title: Tlr5fx/fx SPC-Cre + TLR5-agonist/bleomycin Rep S06

city: RTP

first: Thomas

last: Randall

address: 101 TW Alexander

institute: NIEHS

description: Library name: N219SE2RepS06

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were filtered based on a mean base quality score > 20, and adapters were trimmed by trim_galore
The raw reads were filtered by removing adaptor sequences, contamination and low-quality reads. Cleaned reads were mapped to mouse mm10 using STAR aligner
Subread featureCounts was applied for gene quantification based on the mouse refGene gene annotation available from UCSC Genome Browser website
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count from featureCounts and RPKM normalized counts for each sample

extract_protocol:
Animals were euthanized 36-hours post treatment, lungs were collected and digested as described in Sakamachi et al., 2025 (manuscript provisionally accepted). Briefly, alveolar type II cells were sorted, and RNA was isolated using the NucleoSpin RNA kit for RNA purification (Macherey-Nagel, Catalog# 740955.50). Each sample is comprised by a pool of 3 animals.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Following Barkauskas et al., 2013: SPC-Cre.ERT2 x ROSA-TOMATO mice were injected with Tamoxifen (0.25 mg/10 g to 2.5 mg/10 g body weight) by intraperitoneal administration, every other day for up to 4 treatments to induce TOMATO expression in SPC+ cells. Animals were rested for two-weeks following the final tamoxifen administration prior to bleomycin administration. Animals were treated with Bleomycin, TLR5-agonist/bleomycin, or antibiotics (ABX)/TLR5-agonist/bleomycin, as described in Sakamachi et al., 2025.

value: alveolar type II epithelial cells

value: Tlr5fx/fx SPC-Cre


title: Atherosclerotic plaques, late fibroatheroma (LFA), rep1

status: Public on Apr 03 2026

type: SRA

city: Shanghai

first: Yuanyuan

last: Wei

address: No. 130, Dong'an Road

country: China

institute: Fudan University

library_source: transcriptomic

data_processing:
Skewer software was used to remove splice sequences from the 3' end and low-quality fragments.
STAR software was used to align the sequences to the reference genome.
DEseq2 software was used for statistical differences.
StringTie software was used for transcript assembly.
rMATS software was used for alternative splicing events statistics.
Assembly: hg38
Supplementary files format and content: Raw counts of all genes (including mRNAs and lncRNAs) in the 13 samples
Supplementary files format and content: Raw counts of all transcripts (including mRNAs and lncRNAs) in the 13 samples

molecule: total RNA

organism: Homo sapiens

source_name: Carotid artery

extract_protocol:
Total RNAs were extracted using miRNeasy Mini Kit (Qiagen), followed by subsequent treatment with the RNase-Free DNase Set (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NR603, China) following manufacturer's protocols.

tag: tissue

value: Carotid artery

tag: condition

value: late fibroatheroma (LFA)


title: Tlr5fx/fx SPC-Cre + TLR5-agonist/bleomycin Rep S04

state: NC

country: USA

description: Library name: N219SE2RepS04

organism: Mus musculus

source_name: lung

value: lung

tag: cell type

tag: genotype

tag: treatment

tag: strain


title: Tlr5fx/fx SPC-Cre + bleomycin Rep S05

description: Library name: N219ControlRepS05

value: bleomycin


title: B. subtilis library, bicyclomycin-benzoate, before chloramphenicol selection

city: Cambridge

first: K Julia

last: Dierksheide

state: MA

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

description:
Library name: BCM_plus_preselection
Instrument: Singular Genomics G4

library_source: genomic

data_processing:
First, the paired-end sequencing reads were aligned to the B. subtilis (NC_000964.3) and E. coli (NC_000913.3) genome using the bowtie package (version 1.2.3)57. 40 nt of each read was used for alignment, and alignments with more than 1 mismatch or an insert size of more than 5,000 bp were discarded (bowtie arguments: -trim3 10 -v 1 -X 5000). Any two reads with the same aligned start and end position and UMI were collapsed to a single read. The number of unique reads mapping to each genomic fragment was calculated and normalized to the total number of reads in the sample. Reads mapping to the E. coli genome were combined and used for normalization to total reads in the enrichment calculations, but were not included in further analysis.
Assembly: B. subtilis (NC_000964.3) and E. coli (NC_000913.3)
Supplementary files format and content: Indicates UMI collapsed counts for each fragment in each sample. Fragments are characterized by the columns "fragment_start", "fragment_end", "fragment_strand", which indicate the start position of the aligned read 1, the end position of the aligned read 2, and the strand of the genome the fragment is derived from (+ or - for plus and minus strand). The fragment_id combines all of this information to create a unique identifier for each fragment. The UMI collapsed reads for each sample are in the corresponding columns. The total reads mapping to the E. coli genome in each sample are in the final column under fragment_id "1_4641652_Eco_."

molecule: genomic DNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Reporter library integrated at amyE

extract_protocol:
Sequencing libraries were prepared to quantify the frequency of each genomic fragment variant in the four experimental conditions. gDNA was extracted from the cell pellets using the Wizard Genomic DNA Purification kit (Promega) following manufacturer’s instructions. To reduce RNA contamination, the gDNA was then cleaned up with the genomic DNA clean and concentrator-10 (Zymo Research).
Libraries were generated using a two-step Q5 PCR protocol. To attach UMIs, a 2 cycle PCR was performed using 2 μg of gDNA per 150 μL PCR reaction (scaled as needed for library complexity) with primers oJD180/oJD182. This PCR reaction was cleaned up with two rounds of magnetic bead clean-up at a 1:1 ratio of beads to sample (PCRClean DX bead, Aline Biosciences). Half (pre-selection libraries) or one quarter (post-selection libraries) of this cleaned-up reaction was then amplified in a second PCR with primers oJD181/oJD183. The second PCR reaction was gel-purified using an 8% TBE gel. These libraries were sequenced with 50 bp paired-end reads on a G4 sequencer (Singular Genomics).

treatment_protocol: To perform chloramphenicol selection on the B. subtilis library to enrich for genomic fragments with transcription termination activity, the library was grown in LB for 5 generations, split into +BCM and DMSO control (−BCM) conditions for pre-treatment, and then back-diluted into selective media containing chloramphenicol and BCM or chloramphenicol and DMSO. To begin the initial outgrowth, a single glycerol stock was thawed, resuspended in warm LB, and back-diluted to OD600 0.006 in 50 mL warm LB. This starter culture was grown at 37°C with vigorous shaking to OD600 0.2. A second back-dilution to OD600 0.006 in 25 mL was then performed to pre-treat the cultures with bicyclomycin-benzoate (BCM) or a DMSO control. For this pre-treatment, cells were grown either in LB with 120 ng/mL BCM (+BCM treatment) or 2.5% DMSO (−BCM treatment). The pre-treatment cultures were then grown to OD600 0.2, at which point both cultures were harvested (pre-selection harvest). At the end of the +BCM pre-treatment, a small amount (3%) of residual chloramphenicol acetyltransferase is expected to remain in cells with inserts driving Rho termination, which may explain the slight increase in +BCM enrichment for these fragments relative to the non-terminated fragments (Fig. 1d). BCM concentration and pre-treatment duration were optimized using the kinB Rho termination site as a positive control. To begin the chloramphenicol selection, the BCM pre-treated culture (+BCM) was back-diluted to OD600 0.013 in 25 mL of LB with 5 μg/mL chloramphenicol and 120 ng/mL BCM, and the untreated culture (−BCM) was back-diluted to OD600 0.0075 in 25 mL of LB with 5 μg/mL chloramphenicol and 2.5% DMSO. The cultures were then grown with vigorous shaking at 37°C for 2.75 h before the post-selection harvest (OD600 0.24–0.27). To harvest cells, 11–14 mL of culture was pelleted at 4°C and then frozen in liquid nitrogen. Cell pellets were stored at −80°C until gDNA extraction. In total, cell pellets for four conditions were collected: +BCM culture before and after chloramphenicol selection; −BCM culture before and after chloramphenicol selection.

tag: cell line

value: Reporter library integrated at amyE

value: bicyclomycin-benzoate


title: B. subtilis library, wild-type background, before chloramphenicol selection

description: Library name: wt_preselection

data_processing:
First, the paired-end sequencing reads were aligned to the B. subtilis (NC_000964.3) and E. coli (NC_000913.3) genome using the bowtie package (version 1.2.3). 36 nt of each read was used for alignment, and alignments with more than 1 mismatch or an insert size of more than 5,000 bp were discarded (bowtie arguments: -trim3 10 -v 1 -X 5000). Any two reads with the same aligned start and end position and UMI (UMIs are present in the first 4nt of each index read) were collapsed to a single read. The number of unique reads mapping to each genomic fragment was calculated and normalized to the total number of reads in the sample. Reads mapping to the E. coli genome were combined and used for normalization to total reads, but were not included in further analysis.
Assembly: B. subtilis (NC_000964.3) and E. coli (NC_000913.3)
Supplementary files format and content: Indicates UMI collapsed counts for each fragment in each sample. Fragments are characterized by the columns "fragment_start", "fragment_end", "fragment_strand", which indicate the start position of the aligned read 1, the end position of the aligned read 2, and the strand of the genome the fragment is derived from (+ or - for plus and minus strand). The fragment_id combines all of this information to create a unique identifier for each fragment. The UMI collapsed reads for each sample are in the corresponding columns. The total reads mapping to the E. coli genome in each sample are in the final column under fragment_id "1_4641652_Eco_."

extract_protocol:
Sequencing libraries were prepared to quantify the frequency of each genomic fragment variant in the four experimental conditions. gDNA was extracted from the cell pellets using the Wizard Genomic DNA Purification kit (Promega) following manufacturer’s instructions.
To attach UMIs, a 2 cycle PCR was performed using 1.6 μg of gDNA per 100 μL PCR reaction (scaled as needed for library complexity) with primers oCEK071/oCEK083. This PCR reaction was then cleaned up with a DNA Clean & Concentrator-5 column, followed by a one-sided selection with a Select-a-Size DNA Clean & Concentrator MagBead Kit (Zymo Research) using a 260-bp cutoff, followed by a second clean up with the DNA Clean & Concentrator-5 column. This size-selected reaction was then amplified in a second PCR with primers oJT895/oCEK087. The second PCR reaction was concentrated using a DNA Clean & Concentrator-5 column, then gel-purified using an 8% TBE gel. These libraries were sequenced with 36-bp paired-end reads on a NextSeq500 (Illumina).

treatment_protocol: To perform chloramphenicol selection on the wild-type and Δrho B. subtilis libraries to enrich for genomic fragments with transcription termination activity, the libraries were grown in LB for ~10 doublings then back-diluted into selective media containing chloramphenicol. To begin the initial outgrowth, a single glycerol stock for each library was thawed and resuspended in 200 mL warm LB. These starter cultures were grown at 37°C with vigorous shaking to OD600 0.2. The wild-type and Δrho cultures were then back-diluted to OD600 0.003 and 0.015 in 200 mL warm LB, respectively.  Once the cultures reached OD600 0.2, they were harvested (pre-selection harvest). To begin the chloramphenicol selection, each culture was then back-diluted to OD600 0.002 in 100 mL of LB with 5 μg/mL chloramphenicol. The cultures were then grown with vigorous shaking at 37°C for 2.5 h and then harvested (post-selection harvest). To harvest cells, 11–14 mL of culture was pelleted at 4°C and then frozen in liquid nitrogen. Cell pellets were stored at −80°C until gDNA extraction.


title: Tlr5fx/fx SPC-Cre + bleomycin Rep S03

description: Library name: N219ControlRepS03


title: Atherosclerotic plaques, early fibroatheroma (EFA), rep4

value: early fibroatheroma (EFA)


title: B. subtilis library, DMSO,after chloramphenicol selection

description:
Library name: BCM_minus_postselection
Instrument: Singular Genomics G4

value: DMSO control


title: PNR_4_naive_cd4+_baseline

city: Bethesda

first: Michael

last: Sack

state: MD

address: 10 Center Dr

institute: NHLBI/NIH

description: Library name: SH8867_5

data_processing:
The RNA sequencing data was processed using default parameters with RNA-seek workflow (https://github.com/OpenOmics/RNA-seek)
preprocessing of the raw sequencing reads to remove low quality bases, adapters, and shorter reads using Cutadapt v1.18
alignment to human hg38 reference genome (GRCh38, Gencode Release 30) using STAR (v.2.7.6a) aligner in two-pass mapping mode
The gene expression counts estimated from number of reads mapping to each annotated gene using RSEM (v.1.3.3)
Assembly: hg38
Supplementary files format and content: tab-delimited file containing RSEM expected counts for each sample
Supplementary files format and content: differential expression results comparing NR vs baseline in activated CD4+ T cells
Supplementary files format and content: differential expression results comparing NR vs baseline in naive CD4+ T cells

source_name: PBMC

extract_protocol:
Total RNA from CD4+ T cells at baseline and after four weeks of Nicotinamide Riboside supplementation were extracted with the miRNeasy Micro Kit (Qiagen) and RNA quality and integrity was assessed by Qubit 3.0 fluorometer (Thermo Fisher Scientific) and Agilent Bioanalyzer (Agilent Technologies).
Libraries were prepared using TruSeq stranded Total RNA HT kit (Illumina) and sequenced in a HISeq 3000 (Illumina)

treatment_protocol: Study subjects were screened prior to signing consent and subjects were given a 4-week supplementation of Nicotinamide Riboside (250 mg bid)

value: PBMC

value: naive CD4+ T cells

tag: time

value: baseline


title: Atherosclerotic plaques, early fibroatheroma (EFA), rep2


title: B. subtilis library, DMSO, before chloramphenicol selection

description:
Library name: BCM_minus_preselection
Instrument: Singular Genomics G4


title: Atherosclerotic plaques, early fibroatheroma (EFA), rep1


title: dcl2 dcl3 dcl4 roots rep2

status: Public on Apr 02 2026

city: Versailles

first: Hervé

last: Vaucheret

country: France

institute: INRAE

description: Library name: 250625002_11

data_processing:
Trimming of the raw data has been performed with CutAdapt (parameter - error-rate = 0,02)
Trimmed reads were aligned to A.thaliana TAIR10 genome using ShortStack (parameter - mmap u). ShortStack produce the count table for the different features annotated in TAIR10. Raw count was then normalized in read-per-million (RPM) using R.
siRNA read count were extracted after alignment with Samtool by extracting 21nt- to 24nt-long reads with a MAPQ-score > 10 that did not mapped on annotated tRNA, miRNA and rRNA. siRNA raw read count were then normalized in RPM using R.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files with read count for each TAIR10 loci (one by sample)
Supplementary files format and content: tab-delimited text files with siRNA read count for each read length (21nt to 24nt) (one by sample)

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Plants were grown in vitro under short-day conditions and transferred in soil 20 days after germination (short-days conditions)

extract_protocol:
Leaves of 67 days-old plants were sampled and total RNA extracted.
Library construction has been realized by Singleron Biotechnologies. Small RNAs between 18nt and 30nt have been pre-sized using the BluePippin system and libraries prepared using the kit NEBNext Small RNA Library Prep Set for Illumina.

treatment_protocol: Six days after germination, plant were either let in vitro are grafted. In this case, roots of the indicated genotypes were grafted with WT L1 shoots.

value: roots

tag: transgenes

value: dcl2-1 dcl3-1 dcl4-2

value: non-grafted


title: Tlr5fx/fx SPC-Cre + TLR5-agonist/bleomycin Rep S02

description: Library name: N219SE2RepS02


title: dcl2 dcl3 dcl4 OE RTL1 roots rep2

description: Library name: 250625002_14


title: PNR_1_naive_cd4+_baseline

description: Library name: SH8867_1


title: sci-RNA-seq3_Arabidopsis_Day5_to_Day8_Biological_Replicate_1_Technical_Replicate_2

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_Day5_to_Day8_Biological_Replicate_1_Technical_Replicate_2
sci-RNA-seq3

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

molecule: nuclear RNA

source_name: leaf

growth_protocol: Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

value: leaf

tag: age

value: mature rosttes


title: Atherosclerotic plaques, early fibroatheroma (EFA), rep3


title: PNR_1_naive_cd4+_NR

description: Library name: SH8867_2

value: NR


title: Tlr5fx/fx SPC-Cre + bleomycin Rep S01

description: Library name: N219ControlRepS01

value: alveolar type II epithelial cells

value: Tlr5fx/fx SPC-Cre


title: dcl2 dcl3 dcl4 OE RTL1 roots rep1

description: Library name: 250625002_13


title: LCMV Clone 13, Day 21, sgKlf2, GEX

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description:
Library name: scMulti_Cl13D21_P14_sgKlf2_GEX
10x scMultiome-seq GEX library

data_processing:
FASTQ generation and alignment to mouse mm10 genome were performed using Cell Ranger ARC (10x Genomics) with the default settings.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: filtered_feature_bc_matrix.h5; atac_fragments.tsv.gz; atac_fragments.tsv.gz.tbi

source_name: Spleen

extract_protocol:
P14 CD8 T cells were sorted from spleens of LCMV Cl13-infected mice at day 21 p.i. Cells from 3-4 mice per condition were pooled (about 100,000 total). Nuclei were extracted per 10x protocol (CG000365).
scMultiome libraries were generated using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Libraries were constructed per manufacturer's instructions (CG000338).

value: Spleen

value: P14 CD8 T cells

value: CRISPR sgKlf2

tag: batch


title: dcl2 dcl3 dcl4 roots rep1

description: Library name: 250625002_10


title: dcl2 dcl3 dcl4 OE RTL1 roots rep3

description: Library name: 250625002_15


title: L1 leaves rep1

description: Library name: 250625002_16

source_name: leaves

value: leaves

value: p35S:GUS (L1)

value: WT


title: dcl2 dcl3 dcl4 roots rep3

description: Library name: 250625002_12


title: L1 leaves rep2

description: Library name: 250625002_17


title: L1 leaves rep3

description: Library name: 250625002_18


title: L1 roots rep3

description: Library name: 250625002_9


title: sci-RNA-seq3_Arabidopsis_HA_Stress_Biological_Replicate_2_and_3

description:
Library name: Arabidopsis_HA_Stress_Biological_Replicate_2_and_3
sci-RNA-seq3

growth_protocol: Plants were grown on hard agar (HA) stress at different stress levels

value: seedlings


title: L1 roots rep2

description: Library name: 250625002_8


title: L1 // dcl2 dcl3 dcl4 OE RTL1 roots rep3

description: Library name: 250625002_6

value: grafted


title: BAT_Stim1/2_fl/fl_room_temp_rep2

city: Berkeley

first: Gunes

last: Parlakgul

address: 119 Morgan Hall

department: Metabolic Biology and Nutrition

institute: University of California, Berkeley

description: Library name: 153L_TAG0238

data_processing:
Six-base pair unique molecular identifiers (UMIs) were extracted from single-end 100-bp reads using umi-tools v1.1.2.
Adapter sequences and low-quality bases (Q < 30) were removed using Trim Galore v0.6.7, and reads shorter than 30 bp after trimming were discarded.
Reads passing quality control were aligned to the mouse reference genome GRCm39 using STAR v2.7.10b with GENCODE  vM29.
PCR duplicates were removed using umi-tools v1.1.2 based on UMI information.
Gene-level read counts were generated using HTSeq-count from HTSeq v0.12.3.
Lowly expressed genes were filtered using filterByExpr in edgeR, and count data were normalized using the TMM method.
Differential expression analysis was performed using limma-voom, and multiple testing correction was performed using the Benjamini-Hochberg method.
Ingenuity Pathway Analysis was used to identify enriched pathways.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing raw gene counts for all samples.

source_name: Mouse brown adipose tissue, room temperature, control

growth_protocol: Mice were maintained at room temperature or exposed to cold (4°C) for 6 hours prior to tissue collection.

extract_protocol:
Brown adipose tissue was homogenized in TRIzol reagent using a TissueLyser. Following phase separation with chloroform and centrifugation, the aqueous phase was collected and mixed with ethanol. Total RNA was purified using the NucleoSpin RNA kit according to the manufacturer’s instructions and eluted in RNase-free water.
Libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) following manufacturer instructions.

value: Brown Adipose Tissue


title: L1 // dcl2 dcl3 dcl4 roots rep2

description: Library name: 250625002_2

value: roots


title: L1 // dcl2 dcl3 dcl4 roots rep1

description: Library name: 250625002_1

value: dcl2-1 dcl3-1 dcl4-2


title: BAT_Stim1/2_Adp-Cre_room_temp_rep1

description: Library name: 176R_TAG0238

source_name: Mouse brown adipose tissue, room temperature, KO


title: BAT_Stim1/2_Adp-Cre_cold_rep2

description: Library name: 164B_TAG0238

source_name: Mouse brown adipose tissue, cold exposure 6h, KO

value: cold


title: BAT_Stim1/2_Adp-Cre_room_temp_rep3

description: Library name: 152R_TAG0238


title: L1 // dcl2 dcl3 dcl4 OE RTL1 roots rep2

description: Library name: 250625002_5


title: L1 // dcl2 dcl3 dcl4 roots rep3

description: Library name: 250625002_3


title: BAT_Stim1/2_fl/fl_room_temp_rep1

description: Library name: 175RR_TAG0238


title: BAT_Stim1/2_Adp-Cre_cold_rep4

description: Library name: 168L_TAG0238


title: L1 roots rep1

description: Library name: 250625002_7

value: non-grafted


title: BAT_Stim1/2_fl/fl_cold_rep3

description: Library name: 167R_TAG0238

source_name: Mouse brown adipose tissue, cold exposure 6h, control


title: L1 // dcl2 dcl3 dcl4 OE RTL1 roots rep1

description: Library name: 250625002_4


title: BAT_Stim1/2_fl/fl_cold_rep2

description: Library name: 166N_TAG0238


title: BAT_Stim1/2_Adp-Cre_cold_rep3

description: Library name: 165RR_TAG0238


title: BAT_Stim1/2_Adp-Cre_room_temp_rep2

description: Library name: 178B_TAG0238


title: ATAC HIRAfl/fl_Tbg-Cre_female_rep1

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: Library name: sample 3

data_processing:
Reads were trimmed using Cutadapt v2.3 and then aligned against chrM mm10 using Bowtie2.
Duplicate reads were removed using Picard MarkDuplicates v2.22.0.
MACS2 v2.2.9.1 was used to call peaks.
Reproducible peaks for replicates (n=2) were determined using IDR v2.0.4.2.
Differential accessibility of peaks were tested using edgeR v3.38.4
Assembly: mm10
Supplementary files format and content: genome track files as bigWig

source_name: liver

extract_protocol:
DNA was extracted from cells using the ATAC-seq kit (Active Motif, 53150)
ATAC libraries were prepared using the ATAC-seq kit (Active Motif, 53150) following the manufacturer's protocol.

treatment_protocol: Virus suspension was injected at a dose of 3.33 x 1011 viral genomes per mouse in 100 µl sterile PBS retro-orbitally.

value: liver

value: HIRA fl/fl

value: AAV8 Tbg-Cre


title: BAT_Stim1/2_fl/fl_cold_rep1

description: Library name: 160L_TAG0238


title: BAT_Stim1/2_Adp-Cre_cold_rep1

description: Library name: 161B_TAG0238


title: ATAC WT_Tbg-Cre_female_rep2

description: Library name: sample 2

value: wildtype


title: BAT_Stim1/2_fl/fl_cold_rep4

description: Library name: 171L_TAG0238


title: WT_CRISPR_sgHIRA_female_6months_rep5

description: Library name: sample 20

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: mm10
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene

molecule: polyA RNA

extract_protocol:
RNA was extracted from tissue using a bead homogenizer with TRIzol and Direct-zol RNA MiniPrep Plus kits (Zymo R2072).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).


title: WT_CRISPR_sgHIRA_female_6months_rep4

description: Library name: sample 19


title: WT_CRISPR_sgHIRA_female_6months_rep2

description: Library name: sample 17


title: ATAC HIRAfl/fl_Tbg-Cre_female_rep2

description: Library name: sample 4


title: WT_CRISPR_sgHIRA_female_6months_rep3

description: Library name: sample 18


title: WT_CRISPR_sgHIRA_female_3weeks_rep1

description: Library name: sample 6


title: WT_CRISPR_sgRosa26_female_6months_rep5

description: Library name: sample 15


title: WT_CRISPR_sgRosa26_female_3weeks_rep5

description: Library name: sample 5


title: WT_CRISPR_sgHIRA_female_3weeks_rep3

description: Library name: sample 8


title: ATAC WT_Tbg-Cre_female_rep1

description: Library name: sample 1


title: WT_CRISPR_sgRosa26_female_6months_rep4

description: Library name: sample 14


title: WT_CRISPR_sgHIRA_female_3weeks_rep2

description: Library name: sample 7


title: WT_CRISPR_sgHIRA_female_3weeks_rep5

description: Library name: sample 10


title: WT_CRISPR_sgRosa26_female_6months_rep1

description: Library name: sample 11


title: WT_CRISPR_sgHIRA_female_6months_rep1

description: Library name: sample 16


title: WT_CRISPR_sgHIRA_female_3weeks_rep4

description: Library name: sample 9


title: WT_CRISPR_sgRosa26_female_3weeks_rep3

description: Library name: sample 3


title: WT_CRISPR_sgRosa26_female_6months_rep3

description: Library name: sample 13


title: WT_CRISPR_sgRosa26_female_3weeks_rep2

description: Library name: sample 2


title: WT_CRISPR_sgHIRA_male_after_rep2

description: Library name: sample 16


title: WT_CRISPR_sgRosa26_female_3weeks_rep4

description: Library name: sample 4


title: WT_CRISPR_sgRosa26_female_6months_rep2

description: Library name: sample 12


title: WT_CRISPR_sgHIRA_male_after_rep1

description: Library name: sample 15


title: HIRAfl/fl_Tbg-Cre_male_after_rep1

description: Library name: sample 13


title: WT_CRISPR_sgRosa26_male_after_rep1

description: Library name: sample 11


title: WT_CRISPR_sgHIRA_male_before_rep2

description: Library name: sample 8


title: WT_Tbg-Cre_male_after_rep2

description: Library name: sample 10


title: HIRAfl/fl_Tbg-Cre_male_after_rep2

description: Library name: sample 14


title: WT_Tbg-Cre_male_after_rep1

description: Library name: sample 9


title: WT_Tbg-Cre_female_rep3

description: Library name: sample 18


title: WT_CRISPR_sgRosa26_male_before_rep1

description: Library name: sample 3


title: WT_Tbg-Cre_male rep3

description: Library name: sample 15


title: WT_Tbg-Cre_female_rep2

description: Library name: sample 17


title: HIRAfl/fl_Tbg-Cre_male_before_rep2

description: Library name: sample 6


title: WT_CRISPR_sgHIRA_male_before_rep1

description: Library name: sample 7


title: WT_CRISPR_sgRosa26_female_3weeks_rep1

description: Library name: sample 1


title: WT_CRISPR_sgRosa26_male_before_rep2

description: Library name: sample 4


title: WT_Tbg-Cre_male rep1

description: Library name: sample 13


title: HIRAfl/fl_Tbg-Cre_male_before_rep1

description: Library name: sample 5


title: WT_CRISPR_sgRosa26_male_after_rep2

description: Library name: sample 12


title: WT_Tbg-Cre_female_rep1

description: Library name: sample 16


title: WT_Tbg-Cre_male_before_rep2

description: Library name: sample 2


title: HIRAfl/fl_MCS_female_rep3

description: Library name: sample 12

value: AAV8 Tbg-MCS


title: WT_Tbg-Cre_male rep2

description: Library name: sample 14


title: WT_Tbg-Cre_male_before_rep1

description: Library name: sample 1


title: HIRAfl/fl_MCS_female_rep2

description: Library name: sample 11


title: HIRAfl/fl_MCS_male_rep2

description: Library name: sample 8


title: HIRAfl/fl_MCS_female_rep1

description: Library name: sample 10


title: HIRAfl/fl_MCS_male_rep1

description: Library name: sample 7


title: HIRAfl/fl_Tbg-Cre_female_rep3

description: Library name: sample 6


title: HIRAfl/fl_Tbg-Cre_male_rep2

description: Library name: sample 2


title: HIRAfl/fl_Tbg-Cre_male_rep1

description: Library name: sample 1


title: HIRAfl/fl_Tbg-Cre_male_rep3

description: Library name: sample 3


title: HIRAfl/fl_Tbg-Cre_female_H3.3_rep2

description: Library name: sample 17

data_processing:
Raw reads were aligned to mm10 using bowtie2
Duplicates were removed using Picard MarkDuplicates
Signal was normalized by uniquely aligned non-duplicated E.coli spike-in reads
Assembly: mm10
Supplementary files format and content: E.coli spike-in normalized bigWig files
Library strategy: CUT&Tag

extract_protocol:
DNA was extracted from cells using the Cut&Tag-IT kit (Active Motif, 53160, 53165)
Cut&Tag libraries were prepared using the Cut&Tag-IT kit (Active Motif, 53150) following the manufacturer's protocol.


title: HIRAfl/fl_Tbg-Cre_female_rep1

description: Library name: sample 4


title: HIRAfl/fl_Tbg-Cre_female_H3.3_rep1

description: Library name: sample 16


title: HIRAfl/fl_MCS_male_rep3

description: Library name: sample 9


title: WT_Tbg-Cre_female_H3.3_rep1

description: Library name: sample 13


title: HIRAfl/fl_Tbg-Cre_female_H3.3_rep3

description: Library name: sample 18


title: HIRAfl/fl_Tbg-Cre_female_rep2

description: Library name: sample 5


title: HIRAfl/fl_Tbg-Cre_female_H3K36me3_rep1

description: Library name: sample 10


title: WT_Tbg-Cre_female_H3K36me3_rep3

description: Library name: sample 9


title: WT_Tbg-Cre_female_H3.3_rep3

description: Library name: sample 15


title: WT_Tbg-Cre_female_H3.3_rep2

description: Library name: sample 14


title: HIRAfl/fl_Tbg-Cre_female_H3K27ac_rep3

description: Library name: sample 6


title: HIRAfl/fl_Tbg-Cre_female_H3K36me3_rep2

description: Library name: sample 11


title: HIRAfl/fl_Tbg-Cre_female_H3K36me3_rep3

description: Library name: sample 12


title: WT_Tbg-Cre_female_H3K36me3_rep2

description: Library name: sample 8


title: WT_Tbg-Cre_female_H3K36me3_rep1

description: Library name: sample 7


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep2

description: Library name: sample 8


title: WT_Tbg-Cre_female_H3K27ac_rep1

description: Library name: sample 1


title: WT_Tbg-Cre_male_rep2

description: Library name: sample 2


title: WT_Tbg-Cre_male_rep1

description: Library name: sample 1


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep4

description: Library name: sample 10


title: HIRAfl/fl_Tbg-Cre_female_H3K27ac_rep1

description: Library name: sample 4


title: H3f3afl/fl_H3f3bfl/fl_MCS_male_rep3

description: Library name: sample 6


title: HIRAfl/fl_Tbg-Cre_female_H3K27ac_rep2

description: Library name: sample 5


title: WT_Tbg-Cre_female_H3K27ac_rep3

description: Library name: sample 3


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep3

description: Library name: sample 9


title: WT_Tbg-Cre_female_H3K27ac_rep2

description: Library name: sample 2


title: H3f3afl/fl_H3f3bfl/fl_MCS_male_rep1

description: Library name: sample 4


title: WT_Tbg-Cre_male_rep3

description: Library name: sample 3


title: HCC827 with CAFs

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

description: Library name: Sample 8

data_processing:
CLC Genomics Workbench 21.0.5
RNA-Seq Analysis tool was used by default parameter setting.
Assembly: Homo_sapiens_refseq_GRCh38.p13_no_alt_analysis_set
Supplementary files format and content: Each Excel file includes both RPM and raw count values

source_name: HCC827 with CAFs

growth_protocol: NSCLC cells or NSCLC cells and CAFs were mainhtained RPMI supplementede with 5% FBS with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from NSCLC cells using RNeasy Mini Kit (Qiagen, Venlo, Netherlands), and RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA).
RNA-seq libraries were prepared using NEBNext rRNA Depletion Kit (NEB, MA, USA) and MGIEasy RNA Directional Library Prep Set (MGI Tech, Shenzhen, Guangdong, China), according to the manufacturer’s instructions. The library samples were sent to Genome-Lead Co., Ltd. (Takamatsu, Japan) for RNA-seq analysis (DNBSEQ-G400RS, MGI)) using a 2 × 150-bp paired-end protocol. All sequence reads were converted to FASTQ format using Bcl-2fastq.

treatment_protocol: NSCLC cells or NSCLC cells and CAFs were incubated for 48h.

value: HCC827 with CAFs

value: NSCLC cell line

value: co-culture with CAFs


title: H3f3afl/fl_H3f3bfl/fl_MCS_male_rep2

description: Library name: sample 5


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep1

description: Library name: sample 7


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_H3.3_rep1

description: Library name: sample 2

value: H3f3afl/fl; H3f3bfl/fl


title: HCC827

description: Library name: Sample 7

value: WT


title: H1975 with CAFs

description: Library name: Sample 6

source_name: H1975 with CAFs

value: H1975 with CAFs


title: WT_Tbg-Cre_male_H3.3_rep1

description: Library name: sample 1


title: mouse-tumor,OD10_3

city: Beijing

first: Xingru

last: Tan

address: No. 1 Shuaifuyuan, Dongcheng District, Beijing

institute: peking union medical college

description:
Library name: sample45
TOD103

data_processing:
2. Bioinformatics Analysis  2.1 Data Quality Control Raw reads were first processed using fastp software. In this step, clean reads were obtained by removing reads containing adapters, poly-N, and low-quality reads from the raw data. Meanwhile, Q20, Q30, and GC content of the clean data were calculated. All downstream analyses were based on these high-quality clean data.  2.2 Sequence Alignment to the Reference Genome The reference genome and gene model annotation files were downloaded from a genome website. An index of the reference genome was constructed using HISAT2 (v2.2.1), and paired-end clean reads were aligned to the reference genome using HISAT2. HISAT2 can generate a database of splice junctions based on the gene model annotation file, offering better alignment performance than other non-splice-aware aligners.  2.3 Novel Transcript Prediction StringTie (v2.2.3) was used for novel gene prediction. StringTie applies a network flow algorithm and optional de novo assembly to assemble transcripts. Compared to software such as Cufflinks, StringTie offers the following advantages: (1) assembles more complete transcripts; (2) assembles more accurate transcripts; (3) provides better estimation of transcript expression levels; (4) faster assembly speed.  2.4 Quantification of Gene Expression Levels featureCounts (v2.0.6) was used to count the reads mapped to each gene. Then, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene was calculated based on gene length and the read count mapped to the gene. FPKM considers the effects of both sequencing depth and gene length on read counts and is currently the most commonly used method for estimating gene expression levels.  2.5 Differential Expression Analysis For samples with biological replicates: Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (v1.42.0). DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg approach to control the false discovery rate. Genes with padj <= 0.05 and |log2(fold change)| >= 1 were considered significantly differentially expressed. For samples without biological replicates:Before differential gene expression analysis, read counts were adjusted for each sequencing library using scaling normalization factors with the edgeR R package (v4.0.16) to eliminate differences in sequencing depth between samples. Differential expression analysis was then performed. The resulting P-values were adjusted using the Benjamini and Hochberg approach to control the false discovery rate. Genes with padj <= 0.05 and |log2(fold change)| >= 1 were considered significantly differentially expressed.  2.6 GO and KEGG Enrichment Analysis of Differentially Expressed Genes GO enrichment analysis of differentially expressed genes was performed using the clusterProfiler (v4.8.1) software, which corrects for gene length bias. GO terms with an adjusted P-value < 0.05 were considered significantly enriched by differentially expressed genes. KEGG is a database resource for understanding high-level functions and utilities of biological systems, such as cells, organisms, and ecosystems, from molecular-level information, particularly large-scale molecular datasets generated by genome sequencing and other high-throughput technologies. Statistical enrichment of differentially expressed genes in KEGG pathways was analyzed using the clusterProfiler software.  2.7 Gene Set Enrichment Analysis (GSEA) Gene Set Enrichment Analysis (GSEA) does not require specifying a threshold for differentially expressed genes. It uses predefined gene sets (usually derived from functional annotations or previous experimental results), ranks genes based on their differential expression between two classes of samples, and tests whether the predefined gene sets are enriched at the top or bottom of this ranked list. GSEA detects expression changes of gene sets rather than individual genes, thus capturing subtle expression changes and potentially yielding more insightful results. GSEA was performed on GO and KEGG datasets for this species using the local version of the GSEA tool (http://www.broadinstitute.org/gsea/index.jsp).  2.8 Protein-Protein Interaction (PPI) Network Analysis of Differentially Expressed Genes PPI analysis of differentially expressed genes was based on the STRING database, which contains known and predicted protein-protein interactions. For species present in the database, the network was constructed by extracting the target gene list from the database. Otherwise, target gene sequences were aligned to selected reference protein sequences using DIAMOND, and the network was constructed based on the known interactions of the chosen reference species.  2.9 Alternative Splicing Analysis Alternative splicing is an important mechanism for regulating gene expression and protein diversity. rMATS (v4.3.0) was used to analyze alternative splicing (AS) events, mainly including five types: Skipped Exon (SE), Retained Intron (RI), Mutually Exclusive Exons (MXE), Alternative 5' Splice Site (A5SS), and Alternative 3' Splice Site (A3SS).  2.10 SNP Analysis Variant calling was performed on the sample data using the GATK (v4.6.0.0) software.  2.11 Weighted Gene Co-expression Network Analysis (WGCNA) Weighted Gene Co-expression Network Analysis (WGCNA) is a systems biology method for describing gene association patterns among different samples. It can be used to identify modules of highly co-expressed genes and to identify candidate biomarker genes or therapeutic targets based on the interconnectivity of gene sets and the association between gene sets and phenotypes. The WGCNA R package (v1.71) is a comprehensive collection of functions for performing various weighted correlation network analyses, including network construction, gene selection, module identification, topological property calculation, data simulation, and visualization. WGCNA is suitable for datasets with multiple samples, typically requiring more than 15 samples. Better results are achieved with more than 20 samples; the more samples, the more stable the results. The input files include a sample information file (a matrix describing sample traits: traits used for correlation analysis must be numeric; for categorical variables, they should be converted into a 0-1 matrix) and a gene expression data file (for transcriptome sequencing, FPKM values can be used).
Assembly: （Mus musculus）GRCm38
Supplementary files format and content: Format: .txt Content: 1、all_compare_LN.txt: Rows represent gene identifiers (Ensembl Gene ID).Columns represent individual lymph node samples. Includes FPKM values for all genes across all samples, log2FC, pvalue, padj for each gene. 2、all_compare_tumor.txt: Rows represent gene identifiers (Ensembl Gene ID).Columns represent individual tumor samples. Includes FPKM values for all genes across all samples, log2FC, pvalue, padj for each gene.

source_name: tumor

extract_protocol:
Total RNA was isolated from mouse tumor and lymph node tissues (including popliteal and inguinal lymph nodes) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Briefly, tissues were homogenized in 1 mL of TRIzol reagent, followed by chloroform phase separation. RNA was precipitated from the aqueous phase with isopropanol, washed with 75% ethanol, and then dissolved in RNase-free water.
1.Library Construction and Quality Control.Conventional Library Construction:mRNA was enriched from total RNA using Oligo(dT) magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. After end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification, the library was constructed. Library quantification was performed using a Qubit fluorometer and real-time quantitative PCR (qPCR), and the fragment size distribution was assessed using a Bioanalyzer. Strand-Specific Library Construction:mRNA was enriched from total RNA using Oligo(dT) magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers. Subsequently, second-strand cDNA was synthesized with dUTP substituting for dTTP. After end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification, the directional library was constructed.Library quantification was performed using a Qubit fluorometer and real-time quantitative PCR (qPCR), and the fragment size distribution was assessed using a Bioanalyzer.

value: tumor

value: Tumor cells


title: H1975

description: Library name: Sample 5


title: mouse-tumor,OD10_1

description:
Library name: sample43
TOD101


title: mouse-tumor,OD7_1

description:
Library name: sample40
TOD71


title: PC9

description: Library name: Sample 1


title: mouse-tumor,OD3_3

description:
Library name: sample38
TOD33


title: mouse-tumor,OXA_3

description:
Library name: sample35
TOXA3


title: mouse-tumor,OD7_2

description:
Library name: sample41
TOD72


title: AP-Seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

city: Paris

first: Anton

last: Granzhan

address: 45 rue des Saints-Pères

department: UMR8601 LCBPT

institute: Université Paris Cité

description: Library name: Rep3 M2 AP Seq

data_processing:
Data management, quality control, and primary analysis were carried out by the Institut Curie Bioinformatics platform.
Unless stated otherwise, data processing was performed using DeepTools following key tools, including BigwigCompare, multiBigwigSummary, plotCorrelation, computeMatrix, and plotProfile. The BigwigCompare tool was used to calculate the relative enrichment of AP sites by comparing the BigWig file of the enriched sample against the input. This comparison was performed using a log2 transformation across various bin sizes: 100bp, 1kb, 10kb, 100kb, and 1Mb. The resulting relative enrichment files were then processed with multiBigwigSummary to generate a matrix, which was subsequently subjected to statistical correlation analysis using Pearson or Spearman correlation. Data were visualized with the Integrative Genomics Viewer version 2.17.2 (http://software.broadinstitute.org/software/igv/). Genome-wide feature sets were obtained from the UCSC Genome Browser. Chromatin features for HepG2 cells were retrieved from the data repository generated in the context of the ENCODE consortium
BigWig files were generated using the GenomicRanges package in R, where scores correspond to normalized fragment coverage across genomic coordinates. Peaks were identified using MACS2 (v2) with default parameters, and reported in narrowPeak format, representing enriched regions of binding.
AP site enrichment was analyzed with DeepTools using BigwigCompare (log2-transformed, 100 bp–1 Mb bins), multiBigwigSummary for correlation with samples and HepG2 histone marks, and computeMatrix for distribution across genomic features (TSS, TTS, 5′/3′UTRs). Visualization was done with plotCorrelation, plotProfile, and IGV.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: HepG2 were purchased from ATCC and cultivated at 37 °C and 5% CO2 in Dulbecco’s modified Eagle medium (Gibco DMEM+GlutaMax, ThermoFisher, cat. n° 31966021) supplemented with 1% penicillin/ streptomycin, and 10% heat-inactivated fetal bovine serum (FBS) in 75-T flask. Cells were harvested using 1X trypsin (Gibco TrypLE Express, ThermoFisher, cat. n° 12605-010,) and, when needed, cell washing was done using 1X DPBS (Gibco, ThermoFisher, cat. n° 14190-094).

extract_protocol:
Total genomic DNA was extracted from washed cell pellets using the DNeasy Blood & Tissue Kit (Qiagen, cat. n° 69506), following the manufacturer's instructions with slight modifications. Briefly, each washed cell pellet was resuspended in 200 µL of fresh, cold PBS. To this, 4 µL of RNase A (Qiagen, cat. n° 19101) was added, and the mixture was incubated at room temperature for 2 minutes. Subsequently, 20 µL of Proteinase K (Qiagen, cat. n° 19131) and 200 µL of Buffer AL (without ethanol) were added, and the mixture was thoroughly mixed and incubated at 37 °C for 10 minutes. After incubation, samples were vortexed until homogeneous, and 200 µL of cold absolute ethanol was added to precipitate the DNA. The mixture was transferred to a spin column and centrifuged at 6000 × g for 1 minute at 4 °C. The flow-through was discarded, and the column was washed with 500 µL of Buffer AW1, followed by centrifugation at 6000 × g for 1 min at 4 °C. A second wash was performed using 500 µL of Buffer AW2, followed by centrifugation at 20,000 × g for 3 min at 4 °C to ensure complete drying. Each wash was done in a new Eppendorf tube. Genomic DNA was then eluted by adding 150–200 µL of sterile water to the column, incubating at room temperature for 3 minutes, and centrifuging at 6000 × g for 1 min at 4 °C. DNA concentration and purity (A260 / A280 > 1.8) were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific). Throughout the extraction process, samples were kept on ice until processed for DNA-adduct formation analysis.
Library preparation and sequencing were performed by the Institut Curie NGS platform. ChIP-seq libraries were prepared using a 150-bp paired-end (PE150) protocol with the KAPA Biosystems library preparation kit (Ref. No. 07962363001). Sequencing was carried out on the Illumina NextSeq 2000 system in PE150 mode, using P1, P2, or P3 flow cell formats depending on the sequencing run. Data generated from different flow cells were subsequently combined. Briefly, fragmented DNA underwent end-repair and A-tailing in a single enzymatic step by incubation with End Repair & A-Tailing Buffer and Enzyme Mix at 20°C for 30 minutes, followed by 65°C for 30 minutes. Adapter ligation was then performed at 20°C for 15 minutes using KAPA dual-indexed adapters. Post-ligation cleanup was conducted using a 0.8× volume of KAPA HyperPure Beads. Libraries were optionally amplified by PCR using KAPA HiFi HotStart ReadyMix with 14–15 cycles, depending on the input DNA amount. Amplified libraries underwent a second bead-based cleanup, and final elution was performed in H₂O. Library quality and concentration were assessed using Qubit fluorometry and a Bioanalyzer to confirm fragment size distribution and ensure suitability for Illumina sequencing. High-throughput sequencing was performed by the ICGex NGS platform at Institut Curie.

treatment_protocol: To prepare samples for APX-seq and AP-seq, approximately 3–4 × 10⁶ cells were initially seeded in a T-75 flask and cultured for 3–4 days to reach a final count of approximately 9–12 × 10⁶ cells. These were then divided into four groups: untreated, two MMS-treated groups, and X-ray irradiated group. For the MMS-treated groups, cells were incubated for 1 hour in pre-warmed DMEM containing either 5 mM or 10 mM MMS. For the X-ray irradiated group, cells were exposed to 6 Gy of X-ray using an X-RAD 320 Dx irradiator (320 kV), followed by a 30-minute incubation. The untreated control group was maintained in DMEM and processed in parallel, following identical washing and harvesting steps. Following treatment or incubation, the medium was removed and cells were washed with 10 mL of pre-warmed 1X DPBS. Cells were then harvested using 5 mL of 1X trypsin and incubated for 10 minutes at 37°C until fully detached. To neutralize the trypsin, 5 mL of pre-warmed fresh DMEM was added, resulting in a total volume of 10 mL. Cell counts were recorded, and the suspensions were centrifuged at 1200 rpm for 5 minutes. The resulting cell pellets were transferred to 1.5 mL Eppendorf tubes and washed twice with 1 mL of cold 1X PBS, centrifuging at 1200 rpm for 5 minutes at 4 °C each time. The final washed cell pellets were kept on ice and immediately processed for genomic DNA extraction.

value: Human hepatocellular carcinoma

value: 10 mM MMS 1h

value: Replicate 3


title: Input DNA control for AP-Seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 AP input

value: 5 mM MMS 1h


title: PC9 with CAFs

description: Library name: Sample 2

source_name: PC9 with CAFs

value: PC9 with CAFs


title: H1299 with CAFs

description: Library name: Sample 4

source_name: H1299 with CAFs

value: H1299 with CAFs


title: mouse-tumor,OD7_3

description:
Library name: sample42
TOD73


title: mouse-tumor,OD10_2

description:
Library name: sample44
TOD102


title: mouse-tumor,OXA_2

description:
Library name: sample34
TOXA2


title: mouse-tumor,OD3_1

description:
Library name: sample36
TOD31


title: Input DNA control for AP-Seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR AP input

value: 6 Gy X-ray 30min


title: mouse-tumor,OD3_4

description:
Library name: sample39
TOD34


title: Input DNA control for AP-Seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 AP input


title: AP-Seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR AP Seq


title: mouse-tumor,OD3_2

description:
Library name: sample37
TOD32


title: AP-Seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 AP Seq


title: Input DNA control for AP-Seq in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C AP input


title: mouse-tumor,OXA_1

description:
Library name: sample33
TOXA1


title: AP-Seq of AP sites in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C AP Seq


title: mouse-tumor,DC_5

description:
Library name: sample32
TDC5


title: mouse-tumor,DC_4

description:
Library name: sample31
TDC4


title: mouse-tumor,DC_3

description:
Library name: sample30
TDC3


title: mouse-tumor,CON_5

description:
Library name: sample28
TCON5


title: AP-Seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR AP Seq

value: Replicate 2


title: AP-Seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 AP Seq


title: mouse-tumor,DC_2

description:
Library name: sample29
TDC2


title: Input DNA control for AP-Seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 AP input


title: Input DNA control for AP-Seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 AP input


title: AP-Seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 AP Seq


title: Input DNA control for AP-Seq in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C AP input


title: mouse-FLN,YF,CON_1

description:
Library name: sample25
FLNdd1

source_name: Lymph Nodes

value: Lymph Nodes

value: Lymphocytes


title: mouse-tumor,CON_4

description:
Library name: sample27
TCON4


title: mouse-FLN,YF,d10_1

description:
Library name: sample24
FLNc1


title: Input DNA control for AP-Seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR AP input


title: mouse-FLN,YF,d7_1

description:
Library name: sample23
FLNb1


title: Input DNA control for AP-Seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR AP input

value: Replicate 1


title: mouse-tumor,CON_1

description:
Library name: sample26
TCON1


title: AP-Seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR AP Seq


title: AP-Seq of AP sites in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C AP Seq


title: mouse-FLN,YF,d3_1

description:
Library name: sample22
FLNa1


title: mouse-PLN,YF,CON_1

description:
Library name: sample21
PLNdd1


title: Input DNA control for AP-Seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 AP input


title: AP-Seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 AP Seq


title: H1299

description: Library name: Sample 3

value: NSCLC cell line


title: mouse-PLN,YF,d7_1

description:
Library name: sample19
PLNb1


title: AP-Seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 AP Seq


title: mouse-PLN,YF,d3_1

description:
Library name: sample18
PLNa1


title: mouse-FLN,OD10_1

description:
Library name: sample16
FLN71


title: Input DNA control for AP-Seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 AP input


title: Input DNA control for AP-Seq in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C AP input


title: mouse-FLN,OD3_1

description:
Library name: sample14
FLN41


title: APX-seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR APX Seq


title: mouse-PLN,YF,d10_1

description:
Library name: sample20
PLNc1


title: Input DNA control for APX-seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR APX input


title: mouse-FLN,OD7_1

description:
Library name: sample15
FLN61


title: mouse-FLN,OD14_1

description:
Library name: sample17
FLN81


title: APX-seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 APX Seq


title: AP-Seq of AP sites in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C AP Seq


title: Input DNA control for APX-seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 APX input


title: Input DNA control for APX-seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 APX input


title: mouse-PLN,OD14_1

description:
Library name: sample12
PLN81


title: mouse-PLN,OD10_1

description:
Library name: sample11
PLN71


title: APX-seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 APX Seq


title: mouse-PLN,OD14_2

description:
Library name: sample13
PLN82


title: mouse-PLN,OD7_1

description:
Library name: sample10
PLN61


title: APX-seq of AP sites in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C APX Seq


title: Input DNA control for APX-seq in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C APX input


title: Input DNA control for APX-seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR APX input


title: mouse-PLN,ICD,d3_1

description:
Library name: sample1
PLND1


title: Input DNA control for APX-seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 APX input


title: Input DNA control for APX-seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 APX input


title: mouse-FLN,ICD,d3_1

description:
Library name: sample5
FLND1


title: Input DNA control for APX-seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR APX input


title: APX-seq of AP sites in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C APX Seq


title: mouse-FLN,ICD,d14_1

description:
Library name: sample8
FLNH1


title: mouse-PLN,OD3_1

description:
Library name: sample9
PLN41


title: APX-seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR APX Seq


title: APX-seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR APX Seq


title: mouse-FLN,ICD,d10_1

description:
Library name: sample7
FLNG1


title: APX-seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 APX Seq


title: mouse-PLN,ICD,d10_1

description:
Library name: sample3
PLNG1


title: APX-seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 APX Seq


title: HIRAfl/fl_Tbg-Cre_female_rep4

type: genomic

description: mouse DNA methylation array was performed on Illumina iScan System

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium Mouse Methylation BeadChip (Illumina) following the manufacturer's standard protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system at the UCSD Institute for Genomic Medicine (IGM) Genomics Core.

data_processing: SeSAMe package (v1.26.0) in R environment (v4.5.1) with TQCDPB preprocessing

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was isolated from mouse liver tissue using the Monarch Genomic DNA Purification Kit.

value: liver

value: HIRA fl/fl

value: AAV8 Tbg-Cre


title: Input DNA control for APX-seq in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C APX input


title: mouse-PLN,ICD,d7_1

description:
Library name: sample2
PLNF1


title: mouse-FLN,ICD,d7_1

description:
Library name: sample6
FLNF1


title: HIRAfl/fl_Tbg-Cre_female_rep3


title: HIRAfl/fl_Tbg-Cre_female_rep2


title: Input DNA control for APX-seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 APX input


title: HIRAfl/fl_Tbg-Cre_female_rep1


title: mouse-PLN,ICD,d14_1

description:
Library name: sample4
PLNH1


title: WT_Tbg-Cre_female_rep4

value: wildtype


title: APX-seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 APX Seq


title: APX-seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 APX Seq


title: WT_Tbg-Cre_female_rep3


title: WT_Tbg-Cre_female_rep2


title: Input DNA control for APX-seq in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C APX input


title: APX-seq of AP sites in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C APX Seq


title: WT_Tbg-Cre_female_rep1


title: HIRA_KO_FOV_49

type: RNA

description:
R6289_E3_Liver_exprMat_file.csv
R6289_E3_Liver_metadata_file.csv
R6289_E3_Liver_tx_file.csv
R6289_E3_Liver_fov_positions_file.csv
R6289_E3_Liver-polygons.csv
NanoString CosMx Spatial Molecular Imager

data_processing: AtoMx Spatial Informatics Platform was used to decode transcripts and segment cells from CosMx SMI raw image data.

extract_protocol: Transcript were detected in situ on FFPE tissue sections using the NanoString CosMx Spatial Molecular Imager. FFPE tissue blocks were sectioned at 5 μm thickness and processed according to the manufacturer's CosMx SMI FFPE slide preparation protocol.


title: HIRA_KO_FOV_50


title: Input DNA control for APX-seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 APX input


title: Non-agedNeu-2

city: Chongqing

first: Yaqian

last: Duan

address: 76 Linjiang Road, Yuzhong District

institute: The Second Affiliated Hospital of Chongqing Medical University

description: Library name: Sample 5

data_processing:
RNA sequencing (RNA-seq) data analysis was performed as follows. Raw sequencing reads were subjected to quality assessment, alignment to the reference genome, and differential expression analysis.
Gene expression levels were normalized using the Trimmed Mean of M-values (TMM) method. For samples where TMM normalization was not applicable due to insufficient sample number, transcript expression was normalized using transcripts per kilobase million (TPM).
Reads were aligned to the reference genome using HISAT2 (v2.1.0), a splice-aware aligner.
Assembly: hg38
Supplementary files format and content: gene_fpkm.csv

source_name: blood tissue

extract_protocol:
Total RNA was extracted from the samples. RNA integrity was assessed using the Agilent 2100 Bioanalyzer, and RNA concentration was precisely measured using a NanoDrop spectrophotometer.
mRNA was isolated from total RNA using oligo(dT)-coated magnetic beads, and the captured mRNA was subjected to fragmentation. First-strand and second-strand cDNA were then synthesized using reverse transcriptase. The resulting double-stranded cDNA underwent end repair, followed by addition of an adenine (A) base to the 3′ ends. Subsequently, the fragments were ligated to sequencing adapters. After purification to remove unligated products and adapter dimers, the ligation products were amplified by PCR using primers complementary to the adapter sequences. Finally, the sequencing library was purified using magnetic beads.

value: blood tissue

value: neutrophils


title: HIRA_KO_FOV_46


title: Non-agedNeu-1

description: Library name: Sample 4


title: AgedNeu-2

description: Library name: Sample 2


title: HIRA_KO_FOV_48


title: AgedNeu-3

description: Library name: Sample 3


title: Non-agedNeu-3

description: Library name: Sample 6


title: HIRA_KO_FOV_45


title: AgedNeu-1

description: Library name: Sample 1


title: HIRA_KO_FOV_44


title: HIRA_KO_FOV_47


title: WT_FOV_41

value: WT


title: WT_FOV_39


title: WT_FOV_42


title: WT_FOV_38


title: hTERT-RPE1 cells, knockdown ccnd1, dox, day 4, rep2

city: Stanford

first: Dong Shin

last: You

address: 327 Campus Drive

institute: Stanford University

description:
Library name: shccnd1-dox-d4-rep2
Column name in rep2.TPM.table.txt: d4-null-dox

data_processing:
RNA-seq reads were aligned to the H. sapiens hg38 genome assembly and the transcriptome annotation from H. sapiens gene models from the v29 version of the GENCODE annotation (PMID: 30357393). For the purposes of RNA-seq data quality evaluation, genome browser track generation, reads were aligned against the genomes and set of splice junctions using the STAR aligner (version 2.5.3a; settings: --limitSjdbInsertNsj 10000000 --outFilterMultimapNmax 50 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --twopassMode Basic --twopass1readsN -1) (PMID: 23104886). Read mapping statistics and genome browser tracks were generated using custom Python scripts. For quantification purposes, reads were aligned as 2x50mers in transcriptome space against an index generated from annotations described above using Bowtie (version 1.0.1; settings: -e 200 -a -X 1000) (PMID: 19261174). Alignments were then quantified using eXpress (version 1.5.1) (PMID: 23160280) before effective read count values and TPM (Transcripts Per Million transcripts) were quantified.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM for each gene in each Sample for each replicate

growth_protocol: Cells were cultured at 37℃ and 5% CO2 in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (Corning; 10-092-CV) supplemented with 10% heat-inactivated fetal bovine serum (Corning; 35-011-CV) and 1% penicillin/streptomycin (Gibco; 15140-122).

extract_protocol:
After PBS wash, cells were lysed using TRIReagent (Zymo Research; R2050-1-50), and RNA was extracted by Direct-zolTM RNA Microprep Kit (Zymo Research; R2051-A).
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760) was then used to prepare libraries for paired-end (2x150bp) Illumina sequencing (Novogene). More than 20 million reads were sequenced per sample.

treatment_protocol: To induce cyclin D1 knockdown or overexpression, 0.5 ug/mL doxycycline was added to the culture medium for 4 or 5 days.

value: epithelial cell

value: inducible ccnd1 knockdown

value: doxycycline-induced ccnd1 knockdown

value: Day 4


title: hTERT-RPE1 cells, overexpression ccnd1, dmso, day 4, rep2

description:
Library name: wtccnd1-dmso-d4-rep2
Column name in rep2.TPM.table.txt: d4-wt-dmso

value: inducible ccnd1 knockdown; inducible ccnd1 overexpression

value: dmso control


title: WT_FOV_37


title: hTERT-RPE1 cells, overexpression ccnd1, dox, day 4, rep2

description:
Library name: wtccnd1-dox-d4-rep2
Column name in rep2.TPM.table.txt: d4-wt-dox


title: hTERT-RPE1 cells, overexpression ccnd1, dox, day 5, rep2

description:
Library name: wtccnd1-dox-d5-rep2
Column name in rep2.TPM.table.txt: d5-wt-dox

value: Day 5


title: HIRA_KO_FOV_43


title: WT_FOV_36


title: hTERT-RPE1 cells, knockdown ccnd1, dox, day 5, rep2

description:
Library name: shccnd1-dox-d5-rep2
Column name in rep2.TPM.table.txt: d5-null-dox


title: hTERT-RPE1 cells, knockdown ccnd1, dox, day 5, rep1

description:
Library name: shccnd1-dox-d5-rep1
Column name in rep1.TPM.table.txt: d5-null-dox


title: hTERT-RPE1 cells, overexpression ccnd1, dmso, day 5, rep2

description:
Library name: wtccnd1-dmso-d5-rep2
Column name in rep2.TPM.table.txt: d5-wt-dmso


title: WT_FOV_40


title: hTERT-RPE1 cells, knockdown ccnd1, dmso, day 5, rep2

description:
Library name: shccnd1-dmso-d5-rep2
Column name in rep2.TPM.table.txt: d5-null-dmso


title: WT_FOV_35


title: hTERT-RPE1 cells, knockdown ccnd1, dmso, day 5, rep1

description:
Library name: shccnd1-dmso-d5-rep1
Column name in rep1.TPM.table.txt: d5-null-dmso


title: hTERT-RPE1 cells, overexpression ccnd1, dmso, day 5, rep1

description:
Library name: wtccnd1-dmso-d5-rep1
Column name in rep1.TPM.table.txt: d5-wt-dmso


title: hTERT-RPE1 cells, knockdown ccnd1, dmso, day 4, rep2

description:
Library name: shccnd1-dmso-d4-rep2
Column name in rep2.TPM.table.txt: d4-null-dmso


title: hTERT-RPE1 cells, overexpression ccnd1, dox, day 5, rep1

description:
Library name: wtccnd1-dox-d5-rep1
Column name in rep1.TPM.table.txt: d5-wt-dox


title: HIRA_KO_FOV_33


title: HIRA_KO_FOV_32


title: HIRA_KO_FOV_31


title: hTERT-RPE1 cells, overexpression ccnd1, dmso, day 4, rep1

description:
Library name: wtccnd1-dmso-d4-rep1
Column name in rep1.TPM.table.txt: d4-wt-dmso


title: hTERT-RPE1 cells, knockdown ccnd1, dox, day 4, rep1

description:
Library name: shccnd1-dox-d4-rep1
Column name in rep1.TPM.table.txt: d4-null-dox


title: HIRA_KO_FOV_34


title: hTERT-RPE1 cells, knockdown ccnd1, dmso, day 4, rep1

description:
Library name: shccnd1-dmso-d4-rep1
Column name in rep1.TPM.table.txt: d4-null-dmso


title: ASPS02_D22, VDJ

city: Calgary

first: Sorana

last: Morrissy

state: Alberta

address: 3330 Hospital Dr NW

department: Department of Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description:
Library name: scTCR_longPB__D22
VDJ (5' mRNA library)

data_processing:
GEX and VDJ(TCR) libraries were demultiplexed using cellranger mkfastq.
Demultiplexed data was processed using the cellranger multi pipeline using the Human-GCAR1 customized reference.
Assembly: GRCh38-2024-A
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: TCR-Seq

source_name: peripheral blood

extract_protocol:
Patient’s PBMCs samples were thawed and washed with warm DMEM + 10% FBS followed by automated cell count. Cells were resuspended in 1X PBS + 1% BSA on a range of 100-2,000 cells/μl. The number of cells loaded on the 10X Genomics Single Cell Chromium Controller was adjusted according to differences in samples concentrations aiming to achieve the highest targeted cell recovery number.
After the generation of the single cell gel beads (GEMs), captured cells were lysed, and barcoded full-length cDNA from poly-adenylated mRNA was produced and amplified. An additional amplification was performed with primers specific to TCR constant regions prior to TCR library construction. GEM-X and TCR libraries were prepared according to the manufacturer’s protocols (10x Genomics Chromium GEM-X Single Cell V(D)J + 5′ Gene Expression (v3) kit).

value: peripheral blood

value: T cell

tag: library type

value: VDJ


title: ASPS02_D17, VDJ

description:
Library name: scTCR_longPB__D17
VDJ (5' mRNA library)


title: ASPS02_D31, VDJ

description:
Library name: scTCR_longPB__D31
VDJ (5' mRNA library)


title: ASPS02_D46, VDJ

description:
Library name: scTCR_longPB__D46
VDJ (5' mRNA library)


title: HIRA_KO_FOV_26

description:
R6289_E3_Liver_exprMat_file.csv
R6289_E3_Liver_metadata_file.csv
R6289_E3_Liver_tx_file.csv
R6289_E3_Liver_fov_positions_file.csv
R6289_E3_Liver-polygons.csv
NanoString CosMx Spatial Molecular Imager

value: liver


title: WT_FOV_25


title: HIRA_KO_FOV_30


title: HIRA_KO_FOV_27


title: WT_FOV_24


title: HIRA_KO_FOV_29


title: HIRA_KO_FOV_28


title: ASPS02_D15, VDJ

description:
Library name: scTCR_longPB__D15
VDJ (5' mRNA library)


title: hTERT-RPE1 cells, overexpression ccnd1, dox, day 4, rep1

description:
Library name: wtccnd1-dox-d4-rep1
Column name in rep1.TPM.table.txt: d4-wt-dox


title: WT_FOV_23


title: WT_FOV_22


title: ASPS02_D8, VDJ

description:
Library name: scTCR_longPB__D8
VDJ (5' mRNA library)


title: Variation_MPRA_Barcode_Association

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: Variation_MPRA_Barcode_Association

library_source: other

data_processing:
Adapters were trimmed from sequeincing during demuxing using bcl2fastq --use-bases-mask=N15Y136,Y15,I10,N15Y136
The barcode association dictionary was generated using MPRAflow for each size present in the design (219bp, 218bp, 216bp, 214bp, 212bp, 210bp, 208bp) using ---mapq 0 and a cigar score flag for the length of the oligo to require an exact match (ex: --cigar 219M) dictionaries were converted to tsvs, combined, and repeat barcodes were removed.
Assembly: hg38
Supplementary files format and content: The barcode association dictionary is a tsv file of barcodes and oligo names.
Supplementary files format and content: The design file is the fasta file sent to Twist biosciences to generate the oligo pool.

molecule: other

source_name: NEB 10-beta electrocompetent cells

extract_protocol:
Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

value: NEB 10-beta electrocompetent cells


title: ASPS02_product, VDJ

description:
Library name: scTCR_longPB__product
VDJ (5' mRNA library)

value: GCAR1 harvest


title: SAT59

city: Los Angeles

first: Kyla

last: Gelev

email: kylagelev@gmail.com, kzg@g.ucla.edu

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

description:
Library name: SAT59
10x Genomics

data_processing:
Alignment was performed using STAR v2.7.10a, with parameter ‘--soloFeatures Gene GeneFull SJ Velocyto’ to the GRCh38 human genome reference with Gencode v42 gene annotations.
To demultiplex the samples within the batches, we used demuxlet v2 via popscle.
To remove empty droplet and contaminated reads, we used DIEM v2.4.1 and DecontX (celda v1.16.1).
To remove heterotypic doublets, we used DoubletFinder v2.0.3.
Assembly: GRCh38
Supplementary files format and content: Gene counts are found in matrix market file format.
Supplementary files format and content: Barcodes, gene names, and meta data are in tab-separated value formats.

source_name: subcutaneous adipose tissue

extract_protocol:
Frozen subcutaneous adipose tissue biopsies were incubated in ice cold lysis buffer (1mL per 100mg). Lysis buffer was composed of 10mM Tris-HCl, 10nM NaCl, 3mM MgCl2, 0.1% of IGEPAL, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). We immediately ran the gentleMACS dissociator gentleMACS Programs 4C_nuclei_1a and 4C_nuclei_1b in succession (5 min total). The lysate was further incubated for another 10 minutes. Following a total 15 minute incubation period, the lysate was filtered through MACS 30μm strainer (Miltenyi Biotec #130-110-915). It was then centrifuged at 500 x g for 5 minutes at 4°C. The pellet was re-suspended with 1mL wash buffer consisting of 2.0% BSA, 1X PBS, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). Then, the lysate was filtered through another MACS 30μm strainer (Miltenyi Biotec #130-110-915). It was then centrifugated at 500 x g for 5 minutes at 4°C. Supernatant was removed and the pellet was re-suspended in 70 uL wash buffer wherein it was ready for library construction.
Libraries were prepared using the 10x Chromium Single Cell 3' Reagent kit v3.1.

value: subcutaneous adipose tissue

tag: cohort

value: Kuopio OBesity Surgery study (KOBS)


title: SAT58

description:
Library name: SAT58
10x Genomics


title: ASPS02_apheresis, VDJ

description:
Library name: scTCR_longPB__apheresis
VDJ (5' mRNA library)

value: apheresis


title: SAT56

description:
Library name: SAT56
10x Genomics


title: WT_FOV_19

value: WT

value: AAV8 Tbg-Cre


title: SAT55

description:
Library name: SAT55
10x Genomics


title: WT_FOV_21


title: SAT54

description:
Library name: SAT54
10x Genomics


title: SAT53

description:
Library name: SAT53
10x Genomics


title: ASPS02_D46, GEX

description:
Library name: scRNA_longPB__D46
GEX (5' mRNA library)

data_processing:
GEX and VDJ(TCR) libraries were demultiplexed using cellranger mkfastq.
Demultiplexed data was processed using the cellranger multi pipeline using the Human-GCAR1 customized reference.
Assembly: GRCh38-2024-A
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: Peripheral blood mononuclear cell (PBMC)

value: GEX


title: SAT51

description:
Library name: SAT51
10x Genomics


title: WT_FOV_20


title: ASPS02_D31, GEX

description:
Library name: scRNA_longPB__D31
GEX (5' mRNA library)


title: SAT57

description:
Library name: SAT57
10x Genomics


title: WT_FOV_18


title: SAT52

description:
Library name: SAT52
10x Genomics


title: SAT48

description:
Library name: SAT48
10x Genomics


title: HIRA_KO_FOV_16


title: ASPS02_D17, GEX

description:
Library name: scRNA_longPB__D17
GEX (5' mRNA library)


title: ASPS02_D22, GEX

description:
Library name: scRNA_longPB__D22
GEX (5' mRNA library)


title: SAT49

description:
Library name: SAT49
10x Genomics


title: HIRA_KO_FOV_17


title: SAT50

description:
Library name: SAT50
10x Genomics


title: HIRA_KO_FOV_15


title: SAT46

description:
Library name: SAT46
10x Genomics


title: SAT47

description:
Library name: SAT47
10x Genomics


title: SAT45

description:
Library name: SAT45
10x Genomics


title: SAT43

description:
Library name: SAT43
10x Genomics


title: SAT37

description:
Library name: SAT37
10x Genomics


title: HIRA_KO_FOV_13


title: ASPS02_D8, GEX

description:
Library name: scRNA_longPB__D8
GEX (5' mRNA library)


title: SAT36

description:
Library name: SAT36
10x Genomics


title: HIRA_KO_FOV_11


title: HIRA_KO_FOV_10


title: HIRA_KO_FOV_14


title: SAT42

description:
Library name: SAT42
10x Genomics


title: scRNA-seq of matched adjacent normal tissues6

city: Nanjing

first: Yueming

last: Sun

state: Prof.

address: 140 Hanzhong Road, Gulou District, Nanjing, Jiangsu

department: Department of General Surgery

institute: The First Affiliated Hospital of Nanjing Medical University

description:
Library name: CRC_N6
10x Genomics

data_processing:
Raw sequencing data (FASTQ files) were generated using 10x Genomics Cell Ranger mkfastq (v7.1.0).
Assembly: GRCh38 (Human Genome Reference Consortium, hg38)
Supplementary files format and content: Gene-barcode matrices (filtered and unfiltered) in 10x Genomics format (including barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz). Additionally, Seurat object (.rds) and/or AnnData object (.h5ad) containing normalized expression, cluster labels, UMAP coordinates, and cell type annotations are provided.

source_name: Adjacent normal tissue

extract_protocol:
Fresh tissue samples were immediately processed after surgical resection. Tissues were minced and enzymatically dissociated using a cocktail of collagenase IV, DNase I, and hyaluronidase at 37°C for 30–45 minutes to generate single-cell suspensions. Red blood cells were lysed, and cells were filtered through a 40-μm strainer. Cell viability was assessed by trypan blue exclusion and maintained above 85%.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit (v3). Approximately 10,000 cells per sample were loaded onto the Chromium Controller to generate gel bead-in-emulsions (GEMs). Reverse transcription, cDNA amplification, and library construction were performed according to the manufacturer’s instructions.

value: Adjacent normal tissue


title: ASPS02_D15, GEX

description:
Library name: scRNA_longPB__D15
GEX (5' mRNA library)


title: SAT40

description:
Library name: SAT40
10x Genomics


title: ASPS02_product, GEX

description:
Library name: scRNA_longPB__product
GEX (5' mRNA library)


title: scRNA-seq of primary colorectal cancer6

description:
Library name: CRC_T6
10x Genomics

source_name: Colorectal cancer

value: Colorectal cancer


title: SAT39

description:
Library name: SAT39
10x Genomics


title: ASPS02_apheresis, GEX

description:
Library name: scRNA_longPB__apheresis
GEX (5' mRNA library)


title: HIRA_KO_FOV_12


title: SAT35

description:
Library name: SAT35
10x Genomics


title: SAT38

description:
Library name: SAT38
10x Genomics


title: SAT41

description:
Library name: SAT41
10x Genomics


title: SAT44

description:
Library name: SAT44
10x Genomics


title: WT_FOV_9


title: scRNA-seq of primary colorectal cancer5

description:
Library name: CRC_T5
10x Genomics


title: WT_FOV_7


title: SAT26

description:
Library name: SAT26
10x Genomics


title: scRNA-seq of matched paired liver metastases3

description:
Library name: CRC_LM3
10x Genomics

source_name: Colorectal cancer liver metastase

value: Colorectal cancer liver metastase


title: SAT34

description:
Library name: SAT34
10x Genomics


title: SAT24

description:
Library name: SAT24
10x Genomics


title: scRNA-seq of primary colorectal cancer4

description:
Library name: CRC_T4
10x Genomics


title: scRNA-seq of matched adjacent normal tissues3

description:
Library name: CRC_N3
10x Genomics


title: SAT27

description:
Library name: SAT27
10x Genomics


title: scRNA-seq of primary colorectal cancer3

description:
Library name: CRC_T3
10x Genomics


title: SAT23

description:
Library name: SAT23
10x Genomics


title: scRNA-seq of matched adjacent normal tissues4

description:
Library name: CRC_N4
10x Genomics


title: WT_FOV_4


title: SAT28

description:
Library name: SAT28
10x Genomics


title: scRNA-seq of matched adjacent normal tissues5

description:
Library name: CRC_N5
10x Genomics


title: SAT29

description:
Library name: SAT29
10x Genomics


title: SAT25

description:
Library name: SAT25
10x Genomics


title: SAT33

description:
Library name: SAT33
10x Genomics


title: WT_FOV_8


title: SAT30

description:
Library name: SAT30
10x Genomics


title: WT_FOV_6


title: SAT31

description:
Library name: SAT31
10x Genomics


title: SAT32

description:
Library name: SAT32
10x Genomics


title: WT_FOV_5


title: SAT22

description:
Library name: SAT22
10x Genomics


title: WT_FOV_3


title: SAT21

description:
Library name: SAT21
10x Genomics


title: WT_FOV_2


title: SAT17

description:
Library name: SAT17
10x Genomics


title: scRNA-seq of primary colorectal cancer2

description:
Library name: CRC_T2
10x Genomics


title: SAT20

description:
Library name: SAT20
10x Genomics


title: scRNA-seq of matched paired liver metastases2

description:
Library name: CRC_LM2
10x Genomics


title: SAT16

description:
Library name: SAT16
10x Genomics


title: SAT19

description:
Library name: SAT19
10x Genomics


title: SAT15

description:
Library name: SAT15
10x Genomics


title: WT_FOV_1


title: SAT13

description:
Library name: SAT13
10x Genomics


title: CNP_IVM_OOCYTE_10

city: Baton Rouge

first: Hao

last: Ming

state: Louisiana

address: 39 Forestry Ln

department: School of Animal Science

institute: Louisiana State University

description: Library name: sample30

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide tpm (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: UCD1.3
Supplementary files format and content: csv, normalized read counts

organism: Bos taurus

source_name: OOCYTE

growth_protocol: Immature COCs were recovered and transferred to either conventional or modified maturation systems. Maturation was performed using Tissue Culture Medium 199 (TCM199) supplemented with 10% fetal bovine serum, 2 mM glutamine, 0.2 mM sodium pyruvate, 1% penicillin-streptomycin, 50 ng/mL epidermal growth factor (EGF), and 5 µg/mL FSH. The pre-maturation medium used the same formulation excluding EGF and was supplemented with 200 nM CNP (Sigma 05-23-0310) for the 6-hour treatment period. Oocytes were divided between conventional and CNP maturation systems and incubated under 5% CO2 at 38.5°C. Conventional maturation lasted 22 hours while the modified system included a 6-hour pre-maturation CNP culture followed by 22 hours of maturation. After maturation, COCs were denuded in hyaluronidase and nuclear maturation was verified by the presence of a polar body. Individual GV and MII oocytes were collected for subsequent analyses.

extract_protocol:
Individual oocytes were washed three times in Dulbecco’s phosphate buffered saline (DPBS) and transferred to a 1.5 mL tube with 1 µL of media. Once in the 1.5 mL, individual oocytes were snap-frozen and stored at -80°C until RNA extraction and library preparation. RNA extraction was performed using the SMART-Seq® v4 Ultra® Low Input RNA Kit for sequencing (Takara Bio USA, Inc., San Jose, CA, USA) according to the manufacturer’s protocol.
The RNA-seq libraries were generated from oocytes by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

value: OOCYTE

value: in vitro maturation


title: SAT18

description:
Library name: SAT18
10x Genomics


title: CNP_IVM_OOCYTE_8

description: Library name: sample28


title: scRNA-seq of matched paired liver metastases1

description:
Library name: CRC_LM1
10x Genomics


title: CNP_IVM_OOCYTE_9

description: Library name: sample29


title: SAT14

description:
Library name: SAT14
10x Genomics


title: scRNA-seq of matched adjacent normal tissues2

description:
Library name: CRC_N2
10x Genomics


title: CNP_IVM_OOCYTE_7

description:
Library name: sample27
colname in express_tpm.csv: O27


title: SAT11

description:
Library name: SAT11
10x Genomics


title: SAT12

description:
Library name: SAT12
10x Genomics


title: SAT10

description:
Library name: SAT10
10x Genomics


title: scRNA-seq of primary colorectal cancer1

description:
Library name: CRC_T1
10x Genomics


title: scRNA-seq of matched adjacent normal tissues1

description:
Library name: CRC_N1
10x Genomics


title: SAT9

description:
Library name: SAT9
10x Genomics


title: SAT8

description:
Library name: SAT8
10x Genomics


title: SAT6

description:
Library name: SAT6
10x Genomics


title: SAT3

description:
Library name: SAT3
10x Genomics


title: SAT5

description:
Library name: SAT5
10x Genomics


title: SAT4

description:
Library name: SAT4
10x Genomics


title: CNP_IVM_OOCYTE_3

description:
Library name: sample23
colname in express_tpm.csv: O23


title: HEK293_Swap_TTseq_rep1

city: Austin

first: Yan Jessie

last: Zhang

state: TX

address: 100 E 24th St

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
Library name: Swap_TTseq_rep1
TT-seq; swap1

data_processing:
Reads were trimmed and filtered using TrimGalore v 0.6.10 and aligned to the hg38 human genome (Ensembl) and spike-in genomes with and STAR.
PCR duplicates were removed using Picard Tools (version 3.1.1).
Alignment files were converted to Bam files with Samtools (version 1.14) for downstream analysis.
Reads mapped to exons and genes were quantified using featureCounts v2.0.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text file of counts
Supplementary files format and content: bigWig

source_name: Human embryonic kidney

growth_protocol: HEK293 degron were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were lysed in 3 mL Trizol. Total RNA was extracted, and 150 μg was used per experiment. Yeast RNA from 4TU-labeled cells was added as spike-in controls (1:100 ratio) for normalization. RNA fragmentation was achieved by adding 1 M NaOH to a final concentration of 0.2 M, followed by incubation on ice for 20 min. Fragmentation was stopped by adding 1 M Tris buffer (pH 6.8) to a final concentration of 0.5 M. RNA samples were biotinylated with MTSEA biotin-XX linker (dissolved in DMF), incubated in the dark for 40 min at room temperature, and purified using phenol/chloroform/isoamyl alcohol (25:24:1, vol/vol/vol). Biotinylated RNA was enriched using μMACS Streptavidin MicroBeads (μMACS Streptavidin Kit).
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: Approximately 20 million cells were pulse-labeled with 1 mM 4-thiouridine (4SU, Sigma-Aldrich) for 20 min at 37 °C.

value: Human embryonic kidney

value: Trasfected with an RPB1 that has a 26X Y1T and T4Y CTD


title: HEK293_Swap_TTseq_rep2

description:
Library name: Swap_TTseq_rep2
TT-seq; swap2


title: SAT7

description:
Library name: SAT7
10x Genomics


title: CNP_IVM_OOCYTE_5

description:
Library name: sample25
colname in express_tpm.csv: O25


title: CNP_IVM_OOCYTE_4

description:
Library name: sample24
colname in express_tpm.csv: O24


title: SAT2

description:
Library name: SAT2
10x Genomics


title: HEK293_yCTD_TTseq_rep1

description:
Library name: yCTD_TTseq_rep1
TT-seq; yCTD1

value: Trasfected with an RPB1 that has a 26X wildtype CTD


title: HEK293T_Swapped_2rep

description: Library name: Swapped_2rep

data_processing:
Reads were trimmed and filtered using cutadapt v.4.6.
Reads were aligned to the hg38 human genome (Ensembl) with Bowtie2 v.2.4.5 for Chip.
Alignment files were converted to Bam files with Samtools (version 1.14) for downstream analysis.
bamCompare v.3.5.5 was used to generate bigWig files normalized to Input (control) for each sample using the log2 ratio of mapped reads (MAPQ > 10).
Data matrices were generated using the computeMatrix function in Deeptools v3.5.1, from which metagene plots and heatmaps were derived.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: HEK293T were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature, followed by quenching with 0.125 M glycine for 5 min. Cells were sequentially lysed in 1 mL LB1 buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and 1×protease and phosphatase inhibitor (1×PPI)) at 4°C for 10 min. After centrifugation and supernatant removal, the pellet was washed with 1 mL LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1×PPI) at 4°C for 5 min. The pellet was collected by centrifugation and resuspended in 300 μL LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1×PPI). Chromatin was sonicated to an average fragment size of approximately 200–500 bp using a Q800R3 Sonicator (30 s ON, 30 s OFF, for 20 min). For immunoprecipitation, 5 μg of GFP antibody (Proteintech, 50430-2-AP), pre-incubated with 50 μL Dynabeads Protein A (Invitrogen), was added to the chromatin samples along with 1% Triton X-100 and incubated overnight at 4°C. Beads were washed twice with low-salt wash buffer (0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), once with high-salt wash buffer (0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), once with LiCl wash buffer (250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.0), and twice with TE buffer. Chromatin was reverse crosslinked overnight at 65°C with shaking at 800 rpm in reverse crosslinking buffer (1% SDS and 0.1 M NaHCO₃). DNA was purified using phenol-chloroform extraction and resuspended in 10 mM Tris-HCl pH 8.0.
ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Cells transfected with an engineered RPB1 containing an modified CTD

value: Transfected with engineered RPB1 containing Y1T and T4Y mutant CTD repeats


title: HEK293_yCTD_TTseq_rep2

description:
Library name: yCTD_TTseq_rep2
TT-seq; yCTD2


title: SAT1

description:
Library name: SAT1
10x Genomics


title: CNP_IVM_OOCYTE_6

description:
Library name: sample26
colname in express_tpm.csv: O26


title: CNP_IVM_OOCYTE_2

description:
Library name: sample22
colname in express_tpm.csv: O22


title: CNP_IVM_OOCYTE_1

description:
Library name: sample21
colname in express_tpm.csv: O21


title: PDX derived 48396 #325, KTX-049 treated, 24 hours, rep3

city: Boston

first: Andrew

last: Cherniack

state: Mass

address: 450 Brookline Ave

department: Molecular Oncology

institute: Dana Farber Cancer Institute

description:
Library name: 48396_325_KTX-049_3
I6
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_325_KTX_049_1, 48396_325_KTX_049_2, 48396_325_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

data_processing:
Reads containing adapters, containing N > 10% or with a Qscore <= 5 were removed by Novogene.
Reads were mapped to hg38 using STAR with GENCODE v47 for gene annotation. STAR was run with quantMode GeneCounts to retrieve raw read counts per gene.
Only genes with counts of 10 or higher in at least 3 samples were kept for further analysis. DESeq2 v1.42.1 was used to derive normalized counts.
Assembly: hg38
Supplementary files format and content: treated_vs_untreated_counts csv file contains normalized counts from running DESeq only on samples treated with DMSO and KTX-049. Additionally, MKL-1 is excluded from this file.
Supplementary files format and content: WaGa_counts csv file contains normalized counts from running DESeq on KTX and DMSO treated MCC / PDX 48396 samples
Supplementary files format and content: WaGa_counts csv file contains normalized counts from running DESeq on KTX and DMSO treated WaGa and WaGa CDX samples only
Supplementary files format and content: WaGa_parental_counts csv file contains normalized counts form running DESeq on WaGa parental samples only but all treatments
Supplementary files format and content: MKL_counts csv file contains normalized counts from running DESeq on MKL samples only but all treatments

source_name: PDX derived cell line 48396 #325

growth_protocol: MKL-1, WaGa and WaGa CDX derived  cell lines were cultured in RPMI medium supplemented with 10% FBS, 1% Penicillin and Streptomycin and 1% GlutaMAX. MCC-301 and PDX derived cell lines were cultured in NeuroCult NS-A medium with 10% proliferation supplement, 1% Penicillin and Streptomycin, EGF, FGF (10mL of 100mg/mL stock solutions in 50 mL medium) and 0.02% Heparin. The cells were grown in an 37˚C incubator with 5% CO2.

extract_protocol:
Cells were collected by centrifugation, resuspended in TRIzol LS reagent followed by incubation at room temperature for five minutes. The homogenized samples were incubated with chloroform followed by centrifugation. The aqueous layer was transferred to an RNAeasy spin column and the Qiagen kit protocol for RNA extraction was followed (Qiagen # 74134). RNA QC analysis, mRNA library preparation (poly A enrichment) and sequencing (PE150, 15G raw data per sample) using NovaSeq X plus Series was carried out by Novogene Corporation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. (cited from Novogene sequencing report)

treatment_protocol: Cells were seeded in the appropriate media and treated with DMSO, KTX-049 or DS-3032 for 24 hours.

value: PDX derived cell line 48396 #325

value: Merkel cell carcinoma cells

value: 1nM KTX-049

value: 24 hours


title: PDX derived 48396 #346, KTX-049 treated, 24 hours, rep3

description:
Library name: 48396_346_KTX-049_3
J6
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_346_KTX_049_1, 48396_346_KTX_049_2, 48396_346_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

source_name: PDX derived cell line 48396 #346

value: PDX derived cell line 48396 #346


title: HEK293T_Swapped_1rep

description: Library name: Swapped_1rep


title: Patient derived MCC-301, KTX-049 treated, 24 hours, rep3

description:
Library name: MCC-301_KTX-049_3
H6
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: MCC_301_KTX_049_1, MCC_301_KTX_049_2, MCC_301_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

source_name: Patient derived cell line MCC-301

value: Patient derived cell line MCC-301


title: Ctrl_IVM_OOCYTE_8

description:
Library name: sample18
colname in express_tpm.csv: O18

value: WT