title: t(7;12) HSPC_rep1_cellline36

description: NlaIII/Csp6I, vp coordinate chr7:156803000

data_processing:
4C-fastq single read data was processed using the pipe4C platform as described (PMID: 31351925).
Reads were aligned using bowtie2, version 2.3.5.1. (PMID: 22388286) and samtools 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Final processing was done under R3.6.2 using the pipe4C script with default parameters. Reads mapped to the 4C fragment end library were normalized according to the default normalizeFactor 1000000. 3′-ends of sequences were trimmed using a sliding window (size 21) as soon as 2 out of 5 nucleotides had a quality encoding less than the default Q-score. The quality cutoff and trimlength were 0, the minimum amount of reads was 1000. NonBlind and mapUnique were set to FALSE.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: 4C-Seq

extract_protocol:
Circular chromosome conformation capture (4C) was done essentially as described (PMID: 22961246) using two million cells and two rounds of restriction digestion with either HindIII and DpnII, or with NlaIII and Csp6I, depending on the viewpoint, each time followed by ligation.
First PCR 98°C for 30 sec, 10 cycles with 98°C for 15 sec, 61°C, 60°C or 54°C depending on the viewpoint for 20 sec with 0.5°C touch-down per cycle, 72°C for 2 min, then 30 or 25 cycles with 98°C for 15 sec, 56°C, 55°C or 49°C, depending on the viewpoint  for 20 sec, 72°C for 2 min, finally followed by 72°C for 1 min. Second PCR with 95°C, 3 min (initial melting) and 95°C, 20 sec, 62°C, 15 sec, 72°C, 40 sec (8 cycles).
4C sequencing libraries were generated in two PCR steps. In the first step, the  second ligation products, inverse primers and Q5 high fidelity enzyme were used. Libraries were generated in the second step with DNA from the first step essentially according to (PMID: 29224141) under real-time conditions.

value: translocation t(7;12)


title: THP1_IL6_48h

status: Public on Aug 21 2024

type: SRA

city: Sendai

first: Takuya

last: Saito

state: Miyagi

address: 1-1 Seiryomachi, Aobaku

department: Department of Respiratory Medicine

country: Japan

institute: Tohoku University Graduate School of Medicine

library_source: transcriptomic

data_processing:
The FASTQ reads of each sample were aligned to the GENCODE human reference genome GRCh38, and the expression levels for each gene were calculated.
The calculated gene expression data were incorporated into Subio Platform (Subio inc., Japan) and analyzed with Basic and Advanced Plug-ins.
Assembly: hg38
Supplementary files format and content: Text files include normalized processed signals for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
total RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Total RNA was subjected to amplification with the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (CloneTech). A cDNA library was prepared with the Nextera XT DNA Library Prep Kit (illumina) and analyzed on NovaSeq 6000 (illumina).

tag: cell line

tag: agent

tag: time point


title: HSPC_rep1_cellline36

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

library_source: genomic

molecule: genomic DNA

source_name: HSPC

growth_protocol: Cell line ChiPSC22 and its t(7;12) derivatives were grown in the feeder free DEF-CS culture system (Cellartis/Takara Bio Europe) under standard conditions.

treatment_protocol: Before differentiation of CHIPSC22 and its t(7;12) derivatives to HSPCs, they were transferred to Matrigel (BD Biosciences, Stockholm, Sweden) and mTeSR1 medium (StemCell Technologies Inc., Grenoble, France) for 2-3 passages. They were then grown for 3-4 passages as clusters using Gentle Cell Dissociation Reagent (Stemcell Technologies Inc.). The STEMdiff Hematopoietic kit (Stemcell Technologies Inc.) was used for the differentiations according to the protocol. On day 12 of the differentiation, the hematopoietic cells were harvested and analyzed by ATAC-seq.

tag: tissue

value: HSPC

tag: cell type


title: K14 CTRL 1

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adaptor sequences were removed with Trimmomatic PE using options ‘HEADCROP:10 CROP:70 ILLUMINACLIP: adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50’.
ATAC–seq paired-end reads were then aligned to mouse reference genome mm10 using Bowtie2 (v.2.3.4.2) using options ‘‘-X 2000 -q -p 6 -t –fr –very-sensitive –no-discordant –no-unal –no-mixed’.
Mitochondrial reads, reads from unmapped or random counting and reads with a mapping quality <20 was removed using SAM tools.
Duplicate reads were removed by Picard MarkDuplicates module.
Peak calling was performed on each individual sample by MACS2 (v.2.1.0.20151222) using options ‘-f BAMPE -g mm -q 0.01 –nomodel –shift 0.
Peaks from the different subpopulations were merged for downstream analysis
Reads counts of each merged peak for each individual sample were calculated by HTSeq-count using options ‘-f bam -r pos -m intersection-nonempty’.
These counts were normalized for one million mapped reads in merged peaks and fold-change was calculated compared to control.
Peaks were associated to genes with GREAT software (v4.0.4) with the following parameters: 5.0 kb in proximal upstream, 1.0 kb in proximal downstream and 100.0 kb in distal.
Assembly: mm10
Supplementary files format and content: .csv / normalized peak intensity

organism: Mus musculus

source_name: Skin epidermis

extract_protocol:
For ATAC-seq, 50000 sorted basal cells (α6High/CD34-/Lrig1-/YFP+/GFP+/RFP+) were collected in 1 ml PBS supplemented with 3% FBS at 4 °C. Cells were centrifuged and cell pellets were resuspended in 100 μl lysis buffer (TrisHCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0.1%) and centrifuged at 500g for 25 min at 4 °C. Supernatant was carefully discarded and nuclei were resuspended in 50 μl reaction buffer (Tn5 transposase 2.5 μl, TD buffer 22.5 μl, from Nextera DNA sample preparation kit, Illumina, and 25 μl H20). The reaction was performed at 37 °C for 30 min and was stopped by adding 5 μl clean up buffer (NaCl 900 mM, EDTA 300 mM). DNA was purified using the MiniElute purification kit (QIAGEN) following the manufacturer’s protocol.
DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800 bp (BluePippin, Sage Sciences), following the manufacturer’s recommendations.

value: Skin epidermis

value: Epithelial

tag: genotype

value: WT


title: THP1_IL6_24h


title: t(7;12) iPSC_rep1_cellline35

source_name: iPSC

value: iPSC


title: iPSC_rep1_cellline35


title: t(7;12) HSPC_rep2_cellline10

description: HindIII/DpnII, vp coordinate chr7:156806000


title: THP1_IL6_6h


title: K14-CTR-K14-Exp-Lrig1-Exp

description: Multiplexed 10X sequencing composed of WT(K14_CTL), basal lineage ablation with K14 tracing(K14_Exp) and basal lineage ablation with Lrig1 tracing(Lrig1_Exp).

library_source: transcriptomic single cell

data_processing:
Demultiplexing of samples from the raw datasets are done by CellRanger (v6.1.1) with multi module.
Sequencing reads were aligned and annotated with the mm10-2020-A reference dataset as provided by 10X and CellRanger with default parameters.
Further downstream analyses were carried out individually for each of the three samples (K14CTL, K14Exp, Lrig1Exp).
Quality control and downstream analysis were performed on R (version 4.1.0), using the Seurat R package (v.4.1.0)
For each sample, all the cells passed the following criteria: showed expression of more than 1500 and less than 6000 unique genes and had less than 10% UMI counts belonging to mitochondrial sequences.
Read counts were normalized by NormalizeData function of Seurat, with parameter ‘normalization.method = "LogNormalize" and scale.factor=10000’.
A PCA for each sample was calculated using the scaled expression data of the most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes).
UMAP calculation and graph-based clustering were done for each sample using the appropriate functions from Seurat (default parameters) with the respective PCA results as input.
The clusters expressing fibroblast markers (Vim, Fn1, Ctsk) and immune-related genes (Cd74, Cxcl2, Cxcl4, Fcer1g) are excluded and dimensionality has been recalculated.
Assembly: mm10-2020-A
Supplementary files format and content: .tsv.gz / cell barcode and features
Supplementary files format and content: .mtx.gz / count matrix

extract_protocol:
We sorted α6High/CD34-/Lrig1-/YFP+/GFP+/RFP+ for K14 CTRL and K14 Exp mice and for Lrig1 Exp we sort α6High/CD34-/Lrig1+/RFP+ cells. Total10,000 cells were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment.
The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics).


title: Lrig1 Abl 2

data_processing:
The adaptor sequences and low-quality regions were trimmed by Trimmomatic PE (paired-end mode).
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments for each sample.
Duplicated reads are suppressed by picard (http://broadinstitute.github.io/picard/)  MarkDuplicates.
After transcripts assembling, gene level counts were obtained using Htseq-count (v.0.11.1) and normalized to 20 million of aligned reads.
Average expression for each gene for the different populations was computed based on at least 2 biological replicates and fold changes were calculated between the subpopulations.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .csv / normalized gene expression

molecule: polyA RNA

extract_protocol:
FACS isolated cells were collected into 350µl of lysis buffer (RLT buffer, RNeasy Microkit, Qiagen) supplemented with β-mercaptoethanol. RNA extraction was then carried out using RNeasy Micro kit (QIAGEN) according to the manufacturer’s recommendations. Prior to sequencing, the quality of RNA was evaluated by Bioanalyzer 2100 (Agilent).
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: Basal lineage ablation


title: TOP1cc-seq WT Input rep1

city: Chicago

first: Mannan

last: Bhola

state: IL

address: 303 E Superior St

department: BMG

country: USA

institute: Northwestern university

description: CHIP-seq / TOP1cc-seq

data_processing:
The quality control of raw data was evaluated with FastQC and MultiQC (Ewels et al., 2016b).Trimgalore was used to filter out low quality reads (with a phred score threshold of 30) and adapter sequences.
The samples were aligned using Bowtiev2.4.5 to GRCh38 (+major SNVs). Only reads with high mapping quality were considered using a MAPQ threshold of 10 in Samtools v1.6. The BAM files were further deduplicated using Samtools.
The samples were also aligned to Drosophila melanogaster genome (BDGP6) using Bowtie2 for spike-in normalization.
Deeptools v3.5.1 (Ramirez et al., 2014) was used to generate normalized bigwig files, heatmap, and profile plots. The bins per million mapped normalized reads were used and the log2 ratio between the IP over the Input was calculated. The bigwig files were visualized in IGV (Thorvaldsdottir et al., 2013).
Assembly: GRCh38
processed data files format and content: BigWig

growth_protocol: TOP1 knockdown Human SW480 cells were grown at 37°C, supplied with 5% CO₂ in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 10% FBS and 1.5 mg/mL puromycin

extract_protocol:
Cell resuspensions were next dounced ten times in a prechilled glass homogenizer. Nuclei were collected and resuspended in shearing buffer (0.1% SDS, 0.5% N-lauroylsarcosine, 1% Triton X-100, 10 mM Tris-HCl pH 8.1, 100 mM NaCl, 1 mM EDTA, 1 mM PMSF, PICs) and incubated on ice for 30 min. Chromatin was fragmented using an E220 Focused-Ultrasonicator (Covaris) to an average size of 200-600 bp.
The eluted DNA was quantified with a Qubit 4.0 fluorometer, and 10 ng of DNA was used to prepare the sequencing libraries using KAPA Hyper Prep Kit according to the manufacturer’s instructions. Briefly, purified DNA was subjected to end-repair, adaptor ligation followed by indexed PCR. Libraries were size selected for average size of 300 bp. The sequencing was done using Illumina NovaSeq 6000 with a read length configuration of 150 PE for 50 M PE reads per sample (25M in each direction).

treatment_protocol: SW480 cells transiently expressing EV, GFP-FLAG-TOP1 WT or GFP-FLAG-TOP1 RBR were treated with 10 mM CPT for 4 min followed by immediate washing with ice-cold 1X PBS, scraped, and resuspended in lysis buffer (20 mM Tris-HCl pH 7.5, 300 mM NaCl, 2 mM EDTA, 0.5% NP40, 1% Triton X-100, 1 mM PMSF, PICs), and incubated on ice for 30 min.

value: Colorectal Cancer Cell

tag: chip antibody


title: THP1_ctrl_48h

value: ctrl


title: t(7;12) HSPC_rep1_cellline10


title: t(7;12) iPSC_rep2_cellline09


title: t(7;12) iPSC_rep1_cellline09


title: Lrig1 CTRL 2


title: THP1_ctrl_24h


title: Lrig1 Abl 1


title: iPSC_rep1_cellline09


title: wt_HSPC_3

data_processing:
TrimGalore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was deployed together with Cutadapt v. 1.14 (https://cutadapt.readthedocs.io/en/stable/) using the non-default parameters “--paired”, “--nextera”, “--length_1 35”, and “--length_2 35” to perform adapter and quality trimming.
Bowtie2 v. 2.2.6 (PMID: 22388286) was used with the “--very-sensitive” flag and a maximum insertion length of 2500 bp to map trimmed reads against the GRCh37/hg19 reference genome.
Aligned reads belonging to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).  PCR duplicates were removed by means of Picard MarkDuplicates v. 2.17.4 (https://broadinstitute.github.io/picard/).
Discordant mappings and alignments with a Phred score below 20 were removed using SAMtools view.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)

extract_protocol:
Cell permeabilization of native cells and tagmentation reaction with a Tn5 transposome for "Assay for transposase-accessible chromatin by sequencing (ATAC-seq)" according to Corces et al. (PMID: 28846090). Tagmented DNA was purified with HighPrep beads (Biozym) after guanidinium-mediated inactivation of the transposome according to Weichenhan et al. (PMID: 29224141).
Libraries were prepared according to Weichenhan et al. (PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.
Assay for transposase-accessible chromatin by sequencing (ATAC-seq)

value: wt


title: THP1_ctrl_6h


title: wt_iPSC_2


title: wt_HSPC_2


title: K14 Abl 2


title: Lrig1 CTRL 1


title: IL6Rneg_mono_3

source_name: lung

value: lung

value: CD14+IL-6R- monocyte


title: wt_HSPC_1


title: IL6Rhi_mono_3

value: CD14+IL-6Rhi monocyte


title: wt_iPSC_1


title: translocation_HSPC_3


title: translocation_iPSC_3


title: K14 CTRL 2


title: HSPC_rep1_cellline10


title: IL6Rhi_mono_2


title: translocation_HSPC_1


title: K14 CTRL 1


title: translocation_iPSC_2


title: IL6Rneg_mono_1


title: wt_iPSC_3


title: translocation_iPSC_1


title: KO_CTX3

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
STAR (v2.7.10a) was used for sequence alignments to mouse genome (GRCm38). Genes with zero expression in all samples were removed and DESeq2 (alpha = 0.05 and Independent Filtering feature= T) was used to obtain differentially expressed genes. Gene-set enrichment analysis was performed on Hallmark. Collection using fgsea package.
Assembly: GRCm38
Supplementary files format and content: raw counts

source_name: Prostate

growth_protocol: Ptenpc−/− and F10fl/fl; LysM-Cre mice were maintained under specific pathogen-free conditions.

extract_protocol:
Mouse prostate tumor tissues were quickly excised and homogenized for RNA extraction. RNA was extracted using TRIzol RNA isolation reagent (Invitrogen, Cat n=15596026), followed by RNase-Free DNase set (Qiagen, Cat n=79254) treatment, following manufacturers’ guidelines. RNA integrity was checked with Agilent 2100 Bioanalyzer system.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (New England BioLabs Inc) and NEBNext poly (A) mRNA magnetic isolation module (New England BioLabs Inc) were used for cDNA synthesis. The libraries were sequenced using the NextSeq 2000 and P2 kit High (100 cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

treatment_protocol: Bone marrow reconstitution with F10fl/fl precursors was performed on 6-week-old Ptenpc−/− mice. Recipient Ptenpc-/- mice were lethally irradiated (900 rad) and transplanted i.v. two hours later with 1 x 107 viable bone marrow cells from either F10fl/fl; LysM-Cre+ or F10fl/fl; LysM-Cre –mice. Bone marrow were flushed under sterile conditions with PBS using a 21-gauge needle. Red blood cells were removed by using ACK lysing buffer (Gibco; A1049201) and cell suspensions were filtered and checked for viability using trypan blue. Surgical castration was performed on 8-week-old Ptenpc-/- mice under anesthesia with isoflurane. Prostate tumors were resected 16 weeks after surgical castration.

value: Prostate

tag: treatment

value: F10fl/fl; LysM-Cre+; Ptenpc-/- mouse


title: K14 Abl 1


title: Granulosa cells, SFRP4-3

city: Saint-Hyacinthe

first: Michael

last: Bérubé

state: QC

address: 3200, Sicotte street

country: Canada

institute: University of Montreal

data_processing:
Fastq data was processed using the GenPipes v.3.1.2 pipeline.
Briefly, raw reads were quality and adaptor trimmed using Trimmomatic, then aligned to the mm10 (mouse) reference genome using the STAR aligner.
Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1.
PCR duplicates and fragments with poor mapping quality (q < 255) were filtered out.
Gene transcription levels was quantitated over annotated Ensembl genes, and differential gene expression was measured between the control and SFRP4 condition using DESeq2 (corrected p-value < 0.05, LOG2 fold-change > 2)
Assembly: mm10 (mouse) reference genome
Supplementary files format and content: bw

source_name: Ovary

growth_protocol: Granulosa cells were cultured in MEM containing 1% fetal bovine serum, 0.25 nM sodium pyruvate, and 3 mM L-glutamate. GCs were seeded in 96-well culture plates (each well receiving the granulosa cells isolated from 0.5 ovary) and incubated for 3h at 37ºC in 5% CO2/95% air. Culture medium was then replaced with serum-free medium for 2h before the treatments

extract_protocol:
RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
250 ng RNA was used for ribosomal RNA depletion using the NEBNext rRNA Depletion Kit (Cat# E6310X) according to the manufacturer’s instructions.
Double-stranded cDNA was then synthesized using the NEBNext Ultra II RNA First Strand Synthesis (Cat# E7771) and the NEBNext Ultra II Directional RNA Second Strand Synthesis (Cat# E7550L) modules.
Libraries were constructed using NEBNext Ultra II End Repair/dA-Tailing (Cat# E7546L) and NEBNext Ultra II Ligation (Cat# E7595L) modules.
Each library was amplified for 9 PCR cycles using NEBNext High-Fidelity 2X PCR Master Mix (Cat# M0541L) and NEBNext Multiplex Oligos for Illumina (UDI) (Cat# E6440S)

treatment_protocol: Treated (or not) with exogenous SFRP4 during 3h

value: Ovary

value: Primary culture

value: Granulosa cells


title: IL6Rhi_mono_1


title: Granulosa cells, SFRP4-2


title: IL6Rneg_mono_2


title: WT_CTX3

value: F10fl/fl; Ptenpc-/- mouse


title: HeLa cells, PINX1-KO_PINX1, IP, rep2

city: Shanghai

first: Mei

last: Huang

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Novaseq output
The ChIP-seq reads were trimmed using Cutadapt (version 1.9.1), which involved removing adapter sequences, cutting off bases with a quality score below 20 or containing 'N's at the ends, and discarding any reads that were reduced to less than 75 base pairs in length.
ChIP-seq reads were aligned to the UCSC hg38 genome using bowtie2(Version: 2.2.6).To create ChIP-seq coverage plots, the locations of the mapped ChlP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format
Peaks were called using MACS2 with the significance cut-off p-value <= 0.001. Different peak analysis: Combine the peaks of two different experimental groups with bedtools (version, 2.25.0) software, and then readcounts are counted in the combined peaks area. Difference analysis was performed using edgeR (V3.4.6) of the Bioconductor software package.
Merging peaks: To find the common and unique peaks of several groups, HOMER(V2) toolkit is used to treat the peaks with 200bp overlapping peaks as common and vice versa.
Assembly: GRCh38.p14
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: HeLa

extract_protocol:
Two biological replicates were prepared for each condition. Cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 minutes at room temperature, and quenched in 125 mM glycine in PBS for 5 minutes. Cells were washed twice with ice-cold PBS and collected by centrifugation at 5,000 × g for 5 minutes, then sonicated in nuclei lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, 1× protease inhibitor cocktail) with Bioruptor Plus (Diagenode) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation at 20,000 × g for 10 minutes at 4℃ and diluted 10-fold in dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, 16.7 mM Tris-HCl pH 7.9, 1× protease inhibitor cocktail), and pre-cleared with protein A/G agarose beads at 4℃ for 1 hour. The pre-cleared, chromatin-containing supernatant was incubated with anti-PARP1 antibody (Cell Signaling, Cat# 9532) or rabbit IgG (Cell Signaling, Cat# 2729) as a control at 4℃ overnight. Protein A/G beads were added, incubated at 4℃ for 1 hour, and washed once in sequence with the following buffers: low salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0) and finally washed twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The immunoprecipitated protein-DNA complex was eluted with elution buffer (1% SDS, 0.1M NaHCO3), and cross-linking was reversed by adjusting to 200 mM NaCl and incubating for 6 hours at 65°C. Residual RNA and protein were cleared by digestion with RNase and proteinase K, respectively. ChIP-enriched and corresponding input DNA was purified with a MinElute PCR Purification Kit (QIAGEN).
ChIP DNA samples were quantified using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad,  CA, USA) and qualified by Agilent Bioanalyzer 2100(Agilent Technologies, Palo Alto, CA,  USA). Next generation sequencing library preparations were constructed following the  manufacturer’s protocol. For each sample, ChIP product was used for library preparation. The  ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and  dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor_x0002_ ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5  and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform  bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were  cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit  3.0 Fluorometer.

value: HeLa

value: PINX1-KO and reconstituted with PINX1

value: enriched PARP1-bound chromatin


title: WT_CTX4

value: F10fl/fl; ; Ptenpc-/- mouse


title: KO_CTX1


title: WT_CTX1


title: Riba-22_A

city: Shanghai City

first: Yue

last: Dong

address: 800 Xiangyin Road

institute: Naval Medical University

data_processing:
Data evaluation, adapter trimming, and host removal.Meta-transcriptome sequencing and Human transcriptome sequencing:  Starting with clean data processed from the raw sequencing data provided by the sequencing company, the data was treated using KneadData (version 0.12.0). The specific processing steps included: 1. Data assessment was conducted using FastQC (version 0.12.1). 2. Adapter sequences and low-quality sections were removed using Trimmomatic (version 0.39). 3. Tandem repeat sequences were identified and eliminated using trf (version 4.09.1). 4. Alignment was performed against the reference sequence hg37_and_human_contamination using Bowtie 2 (version 2.5.4).
Transcriptome assembly. .Meta-transcriptome sequencing and Human transcriptome sequencing: 1. Ribosomal RNA was removed using SortmeRNA (version 4.3.6). 2. Normalization of reads was performed using bbnorm and bbcms from bbtools (version 39.06).3. Transcriptome assembly was conducted using Megahit (version 1.2.9). 4. The assembled results were aligned using Bowtie 2 (version 2.5.4), followed by an additional assembly using MegaHit (version 1.2.9). 5. Redundancy reduction was carried out using MMseqs2 (version 14.7e284). 6. The assembly was evaluated using QUAST (version 5.2.0).
Meta-transcriptome: [Viral sequence identification.]A combined approach of database alignment identification and software identification was employed, as detailed below:Database Alignment Identification Method:1. Sequences were aligned using blastn (version 2.15.0) against the hg38 host reference sequence. 2. Alignments were also performed using blastn (version 2.15.0) with the [virus genomes] and [Nt virus] databases.3. Assembly results were aligned against the [Nr virus] database using diamond (version 2.1.9).Software Identification Method:1.Results from the [diamond] and [blastn] alignments were merged. 2. Virus identification was conducted using VirSorter2 (version 2.2.4). 3. VirFinder (version 1.1) was used for virus identification. 4. Phage identification was performed using PPR-Meta (version 1.1). 5. The geNomad method was applied for virus identification. 6. The viralVerify method was used for virus identification. 7. RNA virus identification was conducted using VirBot. 8.Phage identification was carried out using the VIBRANT method. [Viral Sequence Species Annotation.] 1. Species annotation was performed using BASTA (version 1.4). 2. Uncharacterized sequences were annotated using HMMER (version 3.1b2) for alignment with the ViPhOGs database. The results from the above two methods were then merged. [Viral Sequence Functional Annotation.] The final assembly results were aligned using eggnog-mapper (version not specified) against the EggNOG database. This alignment provided annotations for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Carbohydrate-Active enZYmes (CAZy).
Meta-transcriptome Viral Quantification: 1. Quantification of assembly results: Contig sequences were quantified using RSEM. 2. Species quantification: The quantified assembly results were combined with species annotations from the assembly, enabling quantification across seven taxonomic levels.3. Functional quantification. Human transcriptome sequencing: Host reads were aligned to GRCh38.84 using the STAR v2.7.11b (Princeton, NJ), and quantification was performed with RSEM v1.2.28 (Madison, WI).
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include normalized FPKM values for each Sample

source_name: nose swab sample

extract_protocol:
Total RNA was extracted from nose swab samples using Trizol, and the RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
Upon confirming the RNA quality standards (total RNA ≥ 500ng, RNA integrity number ≥ 5.8), the RNA library for meta-transcriptome sequencing was prepared by depleting ribosomal RNA using an rRNA Removal Kit, fragmenting the RNA into 250-300 bp pieces, and reverse-transcribing these into cDNA. Subsequent steps included end repair, adenylation, and adaptor ligation. The library was then size-selected, amplified, and its concentration and insert size were validated using Qubit® fluorometer, Agilent 2100 Bioanalyzer, and qPCR before sequencing.

value: nose swab sample

value: WT

value: Ribavirin


title: HeLa cells, PINX1-KO_PINX1, IP, rep1


title: Riba-22_B


title: Granulosa cells, SFRP4-1


title: Granulosa cells, PBS-3

value: PBS


title: translocation_HSPC_2

value: HSPC

value: translocation t(7;12)


title: HeLa cells, PINX1-KO, IP, rep2

value: PINX1-KO and infected with empty vector


title: Granulosa cells, PBS-2


title: Riba-16_A


title: Riba-15_B


title: HeLa cells, PINX1-KO, IP, rep1


title: KO_CTX4

value: Prostate


title: Riba-15_A


title: Granulosa cells, PBS-1


title: HeLa cells, WT, IP, rep2

value: WT infected with empty vector


title: Riba-14_A


title: Riba-11_A


title: Vehicle

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger-5.0.0 software (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Nasal mucosa

extract_protocol:
The specific method involves obtaining mouse nasal mucosa and digesting it into a single-cell suspension using hyaluronidase (250U ml-1), collagenase I (114U ml-1), and DNase I (25μg ml-1). Subsequently, CD45+ cells are isolated using Magnetic Activated Cell Sorting (MACS) to prepare a CD45+ single-cell suspension, which is then subjected to single-cell sequencing.
1. The prepared CD45+ single-cell suspension, 10X barcode gel beads, and oil are each added to different chambers of the Chromium Chip M, and GEMs (Gel Beads-in-emulsion) are formed using the 10X Genomics Chromium X system. 2. GEMs are transferred to a PCR machine for reverse transcription, where gel beads containing reverse transcription primers with a 30nt oligo-dT enable the reverse transcription of poly-A RNA in the cells into single-stranded cDNA with Barcode and UMI information. 3. The single-stranded cDNA is purified using magnetic beads. 4. The purified cDNA undergoes PCR amplification. 5. The cDNA concentration is measured using Qubit, and fragment size is assessed using Agilent 2100. 6. After amplification of cDNA, the fragments are enzymatically sheared and size-selected with magnetic beads, followed by end repair, A-tailing, and adaptor ligation with Read2 sequencing primers. A cDNA library with P5 and P7 adaptors is then constructed using PCR. 7. The library is purified using magnetic beads. 8. The library concentration is measured using Qubit, and fragment size is assessed using Agilent 2100.

value: Nasal mucosa

value: CD45+ cells

tag: strain

tag: age

value: 8 weeks

value: Vehicle


title: Riba-10_B


title: HeLa cells, WT, IP, rep1

value: HeLa


title: Riba-11_B


title: HeLa cells, PINX1-KO_PINX1, input, rep2

value: PINX1-KO and reconstituted with PINX1


title: Vehicle-OVA

value: Vehicle-OVA


title: Ribavirin


title: Riba-10_A


title: HeLa cells, PINX1-KO_PINX1, input, rep1

value: enriched PARP1-bound chromatin


title: Ribavirin-OVA

value: Ribavirin-OVA


title: Riba-7_B

value: nose swab sample

value: WT


title: Riba-7_A

value: Ribavirin


title: Riba-9_A


title: HeLa cells, PINX1-KO, input, rep2


title: Riba-5_B


title: Riba-4_B


title: Riba-5_A


title: HeLa cells, PINX1-KO, input, rep1


title: PGCs, HFD, E18.5, RNA, rep1

city: Nanjing

first: Qiuzhen

last: Chen

address: 101 Longmian Rd, Nanjing, Jiangsu, 211166 China

institute: Nanjing Medical University

data_processing:
Checked the quality control of reads data by FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to mm10 using HISAT2
Read count extraction was performed using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts values for each sample,  each file contain 2 columns, the first column represents gene id, the second column represents the counts.

source_name: ovary

extract_protocol:
The SSEA-1-positive female germ cells were obtained through FACS, and then the cells were lysed for cDNA synthesis.
SMART-Seq2

value: ovary

value: germline

value: primordial germ cells

value: high-fat diet for 4 months

tag: replicate


title: Riba-4_A


title: Riba-2_B


title: PGCs, HFD, E18.5, RNA, rep2


title: HeLa cells, WT, input, rep2

value: WT infected with empty vector


title: Riba-2_A


title: PGCs, ND, E18.5, RNA, rep2

value: normal diet for 4 months


title: PGCs, ND, E18.5, RNA, rep1


title: Placebo-20_B

value: Placebo


title: HeLa cells, WT, input, rep1


title: Placebo-20_A


title: Placebo-18_B


title: ribo-dep,MSC,2000Pa,48hr,n2

city: Toronto

first: Justin

middle: Jisu

last: Lim

address: 160 College Street

department: Moleuclar Genetics

institute: University of Toronto

description: ribosomal RNA-depleted library

data_processing:
For ribo-depeleted RNA-seq samples, reads were first trimmed for adaptor sequences with fastp 0.23.2. No trimming was necessary for poly(A)-enriched samples.
Reads were then pseudo-aligned to GENCODE GRCh38 V38 transcripts with Salmon 0.14.1.
Assembly: hg38
Supplementary files format and content: tab-delimited .txt files include raw transcript counts for each sample.

source_name: Bone marrow aspirates

growth_protocol: MSCs were maintained in MEM-α supplemented with 10% heat-inactivated fetal bovine serum and 10ng/mL fibroblast growth factor.

extract_protocol:
RNA was harvest using the RNeasy mini kit (Qiagen) or mirVana kit (Invitrogen) for poly(A)-enriched and ribosomal RNA-depleted sequencing libraries, respectively.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA kits follwing manufaturer's protocol by the Donnelly Sequencing Centre at the University of Toronto.

treatment_protocol:
Passage 4 MSCs were encapsulated in IPNs with storage moduli of 150, 500, and 2000 Pa.
For the poly(A)-enriched RNA-seq, the cells were additionally treated with either 0.04% (v/v) DMSO or 10uM blebbistatin.

value: Bone marrow aspirates

value: mesenchymal stromal cell

tag: stiffness

tag: time

value: 48 hours


title: Placebo-17_A


title: Placebo-18_A


title: ribo-dep,MSC,2000Pa,48hr,n3

description: ribosomal RNA-depleted library


title: Macrophage-P-MLE15CM3

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
Trimmed data were aligned with mm10 genome using Star aligner on Galaxy Server
Assembly: mm10
Supplementary files format and content: csv file of raw counts for each sample
Supplementary files format and content: csv file of normalized tpm for each sample

extract_protocol:
QIAGEN RNEasy Mini Kit
Library construction was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core using the Lexogen RiboCop rRNA Depletion kit and Swift Biosciences RNA Library Sciences.

treatment_protocol: Raw 264.7 cells (ATCC, TIB-71) were seeded in 12-well plates at a density of 5x105cells per well in 500 µL of RPMI supplemented with 10% FBS (Cytiva, 16777-014) and incubated at 37°C. The following day, Raw 264.7 cells were rinsed once with PBS, and 500 µL of eosinophil conditioned media, with or without 2 µg of Isotype or MBP-1 antibody, or MBP-1, or control concentrated conditioned media from transfected HEK cells, was added to the Raw 264.7 cells for a 24-hour incubation period. MLE15 conditioned media was used as control. RNA extraction was performed using the RNeasy mini kit (Qiagen – 74104), and the extracted RNA was stored at -80°C for subsequent RNA-Sequencing analysis.

value: Macrophage

value: Macrophage with MLE15 conditioned media


title: Macrophage-P-MLE15CM2


title: Macrophage-P-MLE15CM1


title: ribo-dep,MSC,2000Pa,48hr,n1

description: ribosomal RNA-depleted library


title: Placebo-14_B


title: Placebo-15_B


title: Placebo-14_A


title: ribo-dep,MSC,500Pa,48hr,n3

description: ribosomal RNA-depleted library


title: Placebo-13_A


title: Placebo-13_B


title: ribo-dep,MSC,500Pa,48hr,n2

description: ribosomal RNA-depleted library


title: Placebo-12_A


title: Macrophage-P-EosCM-P-MBP-1-3

value: Macrophage with eosinophil conditioned media and MBP1 antibody


title: Macrophage-P-EosCM-P-MBP-1-2


title: ribo-dep,MSC,500Pa,48hr,n1

description: ribosomal RNA-depleted library


title: Macrophage-P-EosCM-P-MBP-1-1


title: Placebo-10_B


title: Placebo-10_A


title: Macrophage-P-EosCM-P-Isotype3

value: Macrophage with eosinophil conditioned media and isotope control


title: Placebo-8_B

value: nose swab sample


title: ribo-dep,MSC,150Pa,48hr,n3

description: ribosomal RNA-depleted library

value: WT


title: Placebo-5_B


title: Placebo-5_A


title: Macrophage-P-EosCM-P-Isotype1


title: Placebo-15_A


title: Macrophage-P-EosCM-P-Isotype2


title: Placebo-3_B


title: Placebo-3_A


title: ribo-dep,MSC,150Pa,48hr,n2

description: ribosomal RNA-depleted library


title: ribo-dep,MSC,150Pa,48hr,n1

description: ribosomal RNA-depleted library


title: poly(A),MSC,2000Pa,48hr,blebb,n3

description: poly(A)-enriched library

value: Blebbistatin


title: Macrophage-P-EosCM3

value: Macrophage with eosinophil conditioned media


title: Placebo-2_B


title: Placebo-2_A


title: poly(A),MSC,2000Pa,48hr,blebb,n2

description: poly(A)-enriched library


title: HC_50


title: HC_49


title: Macrophage-P-EosCM1


title: HC_48


title: HC_47


title: poly(A),MSC,2000Pa,48hr,dmso,n3

description: poly(A)-enriched library

value: DMSO


title: HC_44


title: poly(A),MSC,2000Pa,48hr,blebb,n1

description: poly(A)-enriched library


title: Placebo-8_A


title: HC_42


title: Macrophage-P-EosCM2


title: translocation_HSPC_H3K4me1_3

data_processing:
TrimGalore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was deployed together with Cutadapt v. 1.14 (https://cutadapt.readthedocs.io/en/stable/) using the non-default parameters “--paired”, “--nextera”, “--length_1 35”, and “--length_2 35” to perform adapter and quality trimming.
Bowtie2 v. 2.2.6 (PMID: 22388286) was used with the “--very-sensitive” flag and a maximum insertion length of 2500 bp to map trimmed reads against the GRCh37/hg19 reference genome.
Aligned reads belonging to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Discordant mappings and alignments with a Phred score below 20 were removed using SAMtools view.
Trimmed reads were additionally aligned against the S. cerevisiae R64 reference genome followed by post-alignment filtering as described above. To derive a library-specific scaling factor, the multiplicative inverse of the number of filtered alignments against the yeast genome were calculated. Coverage tracks were generated using the bamCoverage functionality of Deeptools v. 3.1.1 (https://anaconda.org/bioconda/deeptools/files?version=3.1.1) with the non-default parameters “--ignoreForNormalization chrM chrY chrX” and “--effectiveGenomeSize 2652783500” as well as the “--scaleRatio” option to specify the spike-in-derived scaling factor.
Peak calling was performed with MACS v.2.2.6 (https://pypi.org/project/MACS2/) using a wrapper script callpeaks provided by Encode (https://www.encodeproject.org/chip-seq/histone/); to identify HSPC-specific peaks, ACT-seq data from corresponding iPSCs were used as reference.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: Antibody-guided chromatin tagmentation (ACT-seq)

extract_protocol:
Cell permeabilization of native cells and tagmentation reaction with pA-Tn5 transposome-antibody complex for "Antibody-guided chromatin tagmentation (ACT-seq)" according to Carter et al (PMID: 31431618). For normalization of sequence reads between biological replicates, ~4,000 permeabilized nuclei of yeast Saccharomyces cerevisiae, prepared according to (PMID: 25827087) and incubated with pA-Tn5ome-ab complex targeting yeast H2B, were spiked into each mix of cells and pA-Tn5ome-ab complex.  Tagmented DNA was purified with MinElute (Qiagen) columns (ACTseq) according to the provider's instruction.
Libraries were prepared according to Weichenhan et al. (PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.

value: HSPC

value: H3K4me1 (Abcam ab8895)

value: translocation t(7;12)


title: LG31E4_54

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with a unique gene count over 5000 or less than 300, cells with UMI counts over 15000, and cells with a high fraction of mitochondrial reads (>1%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4.0.0 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: hippocampus

tag: Sex

value: Female

value: Human ApoE4:E4/E4; P301S tau:+; R47H Human TREM2 KI:+/+


title: HC_37


title: HC_35


title: poly(A),MSC,2000Pa,48hr,dmso,n1

description: poly(A)-enriched library

value: Bone marrow aspirates

value: mesenchymal stromal cell


title: LG31E4_45

description: mRNA expression in mouse hippocampus

value: Human ApoE4:E4/E4; P301S tau:+; R47H Human TREM2 KI:+/KI


title: HC_32


title: LG31E4_73

description: mRNA expression in mouse hippocampus


title: poly(A),MSC,2000Pa,24hr,blebb,n3

description: poly(A)-enriched library

value: 24 hours


title: HC_23


title: LG31E4_33

description: mRNA expression in mouse hippocampus


title: HC_22


title: poly(A),MSC,2000Pa,24hr,blebb,n2

description: poly(A)-enriched library


title: poly(A),MSC,2000Pa,24hr,blebb,n1

description: poly(A)-enriched library


title: HC_24


title: HC_19


title: HC_38


title: LG31E4_27

description: mRNA expression in mouse hippocampus

value: Human ApoE4:E4/E4; P301S tau:-; R47H Human TREM2 KI:+/+


title: HC_16


title: poly(A),MSC,2000Pa,24hr,dmso,n3

description: poly(A)-enriched library


title: HC_13


title: poly(A),MSC,2000Pa,24hr,dmso,n2

description: poly(A)-enriched library


title: LG31E4_25

description: mRNA expression in mouse hippocampus


title: HC_11


title: poly(A),MSC,2000Pa,24hr,dmso,n1

description: poly(A)-enriched library


title: HC_25


title: HC_9


title: LG31E4_22

description: mRNA expression in mouse hippocampus


title: HC_8


title: poly(A),MSC,2000Pa,48hr,dmso,n2

description: poly(A)-enriched library

value: 48 hours


title: LG31E3_9

description: mRNA expression in mouse hippocampus

value: Human ApoE3:E3/E3; P301S tau:-; R47H Human TREM2 KI:+/+


title: HC_12

value: nose swab sample

value: WT


title: LG31E4_44

description: mRNA expression in mouse hippocampus


title: HC_7


title: poly(A),MSC,500Pa,48hr,blebb,n2

description: poly(A)-enriched library

value: Blebbistatin


title: HC_5


title: LG31E4_28

description: mRNA expression in mouse hippocampus


title: HC_4


title: LG31E3_40

description: mRNA expression in mouse hippocampus


title: HC_21


title: HC_17


title: poly(A),MSC,500Pa,48hr,blebb,n1

description: poly(A)-enriched library


title: HC_3


title: HC_1


title: poly(A),MSC,500Pa,48hr,dmso,n3

description: poly(A)-enriched library

value: DMSO


title: poly(A),MSC,500Pa,48hr,dmso,n2

description: poly(A)-enriched library


title: PGCs, HFD, E18.5, WGBS, rep1

data_processing:
Checked the quality control of reads data by FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to mm10 using Bismark
Assembly: mm10
Supplementary files format and content: tab-delimited bedGraph files include methylation sites and methylation level for each sample,  each file contain 4 columns, the first three columns represent methylated sites on the genome , the fourth column represents the  methylation level

extract_protocol:
The SSEA-1-positive female germ cells obtained through FACS were washed with PBS, and DNA was isolated from the cell pellets using DNeasy Blood & Tissue Kits (QIAGEN).
Bisulfite conversion was first performed. The converted DNA was then amplified by nested PCR.

value: ovary

value: germline

value: primordial germ cells

value: high-fat diet for 4 months


title: LG31E3_18

description: mRNA expression in mouse hippocampus

value: hippocampus

value: Female

value: Human ApoE3:E3/E3; P301S tau:+; R47H Human TREM2 KI:+/+


title: PGCs, ND, E18.5, WGBS, rep2

value: normal diet for 4 months


title: poly(A),MSC,500Pa,48hr,blebb,n3

description: poly(A)-enriched library

value: Bone marrow aspirates

value: mesenchymal stromal cell


title: PGCs, ND, E18.5, WGBS, rep1


title: LG31E3_17

description: mRNA expression in mouse hippocampus


title: PGCs, HFD, E13.5, WGBS, rep1


title: poly(A),MSC,500Pa,24hr,blebb,n3

description: poly(A)-enriched library

value: 24 hours


title: PGCs, ND, E13.5, WGBS, rep2


title: poly(A),MSC,500Pa,24hr,blebb,n2

description: poly(A)-enriched library


title: LG31E3_12

description: mRNA expression in mouse hippocampus

value: Human ApoE3:E3/E3; P301S tau:+; R47H Human TREM2 KI:+/KI


title: PGCs, ND, E13.5, WGBS, rep1


title: LG31E3_4

description: mRNA expression in mouse hippocampus


title: poly(A),MSC,500Pa,24hr,dmso,n3

description: poly(A)-enriched library


title: LG31E3_38

description: mRNA expression in mouse hippocampus


title: poly(A),MSC,500Pa,24hr,blebb,n1

description: poly(A)-enriched library


title: HC_2


title: LG31E3_11

description: mRNA expression in mouse hippocampus


title: LG31E3_1

description: mRNA expression in mouse hippocampus


title: 155688 WT 12M TI

city: Hobart

first: Phillippa

middle: Claire

last: Taberlay

state: Tasmania

address: 17 Liverpool St

department: College of Health and Medicine

country: Australia

institute: University of Tasmania

description: Total input control.

data_processing:
Sequenced using HiSeq 2500 - mean read depth 13.9M H3K4me3, 16.2M H3K27ac.
Removed library tags.
Pseudoreplicates generated.
Mapped to MM10 using bowtie2.
bigwigs generated.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files for pseudoreplicates.

source_name: C57/BL6 mouse forebrain

extract_protocol:
Flash Frozen forebrains were extracted in nuclei extraction buffer, labelled with NeuN for 1hr then sorted with FACS. NeuN+ nuclei were pelleted, then split into ~200K aliquots for ChIP-seq. Nuclei were sonicated into 300bp fragments, then H3K4me3 or H3K27ac ChIP was performed.
Nugen Ovation Ultralow V2 library preparation - amplification for 17 cycles (H3K27ac), or 18 cycles (H3K4me3) 0347 V2 1-96/0344 V2 1-16.

value: NeuN+ neuronal nuclei

value: 12 months


title: 512 WT 3M TI

description: Total input control.

value: 3 months


title: PGCs, HFD, E18.5, WGBS, rep2


title: 163734 WT 6M TI

description: Total input control.

value: 6 months


title: 158028 WT 24M H3K27ac

description: H3K27ac ChIP-seq from NeuN+ nuclei of 24m old C57/BL6 mice.

value: 24 months


title: 154468 WT 24M H3K27ac


title: poly(A),MSC,500Pa,48hr,dmso,n1

description: poly(A)-enriched library

value: WT

value: 48 hours

value: DMSO


title: PGCs, HFD, E13.5, WGBS, rep2

value: ovary

value: germline

value: primordial germ cells

value: high-fat diet for 4 months


title: poly(A),MSC,500Pa,24hr,dmso,n2

description: poly(A)-enriched library


title: 158027 WT 24M TI

description: Total input control.


title: E4_R47H_Tau_1

description: mRNA expression in primary microglia

data_processing:
RNA-seq reads were mapped using the BlueBee genomics platform and the GENCODE GRCm38 mouse genome (Lexogen QuantSeq 2.2.3) as reference genome.
Counts were normalized using the median of ratios method.
Differential gene expression was analyzed with the DESeq2 1.38.3 package
To control for multiple testing, we used the Benjamini–Hochberg approach to constrain the FDR
Assembly: mm10 genome
Supplementary files format and content: csv: read counts

source_name: brain cortex

extract_protocol:
RNA was isolated from microglia using the Quick-RNA MicroPrep Kit (Zymo Research, R1051)
cDNA library generation was done using the QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) for Illumina (K01596, Lexogen) following manufacturer’s instructions.

value: brain cortex

value: microglia

value: not determined

value: postnatal day 1-3

value: 0N4R tau fibrils


title: poly(A),MSC,500Pa,24hr,dmso,n1

description: poly(A)-enriched library

value: Bone marrow aspirates

value: mesenchymal stromal cell

value: 24 hours


title: 156508 WT 12M H3K27ac

description: H3K27ac ChIP-seq from NeuN+ nuclei of 12m old C57/BL6 mice.

value: NeuN+ neuronal nuclei

value: 12 months


title: 156509 WT 12M H3K27ac


title: E4_R47H_Tau_3

description: mRNA expression in primary microglia


title: 155668 WT 12M H3K27ac


title: 163736 WT 6M H3K27ac

description: H3K27ac ChIP-seq from NeuN+ nuclei of 6m old C57/BL6 mice.

value: 6 months


title: poly(A),MSC,150Pa,48hr,blebb,n2

description: poly(A)-enriched library

value: WT

value: 48 hours

value: Blebbistatin


title: poly(A),MSC,150Pa,48hr,blebb,n3

description: poly(A)-enriched library


title: E4_R47H_3

description: mRNA expression in primary microglia

value: Vehicle


title: 325 WT 6M H3K27ac


title: E4_R47H_2

description: mRNA expression in primary microglia


title: E4_R47H_Tau_2

description: mRNA expression in primary microglia


title: 517 WT 3M H3K27ac

description: H3K27ac ChIP-seq from NeuN+ nuclei of 3m old C57/BL6 mice.

value: 3 months


title: 512 WT 3M H3K27ac


title: E4_R47H_1

description: mRNA expression in primary microglia


title: 513 WT 3M H3K27ac


title: E4_CV_Tau_3

description: mRNA expression in primary microglia


title: 363 WT 3M H3K27ac


title: poly(A),MSC,150Pa,48hr,dmso,n2

description: poly(A)-enriched library

value: DMSO


title: 158027 WT 24M H3K4me3

description: H3K4me3 ChIP-seq from NeuN+ nuclei of 24m old C57/BL6 mice.

value: 24 months


title: 158028 WT 24M H3K4me3


title: E4_CV_Tau_2

description: mRNA expression in primary microglia

value: brain cortex

value: microglia


title: 154469 WT 24M H3K4me3


title: poly(A),MSC,150Pa,48hr,dmso,n1

description: poly(A)-enriched library


title: 154468 WT 24M H3K4me3


title: 17 WT 6M H3K27ac


title: E4_CV_Tau_1

description: mRNA expression in primary microglia

value: not determined

value: postnatal day 1-3


title: 155668 WT 12M H3K4me3

description: H3K4me3 ChIP-seq from NeuN+ nuclei of 12m old C57/BL6 mice.


title: poly(A),MSC,150Pa,48hr,dmso,n3

description: poly(A)-enriched library

value: Bone marrow aspirates


title: E4_CV_3

description: mRNA expression in primary microglia


title: 156508 WT 12M H3K4me3


title: 325 WT 6M H3K4me3

description: H3K4me3 ChIP-seq from NeuN+ nuclei of 6m old C57/BL6 mice.


title: 163736 WT 6M H3K4me3


title: poly(A),MSC,150Pa,24hr,blebb,n3

description: poly(A)-enriched library

value: mesenchymal stromal cell


title: poly(A),MSC,150Pa,24hr,blebb,n2

description: poly(A)-enriched library

value: 24 hours


title: liver, KO5_AP_6h

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text file includes counts and FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: injected intraperitoneally with 500mg/kg acetaminophen for 6h

value: Liver

value: Optn-/-

value: acetaminophen


title: E4_CV_1

description: mRNA expression in primary microglia


title: poly(A),MSC,150Pa,24hr,blebb,n1

description: poly(A)-enriched library

value: WT


title: liver, KO4_AP_6h


title: 512 WT 3M H3K4me3

description: H3K4me3 ChIP-seq from NeuN+ nuclei of 3m old C57/BL6 mice.

value: NeuN+ neuronal nuclei


title: E3_R47H_Tau_3

description: mRNA expression in primary microglia

value: 0N4R tau fibrils


title: poly(A),MSC,150Pa,24hr,dmso,n3

description: poly(A)-enriched library


title: 513 WT 3M H3K4me3


title: poly(A),MSC,150Pa,24hr,dmso,n2

description: poly(A)-enriched library


title: poly(A),MSC,150Pa,48hr,blebb,n1

description: poly(A)-enriched library

value: 48 hours

value: Blebbistatin


title: liver, WT1_AP_6h

value: wild type


title: 517 WT 3M H3K4me3

value: 3 months


title: liver, WT6_con

treatment_protocol: injected intraperitoneally with 200ul PBS for 6h

value: control


title: E3_R47H_Tau_2

description: mRNA expression in primary microglia

value: brain cortex

value: microglia


title: liver, WT4_AP_6h


title: E3_R47H_3

description: mRNA expression in primary microglia

value: not determined

value: postnatal day 1-3

value: Vehicle


title: E3_R47H_Tau_1

description: mRNA expression in primary microglia


title: poly(A),MSC,150Pa,24hr,dmso,n1

description: poly(A)-enriched library

value: Bone marrow aspirates

value: mesenchymal stromal cell

value: 24 hours

value: DMSO


title: HeLa cells, siUSP50-2

city: Birmingham

first: Joanna

middle: Ruth

last: Morris

state: West Midlands

address: IBR West 2nd floor, Medical School, Vincent Drive, WX 2.45, Egdbaston

country: United Kingdom

institute: University of Birmingham

description:
Mor-11_S26_merge_R1
Oligo-Diff.txt
Fasta_clean_up_on_Umix-NTC_(remove_duplicates)].fasta

data_processing:
alignments were converted to Bed files and intersects between biological repeats generated using interesct interval (galaxy)
These were used to generate fasta sequences using Getfasta
RSAT Oligo-diff was then run comparing the USP50 and NTC data sets to return oligos significantly enriched in one file relative to the other
Assembly: Hg38
Supplementary files format and content: Text file that summarizes the output of RSAT-Oligo-Diff. Column 1: seq oligonucleotide sequence, Column 2: id: oligonucleotide identifier. Column 3: occ_tst occurrences (USP50 depletion) in file tmp/www-data/2024/06/10/oligo-diff_2024-06-10.110535_cg5KBU_upload_test_seq.fasta. Column 4 occ_ctl occurrences in file tmp/www-data/2024/06/10/oligo-diff_2024-06-10.110535_cg5KBU_upload_ctrl_seq.fasta. Column 5: exp_tst:random expectation for occ_tst. Column 6: exp_ctl: random expectation for occ_ctl. Column 7: freq_test (USP50) frequency (=occurrences per position) in test sequences. Column8: freq_ctrl: frequency (=occurrences per position) in control sequences. Column 9: occ_P: Hypergeometric P-value. P(X >= occ).  Column 10: occ_E: Hypergeometric E-value. occ_E = nb_test * occ_P. Column 11:occ_sig: Hypergeometric significance. occ_sig = -log10(occ_E). Column 12: ratio: Ratio between test(USP50) and control frequencies. R = freq_test / freq_ctrl. Column 13: rank: Rank of the patterns sorted by decreasing significance. Column 14: side: side of the higher representation (test or ctrl).

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle Media supplemented with 10% FBS and 1% PS.

extract_protocol:
Cells were harvested in Dulbecco’s phosphate-buffered saline (PBS) and counted. Cells (120,000 per well) were adhered onto a poly-L-lysine–coated 96-well plate and cross-linked in methanol-free paraformaldehyde (final concentration 4%) for 10 min. The PFA was removed, and the wells were washed twice in PBS and stored in 200 μl PBS. Plates were sealed and stored at 4°C until downstream library preparation
Library and INDUCE-Seq protocol are here: https://doi.org/10.1038/s41467-022-31702-9
INDUCE-Seq DNA double-strand break sequencing.

treatment_protocol: siRNA transfections were carried out using the transfection reagent Dharmafect1 (Dharmacon) following the manufacturer’s instructions. with either 25 control siRNA, CUUACGCUGAGUACUUCGA, or a mix of USP50 siRNAs (CAACACAUGCUGCGUGAAU, CUACCCAGCAUUUACGAAA, GGACCUCACUCCUUAUAUU).

value: HeLa

value: Cervical cancer

value: WT

value: USP50 siRNAs


title: E4_CV_2

description: mRNA expression in primary microglia


title: LNCaP_RNAseq_M1-IKK_rep3

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: 150 PE

data_processing:
Low quality nucleotides and adapter sequences were removed from raw reads using trimmomatic PE (v. 0.36; PE, LEADING:3, TRAILING:3, MINLEN:36).
Abundant sequences (sequencing adapters, mitochondrial and ribosomal sequences) were removed, and remaining reads were mapped to human genome hg38 with bwa mem aligner (v.0.7.17).
Transcript-level count matrix (rawCounts.LNCaP_RNAseq.txt) was produced using analyzeRepeats function (analyzeRepeats.pl rna hg38 -raw) in homer (v4.10).
Assembly: hg38
Supplementary files format and content: tab-delimited file with refSeq transcript ID and counts for each sample.

source_name: M1 conditioned medium IKK16 3

growth_protocol: LNCaP cells were cultured in RPMI containing 10 % FBS, supplemented with 1 % penicillin-streptomycin and 1 % L-glutamine. Cell were grown in  37°C under 5.0% CO2.

extract_protocol:
The total RNA was extracted from LNCaP cells by following instructions from RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
Library was constructed at Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: LNCaP cells were seeded on 6-well plate. On the next day, the cells were pre-incubated with RPMI 1 % heat-inactivated FBS, supplemented with 1 % penicillin-streptomycin and 1 % L-glutamine. Pre-incubation medium was then replaced to conditioned medium (CM) collected from M0 THP-1 macrophages or M1 or M2 -polarized THP-1 macrophages. CM from M0, M1 and M2 macrophages was diluted with RPMI containing 10% heat-inactivated FBS at a ratio of 1:4. RPMI containing 10% heat-inactivated FBS with 1% penicillin-streptomycin and L-glutamine represented as control treatment.  For inhibitory assay, LNCaP cell were treated with M1 CM in combination with NFκB inhibitor IKK16 (0.7 μmol/l) or equal amount of DMSO.  LNCaP cells were exposed to the respective treatment media for 48 hours

value: LNCaP

value: Prostate cancer cells

value: M1 conditioned medium IKK16


title: liver, WT3_con

value: Liver

value: wild type

value: control


title: 363 WT 3M H3K4me3

value: NeuN+ neuronal nuclei

value: 3 months


title: E3_R47H_2

description: mRNA expression in primary microglia

value: brain cortex

value: microglia

value: not determined

value: postnatal day 1-3

value: Vehicle


title: HeLa cells, siControl-2

description:
Mor-07_S22_merge_R1
Oligo-Diff.txt
fasta_clean_up_NTC_(remove_duplicates)].fasta

value: HeLa

value: control siRNA


title: LNCaP_RNAseq_M1-IKK_rep2

description: 150 PE

source_name: M1 conditioned medium IKK16 2

value: WT


title: HeLa cells, siUSP50-1

description:
Mor-05_S20_merge_R1
Oligo-Diff.txt
Fasta_clean_up_on_Umix-NTC_(remove_duplicates)].fasta

value: Cervical cancer

value: USP50 siRNAs


title: ChIP-seq H3K27me2me3 WT strain: N3753

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

data_processing:
Sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with default option.
Reads with low mapping quality (MapQ < 10) and from repetitive seuqnces were discarded.
Pileup score were calculated using Homer software (version 4.10.1).
ChIP-seq scores correspond to the total number of mapped tags after normalizing to 10 million reads.
Assembly: neurospora crassa genome (OR74A)
Supplementary files format and content: bigwig of pileup graph

organism: Neurospora crassa

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC (supplemented with histidine for strain N6279).

extract_protocol:
Lysates were cleared by centrifugation and 1/20th input was saved. H3K27me2/3 antibody (Active Motif, 2uL), H3K9ac antibody (Diagenode, 2 uL), or H3K14ac antibody (Millipore, 2 uL) was added and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl wash buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the Qiagen MinElute PCR purification kit and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions. AMPure XP beads (Beckman Coulter A63881) were used for size selection of ~200-800 bp fragments. Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses.  Sonicated chromatin was lysed for 2 x 90s on a Mini-beadbeater-16 (Biospec Products) and then sheared using a Bioruptor (Diagenode) for 2 x 5 min with a cycle of 30 sec on followed by 30 sec off, at high power.

tag: antibody


title: LNCaP_RNAseq_M1-DMSO_rep3

description: 150 PE

source_name: M1 conditioned medium DMSO 3

value: LNCaP

value: Prostate cancer cells

value: M1 conditioned medium DMSO


title: LNCaP_RNAseq_M1-IKK_rep1

description: 150 PE

source_name: M1 conditioned medium IKK16 1

value: M1 conditioned medium IKK16


title: HeLa cells, siControl-1

description:
Mor-01_S16_merge_R1
Oligo-Diff.txt
fasta_clean_up_NTC_(remove_duplicates)].fasta


title: E3_CV_Tau_3

description: mRNA expression in primary microglia

value: 0N4R tau fibrils


title: MNase-seq ∆rlp1 (∆NCU09007) strain: N8186

data_processing:
Paired-end sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with the option “-q -p 4 -X 250 --no-discordant --no-mixed --no-unal” (Paired-end alignment reads with maximum 250bp distance gap between them were used in subsequent analysis. This length correspond to mono-nucleosome)
Only correctly aligned paired-end alignment reads were filtered using samtools (version 1.5) commands “samtools view –hf 0x2 input.bam | grep –v “XS:i:” “
Dyad Coverage was calculated using the scripts (03_PNA_SDE.R) from Baldi et al (Baldi, S. et al. Genome-wide Rules of Nucleosome Phasing in Drosophila. Mol. Cell 72, 661-672.e4 (2018))
The spectral density (SD) score correspond to periods of 182bp was calculated using the scripts (cov2spec.R) from Baldi et al. SD score was normalized as Z-score :  (log2(SD score) – average) / standard deviation.
Regions with the average Z-score threshold of 2 were defined as the domain of a regular nucleosome array.
Assembly: neurospora crassa genome (OR74A)
Supplementary files format and content: bigwig of dyad coverage and spectral density

growth_protocol: A 50 ml culture of Vogel’s medium and 1.5% sucrose was inoculated with 2.5E7 cells, harvested from freshly grown conidia, and grown at 32oC with shaking for ~3.5 hours, until at least 70% of conidia have germinated as determined by microscopy

extract_protocol:
Cells were treated with 2 mg of zymolyase (100T) in a 1 ml solution of spheroplast buffer (1M sorbitol, 50mM Tris pH 7.5, 10mM BME) for 15 minutes while rotating at room temperature. Cells were pelleted at full speed and resuspended in 100 ul MNase digestion buffer (1M sorbitol, 50mM NaCl, 10mM Tris pH 7.5, 5mM MgCl2, 1mM CaCl2, 0.075% (v/v) IGEPAL (Sigma), 0.5mM spermidine and 1mM BME). Exonuclease III (NEB) (30 units) and micrococcal nuclease (Takara) were added to samples and rapidly mixed. Digestion proceeded for 10 minutes at 37oC and was quenched with final concentration of 5mM EGTA and 5mM EDTA (from 50mM/50mM stock). MNase concentration was optimized for each strain to yield ~80-90% mononucleosomes (20 units for N8185, N8186, N8193; 40 units for N3752, N8194; 60 units for 3753). RNase (40 ug) treatment was for 1.5 hours at 42C and proteinase K (200 ug) treatment was for 1 hour at 65 C.
10 ug of gel-purified (minelute, Qiagen) mononucleosome DNA was prepared for high-throughput sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: Cells were crosslinked by addition of fresh formaldehyde for a final concentration of 1%, then shaken at room temperature for 10 minutes. The crosslinking reaction was quenched by the addition of 6.8 ml of 1M Tris-HCl pH 8 to a final concentration of 125mM for 10 minutes, shaking at room temperature. Conidia were then harvested by centrifugation.

value: [delta]rlp1 ([delta]NCU09007)


title: LNCaP_RNAseq_M1-DMSO_rep2

description: 150 PE

source_name: M1 conditioned medium DMSO 2


title: E3_CV_Tau_2

description: mRNA expression in primary microglia


title: M2 conditioned medium 3

description: 75 SE

data_processing:
Reads were aligned to human genome hg38 using STAR aligner (v. 2.6.1b).
Transcript-level count matrix (rawCounts.C42B_RNAseq.txt) was produced using analyzeRepeats function (analyzeRepeats.pl rna hg38 -raw) in homer (v4.10).
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample.

growth_protocol: LNCaP-C42B cells were cultured in RPMI containing 10 % FBS, supplemented with 1 % penicillin-streptomycin and 1 % L-glutamine. Cell were grown in  37°C under 5.0% CO2.

extract_protocol:
The total RNA was extracted from LNCaP-C42B cells by following instructions from RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
Library was constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England BioLabs, Ipswich, MA) and NEBNext Ultra II Directional RNA Library Prep Kit (E7765, New England BioLabs, Ipswich, MA) according to manufacturer’s protocol.

treatment_protocol: LNCaP-C42B cells were seeded on 6-well plate. On the next day, the cells were pre-incubated with RPMI 1 % heat-inactivated FBS, supplemented with 1 % penicillin-streptomycin and 1 % L-glutamine. Pre-incubation medium was then replaced to conditioned medium (CM) collected from M0 THP-1 macrophages or M1 or M2 -polarized THP-1 macrophages.  RPMI containing 10% heat-inactivated FBS with 1% penicillin-streptomycin and L-glutamine represented as control treatment.  LNCaP -C42B cells were exposed to the respective treatment media for 48 hours

value: M2 conditioned medium


title: LNCaP_RNAseq_M1-DMSO_rep1

description: 150 PE

source_name: M1 conditioned medium DMSO 1


title: M2 conditioned medium 2

description: 75 SE


title: E3_CV_Tau_1

description: mRNA expression in primary microglia

value: brain cortex


title: LNCaP_RNAseq_M2_rep3

description: 150 PE

source_name: M2 conditioned medium 3


title: MNase-seq WT strain: N3753


title: M2 conditioned medium 1

description: 75 SE


title: ChIP-seq H3K27me2me3 WT strain: N3752


title: E3_R47H_1

description: mRNA expression in primary microglia

value: microglia


title: E3_CV_3

description: mRNA expression in primary microglia

value: not determined


title: E3_CV_2

description: mRNA expression in primary microglia

value: postnatal day 1-3


title: M1 conditioned medium 2

description: 75 SE

value: M1 conditioned medium


title: LNCaP_RNAseq_M2_rep1

description: 150 PE

source_name: M2 conditioned medium 1


title: MNase-seq ∆rlp2 (∆NCU02898) strain: N6708

value: [delta]rlp2 ([delta]NCU02898)


title: M1 conditioned medium 3

description: 75 SE


title: LNCaP_RNAseq_M2_rep2

description: 150 PE

source_name: M2 conditioned medium 2


title: MNase-seq WT strain: N3752


title: E3_CV_1

description: mRNA expression in primary microglia

value: Vehicle


title: MNase-seq ∆rlp2 (∆NCU02898) strain: N6706


title: CtlPR8HTO

data_processing:
CellRanger v7.0.0 software
Assembly: mm10 mouse reference genome 2020A version provided by 10x Genomics
Supplementary files format and content: .h5

source_name: mouse lung

extract_protocol:
The lungs from different treatment (N= 4 for treatment A, N= 4 for treatment B) were removed for single-cell suspension procedures using enzymatic digestion with elastase and lipase/DNAse.
Single cell capture and library construction followed 10x Genomics Single Cell 3’ Reagent Kits v3 user guide

value: mouse lung

value: all cells


title: LNCaP_RNAseq_M1_rep3

description: 150 PE

source_name: M1 conditioned medium 3

value: WT


title: LNCaP_RNAseq_M1_rep2

description: 150 PE

source_name: M1 conditioned medium 2

value: LNCaP


title: MNase-seq ∆sds3 (∆NCU01599) strain: N8193

value: [delta]sds3 ([delta]NCU01599)


title: M0 conditioned medium 3

description: 75 SE

value: Prostate cancer cells

value: M0 conditioned medium


title: LNCaP_RNAseq_M1_rep1

description: 150 PE

source_name: M1 conditioned medium 1


title: MNase-seq ∆sds3 (∆NCU01599) strain: N8194


title: MNase-seq ∆rlp1 (∆NCU09007) strain: N8185


title: M0 conditioned medium 2

description: 75 SE


title: AbxUIHTO

value: VNAM control


title: exo3

first: Lina

last: Antounians

state: Ontario

address: 686 Bay St

institute: The Hospital for Sick Children

data_processing:
FastQ files were obtained using Cell Ranger (10X Genomics, cellranger-6.0.0), aligned to the Rattus norvegicus version 6 genome, and quantified with Cell Ranger count function using default settings. Data were analyzed either by replicate or by pooling reads by condition. Filtering of data was performed to remove cells with raw data was log normalized and scaled using default values. Variable features and principal components were then calculated using default values. Ribosomal genes were removed with pattern = "^Rp[sl][[:digit:]]|^Rplp[[:digit:]]|^Rpsa" from normalized data.
Assembly: rn6

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Nuclei were extracted from frozen lung tissue using Singulator TM 100 (S2 Genomics), with the following settings: nuclear reagent, S2; incubation temp, cold; mixing type, top; mixing speed,  fastest; disruption type, default; disruption speed, medium. RNase inhibitor was added to the Singulator Cartridge to reach a final concentration of 0.2U/μl. Nuclei collected from the Singulator was spun at 800g, at 4°C for 10min. Supernatant was removed, following by resuspending nuclei in freshly made cold Wash and Resuspension Buffer (1X PBS, 1% BSA, 0.2U/μl). The wash was repeated twice before proceeding into the 10X Genomics single-cell 3’ v3.1 assay and processed as described by the protocol provided by the 10X Genomics.
Libraries construction and library sequencing were proceeded as described in the 10X Genomics protocol using NovaSeq 6000.

value: Lung

value: E21 fetus

value: hypoplastic+ amniotic fluid stem cell extracellular vesicles treated


title: M0 conditioned medium 1

description: 75 SE


title: AbxPR8HTO


title: exo2


title: LNCaP_RNAseq_M0_rep2

description: 150 PE

source_name: M0 conditioned medium 2


title: RPMI 3

description: 75 SE

value: RPMI medium


title: M1 conditioned medium 1

description: 75 SE


title: CtlPR8


title: nitro3

value: hypoplastic (injury)


title: CtlUI

value: normal control


title: RPMI 2

description: 75 SE


title: LNCaP_RNAseq_M0_rep1

description: 150 PE

source_name: M0 conditioned medium 1


title: LNCaP_RNAseq_CTRL_rep3

description: 150 PE

source_name: RPMI 3


title: RPMI 1

description: 75 SE


title: exo1


title: AbxUI


title: nitro2


title: ESCC_KYSE30-Luc-GFP, in vivo  metastasis 2 months, rep1

city: Hong Kong

first: Ching Ngar

last: Wong

state: Hong Kong

address: Lab Block, 21 Sassoon Road,

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

description: Chromium 10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were done using Cell Ranger version 3
Assembly: Human Genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ESCC cell line

growth_protocol: In vitro, In vivo (6h, 48h, 2mo, 4mo)

extract_protocol:
Flow cytometry cell sorting
10X Genomics Chromium Next GEM Single Cell 3'

treatment_protocol: Lung dissection, single cell dissociation, lung cell removal, flow cytometry cell sorting

value: ESCC cell line

value: pulmonary metastasis 2 months


title: LNCaP_RNAseq_CTRL_rep1

description: 150 PE

source_name: RPMI 1


title: ESCC_KYSE30-Luc-GFP, in vivo  metastasis 4 months, rep1

description: Chromium 10X Genomics

value: pulmonary metastasis 4 months


title: LNCaP_RNAseq_CTRL_rep2

description: 150 PE

source_name: RPMI 2


title: AbxPR8

value: mouse lung


title: nitro1


title: LNCaP_RNAseq_M0_rep3

description: 150 PE

source_name: M0 conditioned medium 3


title: control 2

value: control


title: PA59 TCR CD8 T cell, lung, influenza, rep03

city: BOSTON

first: Aoi

last: Akitsu

state: MA

address: 35 Binney St., Boston

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
PA59_Lung_m03
STAR_Gene_Counts.csv

data_processing:
Adapters trimmed using FastqMcf (v1.05) and Cutadapt (v4.4).
RNA-Seq pipeline Viper
Sequenced RNA-Seq reads were aligned to the mouse genome (mm10) using the STAR (2.4.2a)
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

source_name: lung

extract_protocol:
Total RNA isolated using RNAaqueous-4PCR protocol (ThermoFisher) according to manufacturer's guidelines
Libraries were constructed using the SMART-Seq v4 Ultra low Input RNA kit (Takara) according to manufacturer's guidelines

value: lung

value: CD8+ T cells

value: responding to influenza A virus


title: Channel 16

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

data_processing:
For each of the 16 channels, all three types of sequencing libraries (mRNA, sgRNA, cell hashing) were uniquely indexed with the same Illumina index sequence. This results in a single pair of fastq files for each channel, necessitating computational separation of the three library types. Transcriptomic reads were mapped using STAR and STARsolo 2.7.10a against a custom gtf annotation based on gencode.v34.annotation.gtf (hg38). Reads that did not map to the transcriptome reference were subsequently mapped and counted using STARsolo against a custom fasta reference containing guide sequences and a fasta reference with hash label sequences.
The output transcriptome matrices from STARsolo underwent initial filtering, akin to the 10x Cell Ranger EmptyDrops filtering method. This retained cells with at least 10% UMI count of the 99th percentile UMI counts of the top expected cells number. From these filtered matrices, an initial Seurat object was created using CreateSeuratObject function with parameters min.cells = 5, min.features = 10, and all other parameters at default values. Mitochondrial and mRNA content (percent.mt, nCount_RNA) were used to filter out outlier cells. To identify cell multiplets and determine cell population (untreated or activated), cell labels (hashes) were called using MULTI-seq approach (deMULTIplex::classifyCells in R). Only cells with exactly one known label were retained. Then, sgRNA calling was performed using a binomial test, with total sgRNA UMI counts used to derive background frequencies. A threshold of 0.05 on Benjamini-Hochberg- corrected p-values (per channel) was used to generate the final calls.
The sgRNA assays produced sparse matrices where a value of 1 indicates that the respective cell is carrying the corresponding sgRNA, and 0 elsewhere. Following these steps, results from 16 channels were merged together, and the merged counts were normalized using NormalizeData and scaled using ScaleData. Cell cycle scoring was performed via CellCycleScoring , PCA was calculated using RunPCA, and UMAP was calculated on first 30 principal components using RunUMAP in Seurat.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Perturb-seq

source_name: Jurkat

extract_protocol:
We chose the Jurkat E6 cell line expressing dCas9-KRAB as our model to study. We transduced them with a genome-wide CRISPRi CROP-seq library at a high multiplicity of infection (MOI). The FACS-measured percentage of GFP positive cells was 99.6%, translating to an estimated MOI of ~6. From experience, we know that real MOI is typically higher than what is estimated from GFP positivity rate. After infection, we split the cells into two populations, including untreated cells and activated cells (cells treated with anti-TCR and anti-CD28 antibodies for approximately 24 hours to stimulate TCR signaling). Cells were then labelled with cell hashing antibodies. Multiple labels were used for the activated population to help with cell multiplet detection. Cells were loaded on 16 channels of 10x Chromium X instrument. We loaded on 115,000 cells per channel and the expected recovery rate was 60,000 cells per channel, including 24% multiplets. Samples were pooled unequally before they were loaded on the Chromium X: 10% untreated cells, 90% treated cells. A sequencing library was prepared using 3’Chemistry with a targeted primer panel: custom multiplex PCR step to enrich for specific transcript. Libraries were sequenced on NovaSeq S4 PE100 in asymetric read mode (R1: 28 cycles; R2: 172 cycles), with PhiX concentration of 1%. The expected coverage is around 9,000 to 10,000 input reads per cell.
The genome-wide CRISPRi sgRNA library was designed to target the transcription start site (TSS) coordinates, calculated from publicly available FANTOM CAGE peaks data. In total 18,595 genes were targeted, with 4 sgRNAs per gene. Additionally, we designed another CRISPRi library targeting 3,220 genes with 4 sgRNAs per gene. This library was designed using TSS data specific to Jurkat cells, calculated from publicly accessible Jurkat CAGE-seq datasets. Both libraries were combined into a final library targeting 3,220 genes with 8 sgRNAs per gene and 15,375 genes with 4 sgRNAs per gene.

value: Jurkat

value: T cell


title: control 1


title: PA59 TCR CD8 T cell, lung, influenza, rep02

description:
PA59_Lung_m02
STAR_Gene_Counts.csv


title: ESCC_KYSE30-Luc-GFP, in vivo metastasis 6 hours, rep1

description: Chromium 10X Genomics

value: pulmonary metastasis 6 hours


title: PA59 TCR CD8 T cell, lung, influenza, rep01

description:
PA59_Lung_m01
STAR_Gene_Counts.csv


title: Wing disc after cell death CR40469-KO rep3

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

country: Spain

institute: University of Barcelona

data_processing:
Transcriptomic data was processed using the grape-nf pipeline (https://github.com/guigolab/grape-nf)
Sequence reads were aligned to the fly genome using STAR v2.4.0j with up to 4 mismatches per paired alignment
Genes and transcripts were quantified in TPMs using RSEM v1.2.21
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Drosophila melanogaster

source_name: Third instar larvae wing imaginal discs

extract_protocol:
RNA was isolated using Quick-RNA Microprep Kit (Zymo Research) followed by RNA Clean and Concentrator-5 Kit (Zymo Research). 500 ng of total RNA was used for the construction of sequencing libraries.
Total RNA for RNA libraries was reverse trancripted and ribosomal RNA was depleted by selecting the poly-A transcripts.

value: Third instar larvae wing imaginal discs

value: Ectopic expression of rpr for 16 hours


title: PA59 TCR CD8 T cell, lymph node, influenza, rep03

description:
PA59_LN_m03
STAR_Gene_Counts.csv

source_name: lymph node

value: lymph node


title: PA59 TCR CD8 T cell, lymph node, influenza, rep02

description:
PA59_LN_m02
STAR_Gene_Counts.csv


title: Wing disc after cell death CR40469-KO rep1


title: Wing disc after cell death CR40469-KO rep2


title: ESCC_KYSE30-Luc-GFP, in vitro, rep1

description: Chromium 10X Genomics

value: in vitro


title: Channel 12


title: PA59 TCR CD8 T cell, lymph node, influenza, rep01

description:
PA59_LN_m01
STAR_Gene_Counts.csv


title: ESCC_KYSE30-Luc-GFP, in vivo  metastasis 48 hours, rep1

description: Chromium 10X Genomics

value: pulmonary metastasis 48 hours


title: Channel 14


title: PA27 TCR CD8 T cell, lung, influenza, rep03

description:
PA27_Lung_m03
STAR_Gene_Counts.csv


title: antiCXCR2_early

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

institute: Institute of oncology research

data_processing:
Sequencing data were processed by CellRanger (version 3.1.0)
To reduce the ‘dropout’ phenomenon, RMagic package was used on gene-counts71
To filter the cells, we removed those that had more than 25% expression on mitochondrial genes, fewer than 100 total genes expressed and we considered only protein-coding genes defined using getBM (biomaRt package). All the samples were integrated using Seurat package (FindIntegrationAnchors and IntegrateData functions). Principal component analysis (PCA) dimensionality reduction considered the top 2000 most variable features identified. Moreover, the dimensional reduction technique t-distributed stochastic neighbor embedding (t-SNE) and UMAP were applied using the RunTSNE and RunUMAP functions from Seurat.
Differentially expressed genes (DEGs) were identified using FindAllMarkers or FindMarker functions (test.use=MAST). Genes were identified as differentially expressed in a particular set of cells if FDR < 0.05 and minimum expression in at least 30% of cells.
Assembly: mm10
Supplementary files format and content: rmagic counts

source_name: CD45+ cells

growth_protocol: TRAMP-C1 cells (2.5x106) were injected in 8-week-old male C57BL6/N mice. Mice were maintained under specific pathogen-free conditions.

extract_protocol:
TRAMP-C1 allografts were resected from C57/BL6N-tumor bearing mice either 12 days (Early phase) or 24 days (Late phase) after the initiation of the treatment. Enzalutamide, Enzalutamide + anti-IL-23 and Enzalutamide + aCXCR2 therapies were started the day after surgical castration.For single-cell RNAseq, tissues were digested in Digestion Buffer composed by RPMI 1640 Normal medium, Collagenase D (1 mg/mL), DNAse (100 U/mL) and HEPES (25 mM), in the presence of RNase Inhibitor Murine (New England Biolabs). The cell suspension was incubated for 40 min at 37 °C on a rocker. The digestion was stopped adding Normal medium and cell suspension was filtered by a 100 mm cell strainer and kept on ice for 4 min. After further filtering, cell suspension was spun down at 1500 rpm for 5 min at 4°C and Cell subsets were enriched by FACS sorting. Flow Cytometry staining of tumors was performed using the following antibodies: anti-CD45-bv605 (clone 30-F11), and anti-CD11b-bv421 (clone M1/70); and anti-Gr1-APC (clone RB6-8C5), and 7AAD (eBioscience). The 7AAD negative cells were sorted as follows: i) CD45+/CD11b+/Gr1+; ii) CD45+/CD11b-/Gr1-; iii) CD45-. After counting, cells were mixed together in ratio 1:1:1 to perform single-cells sequencing.
Single-cell suspensions were processed with Single Cell 3′ Reagent Kit v3 (Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Single Cell G Chip Kit, 10x Genomics) and Chromium Controller (10x Genomics) according to the protocol at the BIOS+ Genomics Facility in Bellinzona. The generated libraries were sequenced using Illumina NextSeq500 Systems accordingly with the 10x Genomics manual.

treatment_protocol: Surgical castration was performed when tumors were approximately 100 mm3, under anesthesia with isoflurane. Enzalutamide was administered on a Monday through Friday schedule by oral gavage; anti-IL-23 monoclonal antibody and Rat IgG1 kappa Isotype Control were intraperitoneally injected twice a week (100μg/mouse). αCXCR2 (AZD5069; AstraZeneca) was administered with daily intraperitoneal injections at a final concentration of 100mg/kg on a Monday through Friday schedule. Based on tumor growth curves, early phase of therapy response was defined as the first two weeks of treatment.

value: CD45+ cells


title: antiIL23_early2


title: Channel 13


title: Wing disc after cell death control rep3

value: salE/Pv-LHG:tub-Gal80TS; lexO-rpr


title: antiIL23_early


title: Channel 15


title: Wing disc after cell death control rep1


title: CtlUI HTO

source_name: mouse lung

value: all cells

value: normal control


title: ENZA_early2

value: Enzalutamide


title: Channel 10


title: PA27 TCR CD8 T cell, lung, influenza, rep02

description:
PA27_Lung_m02
STAR_Gene_Counts.csv


title: PA27 TCR CD8 T cell, lung, influenza, rep01

description:
PA27_Lung_m01
STAR_Gene_Counts.csv


title: PA27 TCR CD8 T cell, lymph node, influenza, rep03

description:
PA27_LN_m03
STAR_Gene_Counts.csv


title: ENZA_early


title: Channel 9


title: A375-M8-miR-876

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
RNA-Seq FASTQ files underwent pseudoalignment to the human transcriptome (Ensembl version 72) with the software Kallisto, using AltAnalyze v.2.1.4. Differential expression analyses were performed in AltAnalyze using an empirical Bayes moderated t-test (fold>1.2, p<0.05).
Assembly: hg19
Supplementary files format and content: Table delimited text file of TPM values

source_name: Skin

growth_protocol: A panel of melanoma cell lines was utilized to assess the expression of miR-876, including C8161.9 (obtained from Dr. D. Welch, UAB, USA), A375 (ATCC, Manassas, VA), LOX (a gift from Dr. Oystein Fodstad, University of Oslo, Norway), 1205-Lu (Coriell Institute, Camden, NJ), and Ma-Mel-12, a short-term melanoma culture (a gift from Dr. Dirk Schadendorf, University of Essen, Germany), as previously described [13]. Human epidermal melanocytes (HEM), used as a control, were obtained from Zen-Bio (Durham, NC).  Further characterization of the role of miR-876 was performed in C8161.9 and A375 cells. C8161.9 cells were grown in DMEM/F12 with 5% fetal bovine serum (FBS) (Invitrogen Life Technologies, Carlsbad, CA), and A375 cells were grown in RPMI-1640 with 5% FBS. Cell culture media was supplemented with 1X penicillin/streptomycin (Thermo Fisher Scientific, South San Francisco, CA) and cells were grown at 37ºC and 5% CO2. All cell lines were routinely tested for mycoplasma contamination using the MycoFluor Mycoplasma Detection Kit (Thermo Fisher Scientific, South San Francisco, CA) following the manufacturer’s instructions.

extract_protocol:
RNA was extracted using Qiagen Rneasy Kit, 500 ng of total RNA was used to construct libraries.
The RNA-Seq libraries were prepared from the purified RNA by using TruSeq RNA Library Prep Kit v2 (Illumina) for gene expression analyses.
Paired-end RNA-Seq was performed with HiSeq (Illumina). An average of ~40 million paired-end reads, stranded reads on an Illumina 2500

value: Skin

value: Melanoma

value: BRAF Mutant (V600E)


title: UNCTX

value: Untr


title: A375-M7-miR-876


title: CTXnoENZA

value: Castration


title: A375-M16-miR-876


title: Channel 7

value: Jurkat

value: T cell


title: Channel 8


title: PA27 TCR CD8 T cell, lymph node, influenza, rep02

description:
PA27_LN_m02
STAR_Gene_Counts.csv

value: CD8+ T cells

value: responding to influenza A virus


title: antiCXCR2_late


title: Wing disc after cell death control rep2

value: Third instar larvae wing imaginal discs

value: Ectopic expression of rpr for 16 hours


title: PA27 TCR CD8 T cell, lymph node, influenza, rep01

description:
PA27_LN_m01
STAR_Gene_Counts.csv

value: lymph node


title: Channel 6


title: Channel 11


title: A375-M1-Control-miR

description: Control-miR

value: Control-miR


title: PA25 TCR CD8 T cell, lung, influenza, rep03

description:
PA25_Lung_m03
STAR_Gene_Counts.csv

value: lung


title: A375-M9-Control-miR

description: Control-miR


title: PTEN_CTX_2

description: 10x Genomics

data_processing:
Sequencing data were processed by CellRanger (version 3.1.0)
To reduce the ‘dropout’ phenomenon, RMagic package was used on gene-counts71
To filter the cells, we removed those that had more than 25% expression on mitochondrial genes, fewer than 100 total genes expressed and we considered only protein-coding genes defined using getBM (biomaRt package). All the samples were integrated using Seurat package (FindIntegrationAnchors and IntegrateData functions). Principal component analysis (PCA) dimensionality reduction considered the top 2000 most variable features identified. Moreover, the dimensional reduction technique t-distributed stochastic neighbor embedding (t-SNE) and UMAP were applied using the RunTSNE and RunUMAP functions from Seurat.
Differentially expressed genes (DEGs) were identified using FindAllMarkers or FindMarker functions (test.use=MAST). Genes were identified as differentially expressed in a particular set of cells if FDR < 0.05 and minimum expression in at least 30% of cells.
Assembly: mm10
Supplementary files format and content: Rmagic counts of all samples

source_name: prostate

growth_protocol: Ptenpc−/− mice were maintained under specific pathogen-free conditions.

extract_protocol:
All prostate lobes were collected and processed to obtain a single-cell suspension. Tumors were collected 16 weeks after either sham-operation or surgical castration. Tissues were digested in Digestion Buffer composed by RPMI 1640 Normal medium, Collagenase D (1 mg/mL), DNAse (100 U/mL) and HEPES (25 mM), in the presence of RNase Inhibitor Murine (New England Biolabs). The cell suspension was incubated for 40 min at 37 °C on a rocker. The digestion was stopped adding Normal medium and cell suspension was filtered by a 100 mm cell strainer and kept on ice for 4 min. After further filtering, cell suspension was spun down at 1500 rpm for 5 min at 4°C and Cell subsets were enriched by FACS sorting. Flow Cytometry staining of tumors was performed using the following antibodies: anti-Epcam-FITC (clone G8.8), anti-CD45-bv605 (clone 30-F11), and anti-CD11b-bv421 (clone M1/70); and anti-Gr1-APC (clone RB6-8C5), and 7AAD (eBioscience). the 7AAD negative cells were sorted: i) Epcam+, ii) Epcam-/CD45+ and iii) Epcam-/CD45-. After counting, cells were mixed together in ratio 1:1:1 to perform single-cells sequencing.
Single-cell suspensions were processed with Single Cell 3′ Reagent Kit v3 (Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Single Cell G Chip Kit, 10x Genomics) and Chromium Controller (10x Genomics) according to the protocol at the BIOS+ Genomics Facility in Bellinzona. The generated libraries were sequenced using Illumina NextSeq500 Systems accordingly with the 10x Genomics manual.

treatment_protocol: Surgical castration was performed on 8-week-old Ptenpc-/- mice under anesthesia with isoflurane. Prostate tumors were resected from either 10-week-old, sham-operated (hormone-sensitive, HS) or castration-resistant (16 weeks after surgical castration, CR) 24-week-old Ptenpc−/− mice.

value: prostate


title: A375-M6-Control-miR

description: Control-miR


title: Channel 3


title: antiIL23_late

value: CD45+ cells


title: PA25 TCR CD8 T cell, lymph node, influenza, rep03

description:
PA25_LN_m03
STAR_Gene_Counts.csv


title: ENZA_late

value: Enzalutamide


title: PA25 TCR CD8 T cell, lung, influenza, rep02

description:
PA25_Lung_m02
STAR_Gene_Counts.csv


title: Channel 5


title: Channel 4


title: Channel 2


title: tho2d, INPUT, 8

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

country: South Korea

institute: Kyungpook National University

data_processing:
All FASTA RAW sequences were quality controlled using FastQC v0.11.7
ChIP-seq reads were trimmed using Trimmomatic v0.38
ChIP-seq reads were aligned to the Saccharomyces cerevisiae reference genome (sacCer3) using BowTie v1.1.2
Peaks were called using MACS2 v2.1.1.20160309
Assembly: sacCer3
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

source_name: yeast cells

extract_protocol:
Formaldehyde was added to mid-log phase cells to a final concentration of 1% for 20 min. Crosslinking was quenched by addition of glycine to 240 mM. Crosslinked cells were collected via centrifugation, washed twice in TBS, and then lysed with glass beads in FA lysis buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS, protease inhibitor cocktail [Roche, 11697498001], and 1 mM PMSF [AmericanBio, AB01620]).
ChIP-seq libraries were prepared using the TruSeq DNA Sample prep kit according to manufacturer's protocols (TruSeq ChIP Sample preparation guide 15023092 Rev. B) and sequenced using 100 bp paired-end sequencing on an Illumina NovaSeq 6000 following manufacturer’s protocols.

value: yeast cells


title: PA25 TCR CD8 T cell, lung, influenza, rep01

description:
PA25_Lung_m01
STAR_Gene_Counts.csv


title: PA25 TCR CD8 T cell, lymph node, influenza, rep02

description:
PA25_LN_m02
STAR_Gene_Counts.csv


title: PTEN_CTX_1

description: 10x Genomics


title: ESCC_KYSE30-Luc-GFP, CD44 Negative (CD44 Low group), rep1

data_processing:
Software from Illumina (bcl2fastq) was used
Assembly: Human Genome GRCh38

growth_protocol: In vitro cell culture

extract_protocol:
Total RNA extraction
cDNA libraries prepared by KAPA mRNA HyperPrep Kit, targeting Poly-A containing mRNA

treatment_protocol: Antibody staining, flow cytometry cell sorting

value: ESCC cell line

value: FACS CD44 Negative


title: PA25 TCR CD8 T cell, lymph node, influenza, rep01

description:
PA25_LN_m01
STAR_Gene_Counts.csv


title: tho2d, INPUT, 2