title: TRIBEID_5-SS3_5-SS3-D11


title: TRIBEID_5-SS3_5-SS3-C9

status: Public on Sep 15 2025

type: SRA

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: 1088 Xueyuan Avenue, Shenzhen 518055,P.R. China

department: Department of Systems Biology

country: China

institute: Southern University of Science and Technology

library_source: transcriptomic single cell

data_processing:
Sequencing reads were preprocessed and mapped to hg38 assembly. PCR duplicates were removed using Picard MarkDuplicates (v2.27.4, https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard) with the option REMOVE_DUPLICATES=true. FeatureCounts (v2.0.1) was used to quantify uniquely mapped reads with parameters: -p -B -C -g gene_name -Q 30. Cells with > 7,000?detected genes and > 150,000 deduplicated reads were included in downstream analysis. Genes with < 10 mapped reads across all cells were excluded. Feature counts for each cell were normalized using the NormalizeData function from Seurat (v5.0.3), with the LogNormalize method and a scale factor of 10,000.
Assembly: hg38 reference genome
Supplementary files format and content: Expression value for quality control-processed single cells

molecule: total RNA

organism: Homo sapiens

extract_protocol: For the single-cell RNA sequencing, single cells were sorted into each well of 96-well plates containing 3 µL lysis buffer (0.3 µL 1% Triton X-100 (Sigma Aldrich, T9284), 0.05 µL 10 µM Oligo dT primer, 0.2 µL 10 mM dNTPs mix (Thermo Scientific, R0191), 0.03 µL 40 U/µL RNase inhibitor (Takara, 2313A), 0.4 µL 50% PEG8000 (Sigma Aldrich, 89510) and 2.02 µL ddH2O). Single-cell RNA sequencing libraries were generated using the Smart-seq3xpress protocol.

tag: cell line

tag: cell type

value: Human embryonic kidney cells


title: TRIBEID_5-SS3_5-SS3-D10


title: TRIBEID_5-SS3_5-SS3-C4


title: TRIBEID_5-SS3_5-SS3-C5


title: TRIBEID_5-SS3_5-SS3-C3


title: TRIBEID_5-SS3_5-SS3-C6


title: TRIBEID_5-SS3_5-SS3-E3


title: TRIBEID_5-SS3_5-SS3-E2


title: TRIBEID_5-SS3_5-SS3-E5


title: TRIBEID_5-SS3_5-SS3-C2


title: TRIBEID_5-SS3_5-SS3-C10


title: TRIBEID_5-SS3_5-SS3-C11


title: TRIBEID_5-SS3_5-SS3-B9


title: TRIBEID_5-SS3_5-SS3-B8


title: TRIBEID_5-SS3_5-SS3-B6


title: TRIBEID_5-SS3_5-SS3-B5


title: TRIBEID_5-SS3_5-SS3-B3


title: TRIBEID_5-SS3_5-SS3-B2


title: TRIBEID_5-SS3_5-SS3-B12


title: TRIBEID_5-SS3_5-SS3-B11


title: ctrl_4-SS3_4-SS3-H9


title: ctrl_4-SS3_4-SS3-H7


title: ctrl_4-SS3_4-SS3-H6


title: ctrl_4-SS3_4-SS3-H4


title: ctrl_4-SS3_4-SS3-H3


title: ctrl_4-SS3_4-SS3-H5


title: ctrl_4-SS3_4-SS3-H2


title: TRIBEID_5-SS3_5-SS3-C1


title: TRIBEID_5-SS3_5-SS3-C12


title: ctrl_4-SS3_4-SS3-H12


title: TRIBEID_4-SS3_4-SS3-G9


title: TRIBEID_4-SS3_4-SS3-G7


title: ctrl_4-SS3_4-SS3-H11


title: ctrl_4-SS3_4-SS3-H10


title: TRIBEID_4-SS3_4-SS3-G6


title: TRIBEID_4-SS3_4-SS3-G5


title: TRIBEID_4-SS3_4-SS3-G4


title: TRIBEID_4-SS3_4-SS3-G2


title: TRIBEID_4-SS3_4-SS3-G1


title: TRIBEID_4-SS3_4-SS3-G11


title: TRIBEID_4-SS3_4-SS3-G10


title: TRIBEID_4-SS3_4-SS3-F9


title: TRIBEID_4-SS3_4-SS3-F8


title: TRIBEID_4-SS3_4-SS3-F7


title: TRIBEID_5-SS3_5-SS3-B10


title: TRIBEID_4-SS3_4-SS3-F6


title: TRIBEID_4-SS3_4-SS3-F4


title: TRIBEID_4-SS3_4-SS3-F3


title: TRIBEID_4-SS3_4-SS3-F2


title: TRIBEID_4-SS3_4-SS3-F1


title: TRIBEID_4-SS3_4-SS3-F12


title: TRIBEID_4-SS3_4-SS3-F11


title: TRIBEID_4-SS3_4-SS3-G8


title: TRIBEID_4-SS3_4-SS3-E8


title: TRIBEID_4-SS3_4-SS3-E9


title: TRIBEID_4-SS3_4-SS3-E7


title: TRIBEID_4-SS3_4-SS3-E5


title: TRIBEID_4-SS3_4-SS3-E6


title: TRIBEID_4-SS3_4-SS3-E4


title: TRIBEID_4-SS3_4-SS3-E1


title: TRIBEID_4-SS3_4-SS3-D8


title: TRIBEID_4-SS3_4-SS3-D9


title: TRIBEID_4-SS3_4-SS3-E11


title: TRIBEID_4-SS3_4-SS3-D7


title: TRIBEID_4-SS3_4-SS3-E12


title: TRIBEID_4-SS3_4-SS3-D4


title: TRIBEID_4-SS3_4-SS3-E3


title: TRIBEID_4-SS3_4-SS3-D6


title: TRIBEID_4-SS3_4-SS3-E2


title: TRIBEID_4-SS3_4-SS3-D5


title: TRIBEID_4-SS3_4-SS3-F5


title: TRIBEID_4-SS3_4-SS3-D3


title: TRIBEID_4-SS3_4-SS3-D1


title: TRIBEID_4-SS3_4-SS3-D12


title: TRIBEID_4-SS3_4-SS3-D2


title: TRIBEID_4-SS3_4-SS3-D10


title: TRIBEID_4-SS3_4-SS3-C9


title: TRIBEID_4-SS3_4-SS3-D11


title: TRIBEID_4-SS3_4-SS3-C8


title: TRIBEID_4-SS3_4-SS3-C7


title: TRIBEID_4-SS3_4-SS3-C5


title: TRIBEID_4-SS3_4-SS3-C4


title: TRIBEID_4-SS3_4-SS3-C3


title: TRIBEID_4-SS3_4-SS3-C2


title: TRIBEID_4-SS3_4-SS3-C12


title: TRIBEID_4-SS3_4-SS3-C11


title: TRIBEID_4-SS3_4-SS3-C10


title: TRIBEID_4-SS3_4-SS3-B9


title: TRIBEID_4-SS3_4-SS3-B4


title: TRIBEID_4-SS3_4-SS3-B5


title: TRIBEID_4-SS3_4-SS3-B1


title: TRIBEID_4-SS3_4-SS3-B3


title: TRIBEID_4-SS3_4-SS3-B6


title: TRIBEID_4-SS3_4-SS3-B8


title: TRIBEID_4-SS3_4-SS3-B7


title: TRIBEID_4-SS3_4-SS3-B12


title: TRIBEID_4-SS3_4-SS3-B11


title: TRIBEID_4-SS3_4-SS3-B10


title: TRIBEID_4-SS3_4-SS3-A8


title: TRIBEID_4-SS3_4-SS3-A2


title: TRIBEID_4-SS3_4-SS3-A12


title: TRIBEID_4-SS3_4-SS3-A6


title: TRIBEID_4-SS3_4-SS3-A7


title: TRIBEID_4-SS3_4-SS3-A1


title: TRIBEID_4-SS3_4-SS3-A11


title: TRIBEID_4-SS3_4-SS3-A5


title: ctrl_3-SS3_3-SS3-H9


title: TRIBEID_4-SS3_4-SS3-A10


title: TRIBEID_4-SS3_4-SS3-C6


title: TRIBEID_4-SS3_4-SS3-C1


title: ctrl_3-SS3_3-SS3-H5


title: ctrl_3-SS3_3-SS3-H3


title: ctrl_3-SS3_3-SS3-H4


title: ctrl_3-SS3_3-SS3-H1


title: ctrl_3-SS3_3-SS3-H2


title: ctrl_3-SS3_3-SS3-H10


title: TRIBEID_3-SS3_3-SS3-G6


title: ctrl_3-SS3_3-SS3-H11


title: TRIBEID_3-SS3_3-SS3-G5


title: TRIBEID_3-SS3_3-SS3-G3


title: TRIBEID_3-SS3_3-SS3-G4


title: TRIBEID_3-SS3_3-SS3-G1


title: TRIBEID_3-SS3_3-SS3-G8


title: TRIBEID_3-SS3_3-SS3-G2


title: ctrl_3-SS3_3-SS3-H12


title: TRIBEID_3-SS3_3-SS3-G12


title: TRIBEID_3-SS3_3-SS3-G10


title: TRIBEID_3-SS3_3-SS3-F6


title: TRIBEID_3-SS3_3-SS3-G11


title: TRIBEID_3-SS3_3-SS3-F3


title: ctrl_3-SS3_3-SS3-H6


title: TRIBEID_3-SS3_3-SS3-F2


title: TRIBEID_3-SS3_3-SS3-F4


title: TRIBEID_3-SS3_3-SS3-F11


title: TRIBEID_3-SS3_3-SS3-F9


title: TRIBEID_3-SS3_3-SS3-E8


title: TRIBEID_3-SS3_3-SS3-E9


title: TRIBEID_3-SS3_3-SS3-E7


title: TRIBEID_3-SS3_3-SS3-F10


title: TRIBEID_3-SS3_3-SS3-E3


title: TRIBEID_3-SS3_3-SS3-E4


title: TRIBEID_3-SS3_3-SS3-E5


title: TRIBEID_3-SS3_3-SS3-G9


title: TRIBEID_3-SS3_3-SS3-E1


title: TRIBEID_3-SS3_3-SS3-E12


title: TRIBEID_3-SS3_3-SS3-D1


title: TRIBEID_3-SS3_3-SS3-D9


title: TRIBEID_3-SS3_3-SS3-E10


title: TRIBEID_3-SS3_3-SS3-D2


title: TRIBEID_3-SS3_3-SS3-E11


title: TRIBEID_3-SS3_3-SS3-E2


title: TRIBEID_3-SS3_3-SS3-D12


title: TRIBEID_3-SS3_3-SS3-F8


title: TRIBEID_3-SS3_3-SS3-D8


title: TRIBEID_3-SS3_3-SS3-F5


title: TRIBEID_3-SS3_3-SS3-C9


title: TRIBEID_3-SS3_3-SS3-D11


title: TRIBEID_3-SS3_3-SS3-C7


title: TRIBEID_3-SS3_3-SS3-C2


title: TRIBEID_3-SS3_3-SS3-C3


title: TRIBEID_3-SS3_3-SS3-D10


title: TRIBEID_3-SS3_3-SS3-C1


title: TRIBEID_3-SS3_3-SS3-C12


title: TRIBEID_3-SS3_3-SS3-C11


title: TRIBEID_3-SS3_3-SS3-C10


title: TRIBEID_3-SS3_3-SS3-C6


title: TRIBEID_3-SS3_3-SS3-B8


title: TRIBEID_3-SS3_3-SS3-B5


title: TRIBEID_3-SS3_3-SS3-B6


title: TRIBEID_3-SS3_3-SS3-B3


title: TRIBEID_3-SS3_3-SS3-B2


title: TRIBEID_3-SS3_3-SS3-D6


title: TRIBEID_3-SS3_3-SS3-B1


title: TRIBEID_3-SS3_3-SS3-B11


title: TRIBEID_3-SS3_3-SS3-B12


title: TRIBEID_3-SS3_3-SS3-A6


title: TRIBEID_3-SS3_3-SS3-B10


title: TRIBEID_3-SS3_3-SS3-A8


title: T-SCLC17

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

country: USA

institute: MSKCC

description: Library name: EPIC_T-SCLC17

library_source: genomic

data_processing:
The Bismark pipeline was adopted to map bisulfite-treated EPIC sequencing reads and determine cytosine methylation states.
Trim Galore v0.6.4 was used to remove raw reads with low-quality (less than 20) and adapter sequences.
The trimmed sequence reads were C(G) to T(A) converted and mapped to similarly converted reference human genome (hg19) using default Bowtie 2 settings within Bismark.
Duplicated reads were discarded. The remaining alignments were then used for cytosine methylation calling by Bismark methylation extractor.
bigWig files were generated using bedGraphToBigWig from kentUtils.
Assembly: hg19
Supplementary files format and content: bigWig for cytosine read coverage
Supplementary files format and content: bigWig for cytosine methylation rate

molecule: genomic DNA

source_name: Lung

extract_protocol:
FFPE sections were deparaffinized in mineral oil. Briefly, 800µL mineral oil (Fisher Scientific, #AC415080010) and 180µL Buffer PKD were mixed with the sections, Proteinase K was added for tissue digestion, and the sample was incubated at 56 °C for 15 min. Phase separation was encouraged with centrifugation, and the aqueous phase was chilled 3 min to precipitate RNA. After centrifugation for 15 min at 20,000 g, RNA-containing supernatant was removed for extraction, while DNA remained in the pellet. Nucleic acids were subsequently extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer ATE.
After PicoGreen quantification (ThermoFisher, #P11496) and quality control by Agilent BioAnalyzer, 170–750 ng of genomic DNA was sheared using a LE220-plus Focused-ultrasonicator (Covaris, #500569). Samples were cleaned using Sample Purification Beads from the TruSeq Methyl Capture EPIC LT Library Prep Kit (Illumina, #FC-151-1002) according to the manufacturer’s instructions with modifications. Briefly, samples were incubated for 5 min after addition of SPB, 50 µL RSB was added for resuspension, and resuspended samples were incubated for 2 min. Sequencing libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) without PCR amplification. Post-ligation cleanup proceeded according to Illumina’s instructions with 110 µL Sample Purification Mix. After purification, 3–4 samples were pooled equimolar and methylome regions were captured using EPIC oligos. Capture pools were bisulfite converted and amplified with 11–12 cycles of PCR. Pools were sequenced on a NovaSeq 6000 or HiSeq 4000 in a 150/150 bp or 100 bp/100 bp paired end run, using the NovaSeq 6000 S4 Reagent Kit (300 Cycles) or HiSeq 3000/4000 SBS Kit (Illumina). The average number of read pairs per sample was 51 million.

tag: tissue

value: Lung

value: Transformed SCLC

tag: genotype

value: Transforming


title: T-SCLC13

description: Library name: EPIC_T-SCLC13


title: T-SCLC11

description: Library name: EPIC_T-SCLC11


title: TRIBEID_3-SS3_3-SS3-A4


title: TRIBEID_3-SS3_3-SS3-A5


title: TRIBEID_3-SS3_3-SS3-A2


title: TRIBEID_3-SS3_3-SS3-B9


title: T-SCLC9

description: Library name: EPIC_T-SCLC9


title: TRIBEID_3-SS3_3-SS3-A3


title: ctrl_2-SS3_2-SS3-H9


title: T-SCLC5

description: Library name: EPIC_T-SCLC5


title: TRIBEID_3-SS3_3-SS3-A1


title: ctrl_2-SS3_2-SS3-H8


title: T-SCLC10

description: Library name: EPIC_T-SCLC10


title: T-SCLC6

description: Library name: EPIC_T-SCLC6


title: ctrl_2-SS3_2-SS3-H7


title: T-SCLC7

description: Library name: EPIC_T-SCLC7


title: T-SCLC3

description: Library name: EPIC_T-SCLC3


title: ctrl_2-SS3_2-SS3-H3


title: T-SCLC4

description: Library name: EPIC_T-SCLC4


title: ctrl_2-SS3_2-SS3-H6


title: T-SCLC2

description: Library name: EPIC_T-SCLC2


title: T-LUAD16

description: Library name: EPIC_T-LUAD16

value: Lung adenocarcinoma


title: ctrl_2-SS3_2-SS3-H1


title: T-LUAD11

description: Library name: EPIC_T-LUAD11


title: ctrl_2-SS3_2-SS3-H12


title: T-LUAD15

description: Library name: EPIC_T-LUAD15


title: ctrl_2-SS3_2-SS3-H11


title: TRIBEID_3-SS3_3-SS3-A12


title: T-LUAD10

description: Library name: EPIC_T-LUAD10


title: ctrl_2-SS3_2-SS3-H10


title: TRIBEID_2-SS3_2-SS3-G9


title: TRIBEID_2-SS3_2-SS3-G4


title: T-LUAD4

description: Library name: EPIC_T-LUAD4


title: T-LUAD7

description: Library name: EPIC_T-LUAD7


title: TRIBEID_2-SS3_2-SS3-G3


title: T-LUAD3

description: Library name: EPIC_T-LUAD3


title: TRIBEID_2-SS3_2-SS3-G2


title: SCLC19

description: Library name: EPIC_SCLC19

value: small cell lung cancer cell

value: Control


title: SCLC15

description: Library name: EPIC_SCLC15


title: SCLC14

description: Library name: EPIC_SCLC14


title: TRIBEID_2-SS3_2-SS3-G6


title: T-LUAD2

description: Library name: EPIC_T-LUAD2


title: TRIBEID_2-SS3_2-SS3-F8


title: SCLC17

description: Library name: EPIC_SCLC17


title: SCLC13

description: Library name: EPIC_SCLC13


title: SCLC12

description: Library name: EPIC_SCLC12


title: TRIBEID_2-SS3_2-SS3-F9


title: T-LUAD9

description: Library name: EPIC_T-LUAD9


title: ctrl_2-SS3_2-SS3-H2


title: SCLC11

description: Library name: EPIC_SCLC11


title: TRIBEID_2-SS3_2-SS3-F4


title: TRIBEID_2-SS3_2-SS3-F6


title: SCLC10

description: Library name: EPIC_SCLC10


title: TRIBEID_2-SS3_2-SS3-F2


title: SCLC8

description: Library name: EPIC_SCLC8


title: SCLC9

description: Library name: EPIC_SCLC9


title: TRIBEID_2-SS3_2-SS3-F12


title: SCLC7

description: Library name: EPIC_SCLC7


title: TRIBEID_2-SS3_2-SS3-G12


title: TRIBEID_2-SS3_2-SS3-G11


title: TRIBEID_2-SS3_2-SS3-F11


title: TRIBEID_2-SS3_2-SS3-E9


title: SCLC5

description: Library name: EPIC_SCLC5


title: TRIBEID_2-SS3_2-SS3-F10


title: SCLC4

description: Library name: EPIC_SCLC4


title: SCLC2

description: Library name: EPIC_SCLC2


title: TRIBEID_2-SS3_2-SS3-E7


title: SCLC1

description: Library name: EPIC_SCLC1


title: Br5844_Nuc_SETD1A_Atlas_8G

city: Baltimore

first: Tomoyo

last: Sawada

state: MD

address: 855 N Wolfe St

department: Molecular Neurogenetics

institute: Lieber Institute for Brain Development

description: Library name: Br5844_Nuc_Atlas_8G

data_processing:
Fastq files were quality-checked using FastQC (ver. 0.11.3) and MultiQC101 (ver.1.12).
Paired-end reads were aligned to the human genome version hg38.p12 using bowtie2109 (ver. 2.4.5) with the following parameters: ‘--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700’. The reads were not trimmed, and we did not perform spike-in calibration. Duplicated reads were marked and removed using Picard (ver. 2.21.1) from each sample to generate .sam files. Each file was sorted and filtered based on the read quality (‘minQualityScore = 2’) with samtools110 (ver. 1.14) and converted to .bam and .bedgraph files with bedtools111 (ver. 2.30.0). To evaluate the reproducibility among the samples, the read counts were split into 500 base pair (bp) bins and applied Spearman’s rank correlation between all pairwise brain samples and antibodies.
For the human prenatal cortical samples, sparse enrichment analysis for CUT&RUN (SEACR) was used for peak calling. Peaks for the reads from each antibody were identified using the reads from control IgG as a background. SEACR normalization ‘norm’ and ‘stringent’ arguments were used. For iPSC-derived NPCs and neurons, we used MACS2113 (v.2.2.9.1) using the command ‘-macs2 callpeak -t <sample_input.bam> -c <IgG_input.bedgraph> -f BAM -g hs --keep-dup all -n <sample_id> --outdir ./ -B –trackline’ on .bam files of each sample.
Assembly: hg38.p12
Supplementary files format and content: BigWig track format file for each sample
Library strategy: CUT&Tag

source_name: Prenatal Frontal Lobe

growth_protocol: Two iPSC lines from postmortem dura-derived fibroblasts of two neurotypical individuals (LIBD2c1 and LIBD7c6) were maintained on a tissue culture plate coated with Cultrex Reduced Growth Factor Basement Membrane Matrix (R&D Systems) in StemFlex medium (Thermo Fisher Scientific)

extract_protocol:
Nuclei were isolated from human prenatal frontal lobes (110-170 mg tissues). The nuclear pellets were resuspended gently in nuclei storage buffer (NSB) (167 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, Tris-HCl (pH 7.5) and 1× protease inhibitor) and incubated on ice until the pellet is loosened. NPCs were dissociated with Accutase at 37°C for 2 min. Four-week-old neurons were dissociated with Papain (Worthington Biochemical) dissolved in 1:1 solution of Accutase and 1× PBS at 37°C for 30 min. Dissociated neurons were then washed with Neurobasal medium supplemented with 1× GlutaMax and 2,000 U/mL DNase I (Worthington Biochemical). 1× 105 nuclei or cells for histone marks and 1× 106 nuclei or cells for SETD1A were used.
Libraries were sequenced on HiSeq2500 (Illumina) with a read length of 50-bp paired-end by Psomagen.

treatment_protocol: To generate isogenic SETD1A mutant lines, an oligonucleotide (sgRNA) targeting around the splice acceptor of intron 15 in SETD1A was designed and cloned into U6-gRNA:CMV-CAS9-2A-tGFP vector by MilliporeSigma. Single-strand oligonucleotide (ssODN) carrying SETD1A c.4582-2delAG>- mutation and PAM blocking mutation was also designed by MilliporeSigma. Tn5-adapter complex was purchased from EpiCypher. The control IgG and antibodies against H3K4me marks were used at 1:100 and the antibodies against H3K27ac and SETD1A were used at 1:50. Index primer mix (Nextera DNA UD Indexes Set A) was purchased from Illumina.

value: Prenatal Frontal Lobe

value: Neurotypical

tag: antibody

tag: batch

tag: ab host

value: Rabbit

tag: histone marker


title: TRIBEID_2-SS3_2-SS3-E4


title: Br5844_Nuc_SETD1A_CST_8F

description: Library name: Br5844_Nuc_CST_8F


title: TRIBEID_2-SS3_2-SS3-E5


title: Br5844_Nuc_H3K27ac_8E

description: Library name: Br5844_Nuc_Ac_8E


title: TRIBEID_2-SS3_2-SS3-F3


title: TRIBEID_2-SS3_2-SS3-E3


title: Br5844_Nuc_H3K4me3_8D

description: Library name: Br5844_Nuc_me3_8D


title: TRIBEID_2-SS3_2-SS3-E11


title: Br5844_Nuc_Rb_IgG_8A

description: Library name: Br5844_Nuc_IgG_8A


title: TRIBEID_2-SS3_2-SS3-D8


title: SCLC6

description: Library name: EPIC_SCLC6


title: Br5774_Nuc_SETD1A_Atlas_7H

description: Library name: Br5774_Nuc_Atlas_7H


title: TRIBEID_2-SS3_2-SS3-E8


title: Br5774_Nuc_H3K4me3_7E

description: Library name: Br5774_Nuc_me3_7E


title: TRIBEID_2-SS3_2-SS3-D5


title: TRIBEID_2-SS3_2-SS3-D3


title: Br5774_Nuc_H3K27ac_7F

description: Library name: Br5774_Nuc_Ac_7F


title: TRIBEID_2-SS3_2-SS3-E6


title: Br5774_Nuc_H3K4me1_7C

description: Library name: Br5774_Nuc_me1_7C


title: TRIBEID_2-SS3_2-SS3-D2


title: Br5774_Nuc_Rb_IgG_7B

description: Library name: Br5774_Nuc_IgG_7B


title: TRIBEID_2-SS3_2-SS3-D11


title: TRIBEID_2-SS3_2-SS3-D10


title: Br6184_Nuc_SETD1A_CST_6H

description: Library name: Br6184_Nuc_CST_6H


title: TRIBEID_2-SS3_2-SS3-C9


title: Br6184_Nuc_SETD1A_Atlas_7A

description: Library name: Br6184_Nuc_Atlas_7A


title: TRIBEID_2-SS3_2-SS3-C8


title: TRIBEID_2-SS3_2-SS3-E12


title: Br5844_Nuc_H3K4me1_8B

description: Library name: Br5844_Nuc_me1_8B


title: TRIBEID_2-SS3_2-SS3-C7


title: Br6184_Nuc_H3K27ac_6G

description: Library name: Br6184_Nuc_Ac_6G


title: Br6184_Nuc_H3K4me3_6F

description: Library name: Br6184_Nuc_me3_6F


title: Br6184_Nuc_H3K4me1_6D

description: Library name: Br6184_Nuc_me1_6D


title: TRIBEID_2-SS3_2-SS3-C6


title: Br5774_Nuc_SETD1A_CST_7G

description: Library name: Br5774_Nuc_CST_7G


title: TRIBEID_2-SS3_2-SS3-D6


title: Br6184_Nuc_Rb_IgG_6C

description: Library name: Br6184_Nuc_IgG_6C


title: 7c6_CA137_69_NPC_SETD1A_Atlas2_10F

description: Library name: 7c6_CA137_69_NPC_SETD1A_Atlas2_10F

source_name: iPSC-derived Neural Progenitor Cells

value: iPSC-derived Neural Progenitor Cells

value: NPCs

value: Patient mutant


title: TRIBEID_2-SS3_2-SS3-C5


title: TRIBEID_2-SS3_2-SS3-C4


title: 7c6_CA137_69_NPC_SETD1A_Atlas1_10E

description: Library name: 7c6_CA137_69_NPC_SETD1A_Atlas1_10E


title: TRIBEID_2-SS3_2-SS3-C2


title: TRIBEID_2-SS3_2-SS3-C1


title: 7c6_CA137_69_NPC_SETD1A_CST1_10C

description: Library name: 7c6_CA137_69_NPC_SETD1A_CST1_10C


title: TRIBEID_2-SS3_2-SS3-C11


title: 7c6_CA137_69_NPC_H3K4me3_Thermo_10A

description: Library name: 7c6_CA137_69_NPC_me3_Thermo_10A


title: 7c6_CA137_69_NPC_H3K4me3_CST_9H

description: Library name: 7c6_CA137_69_NPC_me3_CST_9H


title: 7c6_CA137_69_NPC_SETD1A_CST2_10D

description: Library name: 7c6_CA137_69_NPC_SETD1A_CST2_10D


title: 7c6_CA137_69_NPC_Rb_IgG_9D

description: Library name: 7c6_CA137_69_NPC_Rb_IgG_9D


title: TRIBEID_2-SS3_2-SS3-B7


title: TRIBEID_2-SS3_2-SS3-B6


title: 7c6_CM130_78_NPC_SETD1A_Atlas2_9C

description: Library name: 7c6_CM130_78_NPC_SETD1A_Atlas2_9C

value: WT


title: 7c6_CM130_78_NPC_SETD1A_Atlas1_9B

description: Library name: 7c6_CM130_78_NPC_SETD1A_Atlas1_9B


title: TRIBEID_2-SS3_2-SS3-B8


title: TRIBEID_2-SS3_2-SS3-B4


title: 7c6_CM130_78_NPC_SETD1A_CST1_8H

description: Library name: 7c6_CM130_78_NPC_SETD1A_CST1_8H


title: 7c6_CM130_78_NPC_SETD1A_CST2_9A

description: Library name: 7c6_CM130_78_NPC_SETD1A_CST2_9A


title: TRIBEID_2-SS3_2-SS3-B2


title: TRIBEID_2-SS3_2-SS3-B3


title: 7c6_CM130_78_NPC_H3K4me3_Thermo_8F

description: Library name: 7c6_CM130_78_NPC_me3_Thermo_8F


title: TRIBEID_2-SS3_2-SS3-B11


title: TRIBEID_2-SS3_2-SS3-B12


title: 7c6_CM130_78_NPC_H3K4me3_8E

description: Library name: 7c6_CM130_78_NPC_me3_CST_8E


title: 7c6_CM130_78_NPC_Rb_IgG_8A

description: Library name: 7c6_CM130_78_NPC_Rb_IgG_8A


title: 7c6_CM130_30_Neuron_SETD1A_CST_6A

description: Library name: 7c6_CM130_30_Neuron_CST_6A

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: Neurons


title: Rep-3_1% Nitrate_5 _DO_biofilms

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

description: Library name: Sample 12

library_source: transcriptomic

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_008596) using bowtie v1.1.2
Maximum insert size of 1000 and two maximum mismatches after trimming 3 bp at the 3' ends.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments packageintersection mode
The dispersion and differential expression level of each gene were estimated using DESeq2
Transcripts per Million (TPM) were calculated by DESeq2
Assembly: NC_008596
Supplementary files format and content: xlsx, TPM counts

organism: Mycolicibacterium smegmatis MC2 155

source_name: Whole cell

growth_protocol: Biofilms were grown in 24-well plates containing 1.5 mL Sauton's media with or without 1% sodium nitrate supplementation for 4, 5 or 6 days.

extract_protocol:
RNA extraction was performed using the Qiagen miRNeasy Mini kit (Cat. No. 1038703). The samples were homogenized and lysed in TRIzol reagent using Tissuelyser at 20 Hz for 1 minute, extracted with chloroform and the aqueous phase separated and mixed with 1.5 times (v/v) chilled ethanol (100%). This homogeneous mix was loaded on the column (provided by kit), centrifuged for 8,000 Xg for 60 seconds and the flow-through was drained off. The subsequent steps were followed as instructed on the kit, with an on-column DNase I digestion step to remove contaminating DNA and to elute RNA with 50 μl of RNase free water.
250ng of RNA sample was used for ribodepletion by using NEBNext rRNA depletion kit Bacteria (Cat. no. NEB E7850X), according to the manufacturer’s protocol. The NEBNext Ultra II Directional RNA Library prep kit for Illumina (Cat. no. E7760L), was used to construct double-stranded cDNA libraries.

treatment_protocol: Biofilm along with the cells were harvested from two wells for each sample. The samples were then centrifuged at 4000 rpm for 10 mins. The supernatant was discarded and the pellets were resuspended into 1 mL of invitrogen TRIzol Reagent and stored in -80℃ till further processing.

value: Whole cell

tag: strain


title: 7c6_CM130_30_Neuron_H3K4me3_5G

description: Library name: 7c6_CM130_30_Neuron_me3_5G


title: TRIBEID_2-SS3_2-SS3-A9

value: Human embryonic kidney cells


title: 7c6_CM130_30_Neuron_Rb_IgG_5D

description: Library name: 7c6_CM130_30_Neuron_IgG_5D


title: Rep-1_1% Nitrate_5 _DO_biofilms

description: Library name: Sample 10


title: 7c6_CM130_78_Neuron_SETD1A_Atlas_5C

description: Library name: 7c6_CM130_78_Neuron_Atlas_5C


title: TRIBEID_2-SS3_2-SS3-A8


title: TRIBEID_2-SS3_2-SS3-B5


title: 7c6_CM130_78_Neuron_H3K4me3_4H

description: Library name: 7c6_CM130_78_Neuron_me3_4H


title: TRIBEID_2-SS3_2-SS3-A7


title: 7c6_CM130_78_Neuron_SETD1A_CST_5B

description: Library name: 7c6_CM130_78_Neuron_CST_5B


title: Rep-3_0% Nitrate_6 _DO_biofilms

description: Library name: Sample 9


title: TRIBEID_2-SS3_2-SS3-A6


title: 7c6_CA137_69_Neuron_SETD1A_CST_2E

description: Library name: 7c6_CA137_69_Neuron_CST_2E


title: TRIBEID_2-SS3_2-SS3-A5


title: TRIBEID_2-SS3_2-SS3-D9


title: 7c6_CA137_69_Neuron_Rb_IgG_1H

description: Library name: 7c6_CA137_69_Neuron_IgG_1H


title: 7c6_CA137_69_Neuron_SETD1A_Atlas_2F

description: Library name: 7c6_CA137_69_Neuron_Atlas_2F


title: 7c6_CA137_69_Neuron_H3K4me3_2C

description: Library name: 7c6_CA137_69_Neuron_me3_2C


title: TRIBEID_2-SS3_2-SS3-B10


title: 7c6_CA137_109_Neuron_SETD1A_Atlas_1G

description: Library name: 7c6_CA137_109_Neuron_Atlas_1G


title: TRIBEID_2-SS3_2-SS3-A3


title: Rep-3_0% Nitrate_5 _DO_biofilms

description: Library name: Sample 6


title: Rep-1_0% Nitrate_6 _DO_biofilms

description: Library name: Sample 7


title: Rep-2_0% Nitrate_5 _DO_biofilms

description: Library name: Sample 5


title: 7c6_CA137_109_Neuron_H3K4me3_1D

description: Library name: 7c6_CA137_109_Neuron_me3_1D


title: 7c6_CM130_30_Neuron_SETD1A_Atlas_6B

description: Library name: 7c6_CM130_30_Neuron_Atlas_6B


title: 7c6_CA137_109_Neuron_SETD1A_CST_1F

description: Library name: 7c6_CA137_109_Neuron_CST_1F


title: Rep-2_1% Nitrate_5 _DO_biofilms

description: Library name: Sample 11


title: TRIBEID_2-SS3_2-SS3-A2


title: 7c6_CA137_109_Neuron_Rb_IgG_1A

description: Library name: 7c6_CA137_109_Neuron_IgG_1A


title: bTMPSEQ, RPE1sunTag, supercoil,rep2

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
bTMP-seq reads were subjected to quality control using FastQC v0.11.6. Reads were aligned to the human reference genome (GRCh38, GRCh38_no_alt_analysis_set_GCA_000001405.15; https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/) using STAR 2.5.4a (Dobin et al. 2013) with parameters --clip5pNbases 0 --outWigStrand Unstranded. Gene-level count tables were generated while mapping using Gencode v24 primary assembly annotations.
Genome_build: GRCh38
Assembly: hg38
Supplementary files format and content: BigWig files

source_name: RPE1 SunTag

growth_protocol: hTERT=RPE1 cell line was mantained in DMEM (Gibco), FBS 10% and Pen strep 1% and grow at 37 degrees in humified incubator at 5% CO2.  Cells were routinely checked for Mycoplasma contamination.

extract_protocol:
bTMP-seq was performed as previously described {Naughton, 2013, 23416946} with some modifications necessary for next generation sequencing. Cells or control genomic DNA were treated with 500 μg/ml bTMP for 20 min at room temperature in the dark. bTMP was UV cross-linked to DNA at 365 nm UV 800mJ/cm2 (UVP’s CL-1000). DNA was purified from cells using SDS and proteinase K digestion followed by phenol-chloroform-isoamyl alcohol extraction. DNA was fragmented by sonication to a range of 200-500 bp fragments. The bTMP−DNA complex in TE was immunoprecipitated using avidin conjugated to magnetic beads (Dynabeads MyOne Streptavidin Invitrogen, 65001) overnight at 4 °C. Beads were washed sequentially for 5 min each at room temperature with TSE I (20 mM Tris, pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100 and 0.1% SDS), TSE II (20 mM Tris, pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100 and 0.1% SDS) and buffer III (10 mM Tris, pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% NP40 and 1% deoxycholate). Beads were then washed twice with TE buffer for 5 min. bTMP enriched DNA was then “on-bead” end-repaired and A-tailed prior to ligation of Illumina sequencing adapters. Adapter-ligated bTMP-bound DNA was then eluted from the Dynabeads in 25 μl water by heating for 10 min at 98°C. Library preparation was continued using the NEB NEBNext® UltraTM II DNA Library Prep Kit for Illumina (NEB #E7645S) starting at “Step 4 : PCR amplification of adapter-ligated DNA” where 10 μl of the DNA was used. Final libraries were sized and quality controlled on a D1000 Tapestation tape (Agilent). Single-end DNA-sequencing of 50 bp read length was performed on Illumina Hi-Seq 4000 (UMC, Amsterdam).
Libraries were prepared using the TruSeq® RNA LT kit and TruSeq RNA Single Indexes (Illumina). Libraries were sequenced with single-end 65-bp reads on a HiSeq 2500 platform

value: RPE1 SunTag

value: control

value: streptavidin-biotin


title: bTMPSEQ, RPE1sunTag, supercoil,rep1


title: TRIBEID_2-SS3_2-SS3-A1


title: Rep-2_0% Nitrate_6 _DO_biofilms

description: Library name: Sample 8


title: Rep-3_0% Nitrate_4 _DO_biofilms

description: Library name: Sample 3


title: 7c6_CM130_78_Neuron_Rb_IgG_4E

description: Library name: 7c6_CM130_78_Neuron_IgG_4E


title: RNASEQ, RPE1sunTag, TOP2BKD, replicate2

data_processing:
RNA-seq reads were subjected to quality control using FastQC v0.11.6. Reads were aligned to the human reference genome (GRCh38, GRCh38_no_alt_analysis_set_GCA_000001405.15; https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/) using STAR 2.5.4a (Dobin et al. 2013) with parameters --clip5pNbases 0 --outWigStrand Unstranded. Gene-level count tables were generated while mapping using Gencode v24 primary assembly annotations.
Genome_build: GRCh38
Assembly: hg38
Supplementary files format and content: Rawcounts

molecule: polyA RNA

growth_protocol: An RPE1 cell line that expresses the SunTag system  was used to perform TOP2B depletions. This cell line was mantained in DMEM (Gibco), FBS 10% and Pen strep 1% and grow at 37 degrees in humified incubator at 5% CO2.  Cells were routinely checked for Mycoplasma contamination.

extract_protocol:
One million cells were harvested, washed once in cold PBS, resuspended in 600 µL of RTL buffer (RNeasy Mini kit, 74104, Qiagen) and stored at -80°C until subsequent RNA isolation. RNA was isolated using the RNeasy Mini kit (74104, Qiagen).
Libraries were prepared using the TruSeq® RNA LT kit and TruSeq RNA Single Indexes (Illumina). Libraries were sequenced with single-end 65-bp reads on a HiSeq 2500 platform

treatment_protocol: 5,4 X105 cells were transfected in suspension in a 10 cm-dish with 10 nM of siRNA and 1:1000 of Lipofectamin RNAimax reagent (ThermoFisher,13778075). 48 hours after transfection cells were detached and expanded in four 10-cm dishes and transfected again in the same conditions. All experiments were performed at 72 hours following the second round of transfection. Knockodown efficiency was routinely checked by western blot analysis. We used: Silencer™ Select Negative Control No. 2 siRNA (ThermoFisher, 4390846) as negative control siRNA . Cell lines transfected with these two siRNAs showed an high degree of correlation for DNA/NL contacts (R >0.9), although some differences in LAD strenght could be detected. When possible, and as indicated in figure legends, the two datasets were averaged together. For TOP2B depletion we used: Dharmacon on target plus smart pool Human TOP2B siRNA (Horizon Discovery, L-004240-00-0005).

value: TOP2B Knockdown


title: TRIBEID_2-SS3_2-SS3-A10


title: bTMPSEQ, RPE1sunTag, genomic control


title: Rep-2_0% Nitrate_4 _DO_biofilms

description: Library name: Sample 2


title: RNASEQ, RPE1sunTag, TOP2BKD, replicate1


title: RNASEQ, RPE1sunTag, scramble, replicate2


title: RNASEQ, RPE1sunTag, scramble, replicate1


title: ctrl_1-SS3_1-SS3-H9


title: Rep-1_0% Nitrate_4 _DO_biofilms

description: Library name: Sample 1


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LB1_r2

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 20 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig files of log2-normalized LaminB2  pA-DamID scores for 20 kb genomic bins.

source_name: retina

growth_protocol: Two different hTERT immortalized RPE1 cell lines were used in this study. An RPE1 cell line that expresses the SunTag system (ref, ref) was used to perform TOP1, TOP2A and TOP2B depletions and the mapping of heterochromatin components. This cell line was mantained in DMEM (Gibco), FBS 10% and Pen strep 1%.  A second RPE1  cell line expressing and inducible Cas9 (ref) was used for the generation of LBR knockout and all the other experiments. This cell line was mantained in DMEM:F12 (Gibco), FBS 10% and pen/strep 1%. HCT116 were mantained in McCoy medium (Gibco) FBS10% and pen-strep 1%. K562 cell lines were mantained in IMDM medium (Gibco), FBS10% and pen-strep 1%. HCT116 and K562 TOP2B knockout cell lines were a kind gift from Vassilis Roukos. All cells were routinely checked for Mycoplasma contamination.

extract_protocol:
LMNB2 pA-DamID maps were generated as previously described (van Shaik, 2022, 36050765). Briefly, one million of RPE1, HCT116 or K562 were collected by centrifugation (500 g, 3 min) and washed sequentially in ice-cold PBS and digitonin wash buffer (D-Wash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 hours at 4 °C in 200 μL D-Wash with 1:200 of: LMNB2 (Abcam, ab8983,), LMNB1 (Abcam, ab16048), LBR (Abcam, ab32535), H3K9me3 (Diagenode, C15410193), H3K9me2 (Active Motif, 39239) , H3K27me3 (Diagenode, C15410195), TOP2B (Novus Biological, NB100-40842),  followed by a wash step with D-Wash. Following this step, cells were incubated with a solution of D-Wash buffer and Rabbit-anti-mouse IgG (1:200, Abcam, ab6709), followed by a wash step. This incubation was repeated with a 1:200 pA-Dam solution (equivalent to nearly 60 Dam units from NEB), followed by two wash steps. Dam activity was induced by incubation for 30 min at 37 °C in 100 μL D-Wash supplemented with the methyl donor SAM (30 µM) while gently shaking (500 rpm). Genomic DNA was isolated and processed similarly to DamID, except that the DpnII digestion was omitted, and 65-bp reads were sequenced. For every condition, another 1 million cells were processed in only D-Wash and, during Dam activation, incubated with 4 units of Dam enzyme (NEB, M0222L). We use Dam control samples to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C). Libraries were sequenced on Illumina platform Hiseq2500 with single end 65 bp reads.

value: retina

value: LBRKO+TOP2B KD


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LB2_r2


title: 48hpa-LY

city: Vienna

first: Juan

middle: Daniel

last: Montenegro

state: Vienna

address: Djerassiplatz 1

department: Department of neurobiology and developmental biology

country: Austria

institute: University of Vienna

description: Library name: F10_2d_LY

data_processing:
Sequencing reads were mapped to the Nematostella vectensis genome (Zimmermann et al. 2023) using standard parameters of Cellranger v7.1.0 (Zheng et al. 2017). Filtered matrices were then used to proceed with analysis using Seurat v5 (Butler et al. 2018; Stuart et al. 2019). The libraries were filtered for cells with low read and feature counts and analyzed using our scripts (complete details at https://github.com/technau/Gast ruloids ).
Assembly: Nvec200 (https://simrbase.stowers.org/starletseaanemone)
Supplementary files format and content: Seurat object

organism: Nematostella vectensis

source_name: aggregates

extract_protocol:
Samples were washed with ice cold Calcium Magnesium Free (CMF) seawater briefly and the samples were allowed to settle. The CMF was then removed and they were resuspended in ACME (ACetic-MEthanol) prepared as described previously (Garcia-Castro et al. 2021) and tubes were left on the rocker for 20 min. The samples were then dissociated using a cut pipette tip every 5 min during the 20 min window and their dissociation status was checked until sufficient. Tubes were then spun at 400 rcf for 4 min at 4℃ and the supernatant was carefully removed without disturbing the loose cell pellet. The pellet was then resuspended with 1xPBS + 0.5% BSA + RNaseOUT (40U/ml) and DMSO was added to be 10% of the final volume. This cell mix was then stored at -80℃ until the day of  library preparation. On library preperation day, the tubes were left to thaw at RT and then spun again at 400 rcf for 4 min at 4℃ after which the cell pellet was resuspended in 1xPBS + 0.5% BSA + RNaseOUT (40U/ml) and the viability and concentration were then quantified using ViaStain™AOPI staining solution (Nexcelom) and the Cellometer X2.
Libraries for sequencing were prepared using the standard 10X pipeline for scRNAsequencing

value: aggregates

tag: treatment

value: LY


title: ctrl_1-SS3_1-SS3-H7


title: 48hpa-DMSO

description: Library name: F9_2d_DMSO

value: DMSO


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LB2_r2


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_DAM_r2

value: Dam only


title: ctrl_1-SS3_1-SS3-H6


title: ctrl_1-SS3_1-SS3-H5


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LB1_r2


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_DAM_r2


title: 48hpa-run2

description: Library name: Nvagg48

value: wt


title: Rep-1_0% Nitrate_5 _DO_biofilms

description: Library name: Sample 4


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB1_r2

value: TOP2B KD


title: 24hpf

description: Library name: gast5.ACME

source_name: gastrula

value: gastrula


title: pA-DamID_RPE1_iCUT_WT_SCII_LB2_r2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_DAM_r2


title: pA-DamID_RPE1_iCUT_WT_SCII_LB1_r2


title: ctrl_1-SS3_1-SS3-H3


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB2_r2


title: ctrl_1-SS3_1-SS3-H4


title: 48hpa-run1

description: Library name: D4_48hrAggSN


title: 24hpa-run2

description: Library name: Nvagg24


title: pA-DamID_RPE1_iCUT_WT_SCII_DAM_r2


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LB2_r1


title: ctrl_1-SS3_1-SS3-H8


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LB1_r1


title: 24hpa-run1

description: Library name: 18_NvAgg24hr


title: ctrl_1-SS3_1-SS3-H1


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LB2_r1


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LB1_r1


title: ctrl_1-SS3_1-SS3-H12


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_DAM_r1


title: 12hpa

description: Library name: 17_NvAgg12hr


title: 4hpa

description: Library name: 16_NvAgg4hr


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_DAM_r1


title: ctrl_1-SS3_1-SS3-H11


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB1_r1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB2_r1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_DAM_r1


title: ctrl_1-SS3_1-SS3-H10


title: Lungs from Gprc5a-/- mouse 24 at 3 months post-saline

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Library name: KOS3_28

data_processing:
Raw scRNA-seq data were pre-processed (demultiplex cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite (version 3.0.1) provided by 10X Genomics. For read alignment of human and mouse scRNA-seq data, the human reference GRCh38 (hg38) and mouse reference GRCm38 (mm10) genomes were used, respectively. Detailed quality control (QC) metrics were generated and evaluated, and cells were carefully and rigorously filtered to obtain high-quality data for downstream analyses. Briefly, for basic quality filtering, cells with low complexity libraries (in which detected transcripts are aligned to < 200 genes such as cell debris, empty drops, and low-quality cells) were filtered out and excluded from subsequent analyses. Likely dying or apoptotic cells where > 15% of transcripts derived from the mitochondrial genome were also excluded.  For scRNA-seq data of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mice, we further removed potential droplets/dead cells with nFeature smaller than or equal to 500 and mitochondrial gene fraction larger than or equal to 15% using Seurat.
For scRNA-seq data, likely doublets or multiplets were identified and carefully removed through a multi-step approach. Briefly, doublets or multiplets were identified based on library complexity, whereby cells with high-complexity libraries in which detected transcripts are aligned to > 6,500 genes were removed, and also, based on cluster distribution and marker gene expression, whereby doublets or multiplets forming distinct clusters with hybrid expression features and/or exhibiting an aberrantly high gene count were also removed. Expression levels and proportions of canonical lineage-related marker genes in each identified cluster were carefully reviewed. Clusters co-expressing discrepant lineage markers were identified and removed. Doublets or multiplets were also identified using the doublet detection algorithm DoubletFinder. The proportion of expected doublets was estimated based on cell counts obtained prior to scRNA-seq library construction. Data normalization was then performed using Seurat on the filtered gene-cell matrix. Statistical assessment of possible batch effects was performed on non-malignant epithelial cells using the R package k-BET48 as described in our previous studies and Harmony was run with default parameters to remove batch effects present in the PCA space.  For ST profiling data, demultiplexed clean reads were aligned against the GRCm38 (mm10) mouse reference genomes by Spaceranger (version 2.0.0 for mouse ST data) with the Visium transcriptome probe set (mouse data probeset v1.0) and default parameter settings. Generated ST gene expression count matrices were then analyzed using Seurat v4.1.0 to perform unsupervised clustering analysis.
Assembly: mm10
Supplementary files format and content: Comma-separated values and matrix files

organism: Mus musculus

extract_protocol:
Murine lung single cells were  stained with a cocktail of antibodies (1:250 each) against CD45-PE/Cy7 (103114, BioLegend), Icam2-A647 (A15452, Life Technologies), Epcam-BV421 (118225, BioLegend), and Ecad-A488 (53-3249-80, eBioscience). Stained cells were then washed, filtered using 40 μm filters, stained with SYTOX Blue and processed on a FACS Aria I instrument. Doublets and dead cells were eliminated, and viable (SYTOX-negative) epithelial singlets were collected in PBS containing 2% FBS. Cells were washed again to eliminate ambient RNA, and a sample was taken for counting by Trypan Blue exclusion before loading on 10XGenomics Chromium microfluidic chips. Spatial transcriptomic (ST) profiling of FFPE tissues of three Gprc5a-/- mouse samples was performed using the Visium platform from 10X Genomics according to manufacturer’s recommendations and as previously reported by our group.
Up to 10,000 cells per sample were partitioned into nanoliter-scale Gel beads-in-emulsion (GEMs) using Chromium Next GEM Single Cell 5' Gel Bead Kit v1.1 (1000169, 10XGenomics, ) and by loading onto Chromium Next GEM Chips G (1000127, 10XGenomics, Pleasanton, CA). GEMs were then recovered to construct single-cell gene expression libraries using the Chromium Next GEM Single Cell 5’ Library kit (1000166, 10XGenomics) according to the manufacturer’s protocol. Briefly, recovered barcoded GEMs were broken and pooled, followed by magnetic bead clean-up (Dynabeads MyOne Silane, 37002D, Thermo Fisher Scientific). 10X-barcoded full-length cDNA was then amplified by PCR and analyzed using Bioanalyzer High Sensitivity DNA kit (5067-4626, Agilent). Up to 50 ng of cDNA was carried over to construct gene expression libraries and was enzymatically fragmented and size-selected to optimize the cDNA amplicon size prior to 5’ gene expression library construction. Further, samples were subject to end-repair, A-tailing, adaptor ligation, and sample index PCR using Single Index Kit T Set A (2000240, 10XGenomics) to generate Illumina-ready barcoded gene expression libraries. Library quality and yield was measured using Bioanalyzer High Sensitivity DNA (5067-4626, Agilent) and Qubit dsDNA High Sensitivity Assay (Q32854, Thermo Fisher Scientific) kits. Indexed libraries were normalized by adjusting for the ratio of the targeted cells per library as well as individual library concentration and then pooled to a final concentration of 10 nM. Library pools were then denatured and diluted as recommended for sequencing on the Illumina NovaSeq 6000 platform. For ST profiling, regions of interest per tissue/sample, each comprising a 6.5 x 6.5 mm capture area, were selected based on careful annotation of Hematoxylin and Eosin (H&E)-stained slides that were digitally acquired using the Aperio ScanScope Turbo slide scanner (Leica Microsystems Inc., Buffalo Grove, IL). HALO software (Indica Labs, Albuquerque, NM) was used for pathological annotation (tumour areas, blood vessels, bronchioles, lymphoid cell aggregates, macrophages, muscle tissue, normal parenchyma, and reactive pneumocytes) of H&E histology images. Spot-level histopathological annotation visualization was generated using loupe browser (v6.3.0). Briefly, cloupe file generated from Spaceranger was loaded into loupe browser along with the annotation table file , the annotation visualization was then generated in svg format using the export plot tool. Spatial transcriptomic RNA-seq libraries were generated according to manufacturer’s instructions, each with up to ~3,600 uniquely barcoded spots. Libraries were sequenced on Illumina NovaSeq 6000 platform to achieve a depth of at least 50,000 mean read pairs/spot and at least 2,000 median genes/spot
For scRNA-seq analysis of lung tissues from Gprc5a-/- mice, lung single cells were stained with a cocktail of antibodies (1:250 each) against CD45-PE/Cy7 (103114, BioLegend), Icam2-A647 (A15452, Life Technologies), Epcam-BV421 (118225, BioLegend), and Ecad-A488 (53-3249-80, eBioscience) to sort out epithelial and non-epithelial cells. Stained cells were then washed, filtered using 40 μm filters, stained with SYTOX Blue and processed on a FACS Aria I instrument. Doublets and dead cells were eliminated, and viable (SYTOX-negative) epithelial singlets were collected in PBS containing 2% FBS. Cells were washed again to eliminate ambient RNA, and a sample was taken for counting by Trypan Blue exclusion before loading on 10X Genomics Chromium microfluidic chips. Cells from Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mice were processed similarly except for sorting by GFP. Spatial transcriptomic (ST) profiling of FFPE tissues was performed using the Visium platform from 10X Genomics according to manufacturer’s recommendations.

value: Mouse lung cells

value: Lung

tag: age

value: 7 months


title: TRIBEID_1-SS3_1-SS3-G9

value: Human embryonic kidney cells


title: Lungs from Gprc5a-/- mouse 23 at 3 months post-saline

description: Library name: KOS3_27


title: pA-DamID_RPE1_iCUT_WT_SCII_LB1_r1


title: TRIBEID_1-SS3_1-SS3-G8


title: pA-DamID_RPE1_iCUT_WT_SCII_DAM_r1


title: pA-DamID_RPE1_iCUT_WT_SCII_LB2_r1


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB2_Cal_r7


title: ctrl_1-SS3_1-SS3-H2


title: Lungs from Gprc5a-/- mouse 22 at 3 months post-saline

description: Library name: KOS3_26


title: pA-DamID_RPE1_SunTag_TOP2BKD_DAM_Cal_r7


title: Lungs from Gprc5a-/- mouse 20 at 3 months post-NNK

description: Library name: KOK3_32


title: pA-DamID_RPE1_SunTag_SCII_LB2_Cal_r7


title: pA-DamID_RPE1_SunTag_SCII_LB1_Cal_r2


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB1_Cal_r2


title: Lungs from Gprc5a-/- mouse 19 at 3 months post-NNK

description: Library name: KOK3_31


title: pA-DamID_RPE1_SunTag_SCII_DAM_Cal_r7


title: TRIBEID_1-SS3_1-SS3-G6


title: TRIBEID_1-SS3_1-SS3-G4


title: Lungs from Gprc5a-/- mouse 18 at 3 months post-NNK

description: Library name: KOK3_30


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB1_Cal_r1


title: pA-DamID_RPE1_SunTag_TOP2BKD_DAM_Cal_r6


title: Lungs from Gprc5a-/- mouse 17 at 3 months post-NNK

description: Library name: KOK3_29


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB2_Cal_r6


title: TRIBEID_1-SS3_1-SS3-G5


title: TRIBEID_1-SS3_1-SS3-G3


title: Lungs from Gprc5a-/- mouse 21 at 3 months post-saline

description: Library name: KOS3_25


title: pA-DamID_RPE1_SunTag_SCII_DAM_Cal_r6


title: TRIBEID_1-SS3_1-SS3-G1


title: DM6-9_S3 Lung tumour. Untreated

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: DM6-9_S3

data_processing:
Alignment was performed with Cell Ranger v3.1.0 against a custom transgenic reference.
Assembly: Custom transgenic reference based on GRCm38 (mouse genome and sequence for iRFP, human MYC and KRAS-G12D).
Supplementary files format and content: h5

extract_protocol:
Lungs from SPC-Cre+ KM genetically engineered mice were microdissected under a stereomicroscope. For obtaining a single cell suspension of tumour total cells, enzymatic dissociation with 1 mg/ml Collagenase D (Roche) and 25 mg/mL DNAse I (Thermo Fisher Scientific) was carried out using the gentleMACS Octo Dissociator (Miltenyi Biotec). Then, tumour suspensions were mashed through a 70 m filter and live cells were enriched using debris removal solution (Miltenyi Biotec).
For single-cell RNA-Seq, 40,000 cells were loaded per channel onto a Chromium Chip G using reagents from the 10x Genomics Chromium Single Cell 3′ v3 chemistry according to the manufacturer’s instructions. Libraries were constructed following the standard 10x Genomics Chromium 3 prime protocol. Library quality and fragment size distributions were evaluated using the Agilent Bioanalyzer High Sensitivity DNA kit. The prepared scRNA-seq libraries were then sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.

value: SPC-Cre+ KrasG12D+/-;MYC+/+ (KM)

value: Untreated


title: TRIBEID_1-SS3_1-SS3-G2


title: pA-DamID_HCT_wt_TOP2A_AID_TOP2BKO_DAM_r3

source_name: colon

value: colon

value: TOP2B KO


title: pA-DamID_RPE1_SunTag_SCII_LB2_Cal_r6

value: retina


title: pA-DamID_RPE1_SunTag_SCII_LB1_Cal_r1


title: DM6-8_S2 Lung tumour. Untreated

description: Library name: DM6-8_S2


title: pA-DamID_HCT_wt_TOP2A_AID_TOP2BKO_LB2_r3


title: pA-DamID_HCT_wt_TOP2A_AID_DAM_C_r3

value: Control WT


title: DM6-7_S1 Lung tumour. Untreated

description: Library name: DM6-7_S1


title: pA-DamID_HCT_wt_TOP2A_AID_LB2_r3


title: pA-DamID_K562_TOP2BKO_DAM_r2


title: pA-DamID_K562_wt_DAM_r2


title: TRIBEID_1-SS3_1-SS3-G12


title: 11-6_S389 Lung tumour. Vehicle (peanut oil)

description: Library name: 11-6_S389

value: Vehicle (peanut oil)


title: TRIBEID_1-SS3_1-SS3-G11


title: pA-DamID_HCT_wt_TOP2A_AID_TOP2BKO_DAM_r2


title: 11-5_S388 Lung tumour. Vehicle (peanut oil)

description: Library name: 11-5_S388


title: TRIBEID_1-SS3_1-SS3-G10


title: TRIBEID_1-SS3_1-SS3-F9


title: 11-4_S387 Lung tumour. Vehicle (peanut oil)

description: Library name: 11-4_S387


title: pA-DamID_HCT_wt_TOP2A_AID_TOP2BKO_r2


title: pA-DamID_K562_wt_LB2_r2

source_name: lymphoblastoid

value: lymphoblastoid


title: pA-DamID_HCT_wt_TOP2A_AID_LB2_r2


title: pA-DamID_HCT_wt_TOP2A_AID_TOP2BKO_DAM_r1


title: 11-3_S386 Lung tumour. Treated with Neratinib for 3 days.

description: Library name: 11-3_S386

value: Treated with Neratinib for 3 days.


title: pA-DamID_K562_TOP2B_KO_DAM_r1

value: Dam only


title: pA-DamID_K562_wt_DAM_r1


title: 11-2_S385 Lung tumour. Treated with Neratinib for 3 days.

description: Library name: 11-2_S385


title: 11-1_S19 Lung tumour. Treated with Neratinib for 3 days.

description: Library name: 11-1_S19


title: TRIBEID_1-SS3_1-SS3-F8


title: pA-DamID_HCT_wt_TOP2A_AID_TOP2BKO_LB2_r1


title: pA-DamID_HCT_wt_TOP2A_AID_DAM_r1


title: TRIBEID_1-SS3_1-SS3-F5


title: pA-DamID_HCT_wt_TOP2A_AID_LB2_r1


title: pA-DamID_HCT_wt_TOP2A_AID_DAM_r2


title: TRIBEID_1-SS3_1-SS3-F3


title: Nanopore_HEK293T_induced_APOBEC1-DDX6_LSM14A-ADAR2dd

description:
ONT long-read sequencing
Median_polyA-tail_length_of_target_mRNAs_in_HEK293T_cells.txt

data_processing:
Data processing for short-read RNA-seq: mRNA-seq libraries were sequenced using a paired-end 150 bp strategy on the Illumina NovaSeq 6000 System (Haplox genomics center). Sequencing quality was assessed with FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences were removed using Cutadapt (v1.18) with parameters: -j 40 -m 20 -q 20. The reads were then filtered for those derived from repetitive elements using sequences from the UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgTables) and afterwards aligned to the hg38 reference genome with STAR (v2.7.9a). Uniquely mapped reads were quantified using featureCounts (v2.0.1) against Gencode annotations (v37, Ensembl 103) with the following parameters: -T 24 -s 2 -p -B -C -g gene_name -Q 30.
RNA editing analysis for short-read mRNA-seq: After aligning reads to the genome, BAM files were further processed using SAILOR (v1.2.0) to identify C-to-U and A-to-I edit sites across the hg38 reference genome. In brief, known SNPs (dbSNP, v155) and potential artifacts were filtered. Candidate edit sites were identified based on the number of C-to-U or A-to-I conversions. Edit sites with confidence value larger than 0.65 were retained. The retained edit sites were further filtered based on the coverage (coverage ≥ 10) and mutation frequency (frequency < 0.95). Subsequently, sites annotated within the 5' UTR, CDS, or 3' UTR were extracted for further analysis. The reads containing the high-confidence edit sites were extracted using biostar214299 (https://www.biostars.org/p/214299/).
Assembly: hg38 reference genome
Supplementary files format and content: Translation efficiency of genes; Editing score of genes; Poly(A)-tail length of genes; TPM of genes

extract_protocol:
For mRNA-seq and ONT long-read sequencing, total RNAs were extracted using TRlzol Reagent (Invitrogen, 15596026) according to the manufacturer’s protocol. For scRNA-seq, single cells were sorted into each well of 96-well plates containing 3 µL lysis buffer (0.3 µL 1% Triton X-100 (Sigma Aldrich, T9284), 0.05 µL 10 µM Oligo dT primer, 0.2 µL 10 mM dNTPs mix (Thermo Scientific, R0191), 0.03 µL 40 U/µL RNase inhibitor (Takara, 2313A), 0.4 µL 50% PEG8000 (Sigma Aldrich, 89510) and 2.02 µL ddH2O).
500 ng total RNA was used as input material for the mRNA-seq library construction (YEASEN, 12309ES96) following the manufacturer’s protocol. Sequencing library was generated using 500 ng-2 µg total RNA was as input for ONT long-read sequencing library construction (ONT, SQK-PCS109). Single-cell RNA sequencing libraries were generated using the Smart-seq3xpress protocol.


title: KO_Stimulated_rep1

first: Pavan

last: Reddy

address: 1 Baylor Plz

institute: Baylor College of Medicine

description:
Library name: KO_Stimulated_rep1
10x Genomics

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the Cell Ranger Pipeline (10x Genomics) was used to align reads and generate count matrices.
Assembly: Mouse mm10
Supplementary files format and content: comma-separated counts matrix files and metadata file

source_name: T cells

extract_protocol:
Primary murine T cells were from WT and SDHA KO mice were purified by magnetic separation (Pan T Cell Isolation Kit II, mouse, 130-095-130, Miltenyi Biotec) from single cell homogenates of spleens and cultured in cell media (1640 RPMI supplemented with 10% heat inactivated FBS, 2 mM L-glutamine, 100 U/mL penicillin-streptomycin, 100 mM HEPES, nonessential amino acids, 1 mM sodium pyruvate, and 50 μM β-mercaptoethanol). Purified T cells were cultured alone, or with 5 μg/mL Ultra-LEAF™ Purified anti-mouse CD3ε (clone 145-2C11, 100359, BioLegend) and 2.5 μg/mL Ultra-LEAF™ Purified anti-mouse CD28 (clone 37.51, 102121, BioLegend) soluble antibodies for 48h. Unstimulated and stimulated T cells were utilized after removing dead cells by Dead Cell Removal Kit (130-090-101, Miltenyi Biotec).
Single cell suspensions were subjected to final cell counting on the LUNA-FX7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 700-1000 cells/µL. 3’ single cell libraries were generated using the 10x Genomics Chromium Controller and following the manufacturer’s protocol for 3’ HT v3.1 chemistry (10x Genomics). Final library quality was assessed using the LabChip GXII HT (PerkinElmer) and libraries were quantified by Qubit (Thermo Fisher Scientific). Pooled libraries were subjected to 28x10x10x151 bp paired-end sequencing according to the manufacturer’s protocol (NovaSeq 6000, Illumina).

value: T cells

value: KO

value: Stimulated


title: WT_Stimulated_rep2

description:
Library name: WT_Stimulated_rep2
10x Genomics

value: WT


title: TRIBEID_1-SS3_1-SS3-F4


title: TRIBEID_1-SS3_1-SS3-F2


title: pA-DamID_K562_TOP2B_KO_LB2_r2


title: iPSC-CM_IndA_Untr_TOP2B_ChIP

city: Galveston

first: Michelle

middle: C.

last: Ward

address: 301 University blvd.

institute: UTMB

description: Library name: IndA_Untr_TOP2B_ChIP

data_processing:
Paired-end ChIP and Input reads were assessed for quality using FastQC (v0.11.9), then aligned to the human genome (GRCh38/hg38) using Bowtie2 (v2.5.1). Uniquely mapped read pairs were retained with bamtools filter, and PCR duplicates were removed using Picard MarkDuplicates with optical duplicate detection. MACS2 (v2.2.7.1) was used for broad peak calling (--broad) with matched input control, using a q-value threshold of 0.05 and broad cutoff of 0.1. Fragment size was estimated with mfold=5–50 and bandwidth=300.
Assembly: hg38
Supplementary files format and content: PAUL_TOP2B_ChIP.bed

growth_protocol: Human iPSC-dervied cardiomyocytes were maintained in Cardiomyocyte Maintenance Media (500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (MT35015CV, Corning), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL Penicillin/Streptomycin) on Matrigel-coated dishes at 37°C, 5% CO2 and atmospheric O2.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed to map TOP2B binding sites in untreated iPSC-derived cardiomyocytes from individual UCSD143i-87-1. Approximately 40 million cells were fixed in 1% formaldehyde, quenched with glycine, and flash-frozen. Chromatin was extracted, sequentially lysed, and sonicated using a Covaris system to generate 250–400 bp fragments. Immunoprecipitation was performed overnight at 4 °C using anti-TOP2B antibody (Abcam ab72334) pre-bound to Dynabeads Protein G. After stringent washes, chromatin was eluted and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then resuspended for library preparation.
ChIP and Input DNA libraries were constructed using the TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1012) following manufacturer instructions with minor modifications. Starting with all the ChIP DNA and 50ng of  input DNA, end repair and A-tailing were performed prior to ligation of indexed adapters (ACAGTG for ChIP, GCCAAT for Input). Adapter-ligated DNA was PCR-amplified for 18 cycles and purified using AMPure XP beads. Libraries were size-selected (250–400 bp) by gel excision, then purified with the MinElute Gel Extraction Kit (Qiagen). Library concentration and size distribution were assessed by Qubit and Agilent Bioanalyzer. Final libraries were sequenced as 40 bp paired-end reads: ChIP library on the Illumina NextSeq 550 (generated 40,380,049 reads) and Input library on the Illumina MiniSeq (20,968,544 reads).

treatment_protocol: Chromatin immunoprecipitation was performed to map endogenous TOP2B binding sites in untreated human iPSC-derived cardiomyocytes. ChIP and matched input DNA were collected from 40 million cells each, derived from a single female donor line (UCSD143i-87-1). No drug treatment was applied prior to cell harvesting.

tag: Sex

value: female

value: induced pluripotent stem cell-derived cardiomyocytes

value: anti-TOP2B polyclonal antibody (Abcam, ab72334)


title: pA-DamID_K562_wt_LB2_r1


title: Prostate cancer organoid cells, KBO159

city: Tokyo

first: Yuto

last: Baba

address: 35 Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

description:
Library name: KBO159
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/jp/software/cell-ranger/downloads#download-links)
Assembly: Human GRCh38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: Prostate

extract_protocol:
Organoids were harvested from Matrigel and enzymatically dissociated into single cells using TrypLE™ Express Enzyme (1X) at 37°C for 10 minutes, with gentle pipetting. Cells were washed and resuspended in washing buffer (Advanced DMEM/F12, Glutamax 100X, HEPES solution 1M, Penicillin/Streptomycin X100). Cell viability>90% was confirmed for each PDO line by luciferase assay.
Single-cell RNA sequencing (scRNA-seq) was performed using the Chromium Single Cell 3’  platform (10x Genomics, Pleasanton, CA, USA). Reverse transcription, cDNA amplification, and library construction were carried out using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) according to the manufacturer’s protocol. Pooled libraries were sequenced on an Illumina NextSeq 2000 using a P3 flow cell with the following cycle configuration for 3’ v3.1 Dual Index.

value: Prostate

value: Prostate cancer cells


title: Nanopore_HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd

description:
ONT long-read sequencing
Median_polyA-tail_length_of_target_mRNAs_in_HCT116_cells.txt

value: Human colon cancer cells


title: pA-DamID_K562_TOP2BKO_LB2_r1

value: TOP2B KO


title: pA-DamID_RPE1_SunTag_TOP2B_K27M3_r2

value: retina

value: TOP2B KD


title: TRIBEID_1-SS3_1-SS3-F6

value: Human embryonic kidney cells


title: WT_Stimulated_rep1

description:
Library name: WT_Stimulated_rep1
10x Genomics


title: KO_Stimulated_rep2

description:
Library name: KO_Stimulated_rep2
10x Genomics


title: KO_Unstimulated_rep2

description:
Library name: KO_Unstimulated_rep2
10x Genomics

value: Unstimulated


title: TRIBEID_1-SS3_1-SS3-F11


title: Prostate cancer organoid cells, KBO152

description:
Library name: KBO152
10x Genomics


title: pA-DamID_RPE1_SunTag_TOP2B_K9M2_r2


title: KO_Unstimulated_rep1

description:
Library name: KO_Unstimulated_rep1
10x Genomics


title: Prostate cancer organoid cells, KBO114

description:
Library name: KBO114
10x Genomics


title: TRIBEID_1-SS3_1-SS3-F10


title: pA-DamID_RPE1_SunTag_TOP2B_K9M3_r2


title: WT_Unstimulated_rep2

description:
Library name: WT_Unstimulated_rep2
10x Genomics


title: Prostate cancer organoid cells, KBO111

description:
Library name: KBO111
10x Genomics


title: TRIBEID_1-SS3_1-SS3-E9


title: pA-DamID_RPE1_SunTag_TOP2BKD_TOP2Bab_r3


title: WT_Unstimulated_rep1

description:
Library name: WT_Unstimulated_rep1
10x Genomics


title: Prostate cancer organoid cells, KBO105

description:
Library name: KBO105
10x Genomics


title: TRIBEID_1-SS3_1-SS3-E6


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB2_r5


title: TRIBEID_1-SS3_1-SS3-F1


title: d7_TRF1FAP_lightdye_3

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5115 Centre Ave.

institute: University of Pittsburgh

description:
Library name: d7_TRF1FAP_lightdye_3
d7_counts.csv

data_processing:
Adapter trimming with Fastp
Transcript quantitation with Salmon
Assembly: GRCm39
Supplementary files format and content: CSV, transcript counts (Gencode M32)

source_name: spleen

extract_protocol: Takara SMART-Seq HT protocol per manufacturer's instructions.

value: spleen

value: CD8+ T cell

value: 18hr plate-bound anti-CD3/CD28 stimulation, 660nm light treated, passaged in the presence of IL-2 for 7 days.


title: TRIBEID_1-SS3_1-SS3-E5


title: pA-DamID_RPE1_SunTag_TOP2BKD_DAM_r5

value: Dam only


title: TRIBEID_1-SS3_1-SS3-E4


title: d7_TRF1FAP_lightdye_2

description:
Library name: d7_TRF1FAP_lightdye_2
d7_counts.csv


title: mouse_MPP2-3-Arid1a-Arid1b dKO, bio rep 2

city: St. Louis

first: George

middle: P.

last: Souroullas

state: MO

address: 660 S. Euclid Av

department: Medicine

institute: Washington University School of Medicine

description: Library name: Sample 29

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
RNA-seq reads were then aligned and quantitated to the appropriate mouse or human genome with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights  function and were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis (SVA).  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Ensembl release 101 for human samples and mouse Ensembl GRCm39.113 for mouse samples
Supplementary files format and content: tab-delimited text file contains CPM and RPKM values for each sample

source_name: Bone marrow

growth_protocol: SUDHL6 cells were cultured in RPMI 1640 supplemented with 20% FBS and 1% Pen/Strep.  Mouse primary multipotent progenitors (MPPs) were harvested from bone marrow, sorted using FACS, and processed for RNA isolation right after.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturer's instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Bone marrow

value: Arid1a-Arid1b dKO


title: mouse_MPP2-3-Arid1a-Arid1b dKO, bio rep 1

description: Library name: Sample 28


title: d7_TRF1FAP_lightdye_1

description:
Library name: d7_TRF1FAP_lightdye_1
d7_counts.csv


title: pA-DamID_RPE1_SunTag_SCII_K27M3_r2


title: TRIBEID_1-SS3_1-SS3-E3


title: mouse_MPP2-3-Ctrl, bio rep 6

description: Library name: Sample 27


title: pA-DamID_RPE1_SunTag_SCII_K9M2_r2


title: d7_TRF1FAP_light_3

description:
Library name: d7_TRF1FAP_light_3
d7_counts.csv


title: mouse_MPP2-3-Ctrl, bio rep 5

description: Library name: Sample 26


title: pA-DamID_RPE1_SunTag_SCII_K9M3_r2


title: d7_TRF1FAP_light_2

description:
Library name: d7_TRF1FAP_light_2
d7_counts.csv


title: TRIBEID_1-SS3_1-SS3-E2


title: TRIBEID_1-SS3_1-SS3-E11


title: mouse_MPP2-3-Ctrl, bio rep 4

description: Library name: Sample 25


title: pA-DamID_RPE1_SunTag_SCII_TOP2Bab_r3


title: d7_TRF1FAP_light_1

description:
Library name: d7_TRF1FAP_light_1
d7_counts.csv


title: TRIBEID_1-SS3_1-SS3-E10


title: pA-DamID_RPE1_SunTag_SCII_LB2_r5


title: mouse_MPP2-3-Arid1a-Arid1b dKO, bio rep 3

description: Library name: Sample 30


title: mouse_MPP2-3-Ctrl, bio rep 3

description: Library name: Sample 24


title: d7_mitoFAP_lightdye_3

description:
Library name: d7_mitoFAP_lightdye_3
d7_counts.csv


title: TRIBEID_1-SS3_1-SS3-D9


title: d7_mitoFAP_lightdye_2

description:
Library name: d7_mitoFAP_lightdye_2
d7_counts.csv


title: mouse_MPP2-3-Ctrl, bio rep 2

description: Library name: Sample 23


title: pA-DamID_RPE1_SunTag_TOP2B_K27M3_r1


title: TRIBEID_1-SS3_1-SS3-D7


title: mouse_MPP2-3-Ctrl, bio rep 1

description: Library name: Sample 22


title: pA-DamID_RPE1_SunTag_TOP2B_K9M2_r1


title: TM.F.T.12 MMTVCre Pik3caf/wt tumor, treated with weekly testosterone cypionate

city: Boston

first: Jan

last: Heng

state: MA

address: 330 Brookline Ave, Dana 517B

department: Pathology

institute: Beth Israel Deaconess Medical Center

description:
Library name: TM.F.T.12
TM.F.T.12

data_processing:
Mouse: Raw data were trimmed using Trimmomatic v.0.36 and mapped to the Mus muscu-lus GRCm38 reference genome using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Human: The Visualization Pipeline for RNAseq (VIPER) version 6816879 processed the Fastq files into raw data counts for downstream analysis.
Assembly: Mus musculus GRCm38 reference genome; Human GRCh37 (hg19)
Supplementary files format and content: raw counts of mouse and human samples are separate
Supplementary files format and content: voomnormalized data for mouse and human samples are separate

source_name: Breast tumor

extract_protocol:
Qiagen RNeasy FFPE Kit for human samples; Qiagen RNA RNeasy Micro Kit for fresh frozen murine tumors.
Mouse RNA sequencing was performed by Azenta Life Sciences.
Human RNA library was prepared using the KAPA RiboErase Kit.

treatment_protocol:
Mice experiment: MMTVCre Pik3caf/wt mice were treated with weekly 200 ng of testosterone cypionate s.c or were untreated (control) starting at age 8 weeks, and were followed until a tumor of 8mm developed.
Human study experiment: Subjects were taking testosterone therapy between 15 and 17 months prior to chest-contouring surgery. The other subjects were age-matched and did not take testosterone therapy.

value: Breast tumor

value: MMTVCre Pik3caf/wt

value: Testosterone


title: TRIBEID_1-SS3_1-SS3-D8

data_processing:
Sequencing reads were preprocessed and mapped to hg38 assembly. PCR duplicates were removed using Picard MarkDuplicates (v2.27.4, https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard) with the option REMOVE_DUPLICATES=true. FeatureCounts (v2.0.1) was used to quantify uniquely mapped reads with parameters: -p -B -C -g gene_name -Q 30. Cells with > 7,000?detected genes and > 150,000 deduplicated reads were included in downstream analysis. Genes with < 10 mapped reads across all cells were excluded. Feature counts for each cell were normalized using the NormalizeData function from Seurat (v5.0.3), with the LogNormalize method and a scale factor of 10,000.
Assembly: hg38 reference genome
Supplementary files format and content: Expression value for quality control-processed single cells

extract_protocol: For the single-cell RNA sequencing, single cells were sorted into each well of 96-well plates containing 3 µL lysis buffer (0.3 µL 1% Triton X-100 (Sigma Aldrich, T9284), 0.05 µL 10 µM Oligo dT primer, 0.2 µL 10 mM dNTPs mix (Thermo Scientific, R0191), 0.03 µL 40 U/µL RNase inhibitor (Takara, 2313A), 0.4 µL 50% PEG8000 (Sigma Aldrich, 89510) and 2.02 µL ddH2O). Single-cell RNA sequencing libraries were generated using the Smart-seq3xpress protocol.


title: d7_mitoFAP_light_2

description:
Library name: d7_mitoFAP_light_2
d7_counts.csv


title: pA-DamID_RPE1_SunTag_TOP2B_K9M3_r1


title: TM.F.T.10 MMTVCre Pik3caf/wt tumor, treated with weekly testosterone cypionate

description:
Library name: TM.F.T.10
TM.F.T.10


title: pA-DamID_RPE1_SunTag_SCII_DAM_r5


title: TRIBEID_1-SS3_1-SS3-D6


title: TM.F.T.8 MMTVCre Pik3caf/wt tumor, treated with weekly testosterone cypionate

description:
Library name: TM.F.T.8
TM.F.T.8


title: TRIBEID_1-SS3_1-SS3-D5


title: d7_mitoFAP_light_3

description:
Library name: d7_mitoFAP_light_3
d7_counts.csv


title: pA-DamID_RPE1_SunTag_TOP2BKD_TOP2Bab_r2


title: TM.F.T.7 MMTVCre Pik3caf/wt tumor, treated with weekly testosterone cypionate

description:
Library name: TM.F.T.7
TM.F.T.7


title: TRIBEID_1-SS3_1-SS3-D4


title: TRIBEID_1-SS3_1-SS3-D2


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB2_r4


title: pA-DamID_RPE1_SunTag_TOP2BKD_DAM_r4


title: TRIBEID_1-SS3_1-SS3-D1


title: d7_mitoFAP_lightdye_1

description:
Library name: d7_mitoFAP_lightdye_1
d7_counts.csv


title: pA-DamID_RPE1_SunTag_SCII_K27M3_r1


title: TM.F.T.5 MMTVCre Pik3caf/wt tumor, treated with weekly testosterone cypionate

description:
Library name: TM.F.T.5
TM.F.T.5


title: TM.F.C.21 MMTVCre Pik3caf/wt tumor, control

description:
Library name: TM.F.C.21
TM.F.C.21

value: Control


title: TRIBEID_1-SS3_1-SS3-D12


title: pA-DamID_RPE1_SunTag_SCII_K9M2_r1


title: Cd8+ T-cells, CSP, WT

city: Melbourne

first: Nikita

last: Potemkin

state: Vic

address: 792 Elizabeth St

department: The Peter Doherty Institute for Infection and Immunity

country: Australia

institute: University of Melbourne

description: Library name: Wild-type_CSP

library_source: other

data_processing:
CITE-seq and multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data were processed using the Cellranger Multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Mouse Small Intestine

extract_protocol:
To discriminate circulating T cells, mice were intravenously injected with 3ug of anti-CD45.2 BV605 (104) or anti-CD8a PE (53-6.7) 3 min prior to CO2 euthanasia where indicated. Small intestine were cleared of luminal contents and Peyer’s patches were excised. Intestines were longitudinally opened and cut into ~1-2cm fragments which were incubated at 37°C (180rpm, 45° rotation) in 20 ml of Ca2+/Mg2+-free HBSS containing 5 mM DTT, 10 mM HEPES, and 2% FCS. The supernatant was collected as the intra-epithelial lymphocyte layer and purified using a 40/80% Percoll gradient centrifugation. Remaining intestinal pieces were then recovered through a 70 μM strainer and washed once with HBSS with 2% FCS, filtered and transferred to GentleMACS C tube with 5 ml of digestion buffer (0.1 W/ml of LiberaseTM, 30 μg/ml Dnase I, 10 mM HEPES in HBSS with 2% FCS) and incubated for 30 min, 37°C with gentle stirring. The suspension was passed over a 70 μM cell strainer, remaining pieces were mashed through the strainer and washed with 20 ml of ice-cold HBSS with 2% FCS before centrifugation at 1,500 rpm at 4°C for 5 minutes. Lamina propria lymphocytes were then isolated by 40/80% percoll gradient centrifugation.
Libraries were performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Mouse Small Intestine

value: P14 CD8+ T cells

value: Wildtype Hobit-TomCre P14 T cells

value: LCMV Armstrong infection; circulating memory cell depletion and secondary rechallenge with Listeria Monocytogenes-GP33


title: TM.F.C.18 MMTVCre Pik3caf/wt tumor, control

description:
Library name: TM.F.C.18
TM.F.C.18


title: Cd8+ T-cells, GEX, WT

description: Library name: Wild-type_GEX

data_processing:
CITE-seq and multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data were processed using the Cellranger Multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: pA-DamID_RPE1_SunTag_SCII_K9M3_r1

value: retina


title: TRIBEID_1-SS3_1-SS3-D11

value: Human embryonic kidney cells


title: PMIA_4

data_processing:
Adapter trimming with Fastp.
Transcript quantitation with Salmon.
Assembly: GRCm39
Supplementary files format and content: CSV, transcript counts (Gencode M32).

source_name: tumor

extract_protocol:
Takara SMART-Seq HT protocol per manufacturer's instructions.
Paired-end

value: tumor

value: B16 xenograft

value: Tumor-infiltrating CD8+ T cell

value: Pre-infusion transduction with PMIA control construct


title: d7_mitoFAP_light_1

description:
Library name: d7_mitoFAP_light_1
d7_counts.csv

value: spleen

value: CD8+ T cell

value: 18hr plate-bound anti-CD3/CD28 stimulation, 660nm light treated, passaged in the presence of IL-2 for 7 days.


title: TM.F.C.16 MMTVCre Pik3caf/wt tumor, control

description:
Library name: TM.F.C.16
TM.F.C.16

value: Breast tumor


title: TRIBEID_1-SS3_1-SS3-D10


title: pA-DamID_RPE1_SunTag_SCII_TOP2Bab_r2


title: TRIBEID_1-SS3_1-SS3-C8


title: Cd8+ T-cells, CSP, KO

description: Library name: Knock-out_CSP

value: Tcf7fl/fl Hobit-TomCre P14 T cells


title: TM.F.C.10 MMTVCre Pik3caf/wt tumor, control

description:
Library name: TM.F.C.10
TM.F.C.10

value: MMTVCre Pik3caf/wt


title: Cd8+ T-cells, GEX, KO

description: Library name: Knock-out_GEX


title: TRIBEID_1-SS3_1-SS3-C7


title: pA-DamID_RPE1_SunTag_SCII_DAM_r4

value: Dam only


title: GPX_4

value: Pre-infusion transduction with GPX1-TRF1 construct


title: NoTransplant, biol rep 2, saline

city: Philadelphia

first: Carleigh

middle: A

last: O'Brien

address: 3600 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: salineNoTx_2NoTx-sal
Column name in raw counts RawGeneCounts.tsv: salineNoTx_2NoTx-sal

data_processing:
Quality control of raw sequencing data was performed using FastQC (v0.11.9) followed by MultiQC (v1.14)
Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.7), a wrapper around Cutadapt (v3.4), with default quality threshold parameters (Phred score < 20) and minimum read length of 20 bp after trimming
Preprocessed reads were aligned to the Mus musculus reference genome (GRCm39 primary assembly) using STAR (v2.7.10a) with default alignment parameters. The reference annotation used was Ensembl release 111 (Mus_musculus.GRCm39.111.gtf.gz)
Aligned reads were quantified at the gene level using featureCounts (Subread package v2.4.5), counting only reads that mapped to exonic regions
Following alignment and quantification, gene-level counts were extracted from the featureCounts output and processed using DESeq2 (v1.36.0)^12^
Prior to differential expression analysis, low abundance genes were filtered by requiring a minimum TPM count of 10 in at least 2 samples. Normalized counts were obtained using the variance stabilizing transformation (VST) method
Assembly: Mus musculus reference genome (GRCm39 primary assembly), Mus_musculus.GRCm39.111.gtf.gz
Supplementary files format and content: plain text file (RawGeneCounts.tsv) includes raw counts for each sample

source_name: brain

extract_protocol:
RNA was isolated from FACS sorted cells using the Rneasy micro kit (Qiagen).
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina following manufacturers protocols, with 8ul RNA input per sample

value: brain

value: microglia

value: CX3CR1-CreER+/-; CSF1R fl/fl

value: saline


title: pA-DamID_RPE1_SunTag_BLEO0_1_LB2_r2

value: retina

value: Bleomycin 100 nM


title: GPX_3

value: tumor

value: B16 xenograft


title: GPX_2

value: Tumor-infiltrating CD8+ T cell


title: TransplantedMonocyte, biol rep 3, saline

description:
Library name: salineMLC_3MLC-sal
Column name in raw counts RawGeneCounts.tsv: salineMG_3MLC-sal

value: monocyte-derived microglia

value: Osb-GFP


title: pA-DamID_RPE1_SunTag_BLEO10_LB2_r2

value: Bleomycin 10 mM


title: pA-DamID_RPE1_SunTag_BLEO0_1_DAM_r2


title: GPX_1


title: TransplantedMonocyte, biol rep 2, saline

description:
Library name: salineMLC_2MLC-sal
Column name in raw counts RawGeneCounts.tsv: salineMG_2MLC-sal


title: TM.F.C.1 MMTVCre Pik3caf/wt tumor, control

description:
Library name: TM.F.C.11
TM.F.C.11

value: Breast tumor

value: Control


title: PMIA_3

value: Pre-infusion transduction with PMIA control construct


title: TRIBEID_1-SS3_1-SS3-C3

value: Human embryonic kidney cells


title: pA-DamID_RPE1_SunTag_BLEO10_DAM_r2

value: Dam only


title: PMIA_1


title: TransplantedMonocyte, biol rep 1, saline

description:
Library name: salineMLC_1MLC-sal
Column name in raw counts RawGeneCounts.tsv: salineMG_1MLC-sal

value: brain


title: TransplantedMicroglia, biol rep 3, saline

description:
Library name: salineMG_3MG-sal
Column name in raw counts RawGeneCounts.tsv: salineMG_3MG-sal

value: transplanted microglia


title: pA-DamID_RPE1_SunTag_CT_LB2_r2


title: TRIBEID_1-SS3_1-SS3-C2


title: pA-DamID_RPE1_SunTag_SCII_LB2_r4


title: TRIBEID_1-SS3_1-SS3-C1


title: pA-DamID_RPE1_SunTag_CT_DAM_r2


title: TRIBEID_1-SS3_1-SS3-C6


title: PMIA_2


title: MitoFAP_lightdye_2

value: spleen

value: CD8+ T cell

value: 18hr plate-bound anti-CD3/CD28 stimulation, 660nm light + MG-2I treatment


title: TransplantedMicroglia, biol rep 2, saline

description:
Library name: salineMG_2MG-sal
Column name in raw counts RawGeneCounts.tsv: salineMG_2MG-sal

value: saline


title: NoTransplant, biol rep 1, saline

description:
Library name: salineNoTx_1NoTx-sal
Column name in raw counts RawGeneCounts.tsv: salineNoTx_1NoTx-sal

value: microglia

value: CX3CR1-CreER+/-; CSF1R fl/fl


title: TRIBEID_1-SS3_1-SS3-C12


title: pA-DamID_RPE1_SunTag_BLEO0_1_LB2_r1

value: retina

value: Bleomycin 100 nM


title: TRIBEID_1-SS3_1-SS3-C5


title: TransplantedMicroglia, biol rep 1, saline

description:
Library name: salineMG_1MG-sal
Column name in raw counts RawGeneCounts.tsv: salineMG_1MG-sal

value: Osb-GFP


title: TRIBEID_1-SS3_1-SS3-C4


title: MitoFAP_lightdye_1


title: pA-DamID_RPE1_SunTag_BLEO0_1_DAM_r1


title: TRIBEID_1-SS3_1-SS3-C11


title: NoTransplant, biol rep 3, seizure

description:
Library name: seizureNoTx_2NoTx-F2
Column name in raw counts RawGeneCounts.tsv: seizureNoTx_1NoTx-F2

value: Kainic acid seizure


title: MitoFAP_light_3

value: 18hr plate-bound anti-CD3/CD28 stimulation, 660nm light treated


title: NoTransplant, biol rep 2, seizure

description:
Library name: seizureNoTx_1NoTx-M1
Column name in raw counts RawGeneCounts.tsv: seizureNoTx_1NoTx-M1


title: MitoFAP_light_2


title: MitoFAP_lightdye_3


title: TRIBEID_1-SS3_1-SS3-B9


title: NoTransplant, biol rep 1, seizure

description:
Library name: seizureNoTx_1NoTx-F1
Column name in raw counts RawGeneCounts.tsv: seizureNoTx_1NoTx-F1


title: TRIBEID_1-SS3_1-SS3-C10


title: pA-DamID_RPE1_SunTag_BLEO10_LB2_r1

value: Bleomycin 10 mM


title: MitoFAP_light_1


title: pA-DamID_RPE1_SunTag_CT_LB2_r1

value: Control


title: pA-DamID_RPE1_SunTag_BLEO10_DAM_r1


title: TRF1FAP_lightdye_3


title: TRIBEID_1-SS3_1-SS3-B6

value: Human embryonic kidney cells


title: pA-DamID_RPE1_SunTag_CT_DAM_r1

value: Dam only


title: TransplantedMonocyte, biol rep 6, seizure

description:
Library name: seizureMLC_2MLC11b-F2
Column name in raw counts RawGeneCounts.tsv: seizureMLC_2MLC11b-F2

value: brain

value: monocyte-derived microglia


title: TRIBEID_1-SS3_1-SS3-B5


title: TRF1FAP_lightdye_2

value: spleen


title: pA-DamID_RPE1_SunTag_TOP2BKD_TOP2Bab_r1

value: TOP2B KD


title: TransplantedMonocyte, biol rep 4, seizure

description:
Library name: seizureMLC_2MLC-F2
Column name in raw counts RawGeneCounts.tsv: seizureMLC_1MLC-F2


title: TransplantedMonocyte, biol rep 5, seizure

description:
Library name: seizureMLC_2MLC-M2
Column name in raw counts RawGeneCounts.tsv: seizureMLC_1MLC-M2


title: TRF1FAP_lightdye_1

value: CD8+ T cell

value: 18hr plate-bound anti-CD3/CD28 stimulation, 660nm light + MG-2I treatment


title: TRIBEID_1-SS3_1-SS3-B4


title: TransplantedMonocyte, biol rep 3, seizure

description:
Library name: seizureMLC_1MLC11b-M1
Column name in raw counts RawGeneCounts.tsv: seizureMLC_1MLC11b-M1


title: TRF1FAP_light_3


title: TRIBEID_1-SS3_1-SS3-B12


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB2_r3


title: TRIBEID_1-SS3_1-SS3-B8


title: TRF1FAP_light_1


title: TRIBEID_1-SS3_1-SS3-B11


title: TRF1FAP_light_2


title: pA-DamID_RPE1_SunTag_SCII_LB2_r3


title: TransplantedMicroglia, biol rep 4, seizure

description:
Library name: seizureMG_2MG-M2
Column name in raw counts RawGeneCounts.tsv: seizureMG_1MG-M2

value: transplanted microglia


title: TransplantedMonocyte, biol rep 1, seizure

description:
Library name: seizureMLC_1MLC-F1
Column name in raw counts RawGeneCounts.tsv: seizureMLC_1MLC-F1


title: aPabC_5

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

data_processing:
fastP was used to perform quality control and read trimming
The trimmed reads were aligned to a combined Mus musculus (GRCm39 Primary Assembly) and P. gingivalis ATCC 33277 genome (accession AP009380.1) using the Hisat2 aligner to generate SAM files that were subsequently converted to coordinate-sorted BAM files. Reads aligning only to P. gingivalis were split into separate BAM files.
Raw counts were generated by parsing the P. gingivalis-only BAM files using featureCounts. A count for a gene was considered valid if a read overlapped at least 7 basepairs with the gene. Any counts remaining for deleted genes in the corresponding deletion mutant strains were manually set to 0 after inspecting the alignment and ensuring no genuine reads mapped to these deleted genomic regions.
Assembly: Mus musculus (GRCm39 Primary Assembly) and P. gingivalis ATCC 33277 genome (accession AP009380.1)
Supplementary files format and content: Processed files are raw counts as generated from featureCounts and are in the form of a tab-delimited text file, where rows are gene features with each column containing sample counts
Supplementary files format and content: Processed files are raw counts as generated from featureCounts and are in the form of a tab-delimited text file, where rows are gene features and columns are individual sample counts

organism: Porphyromonas gingivalis

source_name: Mouse Abscess Material

growth_protocol: Bacteria were cultured anaerobically (85% Nitrogen, 10% carbon dioxide, 5% hydrogen), at 37 degrees Celsius in trypticase soy broth (TSB) supplemented with 1 mg/ml yeast extract, 5 ug/ml hemin, and 1 ug/ml menadione. When necessary, erythromycin (10 ug/mL) or gentamicin (50 ug/ml) was added to the medium for isogenic mutants.

extract_protocol:
Collected abscess material was briefly spun at  150 x g for 3 min at 4 degress Celsius to pellet any mouse cells present. The supernatant was transferred to a new tube and spun at 5000 x g for 5 min at 4 degrees Celsius to pellet bacteria cells. The supernatant was removed and cell pellet resuspened into TRIzol™ Reagent (Invitrogen cat #15596026) and total RNA extraction was caried out using the Qiagen RNeasy Plus Mini Kit (Qiagen cat #74136) following manufacturer protocol including an optional DNAse treatment step and eluting into nuclease-free water. Each sample of total RNA suspended in nuclease-free water was then shipped on dry ice to a commercial vendor for RNA sequencing.
Library construction was performed by Novogene. In brief, a strand-specific library was constructed with rRNA removal for 150-bp paired-end sequencing on an Illumina NovaSeq 6000.

treatment_protocol: 6-8 week old Balb/cJ mice were inoculated subcutaneously in the ventral surface of the right thigh with 1.5x10^9 bacterial cells grown to mid-logarithmic growth phase from on eo fthe following Pg strains: paraental wildtype ATCC 33277 (WT), ΔpabC, or Δptk1. The abscess was allowed to develop for 24-48 hours, after which abscess material was collected via sterile swab into chilled sterile, pre-reduced PBS solution.

value: Mouse Abscess Material

value: {delta}pabC


title: pA-DamID_RPE1_SunTag_SCII_DAM_r3

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 20 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig files of log2-normalized LaminB2  pA-DamID scores for 20 kb genomic bins.

value: retina


title: TransplantedMicroglia, biol rep 3, seizure

description:
Library name: seizureMG_2MG-F2
Column name in raw counts RawGeneCounts.tsv: seizureMG_1MG-F2

value: Osb-GFP


title: TransplantedMonocyte, biol rep 2, seizure

description:
Library name: seizureMLC_1MLC-M1
Column name in raw counts RawGeneCounts.tsv: seizureMLC_1MLC-M1

value: Kainic acid seizure


title: aPabC_4


title: pA-DamID_RPE1_SunTag_TOP2AKD_LB2_r3

value: TOP2A KD


title: TRIBEID_1-SS3_1-SS3-A7

first: Wei

last: Chen

address: 1088 Xueyuan Avenue, Shenzhen 518055,P.R. China

institute: Southern University of Science and Technology


title: aPabC_3


title: TransplantedMicroglia, biol rep 2, seizure

description:
Library name: seizureMG_1MG-M1
Column name in raw counts RawGeneCounts.tsv: seizureMG_1MG-M1


title: TRIBEID_1-SS3_1-SS3-A6


title: TransplantedMicroglia, biol rep 1, seizure

description:
Library name: seizureMG_1MG-F1
Column name in raw counts RawGeneCounts.tsv: seizureMG_1MG-F1


title: aPabC_2


title: TRIBEID_1-SS3_1-SS3-A5


title: pA-DamID_RPE1_SunTag_TOP2BKD_DAM_r3


title: pA-DamID_RPE1_SunTag_SCI_LB2_r3


title: Cartilage, Prx1Dnmt1_vivo_cKO_rep4

city: Toon

first: Yuta

last: Yanagihara

state: Ehime

address: Shitsukawa

department: Division of Integrative Pathophysiology, Proteo-Science Center

institute: Ehime university

description:
Library name: Prx1Dnmt1_vivo_cKO_rep4
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
cKO_female_2

data_processing:
Read1(barcode read) was extracted by using UMI-tools(1.1.1) with the following command “ umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC --read2-stdout ”. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (0.6.7) , and reads were mapped to the GRCm38 reference using HISAT2 (2.2.1). Read counts for each gene and each sample was obtained by summarizing bam file which was produced by featureCounts(2.0.1). Differentially expressed genes were extracted with DESeq2 (1.34.0) using |log2FC| > 1 and padj < 0.1 as threshold values.
Assembly: GRCm38(mouse)
Supplementary files format and content: Comma-separated values file includes raw counts for each Sample

source_name: Cartilage

extract_protocol:
Cartilage was extracted from P5 mice. To exclude connective tissue, cartilage tussues were treated with collagenase. Total RNA was extracted from cartilage tissues using Isogene (Nippon Gene) and RNeasy spin column kit (QIAGEN), followed by treatment with DNase I (QIAGEN).
BRB-seq(Alpern D et al.) was performed for preparing libraries with some following modifications. Barcoded oligo-dT based primer(5’-GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNNNNNCCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTTV -3’ ; (10)N=UMI, (9)C=cell barcode) was used for single-stranded synthesis and Second Strand Synthesis Module (NEB, #E6111) was used for double-stranded cDNA synthesis. In-house MEDS-B Tn5 transposase (Picelli S et al., Sato et al.) was used for tagmentation and amplified by 10 cycles of PCR using Phusion High-Fidelity DNA Polymerase(Thermo Scientific, #M0530) and following primers(5’- AATGATACGGCGACCACCGAGATCTACACindexGTTCAGAGTTCTACAGTCCGA-3',5’-CAAGCAGAAGACGGCATACGAGATindex GTCTCGTGGGCTCGGAGATGT-3' ). 15bp of barcode read (Read1) and 81bp of insert read (Read2) were obtained on Illumina NovaSeq6000.

value: Cartilage

value: cKO

value: female


title: pA-DamID_RPE1_SunTag_SCII_TOP2Bab_r1

extract_protocol:
LMNB2 pA-DamID maps were generated as previously described (van Shaik, 2022, 36050765). Briefly, one million of RPE1, HCT116 or K562 were collected by centrifugation (500 g, 3 min) and washed sequentially in ice-cold PBS and digitonin wash buffer (D-Wash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 hours at 4 °C in 200 μL D-Wash with 1:200 of: LMNB2 (Abcam, ab8983,), LMNB1 (Abcam, ab16048), LBR (Abcam, ab32535), H3K9me3 (Diagenode, C15410193), H3K9me2 (Active Motif, 39239) , H3K27me3 (Diagenode, C15410195), TOP2B (Novus Biological, NB100-40842),  followed by a wash step with D-Wash. Following this step, cells were incubated with a solution of D-Wash buffer and Rabbit-anti-mouse IgG (1:200, Abcam, ab6709), followed by a wash step. This incubation was repeated with a 1:200 pA-Dam solution (equivalent to nearly 60 Dam units from NEB), followed by two wash steps. Dam activity was induced by incubation for 30 min at 37 °C in 100 μL D-Wash supplemented with the methyl donor SAM (30 µM) while gently shaking (500 rpm). Genomic DNA was isolated and processed similarly to DamID, except that the DpnII digestion was omitted, and 65-bp reads were sequenced. For every condition, another 1 million cells were processed in only D-Wash and, during Dam activation, incubated with 4 units of Dam enzyme (NEB, M0222L). We use Dam control samples to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C). Libraries were sequenced on Illumina platform Hiseq2500 with single end 65 bp reads.


title: TRIBEID_1-SS3_1-SS3-B10

city: Shenzhen

value: Human embryonic kidney cells


title: TRIBEID_1-SS3_1-SS3-A4


title: pA-DamID_RPE1_SunTag_SCI_DAM_r3

value: Dam only


title: TRIBEID_1-SS3_1-SS3-A9


title: aPtk1_5


title: TRIBEID_1-SS3_1-SS3-A3


title: pA-DamID_RPE1_SunTag_TOP2BKD_LB2_r2


title: Cartilage, Prx1Dnmt1_vivo_cKO_rep3

description:
Library name: Prx1Dnmt1_vivo_cKO_rep3
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
cKO_female_1


title: aPtk1_4


title: Cartilage, Prx1Dnmt1_vivo_cKO_rep2

description:
Library name: Prx1Dnmt1_vivo_cKO_rep2
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
cKO_male_2

value: male


title: TRIBEID_1-SS3_1-SS3-A2


title: aPtk1_3


title: Cartilage, Prx1Dnmt1_vivo_cKO_rep1

description:
Library name: Prx1Dnmt1_vivo_cKO_rep1
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
cKO_male_1


title: TRIBEID_1-SS3_1-SS3-G7


title: TRIBEID_1-SS3_1-SS3-A1


title: pA-DamID_RPE1_SunTag_TOP2AKD_DAM_r3


title: pA-DamID_RPE1_SunTag_TOP2BKD_DAM_r2


title: pA-DamID_RPE1_SunTag_SCII_LB2_r2


title: Cartilage, Prx1Dnmt1_vivo_flox_rep4

description:
Library name: Prx1Dnmt1_vivo_flox_rep4
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
flox_female_2

value: flox


title: aPtk1_2


title: pA-DamID_RPE1_SunTag_SCII_DAM_r2


title: Cartilage, Prx1Dnmt1_vivo_flox_rep3

description:
Library name: Prx1Dnmt1_vivo_flox_rep3
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
flox_female_1


title: aPtk1_1


title: TRIBEID_1-SS3_1-SS3-A11


title: aPabC_1


title: pA-DamID_RPE1_SunTag_TOP2AKD_LB2_r2


title: Cartilage, Prx1Dnmt1_vivo_flox_rep2

description:
Library name: Prx1Dnmt1_vivo_flox_rep2
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
flox_male_2


title: pA-DamID_RPE1_iCUT_WT_EnzTop2A_LB2_r3

value: Control WT


title: pA-DamID_RPE1_SunTag_TOP2AKD_DAM_r2


title: aWT_5

value: Wildtype (WT)


title: Cartilage, Prx1Dnmt1_vivo_flox_rep1

description:
Library name: Prx1Dnmt1_vivo_flox_rep1
Library-CB.txt
Count data_in_vivo.tsv
RawCountData_in_vivo.csv
flox_male_1


title: aWT_4


title: pA-DamID_RPE1_SunTag_SCI_LB2_r2


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_LB2_r4