title: BY4741, Ioc3-KO, replicate1, MNase-seq

first: Pengjing

last: Hu

state: Beijing

address: 30 Shuangqing Rd, Haidian District

department: School of Life Science

institute: Tsinghua University

description:
dioc3_smooth.bw
dioc3_pos.txt

data_processing:
Pair-end sequencing reads were trimmed by Trimmomatic and were mapped to sacCer3 reference genome using Bowtie2.
Reads in the range of 120-180bp were selected, and those mapped to repetitive rRNA locus (chrXII: 451275–469084) were excluded.
SAMtools was used to remove possible PCR duplicates.
Data from two biological replicates were merged, and an equal number of reads (10345423 reads) was randomly selected for each sample.
Nucleosome positions were identified using algorithm as described for GeneTrack.
Assembly: sacCer3
Supplementary files format and content: bigWig, guassian smoothed peak
Supplementary files format and content: tab-delimited text files, nucleosome dyad position

organism: Saccharomyces cerevisiae

growth_protocol: 30℃, YPD, mid-log phase

extract_protocol:
Cells were harvested and converted to spheroplasts using 0.25 mg ml–1 zymolase100T (MP Biomedicals cat#320932). Spheroplasts were digested with micrococcal nuclease (NEB M0247S) at concentrations of 600/1200/2400 gel unit/ml. Samples were treated with proteinase K (25 μg ml–1, Tiangen RT403) 30 mins at 65 °C to remove protein. Phenol:chloroform was used to extract the DNA. We incubated the sample with RNase A (100 μg ml–1, Tiangen RT405) to remove RNA.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB #E7645S)


title: First RNAseq dataset: DI222-treated IFNAR-/- mouse #F2

status: Public on May 15 2023

type: SRA

city: Bethesda

first: Matthew

last: Chung

state: MD

address: 50 South Dr

country: USA

institute: NIAID (National Institute of Allergy and Infectious Diseases)

library_source: transcriptomic

data_processing:
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
Assembly: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary files format and content: For the RNA-seq dataset, a tab-delimited text file containing the raw gene counts for all the samples was provided.

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen), followed by poly(A) mRNA enrichment.
The enriched poly(A) mRNAs were subject to RNA-seq library preparatin with NEBNext Ultra II RNA library prep kit for Illumina following the manufacturer’s protocol.

tag: tissue

value: Lung

tag: mouse strain

value: IFNAR-/-

tag: treatment

value: DI222 co-treatment


title: WT_4h_A

city: Martinsried/Planegg

first: Martin

last: Mueller

address: Am Klopferspitz 18

country: Germany

institute: MPI of Biochemistry

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts or comma-delimited text file with half-lives and CPM

molecule: total RNA

organism: Homo sapiens

growth_protocol: The Bristol strain N2 was used as wild-type. Strains used in this study are listed in the Key Resource Table. Worms were grown on nematode growth medium (NGM) seeded with OP50 bacteria and maintained at 20°C unless otherwise indicated. For liquid culture, worm eggs were collected by bleaching and synchronized populations of L1 larvae were obtained by overnight growth in M9 medium. The L1 larvae were grown in S Basal in presence of OP50 bacteria.

extract_protocol:
C. elegans  Synchronized nematodes were transferred to 1 l S-Basal and grown in liquid culturentil D1 of adulthood or until D6, when indicated. FUdR (200 µM) was added when the culture had reached the L4/young adult stage. After thorough washing in M9, the nematodes were frozen in lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide) by dropwise transfer into liquid nitrogen. The nematodes were lysed with a Retsch Cryomill MM400 at 30 Hz for 3 times 90 s with cooling between cycles. The lysate was cleared for 10 min at 20,000 x g and 4oC. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.  HEK293T cells  HEK293T cells were seeded into 15 cm plates 24 h prior to treatment. The cells were treated with 10 nM CC-885 and 20 μg/ml G418 for 4 h. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.
C. elegans  The procedure for immunoprecipitation (IP) of GCN-1 bound ribosomes was adapted from {Matsuo, 2021 #75}. Nematodes were synchronized by bleaching. L1 larvae were transferred to 1 L S-Basal. The animals were harvested at D1 of adulthood. Bacteria were removed by repeated washes in M9. In the last washing step, M9 was replaced by lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide). After a quick spin, the worms were flash frozen in liquid nitrogen. The frozen worms were lysed with a Retsch cryomill MM400 at 30 Hz as above. The lysate was thawed on ice and clarified by centrifugation at 4,000 x g for 10 min at 4oC. Protein concentration was determined by Bradford assay. The supernatant fraction (80 mg of total protein) was partially digested with 3 units per 1 mg RNA RNase I (Epicenter) at 4oC for 1 h. Ribosomes were pelleted through a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC and resuspended in lysis buffer supplemented with 10% glycerol. The IP was performed at 4oC for 1 h using M2 anti-FLAG magnetic agarose beads (Invitrogen). The beads were washed 10 times with lysis buffer and bound material was digested with 12.5 units of RNase I (Epicenter) at 23oC for 45 min (strong RNase I treatment). Ribosome protected mRNA fragments were eluted by adding TRIzol reagent (Invitrogen). Libraries were prepared as previously described (McGlincy, 2017 #78) and sequenced on an Illumina NextSeq 500 system.  HEK293T cells  SLAM-seq was performed using the Lexogen SLAM-seq kinetics kit following the manufacturer's instructions.
Ribo-seq (disome) and mRNAseq (SLAMseq)

treatment_protocol: HEK293T cells were cultured in DMEM (Thermo Scientific, 11995073) supplemented with 10% FBS (Gibco, 10270106) at 5% CO2 and 37°C.

tag: cell line

tag: cell type

value: embryonic kidney

tag: genotype

value: WT

value: 100uM 4sU fed for 24h, then washed out for chase over 8h


title: CMP, KO5

city: Shanghai

first: Shaoqin

last: Rong

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

description:
T2KO5-CMP
TET2_project_counts.csv

data_processing:
For RNA data, the raw data were trimmed by Trim Galore (v0.6.7) with default settings.
Then, the clean RNA-seq FASTQ data were mapped to mm10 using Hisat2 (v7.5.0) with default parameters.
DEG analysis was performed by using DESeq2 package with the raw count. Only genes with padj less than 0.05 and at least 2-fold-change were considered to be differentially expressed.
Assembly: mm9
Supplementary files format and content: raw count

source_name: Bone marrow

extract_protocol:
Different populations of hematopoietic stem/progenitor cells (LT-HSC, ST-HSC, CMP, GMP, MEP, CLP) from bone marrow cells of different genotypes of mice (WT, Sting-KO, Tet2-KO, Tet2/Sting-dKO) were sorted by  FACS with a number of 200 cells. The sorted cells were lysed with the lysis buffer obtained by SMART-seq construction Kit (Cat. N712, Vazyme) immediately and followed the library construction protocol from the Kit to generate cell full length mRNA library.
RNA libraries of pre-malignant cells were constructed by Smart-seq2 protocol, Nat. Methods 10, 1096–1098 (2013). RNA libraries of mouse hematopoietic cells were constructed by kit (Vazyme, NR611)

value: Bone marrow

value: CMP

value: Hematopoietic stem/progenitor cells

value: Tet2 knockout


title: BY4741, Ioc3-Q251K/ D252K, replicate2, MNase-seq

city: Beijing

description:
dH4_smooth.bw
dH4_pos.txt

library_source: genomic

molecule: genomic DNA


title: BY4741, Ioc3-Q251K/ D252K, replicate1, MNase-seq

description:
dH4_smooth.bw
dH4_pos.txt


title: ST-HSC, KO5

description:
T2KO5-ST
TET2_project_counts.csv

value: ST-HSC


title: WT_2h_B


title: First RNAseq dataset: DI222-treated IFNAR-/- mouse #F1


title: BY4741, Ioc3-R739E/R742E, replicate2, MNase-seq

description:
dAP_smooth.bw
dAP_pos.txt


title: WT_2h_A


title: cSiah1a/2f/f::CD11ccre alveolar macrophage, replicate 1

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapters and polyA/polyT sequences were trimmed from raw reads using Cutadapt version 2.3.
Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 adopting alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
RSEM version 1.3.1 was used to obtain gene level estimated counts and transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes TPM (Transcripts Per Million) values for each sample.

source_name: lung

extract_protocol:
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Barcoded libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, Ipswich MA). Libraries were pooled and sequenced single-end (1X75) on an Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: lung

value: alveolar macrophage


title: CLP, KO5

description:
T2KO5-CLP
TET2_project_counts.csv

value: CLP


title: LT-HSC, KO5

description:
T2KO5-LT
TET2_project_counts.csv

value: LT-HSC


title: WT_0h_C


title: cSiah1a/2f/f::Lyz2cre alveolar macrophage, replicate 2


title: First RNAseq dataset: DI222-treated IFNAR-/- mouse #M2


title: CLP, KO4

description:
T2KO4-CLP
TET2_project_counts.csv


title: WT_4h_C


title: MEP, KO4

description:
T2KO4-MEP
TET2_project_counts.csv

value: MEP


title: BY4741, Ioc3-R739E/R742E, replicate1, MNase-seq

description:
dAP_smooth.bw
dAP_pos.txt


title: WT_4h_B


title: WT_0h_B


title: cSiah1a/2f/f::Lyz2cre alveolar macrophage, replicate 1


title: GMP, KO5

description:
T2KO5-GMP
TET2_project_counts.csv

value: GMP


title: BY4741, Ioc3-KO, replicate2, MNase-seq

description:
dioc3_smooth.bw
dioc3_pos.txt


title: GMP, KO4

description:
T2KO4-GMP
TET2_project_counts.csv


title: BY4741, WT3, replicate1, MNase-seq

description:
wt3_smooth.bw
wt3_pos.txt


title: WT_0h_A


title: WT_2h_C


title: WT alveolar macrophage, replicate 3

value: CD11c+ F480+ SiglecF+ WT


title: BY4741, WT2, replicate2, MNase-seq

description:
wt2_smooth.bw
wt2_pos.txt


title: WT alveolar macrophage, replicate 2


title: BY4741, WT2, replicate1, MNase-seq

description:
wt2_smooth.bw
wt2_pos.txt


title: cSiah1a/2f/f::Lyz2cre alveolar macrophage, replicate 3


title: WT alveolar macrophage, replicate 1


title: BY4741, WT3, replicate2, MNase-seq

description:
wt3_smooth.bw
wt3_pos.txt


title: LT-HSC, KO4

description:
T2KO4-LT
TET2_project_counts.csv


title: WT MCF-7 scRNA-seq repeat 2

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

description: raw data currently unavailable due to unstable network.

library_source: transcriptomic single cell

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)

source_name: whole cell

growth_protocol: Regular MCF7 cell lines were obtained from ATCC. These cell lines were cultured using Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal calf serum (FBS) and 100 units/mL penicillin, and 100 mg/mL streptomycin, 2 mM l-glutamine.

extract_protocol:
CUT&Tag was performed as previously reported(Kaya-Okur HS et al., 2019)
CUT&Tag library PCR amplification was performed with NEBNext 2× PCR Master Mix and standard Illumina Nextera indexing primers. The libraries were purified with Ampure XP beads at a ratio of 1:1. ChIP-seq libraries were prepared from 10 ng EZH2 ChIP, 100 ng H3K36me2 ChIP and input DNA using the KAPA Hyper prep kit (KAPA).

tag: media

value: DMEM

tag: chip antibody


title: CLP, KO3

description:
T2KO3-CLP
TET2_project_counts.csv


title: ST-HSC, KO4

description:
T2KO4-ST
TET2_project_counts.csv


title: MCM2-2A MCF-7 H3K36me3 espan 1h

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)
Library strategy: CUT&TAG

value: Anti-H3K36me3 Antibody (Active Motif_61021)


title: WT MCF-7 H3K36me3 espan 1h


title: MEP, KO3

description:
T2KO3-MEP
TET2_project_counts.csv


title: POLE3 KO MCF-7 H3K27me3 CUT&Tag repeat 2

value: POLE3 KO

value: Anti-H3K27me3 Antibody (CST_9733)


title: BY4741, WT1, replicate2, MNase-seq

description:
wt1_smooth.bw
wt1_pos.txt

value: WT


title: miRNA-seq dataset: mock-infected IFNLR-/- mouse #3

description:
FDK287_LM3
DIinfKOmice_miRNAseq_counts.txt

data_processing:
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the miRNA-seq dataset, miRNA primary quantification was performed in the GeneGlobe Data Analysis Center (Qiagen) for trimming, mapping, and unique molecular indices (UMI) analysis. Although both miRNAs and piRNAs were detected in the small RNA libraries, only miRNAs were used in the downstream analyses.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment.
Genome_build: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary_files_format_and_content: For the RNA-seq and miRNA-seq datasets, a tab-delimited text file containing the raw gene or miRNA counts for all the samples was provided.

source_name: Whole lungs of mock-infected IFNLR-/- mouse

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen).
Total RNAs in the lung homogenate were subject to miRNA sequencing library preparation with QIAseq miRNA library kit for Illumina (Qiagen).

treatment_protocol: Mice were intranashally inoculated with 50µL PBS.

value: Lung

value: IFNLR-/-

value: Mock infection


title: miRNA-seq dataset: mock-infected IFNAR-/- IFNLR-/- mouse #3

description:
DJA269_DOM3
DIinfKOmice_miRNAseq_counts.txt

source_name: Whole lungs of mock-infected IFNAR-/- IFNLR-/- mouse

value: IFNAR-/- IFNLR-/-


title: miRNA-seq dataset: mock-infected IFNAR-/- IFNLR-/- mouse #1

description:
DJA248_DOM1
DIinfKOmice_miRNAseq_counts.txt


title: miRNA-seq dataset: mock-infected IFNAR-/- IFNLR-/- mouse #2

description:
DJA270_DOM2
DIinfKOmice_miRNAseq_counts.txt


title: CMP, KO4

description:
T2KO4-CMP
TET2_project_counts.csv

value: Bone marrow

value: CMP

value: Hematopoietic stem/progenitor cells

value: Tet2 knockout


title: BY4741, WT1, replicate1, MNase-seq

description:
wt1_smooth.bw
wt1_pos.txt


title: POLE3 KO MCF-7 H3K27me3 CUT&Tag repeat 1


title: CMP, KO3

description:
T2KO3-CMP
TET2_project_counts.csv


title: ST-HSC, KO3

description:
T2KO3-ST
TET2_project_counts.csv

value: ST-HSC


title: IgE+Monocytes, Healthy, Clinical Phase EL28

city: Ithaca

first: Bettina

last: Wagner

state: NY

address: 240 Farrier Drive

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

description: IgE+Monocytes, Healthy, Clinical Phase

data_processing:
Raw sequencing reads were initially processed by Cornell’s TREx Facility using pipelines built around ENCODE standards and practices. First, raw fastq files were processed with TrimGalore v0.6.0 to remove low quality bases and adaptor sequences.
Reads were then mapped to the EquCab3.0 genome using STAR v2.7.0e.
Read count data was further analyzed using iDEP.96 (integrated Differential Expression and Pathway analysis). Counts data was transformed using EdgeR (log2(CPM+4)) on all genes with a minimum of 0.5 counts per million (CPM) in at least 1 library. Samples from each phase were normalized separately.
Assembly: EquCab3.0 genome
Supplementary files format and content: tab-delimited text files include counts per million (CPM) values for each Sample

organism: Equus caballus

source_name: IgE-binding Monocyte

extract_protocol:
Frozen IgE-binding monocytes were thawed at 37ºC and slowly resuspended into 10ml PBS-FCS (PBS supplemented with 20% FCS and 2mM EDTA (Boston BioProducts, Boston, NY, USA) at RT. Cells were pelleted at 100xg, 5 min, RT and washed once in 1ml PBS-FCS. Cells were resuspended in 250µl PBS-FCS and 750µl Trizol LS solution (Invitrogen, Waltham, MA, USA). Then, 200µl chloroform (Fisher Scientific, Pittsburgh, PA, USA) was added. Tubes were vigorously shaken for 15 seconds and centrifuged at 16000xg, 15 min, 4ºC. The aqueous phase was collected and added to an additional 600µl chloroform in Phase Lock Gel tubes (Quantabio, Beverly, MA, USA). To improve RNA recovery, 2µl of a glycogen carrier (GlycoBlue, ThermoFisher Scientific, Waltham, MA, USA) was added. Last, 500µl isopropanol was added and incubated on ice for 1 hour, then washed three times in 75% ice-cold ethanol. All wash spins were performed at 16000xg, 10 min, 4ºC. Extracted RNA was air dried in a laminar flow hood at RT, then resuspended in 20µl RNase-free water (Invitrogen, Waltham, MA, USA), and stored at -80ºC until submitted for sequencing.
RNA was first poly-A selected with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and TruSeq-barcoded RNA-seq libraries were generated using the NEBNext® Ultra™ II Directional RNA Library Prep kit (New England Biolabs, Ipswich, MA, USA). Libraries were sequenced on an Illumina instrument with a read length of 75bp single end reads at a depth of 20 million reads per sample.

tag: cell source

value: Heparinized Blood

value: IgE-binding Monocyte

tag: allergy status

value: Healthy

tag: disease stage

value: Clinical Phase


title: IgE+Monocytes, Healthy, Clinical Phase EL27

description: IgE+Monocytes, Healthy, Clinical Phase


title: IgE+Monocytes, Healthy, Clinical Phase EL23

description: IgE+Monocytes, Healthy, Clinical Phase


title: MCM2-2A MCF-7 scRNA-seq repeat 2

value: DMEM


title: POLE3 KO MCF-7 H3K36me3 espan 1h

value: POLE3 KO

value: Anti-H3K36me3 Antibody (Active Motif_61021)


title: miRNA-seq dataset: mock-infected IFNLR-/- mouse #1

description:
FDK262_LM1
DIinfKOmice_miRNAseq_counts.txt


title: IgE+Monocytes, Healthy, Clinical Phase EL22

description: IgE+Monocytes, Healthy, Clinical Phase


title: miRNA-seq dataset: mock-infected IFNAR-/- mouse #4

description:
DG4601_AM4
DIinfKOmice_miRNAseq_counts.txt

source_name: Whole lungs of mock-infected IFNAR-/- mouse

value: IFNAR-/-


title: Endo_Failed_26

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using bcl2fastq version 2.20.0
RNA-seq and ChIP-seq reads were aligned to the mm10 (for mice) or hg38 (for humans) genome using Hisat2 version 2.1.0. and bowtie2 version 2.3.3.1.
For RNA-seq analysis, To quantify uniquely aligned reads on respective annotated transcript loci (NCBI RefSeq transcripts), the htseq-count function with  –s reverse option, part of the HTSeq package
For ChIP-seq analysis, Pearson correlation coefficient (R) in 2kb bins between biological replicates were calculated with R. Peak calling for ChIP-seq data were performed by MACS 2.1.1 with default arguments; a cut-off P value of 10-2 was used.  Relative ChIP-seq enrichments in respective peak regions were calculated by dividing input controls.
Assembly: mm10 for mice, hg38 for humans
Supplementary files format and content: bam files were generated from each alignment step

source_name: Human endometria

growth_protocol: For RNA-seq analysis using mouse uteri, all mice were housed in 12h/12h light cycle. Mice were mated with fertile males to get pregnant. The day vaginal plugs found is considered as day 1 of pregnancy. On day 4 or day 6 morning, uteri were collected.

extract_protocol:
For RNA-seq analysis , total RNA were collected using NucleoSpin RNA (MACHEREY-NAGEL) for mice and the RNeasy Plus Mini Kit (Qiagen) for humans, with genomic DNA elimination. For ChIP-seq analysis, to extract chromatin, isolated day 6 endometrial cells were suspended in 20 µl of Nuclei EZ Lysis Buffer (SIGMA), and extensively digested chromatin with 20 IU/µl Micrococcal Nuclease (MNase, NEB) at 37℃ for 5 min.
RNA-seq library preparation was carried out using TruSeq Stranded mRNA Library Prep kit (Illumina) following manufacturer’s instructions. ChIP-seq library preparation was carried out by NEBNext ChIP-seq for Illumina (NEB) following manufacturer’s instructions.

treatment_protocol: For RNA-seq analysis using human endometria, fertile or RIF patients were treated with P4. Their endometria were collected 7days later.

tag: no. of passages and ages of weeks

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans

tag: genotype/treatment condition

value: P4 was treated during a hormonal replacement cycle

tag: background strain

value: Human


title: CLP, KO2

description:
T2KO2-CLP
TET2_project_counts.csv

value: CLP


title: Endo_Failed_27


title: GMP, KO3

description:
T2KO3-GMP
TET2_project_counts.csv

value: Bone marrow

value: GMP


title: Endo_Failed_25


title: miRNA-seq dataset: mock-infected IFNAR-/- mouse #3

description:
DG4579_AM3
DIinfKOmice_miRNAseq_counts.txt

value: Lung

value: Mock infection


title: MEP, KO2

description:
T2KO2-MEP
TET2_project_counts.csv

value: MEP

value: Hematopoietic stem/progenitor cells

value: Tet2 knockout


title: IgE+Monocytes, Healthy, Clinical Phase EL25

description: IgE+Monocytes, Healthy, Clinical Phase

value: Heparinized Blood

value: IgE-binding Monocyte

value: Healthy


title: miRNA-seq dataset: mock-infected IFNLR-/- mouse #2

description:
FDK241_LM2
DIinfKOmice_miRNAseq_counts.txt

value: IFNLR-/-


title: Endo_Failed_24


title: IgE+Monocytes, Allergic, Clinical Phase EL20

description: IgE+Monocytes, Allergic, Clinical Phase

value: Allergic

value: Clinical Phase


title: Endo_Failed_23

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans


title: IgE+Monocytes, Allergic, Clinical Phase EL21

description: IgE+Monocytes, Allergic, Clinical Phase


title: GMP, KO2

description:
T2KO2-GMP
TET2_project_counts.csv


title: miRNA-seq dataset: mock-infected IFNAR-/- mouse #2

description:
DG4476_AM2
DIinfKOmice_miRNAseq_counts.txt

value: IFNAR-/-


title: miRNA-seq dataset: mock-infected IFNAR-/- mouse #1

description:
DG4450_AM1
DIinfKOmice_miRNAseq_counts.txt


title: CMP, KO2

description:
T2KO2-CMP
TET2_project_counts.csv

value: CMP


title: IgE+Monocytes, Allergic, Clinical Phase EL18

description: IgE+Monocytes, Allergic, Clinical Phase


title: RNA-seq dataset: mock-infected IFNAR-/- IFNLR-/- mouse #3

description:
DJA269_DOM3
DIinfKOmice_mRNAseq_counts.txt

value: IFNAR-/- IFNLR-/-


title: Endo_Failed_21

value: P4 was treated during a hormonal replacement cycle

value: Human


title: Endo_Failed_22


title: ST-HSC, KO2

description:
T2KO2-ST
TET2_project_counts.csv

value: Bone marrow

value: ST-HSC


title: LT-HSC, KO3

description:
T2KO3-LT
TET2_project_counts.csv

value: LT-HSC


title: IgE+Monocytes, Allergic, Clinical Phase EL16

description: IgE+Monocytes, Allergic, Clinical Phase


title: IgE+Monocytes, Allergic, Clinical Phase EL17

description: IgE+Monocytes, Allergic, Clinical Phase


title: Endo_Failed_20


title: Endo_Failed_19


title: RNA-seq dataset: mock-infected IFNLR-/- mouse #3

description:
FDK287_LM3
DIinfKOmice_mRNAseq_counts.txt

value: Lung

value: Mock infection


title: IgE+Monocytes, Allergic, Clinical Phase EL15

description: IgE+Monocytes, Allergic, Clinical Phase

value: Heparinized Blood


title: LT-HSC, KO2

description:
T2KO2-LT
TET2_project_counts.csv

value: Hematopoietic stem/progenitor cells

value: Tet2 knockout


title: IgE+Monocytes, Healthy, Remission Phase EL14

description: IgE+Monocytes, Healthy, Remission Phase

value: IgE-binding Monocyte

value: Healthy

value: Remission Phase


title: MEP, WT5

description:
WT5-MEP
TET2_project_counts.csv

value: MEP

value: WT


title: CLP, WT5

description:
WT5-CLP
TET2_project_counts.csv

value: CLP


title: Endo_Failed_18

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans


title: IgE+Monocytes, Allergic, Clinical Phase EL19

description: IgE+Monocytes, Allergic, Clinical Phase

value: Allergic

value: Clinical Phase


title: RNA-seq dataset: mock-infected IFNLR-/- mouse #2

description:
FDK241_LM2
DIinfKOmice_mRNAseq_counts.txt

value: IFNLR-/-


title: RNA-seq dataset: mock-infected IFNLR-/- mouse #1

description:
FDK262_LM1
DIinfKOmice_mRNAseq_counts.txt


title: CMP, WT5

description:
WT5-CMP
TET2_project_counts.csv

value: Bone marrow

value: CMP


title: Endo_Failed_17

value: P4 was treated during a hormonal replacement cycle

value: Human


title: GMP, WT5

description:
WT5-GMP
TET2_project_counts.csv

value: GMP


title: RNA-seq dataset: mock-infected IFNAR-/- mouse #4

description:
DG4601_AM4
DIinfKOmice_mRNAseq_counts.txt

value: Lung

value: IFNAR-/-

value: Mock infection


title: ST-HSC, WT5

description:
WT5-ST
TET2_project_counts.csv

value: ST-HSC

value: Hematopoietic stem/progenitor cells


title: IgE+Monocytes, Healthy, Remission Phase EL11

description: IgE+Monocytes, Healthy, Remission Phase

value: Heparinized Blood

value: IgE-binding Monocyte

value: Healthy

value: Remission Phase


title: RNA-seq dataset: mock-infected IFNAR-/- IFNLR-/- mouse #2

description:
DJA270_DOM2
DIinfKOmice_mRNAseq_counts.txt

value: IFNAR-/- IFNLR-/-


title: Endo_Failed_15

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans


title: Endo_Failed_16


title: RNA-seq dataset: mock-infected IFNAR-/- mouse #3

description:
DG4579_AM3
DIinfKOmice_mRNAseq_counts.txt


title: LT-HSC, WT5

description:
WT5-LT
TET2_project_counts.csv

value: LT-HSC

value: WT


title: IgE+Monocytes, Healthy, Remission Phase EL13

description: IgE+Monocytes, Healthy, Remission Phase


title: IgE+Monocytes, Healthy, Remission Phase EL9

description: IgE+Monocytes, Healthy, Remission Phase


title: IgE+Monocytes, Healthy, Remission Phase EL8

description: IgE+Monocytes, Healthy, Remission Phase


title: Endo_Failed_14


title: CLP, WT4

description:
WT4-CLP
TET2_project_counts.csv

value: Bone marrow

value: CLP


title: RNA-seq dataset: mock-infected IFNAR-/- mouse #2

description:
DG4476_AM2
DIinfKOmice_mRNAseq_counts.txt


title: RNA-seq dataset: mock-infected IFNAR-/- IFNLR-/- mouse #1

description:
DJA248_DOM1
DIinfKOmice_mRNAseq_counts.txt


title: IgE+Monocytes, Allergic, Remission Phase EL7

value: Allergic


title: RNA-seq dataset: mock-infected IFNAR-/- mouse #1

description:
DG4450_AM1
DIinfKOmice_mRNAseq_counts.txt


title: IgE+Monocytes, Allergic, Remission Phase EL6


title: Endo_Failed_13

value: P4 was treated during a hormonal replacement cycle

value: Human


title: GMP, WT4

description:
WT4-GMP
TET2_project_counts.csv

value: GMP


title: IgE+Monocytes, Allergic, Remission Phase EL5


title: JC_T1_3D_6

city: San Francisco

first: Alex

middle: G

last: Lee

address: 1550 4th Street

institute: UCSF

data_processing:
Original fastq files for each GAIIx run were composed of 30-60 multiplexed samples. Each fastq was split by a barcode identifier using the FASTX-toolkit barcode_splitter.pl script
Count files were created in R (v. 3.1.1) using the edgeR package (v. 3.6.8) processHairpinReads function with no mismatches or shifting allowed, shRNAs with no counts were filtered out and all shRNAs were given an extra count to avoid dividing by zero counts
Analysis of shRNA abundance was performed in edgeR using a time-course design and generalized linear models to compare the initial (T0) and final (T1) timepoints (using the glmFit function) and perform a likelihood ratio test (using the glmLRT function) to report log2 fold change scores and significance.
Assembly: no alignment necessary
Supplementary files format and content: tab delimited text file

source_name: primary murine lung tumor organoids

growth_protocol: Primary lung tumor cells isolated from the KRAS/P53/YFP GEMM were depleted for CD45, CD31, and TER119, and 2x10^6 cells were spinfected with lentiviral shRNA libraries (100-150 shRNA/pool at an MOI <0.5) and seeded in equal parts Matrigel and 2x SCM (DMEM;F12, 10% FBS, and supplemented with N2 supplement, BPE, 10 ng/mL EGF, 10ng/mL FGF, and antibiotic/antimycotic) and overlayed with 1x SCM to grow into primary tumor spheres.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue kit
Lentiviral pLKO shRNA vectors were amplified using PCR with ExTaq, and each sample was given direct barcodes for multiplexing and Illumina compatible adapters using a secondary PCR step

treatment_protocol: Primary tumor spheres were selected with 1ug/mL Puromycin from 24h-72 hours in culture. After 7 days in culture, the first timepoint was collected as genomic DNA from 50% of cells, and the remaining 50% of cells were re-seeeded to form secondary spheres which were collected as genomic DNA after day 7 as secondary spheres.

tag: timepoint

tag: replicate

tag: condition

tag: pool

value: JC

tag: strain


title: Endo_Failed_11


title: Endo_Failed_12


title: JC_T1_3D_5


title: Endo_Succeed_40


title: CLP, WT3

description:
WT3-CLP
TET2_project_counts.csv

tag: tissue


title: JC_T1_3D_3


title: Endo_Succeed_39


title: IgE+Monocytes, Allergic, Remission Phase EL3


title: Endo_Succeed_38


title: GMP, WT3

description:
WT3-GMP
TET2_project_counts.csv

tag: cell line


title: MEP, WT3

description:
WT3-MEP
TET2_project_counts.csv

value: MEP

tag: cell type


title: IgE+Monocytes, Allergic, Remission Phase EL1


title: CMP, WT4

description:
WT4-CMP
TET2_project_counts.csv

value: CMP

value: Hematopoietic stem/progenitor cells

tag: genotype


title: CMP, WT3

description:
WT3-CMP
TET2_project_counts.csv


title: MEP, WT4

description:
WT4-MEP
TET2_project_counts.csv


title: IgE+Monocytes, Allergic, Remission Phase EL2

value: Heparinized Blood

value: IgE-binding Monocyte


title: Endo_Succeed_37


title: JC_T1_2D_6

source_name: LKR10 cell line


title: JC_T1_3D_2


title: JC_T1_3D_4


title: 1_xlg_4h rep2

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

data_processing:
1-4: STAR for genome mapping
Assembly: Arabidopisis: TAIR10; Marantia v3.1, v5.1; Rice: IRGSP 1.0
Supplementary files format and content: 1-4: raw counts

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: 1: 7-day-old arabidopsis seedlings liquid grown in 1/2 MS, continuous light; 2-3: 7-day-old marchantia gemma liquid grown in 1/2 B5, continuous light;  4: 7-day-old NB seedlings grwon on 1/2 MS plates, 16/8 Light/Dark cycle

extract_protocol:
1-4: Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen)
1-4: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1/2 Ms + 100 mM NaCl treatment for 0, 2 and 24 hr, 1/2 MS + 0.3 ug/ mL tunicamycin for 4 hr

value: Seedlings

tag: age


title: Endo_Succeed_35

tag: chip antibody


title: 1_xlg_4h rep1


title: ST-HSC, WT3

description:
WT3-ST
TET2_project_counts.csv

value: ST-HSC


title: JC_T1_3D_1


title: JC_T1_2D_5


title: Endo_Succeed_36

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans


title: LT-HSC, WT3

description:
WT3-LT
TET2_project_counts.csv

value: LT-HSC


title: IgE+Monocytes, Allergic, Remission Phase EL4

tag: cell source

value: Remission Phase


title: JC_T1_2D_4


title: Endo_Succeed_34


title: CLP, WT2

description:
WT2-CLP
TET2_project_counts.csv

value: Bone marrow

value: WT


title: 1_agb_4h rep1


title: MEP, WT2

description:
WT2-MEP
TET2_project_counts.csv


title: JC_T1_2D_2


title: Endo_Succeed_32


title: 1_gpa_4h rep1


title: JC_T1_2D_1


title: Endo_Succeed_31


title: JC_T1_2D_3


title: 1_col-0_4h rep2

value: col-0, WT


title: JC_T0_3D_6


title: Endo_Succeed_33

value: P4 was treated during a hormonal replacement cycle


title: 1_col-0_4h rep1


title: 1_gpa_4h rep2


title: JC_T0_3D_5


title: CMP, WT2

description:
WT2-CMP
TET2_project_counts.csv


title: ST-HSC, WT2

description:
WT2-ST
TET2_project_counts.csv


title: 1_xlg_24h rep3


title: 1_agb_4h rep2


title: Endo_Succeed_29

value: Human


title: LT-HSC, WT2

description:
WT2-LT
TET2_project_counts.csv


title: 1_xlg_24h rep2


title: Endo_Succeed_28


title: JC_T0_3D_3


title: Endo_Succeed_27


title: 1_xlg_24h rep1


title: Endo_Succeed_26


title: GMP, WT2

description:
WT2-GMP
TET2_project_counts.csv

value: GMP


title: Murine SCG, scRNAseq, HTO

city: Leiden

first: Monique

last: Jongbloed

address: Einthovenweg 20

department: Cardiology and Anatomy & Embryology

country: Netherlands

institute: Leiden University Medical Center

description: 10x Genomics

data_processing:
CellRanger 7.0.0 pipelines with CellRanger mode intron
Assembly: mm10-2020-A
Supplementary files format and content: H5-format and Tab-separated values files

molecule: nuclear RNA

source_name: superior cervical ganglia (SCG)

extract_protocol:
See publication for isolation protocol. Briefly, left and right SCG were dissected from 4 mice. Follwed by nuclei isolation and HTO barcoding
10X Library preparation according to manufactor's protocol
droplet based scRNA-seq with HTO antibodies per tissue. Illumnia NovaSeq 6000 (150bp PE) with 10X Genomics Single cell 3' v3

value: superior cervical ganglia (SCG)


title: Murine SCG, scRNAseq, GEX

description: 10x Genomics


title: Endo_Succeed_30


title: JC_T0_3D_2

value: JC


title: JC_T0_3D_1


title: Endo_Succeed_25


title: 1_agb_24h rep3


title: hippocampus 1_IgG

city: nanjing

first: jianwei

last: ge

address: zhongshan road

institute: nanjing university

data_processing:
Quality control    Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data   (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads   from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream   analyses were based on the clean data with high quality.
Reads mapping to the reference genome     Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the   adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
Call peak    The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff   qvalue < 0.05.
Motif analysis    The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the   genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with   the Motif database to obtain the Motif.
Peak analysis    Count the results of the annotations and plot the distribution results using R.
Assembly: mm10
Supplementary files format and content: Hippocamous_1.bw
Supplementary files format and content: Hippocamous_1_peaks.narrowPeak

source_name: mice hippocampus

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，  native nuclei were purified from frozen samples as previously described (Corces et al., 2017). Concanavalin A coated magnetic beads were added and incubated at room temperature for 10 min. Bead-bound cells were incubated with rabbit anti-Smad4 (1:50, Cell Signaling Technology, catalog 46535) or IgG control antibody (1:50, Millipore, catalog 12-370) on a rotating platform overnight at 4 °C. Secondary antibody (anti-Rabbit IgG antibody, Millipore, USA) was added and pA-Tn5 adapter complex was prepared in dig-med buffer. Then cells were resuspended in tagmentation buffer (10 mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.   1. Hatice S. Kaya-Okur, Steven J. Wu, Christine A. Codomo, Erica S. Pledger, Terri D. Bryson, Jorja G.Henikoff, Kami Ahmad & Steven Henikoff. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature communications. 2019, 10(1):1930.  2. Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and   enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017) doi:10.1038/nmeth.4396
The size distribution of libraries was determined by Agilent 4200 TapeStation analysis, and libraries were mixed   to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer.   Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s   instructions.
Other: Cut&tag

value: mice hippocampus


title: hippocampus 1_Smad4_CST


title: Endo_Succeed_24


title: 1_agb_24h rep2


title: JC_T0_3D_4


title: JC_T0_2D_5


title: JC_T0_2D_6


title: Endo_Succeed_23


title: 1_agb_24h rep1


title: JC_T0_2D_4


title: 1_gpa_24h rep2


title: Bap1LysM OC 4

city: St Louis

first: nidhi

last: rohatgi

state: MO

address: 660 S Euclid Ave

department: pathology and immunology

institute: washington university in st. louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: osteoclast

extract_protocol: oligo-dT

value: osteoclast

value: Bap1LysM (myeloid deletion

tag: treatment

value: MCSF + RANKL (100 ng/ml)


title: Bap1LysM OC 6


title: Endo_Succeed_22


title: Bap1LysM OC 5


title: JC_T0_2D_3


title: 1_gpa_24h rep1

value: Seedlings


title: Bap1LysM OC 2


title: Endo_Succeed_20


title: Bap1LysM OC 1


title: JC_T0_2D_2


title: Endo_Succeed_19


title: 1_col-0_24h rep3


title: Bap1flox OC 6


title: JC_T0_2D_1


title: 1_col-0_24h rep2


title: Endo_Succeed_18


title: 1_col-0_24h rep1


title: 1_gpa_24h rep3


title: Bap1flox OC 5


title: JB_T1_3D_5

value: JB


title: Endo_Succeed_16

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans


title: Endo_Succeed_21


title: 1_xlg_2h rep2


title: Bap1flox OC 3


title: 1_xlg_2h rep1


title: Endo_Succeed_14


title: Endo_Succeed_15


title: JB_T1_3D_3


title: Bap1flox OC 2


title: Bap1flox OC 1


title: 1_agb_2h rep3


title: JB_T1_3D_6


title: JB_T1_3D_4


title: Endo_Succeed_13


title: Bap1flox OC 4


title: JB_T1_3D_2


title: JB_T1_3D_1


title: Bap1LysM BMM 3

source_name: BMM

value: BMM

value: MCSF


title: 1_agb_2h rep2


title: Endo_Succeed_12


title: Endo_Succeed_17


title: 1_agb_2h rep1


title: Bap1LysM BMM 2


title: JB_T1_2D_6


title: JB_T1_2D_5


title: Endo_Failed_10


title: Bap1LysM BMM 1


title: 1_gpa_2h rep3


title: JB_T1_2D_4


title: Endo_Failed_9


title: 1_gpa_2h rep2


title: Endo_Failed_7


title: Bap1flox BMM 3


title: JB_T1_2D_3


title: Bap1flox BMM 2


title: 1_col-0_2h rep3


title: Bap1flox BMM 1


title: JB_T1_2D_2


title: Endo_Failed_8


title: Endo_Failed_6


title: 1_gpa_2h rep1


title: Endo_Failed_5


title: ipsilateral sham injured astrocytes  a9_11_H_Ipsi

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

description: ipsilateral sham injured astrocytes

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4)
After trimming, only reads with length greater than 30bp were mapped to mm10 by RSEM (v1.2.28) with bowtie2 (v 2.4.1)
The raw counts were used to identify differentially expressed genes by DESeq2 (v 1.36.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Hippocampus

extract_protocol:
Ambion’s PureLink RNA Mini Isolation
TakaraSMARTSeq V4 ultra-low input RNA kit

value: Hippocampus

value: astrocytes

value: WT CD31 Sham

value: Ipsi SHAM

tag: time

value: 4 months post injury


title: JB_T1_2D_1


title: JB_T0_3D_6


title: 1_col-0_2h rep1

value: col-0, WT


title: 1_col-0_2h rep2


title: ipsilateral sham injured astrocytes  a9_10_H_Ipsi

description: ipsilateral sham injured astrocytes


title: Endo_Failed_4

tag: no. of passages and ages of weeks

value: P4 was treated during a hormonal replacement cycle

value: Human


title: ipsilateral sham injured astrocytes  a9_9_H_Ipsi

description: ipsilateral sham injured astrocytes


title: Endo_Failed_3

tag: genotype/treatment condition


title: 1_xlg_0h rep3


title: JB_T0_3D_5


title: JB_T0_3D_4


title: ipsilateral sham injured astrocytes  a8_16_H_Ipsi

description: ipsilateral sham injured astrocytes


title: 1_xlg_2h rep3


title: JB_T0_3D_3


title: 1_xlg_0h rep1


title: 1_xlg_0h rep2


title: ipsilateral sham injured astrocytes  a8_15_H_Ipsi

description: ipsilateral sham injured astrocytes


title: Endo_Failed_2

tag: background strain


title: JB_T0_3D_2

tag: timepoint


title: 1_agb_0h rep3


title: JB_T0_3D_1

tag: replicate


title: ipsilateral injured astrocytes PTE- a9_15_H_Ipsi

description: ipsilateral injured astrocytes PTE-

value: WT CD31 Injured

value: Ipsi PTE-


title: ipsilateral injured astrocytes PTE- a9_16_H_Ipsi

description: ipsilateral injured astrocytes PTE-


title: Endo_Succeed_11


title: Endo_Failed_1


title: 1_agb_0h rep2


title: JB_T0_2D_6

tag: condition


title: 1_agb_0h rep1


title: Endo_Succeed_9


title: ipsilateral injured astrocytes PTE- a9_13_H_Ipsi

description: ipsilateral injured astrocytes PTE-


title: JB_T0_2D_5

tag: pool


title: 1_gpa_0h rep3


title: Endo_Succeed_8


title: ipsilateral injured astrocytes PTE- a9_14_H_Ipsi

description: ipsilateral injured astrocytes PTE-


title: JB_T0_2D_4

tag: strain


title: ipsilateral injured astrocytes PTE- a9_12_H_Ipsi

description: ipsilateral injured astrocytes PTE-

tag: tissue


title: Endo_Succeed_7


title: JB_T0_2D_3


title: 1_gpa_0h rep1


title: Endo_Succeed_6


title: ipsilateral injured astrocytes PTE- a8_14_H_Ipsi

description: ipsilateral injured astrocytes PTE-


title: JB_T0_2D_2


title: Endo_Succeed_10


title: 1_col-0_0h rep3


title: JB_T0_2D_1


title: ipsilateral injured astrocytes PTE- a8_9_H_Ipsi

description: ipsilateral injured astrocytes PTE-


title: Endo_Succeed_5


title: 1_col-0_0h rep2


title: ipsilateral injured astrocytes PTE- a8_11_H_Ipsi

description: ipsilateral injured astrocytes PTE-


title: JA_T1_3D_6

value: JA


title: ipsilateral injured astrocytes PTE+ a9_18_H_Ipsi

description: ipsilateral injured astrocytes PTE+

value: Ipsi PTE+


title: ipsilateral injured astrocytes PTE+ a9_19_H_Ipsi

description: ipsilateral injured astrocytes PTE+


title: Endo_Succeed_3


title: 3_wrky12_24h rep2

organism: Marchantia polymorpha

source_name: Gemmalings

value: Gemmalings


title: JA_T1_3D_4


title: ipsilateral injured astrocytes PTE+ a9_17_H_Ipsi

description: ipsilateral injured astrocytes PTE+


title: JA_T1_3D_5


title: Endo_Succeed_4


title: 1_gpa_0h rep2

value: Seedlings


title: Endo_Succeed_2

value: day 7 of P4 administration during a hormonal replacement cycle, which is considered the peri-implantation period in humans


title: 3_wrky12_2h rep2


title: JA_T1_3D_3


title: JA_T1_3D_2


title: ipsilateral injured astrocytes PTE+ a8_10_H_Ipsi

description: ipsilateral injured astrocytes PTE+


title: MCM2-2A H3K36me3 espan

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)
Library strategy: ESPAN

tag: cell line

tag: media

value: DMEM

value: Anti-H3K36me3 Antibody (Active Motif_61021)


title: 1_col-0_0h rep1

tag: genotype


title: contralateral sham injured astrocytes  a9_10_H_Con

description: contralateral sham injured astrocytes

value: Hippocampus

tag: cell type

value: Contra SHAM


title: 3_wrky6_2h rep2

tag: age


title: 3_wrky6_0h rep2


title: contralateral sham injured astrocytes  a9_9_H_Con

description: contralateral sham injured astrocytes

value: astrocytes

value: WT CD31 Sham


title: JA_T1_2D_6


title: JA_T1_2D_5


title: MCM2-2A scRNA-seq mouse tumor repeat 2

tag: chip antibody


title: Endo_Succeed_1


title: 3_tak-1_24h rep2

value: Tak1, WT


title: 3_tak-1_2h rep2


title: contralateral sham injured astrocytes  a8_15_H_Con

description: contralateral sham injured astrocytes

tag: treatment

value: 4 months post injury


title: contralateral sham injured astrocytes  a8_16_H_Con

description: contralateral sham injured astrocytes

tag: time


title: JA_T1_2D_3


title: JA_T1_2D_4


title: contralateral injured astrocytes PTE- a9_20_H_Con

description: contralateral injured astrocytes PTE-

value: Contra PTE-


title: MCM2-2A scRNA-seq mouse tumor repeat 1


title: 3_wrky12_0h rep2


title: contralateral sham injured astrocytes  a9_11_H_Con

description: contralateral sham injured astrocytes


title: MCM2-2A MCF-7 scRNA-seq


title: 3_wrky6_24h rep2


title: WT H3K36me3 espan

value: WT


title: contralateral injured astrocytes PTE- a9_16_H_Con

description: contralateral injured astrocytes PTE-

value: WT CD31 Injured


title: 3_wrky12_24h rep1


title: JA_T1_3D_1


title: JA_T1_2D_2


title: WT MCF-7 scRNA-seq


title: WT scRNA-seq mouse tumor repeat 2


title: JA_T1_2D_1


title: contralateral injured astrocytes PTE- a9_15_H_Con

description: contralateral injured astrocytes PTE-


title: 3_wrky12_2h rep1


title: WT scRNA-seq mouse tumor repeat 1


title: MCM2-2A MCF-7 RNA-seq repeat 2


title: contralateral injured astrocytes PTE- a9_14_H_Con

description: contralateral injured astrocytes PTE-


title: JA_T0_3D_6


title: MCM2-2A MCF-7 RNA-seq repeat 1


title: JA_T0_3D_5


title: WT MCF-7 RNA-seq repeat 2


title: contralateral injured astrocytes PTE- a9_12_H_Con

description: contralateral injured astrocytes PTE-


title: 3_wrky6_24h rep1


title: WT MCF-7 RNA-seq repeat 1


title: JA_T0_3D_3


title: 3_wrky6_0h rep1


title: MCM2-2A MCF-7 input ChIP-seq repeat 2


title: contralateral injured astrocytes PTE- a8_14_H_Con

description: contralateral injured astrocytes PTE-


title: JA_T0_3D_2


title: MCM2-2A MCF-7 input ChIP-seq repeat 1


title: 3_tak-1_24h rep1


title: 3_tak-1_2h rep1


title: contralateral injured astrocytes PTE- a8_13_H_Con

description: contralateral injured astrocytes PTE-


title: 3_tak-1_0h rep2


title: JA_T0_3D_1


title: contralateral injured astrocytes PTE- a8_11_H_Con

description: contralateral injured astrocytes PTE-


title: contralateral injured astrocytes PTE- a8_9_H_Con

description: contralateral injured astrocytes PTE-


title: 3_wrky12_0h rep1


title: JA_T0_2D_6


title: contralateral injured astrocytes PTE- a9_13_H_Con

description: contralateral injured astrocytes PTE-


title: JA_T0_2D_5


title: contralateral injured astrocytes PTE+ a9_19_H_Con

description: contralateral injured astrocytes PTE+

value: Contra PTE+


title: WT MCF-7 input ChIP-seq repeat 2


title: JA_T0_3D_4

value: JA


title: JA_T0_2D_4


title: 3_wrky6_2h rep1


title: 3_tak-1_0h rep1


title: MCM2-2A MCF-7 H3K36me2 ChIP-seq repeat 2

value: Anti-H3K36me2 Antibody (ab176921)


title: WT MCF-7 input ChIP-seq repeat 1


title: contralateral injured astrocytes PTE+ a9_18_H_Con

description: contralateral injured astrocytes PTE+


title: MCM2-2A MCF-7 H3K36me2 ChIP-seq repeat 1


title: RCMV_Mock_2

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description: polyA enrichment

data_processing:
Sequencing reads were aligned to the rn6 version of the rat genome using hisat2 (Kim et al, 2015) with standard parameters.
Reads were then quantified using quasR (Gaidatzis et al, 2015).
Assembly: rn6
Supplementary files format and content: tab-separated values

organism: Rattus norvegicus

source_name: spleen

growth_protocol: Sprague Dawley rats were bred at the animal facility of the Robert Koch Institute and sacrificed by an isoflurane overdose.

extract_protocol:
Cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: DCs were enriched from spleen homogenates using OX-62 (CD103) microbeads (Miltenyi Biotec), and RNA was either directly extracted after enrichment or 24h hours later following infection with wt/∆vXLC1/UV-irradiated rat CMV at an MOI of 3 or mock infection, as indicated.

value: Sprague Dawley rats

value: spleen

value: Dendritic cells

value: mock infection


title: RCMV_Mock_3

description: polyA enrichment


title: JA_T0_2D_3


title: RCMV_Mock_1

description: polyA enrichment


title: WT MCF-7 H3K36me2 ChIP-seq repeat 2

value: DMEM


title: contralateral injured astrocytes PTE+ a8_17_H_Con

description: contralateral injured astrocytes PTE+

value: Hippocampus


title: JA_T0_2D_2


title: JA_T0_2D_1


title: WT MCF-7 H3K36me2 ChIP-seq repeat 1


title: RCMV_Input_2

description: polyA enrichment


title: contralateral injured astrocytes PTE+ a8_10_H_Con

description: contralateral injured astrocytes PTE+


title: MCM2-2A MCF-7 EZH2 ChIP-seq repeat 2

value: Anti-EZH2 Antibody (CST_5246)


title: RCMV_Input_1

description: polyA enrichment


title: T2D-Bone marrow stroma

city: Phildelphia

first: Fanxin

last: Long

state: Pennsylvania

address: Civc center blvd 3501

institute: Children's Hospital of Philadelphia

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow and digested bone chips

extract_protocol:
For isolation of bone marrow mesenchymal cells, epiphyseal ends of both tibias and femurs were removed and the bone marrow cells were flushed out with M-199 (Thermo Fisher Scientific, USA) supplemented with 10% FBS (heat-inactivated Qualified FBS, Thermo Fisher Scientific, USA) and collected. The bone shaft was then cut into pieces and digested with 1 mg/mL STEMxyme1 (Worthington, Ref#LS004106) and 1 mg/mL Dispase II (ThermoFisher Scientific, Ref#17105041), in M-199 supplemented with 2% FBS for 25 min at 37°C. The digested cells and bone marrow cells were pooled together and passed through a 70mm filter. Cells were then stained in media 199 supplemented with 2% FBS for FACS. Bone marrow mesenchymal cells were enriched as the 7-AAD-/Calcein AM+/ CD71-/ Ter119-/ Lin (CD45/CD3/B220/CD19/Gr-1/CD11b)- fraction.
scRNA-seq libraries were constructed with bone marrow mesenchymal cells from T2D versus CTRL mice with the Single Cell 3’ Reagent Kits v3.1 (10x Genomics).

value: bone marrow stromal cells

value: bone marrow and digested bone chips

value: 22 weeks of age


title: MCM2-2A MCF-7 EZH2 ChIP-seq repeat 1

source_name: whole cell


title: Day6_Ezh2_uKO_3

source_name: mouse uterus

tag: no. of passages and ages of weeks

value: 7-12 weeks, day 6 of pregnancy


title: CB_T1_3D_5

value: CB


title: MC3(6) SAM24397657

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
GSNAP was used to align reads to GRCm38.
The HTSeqGenie Bioconductor package was used to count genes.
Gene models were obtained from an internal database.
Assembly: GRCm38
Supplementary files format and content: Tab-delimeted text files with raw counts, width, and rpkm normalized values for each gene.

source_name: Brain

extract_protocol:
Brain tissue was stored in RNALater. RNA was extracted using the RNeasy Mini QIAcube Kit with a QIACUBE workstation. RNA concentration and purity was determined using a NanoDrop, and purified RNA was stored at -80°C. 1000 ng of RNA per sample was used to prepare RNAseq libraries.
Truseq Stranded mRNA Kit (Illumina).

value: Brain


title: WT MCF-7 EZH2 ChIP-seq repeat 1

value: WT


title: WT MCF-7 EZH2 ChIP-seq repeat 2


title: CTRL-Bone marrow stroma

description: 10x Genomics


title: MC3(6) SAM24397656


title: CB_T1_3D_4


title: Day6_Ezh2_uKO_2

tag: genotype/treatment condition


title: CB_T1_3D_3


title: Day6_floxed_control_3

tag: background strain


title: contralateral injured astrocytes PTE+ a9_17_H_Con

description: contralateral injured astrocytes PTE+

value: astrocytes

value: WT CD31 Injured

value: Contra PTE+

value: 4 months post injury


title: CB_T1_3D_2

tag: timepoint


title: RCMV_Input_3

description: polyA enrichment

value: Sprague Dawley rats

value: spleen


title: MCM2-2A MCF-7 H3.3 CUT&Tag repeat 2

value: Anti-H3 Antibody (ab1791)


title: CB_T1_3D_1

tag: replicate


title: Saline SAM24397654

value: Saline


title: CB_T1_2D_6

tag: condition


title: Saline SAM24397653


title: CB_T1_3D_6

tag: pool


title: Day6_floxed_control_2


title: Day6_floxed_control_1


title: CB_T1_2D_5

tag: strain


title: Day6_Ezh2_uKO_1


title: WT MCF-7 H3.3 CUT&Tag repeat 2

value: DMEM


title: MCM2-2A MCF-7 H3.3 CUT&Tag repeat 1


title: WT MCF-7 H3.3 CUT&Tag repeat 1


title: Saline SAM24397652

tag: tissue


title: MCM2-2A MCF-7 RING1B CUT&Tag repeat 2

tag: cell line

value: Anti-RING1B Antibody (CST_5694)


title: Day4_Ezh2_uKO_2

value: 7-12 weeks, day 4 of pregnancy


title: CB_T1_2D_4


title: Day4_Ezh2_uKO_3


title: Saline SAM24397651


title: MC3(6) SAM24397655


title: MCM2-2A MCF-7 RING1B CUT&Tag repeat 1

tag: media


title: Day4_Ezh2_uKO_1


title: CB_T1_2D_2


title: TA2-MC3(6) (25 ug) SAM24397649


title: Saline SAM24397650


title: WT MCF-7 RING1B CUT&Tag repeat 2

tag: genotype


title: CB_T1_2D_1


title: TA2-MC3(6) (25 ug) SAM24397648


title: Day4_floxed_control_3


title: MCM2-2A MCF-7 SUZ12 CUT&Tag repeat 2

value: Anti-SUZ12 Antibody (CST_3737)


title: TA2-MC3(6) (25 ug) SAM24397647


title: CB_T0_3D_6


title: Day4_floxed_control_2


title: Day4_floxed_control_1


title: CB_T0_3D_5


title: CB_T1_2D_3


title: MCM2-2A MCF-7 SUZ12 CUT&Tag repeat 1


title: WT MCF-7 SUZ12 CUT&Tag repeat 2


title: TA2-MC3(6) (25 ug) SAM24397646


title: CB_T0_3D_4


title: TA2-MC3(6) (25 ug) SAM24397645


title: WT MCF-7 RING1B CUT&Tag repeat 1


title: CB_T0_3D_2


title: Salt2-2

city: Anyang

first: Pengtao

last: Li

address: Huanghe River Avenue

institute: Anyang Institute of Technology

data_processing:
Multiple alignments were separately conducted between the raw scRNA-seq data obtained from eight samples and the G. arboreum reference genome (Du et al., 2018) by Cell Ranger software pipeline v5.0.0 (10× Genomics), and a matrix of gene counts versus cells was produced from normalized aggregate data across samples
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Gossypium arboreum

source_name: Lateral root tips

extract_protocol:
Lateral root tips of 0.5–1-cm were cut into pieces with a sharp blade and placed in a six-well cell culture dish containing 10 mL zymolytic solution (1.5% cellulase R10, 1% pectolyase, 0.4 M mannitol, 0.1 M KCl, 0.08 M MES, 0.02 M CaCl2 and 0.1% BSA). Subsequently, vacuum treatment (0.05 MPa) was conducted under a dark environment for 1 h, and the enzymatic hydrolysis reaction lasted for about 6 h in a constant-temperature shaker with a gentle speed of 80 r/min at 25°C. A 40-μm cell strainer was used to filter the dissociated protoplasts. The protoplasts were collected by centrifugation and washed 2–4 times with WB buffer (0.1 M KCl, 0.08 M MES, 0.4 M mannitol and 0.1% BSA) on standby.
The 10× Genomics 3ʹ Single Cell Platform was adopted in this study to process the high-quality protoplasts according to the corresponding instructions, and single-cell gel beads in emulsions (GEMs) were generated by a microfluidic chip in different lanes, and the scRNA-seq library was then constructed using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics, Pleasanton, CA).

value: Lateral root tips

value: 100 mM NaCl for 1h


title: Salt3-2

value: 150 mM NaCl for 0.5h


title: WT MCF-7 SUZ12 CUT&Tag repeat 1


title: Control2

value: natural growth


title: CB_T0_3D_3

value: CB


title: CB_T0_3D_1


title: Salt1-2

value: 100 mM NaCl for 0.5h


title: MCM2-2A MCF-7 H3K36me3 CUT&Tag repeat 2

value: Anti-H3K36me3 Antibody (Active Motif_61021)


title: TA2 (25 ug) SAM24397642

value: Brain


title: Salt3-1


title: TA2 (25 ug) SAM24397644


title: TA2 (25 ug) SAM24397643


title: WT MCF-7 H3K36me3 CUT&Tag repeat 2

value: WT


title: TA2 (25 ug) SAM24397641


title: Salt2-1


title: WT MCF-7 H3K36me3 CUT&Tag repeat 1


title: Salt1-1


title: CB_T0_2D_5


title: TA2 (25 ug) SAM24397640


title: MCM2-2A MCF-7 H2AK119ub CUT&Tag repeat 2

value: Anti-H2AK119ub Antibody (CST_8240)


title: CB_T0_2D_4


title: GenVoy(1) SAM24397639


title: MCM2-2A MCF-7 H2AK119ub CUT&Tag repeat 1


title: CB_T0_2D_3


title: MCM2-2A MCF-7 H3K36me3 CUT&Tag repeat 1


title: CB_T0_2D_2


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #3 rep#2

city: Bethesda

first: Matthew

last: Chung

address: 50 South Dr

institute: NIAID (National Institute of Allergy and Infectious Diseases)

data_processing:
Library strategy: amplicon sequencing
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the miRNA-seq dataset, miRNA primary quantification was performed in the GeneGlobe Data Analysis Center (Qiagen) for trimming, mapping, and unique molecular indices (UMI) analysis. Although both miRNAs and piRNAs were detected in the small RNA libraries, only miRNAs were used in the downstream analyses.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment.
Genome_build: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary_files_format_and_content: For the RNA-seq and miRNA-seq datasets, a tab-delimited text file containing the raw gene or miRNA counts for all the samples was provided.

organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Whole lungs of DI222-treated IFNAR-/- IFNLR-/- mouse

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen).
Viral genomic RNA (vRNA) in the lung homogenate was amplified using multi-segment reverse-transcription PCR (M-RT-PCR) and then subject to Illumina library preparation with Nextera XT DNA library prep kit.

treatment_protocol: Mice were intranashally inoculated with 1,000 TCID50 units of PR8 virus and approximately 3,000,000 units of DI222 virus in 50µL PBS.

value: Lung

tag: mouse strain

value: IFNAR-/- IFNLR-/-

value: DI222 co-treatment


title: GenVoy(1) SAM24397638


title: GenVoy(1) SAM24397637


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #1 rep#2


title: CB_T0_2D_1


title: TA2-GenVoy(1) (25 ug) SAM24397636

value: TA2-GenVoy(1) (25 ug)


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #2 rep#2


title: MCM2-2A MCF-7 H3K4me1 CUT&Tag repeat 2

value: DMEM

value: Anti-H3K4me1 Antibody (CST_5326)


title: WT MCF-7 H2AK119ub CUT&Tag repeat 1


title: WT MCF-7 H2AK119ub CUT&Tag repeat 2


title: MCM2-2A MCF-7 H3K4me1 CUT&Tag repeat 1


title: TA2-GenVoy(1) (25 ug) SAM24397635


title: TA2-GenVoy(1) (25 ug) SAM24397634


title: CB_T0_2D_6


title: CA_T1_3D_6

value: CA


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #3 rep#2

source_name: Whole lungs of PR8-infected IFNAR-/- IFNLR-/- mouse

treatment_protocol: Mice were intranashally inoculated with 1,000 TCID50 units of PR8 virus in 50µL PBS.

value: PR8-only infection


title: CA_T1_3D_5

source_name: primary murine lung tumor organoids


title: WT MCF-7 H3K4me1 CUT&Tag repeat 2


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #2 rep#2


title: CA_T1_3D_4


title: TA2-GenVoy(1) (25 ug) SAM24397633


title: Control1

value: Lateral root tips


title: WT MCF-7 H3K4me1 CUT&Tag repeat 1


title: CA_T1_3D_3


title: TA2-GenVoy(1) (25 ug) SAM24397632


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #4 rep#2

source_name: Whole lungs of DI222-treated IFNLR-/- mouse

value: IFNLR-/-


title: TA2 (100 ug) SAM24397631


title: MCM2-2A MCF-7 H3K4me3 CUT&Tag repeat 2

value: Anti-H3K4me3 Antibody (Active Motif_39159)


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #3 rep#2


title: MCM2-2A MCF-7 H3K4me3 CUT&Tag repeat 1


title: CA_T1_3D_2


title: TA2 (100 ug) SAM24397630


title: WT MCF-7 H3K4me3 CUT&Tag repeat 2


title: CA_T1_3D_1


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #1 rep#2


title: WT MCF-7 H3K4me3 CUT&Tag repeat 1


title: CA_T1_2D_5

source_name: LKR10 cell line


title: TA2 (100 ug) SAM24397629


title: MCM2-2A MCF-7 H3K9me3 CUT&Tag repeat 2

value: Anti-H3K9me3 Antibody (ab8898)


title: CA_T1_2D_4


title: TA2 (100 ug) SAM24397627


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #1 rep#2


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #5 rep#2

source_name: Whole lungs of PR8-infected IFNLR-/- mouse


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #6 rep#2


title: TA2 (100 ug) SAM24397628


title: Emx2 KO utricles dissected 7

city: Salt Lake City

first: Shihai

last: Jia

state: ut

address: 20 South 2030 East, Room 320 BPRB

department: Department of Neurobiology

institute: University of Utah

data_processing:
mm10, M-musculus_Dec_2011, GRCm38 genome build alignment
DEseq2 and FDR analysis was used to identify differentially expressed transcripts
samples were compared using the Bioconductor DESeq package as well as by post hoc-analysis using Swish. Benjamini-Hirshberg false discover rate was used to normalize data across all transcripts and produce adjusted p-values for significantly downregulated or upregulated genes based on log2-fold changes compared to WT baseline transcript levels.

source_name: utricles

growth_protocol: embryonic tissue harvest at E18.5

extract_protocol:
4-6 utricles were combined per genotype to constitute one biological replicate, and 4 replicates were collected for each. Tissue was transferred to 350ul of RNeasy Lysis buffer (Qiagen 79216) Buffer RLT and lysed using the Qiagen Tissue Lyser LT at 20Hz with one stainless steel bead for 4min. Following centrifugation, supernatant was transferred to a clean tube and RNA isolated using the RNeasy Micro Kit (Qiagen 74004). DNA and RNA concentrations were determined using Qubit broad range DNA and RNA assay kits (Invitrogen Q32853 Q10211) and RNA quality evaluated using the Agilent 2200 TapeStation which returned RNA integrity numbers ranging from 8.3 to 9.1.
Libraries were generated at the Huntsman Cancer Institute Genomic Core facility using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold kits (Illumina 20020598)

value: utricles

tag: developmental stage

tag: cell type

value: tissue

value: Emx2 KO/KO


title: CA_T1_2D_2


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #3 rep#2

tag: treatment


title: Emx2 KO utricles dissected 6


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #2 rep#2


title: MCM2-2A MCF-7 H3K9me3 CUT&Tag repeat 1

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)
Library strategy: CUT&TAG

tag: chip antibody


title: CA_T1_2D_6


title: WT MCF-7 H3K9me3 CUT&Tag repeat 1

value: WT


title: CA_T1_2D_3


title: WT MCF-7 H3K9me3 CUT&Tag repeat 2


title: CA_T1_2D_1


title: Emx2 KO utricles dissected 5


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #2 rep#2


title: Emx2 KO utricles dissected 4


title: MCM2-2A MCF-7 H3K27ac CUT&Tag repeat 2

value: Anti-H3K27ac Antibody (CST_8173)


title: MCM2-2A MCF-7 H3K27ac CUT&Tag repeat 1


title: CA_T0_3D_5


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #1 rep#2

value: Lung


title: CA_T0_3D_6


title: CA_T0_3D_4


title: WT utricles dissected 3

value: Emx2 WT/WT


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #5 rep#2

source_name: Whole lungs of DI222-treated IFNAR-/- mouse

value: IFNAR-/-

value: DI222 co-treatment


title: WT utricles dissected 2


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #4 rep#2


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #4 rep#2


title: WT MCF-7 H3K27ac CUT&Tag repeat 2

value: DMEM


title: CA_T0_3D_3


title: WT MCF-7 H3K27ac CUT&Tag repeat 1


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #3 rep#2


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #2 rep#2


title: WT utricles dissected 1


title: MCM2-2A NPC 7D Sox1 CUT&RUN repeat 1

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)
Library strategy: CUT&Tag

source_name: MCM2-2A NPC

growth_protocol: Mouse embryonic stem cell (ESC) E14TG2a (kind gift from Bing Zhu lab, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China) were cultured on gelatin coated dishes in DMEM/F-12 (Gibco) supplemented with 15% (v/v) fetal bovine serum (Gibco), 1% penicillin/streptomycin (Gibco), 1 mM sodium pyruvate (Gibco), 2 mM GlutaMAX (Gibco), 1% MEM nonessential amino acids (Gibco), 55 μM β-mercaptoethanol (Sigma-Aldrich), and 10 ng/ml mouse leukemia inhibitory factor (Millipore) in a 37°C incubator with a humidified, 5% CO2 atmosphere. Cells were passaged using Trypsin-EDTA (Gibco) and routinely tested for mycoplasma contamination. ESCs were differentiated into Neuronal precursor cell (NPC) as previous described with modifications3. Briefly, ESCs were grown on gelatin coated dishes in N2B27 medium that 1:1 mixed of DMEM/F-12 (Gibco) and Neurobasal media (Gibco) and supplemented with 2 mM GlutaMAX (Gibco), 100 μM β-mercaptoethanol (Sigma-Aldrich), 1× N-2 and 0.5× B-27 supplements (Gibco). After 7 days, ESCs were re-plated in suspension using nonadherent plates to promote the formation of cellular aggregates for 3 additional days. Cellular aggregates were harvested and plated on gelatin coated dishes in N2B27 medium supplemented with 10 ng/ml EGF and FGF, respectively. The aggregates will attach and NPCs will grow out of the attached aggregates on differentiation day 11. Medium was changed every 2 days without exposing the NPC culture to air and passaged using Accutase (Sigma-Aldrich).

extract_protocol:
CUT&Tag was performed as previously reported with modifications4,5. Cells (1-2×105) were washed twice in 1 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1×Protease inhibitor cocktail) at room temperature. Concanavalin-coated magnetic beads (Bangs Laboratories) were washed twice in 1 mL Binding Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were resuspended in 1 mL Wash Buffer and incubated with 10 μL pre-washed Concanavalin-coated magnetic beads at room temperature for 15 min. Beads (bound to cells) were incubated in Antibody Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells, 2 mM EDTA, 0.1% BSA, 1:100 dilution of the appropriate primary antibody) on a rotating platform overnight at 4°C. Prepare mixture of 1 μg appropriate secondary antibody (Table S1) and pAG-Tn5 adapter complex (Novoprotein) at 1:2 molar ratio at room temperature for 1 hour. Beads were washed once with 1 mL Dig-wash Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells) and nutated in 100 μL Dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1×Protease inhibitor cocktail, 0.01% Digitonin) added the secondary antibody bound pAG-Tn5 complex at room temperature for 1 hour. Beads were washed 3 times with 1 mL Dig-300 buffer and resuspended in Tagmentation Buffer (Dig-300 buffer, 10 mM MgCl2) at 37°C for 1 hour. Beads were washed once with 1 mL TAPS Wash Buffer (10mM TAPS, pH 7.5, 0.4 mM EDTA) and incubated in 250 µL Dig-300 buffer containing 15 mM EDTA, 0.1% SDS and 100 µg/mL Proteinase K at 37°C for 1 hour with shaking of 900rpm. Then CUT&Tag DNA was extracted by phenol-chloroform-isoamyl alcohol and purified again by DNA Clean & Concentrator-5 Kit (Zymo Research) to 20 µL EB buffer. CUT&Tag DNA was Incubated by RNase A (1/400) at 37°C for 10 min. To amplify libraries, 10 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, and 12 μL NEBNext 2× PCR mix, and run the following cycling conditions with lid heat on: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 10 s; final extension at 72 °C for 1 min and hold at 10 °C. Post-PCR clean-up was performed by adding 1× volume of Ampure XP beads (24 μL) (Beckman Counter), and libraries were incubated with beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer. The libraries were used for paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq Xten platform by Annoroad Gene Technology Co. Ltd.
RNA-seq library preparation and deep sequencing were performed by Annoroad Gene Technology Co. Ltd.. Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit (10x Genomics).

value: MCM2-2A NPC

value: DMEM/F12：Neurobasal 1：1+N2+B27

value: Ant-Sox1 Antibody(CST_4194)


title: CA_T0_2D_6

value: CA


title: CA_T0_3D_2


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #1 rep#2


title: WT MCF-7 H3K27me3 CUT&Tag repeat 2

extract_protocol:
CUT&Tag was performed as previously reported(Kaya-Okur HS et al., 2019)
CUT&Tag library PCR amplification was performed with NEBNext 2× PCR Master Mix and standard Illumina Nextera indexing primers. The libraries were purified with Ampure XP beads at a ratio of 1:1. ChIP-seq libraries were prepared from 10 ng EZH2 ChIP, 100 ng H3K36me2 ChIP and input DNA using the KAPA Hyper prep kit (KAPA).

value: Anti-H3K27me3 Antibody (CST_9733)


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #5 rep#2

source_name: Whole lungs of PR8-infected IFNAR-/- mouse

value: PR8-only infection


title: CA_T0_3D_1


title: WT NPC 7D Sox1 CUT&RUN repeat 1

source_name: WT NPC

value: WT NPC


title: WT NPC 3D Sox1 CUT&RUN repeat 1


title: CA_T0_2D_5


title: MCM2-2A NPC 3D Sox1 CUT&RUN repeat 1


title: MCM2-2A NPC 7D Olig2 CUT&RUN repeat 1

value: Ant-Olig2 Antibody(Proteintech_133999)


title: MCM2-2A MCF-7 H3K27me3 CUT&Tag repeat 1


title: MCM2-2A MCF-7 H3K27me3 CUT&Tag repeat 2


title: WT MCF-7 H3K27me3 CUT&Tag repeat 1


title: CA_T0_2D_4


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #4 rep#2


title: MCM2-2A MCF-7 ATAC-seq repeat 2

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #2 rep#2


title: WT NPC 7D Olig2 CUT&RUN repeat 1


title: MCM2-2A MCF-7 ATAC-seq repeat 1


title: CA_T0_2D_3


title: WT MCF-7 ATAC-seq repeat 2


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #3 rep#2


title: CA_T0_2D_2


title: MCM2-2A NPC 3D Olig2 CUT&RUN repeat 1


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #1 rep#2


title: CA_T0_2D_1


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #3 rep#1

value: IFNAR-/- IFNLR-/-


title: WT NPC 3D Olig2 CUT&RUN repeat 1


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #2 rep#1


title: A549.siUHRF1.3

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence  then mapped to hg38 genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf from genecode
Sequences were imported into R , scaled, filter for low counts and  TMM normalized using the edgeR package.
log2 cpm, prior.count=1
Assembly: hg38
Supplementary files format and content: single tab delimited file containing   log2 cpm: genes as rows and one sample per column

growth_protocol: Cells were cultured in RPMI medium with 10% serum and passaged twice per week (1:10 for A549, 1:6 for H358).

extract_protocol:
72h post transfection total RNA was extracted using the AllPrep kit (Qiagen) following manufacturer's instructions.
Libraries  created with TruSeq Stranded mRNA kit (Illumina, RS-122-2101) following manufacturer's instructions and sequenced on an Novaseq

treatment_protocol: Cells were seeded into 6-well plates and 24h later transfected with siRNA (10nM) using Lipofectamine RNAiMAX (following manufacturer's instructions for forward transfection).

tag: sirna

tag: lineage

value: Adenocarcinoma

tag: mutation

value: KRAS p.Gly12Ser


title: WT MCF-7 ATAC-seq repeat 1

value: WT


title: A549.siUHRF1.1


title: WT ESC Sox2 CUT&RUN repeat 3

source_name: WT ESC

value: WT ESC

value: Ant-Sox2 Antibody(Abcam_ab92494)


title: MCM2-2A ESC Sox2 CUT&RUN repeat 2

source_name: MCM2-2A ESC

value: MCM2-2A ESC


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #3 rep#1

value: Lung


title: melanoma cells untreated rep5

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
The final libraries for single-read sequencing of 101 base pairs was carried out on an Illumina HiSeq2000. Reads quality was evaluated using FastQC (version 0.11.2, Babraham Institute Cambridge, UK) tool and will be trimmed using TrimGalore software to remove adapter and low-quality bases (Q< 20).
Then reads were mapped to the human Ensembl GRCh38 build reference genome using STAR version 2.5.0a using Gene annotations corresponding to the Ensembl annotation release 99, which was used to build a transcriptome index and provided to STAR during the alignment.
Subsequently, the transcript data normalization and differential gene expression analysis were performed using Bioconductor R package RUVSeq version 1.28 and edgeR version 3.36
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Cutaneous metastasis

extract_protocol:
Total RNA was extracted from purified cell pellets using Qiagen RNeasy Plus.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.

value: Cutaneous metastasis

value: primary melanoma cells

value: metastatic melanoma

value: BRAF WT

value: untreated


title: melanoma cells untreated rep6


title: MCM2-2A ESC Sox2 CUT&RUN repeat 3


title: A549.siKRAS.2

value: siKRAS


title: A549.siUHRF1.2


title: melanoma cells, romidepsin-INF (RI), rep4

value: romidepsin-IFN


title: A549.siKRAS.1


title: melanoma cells untreated rep4


title: melanoma cells, romidepsin-INF (RI), rep6


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #2 rep#1

value: PR8-only infection


title: A549.siKRAS.3


title: MCM2-2A ESC Repli-ATAC-seq 2h repeat 2

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)


title: A549.siNeg.3

value: siNeg


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #1 rep#1

value: IFNAR-/- IFNLR-/-

value: DI222 co-treatment


title: melanoma cells, romidepsin-INF (RI), rep3

value: BRAF V600R


title: MCM2-2A ESC Repli-ATAC-seq 2h repeat 1


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #4 rep#1

value: IFNLR-/-


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #1 rep#1


title: melanoma cells, romidepsin-INF (RI), rep5


title: WT ESC Sox2 CUT&RUN repeat 2

value: WT ESC


title: melanoma cells untreated rep3


title: WT ESC Repli-ATAC-seq 2h


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #3 rep#1


title: A549.siNeg.2

value: Adenocarcinoma

value: KRAS p.Gly12Ser


title: MCM2-2A ESC Repli-ATAC-seq 0h repeat 2

value: MCM2-2A ESC


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #2 rep#1

value: Lung


title: MCM2-2A ESC Repli-ATAC-seq 0h repeat 1


title: Viral genome sequencing dataset: DI222-treated IFNLR-/- mouse #1 rep#1


title: melanoma cells, romidepsin-INF (RI), rep2

value: Cutaneous metastasis

value: primary melanoma cells

value: BRAF V600E


title: WT ESC Repli-ATAC-seq 0h


title: H358.siUHRF1.3

value: KRAS p.Gly12Cys


title: melanoma cells untreated rep2

value: metastatic melanoma

value: untreated


title: melanoma cells untreated rep1


title: H358.siUHRF1.1


title: H358.siUHRF1.2


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #5 rep#1

value: PR8-only infection


title: melanoma cells, romidepsin-INF (RI), rep1

value: romidepsin-IFN


title: MCM2-2A ESC ATAC-seq repeat 3


title: MCM2-2A ESC ATAC-seq repeat 2


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #4 rep#1


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #6 rep#1


title: H358.siKRAS.3

value: siKRAS


title: Glioblastoma OE SRPK1 cells, rep2

city: Campinas

first: Pedro

last: Cruz

address: Av Candido Rondon 400

country: Brazil

institute: UNICAMP

data_processing:
Sequence quality was assessed by fastQC software.
Sequenced reads were trimmed for adaptor sequence, exogeneous RNA, rRNA, and masked for low-complexity or low-quality sequence using Trimmomatic and SortmeRNA
Reads were aligned to the hg38 genome assembly using STAR v2.5.3.

growth_protocol: Human glioblastoma (GBM) cells T98G (ATCC, Manassas, VA, USA)  and A178 (shared by Dr. Roger Frigério Castilho, FCM/UNICAMP) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Invitrogen, Carlsbad, CA, USA) at 37°C with 5% CO2 in a humidified incubator. Transient transfection for overexpression and shRNA in GBM cells was performed in 6-well plates using Lipofectamine 2000 (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions.

extract_protocol:
Total RNA for RNA-seq and RT–PCR was extracted using a PureLink RNA Mini Kit (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions.
The quality of the RNA was assessed by a Bioanalyzer (Agilent Technology, Santa Clara, CA, USA). For library preparation, only samples that presented RNA integrity greater than 8 were selected. mRNA was isolated using poly(A) selection. The mRNA-seq library was prepared following the standard protocol by Illumina, and the sequencing was processed as 101 bp paired-end RNA-seq by the LACTAD facility (UNICAMP, Campinas, BR) using the HiSeq 2000 Sequencing System (Illumina, San Diego, CA, USA).
RNA-seq was performed in duplicate. Approximately 26 million reads were obtained for each sample.

treatment_protocol: The shRNA sequences were cloned into a pLKO.1 plasmid (Addgene, Wathertown, MA, USA), The cDNA used for full-length cloning and overexpression of SRPK1, SRPK2, and CLK1 was obtained from GBM T98G and reverse transcribed using Superscript III Reverse Transcriptase (ThermoFisher Scientific, Waltham, MA, USA) with oligodT and was amplified by Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific, Waltham, MA, USA). The full-length sequences corresponding to the kinases were cloned into the pcDNA3.1 plasmid (Addgene, Wathertown, MA, USA).

value: Glioblastoma multiforme

value: SRPK1 over expression

tag: transfection

value: transient


title: MCM2-2A ESC ATAC-seq repeat 1

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #3 rep#1

value: IFNLR-/-


title: Glioblastoma OE SRPK1 cells, rep1


title: A549.siNeg.1

value: siNeg

value: Adenocarcinoma


title: WT ESC ATAC-seq repeat 3

value: WT ESC


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #2 rep#1

value: Lung


title: Viral genome sequencing dataset: PR8-infected IFNLR-/- mouse #1 rep#1


title: H358.siNeg.3


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #5 rep#1

value: IFNAR-/-

value: DI222 co-treatment


title: H358.siNeg.2


title: Glioblastoma shRNA SRPK1 cells, rep1

value: SRPK1 shRNA knockdown


title: WT ESC ATAC-seq repeat 1