title: ZNF263_KO, Cervical Motor Neurons, RAD21

data_processing:
Sequence reads were mapped to mm10 reference genome with Bowtie 2.
After normalization with the spike-in Drosophila read counts for all (except for normalization with total counts for RAD21), normalized ChIP-seq read densities were visualized in Easeq Software and/or Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin fromDrosophila(1:100 ratio to ESC or MN derived chromatin), andDrosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

value: Cervical Motor Neurons


title: Zebrafish Embryo, 4hpf, rep1

status: Public on Aug 21 2024

type: SRA

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

country: USA

institute: Stowers Institute for Medical Research

library_source: transcriptomic

data_processing:
Raw reads from zebrafish oocytes (stages I-IV) and embryos (0-, 2-, 4-, and 6-hours post fertilization) were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl-convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner (version 2.7.3a), using Ensembl 106 gene models. Counts were converted to TPM values using RSEM (version v1.3.0) and all subsequent analysis was done using TPM.
Assembly: danRer11 Ensembl 106 gene models
Supplementary files format and content: comma-separated files with TPMs from all replicates

molecule: total RNA

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
Isolated oocytes were snap-frozen and RNA was extracted with TRIzol (Invitrogen #15596026) following manufacturer’s protocols. 0-, 2-, 4- and 6-hpf zebrafish embryo RNA was extracted with Direct-zol RNA MicroPrep kit (Zymo Research #R2062) following manufacturer’s protocols.
Ribo-dep Stranded RNA-Seq
Zebrafish embryos (0-, 2-, 4-, and 6-hours post fertilization) total RNA sequencing libraries were generated from 500ng of high-quality total RNA, as assessed using Bioanalyzer (Agilent). Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold (Illumina #20020598), and TruSeq RNA Single Indexes Sets A and B (Illumina #20020492 and #20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Life Technologies). Libraries were pooled, quantified, and sequenced as 75bp single reads on a high-output flow cell using the Illumina NextSeq500 instrument. Following sequencing, Illumina Primary Analysis (version RTA 2.11.3.0) and bcl-convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes (stages I-IV) total RNA-Seq libraries were generated from 100 ng of high-quality total RNA, as assessed by a Bioanalyzer (Agilent Technologies). Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, Cat. No. 20020598), and TruSeq RNA Single Indexes; Sets A and B (Illumina Cat. No. 20020492 and 20020493). Resulting short-fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer (Life Technologies). Libraries were normalized, pooled, and sequenced on a NextSeq 500 instrument (Illumina), as 75 bp single-end reads on a high-output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.

tag: tissue

value: Whole embryo

tag: developmental stage

tag: genotype

value: AB, TF and TLF


title: T26C_CKDL220007706-1a-N706-N503_HN2WWDSX3_L4

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCh38) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide CPM (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: GRCh38
Supplementary files format and content: txt, normalized read counts

organism: Homo sapiens

extract_protocol:
RNA isolation from cultured cells was used Trizol reagent.
RNA-seq libraries were prepared using the NEBNext RNA Library Prep Kit (New England Biolabs, NEB) .

treatment_protocol: TSC lines CT27 (female) and CT-29 (male) were obtained from the RIKEN Cell Engineering Division (https://cell.brc.riken.jp/en/) and cultured as previously described (Okae). In brief, stem-state CTB cells were plated on plates pre-coated with 5 μg/mL collagen IV (Corning, cat # 354277) and maintained in stem state medium containing DMEM/F12 with 0.3 % w/v bovine serum albumin (BSA, FisherSci, BP9704100), 1X insulin, transferrin, selenium- ethanolamine supplement ( ITS-X, ThermoFisher, cat # 51500056), 0.2 % v/v fetal bovine serum (FBS, ThermoFisher, cat # 16141061), 0.1 mM 2-mercaptoethanol, 50 ng/mL epidermal growth factor, 1.5 μg/mL L-ascorbic acid, 0.8 mM valproic acid, 5 μM Y27632 (ReproCell, cat #04-0012), 2 μM CHIR99021 (ReproCell, cat #04-0004), 0.5 μM A83-01 (ReproCell, cat #04-0004), and 1 μM SB431542 (ReproCell, cat #04-0010). Monolayers were rinsed with phosphate-buffered saline, dispersed to single cells with TrypLE Express for approximately 15 min, and passaged at 75% confluence. Undifferentiated TSC were collected for as CTB for downstream analysis.  To induce STB differentiation in TSC, cells were passaged to a plate coated with 2.5 μg/mL collagen IV and seeded at 1 x 105 cells per 35 mm well of a 6 well plate. Cells were differentiated over the course of 6 ds in medium containing DMEM/F12 with 0.3% w/v BSA, 1X ITS-X, 0.1 mM 2-mercaptoethanol, 2.5 μM Y27632, 2 μM Forskolin, and 4% v/v Knockout Serum Replacement (KSR) with medium changes every other day.  To induce EVTB/MTB differentiation in TSC, cells were passaged to a plate coated with 1 μg/mL collagen IV and seeded at 1 x 105 cells per 35 mm well of a 6 well plate. Cells were differentiated over the course of 6 d in medium containing DMEM/F12 with 0.3 % w/v BSA, 1X ITS-X, 0.1 mM 2-mercaptoethanol, 2.5 μM Y27632, 7.5 μM A83-01, 100 ng/mL NRG1, 2% Matrigel, and 4 % v/v KSR with medium changes every other day. On d 3 of differentiation, medium was exchanged with the above recipe without NRG1. On d 6, medium was exchanged with the above recipe without NRG1 and KSR and cells were passaged a final time to enhance EVTB differentiation.   Human embryonic stem cell (hESC) lines H1 (WA01, male, XY) and H9 (WA09, female, XX) were obtained from the WiCell Research in Madison, WI (Thomson et al.) Cells were seeded at a density of 50,000 cells/well onto Matrigel (Corning)-coated 6-well plates in mTESR1 medium (Stem Cell Technologies). Cells were then cultured in basal DMEM/F12 with 20 % v/v KOSR, non-essential amino acids, 2mM L-glutamine, and FGF2 (4 ng/mL)  for 24 h. The trophoblast phenotype was initiated using an established protocol (Amita). Medium was exchanged with the same recipe without FGF2, and additional supplementation of BMP4 (10 ng/mL), A83-01 (1 µm), and PD173074 (0.1 µm) (BAP) each day over the course of 8 days. Upon completion of BAP treatment, cells were dispersed and passed through a cell strainer to separate small, CTB-like cells (<40 μm) and large, STB-like cells (>70 μm) (Yabe; {Yabe, 2016 #8777}. After separation, cells were centrifuged and snap frozen for downstream assays. All cell culture was completed at 37 °C in a humidified incubator at 5% CO2 and atmospheric oxygen.

tag: cell type

value: Trophoblasts

tag: treatment

value: BAP


title: Zebrafish Oocyte, Stage I, rep1

source_name: Oocyte

value: Oocyte

value: Stage I


title: Hypothalamus, 120 day, M4-3

city: Tai'an

first: Qing

last: Li

address: Tai’an, Shandong Province, P.R. China

country: China

institute: College of Animal Science and Veterinary Medicine

data_processing:
Clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNAs. miRBase20.0 was used as the reference, and the modified software mirdeep2 and sRNA-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The software miREvo and mirdeep2 were integrated to predict novel miRNAs.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: ARS1.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

organism: Capra hircus

source_name: hypothalamus

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hypothalamus

value: 120 day


title: WT_E14, Cervical Motor Neurons, RAD21

city: Miami

first: Danny

last: Reinberg

state: Florida

address: 1501 NW 10th Ave

department: Sylvester Cancer Center/Human Genetics

institute: University of Miami

description: WT MNs

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days (Day 0) in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol). Medium was exchanged on Day 2 of differentiation, and further patterning of embryoid bodies was induced by supplementing the ANDFK media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

tag: cell line

tag: chip antibody


title: Retina_06w_S02

city: Leuven

first: Lieve

last: Moons

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

description: 10x Genomics 3' scRNA-seq

library_source: transcriptomic single cell

data_processing:
Sequencing reads were mapped to the custom build transcriptome using CellRanger (v7.0.1)
Mapped scRNA-seq data was processed in Monocle 3 (monocle3_1.2.9)
Assembly: PRJEB5837
Supplementary files format and content: Comma-separated value files and matrix files

molecule: polyA RNA

organism: Nothobranchius furzeri

source_name: Neural Retina

growth_protocol: Killifish of the GRZ-AD inbred strain were housed in a standarised system maintaining constant pH (7.0), conducitivty (600µs) and temperature (28,0°C).

extract_protocol:
Fish were euthanized using 0.1% tris buffered tricaine. Retinas were collected in complete L15 (Leibovitz 15 medium complemented with 2% Penicilin-Streptomycin, 0.5% Gentamycin, 2% heat-inactivated Fetal Bovin Serum, 1% Glutamax, 2% MEM Essential Amino Acids, 2% B27, 25 mM D-Glucose, 25 mM HEPES and brought to pH7.4) after retinal pigment epitheluim removal. Retinas were rinsed three times with complete L15 before enzymetic digesting using papain (16 U/ml) for 30 min at 28°C.  Before mechinal tritruation in sterile PBS with 1% bovine serum albumine (fraction V), digested retinas were rinsed three times with complete L15. Cell clumps were removed using a 40 µm cell strainer.
scRNA-seq was performed using standard 10x Genomics v3 3' sequencing protocol.

value: Neural Retina

value: Wildtype

tag: condition

value: 6 weeks


title: T32C_CKDL220007706-1a-N702-N506_HN2WWDSX3_L4


title: Hypothalamus, 60 day, M2-1

value: 60 day


title: ZNF263_KO, Embryonic stem cells, RAD21

value: Embryonic stem cells


title: Zebrafish Embryo, 0hpf, rep3


title: Zebrafish Embryo, 6hpf, rep3


title: Hypothalamus, 120 day, M4-2


title: Hypothalamus, 1 day, D1-5

value: 1 day


title: T12C_CKDL220007706-1a-N704-N503_HN2WWDSX3_L4

value: Differentiated


title: Zebrafish Embryo, 6hpf, rep2


title: T31C_CKDL220007706-1a-N701-N506_HN2WWDSX3_L4


title: Hypothalamus, 120 day, M4-1


title: Hypothalamus, 1 day, D1-4


title: PATZ1_KO_MNs

description:
Patz1 KO MNs
microc_hiccompare_WT_v_KO_MN.results_related_to_Fig_S12F.txt

data_processing:
The raw data was processed by Dovetail pipeline into the processed files.
Assembly: mm10
Supplementary files format and content: hic
Library strategy: Micro-C sequencing

source_name: Motor Neurons

extract_protocol:
Cells were processed according to the Dovetail Micro-C kit instructions. Briefly, they were trypsinized, counted, washed with 1X PBS and frozen in the recommended numbers at -80 C. They were then processed with the Dovetail Micro-C kit.
Libraries were prepared according to manufacturer’s instructions (Dovetail Micro-C kit compatible with Illumina sequencing) as described in STAR Methods.

value: Motor Neurons


title: T30C_CKDL220007706-1a-N702-N505_HN2WWDSX3_L4


title: Zebrafish Embryo, 6hpf, rep1


title: ZNF263_KO, Embryonic stem cells, HA

value: HA (Abcam, ab9110)


title: Hypothalamus, 60 day, M2-5


title: WT_MNs

description:
wild type MNs
microc_hiccompare_WT_v_KO_MN.results_related_to_Fig_S12F.txt


title: Zebrafish Embryo, 4hpf, rep2

value: Whole embryo


title: T10C_CKDL220007706-1a-N702-N503_HN2WWDSX3_L4


title: Hypothalamus, 60 day, M2-3


title: WT_ESCs

description:
wild type ESCs
microc_hiccompare_WT_v_KO_ESC.results_related_to_Fig_S12E.txt


title: T28C_CKDL220007706-1a-N710-N503_HN2WWDSX3_L4


title: PATZ1_KO, Cervical Motor Neurons, RAD21

value: Cervical Motor Neurons


title: hESC_APLNR+ mesoderm cell_10x

city: 288 Nanjing Rd, Heping

first: Jingjing

last: Zhao

state: TianJin

address: Nanjing Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
10X Genomics CellRanger version 3.0.2 were used to the basecalling.
Cell Ranger (version 3.0.2) software from 10X Genomics (http://www.10xgenomics.com) was used to align and quantify sequencing raw data with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-Separated Values file includes UMI for each cell

source_name: human embryonic stem cells

growth_protocol: hESC aggregates were dissociated by dispase and planted onto the mAGM-S3 cells in mTeSR1 medium for 24 hour. Subsequently, the medium was changed to hematopoietic differentiation medium (IMDM supplemented with 10% (v/v) fetal bovine serum (FBS), VEGF (15 ng/ml), 2-ME (100 mM), L-Ascorbic acid (50 mg/ml), 1% (v/v) nonessential amino acid solution, P/S (10 ng/ml) and human transferrin (7 mg/ml)). Changed medium every day.

extract_protocol: The libraries were constructed and  sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner (sequenced by Novogene).

value: H1 embryonic stem cell line

value: APLNR+ mesoderm cells derived from hESC

tag: development stage

value: after hematopoietic differentiation


title: Citrobacter rodentium transposon mutant library

status: Public on Aug 20 2024

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
reads were trimmed and quality filtered on their right (genomic sequence) ends using PRINSEQ with the command: prinseq-lite.pl -fastq stdin -out_good stdout -out_bad null -min_len 30 -trim_tail_right 2 -trim_ns_right 1 -trim_qual_right 20 -trim_qual_window 3
Reads were filtered for 10 bases matching the expected transposon tag sequence, and filtered reads were then mapped against the appropriate reference genome and plasmid sequences, available at https://github.com/Gardner-BinfLab/EnTrI using the Bio-TraDIS pipeline with the following command line options:    bacteria_tradis -v --smalt_r 0 --smalt_k 8 --smalt_s 1 --smalt_y 0.9 -m 0 -f fastqs.txt -t TAAGAGACAG -r ref.fa
For each gene in each organism, we calculated an insertion index as a measure of gene essentiality. The insertion index is calculated as (ng/lg)(nG/lG) where ng is the number of unique insertion sites in the gene, lg is the length of the gene, nG is the number of insertion sites in the genome, and lG is the length of the genome. We calculated the insertion index for each gene after trimming 5% of the sequence from the 5’ end and 20% of the sequence from the 3’ end
To correct for biases in the insertion index, we used fitted values from a generalized additive model (GAM). For each genome, we fitted a GAM curve (using the MGCV package in R) with the formula y ~ s(x) to the distance vs. insertion index plot for distance normalization. The normalized insertion indices were calculated by dividing the insertion indices by the predicted insertion index from the GAM, then multiplying them by the average insertion index. The same procedure was repeated for G-C normalization.
We used the DBSCAN R package (25) to cluster the normalized insertion indices using the DBSCAN function with parameters minPts = 200 and eps = 0.05.
Supplementary files format and content: Ghomi_SI.xslx: essentiality scores for each gene in each organism
Supplementary files format and content: .plot files: read counts per genomic position

organism: Citrobacter rodentium

extract_protocol:
Qiagen Genomic-tip 100/G kit
~2 μg of genomic DNA was fragmented to a size of ~300 base-pairs using a Covaris Focused ultrasonicator (Covaris), followed by end repair using the NEBNext End Repair module (NEB), A-tailing using the NEBNext dA-Tailing module (NEB), and adapter ligation using the NEBNext Quick Ligation Module with a custom splinkerette adaptor (SplA5). PCR enrichment of fragments containing transposon sequence was then carried out using transposon- and adaptor-specific primers using Kapa HiFi HotStart ReadyMix (Kapa Biosystems) for 10 to 20 cycles. PCR products were analyzed on an Agilent Bioanalyzer using a High Sensitivity DNA kit (Agilent Technologies), and by SYBR green qPCR (Kapa Biosystems). Sequencing was then performed on an Illumina HiSeq 2000 or MiSeq using transposon-specific primers and a custom dark-cycle sequencing protocol at the Wellcome Sanger Institute or the King Abdullah University of Science and Technology Bioscience Core Laboratory (Salmonella Typhimurium A130 and D23580). All custom adaptors, primers, and sequencing protocols are described in Barquist et al. "The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries" Bioinformatics 2016 and publicly available at  https://github.com/sanger-pathogens/Bio-Tradis/tree/master/recipes.
transposon insertion sequencing

tag: strain

value: transposon mutagenesis


title: TDP2seq_Scerevisiae_DNA_SPO11_WT_rep2

city: New York

first: Meret

last: Arter

address: 430 E 67th Street

institute: Memorial Sloan Kettering Cancer Center

description: For mapping in vitro SPO11 cleavage sites, Saccharomyces cerevisiae genomic DNA digested by SPO11 in vitro was embedded in plugs together with wild type C57BL/6J mouse testis cells (0.5–1 million cells per plug), whose DNA acted as carrier during library preparation

data_processing:
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.
Top- and bottom-strand peaks were separately called as nucleotide positions with >3,000, >10 and >15 RPM of strand-specific read counts using averaged pUC19, E. coli, and S. cerevisiae TDP2-seq data, respectively. Positions with less read counts than those located at –1 and +1 positions on top and bottom strands, respectively, were not defined as peaks because those reads could be false-positively enriched due to incomplete fill-in of 5-prime overhangs at DNA ends before adaptor ligation.
Assembly: mm10, pUC19, ASM584v2, SacCer3
Supplementary files format and content: bigWig files contain read counts at positions of DNA double-strand break ends. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.
Supplementary files format and content: bed files contain peak locations. If only one file per experiment is submitted, peaks were determined based on average profiles of the two replicates.
Library strategy: TDP2-seq

organism: Saccharomyces cerevisiae

source_name: Mus musculus, Saccharomyces cerevisiae DNA

extract_protocol:
Testis cells from adult mice were obtained as described previously (ref. 1,2). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing. For in vitro SPO11 treated plasmid or genomic DNA samples, the treated DNA was mixed with wild type B6 (C57BL/6J) mouse testis cells right before plug formation to provide carrier DNA during library preparation. Plugs were treated with SDS, Proteinase K and RNAse as described previously (ref. 1,2). In-plug removal of covalently bound SPO11 using human TDP2 was performed as described with minor modifications (ref. 3). In brief, plugs were equilibrated in TDP2 buffer (0.05 M Tris-HCl pH 8, 0.15 M NaCl, 10 mM Mg2Cl, 0.5 mM Dithriothreitol, 30 μg/ml BSA, 2 mM ATP) and incubated with purified human TDP2 protein (490 pmol per plug, TopoGEN) at 37°C for 30 min according to the TopoGEN protocol. DNA ends were filled-in with T4 DNA polymerase (New England Biolabs) and ligated to biotinylated adaptors as described previously (ref. 1,2,4,5). To minimize the loss of small plasmid fragments through diffusion out of the plugs, the washing step after ligation of the first adaptor was reduced from overnight to 1h for samples containing plasmid DNA. After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously with minor modifications (ref. 1,2,4,5). For end repair after DNA shearing, NEBNext End repair Kit (New England Biolabs) was used. (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Kim et al., Optimized methods for mapping DNA double-strand-break ends and resection tracts and application to meiotic recombination in mouse spermatocytes. bioRxiv 2024.08.10.606181; https://doi.org/10.1101/2024.08.10.606181, (2024).(ref. 3) Gittens et al., A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. Nat Commun 10, 4846 (2019). (ref. 4) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 5) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina NextSeq 1000 sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes.
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.
Sequencing reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.


title: Gpx4 cKO, spleen NKT, Rep3

city: Oklahoma City

first: Sophia

middle: P. M.

last: Sok

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

data_processing:
CLC Genomics Workbench 23.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics workbench (parameter - Quality limit: 0.05)
Trimmed sequence read were mapped to GrCM38/mm10 using CLC genomics workbench (parameters- mismatch cost: 2; insert cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts, TPM and RPKM for each sample.

source_name: Spleen

extract_protocol:
RNA was isolated from sorted T cells using NucleoSpin RNA XS Micro kit (Macherey-Nagel).
The library was prepared using a QIAseq UPXome RNA Lib Kit (QIAGEN).

value: Spleen

value: Natural killer T cells

value: Gpx4 cKO

value: Resting state


title: Hypothalamus, 60 day, M2-2

value: hypothalamus


title: WT, spleen NKT, Rep2

value: WT


title: Zebrafish Embryo, 2hpf, rep2

value: AB, TF and TLF


title: T25C_CKDL220007706-1a-N705-N503_HN2WWDSX3_L4

value: Trophoblasts

value: BAP


title: WT, spleen NKT, Rep1


title: Zebrafish Embryo, 2hpf, rep1


title: rep06

city: Cambridge

first: Jenny

address: 16 Divinity Ave

institute: Harvard

description: 10x Genomics 3' V3

data_processing:
Each replicate has been mapped to the P. maniculatus (GCA_003704035.1) and P. polionotus (GCA_003704135.2) transcriptomes using CellRanger v5.0.0 with default parameters. Transcriptomes were annotated in-house and are available upon request.
Each replicate contains four samples which were computationally demultiplexed using demuxlet. Sample assignments can be found in demultiplexed_sample_barcodes.*.txt
Assembly: GCA_003704035.1, GCA_003704135.2
Supplementary files format and content: Barcodes, features (i.e. gene names) and unfiltered UMI matrix for each replicate mapped to the P. maniculatus (GCA_003704035.1) and P. polionotus (GCA_003704135.2) transcriptomes
Supplementary files format and content: Demultiplexed sample assignments for each replicate.

organism:
Peromyscus maniculatus
Peromyscus polionotus

extract_protocol:
Dissected frozen tissue was placed in a single well of a 6 well plate, with 2 ml of extraction buffer. Mechanical dissociation was performed by trituration using a P1000 pipette, pipetting 1 ml of solution slowly up and down with a 1 ml tip, 20 times. Trituration was repeated 5 times, with 2 minutes of rest between each time. The entire volume of the well was then passed twice through a 26 gauge needle into the same well. The tissue solution was transferred into a 50 ml Falcon tube filled with 30 ml wash buffer and spun in a swinging-bucket centrifuge for 10 min at 600g and 4°C. Following spinning, the majority of supernatant was discarded, leaving 500 μl of tissue solution. DAPI was added (1:1,000) and debris was removed from nuclei by FACS. A detailed protocol can be found at dx.doi.org/10.17504/protocols.io.bi62khge.
Library construction was performed on a 10X Genomics 3’ V3 Chip.

value: MPOA


title: Hypothalamus, 1 day, D1-3

value: 1 day


title: rep04

description: 10x Genomics 3' V3


title: WT_E14, Embryonic stem cells, RAD21

description: WT ESCs

value: Embryonic stem cells


title: T1C_CKDL220007706-1a-N701-N502_HN2WWDSX3_L4

value: Differentiated


title: Zebrafish Embryo, 0hpf, rep2

value: Whole embryo


title: rep01

description: 10x Genomics 3' V3


title: Hypothalamus, 1 day, D1-2


title: Zebrafish Embryo, 0hpf, rep1


title: T11C_CKDL220007706-1a-N703-N503_HN2WWDSX3_L4


title: Hypothalamus, 1 day, D1-1


title: rep02

description: 10x Genomics 3' V3


title: wt_WT_mRNA_rep2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Paired-end reads from RNA-seq were quantified on the transcript level using Salmon version 1.9.0 with parameters --gcBias --seqBias –numGibbsSamples=50. The reference index was constructed based on reference sequences (cDNA and non-coding RNA sequence) obtained from ENSEMBL (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/fungi/fasta/schizosaccharomyces_pombe/cdna/Schizosaccharomyces_pombe.ASM294v2.cdna.all.fa.gz and https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/fungi/fasta/schizosaccharomyces_pombe/ncrna/Schizosaccharomyces_pombe.ASM294v2.ncrna.fa.gz), using the genome sequence (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/fungi/fasta/schizosaccharomyces_pombe/dna/Schizosaccharomyces_pombe.ASM294v2.dna.toplevel.fa.gz) as a decoy127 and a k-mer length of 23.
Assembly: ASM294v2 (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/fungi/fasta/schizosaccharomyces_pombe/dna/Schizosaccharomyces_pombe.ASM294v2.dna.toplevel.fa.gz)
Supplementary files format and content: Counts table and transcripts per million (TPM) table for the RNAseq samples as comma-separated text files.

organism: Schizosaccharomyces pombe

source_name: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)

growth_protocol: Schizosaccharomyces pombe cell cultures were grown exponentially in YES medium at 30°C. For more details see methods of the publication.

extract_protocol:
Total RNA was extracted using the MasterPure Yeast RNA Purification Kit (Lucigen, MPY03100) according to the manufacturer’s protocol. mRNA-seq libraries were generated using the Illumina Stranded mRNA Prep (Illumina, 20040534) according to the manufacturer’s protocol, using 300 ng of total RNA as input.
mRNA-seq libraries were generated using the Illumina Stranded mRNA Prep (Illumina, 20040534) according to the manufacturer’s protocol, using 300 ng of total RNA as input.


title: ntu1_KO_mRNA_rep2

value: h+ ade6-M216 ura4-D18 leu1-32 ntu1D::kanMX

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: ntu_WT_mRNA_rep2


title: TDP2seq_Scerevisiae_DNA_SPO11_YF_rep2

value: Saccharomyces cerevisiae genomic DNA digested by SPO11 in vitro


title: TDP2seq_Scerevisiae_DNA_SPO11_WT_rep1


title: TDP2seq_Scerevisiae_DNA_SPO11_YF_rep1


title: Enterobacter cloacae NCTC 9394 transposon mutant library

organism: Enterobacter cloacae

source_name: NCTC 9394

value: NCTC 9394

value: transposon mutagenesis


title: ntu2_delTMD_ChIP_rep2

data_processing:
Paired-end reads from ChIP-seq were aligned to the reference genome obtained from ENSEMBL (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/fungi/fasta/schizosaccharomyces_pombe/dna/Schizosaccharomyces_pombe.ASM294v2.dna.toplevel.fa.gz) using QuasR version 1.38.0 with default parameters, resulting in read pairs with more than a single genomic hit to be discarded. BigWig files were generated using QuasR (qExportWig using default parameters and binsize=1, scaling=1e6).
Assembly: ASM294v2 (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/fungi/fasta/schizosaccharomyces_pombe/dna/Schizosaccharomyces_pombe.ASM294v2.dna.toplevel.fa.gz)
Supplementary files format and content: BigWig files with normalized fragment densities along the genome.

extract_protocol:
ChIP was perfomed as described in the methods of the publication. In brief, exponentially growing cells were fixed with formaldehyde and lysed by beat-beating and the chromatin was sheared using sonication. The immunoprecipitation was performed for 2h at 4°C. ChIPs were reverse crosslinked overnight at 65°C and the DNA was extracted using AMPure XP beads. ChIP-seq libraries were prepared with the NEBnext Ultra II DNA Library Prep kit (NEB, E7645) according to the manufacturer's instructions, using NEBnext UDI indexes (NEB).
ChIP-seq libraries were prepared with the NEBnext Ultra II DNA Library Prep kit (NEB, E7645) according to the manufacturer's instructions, using NEBnext UDI indexes (NEB).

value: h- leu1-32 ura-D18 ade6-704 ntu2::delTMD(559-581)-6xGly-3xFlag-kanMX

tag: sample type

value: ChIP

value: anti-FLAG M2 (Sigma-Adrich)


title: WT_ZNF263_FH, Embryonic stem cells, HA

description: ZNF263_Flag_HA_expressing ESCs

value: HA (Abcam, ab9110)


title: Klebsiella penumoniae Ecl8 transposon mutant library

organism: Klebsiella pneumoniae


title: Gpx4 cKO, spleen NKT, Rep1

value: Spleen

value: Natural killer T cells

value: Gpx4 cKO

value: Resting state


title: Gpx4 cKO, spleen NKT, Rep2


title: ntu_WT_mRNA_rep3


title: WT, spleen NKT, Rep3

value: WT


title: ntu1_KO_ntu2TAG_IN_rep1

value: h- leu1-32 ura4-D18 ade6-704 ntu2::6xGly-3xFlag-kanMX ntu1D::natMX

value: Input


title: ntu2_KO_ntu1TAG_ChIP_rep2

value: h- leu1-32 ura4-D18 ade6-704 ntu1::6xGly-3xFlag-kanMX ntu2D::natMX


title: rep05

description: 10x Genomics 3' V3

value: hypothalamus

value: MPOA


title: ntu2_KO_ntu1TAG_IN_rep2

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: ntu2_KO_ntu1TAG_IN_rep1


title: ntu2_TAG_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 ntu2::6xGly-3xFlag-kanMX


title: rep03

description: 10x Genomics 3' V3


title: ntu1_TAG_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 ntu1::6xGly-3xFlag-kanMX


title: wt_WT_mRNA_rep3


title: ntu1_TAG_ChIP_rep1


title: wt_WT_mRNA_rep1


title: ntu1_KO_mRNA_rep3

value: h+ ade6-M216 ura4-D18 leu1-32 ntu1D::kanMX


title: ntu1_KO_mRNA_rep1


title: ntu2_KO_mRNA_rep3

value: h+ ade6-M216 ura4-D18 leu1-32 ntu2D::kanMX


title: Untagged_IN_rep2


title: Untagged_IN_rep1


title: ntu2_KO_mRNA_rep2


title: SPCC965.10_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPCC965.10::6xGly-3xFlag-kanMX

value: ChIP

value: anti-FLAG M2 (Sigma-Adrich)


title: ntu2_KO_mRNA_rep1


title: SPCC965.10_ChIP_rep2


title: ntu_WT_mRNA_rep1


title: ntu2_delTMD_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 ntu2::delTMD(559-581)-6xGly-3xFlag-kanMX


title: ntu2_delTMD_IN_rep2


title: ntu2_delTMD_IN_rep1


title: SPCC777.02_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPCC777.02::6xGly-3xFlag-kanMX


title: ntu1_KO_ntu2TAG_ChIP_rep1


title: ntu1_KO_ntu2TAG_ChIP_rep2


title: ntu1_KO_ntu2TAG_IN_rep2


title: ntu2_KO_ntu1TAG_ChIP_rep1


title: ntu1_TAG_IN_rep1


title: ntu2_TAG_ChIP_rep1


title: SPCC757.04_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPCC757.04::6xGly-3xFlag-kanMX


title: SPCC417.09c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPCC417.09c::6xGly-3xFlag-kanMX


title: SPCC757.04_IN_rep2


title: ntu2_TAG_IN_rep1


title: ntu2_TAG_IN_rep2


title: SPCC417.09c_IN_rep2


title: SPCC320.03_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPCC320.03::6xGly-3xFlag-kanMX


title: SPCC757.04_IN_rep1

value: Input


title: ntu1_TAG_IN_rep2


title: Untagged_ChIP_rep1


title: SPCC777.02_ChIP_rep2


title: SPCC320.03_ChIP_rep1


title: Untagged_ChIP_rep2


title: SPCC965.10_IN_rep2


title: SPCC320.03_IN_rep2


title: SPCC757.04_ChIP_rep2


title: SPCC965.10_IN_rep1


title: SPCC18.03_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPCC18.03::6xGly-3xFlag-kanMX


title: SPCC777.02_IN_rep2


title: SPCC777.02_IN_rep1


title: SPCC417.09c_ChIP_rep1


title: SPCC18.03_IN_rep2


title: SPBC56F2.05c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPBC56F2.05c::6xGly-3xFlag-kanMX


title: SPCC320.03_IN_rep1


title: SPCC18.03_ChIP_rep1


title: SPBC56F2.05c_ChIP_rep1


title: SPBC56F2.05c_IN_rep2


title: SPBC56F2.05c_IN_rep1


title: SPCC417.09c_IN_rep1


title: SPBC530.11c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPBC530.11c::6xGly-3xFlag-kanMX


title: SPBC530.11c_ChIP_rep1

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: SPBC530.11c_IN_rep2


title: Ntu2_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 ntu2::6xGly-3xFlag-kanMX


title: SPBC1773.16c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPBC1773.16c::6xGly-3xFlag-kanMX


title: Ntu2_ChIP_rep2


title: SPCC18.03_IN_rep1


title: Ntu2_IN_rep1


title: Ntu2_IN_rep2


title: SPBC1773.16c_ChIP_rep1


title: SPBC16G5.17_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPBC16G5.17::6xGly-3xFlag-kanMX


title: SPBC1773.16c_IN_rep1


title: SPBC1773.12_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPBC1773.12::6xGly-3xFlag-kanMX


title: SPBC1773.12_ChIP_rep2


title: SPBC16G5.17_IN_rep1


title: SPBC16G5.17_ChIP_rep1


title: SPBC530.11c_IN_rep1


title: Ntu1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 ntu1::6xGly-3xFlag-kanMX


title: SPAC3H8.08c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPAC3H8.08c::6xGly-3xFlag-kanMX

value: ChIP


title: SPAC3H8.08c_ChIP_rep1

value: anti-FLAG M2 (Sigma-Adrich)


title: SPBC1773.12_IN_rep2


title: SPAC3F10.12c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPAC3F10.12c::6xGly-3xFlag-kanMX


title: Ntu1_IN_rep2


title: SPAC3F10.12c_IN_rep2


title: Ntu1_ChIP_rep1


title: Ntu1_IN_rep1


title: SPAC3H8.08c_IN_rep1


title: SPAC3H8.08c_IN_rep2


title: SPAC3C7.04_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPAC3C7.04::6xGly-3xFlag-kanMX


title: SPAC3C7.04_IN_rep2


title: SPAC3C7.04_ChIP_rep1


title: SPAC3C7.04_IN_rep1


title: SPAC25B8.11_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPAC25B8.11::6xGly-3xFlag-kanMX


title: SPAC25B8.11_IN_rep1


title: SPBC16G5.17_IN_rep2


title: SPAC2H10.01_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPAC2H10.01::6xGly-3xFlag-kanMX


title: SPAC2H10.01_IN_rep2

value: Input


title: SPAC1F7.11c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPAC1F7.11c::6xGly-3xFlag-kanMX


title: SPBC1773.12_IN_rep1


title: SPAC1327.01c_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPAC1327.01c::6xGly-3xFlag-kanMX


title: SPAC1327.01c_IN_rep2


title: SPAC1327.01c_ChIP_rep2


title: SPAC1F7.11c_IN_rep1


title: SPAC11D3.17_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPAC11D3.17::6xGly-3xFlag-kanMX


title: SPAC2H10.01_IN_rep1

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: SPAC2H10.01_ChIP_rep2


title: SPAC1F7.11c_ChIP_rep1


title: SPAC11D3.11c_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 SPAC11D3.11c::6xGly-3xFlag-kanMX


title: SPAC3F10.12c_ChIP_rep1


title: SPAC11D3.11c_ChIP_rep1


title: SPAC11D3.11c_IN_rep1


title: SPAC3F10.12c_IN_rep1


title: SPAC11D3.17_IN_rep1


title: SPAC1327.01c_IN_rep1


title: SPAC1F7.11c_IN_rep2


title: SPAC25B8.11_ChIP_rep1


title: SPAC25B8.11_IN_rep2


title: SPAC11D3.17_ChIP_rep2


title: Dal81_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 SPAC105.03c::6xGly-3xFlag-kanMX


title: SPAC11D3.11c_IN_rep2


title: Zip1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 zip1::6xGly-3xFlag-kanMX


title: Dal81_IN_rep2


title: Dal81_IN_rep1


title: Toe4_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 toe4::6xGly-3xFlag-kanMX


title: SPAC11D3.17_IN_rep2


title: Zip1_IN_rep2


title: Dal81_ChIP_rep2


title: Zip1_IN_rep1


title: Toe3_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 toe3::6xGly-3xFlag-kanMX


title: Toe2_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 toe2::6xGly-3xFlag-kanMX


title: Toe3_IN_rep1


title: Toe2_ChIP_rep2

value: ChIP


title: Toe1_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 toe1::6xGly-3xFlag-kanMX


title: Toe4_ChIP_rep2

value: anti-FLAG M2 (Sigma-Adrich)


title: Toe4_IN_rep1


title: Toe3_ChIP_rep2


title: Thi5_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 thi5::6xGly-3xFlag-kanMX


title: Toe3_IN_rep2


title: Toe2_IN_rep2


title: Thi5_IN_rep2


title: Toe1_ChIP_rep2


title: Toe2_IN_rep1


title: Toe4_IN_rep2


title: Toe1_ChIP_rep1


title: Thi1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 thi1::6xGly-3xFlag-kanMX


title: Thi5_ChIP_rep2


title: Thi5_IN_rep1


title: Thi1_ChIP_rep1


title: Zip1_ChIP_rep2


title: Ste11_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 ste11::6xGly-3xFlag-kanMX


title: Stb3_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 stb3::6xGly-3xFlag-kanMX


title: Sre1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 sre1::6xGly-3xFlag-kanMX


title: Thi1_IN_rep1

value: Input


title: Toe1_IN_rep1


title: Ste11_IN_rep2


title: Stb3_ChIP_rep1


title: Thi1_IN_rep2


title: Sre1_IN_rep2


title: Ste11_ChIP_rep2


title: Ste11_IN_rep1


title: Stb3_IN_rep2


title: Sre1_ChIP_rep1


title: Klf1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 klf1::6xGly-3xFlag-kanMX


title: Stb3_IN_rep1

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: Klf1_IN_rep2


title: Gsf1_IN_rep1

value: h- leu1-32 ura-D18 ade6-704 gsf1::6xGly-3xFlag-kanMX


title: Sre1_IN_rep1


title: Grt1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 grt1::6xGly-3xFlag-kanMX


title: Gsf1_IN_rep2


title: Klf1_IN_rep1


title: Gsf1_ChIP_rep1


title: Grt1_ChIP_rep1


title: Hsr1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 hsr1::6xGly-3xFlag-kanMX


title: Grt1_IN_rep2


title: Grt1_IN_rep1


title: Hsr1_IN_rep1


title: Sfp1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 sfp1::6xGly-3xFlag-kanMX


title: Hsr1_IN_rep2


title: Hsr1_ChIP_rep2


title: Sep1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 sep1::6xGly-3xFlag-kanMX


title: Sep1_IN_rep2


title: Klf1_ChIP_rep2


title: Sfp1_IN_rep2


title: Sfp1_IN_rep1


title: Sep1_IN_rep1


title: Scr1_IN_rep1

value: h- leu1-32 ura-D18 ade6-704 scr1::6xGly-3xFlag-kanMX


title: Scr1_ChIP_rep1

value: ChIP


title: Sfp1_ChIP_rep1


title: Sep1_ChIP_rep1


title: Scr1_ChIP_rep2


title: Rsv2_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 rsv2::6xGly-3xFlag-kanMX


title: Rsv2_IN_rep1


title: Rsv2_ChIP_rep2

value: anti-FLAG M2 (Sigma-Adrich)


title: Rst2_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 rst2::6xGly-3xFlag-kanMX


title: Rsv2_ChIP_rep1


title: Gsf1_ChIP_rep2


title: Rst2_IN_rep1


title: Res2_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 res2::6xGly-3xFlag-kanMX


title: Res2_IN_rep2


title: Reb1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 reb1::6xGly-3xFlag-kanMX


title: Res2_IN_rep1


title: Reb1_IN_rep2


title: Reb1_ChIP_rep1


title: Prz1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 prz1::6xGly-3xFlag-kanMX


title: Prz1_ChIP_rep2


title: Scr1_IN_rep2


title: Prz1_IN_rep1


title: Prz1_IN_rep2


title: Rst2_ChIP_rep2


title: Prr1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 prr1::6xGly-3xFlag-kanMX


title: Rst2_IN_rep2

value: Input


title: Prt1_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 prt1::6xGly-3xFlag-kanMX


title: Prt1_ChIP_rep1

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: Prt1_IN_rep1


title: Phx1_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 phx1::6xGly-3xFlag-kanMX


title: Res2_ChIP_rep2


title: Prr1_IN_rep1


title: Prr1_ChIP_rep1


title: Prr1_IN_rep2


title: Phx1_ChIP_rep1


title: Php5_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 php5::6xGly-3xFlag-kanMX


title: Php5_IN_rep1


title: Php3_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 php3::6xGly-3xFlag-kanMX


title: Php3_ChIP_rep2


title: Prt1_ChIP_rep2


title: Php5_IN_rep2


title: Php3_IN_rep2


title: SPBC1773.16c_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 SPBC1773.16c::6xGly-3xFlag-kanMX


title: Php3_IN_rep1


title: Php2_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 3xFlag-6xGly::php2


title: Php2_IN_rep1


title: Php2_ChIP_rep1


title: Phx1_ChIP_rep2


title: Pho7_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 pho7::6xGly-3xFlag-kanMX


title: Pho7_IN_rep1


title: Phx1_IN_rep1


title: Pho7_IN_rep2


title: Pcr1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 3xFlag-6xGly::pcr1

value: ChIP


title: Pcr1_ChIP_rep2

value: anti-FLAG M2 (Sigma-Adrich)


title: Php5_ChIP_rep2


title: Pap1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 pap1::6xGly-3xFlag-kanMX


title: Pcr1_IN_rep2


title: Pho7_ChIP_rep2


title: Pap1_ChIP_rep1


title: Pap1_IN_rep1


title: Reb1_IN_rep1


title: Moc3_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 moc3::6xGly-3xFlag-kanMX


title: Moc3_ChIP_rep2


title: Moc3_IN_rep2


title: Php2_ChIP_rep2


title: Mca1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 mca1::6xGly-3xFlag-kanMX


title: Mca1_ChIP_rep2


title: Mca1_IN_rep2


title: Mca1_IN_rep1


title: Mbx2_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 3xFlag-6xGly::mbx2


title: Mbx2_ChIP_rep1


title: Mbx2_IN_rep2


title: Pcr1_IN_rep1


title: Mbx1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 mbx1::6xGly-3xFlag-kanMX


title: Mbx2_IN_rep1

value: Input


title: Mbx1_ChIP_rep1


title: Pap1_IN_rep2


title: Mbx1_IN_rep2


title: Map1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 map1::6xGly-3xFlag-kanMX


title: Mbx1_IN_rep1

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: Map1_IN_rep2


title: Map1_ChIP_rep1


title: Loz1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 loz1::6xGly-3xFlag-kanMX


title: Map1_IN_rep1


title: Loz1_IN_rep2


title: Cbf11_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 3xFlag-6xGly::cbf11


title: Loz1_ChIP_rep1


title: Loz1_IN_rep1


title: Cbf11_ChIP_rep1


title: Cbf11_IN_rep2


title: Zas1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 zas1::6xGly-3xFlag-kanMX


title: Moc3_IN_rep1


title: Cbf11_IN_rep1


title: Zas1_IN_rep1


title: Zas1_IN_rep2


title: Teb1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 teb1::6xGly-3xFlag-kanMX


title: Teb1_ChIP_rep2


title: Teb1_IN_rep2


title: Teb1_IN_rep1


title: Zas1_ChIP_rep2


title: Atf1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 atf1::6xGly-3xFlag-kanMX


title: Atf1_ChIP_rep1


title: Sak1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 sak1::6xGly-3xFlag-kanMX


title: Sak1_IN_rep1


title: Atf1_IN_rep1


title: Sak1_IN_rep2


title: Res1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 res1::6xGly-3xFlag-kanMX


title: Ams2_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 ams2::6xGly-3xFlag-kanMX

value: ChIP


title: Res1_IN_rep1


title: Res1_ChIP_rep1

value: anti-FLAG M2 (Sigma-Adrich)


title: Atf1_IN_rep2


title: Ams2_IN_rep1


title: Res1_IN_rep2


title: Ams2_IN_rep2


title: Adn3_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 adn3::6xGly-3xFlag-kanMX


title: Ams2_ChIP_rep1


title: Adn3_ChIP_rep1


title: Adn3_IN_rep2


title: Hsf1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 hsf1::6xGly-3xFlag-kanMX


title: Hsf1_ChIP_rep2


title: Hsf1_IN_rep2


title: Hsf1_IN_rep1


title: Sak1_ChIP_rep2


title: Gaf1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 gaf1::6xGly-3xFlag-kanMX


title: Gaf1_IN_rep2


title: Adn2_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 adn2::6xGly-3xFlag-kanMX


title: Gaf1_ChIP_rep1


title: Gaf1_IN_rep1

value: Input


title: Adn2_ChIP_rep1


title: Adn2_IN_rep1


title: Adn2_IN_rep2


title: Fkh2_IN_rep1

value: h- leu1-32 ura-D18 ade6-704 fkh2::6xGly-3xFlag-kanMX


title: Fkh2_ChIP_rep2

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)


title: Fkh2_IN_rep2


title: Fil1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 fil1::6xGly-3xFlag-kanMX


title: Fil1_ChIP_rep1


title: Adn3_IN_rep1


title: Fhl1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 fhl1::6xGly-3xFlag-kanMX


title: Fhl1_ChIP_rep2


title: Fil1_IN_rep1


title: Fep1_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 fep1::6xGly-3xFlag-kanMX


title: Fhl1_IN_rep1


title: Fep1_ChIP_rep1


title: Fep1_IN_rep1


title: Esc1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 esc1::6xGly-3xFlag-kanMX


title: Fep1_ChIP_rep2


title: Fil1_IN_rep2


title: Fhl1_IN_rep2


title: Esc1_IN_rep2


title: Esc1_IN_rep1


title: Deb1_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 deb1::6xGly-3xFlag-kanMX


title: Esc1_ChIP_rep1


title: Cuf1_ChIP_rep2

value: h- leu1-32 ura-D18 ade6-704 cuf1::6xGly-3xFlag-kanMX


title: Deb1_IN_rep2


title: Deb1_IN_rep1


title: Deb1_ChIP_rep2


title: Fkh2_ChIP_rep1


title: Cuf1_ChIP_rep1


title: Cuf1_IN_rep1


title: Cdc10_IN_rep2

value: h- leu1-32 ura-D18 ade6-704 cdc10::6xGly-3xFlag-kanMX


title: Cdc10_ChIP_rep1


title: Cdc10_ChIP_rep2


title: Cdc10_IN_rep1


title: IFNγ+PD-L1hi_3

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size were calculated using a protocol from Chepeleve et al., Nucleic Acids Research, 2009.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: tumor cell

extract_protocol:
Briefly, tumor cell were generated and collected after 20 hours of stimulation.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: tumor cell

value: PD-L1 high


title: IFNγ+PD-L1hi_1


title: Ace2_ChIP_rep1

value: h- leu1-32 ura-D18 ade6-704 ace2::6xGly-3xFlag-kanMX

value: ChIP

value: anti-FLAG M2 (Sigma-Adrich)


title: IFNγ+PD-L1all_3

value: PD-L1 all


title: IFNγ+PD-L1all_2


title: IFNγ+PD-L1hi_2


title: Ace2_IN_rep2


title: Ace2_ChIP_rep2


title: IFNγ-PD-L1all_4


title: IFNγ-PD-L1all_3


title: IFNγ+PD-L1all_1


title: CC-5325 strains, set3, mt–, vegetative stage

first: Xiuqi

last: Gui

address: 320 Yue Yang Rd

institute: Shanghai Institute of Nutrition and Health

data_processing:
Bisulfite-converted sequences were aligned to C. reinhardtii (CC-4532 Assembly-version = v6) nuclear genome, chloroplast genome, mitochondria genome using the Bismark alignment pipeline (version: v0.22.3).
To visualize the methylation level or read coverage at individual CpG sites in a genome browser, we created a bigWig format using the output from Bismark.
A sliding window of size 20-kb was used to generate the DNA methylation profiles for genome browser visualization, with a step size of 10-kb along chromosomes.
Assembly: C. reinhardtii reference sequence (CC-4532 Assembly-version = v6)
Supplementary files format and content: bigWig files for visualizing methylation levels at individual CpG sites.
Supplementary files format and content: bigWig files  for visualizing  read coverage at individual CpG sites.
Supplementary files format and content: tab-delimited text files include 5mCG/CG levels for each window in each sample.

organism: Chlamydomonas reinhardtii

growth_protocol: Cells were grown photo mixotrophically in liquid Tris-acetate-phosphate (TAP) medium on a rotary shaker at 22–25°C or on agar-solidified TAP medium under continuous light (50–100 μE∙m-2∙s-1, cool-white fluorescent lamps).

extract_protocol:
To isolate genomic DNA, the procedure was adopted from plant genomic DNA kit (Cat. DP305-03, Tiangen) as follows: Vegetative cells were grown in 100 mL TAP medium to stationary phase and harvested by centrifugation (5 min, 4200 rpm, room temperature). The cell pellet was resuspended in Buffer GD from the kit. The suspension was transferred into lysing matrix E (Cat. 116914050, MP biomedicals) and then incubated for 15 min at 65°C, 1400 rpm. The ensuing steps followed the kit’s protocol.
Covaris S220 was used to interrupt genomic DNA to 200-300bp randomly with negative control (lambda DNA) added. End repair was performed on The broken DNA fragments were end-repaired, added with A-tail and connected with all cytosine methylated sequencing joints. This was followed by Bisulfite treatment (using EZ DNA Methylation Gold Kit, Zymo Research) and PCR amplification.

tag: mate type

value: mt-

tag: Stage

value: vegetative stage

value: SET3 knockout

tag: assay type

value: Bisulfite-Seq


title: Ace2_IN_rep1

value: vegetatively growing cells cultured under optimal conditions (30¬∞C, rich medium)

value: Input


title: IFNγ-PD-L1all_2


title: CC-5325 strains, dnmt1, mt–, vegetative stage

value: DNMT1 knockout


title: IFNγ-PD-L1all_1


title: Cuf1_IN_rep2


title: H2A119Ub_IFNγ-PD-L1all

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Library strategy: CUT&Tag

source_name: cultured pancreatic tumor cell

extract_protocol: CUT&Tag libraries were prepared for sequencing using standard illumina protocols.

value: cultured pancreatic tumor cell

value: PDL1 all

tag: antibody


title: H2A119Ub_IFNγ+PD-L1hi

value: PDL1 high-10ng/ml IFN[gamma]


title: CC-5155 strains, dnmt1, mt+, vegetative stage

value: mt+


title: CC-5155 strains, WT, mt+, vegetative stage

value: WT


title: CC-5325 strains, dnmt1, mt–, vegetative stage, biol rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 2.6.
were aligned using STAR (version 2.7.6) to C. reinhardtii reference sequence (CC-4532 Assembly-version = v6, Annotation-version = v6.1).
Duplicate reads were identified and removed using picard MarkDuplicates v2.27.2.
Read count extraction  were performed using featureCounts.
Read counts were normalized using DEseq2.
Assembly: C. reinhardtii reference sequence (CC-4532 Assembly-version = v6, Annotation-version = v6.1)
Supplementary files format and content: tab-delimited text files include read counts for each Sample
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

extract_protocol:
To obtain total RNA for RNA-seq, the procedure was adopted from KK Fast Plant Total RNA Kit (Cat. ZP405K, Zomanbio) as follows: Vegetative cells were grown to a cell density of 2 × 106 mL-1 in TAP medium and 1 × 107 cells were harvested by centrifugation (3 min, 2500 rpm, 4°C). The cell pellet was resuspended in 1 mL TRIzol (Thermo Fisher). The next procedure followed the kit’s protocol.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: H2A119Ub_IFNγ+PD-L1all

value: PDL1 all-10ng/ml IFN[gamma]


title: CC-5155 strains, dnmt1, mt+, vegetative stage, biol rep2


title: CC-5325 strains, dnmt1, mt–, vegetative stage, biol rep1


title: CC-5325 strains, WT, mt–, vegetative stage


title: H3K27me3_IFNγ+PD-L1hi


title: H3K27me3_IFNγ-PD-L1all


title: CC-5325 strains, WT, mt–, vegetative stage, biol rep2


title: H3K27Ac_IFNγ+PD-L1all


title: H3K27me3_IFNγ+PD-L1all


title: H3K27Ac_IFNγ-PD-L1all


title: CC-5155 strains, set3, mt+, vegetative stage


title: CC-5155 strains, dnmt1, mt+, vegetative stage, biol rep1


title: H3K4me3_IFNγ+PD-L1hi


title: CC-5155 strains, WT, mt+, vegetative stage, biol rep2


title: H3K4me3_IFNγ+PD-L1all


title: H3K27Ac_IFNγ+PD-L1hi


title: CC-5325 strains, WT, mt–, vegetative stage, biol rep1


title: CC-5155 strains, WT, mt+, vegetative stage, biol rep1


title: Klebsiella penumoniae RH201207 transposon mutant library

value: transposon mutagenesis


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K9me3, CST

description: H3K4me3, and H3K9me3 share the same input control with H3K4me1.

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 0.6.7,discarding reads left with < 20 bp
Each read was mapped against the C. reinhardtii reference sequence (CC-4532 v6) using Bowtie 2 version 2.4.2
Duplicate reads were removed by Picard MarkDuplicates
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <0.01.
narrowPeak files were generated using MACS2 callpeak.
bigWig files were generated from aligned reads using deepTools bamCoverage v 3.5.1 with parameter 'normalizeUsing=RPKM'. Scale factors were calculated using reads mapped to non-peak regions across all samples. The RPKM score represents normalized DNA fragment coverage at specific genomic coordinates.
Assembly: C. reinhardtii reference sequence (CC-4532 Assembly-version = v6)
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 0.35% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Covaris S220.
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Cat. ND607, Vazyme). 1 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using VAHTS DNA Clean Beads (Cat. N411, Vazyme).


title: H3K4me3_IFNγ-PD-L1all


title: Salmonella enterica serovar Enteritidis P125109 transposon mutant library

organism: Salmonella enterica subsp. enterica serovar Enteritidis


title: CC-5325 strains, WT, mt–, vegetative stage, H3K9me3, CST


title: CC-5155 strains, WT, mt+, vegetative stage, H3K9me3, CST


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K4me3, ABCAM

value: H3K4me3 (Abcam, #ab8580)


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K4me3, ABCAM


title: CC-5325 strains, WT, mt–, vegetative stage, H3K4me3, ABCAM


title: Control Differentiation Batch 2

city: Ann Arbor

first: Joshua

last: Meisner

state: MI

address: 1540 E. Hospital Drive

department: Pediatrics

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files from Illumina NovaSeq 6000 reads
The reads were trimmed using Cutadapt v2.3(Martin, 2011).
The reads were evaluated with FastQC(Andrews, 2010)(v0.11.8) to determine quality of the data
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a(Dobinet al., 2013)and assigned count estimates to genes with RSEM v1.3.3(Li and Dewey, 2011).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7(Ewelset al., 2016).
Assembly: GRCh38 (ENSEMBL)
Supplementary files format and content: tab delimited text file includes TPM counts per gene for each sample

source_name: iPSC derived cardiomyocytes

growth_protocol: iPSCs were cultured in mTeSR Plus. Cardiomyocytes were differentiated using optimized WNT modulation. iPSC were differentiated in RPMI plus B27 supplement without insulin during day 0–2 (CHIR 4–6 µM and 0-1 mM activin A during first 24 h) followed by CDM3 media (without B27) with IWP4 5 µM during days 3–4. Retinol inhibitor (BMS 453, 1 µM) was included for days 3–6 to minimize atrial lineage differentiation. IPSC-CMs were maintained in CDM3 until spontaneous contractions. After spontaneous contractions were visible, cardiomyocytes were purified in CDM3-lactate using glucose-deprived, lactate-containing media on days 12–16 with RPMI without glutamine and cryopreserved. Purified, cryopreserved iPSC-CMs were thawed and replated as monolayers (400,000 cells/cm2) for 8 additional days (approximately day 24 post differentiation) on stiff PDMS membranes with growth factor reduced Matrigel. iPSC-CMs were maintained in CDM3-lactate media (4 days) and then oxidative phosphorylation promoting RPMI media (Ox-Phos) plus B27 supplement (4 days). Ox-Phos media, adapted from Correia et al. 2017, is based on glucose-free RPMI with B27 supplement and galactose, lactate, glutamax, and pyruvate at final media concentrations of 4, 4, 2, and 0.5 mM, respectively.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan.

value: iPSC derived cardiomyocytes

value: cardiomyocyte

value: control


title: Control Differentiation Batch 1


title: Control Differentiation Batch 3


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K9me3, CST

value: vegetative stage


title: CC-5155 strains, WT, mt+, vegetative stage, H3K4me3, ABCAM


title: pool4_VDJ_TCR

city: Edinburgh

first: Wiebke

last: Nahrendorf

address: Charlotte Auerbach Rd

department: Institute for Immunology and Infection Research

country: United Kingdom

institute: University of Edinburgh

description:
pool 4 third malaria infection (identical to pool 3). T cell receptor alpha and beta chains (after amplification of the V(D)J regions). debarcode to analyse the 6 biological samples.
VDJ3_4_airr_rearrangement.tsv
VDJ3_4_clonotypes.csv
VDJ3_4_consensus_annotations.csv

data_processing:
Cell Ranger multi (v6.0.2) was used to align 5’ gene expression and V(D)J sequencing reads to the GRCh38 reference genome. This initial step was performed independently for first and third infection since both pools used the same set of six TotalSeq-C barcodes - C0251 (GTCAACTCTTTAGCG - first infection pool: baseline volunteer 313, third infection pool: baseline volunteer 301), C0252 (TGATGGCCTATTGGG - first infection pool: baseline volunteer 315, third infection pool: baseline volunteer 308), C0253 (TTCCGCCTCTCTTTG - first infection pool: baseline volunteer 320, third infection pool: baseline volunteer 310), C0254 (AGTAAGTTCAGCGTA - first infection pool: after malaria volunteer 313, third infection pool: after malaria volunteer 301), C0255 (AAGTATCGTTTCGCA - first infection pool: after malaria volunteer 315, third infection pool: after malaria volunteer 308) and C0256 (GGTTGCCAGATGTCA - first infection pool: after malaria volunteer 320, third infection pool: after malaria volunteer 310).
Feature-Barcode matrices were then loaded into R (v4.2.0) using Seurat (v4.3.0). Oligo count matrices were generated from the cell surface library using CITE-seq-Count (v1.4.2) (https://doi.org/10.5281/zenodo.2590196). Datasets were filtered to only include 10X cell barcodes detected in both gene expression and cell surface libraries. PCA-initialised tSNE was used to visualise the oligo expression levels of each sample pool revealing six large clusters that corresponded to single oligo positive cells (i.e. singlets). We therefore used nearest neighbour identification and Louvain clustering to assign each singlet to a sample and exclude cells with multiple oligo tags (doublets).
After debarcoding we pooled data from first and third infection and followed a standard Seurat workflow for quality control. Briefly, we excluded cells with more than 2500 feature counts (or less than 200) and cells with more than 5% mitochondrial transcripts.
To integrate data and reduce individual variation we used Harmony100 (v0.1.0). This analysis identified a persistent and hyperexpanded cluster of TRBV11-3 positive CD4 T cells. These cells were unique to volunteer 305 (the only CMV seropositive volunteer) and did not respond to malaria; we therefore excluded this cluster from all downstream steps to avoid confounding signatures of malaria-induced activation.
Assembly: GRCh38
Supplementary files format and content: tab separated values files and matrix files

source_name: blood

extract_protocol: CD4 T cells were flow sorted from cryopreserved peripheral blood mononuclear cells and labelled with TotalSeqC oligo-tagged antibodies (available from BioLegend) against two ubiquitously expressed cell surface proteins (CD298 and β2 microglobulin). Six individually barcoded samples were pooled (one pool for first infection and a separate pool for third infection) and the concentration of each pool was carefully measured and adjusted to 1262 cells per microlitre. Each pool was then loaded into 2 wells of an A Chip, which itself was loaded onto a 10X Genomics Chromium Controller. Note that we intentionally super-loaded the Controller in order to capture approx. 30,000 singlets for each infection across 2 wells.

treatment_protocol: Healthy malaria-naive adults were infected with P. falciparum (clone 3D7) blood-stage parasites by direct intravenous infusion. Parasite density was measured in real-time by qPCR and anti-malarial treatment was initiated if i) over 10,000 parasites per ml were detected or ii) if volunteers experienced malaria symptoms and had more than 5000 parasites per ml. These clinical trials received ethical approval from the UK NHS Research Ethics Service and were registered at ClinicalTrials.gov (NCT03906474). They were sponsored by the University of Oxford, carried out in the UK at the Centre for Vaccinology and Tropical Medicine and conducted according to the principles of the current revision of the Declaration of Helsinki 2008 (in full conformity with the ICH Guidelines for Good Clinical Practice). More details can be found in Salkeld et al. 2022 (doi.org/10.3389/fimmu.2022.984323)

value: blood

value: CD4 T cells

value: Plasmodium falciparum malaria infection


title: Back skin, None, Control cream, WT3

city: Wonju-si

first: Sung Won

last: Lee

state: Gangwon-do

address: 83 Sangjidae-gil

country: South Korea

institute: Sangji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Back skin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: NGO cream (50 μg/100 μL/mouse) or control cream was applied only on the tape-stripped area. Skin samples were collected 24 hrs after the treatment.

value: Back skin

value: Control cream


title: Back skin, Tape-stripping, NGO cream, WT1

value: NGO cream


title: Back skin, Tape-stripping, NGO cream, WT2


title: Back skin, Tape-stripping, Control cream, WT1


title: Back skin, Tape-stripping, NGO cream, WT3


title: Back skin, None, Control cream, WT2


title: CC-5325 strains, set3, mt–, vegetative stage, H3K9me1, Input

value: mt-

value: SET3 knockout


title: Back skin, Tape-stripping, Control cream, WT2


title: CC-5325 strains, set3, mt–, vegetative stage, H3K9me1, ABCAM

value: H3K9me1 (Abcam, #ab9045)


title: CC-5155 strains, set3, mt+, vegetative stage, H3K9me1, Input

value: mt+


title: Mopholino treated cells, Replicate 2

city: Philadelphia

first: Jo Lynne

last: Rokita

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
STAR v2.7.10a
RSEM v1.3.1
Adaptor seqeuences were trimmed by the illumina universal adapter Truseq 3: Read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC Read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
gencode v39
Assembly: hg38
Supplementary files format and content: tab delimited file with gene_id, transcript_ids, effective length, expected counts, TPM, and FPKM
Supplementary files format and content: tab delimited file with transcript_id, gene_id, effective_length,expected_count,TPM,FPKM,IsoPc

source_name: CNS/brain

extract_protocol:
Total RNA was isolated and treated with DNAse using the Maxwell RSC simplyRNA Cells kit (Promega, AS1390) with the Maxwell RSC48 Instrument (Promega) per the manufacturer’s instructions
rna-seq libraries prepared as per illumina HiSeq2500 manufacturer's protocol

treatment_protocol: A Vivo-Morpholino ACTCTTCTGGAAACGTCAAGTGGGC (Gene Tools, LLC) targeting the intron 3-exon 4 splice junction was used to skip exon 4 in CLK1

value: CNS/brain

value: Mopholino treated cells

value: treated

value: morpholino


title: Mopholino treated cells, Replicate 3


title: pool3_VDJ_TCR

description:
pool 3 third malaria infection (identical to pool 4). T cell receptor alpha and beta chains (after amplification of the V(D)J regions). debarcode to analyse the 6 biological samples.
VDJ3_4_airr_rearrangement.tsv
VDJ3_4_clonotypes.csv
VDJ3_4_consensus_annotations.csv


title: Non-targeting morpholino control cells, Replicate 3

value: Non-targeting morpholino control cells

value: WT

value: untreated


title: Back skin, Tape-stripping, Control cream, WT3


title: Non-targeting morpholino control cells, Replicate 2


title: MPM049_HIGH_SMRP

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

data_processing:
The raw sequence reads were mapped to GRCh38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor

tag: subject status

value: MPM patients receiving ICT

tag: smrp group

tag: smrp (nmol/l)

tag: age at_tx

tag: Sex

value: M

tag: race

value: White

tag: histology

value: Epithelioid

tag: asbestos hx

tag: pd-l1 ihc(%)

tag: ici abs

value: NIVOLUMAB


title: CC-5155 strains, set3, mt+, vegetative stage, H3K9me1, ABCAM

value: vegetative stage

tag: genotype

tag: chip antibody


title: pool3_gene_expression

description:
pool 3 third malaria infection (identical to pool 4). 5’ gene expression. debarcode to analyse the 6 biological samples.
GEX3_4_barcodes.tsv.gz
GEX3_4_features.tsv.gz
GEX3_4_matrix.mtx.gz

tag: tissue

value: blood

tag: cell type

value: CD4 T cells

tag: treatment

value: Plasmodium falciparum malaria infection


title: Non-targeting morpholino control cells, Replicate 1

value: CNS/brain

tag: cell line


title: pool4_gene_expression

description:
pool 4 third malaria infection (identical to pool 3). 5’ gene expression. debarcode to analyse the 6 biological samples.
GEX3_4_barcodes.tsv.gz
GEX3_4_features.tsv.gz
GEX3_4_matrix.mtx.gz


title: T9_Naive

city: Oslo

first: Ankush

last: Sharma

address: 3rd Floor,  Ullernchausseen 70

department: Department of Cancer Immunology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
processed data column: 76
SampleT9-Naive

data_processing:
Adaptors and low quality reads were removed using Trim Galore (v0.6.4).
The remaining high-quality reads were mapped to the Ensembl GRCh37.p75 using Salmon, in order to obtain gene expression estimates in the form of transcripts per million (TPM).
Assembly: Hg19/ GRCh37.p75
Supplementary files format and content: csv

source_name: heatlhy donor tonsil

extract_protocol:
Total RNA was extracted from fresh frozen tissue sections (follicular lymphoma) or from sorted B cell populations (tonsils), using Qiagen RNeasy Miniprep Kit according to manufacturer's guidelines. One ug of total RNA was used for the construction of sequencing libraries.
Illumina TruSeq Stranded mRNA Library Prep kit was used to contruct the sequencing library according to manufacturer´s instructions. Libraries were sequenced on an Illumina Hiseq4000 Intrument with 150bp paired end reads.

treatment_protocol: The tonsils were processed to single-cell suspension by mechanical mincing and stored in liquid nitrogen. The cells were thawed and rested in RPMI w/10% FCS at 37°C for at least 15 min before staining with the following antibodies: IgD-FITC (clone IA6-2), CD20-APC-H7 (clone L27), CD38-PerCP-Cy5.5 (clone HIT2) and CD27-APC (clone M-T271) from BD Biosciences, CD3-PE (clone UCHT1) from Dako. Live B-cell subsets were sorted on FACS Aria II (BD Biosciences): CD3-CD20+IgD+CD38-CD27- naive B cells, CD3-CD20+IgD-CD38-CD27+ memory B cells, and CD3-CD20++IgD-CD38+ GC B cells. The sorted cells were spun down and lysed in lysis buffer (RNeasy kit, Qiagen).

value: heatlhy donor tonsil

value: naive B cells


title: T9_Memory

description:
processed data column: 75
SampleT9-Memory

value: memory B cells


title: T9_GC

description:
processed data column: 74
SampleT9-GC

value: GC B cells


title: pool3_cell_surface

description:
pool 3 third malaria infection (identical to pool 4) 6 cell surface barcodes discriminating 6 biological samples: 3 volunteers analysed at 2 timepoints (baseline and after malaria).
CS3_4_barcodes.tsv.gz
CS3_4_features.tsv.gz
CS3_4_matrix.mtx.gz


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K9me1, Input

tag: strain

tag: mate type

value: mt-

tag: Stage

value: DNMT1 knockout


title: pool4_cell_surface

description:
pool 4 third malaria infection (identical to pool 3) 6 cell surface barcodes discriminating 6 biological samples: 3 volunteers analysed at 2 timepoints (baseline and after malaria).
CS3_4_barcodes.tsv.gz
CS3_4_features.tsv.gz
CS3_4_matrix.mtx.gz


title: Back skin, None, Control cream, WT1

value: Back skin

value: WT

value: Control cream


title: pool2_VDJ_TCR

description:
pool 2 first malaria infection (identical to pool 1). T cell receptor alpha and beta chains (after amplification of the V(D)J regions). debarcode to analyse the 6 biological samples.
VDJ1_2_airr_rearrangement.tsv
VDJ1_2_clonotypes.csv
VDJ1_2_consensus_annotations.csv


title: Mopholino treated cells, Replicate 1

value: Mopholino treated cells

value: treated

value: morpholino


title: pool2_gene_expression

description:
pool 2 first malaria infection (identical to pool 1). 5’ gene expression. debarcode to analyse the 6 biological samples.
GEX1_2_barcodes.tsv.gz
GEX1_2_features.tsv.gz
GEX1_2_matrix.mtx.gz


title: T7_Naive

description:
processed data column: 73
SampleT7-Naive


title: pool2_cell_surface

description:
pool 2 first malaria infection (identical to pool 1) 6 cell surface barcodes discriminating 6 biological samples: 3 volunteers analysed at 2 timepoints (baseline and after malaria).
CS1_2_barcodes.tsv.gz
CS1_2_features.tsv.gz
CS1_2_matrix.mtx.gz


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K9me1, Input

value: mt+

value: vegetative stage


title: T31_Memory

description:
processed data column: 69
SampleT31-Memory


title: T31_GC

description:
processed data column: 68
SampleT31-GC


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K9me1, ABCAM

value: H3K9me1 (Abcam, #ab9045)


title: T25ii_Naive

description:
processed data column: 67
SampleT25ii-Naive


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K9me1, ABCAM


title: T25ii_Memory

description:
processed data column: 66
SampleT25ii-Memory


title: CC-5325 strains, WT, mt–, vegetative stage, H3K9me1, ABCAM


title: P9_2

description:
processed data column: 8
Sample0008

source_name: follicular lymphoma, lymph node

value: follicular lymphoma, lymph node

value: all cell types present in bulk

tag: genes mutated for this sample from patient


title: CC-5325 strains, WT, mt–, vegetative stage, H3K9me1, Input


title: pool1_VDJ_TCR

description:
pool 1 first malaria infection (identical to pool 2). T cell receptor alpha and beta chains (after amplification of the V(D)J regions). debarcode to analyse the 6 biological samples.
VDJ1_2_airr_rearrangement.tsv
VDJ1_2_clonotypes.csv
VDJ1_2_consensus_annotations.csv

value: blood

value: CD4 T cells

value: Plasmodium falciparum malaria infection


title: P8_2

description:
processed data column: 7
Sample0007

source_name: transformed follicular lymphoma, lymph node


title: T25ii_GC

description:
processed data column: 65
SampleT25ii-GC

value: heatlhy donor tonsil

value: GC B cells


title: CC-5155 strains, WT, mt+, vegetative stage, H3K9me1, Input

description: H3K4me3, and H3K9me3 share the same input control with H3K4me1.


title: T7_Memory

description:
processed data column: 72
SampleT7-Memory

value: memory B cells


title: CC-5155 strains, WT, mt+, vegetative stage, H3K9me1, ABCAM


title: P75_3

description:
processed data column: 64
SampleP75-3


title: T7_GC

description:
processed data column: 71
SampleT7-GC


title: P9_1

description:
processed data column: 44
Sample0045


title: pool1_cell_surface

description:
pool 1 first malaria infection (identical to pool 2). 6 cell surface barcodes discriminating 6 biological samples: 3 volunteers analysed at 2 timepoints (baseline and after malaria).
CS1_2_barcodes.tsv.gz
CS1_2_features.tsv.gz
CS1_2_matrix.mtx.gz


title: P75_2

description:
processed data column: 63
SampleP75-2


title: T31_Naive

description:
processed data column: 70
SampleT31-Naive

value: naive B cells


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K4me1, Input

value: mt-

value: DNMT1 knockout


title: P59_1

description:
processed data column: 61
SampleP59-1


title: P6_2

description:
processed data column: 48
Sample0049


title: con_1 input

city: Fuzhou

first: Dongshan

last: Liao

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: rn6
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: myocardium

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: myocardium

value: human myocardial cell line

value: myoblast

value: Wild type

value: Control


title: con_3 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: con_2 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: P61_1

description:
processed data column: 62
SampleP61_1


title: CC-5325 strains, dnmt1, mt–, vegetative stage, H3K4me1, ABCAM

value: vegetative stage

value: H3K4me1 (Abcam, #ab8895)


title: P6_3

description:
processed data column: 6
Sample0006

value: follicular lymphoma, lymph node

value: all cell types present in bulk


title: P58_1

description:
processed data column: 50
Sample0051


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K4me1, ABCAM

value: mt+


title: pool1_gene_expression

description:
pool 1 first malaria infection (identical to pool 2). 5’ gene expression. debarcode to analyse the 6 biological samples.
GEX1_2_barcodes.tsv.gz
GEX1_2_features.tsv.gz
GEX1_2_matrix.mtx.gz

value: blood

value: CD4 T cells

value: Plasmodium falciparum malaria infection


title: CC-5155 strains, dnmt1, mt+, vegetative stage, H3K4me1, Input


title: P57_1

description:
processed data column: 49
Sample0050


title: Mat_3 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv

value: treat with matrine


title: Mat_2 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: CC-5325 strains, WT, mt–, vegetative stage, H3K4me1, Input

value: WT


title: P50_1

description:
processed data column: 39
Sample0040


title: P75_1

description:
processed data column: 42
Sample0043


title: P56_1

description:
processed data column: 40
Sample0041


title: P56_2

description:
processed data column: 41
Sample0042


title: EV_3 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_EV.csv
d_m6A_EV.csv

value: treat with evodiamine


title: Mat_1 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: CC-5325 strains, WT, mt–, vegetative stage, H3K4me1, ABCAM

value: mt-


title: P48_1

description:
processed data column: 36
Sample0037


title: EV_2 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_EV.csv
d_m6A_EV.csv

value: myocardium


title: P49_1

description:
processed data column: 37
Sample0038


title: P49_2

description:
processed data column: 38
Sample0039


title: CC-5155 strains, WT, mt+, vegetative stage, H3K4me1, Input


title: P46_2

description:
processed data column: 47
Sample0048


title: P44_2

description:
processed data column: 33
Sample0034


title: con_3 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv

value: human myocardial cell line


title: CC-5155 strains, WT, mt+, vegetative stage, H3K4me1, ABCAM


title: P46_3

description:
processed data column: 35
Sample0036


title: normal_6, nromal lung tissue from patient_6

city: Nanchang

first: Kaiying

last: Xu

state: Jiangxi

address: No. 17, Yongwai zheng Street

department: Department of Thoracic Surgery

institute: The First Affiliated Hospital of Nanchang University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for circRNA analysis. They were mapped to the reference genome of Homo sapiens.GRCh38 using STAR software (version 2.5.3a) with default parameters. Unmapped reads were used to predict circRNA by find_circ（version 1.2）and CIRCexplorer software（version 2.3.0）, respectively. The intersection of the results predicted by the two softwares was the final circRNA.
The expression of circRNA were counted by in-house scripts and then SRPBM were calculated.
Assembly: hg38
Supplementary files format and content: spreadsheet file include raw counts for each Sample
Supplementary files format and content: spreadsheet file include  SRPBM values of each Sample

source_name: Normal lung tissue

growth_protocol: Fresh tissue samples were immediately frozen in liquid nitrogen and stored at -80℃ until use.

extract_protocol:
Total RNAs were extracted from 4 paired NSCLC tissues and adjacent normal lung tissues using TRIzol Reagent (Invitrogen). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies). 10 μg total RNAs were used as input for rRNA removing by using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina). Then linear RNA was digested by RNase R.
Stranded RNA sequencing library preparation was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: No treatment.

value: Normal lung tissue

tag: disease

value: NSCLC

value: Female

value: No treatment


title: P44_1

description:
processed data column: 32
Sample0033


title: normal_5, nromal lung tissue from patient_5

tag: Sex

value: Male


title: P43_1

description:
processed data column: 31
Sample0032

value: follicular lymphoma, lymph node


title: P46_1

description:
processed data column: 34
Sample0035

value: all cell types present in bulk


title: P43_2

description:
processed data column: 60
SampleP43_2


title: con_2 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv

value: myoblast

value: Wild type

value: Control


title: P42_1

description:
processed data column: 29
Sample0030


title: P42_2

description:
processed data column: 30
Sample0031


title: normal_4, nromal lung tissue from patient_4


title: con_1 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: normal_2, nromal lung tissue from patient_2


title: P4_1

description:
processed data column: 5
Sample0005


title: P36_2

description:
processed data column: 26
Sample0027


title: EV_1 input

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_EV.csv
d_m6A_EV.csv


title: Mat_3 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: Mat_2 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv


title: P40_1

description:
processed data column: 27
Sample0028


title: cancer_5, tumor tissue form patient_5

source_name: Tumor tissue

value: Tumor tissue


title: P34_2

description:
processed data column: 24
Sample0024


title: cancer_6, tumor tissue form patient_6


title: P35_2

description:
processed data column: 25
Sample0026


title: P33_1

description:
processed data column: 23
Sample0023


title: EV_3 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_EV.csv
d_m6A_EV.csv


title: Mat_1 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_Mat.csv
d_m6A_Mat.csv

value: treat with matrine


title: P31_4

description:
processed data column: 22
Sample0022


title: cancer_2, tumor tissue form patient_2


title: cancer_4, tumor tissue form patient_4


title: P31_1

description:
processed data column: 21
Sample0021


title: P30_2

description:
processed data column: 20
Sample0020


title: P31_3

description:
processed data column: 58
SampleP31_3


title: EV_1 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_EV.csv
d_m6A_EV.csv


title: ZJ316_COM, rep3

city: Hangzhou

first: Xiangfeng

last: Chen

address: Xuezheng Street 18

institute: Zhejiang Gongshang University

data_processing:
Differentially expressed genes/transcripts are identified based on read counts data of transcripts obtained from gene expression analysis. Default parameters: p-adjust < 0.05 and |log2FC| >= 1, using BGI Cloud Platform (Dr.Tom) for online analysis, when the corrected P-value (P adjust) < 0.05, it is considered that there is a significant enrichment of this KEGG PATHWAY function.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: colon tissues

extract_protocol:
Excise the entire colon of each animal, rinse with PBS to remove fecal debris snap-frozen in liquid nitrogen, and store at -80 °C. RNA extraction kits were used to extract tissue RNA and reverse transcribed to cDNA for transcriptome sequencing.
Use the DNBSEQ platform

treatment_protocol: Animal model of ulcerative colitis was established by drinking 2.5% Dextran Sulfate Sodium (DSS). C57BL/6 male mice were randomly divided into 2 groups after a week of normal feeding and adaptive culture. Blank control group (C) (n=10): mice were fed normally until the end of the experiment. DSS colitis group (n=50): mice were fed with 2.5% DSS solution instead of pure water under normal diet conditions for 7 consecutive days, and DSS solution was changed every two days during this period to establish a mouse colitis model. After successful establishment of DSS colitis model, the colitis group was divided into 5 groups and treated with different interventions by gavage: PBS group (P): the mice were treated with PBS medium 200 μL/10 g by gavage every day for 5 weeks, until the end of the experiment. ZJ316 group (WT), ZJ316-KO (KO), ZJ316-COM (COM): the WT Lactobacillus plantarum ZJ316 bacteria, ZJ316-KO and ZJ316-COM suspension 200 μL/10 g (about 2.5×109 CFU/mL) was given by gavage respectively for 5 weeks, until the end of the experiment.

value: colon tissues

value: male

value: WT


title: P3_1

description:
processed data column: 45
Sample0046


title: ABZB RP11-350G8.5 KO (REPLICATE 2)

city: Milano

first: FRANCESCO

last: IORIO

address: Viale Rita Levi-Montalcini, 1 (Area MIND)

country: Italy

institute: Human Technopole

description:
Strand-specific cDNA library
ID 4: 548651
S2B_G8_5KO

data_processing:
FASTQ files from RNA sequencing were verified using the FastQC application (Leggett et al, 2013)
Sequences were aligned to the Gencode hg19 genome and raw counts obtained using the Rsubread package (Liao et al 2019)
Assembly: GENECODE hg19
Supplementary files format and content: tab-delimited text-file containing RNA-Seq read counts for each gene across samples

source_name: plasmacytoma

extract_protocol:
Total RNA was extracted from cells through PureLink RNA mini kit (Invitrogen by Thermo Fisher Scientific, Waltham, MA, USA)
RNA sequencing was performed by Eurofins Genomics Company (Ebersberg, Germany) according to their INVIEW Transcriptome Discover Protocol. Briefly, Purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis (strand-specific), adapter ligation and adapter specific PCR amplification and Illumina paired-end read sequencing (2 x 150 bp) were performed. 30 M reads pairs (+/- 3%) were guaranteed per run

value: plasmacytoma

value: ABZB

value: AMO-1 DERIVATIVE SUBCLONE RESISTANT TO BORTEZOMIB

value: BORTEZOMIB 10 NM


title: P29_2

description:
processed data column: 19
Sample0019


title: ZJ316_COM, rep1


title: P28_1

description:
processed data column: 17
Sample0017


title: P32_1

description:
processed data column: 59
SampleP32_1


title: ZJ316_KO, rep4


title: ABZB SCR (REPLICATE 1)

description:
Strand-specific cDNA library
ID 1: 548648
S1B_SCR


title: P27_3

description:
processed data column: 57
SampleP27-3

value: transformed follicular lymphoma, lymph node


title: P29_1

description:
processed data column: 18
Sample0018


title: P25_2

description:
processed data column: 56
SampleP25_2


title: ABZB SCR (REPLICATE 2)

description:
Strand-specific cDNA library
ID 3: 548650
S2B_SCR


title: P23_3

description:
processed data column: 55
SampleP23_3


title: EV_2 IP

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

description:
DESeq2_EV.csv
d_m6A_EV.csv

value: myocardium

value: human myocardial cell line

value: treat with evodiamine


title: ZJ316_COM, rep4


title: P23_2

description:
processed data column: 54
SampleP23-2

value: follicular lymphoma, lymph node

value: all cell types present in bulk


title: P23_1

description:
processed data column: 14
Sample0014


title: P21_2

description:
processed data column: 53
SampleP21_2


title: P27_1

description:
processed data column: 15
Sample0015


title: ZJ316_KO, rep2


title: P3_2

description:
processed data column: 46
Sample0047


title: UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep2 (RNA-seq)

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

description: passage 27+14+1 (cultured in 5iLAF medium for six days)

data_processing:
Raw reads were aligned against the GRCh38 reference grenome using STAR.
Reads were filtered, sorted and marked for duplicates using samtools.
Features were obtained GENCODE reference annotation file v34 and raw counts were correponding to each feature was calculated using HTSEQ. TPM values were calculated using StringTie.
Differentially expressed genes were calculated using DESeq2. Raw counts were normalised for sequencing depth and library complexity using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data includes TPM values provided as a .txt file

source_name: Reverting human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs prior to collection for experiments.

extract_protocol:
Cells were lysed in RNAzol RT reagent and total RNA was purified from cell extracts according to manufacturer's instructions.
mRNA containing polyA tail were enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module and libraries were prepared using the Swift RNA library kit or NEBNext Ultra II RNA Library Prep Kit according to respective manufacturers' instructions.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate or DMSO of equivalent v/v concentration, where specified.

value: Reverting human embryonic stem cells

value: UCLLA1 reverting hESCs

value: Human embryonic stem cells

value: ZIC3-/- clone 20


title: P27_2

description:
processed data column: 16
Sample0016


title: UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep1 (RNA-seq)

description: passage 27+16+1 (cultured in 5iLAF medium for six days)

value: ZIC3-/- clone 2


title: UCLA1 reverting hESC, NT, 5iLAF d6, rep2 (RNA-seq)

description: passage 27+12+1 (cultured in 5iLAF medium for six days)

value: WT clone 2


title: ZJ316_COM, rep2

value: colon tissues

value: male

value: WT


title: P21_1

description:
processed data column: 52
SampleP21-1


title: ABZB RP11-350G8.5 KO (REPLICATE 1)

description:
Strand-specific cDNA library
ID 2: 548649
S1B_G8_5KO

value: plasmacytoma

value: ABZB

value: AMO-1 DERIVATIVE SUBCLONE RESISTANT TO BORTEZOMIB


title: UCLA1 reverting hESC, NT, 5iLAF d6, rep1 (RNA-seq)

value: WT clone 1


title: ZJ316_WT, rep3


title: P2_1

description:
processed data column: 3
Sample0003