title: EpoR-negative TLI-ATS spleen and untreated LN, MULTI

city: Palo Alto

first: Christopher

last: McGinnis

state: CA

address: Biomedical Innovations Building 4600, 240 Pasteur Drive

institute: Stanford University

description:
Library name: Experiment 2 Lane 2 MULTI
MULTI-seq; EpoR-negative TLI-ATS spleen and untreated LN

data_processing:
scRNA-seq library FASTQs were pre-processed using Cell Ranger version 6.0.0 (10x Genomics) and aligned to the mm-10-3.0.0 reference transcriptome.
MULTI-seq and HTO FASTQs were processed using deMULTIplex2 (Zhu, Conrad, and Gartner, Genome Biology, 2024)
Assembly: mm10
Supplementary files format and content: Cellranger output files: mRNA barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: deMULTIplex2 output files: MULTI-seq count table csv

molecule: other

source_name: Spleen and LN

extract_protocol:
Experiment 1: Spleens were obtained from 7-8 week-old EpoR-loxp/loxp or EpoR-loxp/loxp-Xcr1-Cre mice after TLI/ATS treatment or from untreated controls. Samples were dissociated and subjected to MACS negative enrichment with Pan Dendritic Cell Isolation Kit and were tagged by genotpye using TotalSeq-A hashtag antibodies. Lin(CD3e, NK1.1, CD19, B200)-SiglecH-PDCA-1-F4/80-CD11c+MHCII+XCR1+SIRPa- cDC1s were FACS isolated and used for 10x Genomics scRNA-seq. Experiment 2: Spleens and LNs were obtained from 7-8 week-old EpoR-TdTomato-Cre mice after TLI/ATS treatment. Samples were dissociated and subjected to MACS negative enrichment with Pan Dendritic Cell Isolation Kit, split into 2 aliquots per tissue and MULTI-seq barcoded. cDC1s were then FACS isolated according to EpoR expression status (tracked with MULTI-seq barcode), pooled by EpoR status, and used for 10x Genomics scRNA-seq.
Libraries were prepared according to manufacturers instructions (10x Genomics V3.1; BioLegend Total-Seq-A) with a separate MULTI-seq library prep workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019)
scRNA-seq with Cell Hashing or MULTI-seq

value: Spleen and LN

value: EpoR-TdTomato-Cre

value: TLI-ATS spleen, untreated LN


title: aWT_3

status: Public on Sep 15 2025

type: SRA

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

country: USA

institute: University of Louisville

library_source: transcriptomic

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

molecule: total RNA

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.

tag: tissue

value: Mouse Abscess Material

tag: genotype

value: Wildtype (WT)


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_LB2_r4

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

library_source: genomic

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.

molecule: genomic DNA

organism: Homo sapiens

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

tag: cell line

tag: cell type

value: Control WT

tag: antibody


title: aWT_2


title: pA-DamID_RPE1_SunTag_SCI_DAM_r2

value: Dam only


title: EpoR-positive TLI-ATS spleen and untreated LN, MULTI

department: Pathology

description:
Library name: Experiment 2 Lane 1 MULTI
MULTI-seq; EpoR-positive TLI-ATS spleen and untreated LN

library_source: other

organism: Mus musculus

tag: strain

tag: treatment


title: TRIBEID_1-SS3_1-SS3-A12

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

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.

value: Human embryonic kidney cells


title: pA-DamID_RPE1_SunTag_TOP2BKD_CT_LB2_B_r1

value: TOP2B KD


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_DAM_r4


title: TLI-ATS spleen, HASH

description:
Library name: Experiment 1 Lane 2 HASH
Cell Hashing; TLI-ATS spleen

molecule: protein

source_name: Spleen

value: Spleen

value: EpoR-loxp/loxp, EpoR-loxp/loxp-Xcr1-Cre

value: TLI-ATS


title: aWT_1


title: pA-DamID_RPE1_iCUT_WT_EnzTop2A_DAM_r3


title: pA-DamID_RPE1_SunTag_TOP2BKD_CT_DAM_B_r1


title: Untreated spleen, HASH

description:
Library name: Experiment 1 Lane 1 HASH
Cell Hashing; Untreated spleen

value: untreated


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_DAM_r4


title: H11, replicate 1, scRNAseq

city: Bethesda

first: Laura

last: Kerosuo-Pahlberg

state: MD

address: 30 Convent Dr

institute: NIDCR

description:
Library name: Sample9
10x Genomics 3’ GEX v3.1

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v6.1.1 pipeline using default settings.
Secondary analysis was performed using Seurat v4
Assembly: Custom GRCg6a chicken genome, that included extension to the 3’ UTR the gene definitions of the genes Nanog, Klf4, Runx2 and Ets1.
Supplementary files format and content: 10X Genomics Cell Ranger v6.1.1 standard output raw gene counts matrices.
Supplementary files format and content: 10X Genomics Cell Ranger v6.1.1 standard output filtered gene counts matrices.

organism: Gallus gallus

source_name: all tissue at midbrain axial level

extract_protocol:
Cell samples for scRNA-seq were dissociated using the Multi Tissue Dissociation Kit 3 (Miltenyi Biotec, 130-110-204). Briefly, the dissected cranial tissues were rinsed with PBS, followed by the addition of the enzyme mix provided in the kit. Samples were incubated at 37°C for 10 minutes, then gently triturated by pipetting. This was followed by a second 10-minute incubation at 37°C and additional pipetting to obtain a single-cell suspension. The resulting suspensions were washed twice with cold PBS and filtered through a 70 μm MACS SmartStrainer (Miltenyi Biotec) to remove cell clumps.
Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on two lanes of  NovaSeq 6000 sequencer (Illumina).

value: all tissue at midbrain axial level

tag: age

value: stage 11

value: WT

value: total RNA


title: pA-DamID_RPE1_iCUT_WT_EnzTop2A_LB2_r2


title: pA-DamID_RPE1_SunTag_SCII_DAM_r1


title: EpoR-negative TLI-ATS spleen and untreated LN, scRNA-seq

description:
Library name: Experiment 2 Lane 2
10x Genomics; EpoR-negative TLI-ATS spleen and untreated LN

molecule: polyA RNA

value: Spleen and LN

value: EpoR-TdTomato-Cre


title: WJC_405(TCR)

city: Shanghai

first: Changrui

last: Yang

address: 160 Pu Jian Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline  using default parameters. All downstream single-cell analyses were performed using Cell Ranger v7.0.0 and Seurat v4.3.0. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Assembly: GRCh38-2020-A
Supplementary files format and content: tar archive of CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: ovarian cancer

growth_protocol: Freshly resected clinical tumor samples were meticulously minced and enzymatically digested with a cocktail of collagenase II and DNase I at 37°C for 30-60 minutes. This mixture was then filtered through a 70-μm mesh strainer to create a single-cell suspension. Following red blood cell lysis, the cell suspensions (PDTSs) were washed with PBS and resuspended in RPMI 1640 mediumsupplemented with 10% fetal bovine serum (FBS), d-glutamine (2 mM), penicillin (100 U/ml), and streptomycin (100 μg/ml).

extract_protocol:
FACS sorted Live CD45+ cells from PDTSs of an ovarian cancer patient were resuspended in PBS. The viability was confirmed to be >90%.
Single-cell suspensions were loaded on a 10x Genomics Chromium single-cell 3′ v3 chip to prepare the libraries according to the manufacturer’s protocol. Sequencing was performed with Illumina NovaSeq 6000 according to the manufacturer’s instructions (Illumina).

treatment_protocol: PDTSs were treated with control-IgG or Tri-TCE for 3days.

value: ovarian cancer

value: primary cells

value: Tri-TCE


title: EpoR-positive TLI-ATS spleen and untreated LN, scRNA-seq

description:
Library name: Experiment 2 Lane 1
10x Genomics; EpoR-positive TLI-ATS spleen and untreated LN

value: TLI-ATS spleen, untreated LN


title: pA-DamID_RPE1_SunTag_SCII_LB2_r1

value: retina


title: WJC_con(TCR)

value: control-IgG


title: pA-DamID_RPE1_SunTag_TOP2AKD_CT_LB2_r1

value: TOP2A KD


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_LB2_r3

value: Control WT


title: TLI-ATS spleen, scRNA-seq

description:
Library name: Experiment 1 Lane 2
10x Genomics; TLI-ATS spleen

value: Spleen

value: EpoR-loxp/loxp, EpoR-loxp/loxp-Xcr1-Cre


title: WJC_405(RNA)


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_LB2_r3


title: pA-DamID_RPE1_SunTag_TOP2AKD_CT_DAM_r1

value: Dam only


title: pA-DamID_RPE1_iCUT_WT_EnzTop2A_DAM_r2


title: Untreated spleen, scRNA-seq

description:
Library name: Experiment 1 Lane 1
10x Genomics; Untreated spleen

value: untreated


title: pA-DamID_RPE1_SunTag_SCI_LB2_r1


title: XBP1-Rapa60min-Tg75min-Rep2

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
Library strategy: Amplicon sequencing

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.

value: Human embryonic kidney cells


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_DAM_r3


title: CKO-2 scRNAseq

city: Wuhan

first: Yishuang

last: Sun

address: 115 Donghu Road

institute: Medical Research Institute

description: one sample from murine  tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Colon

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Colon

value: Colorectal tumor cell lines

value: Trim25 cKO


title: WJC_con(RNA)


title: XBP1-Rapa60min-Tg75min-Rep1


title: CKO-1 scRNAseq

description: one sample from murine  tissue


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_DAM_r3


title: pA-DamID_RPE1_SunTag_SCI_DAM_r1


title: XBP1-Rapa60min-Tg60min-Rep2


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_LB2_r2


title: pA-DamID_RPE1_SunTag_TOP1KD_DAM_r3

value: TOP1 KD


title: XBP1-Rapa60min-Tg60min-Rep1


title: XBP1-Rapa60min-Tg45min-Rep2


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_DAM_r2


title: WT-1 scRNAseq

description: one sample from murine  tissue

value: WT


title: Gne Heterozygous Knock-out, C3 Knock-out mouse 8, Gne+/-, C3-/-, Sequencing Run 2

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

country: Germany

institute: University Hospital of Bonn

data_processing:
Adapters were trimmed from the reads using Bbmerge/BBDUK. Reads were then aligned to the mouse reference genome mm10 (GRCm38) with the ensemble gene annotation version 101 using STAR [v2.7.3a] (Dobin et al., 2013) with standard parameters. Read count generation was performed using featureCounts/Subread [v2.0.0] (Liao et al., 2014) ignoring multimapping reads.
Assembly: mm10
Supplementary files format and content: tab-deliminated text file including raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing read count values for each gene across all samples. The data were generated using the featureCounts tool from the Subread package. Each row represents a gene, and each column corresponds to a sample. The values represent the number of reads mapped to each gene in each sample, without normalization

source_name: Retina

growth_protocol: Wildtype and knock-out mice were housed at a 12 hours dark/night cycle in a temperature-control facility with ad libitum water and food until reaching nine months of age.

extract_protocol:
RNA was harvested from retinal whole-mounts that were homogenized in QIAzol Lysis reagent (Qiagen), afterwhich chloroform was used to separate the RNA phase and isopropanol to precipitate the RNA. Afterwards, the suspension was washed with 70% ethanol and the final pellet was resuspended in ultra-pure DEPC treated water.
QuantSeq 3′ mRNA-Seq Library Prep Kit, Lexogen with an input of 100 ng total RNA

value: Retina

value: Gne Heterozygous-C3 Knock-out


title: pA-DamID_RPE1_SunTag_SC_LB2_r3


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_LB2_r2


title: pA-DamID_RPE1_SunTag_SC_DAM_r3


title: Gne Heterozygous Knock-out, C3 Knock-out mouse 7, Gne+/-, C3-/-, Sequencing Run 2


title: pA-DamID_RPE1_SunTag_TOP1KD_LB2_r2


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_DAM_r2


title: XBP1-Rapa60min-Tg30min-Rep2


title: Gne Heterozygous Knock-out, C3 Knock-out mouse 6, Gne+/-, C3-/-, Sequencing Run 1


title: XBP1-Rapa60min-Tg45min-Rep1


title: pA-DamID_RPE1_SunTag_TOP1KD_LB2_r3


title: XBP1-Rapa60min-Tg30min-Rep1


title: Gne Heterozygous Knock-out, C3 Knock-out mouse 5, Gne+/-, C3-/-, Sequencing Run 1


title: pA-DamID_RPE1_SunTag_SC_LB2_r2


title: Gne Heterozygous Knock-out, C3 Knock-out mouse 4, Gne+/-, C3-/-, Sequencing Run 1


title: pA-DamID_RPE1_iCUT_WT_EnzTop2A_LB2_r1


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_LB2_r1


title: pA-DamID_RPE1_SunTag_SC_DAM_r2


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_LB2_r1


title: pA-DamID_RPE1_SunTag_TOP1KD_DAM_r2


title: XBP1-Rapa60min-Tg0min-Rep2


title: Gne Heterozygous Knock-out, C3 Knock-out mouse 3, Gne+/-, C3-/-, Sequencing Run 1


title: WT-2 scRNAseq

description: one sample from murine  tissue


title: pA-DamID_RPE1_iCUT_WT_EnzTop2B_DAM_r1


title: C3 Knock-out mouse 9, Gne+/+, C3-/-, Sequencing Run 2

value: C3 Knock-out


title: pA-DamID_RPE1_SunTag_TOP1KD_LB2_r1

value: retina


title: pA-DamID_RPE1_iCUT_WT_EnzTop2A_DAM_r1


title: XBP1-Rapa60min-Tg0min-Rep1


title: XBP1-Rapa0min-Tg75min-Rep1


title: XBP1-Rapa0min-Tg75min-Rep2


title: C3 Knock-out mouse 8, Gne+/+, C3-/-, Sequencing Run 2


title: pA-DamID_RPE1_iCUT_WT_Top2Buffer_DAM_r1


title: pA-DamID_RPE1_SunTag_SC_DAM_r1


title: XBP1-Rapa0min-Tg60min-Rep2


title: C3 Knock-out mouse 7, Gne+/+, C3-/-, Sequencing Run 2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_LBR_r2

value: TOP2B KD2

value: LBR


title: pA-DamID_RPE1_SunTag_SC_LB2_r1


title: C3 Knock-out mouse 6, Gne+/+, C3-/-, Sequencing Run 1


title: XBP1-Rapa0min-Tg60min-Rep1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_LBR_r2

value: TOP2B KD3


title: MDA-MB-231-BRL-50481 treated replicate 3

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
The base calling was performed using RTA 1.18.64.0
The raw fastq sequences were aligned to the human hg38 reference genome (GenBank assembly accession: GCA_000001405.28). The alignments were carried out using STAR (version 2.7.1a) (Dobin et al 2013) with default parameters. Gene expression was quantified as gene level counts using the htseq-count function (version 0.12.3) (Anders et al 2015); the UCSC gene annotations for the human genome were used. Differentially expressed genes were identified using DESeq2 (version 1.28) (Love et al 2014).
Genome_build: human hg38 reference genome (GenBank assembly accession: GCA_000001405.28)
Supplementary_files_format_and_content: Raw read counts in .csv format

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231cells were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: MDA-MB-231  cells were treated with  PDE7A inhibitor (50 micomolar) BRL-50481 for 72  hours,  were harvested and were used for preparing the total RNA and to perfrom RNA Seq.

value: BRL-50481 treated, 5 micromolar, 48 hours


title: C3 Knock-out mouse 5, Gne+/+, C3-/-, Sequencing Run 1


title: MDA-MB-231-BRL-50481 treated replicate 2


title: C3 Knock-out mouse 2, Gne+/+, C3-/-, Sequencing Run 1


title: MDA-MB-231-BRL-50481 treated replicate 1


title: XBP1-Rapa0min-Tg45min-Rep1


title: pA-DamID_RPE1_SunTag_Top1_DAM_r1


title: XBP1-Rapa0min-Tg45min-Rep2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_LB1_r2


title: MDA-MB-231-DMSO treated replicate 3

value: DMSO treated


title: Gne Knock-out mouse 8, Gne+/-, C3+/+, Sequencing Run 2

value: Gne Heterozygous Knock-out


title: C3 Knock-out mouse 1, Gne+/+, C3-/-, Sequencing Run 1


title: XBP1-Rapa0min-Tg30min-Rep2


title: pA-DamID_RPE1_iCUT_WT_SC2_LB1_r2


title: XBP1-Rapa0min-Tg30min-Rep1


title: Gne Knock-out mouse 5, Gne+/-, C3+/+, Sequencing Run 1


title: Gne Knock-out mouse 7, Gne+/-, C3+/+, Sequencing Run 2


title: XBP1-Rapa0min-Tg0min-Rep2


title: MDA-MB-231-DMSO treated replicate 1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_LBR_r1


title: XBP1-Rapa0min-Tg0min-Rep1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_LBR_r1


title: Gne Knock-out mouse 4, Gne+/-, C3+/+, Sequencing Run 1


title: siCKMT2_3

city: Stockholm

first: Salwan

last: Maqdasy

address: Norra Stationsgatan 69

department: Medicine

country: Sweden

institute: Karolinska Institute

description: Library name: Sample 9

data_processing:
Base scalling and demultiplexing was performed using CASAVA software with default settings generating Fastq files aligned to GRCh38 for further downstream mapping and analysis. Raw counts were normalized and analyzed using DESeq2 in R studio.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, includes raw counts for each sample sequenced

source_name: Human Subcutaneous White Adipose Tissue

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Mini kit (Macherey-Nagel) and quantified using NanoDrop 2000 (ThermoFischer)
RNAseq library was carried out using SMARTer library prep kit, per manufacturer´s instruction

value: Human Subcutaneous White Adipose Tissue

value: hMADs

value: human adipose tissue-derived stem cells

value: Adipocytes differentiation

tag: batch


title: pA-DamID_RPE1_iCUT_WT_SC2_LBR_r1


title: pA-DamID_RPE1_iCUT_WT_SC2_LBR_r2


title: Spol embryos RNAseq 168h (7 days) [Embryos_168h_rep2]

city: Barcelona

first: Josep

middle: F

last: ABRIL

state: Catalonia

address: Av Diagonal, 643, edifici Prevosti, planta -1, sala IBUB

department: Genetics, Microbiology & Statistics

country: Spain

institute: Universitat de Barcelona

description: Library name: Embryos_168h_rep2

data_processing:
Sequencing run produced 1,763,225,906 raw reads totaling 178,085,816,506 bp; those reads were cleaned with Trimmomatic version 0.32, (Bolger, Lohse & Usadel 2014) resulting in 1,679,606,938 clean reads longer than 30bp summing up 166,255,109,697 bp. Basic quality control on raw and clean reads was done by FastQC version 0.11.2, (Andrews, 2010).
data processing step RNA reads from all sample replicates were pooled to be de novo assembled into contigs using Trinity version 2.5.1 (Grabherr et al. 2011); this yielded 1,554,770 contigs longer than 100bp (mean length 264.6bp, longest 19,880bp). Other assembly approaches were considered, yet this one recovered more genes when assessing assembly completeness with BUSCO (version 3.0.2) (Simão et al. 2015; Seppey, Manni & Zdobnov 2019).
Nucleotide NCBI-BLAST (megablast, e-value < 10e-25 (Camacho et al. 2009) against RefSeq genomes database (O?Leary et al. 2016) returned 42,271 contigs mapping to other species than Tricladida (i.e. human, bacteria, etc); those alignments had more than 90% coverage and > 90% identity, therefore those contigs were discarded as contaminants. Subsequently, only contigs longer than 1000bp were considered for further downstream analyses, totaling 62,218 transcript sequences (mean length 1,843bp) assigned by Trinity to 23,300 genes. After contamination screen when uploading to NCBI-TSA repository, 1,297 sequences were discarded and 60,921 transcripts were kept (mean length 1,847bp, summing up 112,526,258bp). The Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GLGS00000000. The version described in this paper is the first version, GLGS01000000.
Isoform expression levels were estimated using RSEM algorithm (Li & Dewey 2011) following the integrated Trinity procedures (Haas et al. 2013); such procedure implied a Trimmed Mean of M-values (TMM) normalization by library size to produce the counts' matrix for expression analysis (Robinson & Oshlack 2010).
All downstream analyses were performed using R version 4.2.2 packages (Core, 2022). Only those transcript isoforms having at least five counts per million (CPMs) on at least three replicates were kept to undergo differential gene expression analyses; this left 22,778 transcripts out of 62,218 from previous filtering steps. DGEList object was created from counts? matrix using edgeR package (version 3.40.2) (Robinson, McCarthy & Smyth 2010) yet differentially expressed genes were identified employing the lima-voom pipeline (version 3.54.2) (Ritchie et al. 2015), considering an FDR adjusted p-value cut-off of 0.05 and a log fold change cut-off of +1/-1. All 28-time pair-wise distinct combinations were considered in the contrast design, focussing on the comparisons of each time point samples relative to initial time (ti versus t0, where t0 = 4hpd) and the pairs for a given time related to previous time (ti versus ti-1).
Assembly: GLGS01000000
Supplementary files format and content:
trinity1k.isoforms.RSEM.raw_counts.tsv.gz is a tab-delimited gzipped text file that includes RSEM raw counts for each sample.
trinity1k.isoforms.RSEM.TMM_expression_matrix.tsv.gz is a tab-delimited gzipped text file that includes RSEM TMM normalized counts for each sample.
trinity1k.isoforms.fasta.gz is a gzipped text file with the trinity-assembled transcriptome isoforms in fasta format.

organism: Schmidtea polychroa

source_name: Schmidtea polychroa embryos

growth_protocol: Sexual population of Schmidtea polychroa maintained in the lab as described by Martin-Duran et al, 2008. Planarians were kept at 20C under a day-night light cycle (16h of light followed by 8h of darkness) in glass aquariums in a 1:1 (v:v) mixture of distilled water and tap water. The tanks had a surface of 1800cm^2, and a water depth of 11cm. The animals were fed twice a week with sliced bovine liver.

extract_protocol:
During the breeding period, egg capsules were collected and placed in Petri dishes, where they hatched after approximately 14 to 20 days. Eggs were collected right after deposition (orange color) and were placed in 24-well plates in order to be able to process each cocoon at a specific hour or day post-deposition (4h, 24h, 32h, 48h, 72h, 96h, 120h, and 168h). Plates were maintained at 20C. At each corresponding time point, egg capsules were placed in a microscope concave glass slide and were treated with 1% diluted commercial NaOCl, for no more than 3 min in order to remove the mucus and parasites. Then the cocoons were moved to an eppendorf tube, washed with RNAlater (Invitrogen) and 50% RNAlater/Trizol. Finally, liquids were removed and 100ul of Trizol reagent (Invitrogen) was added. The whole cocoons were triturated with a tissueLyser (Kontes Microtube Pellet Pestle Rods with Motor), and total mRNA extraction was performed as described in Almuedo-Castillo et al. (2014). Three biological replicates were analyzed per time point. Each biological replicate contained 4 whole cocoons.
Library preparation and sequencing were carried out by the Centre Nacional dAnalisi Genomica (CNAG). TruSeq stranded mRNA-seq libraries were sequenced on HiSeq 2000 (Illumina) with a read length of 2x100bp.

treatment_protocol: Egg collection and fixation was conducted as described in (Cardona, Fernandez, et al. 2005; Martin-Duran et al. 2008).

value: Schmidtea polychroa embryos

value: Embryos at 168h post deposition

tag: time


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_LB1_r2


title: Gne Knock-out mouse 3, Gne+/-, C3+/+, Sequencing Run 1


title: siCKMT2_2

description: Library name: Sample 8


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_LB1_r1


title: Spol embryos RNAseq 168h (7 days) [Embryos_168h_rep1]

description: Library name: Embryos_168h_rep1


title: MDA-MB-231-DMSO treated replicate 2


title: Spol embryos RNAseq 120h (5 days) [Embryos_120h_rep3]

description: Library name: Embryos_120h_rep3

value: Embryos at 120h post deposition


title: Gne Knock-out mouse 2, Gne+/-, C3+/+, Sequencing Run 1

value: Retina


title: siCKMT2_1

description: Library name: Sample 7


title: pA-DamID_RPE1_iCUT_WT_SC2_LB1_r1


title: Gne Knock-out mouse 1, Gne+/-, C3+/+, Sequencing Run 1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_LB1_r1


title: siCKB_3

description: Library name: Sample 6

value: siCKB


title: Wildtype mouse 8, Gne+/+, C3+/+, Sequencing Run 2

value: WT


title: siCKB_2

description: Library name: Sample 5


title: Spol embryos RNAseq 120h (5 days) [Embryos_120h_rep1]

description: Library name: Embryos_120h_rep1


title: siCKB_1

description: Library name: Sample 4


title: Wildtype mouse 7, Gne+/+, C3+/+, Sequencing Run 2


title: Spol embryos RNAseq 120h (5 days) [Embryos_120h_rep2]

description: Library name: Embryos_120h_rep2


title: Spol embryos RNAseq 96h (4 days) [Embryos_096h_rep3]

description: Library name: Embryos_096h_rep3

value: Embryos at 96h post deposition


title: Spol embryos RNAseq 168h (7 days) [Embryos_168h_rep3]

description: Library name: Embryos_168h_rep3


title: siC_3

description: Library name: Sample 3

value: siC


title: pA-DamID_RPE1_iCUT_WT_SC2_LB2_r2

value: retina


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_LB2_r2

value: TOP2B KD2


title: Spol embryos RNAseq 96h (4 days) [Embryos_096h_rep2]

description: Library name: Embryos_096h_rep2


title: Wildtype mouse 5, Gne+/+, C3+/+, Sequencing Run 1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD1_r2

value: TOP2B KD


title: siC_2

description: Library name: Sample 2


title: pA-DamID_RPE1_iCUT_WT_SC1_LB2_r2


title: Spol embryos RNAseq 96h (4 days) [Embryos_096h_rep1]

description: Library name: Embryos_096h_rep1


title: Wildtype mouse 4, Gne+/+, C3+/+, Sequencing Run 1


title: siC_1

description: Library name: Sample 1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_DAM_r2

value: Dam only


title: Spol embryos RNAseq 72h (3 days) [Embryos_072h_rep3]

description: Library name: Embryos_072h_rep3

value: Embryos at 72h post deposition


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_DAM_r2

value: TOP2B KD3


title: TC004 subject, control

city: Boston

first: Jan

last: Heng

state: MA

address: 330 Brookline Ave, Dana 517B

institute: Beth Israel Deaconess Medical Center

description:
Library name: TC004
TC004

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 non cancer tissue

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 non cancer tissue

value: Control


title: Wildtype mouse 2, Gne+/+, C3+/+, Sequencing Run 1


title: Spol embryos RNAseq 72h (3 days) [Embryos_072h_rep2]

description: Library name: Embryos_072h_rep2


title: Wildtype mouse 1, Gne+/+, C3+/+, Sequencing Run 1


title: pA-DamID_RPE1_iCUT_WT_SC2_DAM_r2


title: Wildtype mouse 6, Gne+/+, C3+/+, Sequencing Run 1


title: TC002 subject, control

description:
Library name: TC002
TC002


title: Wild type, replicate 3, scRNAseq

city: Dallas

first: Huocong

last: Huang

state: TX

address: NB8.212A, 6000 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research, Department of Surgery and Immunology

institute: UT Southwestern Medical Center

description: 10x Genomics

data_processing:
These fastq files were aligned to the mm10 mouse reference genome and quantified using the Cell Ranger pipeline (version 7.2.0, 10x Genomics). The preliminary filtered data generated from Cell Ranger were utilized for all subsequent analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDAC

extract_protocol:
Single cells were isolated from mouse tumor tissues following a previously established method. Initially, a 10x digestion buffer was prepared in PBS, containing collagenase type I (450 units/ml, Worthington Biochemical), collagenase type II (150 units/ml, Worthington Biochemical), collagenase type III (450 units/ml, Worthington Biochemical), collagenase type IV (450 units/ml, Thermo Fisher Scientific), elastase (0.8 units/ml, Worthington Biochemical), hyaluronidase (300 units/ml, MilliporeSigma), and DNase type I (250 units/ml, MilliporeSigma). Freshly dissected tumor tissues were cut into 1-2 mm³ pieces using a sterile blade, washed with PBS, and then incubated in 50 mL of 1x digestion buffer on a shaker at 37°C for 45 minutes. The resulting cell suspension was filtered through a 40 μm mesh (MilliporeSigma) and centrifuged at 400 g for 5 minutes. After removing the supernatant, the cell pellet was resuspended in ACK lysing buffer (Thermo Fisher Scientific) and incubated on ice for 5 minutes to lyse red blood cells.
Approximately 10,000 cells were used for library construction with the Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics), following the manufacturer’s protocol.

value: PDAC

value: Tumor cells


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD1_DAM_r2


title: TC003 subject, control

description:
Library name: TC003
TC003


title: Spol embryos RNAseq 48h (2 days) [Embryos_048h_rep3]

description: Library name: Embryos_048h_rep3

value: Schmidtea polychroa embryos

value: Embryos at 48h post deposition


title: Spol embryos RNAseq 72h (3 days) [Embryos_072h_rep1]

description: Library name: Embryos_072h_rep1


title: Wild type, replicate 2, scRNAseq

description: 10x Genomics


title: TC001 subject, control

description:
Library name: TC001
TC001


title: pA-DamID_RPE1_iCUT_WT_SC1_DAM_r2


title: Spol embryos RNAseq 48h (2 days) [Embryos_048h_rep2]

description: Library name: Embryos_048h_rep2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_LB2_r1


title: TT004 subject, taking testosterone

description:
Library name: TT004
TT004

value: Testosterone


title: Spol embryos RNAseq 48h (2 days) [Embryos_048h_rep1]

description: Library name: Embryos_048h_rep1


title: Spp1 knockout, replicate 3, scRNAseq

description: 10x Genomics


title: TT003 subject, taking testosterone

description:
Library name: TT003
TT003


title: Spol embryos RNAseq 32h (1.5 days) [Embryos_032h_rep3]

description: Library name: Embryos_032h_rep3

value: Embryos at 32h post deposition


title: pA-DamID_RPE1_iCUT_WT_SC2_LB2_r1


title: Spp1 knockout, replicate 2, scRNAseq

description: 10x Genomics


title: TT002 subject, taking testosterone

description:
Library name: TT002
TT002


title: Spol embryos RNAseq 32h (1.5 days) [Embryos_032h_rep2]

description: Library name: Embryos_032h_rep2


title: TT001 subject, taking testosterone

description:
Library name: TT001
TT001


title: Chondrocyte, cKO, biol rep3

city: Toon

first: Yuta

last: Yanagihara

state: Ehime

address: Shitsukawa

department: Division of Integrative Pathophysiology, Proteo-Science Center

country: Japan

institute: Ehime university

data_processing:
Paired-end reads were trimmed with fastp and mapped to mm10 using Bowtie2
To identify Dnmt1 mediated methylated DNA peaks across samples, BAM files were merged across biological replicates (n = 3) to call peaks with MACS2.
Peak calling was performed using Galaxy with the merged Ctrl BAM file as the “Treatment file” and the merged cKO BAM file as the “Control file” to obtain the supplementary file.
Assembly: GRCm38
Supplementary files format and content: txt

source_name: Knee articular cartilage

growth_protocol: Primary cultured chondrocyte were mainteined DMEM Glutamax supplemented with 10% fetal bovine serum, Antibiotics and Antimycotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Methylated DNA was enriched by MBD2-mediated precipitation and subjected to next-generation sequencing as follows. Extracted DNA from chondrocytes was sonicated with a Covaris sonicator to obtain ∼300 bp fragments. MBD2-mediated enrichment of methylated DNA was performed using the EpiXplore Methylated DNA Enrichment Kit (Takara Bio) according to the manufacturer’s instructions.
Libraries for MBD-Seq analysis were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions and validated for an average size of about 550-600 bp using a High Sensitivity DNA Assay kit.

value: Knee articular cartilage

value: Chondrocyte

value: Prx1-Cre;Dnmt1 flox/flox


title: Spol embryos RNAseq 32h (1.5 days) [Embryos_032h_rep1]

description: Library name: Embryos_032h_rep1


title: E6-Transient8rep3

city: Brookings

first: Ryan

last: Hanson

state: South Dakota

address: 1390 College Avenue, Rm 252 Box 2140D

institute: South Dakota State University

description: Library name: E6-T8rep3

data_processing:
45 samples prepared for NExtSeq500 (1x75bp) High output reads.  Sequencing was performed using 3 runs to get sufficient reads for all samples and performed by the SDSU Genomics Sequencing Core Facility.  All bioinformatic analyses were done using CLC Genomics Workbench (vs 24.0). Trimmed reads were mapped to the human genome vs hg38 as reference using a minimum length fraction of 0.8 and a minimum similarity fraction of 0.8. Differential expression was calculated on a gene basis using an absolute fold change cut-off of 2 and a FDR adjusted p-value of 0.05.
Assembly: hg38
Supplementary files format and content: excel file with all read information including the RPKM and TPM values for each individual sample arranged in separate tabs

growth_protocol: DMEM/F12 with 10% FBS and pen/strep

extract_protocol:
Qiagen Rneasy kit
Illumina TrueSeq mRNA

treatment_protocol: Treated with 50 ng/ml anisomycin to induce JNK activation

value: epithelial

value: transient

tag: timepoint


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD2_DAM_r1

value: retina

value: TOP2B KD2


title: Chondrocyte, cKO, biol rep2


title: Wild type, replicate 1, scRNAseq

description: 10x Genomics


title: E5-Transient6rep3

description: Library name: E5-T6rep3


title: Spol embryos RNAseq 24h (1 day) [Embryos_024h_rep3]

description: Library name: Embryos_024h_rep3

value: Embryos at 24h post deposition


title: Chondrocyte, Control, biol rep3

value: Dnmt1 flox


title: Chondrocyte, cKO, biol rep1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD3_DAM_r1

value: TOP2B KD3

value: Dam only


title: Spol embryos RNAseq 24h (1 day) [Embryos_024h_rep2]

description: Library name: Embryos_024h_rep2


title: E3-Transient6rep2

description: Library name: E3-T6rep2


title: E4-Transient8rep2

description: Library name: E4-T8rep2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD1_DAM_r1

value: TOP2B KD


title: Spol embryos RNAseq 24h (1 day) [Embryos_024h_rep1]

description: Library name: Embryos_024h_rep1


title: Chondrocyte, Control, biol rep2


title: pA-DamID_RPE1_iCUT_WT_SC2_DAM_r1


title: E2-Transient8rep1

description: Library name: E2-T8rep1


title: Spol embryos RNAseq 4h (after deposition) [Embryos_004h_rep3]

description: Library name: Embryos_004h_rep3

value: Embryos at 4h post deposition


title: Spol embryos RNAseq 4h (after deposition) [Embryos_004h_rep2]

description: Library name: Embryos_004h_rep2

value: Schmidtea polychroa embryos


title: Chondrocyte, Control, biol rep1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD1_LB2_r1


title: E1-Transient6rep1

description: Library name: E1-T6rep1


title: Spp1 knockout, replicate 1, scRNAseq

description: 10x Genomics

value: PDAC

value: Tumor cells


title: pA-DamID_RPE1_iCUT_WT_SC1_LB2_r1


title: Spol embryos RNAseq 4h (after deposition) [Embryos_004h_rep1]

description: Library name: Embryos_004h_rep1


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LBR_r2

value: LBRKO+TOP2B KD

value: LBR


title: Chondrocyte, cKO, BMP2, Day3, Biol rep4

data_processing:
RaNA-seq (https://ranaseq.eu/)
Assembly: GRCm38
Supplementary files format and content: tab-delimited csv file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Isogene (Nippon Gene) and RNeasy spin column kit (QIAGEN), followed by treatment with DNase I (QIAGEN).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer’s instructions and subsequently validated for an average size of about 370 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit.

treatment_protocol: Chondrocyte differentiation was indused by BMP2 (100 ng/µl) treatment for 3 days.

value: Knee articular cartilage

value: Chondrocyte

value: Prrx1-Cre;Dnmt1 flox/flox

value: BMP2 treatment for 3days


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LB2_r4

value: retina


title: Chondrocyte, cKO, BMP2, Day3, Biol rep3


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LBR_r2


title: D9-JNKi2rep3

description: Library name: D9-J2rep3

value: epithelial

value: jnki


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_DAM_r4


title: Chondrocyte, cKO, BMP2, Day3, Biol rep2


title: Chondrocyte, cKO, BMP2, Day3, Biol rep1


title: D10-JNKi4rep3

description: Library name: D10-J4rep3


title: Invivo.PAD4KO.lap1

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic
Reads were aligned to mouse reference genome mm10 by STAR aligner
Gene counts were quantified by STRA
Assembly: mm10
Supplementary files format and content: TAB

source_name: Lung tumor

extract_protocol:
Total RNA was extracted from cancer cells using TRIzol™ Reagent according to the manufacturer’s instructions. 1 μg of the total RNA was used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung tumor

value: cancer cells expressing GFP

value: WT

value: laparotomy (in PAD4 KO mice)


title: D8-JNKi8rep2

description: Library name: D8-J8rep2


title: Chondrocyte, Control, BMP2, Day3, Biol rep3

value: Dnmt1 flox


title: Chondrocyte, Control, BMP2, Day3, Biol rep4


title: pA-DamID_RPE1_iCUT_WT_SC1_DAM_r1

value: Dam only


title: Invivo.WT.lap2

value: mice laparotomy


title: Invivo.WT.lap1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LBR_r2

value: TOP2B KD


title: D7-JNKi6rep2

description: Library name: D7-J6rep2


title: Chondrocyte, Control, BMP2, Day3, Biol rep2


title: D6-JNKi4rep2

description: Library name: D6-J4rep2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB2_r4


title: D12-JNKi8rep3

description: Library name: D12-J8rep3


title: Invivo.WT.control2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_DAM_r4


title: D11-JNKi6rep3

description: Library name: D11-J6rep3


title: D5-JNKi2rep2

description: Library name: D5-J2rep2


title: Invivo.PAD4KO.lap2


title: Invivo.WT.control1


title: Invivo.PAD4KO.control2

value: none (PAD4 KO mice)


title: Invivo.PAD4KO.control1


title: Chondrocyte, cKO, biol rep3


title: Chondrocyte, cKO, biol rep2


title: D4-JNKi8rep1

description: Library name: D4-J8rep1


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_DAM_r4


title: D3-JNKi6rep1

description: Library name: D3-J6rep1


title: pA-DamID_RPE1_iCUT_WT_SCII_LB2_r4


title: pA-DamID_RPE1_iCUT_WT_SCII_LBR_r2

value: LBR


title: Chondrocyte, cKO, biol rep1

value: Knee articular cartilage


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LB2_r4


title: D2-JNKi4rep1

description: Library name: D2-J4rep1


title: pA-DamID_RPE1_iCUT_WT_SCII_DAM_r4


title: Invitro.NET1

value: cancer cells

value: NETs in vitro


title: Chondrocyte, Control, biol rep3

value: Chondrocyte


title: Chondrocyte, Control, BMP2, Day3, Biol rep1

value: BMP2 treatment for 3days


title: D1-JNKi2rep1

description: Library name: D1-J2rep1

value: epithelial


title: Invitro.control3


title: Invitro.NET3


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LBR_r1

value: retina

value: LBRKO+TOP2B KD


title: Chondrocyte, Control, biol rep2


title: C12-Pulse8rep3

description: Library name: C12-P8rep3

value: pulsed


title: Invitro.control2

value: WT


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_LB2_r3


title: Chondrocyte, Control, biol rep1


title: C11-Pulse6rep3

description: Library name: C11-P6rep3


title: pA-DamID_RPE1_iCUT_LBRKO_TOP2BKD_DAM_r3


title: Invitro.control1


title: M6A3_input

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

data_processing:
Firstly, clean reads were aligned to mouse genome (version mm10) using HISAT2 (version 2.2.1). Then, the number of reads were mapped and counted using HTSeq (version 0.12.4), with-stranded = no. Thirdly, the target binding regions were identified using MACS2 (version 2.2.7.1) with -nomodel. Significantly high confidence binding regions were identified by P < 0.05 and absolute value of log2(fold change) higher than 1.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: MeRIP-Seq

source_name: oligodendrocyte progenitor cell

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. The RNA integrity was assessed by Bioanalyzer 2100 with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 30μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (Synaptic Systems, cat.202003, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630).
The IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）.An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000.

treatment_protocol: OPC could be obtained from the cortex of C57BL/6J mouse pups at postnatal days 4 (P4). The isolated tissues were cut into pieces and digested into a single-cell suspension with the papain buffer at 37℃ for 20 min. Cells were resuspended with the panning buffer (DPBS with 0.2% BSA) and incubated in dishes successively pre-coated with the second (IgG) and primary antibodies (GalC) for 1h. Subsequently, the cell suspension was transferred into the O4-coated dishes for 2h. After rinsed twice, cells absorbed on dishes were digested with 0.125% trypsin and be purified OPCs. OPCs were plated in poly-D-lysine-coated plates and cultured in medium.

value: oligodendrocyte progenitor cell

tag: fraction

value: input


title: C10-Pulse4rep3

description: Library name: C10-P4rep3


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LBR_r1

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.

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: Invitro.NET2


title: M6A2_input


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_LB2_r3


title: M6A1_input


title: C9-Pulse2rep3

description: Library name: C9-P2rep3


title: C8-Pulse8rep2

description: Library name: C8-P8rep2


title: H1299 cells, shCtrl bio rep 2

city: Guangzhou

first: Jingwei

last: Li

address: Guangzhou University Town, Panyu District

institute: Sun Yat-sen University

description: Library name: Sample 2

data_processing:
CASAVA Base calling, FASTQ, Trimmomatic, HISAT2, RSeQC, Qualimap, BEDTools
The original image data file is converted into the original sequencing sequence through CASAVA base calling analysis (Sequenced Reads)
The quality of the original sequencing data was assessed by FastQC. Quality shearing was performed by Trimmomatic to obtain relatively accurate valid data.
HISAT2 was used to align the sample valid data to the reference genome and statistically analyze the Mapping information. RSeQC was used to perform redundant sequence analysis, insert fragment distribution and other analyses based on the alignment results.
Qualimap was used to perform uniformity distribution checks, genome structure distribution and other analyses based on the alignment results. BEDTools was used to perform statistical analysis of gene coverage and sequencing sequence distribution on chromosomes.
Assembly: GRCH38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Homo

source_name: Lung

growth_protocol: H1299 lung cancer cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using total RNA Extractor (Trizol), 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using VAHTSTM mRNA-Seg V2 Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: H1299 cells infected by lentivirus to knock down genes: H1299 shCtrl and H1299 shIGF2BP3.

value: Lung

value: Epithelial cells


title: C7-Pulse6rep2

description: Library name: C7-P6rep2


title: M6A3_IP

value: IP


title: pA-DamID_RPE1_iCUT_LBRKO_SCII_DAM_r3

value: Dam only


title: C6-Pulse4rep2

description: Library name: C6-P4rep2


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB2_r3

value: TOP2B KD


title: M6A1_IP


title: Wild type Bioreplicate 3

city: Hsinchu

first: Dinh-Dong

last: Le

address: No. 101, Section 2, Guangfu Rd

country: Taiwan

institute: College of Life Science - Instituted of Molecular & Cellular Biology

description: Library name: Wild type Bioreplicate 3

data_processing:
The processed sequence reads were aligned to the reference C. albicans genome SC5314_A22 using HISAT2.3 Differential gene expression was analyzed with Deseq2 package in R based on the criteria: FDR-corrected P.value (Benjamini-Hochberg) (Padj) ≤ 0.05, log2(Foldchange) ≥ 1 or ≤ -1.
Assembly: SC5314_A22
Supplementary files format and content: csv file includes raw counts for each Sample

organism: Candida albicans SC5314

source_name: Candida albicans wildtype

growth_protocol: A single colony was collected and grown overnight in YPD 30°C. The cells were then allowed to grow in fresh-new YPD for an additional 5 hours to their early log phase before harvesting.

extract_protocol:
Total RNA was extracted using the NautiaZ Bacteria Fungi RNA mini kit (Taiwan) following the manufacturer's instructionsni
The purified RNA was used for the preparation of the sequencing library using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, mRNA was purified from total RNA (1 μm) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After generating double-strand cDNA and adenylation on 3’ ends of DNA fragments, adaptors were ligated to the ends of the fragments. The products were enriched with PCR and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The libraries were analyzed and qualified by a Qsep400 Bio-Fragment Analyzer (Bioptic Inc., New Taipei City, Taiwan) and a Qubit 2.0 Fluorometer (Thermo Scientific, Waltham, MA, USA). The qualified libraries were then sequenced on an Illumina NovaSeq platform with 150 bp paired-end reads generated by Genomics BioSci & Tech Co., New Taipei City, Taiwan.

value: Candida albicans wildtype

value: Wild type


title: C5-Pulse2rep2

description: Library name: C5-P2rep2


title: H1299 cells, shCtrl bio rep 1

description: Library name: Sample 1


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_DAM_r3

city: Milano

first: Stefano

last: Manzo

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

institute: University of Milan


title: M6A2_IP


title: C4-Pulse8rep1

description: Library name: C4-P8rep1


title: HA_rip

data_processing:
For data analysis, firstly clean reads were aligned to mouse genome (version mm10) using HISAT2 (version 2.2.1). The number of reads mapped to each gene was counted using HTSeq (version 0.12.4), with-stranded = no. The target binding regions were identified using MACS2 (version 2.2.7.1) with -nomodel. Significantly high confidence binding regions were identified by P < 0.05 and absolute value of log2 (fold change) higher than 1.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: brain

extract_protocol:
Four brains of P4 mice brain were lysed in 8 ml Lysis Buffer (10 mM HEPES pH 7.6, 2 mM EDTA, 150 mM NaCl, 0.5% NP-40, 0.5 mM DTT, cocktail, 400 U/ml RNase inhibitor). Tissue was fully cleaved with a homogenizer and lysates were centrifuged at 12,500rpm for 60 min at 4 °C. Then the lysate (4.0 mg/ml) were incubated with HA-tag Magnetic Beads (#88836, Thermo Scientific, USA) at 4 °C overnight. After washing, the beads collected and resuspended in 1× MN reaction buffer with micrococcal nuclease at 37 °C for 10 min were washed and incubated with 1×PK buffer containing Proteinase K. RNA were extracted by phenol-chloroform method and then used for RNA library construction (Illumina).
RIP products were reversed transcription into cDNA sequencing library using Invitrogen SuperScript™ II Reverse Transcriptase kit (CA, USA, 1896649). RNA-seq libraries were generated with the NEBNext Ultra™ RNA library Prep Kit (NEB E7770S). The libraries were subjected to quality validation using the Agilent Bioanalyzer 2100, and sequenced using Illumina platforms via a 2x150bp paired-end sequencing protocol

value: brain

value: HA-tag Prrc2b knock-in

value: RIP


title: pA-DamID_RPE1_iCUT_WT_SCII_LBR_r1

source_name: retina

value: LBR


title: H1299 cells, shIGF2BP3 bio rep 2

description: Library name: Sample 4

value: IGF2BP3 knockdown


title: C3-Pulse6rep1

description: Library name: C3-P6rep1

value: epithelial


title: H1299 cells, shIGF2BP3 bio rep 1

description: Library name: Sample 3


title: pA-DamID_RPE1_iCUT_WT_SCII_LB2_r3

value: retina


title: hap32 deletion Bioreplicate 3

department: Instituted of Molecular & Cellular Biology

description: Library name: hap32 deletion Bioreplicate 3

source_name: Candida albicans HAP32 deletion strain

value: Candida albicans HAP32 deletion strain

value: hap32 deletion


title: HA_input

value: input


title: C2-Pulse4rep1

description: Library name: C2-P4rep1

value: pulsed


title: WT_rip

value: wildtype


title: hap32 deletion Bioreplicate 2

description: Library name: hap32 deletion Bioreplicate 2


title: WT_input


title: pA-DamID_RPE1_iCUT_WT_SCII_DAM_r3


title: pA-DamID_RPE1_iCUT_WT_TOP2BKD_LBR_r1


title: C1-Pulse2rep1

description: Library name: C1-P2rep1


title: D60_ROs_WeGFP_rep3

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

description: VSX2-eGFP reporter hiPSCs-derived retinal organoids at 60 days post induction

data_processing:
Reads obtained from the sequencing machines were further filtered by fastp (Chen et al., 2018) (version 0.18.0).
Short reads alignment tool Bowtie2 (Langmead and Salzberg, 2012)(version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
Paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 (Kim et al., 2015) with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 (Pertea et al., 2016; Pertea et al., 2015) in a reference-based approach.
For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM (Li and Dewey, 2011) software.
RNAs differential expression analysis was performed by DESeq2 (Love et al., 2014) software between two different groups (and by edgeR (Robinson et al., 2010) between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 was considered differentially expressed genes/transcripts.
Genome_build: Ensembl_release94
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hiPSCs derived retinal organoids

growth_protocol: Two hiPSC lines, BC1-hiPSC (Chou et al., 2011) and VSX2-eGFP hiPSC (Zheng et al., 2020) were used in this study. All hiPSCs had normal karyotype and were confirmed contamination free. The cells were maintained on Matrigel (Corning) coated plates with mTeSR1 medium (Stem Cell Technologies), and passage every 4-6 days at 80% confluences.

extract_protocol:
The differentiation of hiPSCs into retinal organoids (ROs) was according to published protocols (Li et al., 2019; Li et al., 2018; Luo et al., 2018; Zhong et al., 2014). Briefly, on day 0 (D0) of differentiation, hiPSCs were dissociated to induce embryonic bodies (EBs) formation. EBs were gradually transitioned into neural induction medium (NIM) containing DMEM/F12 (1:1) (GIBCO), 1% N2 supplement (GIBCO), 1% minimum essential media-non essential amino acids (NEAAs, GIBCO), 2 mg/ml heparin (Sigma-Aldrich). On D4 to D6, EBs were seeded onto Matrigel-coated dishes containing NIM, and then switched to retinal differentiation medium (RDM) containing DMEM/F12 (12: 5) supplemented with 2% B27 (without vitamin A, GIBCO), 1% NEAAs and 1% antibiotic-antimycotic (GIBCO) on D16. Since the fourth week of differentiation, optic vesicles (OVs) were gradually formed and morphologically identifiable. OVs were lifted up and cultured in suspension with RDM. The medium was supplemented with 10% fetal bovine serum (FBS, Natocor), 100 mM Taurine (Sigma-Aldrich) and 2 mM GlutaMAX (GIBCO) on D42. Since D90, the medium was supplemented with 1% N2 instead of B27 (without vitamin A). VSX2-eGFP hiPSC-derived mixed cultures at D28 and neuralretinas of 3D ROs collected at D55, D118, and D170 were dissociated into single cells by Papain Dissociation System (Worthington Biochemical) according to the manufacture’ instructions. Cell suspension was centrifuged at 400g for 10 minutes (Allegrax-15R, Beckman Coulter), and cell pellets were resuspended in sorting buffer (PBS containing 1 mM EDTA (GIBCO), 2% [vol/vol] FBS). Cells were sorted at 4℃ by FACSAriafusion (Becton Dickinson). eGFP positive and eGFP negative cells were separately collected in collecting buffer (medium plus 50% [vol/vol] FBS). FSC-A and FSC-H were examined for all cells to obtain live single eGFP positive cells. Cells derived from parental hiPSCs were used to determine gate for sorting.Total RNA were extracted using Trizol reagent kit (Invitrogen). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), end repaired, Abaseadded, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: retinal organoids:derived from VSX2-eGFP reporter hiPSCs

tag: day post induction

value: Day 60


title: hap32 deletion Bioreplicate 1

description: Library name: hap32 deletion Bioreplicate 1


title: Wild type Bioreplicate 2

description: Library name: Wild type Bioreplicate 2


title: D60_ROs_WeGFP_rep2


title: hap31hap32 deletion Bioreplicate 3

description: Library name: hap31hap32 deletion Bioreplicate 3

source_name: Candida albicans HAP31HAP32 deletion strain

value: hap31 deletion hap32 deletion


title: B11-Sustained6rep3

description: Library name: B11-S6rep3

value: sustained


title: hap31hap32 deletion Bioreplicate 2

description: Library name: hap31hap32 deletion Bioreplicate 2

value: Candida albicans HAP31HAP32 deletion strain


title: D60_ROs_WeGFP_rep1


title: MYRF NULL Replicate 1

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: null-deleted MYRF mES total RNA-seq replicate 1

data_processing:
Adapters were removed and reads were trimmed using fastP.
Reads were aligned to hg38 using STAR 2.7.
Bedgraphs were generated using deeptools.
Reads were normalized to total library size (RPM).
Assembly: mm10
Supplementary files format and content: .fastq.gz files contain raw trimmed reads.
Supplementary files format and content: .bedgraph.gz files contain mapped reads normalized to library size (RPM).

source_name: ES cells

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin-coated plates in ES medium (DMEM containing 15% FBS, 0.1 mM MEM nonessential amino acids, 1 mM sodium pyruvate, 2 mM GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/mL LIF, 3 mM CHIR99021 [GSK3b inhibitor, Biovision], 1 mM PD0325901 [MEK inhibitor, Invivogen]) and maintained in a pluripotent state in the absence of a feeder layer.

extract_protocol:
Total RNA was collected from ES cells using Trizol (Invitrogen) lysis buffer and subsequent chloroform and isopropanol isolation followingmanufacturesinstructions. RNA isolation wasfollowed by DNaseI digestion.
Libraries were prepared using standard Illumina TruSeq protocols.

value: ES cells

value: mouse embryonic stem cells

value: Myrf -/- (NULL)


title: Wild type Bioreplicate 1

description: Library name: Wild type Bioreplicate 1

value: Candida albicans wildtype

value: Wild type


title: MYRF NULL Replicate 2

description: null-deleted MYRF mES total RNA-seq replicate 2


title: B10-Sustained4rep3

description: Library name: B10-S4rep3

value: epithelial


title: D60_ROs_WOeGFP_rep3

description: hiPSCs-derived retinal organoids at 60 days post induction

value: retinal organoids:derived from hiPSCs


title: hap31hap32 deletion Bioreplicate 1

description: Library name: hap31hap32 deletion Bioreplicate 1


title: MYRF HET Replicate 3

description: heterozygous-deleted MYRF mES total RNA-seq replicate 3

value: Myrf +/- (HET)


title: B9-Sustained2rep3

description: Library name: B9-S2rep3


title: D60_ROs_WOeGFP_rep2


title: hap31 deletion Bioreplicate 3

description: Library name: hap31 deletion Bioreplicate 3

source_name: Candida albicans HAP31 deletion strain

value: Candida albicans HAP31 deletion strain

value: hap31 deletion


title: B8-Sustained8rep2

description: Library name: B8-S8rep2


title: D60_ROs_WOeGFP_rep1


title: MYRF HET Replicate 2

description: heterozygous-deleted MYRF mES total RNA-seq replicate 2


title: hap31 deletion Bioreplicate 2

description: Library name: hap31 deletion Bioreplicate 2


title: D170_eGFPneg_rep2

description: flow sorted eGFP negative cells at 170 days post induction

source_name: Neuralretinas of hiPSC-derived retinal organoids

value: eGFP negative cells derived from VSX2-eGFP reporter hiPSCs

value: Day 170


title: hap31 deletion Bioreplicate 1

description: Library name: hap31 deletion Bioreplicate 1


title: MYRF HET Replicate 1

description: heterozygous-deleted MYRF mES total RNA-seq replicate 1


title: B12-Sustained8rep3

description: Library name: B12-S8rep3


title: MYRF NULL Replicate 3

description: null-deleted MYRF mES total RNA-seq replicate 3


title: MYRF WT Replicate 3

description: wild-type MYRF mES total RNA-seq replicate 3

value: Myrf +/+ (WT)


title: B6-Sustained4rep2

description: Library name: B6-S4rep2


title: D170_eGFPneg_rep1


title: MYRF WT Replicate 2

description: wild-type MYRF mES total RNA-seq replicate 2


title: BnNAC038 DAP-seq, input

city: Beijing

first: Jingrui

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

description: Library name: Sample3

data_processing:
For DAP-seq analysis, low-quality reads were filtered, and the remaining high-quality reads were mapped to the Brassica napus reference genome (zs11) using BWA-MEM_0.7.17 with default parameters.
Peaks were identified using MACS_2.2.9.1, and peak annotations were performed using ChIPseeker.
Representative motifs from the identified peaks were determined with MEME-ChIP_5.5.5.
For peak visualization, the mapping results (BAM files) were processed using Samtools and subsequently converted to BigWig files via the bamCoverage function of deepTools_3.5.1.
Assembly: zs11
Supplementary files format and content: For DAP-seq, BigWig files for two idenpendent replicates

organism: Brassica napus

source_name: whole plant

growth_protocol: Brassica napus seedlings are cultivated in Hoagland's nutrient solution at 25°C under long-day conditions (16 hours of light and 8 hours of darkness).

extract_protocol:
The BnNAC038 was extracted from Escherichia coli BL21 cells. Genomic DNA was extracted from whole plants, and 10 μg of genomic DNA was diluted and used for library construction. Approximately 5–20 μg of purified BnNAC038 protein was incubated with 1 μg of the DNA library for 1 hour at 25°C.
Library was constructed with the NGS0602-TLX DNA-Seq Kit (MICH).

value: whole plant

value: wild-type

value: non treatent


title: B5-Sustained2rep2

description: Library name: B5-S2rep2

value: sustained


title: BnNAC038 DAP-seq, replicate 2

description: Library name: Sample2


title: MYRF WT Replicate 1

description: wild-type MYRF mES total RNA-seq replicate 1

value: ES cells


title: B4-Sustained8rep1

description: Library name: B4-S8rep1


title: D55_eGFPneg_rep2

description: flow sorted eGFP negative cells at 55 days post induction

value: Day 55


title: B3-Sustained6rep1

description: Library name: B3-S6rep1


title: D55_eGFPneg_rep1


title: BnNAC038 DAP-seq, replicate 1

description: Library name: Sample1


title: BnNAC038 over-expression line 2, 20% PEG treatment for 6 hours, biological replicate 3

description:
Library name: Sample45
Column name in OE_RNAseq_All_samples.txt: OE2_PEG6h_rep3

data_processing:
For RNA-seq analysis of knockout line, high-quality reads were mapped to the Brassica napus reference genome (zs11) using HISAT2.2.1. Fragment per kilobase of transcript per million mapped reads (FPKM) values were calculated for each transcript using StringTie2.2.1 to quantify gene expression. Differentially expressed genes (DEGs) were identified using the DESeq2_1.38.3 package with a fold change (FC) ≥ 1.5 and a p-value < 0.05.
For RNA-seq analysis of overexpression line, high-quality reads were used to quantify each transcript using Kallisto_0.51.1. The transcripts per million (TPM) values for each transcript were calculated. Differentially expressed genes between wild-type and BnNAC038-OE plants were identified using the Sleuth_0.30.1 package with FC ≥ 1.5 and a p-value < 0.05.
Assembly: zs11
Supplementary files format and content: For RNA-seq, txt files include FPKM or TPM value for each Sample

source_name: leaves

extract_protocol:
Total RNA from each sample was extracted using TRIzol™ Reagent (Invitrogen) following the manufacturer's protocol.
The mRNA was isolated and used for RNA-seq library construction following the NEBNext Ultra II RNA Library Kit instructions.

treatment_protocol: Wild-type, knockout lines (BnNAC038-KO-1), and overexpression lines (BnNAC038-OE-1, BnNAC038-OE-2) were subjected to treatment with 50 μM ABA and 20% PEG for the specified durations.

value: leaves

value: BnNAC047 over-expression

value: 20% PEG treatment for 6 hours


title: Muscle, 70 days post 35 Gy CONV irradiation, rep 3

city: Pisa

first: Giulia

last: Furini

address: Via Giuseppe Moruzzi 1

department: Institute of Clinical Physiology (IFC)

institute: National Research Council (CNR)

description: Library name: 10_Conv

data_processing:
Dragen BCLConvert (for demultiplexing): raw data
Kallisto 0.5.0
Assembly: mm10
Supplementary files format and content: tsv from kallisto, gene counts

source_name: Muscle

extract_protocol:
Total RNA was extracted from 10–15 mg of frozen skin and muscle tissues, collected from the left hindlimb of both control and irradiated mice. Homogenization was performed with a Qiagen TissueLyser II in 700 µL of TRIzol reagent using stainless steel beads at 30 Hz for 5×30 sec. The aqueous phase obtained after chloroform addition (1/5 volume) and centrifugation (12000 × g for 15 min at 4 °C) was loaded onto Direct-zol RNA Microprep columns (Zymo Research,) and RNA eluted in 15 uL RNAse-free water, as indicated by the manufacturer protocol.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus

treatment_protocol: C57BL/6J mice were exposed to 35 Gy electron irradiation using the ElectronFlash linear accelerator (Linac) available at the Centro Pisano FLASH Radiotherapy (CPFR). The instrument was set on either FLASH or conventional (CONV) modality.  Sham, not irradiated mice served as controls.

value: Muscle

value: WT


title: D170_eGFPpos_rep2

description: flow sorted eGFP positive cells at 170 days post induction

source_name: Neuralretinas of hiPSCs derived retinal organoids

value: eGFP positive cells derived from VSX2-eGFP reporter hiPSCs


title: Muscle, 70 days post 35 Gy CONV irradiation, rep 2

description: Library name: 8_Conv


title: B2-Sustained4rep1

description: Library name: B2-S4rep1

value: epithelial


title: BnNAC038 over-expression line 2, 20% PEG treatment for 6 hours, biological replicate 2

description:
Library name: Sample44
Column name in OE_RNAseq_All_samples.txt: OE2_PEG6h_rep2

value: BnNAC046 over-expression


title: D170_eGFPpos_rep1


title: B1-Sustained2rep1

description: Library name: B1-S2rep1


title: Muscle, 70 days post 35 Gy CONV irradiation, rep 1

description: Library name: 7_Conv


title: D118_eGFPpos_rep2

description: flow sorted eGFP positive cells at 118 days post induction

value: Day 118


title: B7-Sustained6rep2

description: Library name: B7-S6rep2


title: BnNAC038 over-expression line 2, 20% PEG treatment for 6 hours, biological replicate 1

description:
Library name: Sample43
Column name in OE_RNAseq_All_samples.txt: OE2_PEG6h_rep1

value: BnNAC045 over-expression


title: Muscle, 70 days post 35 Gy FLASH irradiation, rep 4

description: Library name: 6_Flash

value: FLASH-RT


title: D118_eGFPpos_rep1


title: ControlRep3

description: Library name: A3-ControlRep3

value: vehicle


title: BnNAC038 over-expression line 2, 50 μM ABA treatment for 3 hours, biological replicate 3

description:
Library name: Sample42
Column name in OE_RNAseq_All_samples.txt: OE2_ABA3h_rep3

value: BnNAC044 over-expression

value: 50 μM ABA treatment for 3 hours


title: BnNAC038 over-expression line 2, 50 μM ABA treatment for 3 hours, biological replicate 2

description:
Library name: Sample41
Column name in OE_RNAseq_All_samples.txt: OE2_ABA3h_rep2

value: BnNAC043 over-expression


title: ControlRep2

description: Library name: A2-ControlRep2


title: Muscle, 70 days post 35 Gy FLASH irradiation, rep 2

description: Library name: 4_Flash


title: D55_eGFPpos_rep1

description: flow sorted eGFP positive cells at 55 days post induction


title: BnNAC038 over-expression line 2, 50 μM ABA treatment for 3 hours, biological replicate 1

description:
Library name: Sample40
Column name in OE_RNAseq_All_samples.txt: OE2_ABA3h_rep1

value: BnNAC042 over-expression


title: Muscle, 70 days post 35 Gy FLASH irradiation, rep 3

description: Library name: 5_Flash


title: Muscle, 70 days post 35 Gy FLASH irradiation, rep 1

description: Library name: 3_Flash


title: D28_eGFPpos_rep2

description: flow sorted eGFP positive cells at 28 days post induction

source_name: hiPSCs derived mixed cultures

value: Day 28


title: D55_eGFPpos_rep2

value: Day 55


title: Muscle, 70 days not irradiated, rep 3

description: Library name: 4_Cnt

value: sham


title: BnNAC038 over-expression line 2, normal cultural condition, biological replicate 3

description:
Library name: Sample39
Column name in OE_RNAseq_All_samples.txt: OE2_CK_rep3

value: leaves

value: BnNAC041 over-expression

value: non treatent


title: D28_eGFPpos_rep1

extract_protocol:
The differentiation of hiPSCs into retinal organoids (ROs) was according to published protocols (Li et al., 2019; Li et al., 2018; Luo et al., 2018; Zhong et al., 2014). Briefly, on day 0 (D0) of differentiation, hiPSCs were dissociated to induce embryonic bodies (EBs) formation. EBs were gradually transitioned into neural induction medium (NIM) containing DMEM/F12 (1:1) (GIBCO), 1% N2 supplement (GIBCO), 1% minimum essential media-non essential amino acids (NEAAs, GIBCO), 2 mg/ml heparin (Sigma-Aldrich). On D4 to D6, EBs were seeded onto Matrigel-coated dishes containing NIM, and then switched to retinal differentiation medium (RDM) containing DMEM/F12 (12: 5) supplemented with 2% B27 (without vitamin A, GIBCO), 1% NEAAs and 1% antibiotic-antimycotic (GIBCO) on D16. Since the fourth week of differentiation, optic vesicles (OVs) were gradually formed and morphologically identifiable. OVs were lifted up and cultured in suspension with RDM. The medium was supplemented with 10% fetal bovine serum (FBS, Natocor), 100 mM Taurine (Sigma-Aldrich) and 2 mM GlutaMAX (GIBCO) on D42. Since D90, the medium was supplemented with 1% N2 instead of B27 (without vitamin A). VSX2-eGFP hiPSC-derived mixed cultures at D28 and neuralretinas of 3D ROs collected at D55, D118, and D170 were dissociated into single cells by Papain Dissociation System (Worthington Biochemical) according to the manufacture’ instructions. Cell suspension was centrifuged at 400g for 10 minutes (Allegrax-15R, Beckman Coulter), and cell pellets were resuspended in sorting buffer (PBS containing 1 mM EDTA (GIBCO), 2% [vol/vol] FBS). Cells were sorted at 4℃ by FACSAriafusion (Becton Dickinson). eGFP positive and eGFP negative cells were separately collected in collecting buffer (medium plus 50% [vol/vol] FBS). FSC-A and FSC-H were examined for all cells to obtain live single eGFP positive cells. Cells derived from  parental hiPSCs were used to determine gate for sorting.Total RNA were extracted using Trizol reagent kit (Invitrogen). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), end repaired, Abaseadded, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: eGFP positive cells derived from VSX2-eGFP reporter hiPSCs


title: SW948_C_4

city: London

first: Daniel

middle: Martinez

last: Martinez

state: London

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Medical Research Council

data_processing:
HiSeq Control Software 2.2.58, RTA 2.11.3 and bcl2fastq2_2.20.0 were used for raw reads quality control and treatment
Raw sequences were quality filtered and trimmed with trimmomatic (v.0.39)
The resulting reads were mapped to the human reference transcriptome from ensembl database.
Quantification of samples was made via salmon (v 1.5.0) with mapping validation and gcbias options activated
Assembly: GRCh38.p13, version 103
Supplementary files format and content: tab-separated file of raw reads from Salmon mapping
Supplementary files format and content: tab-separated file of normalised reads done in deseq2 in R

source_name: Colon

growth_protocol: HCT116, LoVo, DLD-1 and SW948 cells were plated in 6 wells plates with complete medium

extract_protocol:
Samples were prepared using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
RNA-seq libraries were prepared using Illumina Stranded mRNA Prep kit and protocols

treatment_protocol: 10 mM of 2-MiCit was used as a treatment, or vehicle (water) for control condition

value: Colon

value: epithelial

value: wild-type

value: control


title: Muscle, 70 days not irradiated, rep 2

description: Library name: 2_Cnt

value: Muscle

value: WT


title: LoVo_M_4

value: LoVo

value: Micit


title: ControlRep1

description: Library name: A1-ControlRep1

value: vehicle


title: BnNAC038 over-expression line 2, normal cultural condition, biological replicate 1

description:
Library name: Sample37
Column name in OE_RNAseq_All_samples.txt: OE2_CK_rep1

value: BnNAC039 over-expression


title: Muscle, 70 days not irradiated, rep 1

description: Library name: 1_Cnt


title: WA_FRA1 2hrs _Serum Stimulation-2

city: Sudbury

first: Sujeenthar

last: Tharmalingam

address: 935 Ramsey Lake Road

institute: NOSM University

description:
Library name: TLab_224
2hdCas9_vs_2hACT.genes.counts.csv

data_processing:
The sequencing data was processed in-house using various bioinformatics toolkits available through the Illumina Sequence Hub (San Diego, CA, USA), powered by DRAGEN Inc. Briefly, DRAGEN FASTQ was used to assess sequencing quality and perform read trimming. DRAGEN RNA was employed to align reads to the human reference genome (GRCh38.p14; hg38) and quantify transcript abundance. Differential expression analysis was conducted using the DRAGEN Differential Expression pipeline, which incorporates the DESeq2 algorithm. Genes were considered differentially expressed if they exhibited a fold change < −1.5 or > 1.5, an FDR-adjusted p-value < 0.05, and an average transcript abundance of at least 30 transcripts per million (TPM).
Assembly: GRCh38.p14; hg38
Supplementary files format and content: CSV file describing the number of reads mapped to each gene for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent and further purified with the NEB Monarch® RNA Cleanup Kit (T2040L, NEB).
100 ng of high-quality RNA (A260/280 ~2.0 ± 0.1) was used to generate strand-specific libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765S, NEB), which enriches for poly-A mRNA and incorporates the dUTP method for strand specificity.

value: hybrid of fibroblast and HeLa

value: dCas9; FRA1 Overexpression

value: 2h Post Serum Stimulation


title: SW948_M_4


title: LoVo_C_4


title: BnNAC038 over-expression line 1, 20% PEG treatment for 6 hours, biological replicate 3

description:
Library name: Sample36
Column name in OE_RNAseq_All_samples.txt: OE1_PEG6h_rep3

value: leaves

value: BnNAC038 over-expression

value: 20% PEG treatment for 6 hours


title: WA_FRA1 2hrs _Serum Stimulation-1

description:
Library name: TLab_222
2hdCas9_vs_2hACT.genes.counts.csv


title: DLD1_C_4


title: BnNAC038 over-expression line 1, 20% PEG treatment for 6 hours, biological replicate 2

description:
Library name: Sample35
Column name in OE_RNAseq_All_samples.txt: OE1_PEG6h_rep2


title: Skin, 70 days post 35 Gy CONV irradiation, rep 3

description: Library name: 10C_Skin

source_name: Skin

value: Skin


title: Skin, 70 days post 35 Gy CONV irradiation, rep 2

description: Library name: 8C_Skin


title: WA_dCas9 2hrs _Serum Stimulation-2

description:
Library name: TLab_220
2hdCas9_vs_2hACT.genes.counts.csv


title: BnNAC038 over-expression line 1, 20% PEG treatment for 6 hours, biological replicate 1

description:
Library name: Sample34
Column name in OE_RNAseq_All_samples.txt: OE1_PEG6h_rep1


title: WA_dCas9 2hrs _Serum Stimulation-3

description:
Library name: TLab_221
2hdCas9_vs_2hACT.genes.counts.csv


title: HCT116_M_4

value: Colon


title: WA_dCas9 2hrs _Serum Stimulation-1

description:
Library name: TLab_219
2hdCas9_vs_2hACT.genes.counts.csv


title: Skin, 70 days post 35 Gy CONV irradiation, rep 1

description: Library name: 7C_Skin


title: BnNAC038 over-expression line 1, 50 μM ABA treatment for 3 hours, biological replicate 3

description:
Library name: Sample33
Column name in OE_RNAseq_All_samples.txt: OE1_ABA3h_rep3

value: 50 μM ABA treatment for 3 hours


title: WA_KO 2hrs_Serum Stimulation-3

description:
Library name: TLab_218
2hCas9_vs_2hKO.genes.counts.csv

value: Cas9; FRA1 KO


title: BnNAC038 over-expression line 2, normal cultural condition, biological replicate 2

description:
Library name: Sample38
Column name in OE_RNAseq_All_samples.txt: OE2_CK_rep2

value: BnNAC040 over-expression

value: non treatent


title: BnNAC038 over-expression line 1, 50 μM ABA treatment for 3 hours, biological replicate 2

description:
Library name: Sample32
Column name in OE_RNAseq_All_samples.txt: OE1_ABA3h_rep2


title: Skin, 70 days post 35 Gy FLASH irradiation, rep 3

description: Library name: 5F_Skin

value: WT

value: FLASH-RT


title: Skin, 70 days post 35 Gy FLASH irradiation, rep 4

description: Library name: 6F_Skin


title: HCT116_C_4

value: epithelial

value: wild-type

value: control


title: WA_KO 2hrs_Serum Stimulation-2

description:
Library name: TLab_217
2hCas9_vs_2hKO.genes.counts.csv

value: hybrid of fibroblast and HeLa


title: SW948_M_3

value: Micit


title: BnNAC038 over-expression line 1, 50 μM ABA treatment for 3 hours, biological replicate 1

description:
Library name: Sample31
Column name in OE_RNAseq_All_samples.txt: OE1_ABA3h_rep1


title: DLD1_M_4


title: Skin, 70 days post 35 Gy FLASH irradiation, rep 1

description: Library name: 3F_Skin


title: WA_Cas9 2hrs_Serum Stimulation-3

description:
Library name: TLab_215
2hCas9_vs_2hKO.genes.counts.csv

value: 2h Post Serum Stimulation


title: SW948_C_3


title: Skin, 70 days post 35 Gy FLASH irradiation, rep 2

description: Library name: 4F_Skin


title: WA_KO 2hrs_Serum Stimulation-1

description:
Library name: TLab_216
2hCas9_vs_2hKO.genes.counts.csv


title: LoVo_M_3

value: LoVo


title: BnNAC038 over-expression line 1, normal cultural condition, biological replicate 2

description:
Library name: Sample29
Column name in OE_RNAseq_All_samples.txt: OE1_CK_rep2

value: leaves

value: BnNAC038 over-expression


title: Skin, 70 days not irradiated, rep 3

description: Library name: 4CNT_Skin

value: Skin

value: sham


title: WA_Cas9 2hrs_Serum Stimulation-2

description:
Library name: TLab_214
2hCas9_vs_2hKO.genes.counts.csv


title: BnNAC038 over-expression line 1, normal cultural condition, biological replicate 1

description:
Library name: Sample28
Column name in OE_RNAseq_All_samples.txt: OE1_CK_rep1


title: LoVo_C_3

value: Colon


title: Skin, 70 days not irradiated, rep 2

description: Library name: 2CNT_Skin


title: WA_Cas9 2hrs_Serum Stimulation-1

description:
Library name: TLab_213
2hCas9_vs_2hKO.genes.counts.csv


title: DLD1_M_3


title: wilt-type, 20% PEG treatment for 6 hours, biological replicate 3, for BnNAC038-OE

description:
Library name: Sample27
Column name in OE_RNAseq_All_samples.txt: WT_PEG6h_rep3

value: 20% PEG treatment for 6 hours


title: WA_FRA1 0hrs_Serum Stimulation-3

description:
Library name: TLab_212
0hCas9dCas9_vs_0hACT.genes.counts.csv

value: dCas9; FRA1 Overexpression

value: Baseline


title: DLD1_C_3


title: wilt-type, 20% PEG treatment for 6 hours, biological replicate 2, for BnNAC038-OE

description:
Library name: Sample26
Column name in OE_RNAseq_All_samples.txt: WT_PEG6h_rep2


title: HCT116_M_3


title: WA_FRA1 0hrs_Serum Stimulation-2

description:
Library name: TLab_211
0hCas9dCas9_vs_0hACT.genes.counts.csv


title: RNA-Seq of naive CD4 T cells_WT3

city: NEW YORK

first: Jingyao

last: Zhao

state: NY

address: 701 W 168th Street Room 1204

department: Microbiology and Immunology

institute: Columbia University Medical Center

description: Library name: RNA_N_WT3

data_processing:
Galaxy RNA-seq platform.
Assembly: mm10
Supplementary files format and content: csv DEG for RNA-seq. BED  for ATAC-seq

source_name: Spleen and Lymph nodes

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (Zymo Research). 0.5 ug of total RNA was used for the construction of sequencing libraries.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina(NEB) or ATAC-Seq Kit(Active Motif)

value: Spleen and Lymph nodes


title: WA_FRA1 0hrs_Serum Stimulation-1

description:
Library name: TLab_210
0hCas9dCas9_vs_0hACT.genes.counts.csv


title: RNA-Seq of naive CD4 T cells stimulated by Forskolin_WT3

description: Library name: RNA_FSK_WT3


title: wilt-type, 50 μM ABA treatment for 3 hours, biological replicate 3, for BnNAC038-OE

description:
Library name: Sample24
Column name in OE_RNAseq_All_samples.txt: WT_ABA3h_rep3

value: 50 μM ABA treatment for 3 hours


title: wilt-type, 20% PEG treatment for 6 hours, biological replicate 1, for BnNAC038-OE

description:
Library name: Sample25
Column name in OE_RNAseq_All_samples.txt: WT_PEG6h_rep1


title: BnNAC038 over-expression line 1, normal cultural condition, biological replicate 3

description:
Library name: Sample30
Column name in OE_RNAseq_All_samples.txt: OE1_CK_rep3

value: non treatent


title: SW948_M_2

value: epithelial

value: wild-type


title: WA_dCas9 0hrs _Serum Stimulation-2

description:
Library name: TLab_209
0hCas9dCas9_vs_0hACT.genes.counts.csv

value: hybrid of fibroblast and HeLa


title: WA_dCas9 0hrs _Serum Stimulation-1

description:
Library name: TLab_207
0hCas9dCas9_vs_0hACT.genes.counts.csv


title: SW948_C_2

value: control


title: wilt-type, 50 μM ABA treatment for 3 hours, biological replicate 1, for BnNAC038-OE

description:
Library name: Sample22
Column name in OE_RNAseq_All_samples.txt: WT_ABA3h_rep1