 6000 platform.

treatment_protocol: H146 cells were treated with 2.5 µM of valemetostat for 9 days. Drug was replenished every 3rd day.


title: K590_in_m_3m: Intestine 3-month old W326R/+


title: H146, 2.5 µM Valemetostat, Day9, Rep1, RNA-seq

description:
Library name: H146_val9d_rep1 (RNA-seq)
Column name in H146_STAR_salmon_gene_counts.tsv: Val9d_Rep1


title: K591_in_m_3m: Intestine 3-month old W326R/+


title: ESW-1


title: ESW-2


title: H146, Vehicle, Day9, Rep3, RNA-seq

description:
Library name: H146_ctrl_rep3 (RNA-seq)
Column name in H146_STAR_salmon_gene_counts.tsv: Control_Rep3


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 10

city: Tianjin

first: Peishi

last: Jiang

address: No. 190 Jieyuan Road, Hongqiao District

department: Department of Colorectal Surgery

institute: Tianjin Union Medical Center, Nankai University

description:
Library name: RG26
Group: RG

data_processing:
Raw reads were filtered using fastp to remove adaptor sequences, poly-N reads (N content > 10%), and low-quality reads (Q <= 5 bases exceeding 50% of read length).
Clean reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using HISAT2 (v2.2.1).
Gene-level read counts were quantified using featureCounts (v2.0.6) with the gene model annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file (gene_count.xls) containing raw gene read counts for all 26 samples.

source_name: colon

growth_protocol: Twenty-six SPF male C57BL/6 mice (6 weeks old, 20-22 g) were housed under specific pathogen-free conditions (22+/-2 C, 12-hour light/dark cycle) with free access to food and water. After one week of acclimatization, mice were randomly divided into three groups.

extract_protocol:
Total RNA was extracted from colon tissue samples using standard extraction methods. RNA integrity was assessed using the Agilent 2100 Bioanalyzer to ensure sample quality before library construction.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, the first-strand cDNA was synthesized using random hexamer primers. After second-strand cDNA synthesis, end repair, dA-tailing, and adaptor ligation were performed. The library was amplified by PCR and quality-checked using an Agilent 2100 Bioanalyzer. Libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

treatment_protocol: Mice were divided into three groups: normal control (NC, n=8), loperamide-induced constipation model control (MC, n=8), and Rothia mucilaginosa intervention group (RG, n=10). The experimental protocol consisted of three phases: (1) Adaptation phase (days 0-7): baseline data collection; (2) Modeling phase (days 8-21): constipation was induced by daily gavage of loperamide hydrochloride at 10:00 AM (10 mg/kg for days 8-14 [Selleck Chemicals, USA]; 15 mg/kg for days 15-21 [IMODIUM, Xi'an Janssen Pharmaceutical Ltd.], dissolved in 0.5% carboxymethylcellulose sodium solution); (3) Intervention phase (days 22-40): continued daily gavage of loperamide (15 mg/kg) at 10:00 AM, followed by intervention treatment at 11:00 AM, with NC and MC groups receiving 200 uL PBS by gavage, while the RG group received Rothia mucilaginosa suspension (BNCC363031, BeNa Culture Collection, 2x10^8 CFU in 200 uL PBS) by gavage.

value: colon

value: loperamide-induced constipation model + Rothia mucilaginosa gavage (BNCC363031, 2e8 CFU/day)


title: ATAC-seq Apc flox ctrl biol rep 1

description: Library name: Sample 1


title: H146, 2.5 µM Valemetostat, Day9, Rep2, RNA-seq

description:
Library name: H146_val9d_rep2 (RNA-seq)
Column name in H146_STAR_salmon_gene_counts.tsv: Val9d_Rep2

value: Lung

value: SCLC


title: K589_in_w_3m: Intestine 3-month old +/+


title: Control-3

value: No treatment


title: H146, Vehicle, Day9, Rep1, RNA-seq

description:
Library name: H146_ctrl_rep1  (RNA-seq)
Column name in H146_STAR_salmon_gene_counts.tsv: Control_Rep1


title: H146, Vehicle, Day9, Rep2, RNA-seq

description:
Library name: H146_ctrl_rep2 (RNA-seq)
Column name in H146_STAR_salmon_gene_counts.tsv: Control_Rep2


title: K588_in_m_3m: Intestine 3-month old W326R/+


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 9

description:
Library name: RG25
Group: RG


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 8

description:
Library name: RG24
Group: RG


title: H146, 2.5 µM Valemetostat, Day9, Rep3, ATAC-seq

description: Library name: H146_val9d_rep3 (ATAC-seq)

data_processing:
Raw paired-end sequencing reads were trimmed using Trim Galore, aligned to the hg38 reference genome using Bowtie2. PCR duplicates and mitochondrial reads were removed using Picard and samtools, and peaks were called using MACS2 with narrowPeak output. BigWig files were generated using bedtools genomecov with RPM normalization.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
Chromatin accessibility profiling was performed on 50,000 viable nuclei per sample using the Active Motif ATAC-seq kit.
Libraries were sequenced as 100 bp paired-end reads on the Illumina NovaSeq 6000 platform.

value: 2.5 µM Valemetostat, 9 days


title: Control-2


title: k528_in_w_23d: Intestine 23-day old +/+


title: k529_in_w_23d: Intestine 23-day old +/+


title: Umbilical cord blood CD34+, IgG, WT, C&R, CB

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description: Library name: C_R_IgG_CB_forSTAT1experi_Naive

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.
Library strategy: CUT&Run

source_name: Enriched hCD34+ from umbilical cord blood

growth_protocol: Enriched human cord blood CD34+ cells were cultured in SFEM II medium (StemCell Technologies, #09605) supplemented with Penicillin-Streptomycin (50 U/mL), human SCF (100 ng/mL), human TPO (100 ng/mL), and human FLT3L (100 ng/mL). Media were refreshed every other day.

extract_protocol:
All cell sorting was performed using a BD Aria Ilu SORP cell sorter. For scRNA-seq, 10,000 sorted CD34⁺ cells were used to prepare gene expression (GEX) libraries according to the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3 User Guide. For CITE-seq, 10,000 sorted CD34⁺ cells were processed to generate GEX libraries using the 10x Chromium Single Cell 3' Reagent Kits User Guide, v3.1 Chemistry Dual Index, with Feature Barcoding Technology for Cell Surface Protein, User Guide CG000317. For RNA sequencing, approximately 5,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells were sorted, followed by RNA isolation using the NucleoSpin RNA XS kit (Macherey-Nagel #740902.250) and library preparation with the SMARTer Ultra Low RNA Kit (Clontech), according to the manufacturer's instructions. For CUT&Tag, 10,000–20,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells or enriched human cord blood CD34⁺ cells were sorted and processed following the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff's lab (DOI: dx.doi.org/10.17504/protocols.io.bcuhiwt6). For CUT&RUN, libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher #14-1001).
scRNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 (PN-1000075), following the manufacturer's user guide. CITE-seq libraries were constructed using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index Chemistry) along with Feature Barcoding Technology for Cell Surface Protein, according to the Feature Barcoding User Guide (CG000317). Bulk RNA-seq libraries were generated using the SMARTer Ultra Low RNA Kit (Clontech), following the manufacturer's instructions. CUT&Tag libraries were prepared using the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff’s laboratory (DOI: 10.17504/protocols.io.bcuhiwt6). CUT&RUN libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher, #14-1001), according to the manufacturer’s protocols.

treatment_protocol: We used an optimized microRNA lentiviral backbone to carry our shRNAs, as recommended by Fellmann et al. (2013). Lentiviral particles were produced by co-transfecting 293T cells with the packaging plasmids pMD.G, psPAX2, and pSFFV-eGFP-miR-E, in which the miR-E cassette was engineered to target Renilla, JARID2, EZH2, or STAT1. All plasmids were mixed at a 1:1:1 molar ratio. Enriched human cord blood CD34+ cells were transduced with constitutive lentiviral vectors carrying shRNAs, using LentiBOOST (1:100, SIRION Biotech, Cat No. SB-P-LV-101-12) and protamine sulfate (1:1000) to enhance transduction efficiency, as described by Schott et al. (2019).

value: Umbilical cord blood CD34+


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 7

description:
Library name: RG23
Group: RG


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 6

description:
Library name: RG22
Group: RG


title: Control-1


title: k526_in_m_23d: Intestine 23-day old W326R/+


title: GFP+CD34+, IgG, shJARID2 and shRen,  C&R

description: Library name: C_R_IgG_forSTAT1experi

source_name: Sorted GFP+CD34+, shRen and shJARID2, Day8 ex vivo culture

value: Lentivirus


title: H146, 2.5 µM Valemetostat, Day9, Rep1, ATAC-seq

description: Library name: H146_val9d_rep1 (ATAC-seq)


title: H146, 2.5 µM Valemetostat, Day9, Rep2, ATAC-seq

description: Library name: H146_val9d_rep2 (ATAC-seq)


title: H146, Vehicle, Day9, Rep3, ATAC-seq

description: Library name: H146_ctrl_rep3 (ATAC-seq)

value: DMSO vehicle, 9 days


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 4

description:
Library name: RG20
Group: RG


title: k519_in_m_23d: Intestine 23-day old W326R/+


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 5

description:
Library name: RG21
Group: RG


title: H146, Vehicle, Day9, Rep2, ATAC-seq

description: Library name: H146_ctrl_rep2 (ATAC-seq)


title: k518_in_m_23d: Intestine 23-day old W326R/+


title: GFP+CD34+, STAT1, shRen,  C&R

description: Library name: C_R_STAT1_shRen

source_name: Sorted GFP+CD34+, shRen, Day8 ex vivo culture


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 3

description:
Library name: RG19
Group: RG


title: H146, Vehicle, Day9, Rep1, ATAC-seq

description: Library name: H146_ctrl_rep1 (ATAC-seq)


title: Umbilical cord blood CD34+, STAT1, WT, C&R, CB

description: Library name: C_R_STAT1_CB_Naive


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 2

description:
Library name: RG18
Group: RG


title: GFP+CD34+, STAT1, shJARID2,  C&R

description: Library name: C_R_STAT1_shJARID2

source_name: Sorted GFP+CD34+, shJARID2, Day8 ex vivo culture


title: Colon tissue, loperamide-induced constipation + Rothia mucilaginosa gavage, biol rep 1

description:
Library name: RG17
Group: RG


title: MDA-MB-231, CT7311-treated, RPA2-ChIP (biological replicate 2)

city: Boston

first: Eunbee

last: Choi

state: MA

address: 440 Brookline Ave, Mayer-434

institute: Dana farber cancer institute

description: Library name: RPA2 ChIP_CT7311-2

data_processing:
ChIP-seq reads were aligned to the human reference genome (GRCh38) with Bowtie2 (2.5.2). Mapping quality was assessed with Samtools (1.18). Since RPA displays broad occupancy pattern, peak-calling was performed using MACS3 (3.0.1) using the options --broad and --broad-cutoff 0.1. BroadPeak files from the two DMSO replicates were merged using bedtools (2.31.0) to generate a union peak set. To ensure high-confidence results, approximately 2,000 peaks showing non-specific enrichment in the input controls were excluded. BigWig files were generated, and enrichment signals were analyzed and visualized with deepTools (3.5.6) based on the filtered union peak set.
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig for input and ChIP samples, Bed file includes RPA2-enriched sites.

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, BenchMark, GeminiBio), 100 units/mL penicillin, and 100 μg/mL streptomycin (Gibco).

extract_protocol:
Cells treated with either DMSO or CT7311 were crosslinked with 1% formaldehyde for 5 min at room temperature (RT), followed by quenching with 0.125 M glycine for 5 min at RT. Nuclei were extracted using a Lysis buffer (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100, and protease inhibitors) and then sonicated to an average DNA length 200 bp in Shearing buffer (10 mM Tris-HCl [pH 8.1], 0.1% SDS, 1 mM EDTA, and protease inhibitors) using Covaris E220 sonicator. The sonication settings were as follows: 5% duty cycle, 140 Watts peak power, 200 cycle per burst, for 10 min. Following sonication, the chromatin was supplemented with 1% Triton X-100 and 150 mM NaCl, then centrifuged. For each ChIP reaction, chromatin from ~ 10 million cells was incubated with an RPA32 antibody (FORTIS life science) at 4°C overnight. The following day, protein A/G agarose beads were added and incubated for 2 hours with rotation. The beads were subsequently washed with 4 times with the following buffers: Low salt wash buffer (20 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, protease inhibitors), High salt wash buffer (20 mM HEPES-KOH [pH 7.5], 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, protease inhibitors),  Low LiCl wash buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 1% IGEPAL CA-630, 1% Sodium deoxycholate, protease inhibitors), TE buffer (10 mM Tris-HCl [pH 8.0], 0.1 mM EDTA). ChIP and input samples were treated with RNase A and Proteinase K, and reverse crosslinking was performed by incubating at 65 °C overnight. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared by Azenta (Genewiz, NJ, USA).

treatment_protocol: MDA-MB-231 cells were treated with either DMSO or 10 nM CT7311 for 24 h.

value: Breast

value: Triple-negative breast cancer (TNBC) cells


title: k520_in_w_23d: Intestine 23-day old +/+


title: k608_6_in_w_4d: Intestine 4-day old +/+


city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

institute: National Cancer Institute

description:
Library name: Sample 12
mRNA-Seq of HEK293T Cells with siERN1 and Tunicamycin Treatments and OE of ERN1-ΔE18, Replicate 2

data_processing:
Raw FASTQ file reads were trimmed with Cutadapt tool and mapped with STAR aligner. Differential splicing analysis was performed using rMATS tool. Differential expression analysis was performed with DESeq2 tool.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with two sheets: (1) The Sheet 1 contains log2FoldChange (L2FC), pvalues, and adjusted pvalues (padj) from differential expression analysis with DESeq2 tool for all the genes for siERN1 rescue with overexpression of ERN1-FL/ERN1-ΔE18 constructs, along with Tunicamycin treatments and (2) Sheet 2 contains FPKM values for all the expressed genes in all the samples.
Supplementary files format and content: Tab delimited excel file with a single sheet containing PSI, ΔPSI and FDR values from differential splicing analysis with rMATS tool for all the significant exon skipping splicing events that were detected in the  siERN1 rescue with overexpression of ERN1-FL/ERN1-ΔE18 constructs, along with Tunicamycin treatments.

growth_protocol: HEK293T cells were maintained in Dulbecco’s Modified Eagle’s Medium (supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin).

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads.
Library construction was carried out following the TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HEK293T cells were transfected with siRNA targeting ERN1 with stable overexpression of either EV or ERN1-FL or ERN1-ΔE18. Forty-eight hours after transfection, the cells were treated with 10µg/mL of Tunicamycin or DMSO for 4h, before harvesting for total RNA extraction.

value: Human embryonic kidney cell line

value: siERN1, Tunicamycin


title: MDA-MB-231, CT7311-treated, RPA2-ChIP (biological replicate 1)

description: Library name: RPA2 ChIP_CT7311-1

value: WT


description:
Library name: Sample 11
mRNA-Seq of HEK293T Cells with siERN1 and Tunicamycin Treatments and OE of ERN1-ΔE18, Replicate 1


title: k502_5_in_m_4d: Intestine 4-day old W326R/+

value: Dnmt3a W326R/+


title: Colon tissue, loperamide-induced constipation model control, biol rep 8

description:
Library name: MC16
Group: MC

value: loperamide-induced constipation model + PBS gavage


title: k502_4_in_w_4d: Intestine 4-day old +/+

value: Dnmt3a +/+

value: intestine


description:
Library name: Sample 10
mRNA-Seq of HEK293T Cells with siERN1 and DMSO Treatments and OE of ERN1-ΔE18, Replicate 2

value: siERN1, DMSO


title: Colon tissue, loperamide-induced constipation model control, biol rep 7

description:
Library name: MC15
Group: MC

value: colon


title: MDA-MB-231, DMSO-treated, RPA2-ChIP (biological replicate 2)

description: Library name: RPA2 ChIP_DMSO-2

value: DMSO (24 h)


title: k502_3_in_m_4d: Intestine 4-day old W326R/+


description:
Library name: Sample 9
mRNA-Seq of HEK293T Cells with siERN1 and DMSO Treatments and OE of ERN1-ΔE18, Replicate 1


description:
Library name: Sample 8
mRNA-Seq of HEK293T Cells with siERN1 and Tunicamycin Treatments and OE of ERN1-FL, Replicate 2


title: k502_2_in_w_4d: Intestine 4-day old +/+


title: Colon tissue, loperamide-induced constipation model control, biol rep 6

description:
Library name: MC14
Group: MC


title: Colon tissue, loperamide-induced constipation model control, biol rep 5

description:
Library name: MC13
Group: MC


title: Colon tissue, loperamide-induced constipation model control, biol rep 4

description:
Library name: MC12
Group: MC


title: MDA-MB-231, CT7311-treated, Input

description: Library name: Input_CT7311-1


title: k608_1_in_m_4d: Intestine 4-day old W326R/+


description:
Library name: Sample 7
mRNA-Seq of HEK293T Cells with siERN1 and Tunicamycin Treatments and OE of ERN1-FL, Replicate 1


description:
Library name: Sample 6
mRNA-Seq of HEK293T Cells with siERN1 and DMSO Treatments and OE of ERN1-FL, Replicate 2


title: k464_bm_w_1y: Bone marrow 1-year old +/+

value: bone marrow


title: k463_bm_m_1y: Bone marrow 1-year old W326R/+


description:
Library name: Sample 4
mRNA-Seq of HEK293T Cells with siENR1 and Tunicamycin Treatments, Replicate 2


title: MDA-MB-231, DMSO-treated, RPA2-ChIP (biological replicate 1)

description: Library name: RPA2 ChIP_DMSO-1


title: MDA-MB-231, DMSO-treated, Input

description: Library name: Input_DMSO-1


title: MDA-MB-231 cells, TRIM27-KO, siPARP1, 48h, rep3

city: Zhengzhou City

first: Leixi

last: Cao

address: Zhengzhou University People's Hospital, Fengchan Road Subdistrict, Jinshui District, Zhengzhou City, Henan Province

institute: Zhengzhou University People's Hospital, Translational Medicine Research Center

description:
Library name: 6-3
Column name in raw_counts _All _Samples.txt:T27_KO_siP_3

data_processing:
Base-calling：Raw sequencing data were generated using the Illumina sequencing platform with standard base-calling procedures to produce raw reads in FASTQ format. Filtering (Quality control)：Raw reads were filtered using fastp (v0.23.2) to remove adapter sequences, reads without insert fragments caused by adapter self-ligation, low-quality bases with quality score < 20 at the 3′ end; reads containing any bases with quality score < 10 after trimming were discarded. Reads with > 10% ambiguous N bases and reads shorter than 20 bp after trimming were also removed to generate high-quality clean reads. Alignment：Clean reads were mapped to the corresponding reference genome using HISAT2 (v2.2.1) with optimized default parameters for eukaryotic transcriptome sequencing, and unqualified mapped reads were discarded. Generation of normalized abundance measurements：FeatureCounts (v2.0.3) was employed to calculate raw read counts for each gene, and gene expression levels were normalized to FPKM using StringTie (v2.2.1) to construct the gene expression matrix. Sample repeatability and data reliability were further evaluated via sample correlation analysis and principal component analysis (PCA). Differential expression analysis：Differential expression analysis was performed using DESeq2 (v1.38.3) with thresholds of |log2FC| > 1 and padj < 0.05. All data processing steps were performed by Frasergen Bioinformatics Co., Ltd. (Wuhan, China) following standard routine protocols for eukaryotic mRNA sequencing
Assembly: Homo sapiens GRCh38
Supplementary files format and content: gene_fpkm_all_samples.txt: Gene-level FPKM expression values across all samples.
Supplementary files format and content: transcript_fpkm_all_samples.txt: Transcript-level FPKM expression values across all samples.
Supplementary files format and content: total_gene_information.xls: Integrated gene-level file containing sample FPKM values, differential expression results (padj, log2FC, regulation status) for all pairwise comparisons, and comprehensive functional annotations (Nr, Swiss-Prot, KEGG, GO, eggNOG, Pfam, CAZy, SignalP, TMHMM) alongside gene identifiers.

source_name: Breast; Mammary gland

extract_protocol:
Total RNA was isolated from cultured cells using TRIzol reagent. RNA purity and concentration were routinely verified prior to subsequent library construction. Subsequently, 1 μg of high-quality total RNA was utilized to prepare mRNA sequencing libraries. Library sequencing and the following downstream bioinformatics analyses were performed by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).
mRNA was enriched from total RNA via oligo(dT) magnetic beads, followed by fragmentation and cDNA synthesis. The sequencing library was constructed through end repair, A-tailing, adapter ligation, and PCR amplification.

value: Breast; Mammary gland

value: epithelial cell

value: TRIM27 Knockout (TRIM27-KO)

value: siPARP1, 48h


title: MDA-MB-231 cells, TRIM27-KO, siPARP1, 48h, rep2

description:
Library name: 6-2
Column name in raw_counts _All _Samples.txt:T27_KO_siP_2


title: MDA-MB-231 cells, TRIM27-KO, siPARP1, 48h, rep1

description:
Library name: 6-1
Column name in raw_counts _All _Samples.txt:T27_KO_siP_1


title: Colon tissue, loperamide-induced constipation model control, biol rep 2

description:
Library name: MC10
Group: MC


description:
Library name: Sample 3
mRNA-Seq of HEK293T Cells with siERN1 and Tunicamycin Treatments, Replicate 1


description:
Library name: Sample 5
mRNA-Seq of HEK293T Cells with siERN1 and DMSO Treatments and OE of ERN1-FL, Replicate 1


title: MDA-MB-231 cells, TRIM27-WT, siPARP1, 48h, rep3

description:
Library name: 5-3
Column name in raw_counts _All _Samples.txt:T27_WT_siP_3

value: TRIM27 Wild-type (TRIM27-WT)


title: Colon tissue, loperamide-induced constipation model control, biol rep 3

description:
Library name: MC11
Group: MC


title: k462_bm_w_1y: Bone marrow 1-year old +/+


title: Colon tissue, normal control, biol rep 8

description:
Library name: NC8
Group: NC

value: normal control (PBS gavage)


title: k461_bm_m_1y: Bone marrow 1-year old W326R/+


description:
Library name: Sample 2
mRNA-Seq of HEK293T Cells with siERN1 and DMSO Treatments, Replicate 2

value: Human embryonic kidney cell line


title: MDA-MB-231 cells, TRIM27-WT, siPARP1, 48h, rep2

description:
Library name: 5-2
Column name in raw_counts _All _Samples.txt:T27_WT_siP_2


title: k460_bm_m_1y: Bone marrow 1-year old W326R/+


title: Colon tissue, normal control, biol rep 7

description:
Library name: NC7
Group: NC


title: Colon tissue, loperamide-induced constipation model control, biol rep 1

description:
Library name: MC9
Group: MC


title: MDA-MB-231 cells, TRIM27-WT, siPARP1, 48h, rep1

description:
Library name: 5-1
Column name in raw_counts _All _Samples.txt:T27_WT_siP_1


description:
Library name: Sample 1
mRNA-Seq of HEK293T Cells with siERN1 and DMSO Treatments, Replicate 1


title: k458_bm_w_1y: Bone marrow 1-year old +/+


title: MDA-MB-231 cells, TRIM27-KO, Olaparib, 24h, rep3

description:
Library name: 4-3
Column name in raw_counts _All _Samples.txt:T27_KO_Pi_3

value: Olaparib, 24h


title: Colon tissue, normal control, biol rep 6

description:
Library name: NC6
Group: NC


title: Colon tissue, normal control, biol rep 5

description:
Library name: NC5
Group: NC


description:
Library name: Sample 20
mRNA-Seq of HAP1 cells with PladB 24h Tunicamycin Replicate 2

data_processing:
Raw FASTQ file reads were trimmed with Cutadapt tool and mapped with STAR aligner. Differential splicing analysis was performed using rMATS tool. Differential expression analysis was performed with DESeq2 tool.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with multiple sheets containing log2FoldChange (L2FC), pvalue, and adjusted pvalues (padj) from differential expression analysis with DESeq2 tool for all the significant genes identified with different spliceosomal inhibitions. An additional sheet contains FPKM values for all the expressed genes in all the samples.
Supplementary files format and content: Tab delimited excel file with multiple sheets containing PSI, ΔPSI, Pvalue, and FDR values from differential splicing analysis with rMATS tool for all the significant exon skipping splicing events identified with different spliceosomal inhibitions along with Tunicamycin treatments.

growth_protocol: HAP1 cells were maintained in Dulbecco’s Modified Eagle’s Medium (supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin).

treatment_protocol: HAP1 cells were treated with Indisulam (10µM) and Pladienolide B (10nM) for 8h and 24h followed by treatment with either 10µg/mL of Tunicamycin or DMSO for 4h, before harvesting for total RNA extraction.

value: Near-haploid cell line derived from KBM-7 human CML cell line

value: PladB_24h, Tunicamycin


description:
Library name: Sample 19
mRNA-Seq of HAP1 cells with PladB 24h Tunicamycin Replicate 1


title: k542_bm_m_3m: Bone marrow 3-month old W326R/+

value: Dnmt3a W326R/+


title: k543_bm_m_3m: Bone marrow 3-month old W326R/+


title: MDA-MB-231 cells, TRIM27-KO, Olaparib, 24h, rep2

description:
Library name: 4-2
Column name in raw_counts _All _Samples.txt:T27_KO_Pi_2

treatment_protocol: For Olaparib treatment, cells were seeded at a density of 2×10⁵ cells per well in 6-well plates and allowed to adhere overnight. The next day, medium was replaced with fresh medium containing 2 μM Olaparib (or an equivalent volume of vehicle control, DMSO), and cells were incubated for 24 hours prior to RNA extraction. For PARP1 knockdown, cells were transfected with 100 pM PARP1-specific siRNA (or non-targeting control siRNA) using Lipofectamine RNAiMAX reagent, following the manufacturer's instructions. After 48 hours of incubation, cells were harvested for RNA isolation.


description:
Library name: Sample 18
mRNA-Seq of HAP1 cells with PladB 8h Tunicamycin Replicate 2

value: PladB_8h, Tunicamycin


title: MDA-MB-231 cells, TRIM27-WT, Olaparib, 24h, rep3

description:
Library name: 3-3
Column name in raw_counts _All _Samples.txt:T27_WT_Pi_3


title: k541_bm_m_3m: Bone marrow 3-month old W326R/+


title: Colon tissue, normal control, biol rep 4

description:
Library name: NC4
Group: NC


title: k536_bm_w_3m: Bone marrow 3-month old +/+

value: Dnmt3a +/+


title: MDA-MB-231 cells, TRIM27-KO, Olaparib, 24h, rep1

description:
Library name: 4-1
Column name in raw_counts _All _Samples.txt:T27_KO_Pi_1


description:
Library name: Sample 17
mRNA-Seq of HAP1 cells with PladB 8h Tunicamycin Replicate 1


title: Colon tissue, normal control, biol rep 3

description:
Library name: NC3
Group: NC


description:
Library name: Sample 16
mRNA-Seq of HAP1 cells with Indisulam 24h Tunicamycin Replicate 2

value: Indisulam_24h, Tunicamycin


title: Colon tissue, normal control, biol rep 2

description:
Library name: NC2
Group: NC

value: colon


title: MDA-MB-231 cells, TRIM27-WT, Olaparib, 24h, rep2

description:
Library name: 3-2
Column name in raw_counts _All _Samples.txt:T27_WT_Pi_2


title: k535_bm_w_3m: Bone marrow 3-month old +/+


title: Colon tissue, normal control, biol rep 1

description:
Library name: NC1
Group: NC


description:
Library name: Sample 15
mRNA-Seq of HAP1 cells with Indisulam 24h Tunicamycin Replicate 1


title: k529_bm_w_23d: Bone marrow 23-day old +/+


title: MDA-MB-231 cells, TRIM27-KO, rep3

description:
Library name: 2-3
Column name in raw_counts _All _Samples.txt:T27_KO_3


title: k528_bm_w_23d: Bone marrow 23-day old +/+


title: k534_bm_w_3m: Bone marrow 3-month old +/+


title: KO3

city: NEW YORK

first: LEVI

last: MANGARIN

state: NY

address: 413 E 69TH STREET

department: MEYER CANCER CENTER

institute: WEILL CORNELL MEDICINE

description: Library name: KO3

data_processing:
STAR v2.6.0
subread featureCounts v1.5.1
Assembly: GRCm38-2020-A
Supplementary files format and content: Tsv and matrix files

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen, QIACube). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA LT Kit following manufacturer's protocols.

value: tumor

value: Pmel

value: Sirpa-knockout (KO)


description:
Library name: Sample 14
mRNA-Seq of HAP1 cells with Indisulam 8h Tunicamycin Replicate 2

value: Indisulam_8h, Tunicamycin


description:
Library name: Sample 13
mRNA-Seq of HAP1 cells with Indisulam 8h Tunicamycin Replicate 1


title: MDA-MB-231 cells, TRIM27-KO, rep2

description:
Library name: 2-2
Column name in raw_counts _All _Samples.txt:T27_KO_2

value: Breast; Mammary gland

value: epithelial cell

value: TRIM27 Knockout (TRIM27-KO)


title: MDA-MB-231 cells, TRIM27-WT, Olaparib, 24h, rep1

description:
Library name: 3-1
Column name in raw_counts _All _Samples.txt:T27_WT_Pi_1

value: TRIM27 Wild-type (TRIM27-WT)


title: MDA-MB-231 cells, TRIM27-KO, rep1

description:
Library name: 2-1
Column name in raw_counts _All _Samples.txt:T27_KO_1


title: KO2

description: Library name: KO2


title: WT3

description: Library name: WT3

value: Sirpa-wild type (WT)


title: k526_bm_m_23d: Bone marrow 23-day old W326R/+

value: bone marrow


title: k519_bm_m_23d: Bone marrow 23-day old W326R/+


description:
Library name: Sample 11
mRNA-Seq of HAP1 cells with CTL Tunicamycin Replicate 1

value: Near-haploid cell line derived from KBM-7 human CML cell line

value: CTL, Tunicamycin


title: WT2

description: Library name: WT2


title: KO1

description: Library name: KO1


description:
Library name: Sample 12
mRNA-Seq of HAP1 cells with CTL Tunicamycin Replicate 2


title: MDA-MB-231 cells, TRIM27-WT,rep3

description:
Library name: 1-3
Column name in raw_counts _All _Samples.txt:T27_WT_3


title: k520_bm_w_23d: Bone marrow 23-day old +/+


title: k518_bm_m_23d: Bone marrow 23-day old W326R/+

value: Dnmt3a W326R/+


title: MDA-MB-231 cells, TRIM27-WT, rep2

description:
Library name: 1-2
Column name in raw_counts _All _Samples.txt:T27_WT_2


description:
Library name: Sample 9
mRNA-Seq of HAP1 cells with PladB 24h DMSO Replicate 1

value: PladB_24h, DMSO


description:
Library name: Sample 10
mRNA-Seq of HAP1 cells with PladB 24h DMSO Replicate 2


title: TIL_KO

description:
Library name: TIL_KO
10X Chromium v3 scRNAseq FASTQ

library_source: transcriptomic single cell

data_processing:
Cellranger v3.1.0
Assembly: GRCm38-2020-A
Supplementary files format and content: Tsv and matrix files

extract_protocol: 10X Chromium v3 library preparation