title: Myocardian fibroblast, cultured, subject tp321, PF supernatant and TGFbR1i treated

value: subject tp321

value: percardial fluid supernatant + TGFbR1i


title: KD2

status: Public on Dec 06 2024

type: SRA

city: Beijing

first: Junling

last: Fu

address: 北京市长椿街45号

country: China

institute: 首都医科大学宣武医院

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchword
Assembly: mm10
Supplementary files format and content: counts, FPKM

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: brain

tag: Sex

value: male

tag: genotype

value: db/db

tag: treatment

value: ketogenic diet (KD)


title: KD4


title: sdg2_H2Aub_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

library_source: genomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

tag: cell type

value: Arabidopsis seedlings

tag: chip antibody


title: Myocardian fibroblast, cultured, subject tp307, PF supernatant treated

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

data_processing:
Bulk-RNA sequencing (RNASeq) reads were pseudo-mapped to NCBI RefSeq human transcript models using Kallisto 0.42.4
Assembly: GRCh38
Supplementary files format and content: The tab-delimited processed counts file for each sample contains two columns: the NCBI RefSeq transcript accession, and the Transcripts Per Million normalized read count for that transcript.

molecule: polyA RNA

organism: Homo sapiens

source_name: myocardial fibroblast

growth_protocol: Fibroblasts isolated from the right atrial appendage were minced into 0.5-1mm fragments and suspended in Iscove’s Modified Dulbecco’s Medium (IMDM; Lonza, Walkersville, MD) supplemented with 10% fetal bovine serum (Gibco by Life Technologies, Burlington, Canada) and 50,000 units of penicillin-streptomycin (Life Technologies, Burlington, Canada). Tissue suspensions were plated and cultured at 37°C in 5% CO2. Passages 1-4 were used for experiments. All cells were serum starved for 24-hours prior to mRNA isolation.

extract_protocol:
RNeasy kit (Qiagen) per the manufacturer’s protocol
NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Isolation Module

value: myocardial fibroblast

tag: individual

value: subject tp307

value: percardial fluid supernatant


title: cspg4-cKO_spinalcord_EAE_2

city: Taipei

first: Pei-Lin

last: Cheng

address: No. 128 Acdemia Rd., Section 2, Nankang

country: Taiwan

institute: Institue of Molecular Biology, Academia Sinica

data_processing:
The paired-end, 150-bp raw sequencing reads for each sample were aligned to the mouse reference genome and transcriptome (GRCm39) using STAR (v 2.7.10)
The expected read counts of each gene were estimated by RSEM (v1.3.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes the raw read count for each sample

source_name: spinal cord

growth_protocol: non

extract_protocol:
Total RNA was extracted utilizing the RNeasy Mini Kit (Qiagen; Cat# 74104) and its concentration was determined using a Nanodrop 2000 spectrophotometer and a Qubit fluorometer (both from ThermoFisher Scientific). The quality of the extracted RNA was evaluated using a 2100 Bioanalyzer (Agilent).
For bulk transcriptomics of EAE-affected spinal cords, library preparation was performed using the SureSelect Strand-Specific RNA Library Prep System (Agilent; Cat# G9691) following the manufacturer’s protocols. These samples were sequenced on the NovaSeq 6000 System (Illumina), achieving a sequencing depth of over 30 million 2x150bp paired-end reads.

treatment_protocol: Hooke Kits™ for EAE Induction in C57BL/6 Mice with MOG35-55/CFA emulsion and pertussis toxin was purchased from Hook laboratory (Cat# EK-2110). 9 to 13 weeks old female and male mice were used for immunization and EAE development.

value: spinal cord

tag: cell line

value: bulk

value: EAE


title: Myocardian fibroblast, cultured, subject tp300, PF supernatant and TGFbR1i treated

value: subject tp300


title: Col-0_H2Aub_rep5

value: wild type


title: KD1


title: NC1-8.2_2

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

country: USA

institute: Princeton

data_processing:
Micro-C data for D. melanogaster were aligned to the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly with BWA-MEM 82 using parameters -S -P -5 -M.
The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with pairtools (https://github.com/mirnylab/pairtools).  We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three.
The resultant files were indexed with pairix (https://github.com/4dn-dcic/pairix).
The pairs files for individual replicates were merged with pairtools, and then used to generate contact matrices at 100bp resolution with Cooler.
Finally, balancing and mcool file generation was performed using Cooler’s zoomify tool.
Assembly: dm6
Supplementary files format and content: mcool
Library strategy: Micro-C

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
Embryos were collected on yeasted apple juice plates in population cages. For nc1-8 embryos, plates were changed every 30 mins, and subjected to immediate fixation. For nc14 embryos, plates were laid for 1 hour, then collected, incubated for 2 hours at 25℃, and subjected to fixation. For stage 10-12 embryos, plates were laid for 2 hours, incubated for 6 hours at 25C, and subjected to fixation.
Micro-C libraries were prepared as previously described in Batut…Levine 2022.

value: embryo

value: wt

tag: Stage


title: Myocardian fibroblast, cultured, subject tp308

value: subject tp308


title: C4

value: control


title: 0731 LAL KO hLAL mRNA

city: Montreal

first: Simon-Pierre

last: Gravel

state: QC

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

institute: University of Montreal

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed sequences were aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
Gene expressions were obtained from STAR both as readcounts and TPM values as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in FPKM and TPM values, for these stranded RNA libraries
DESeq2 version 1.30.1 was then used to normalize gene readcounts.
Assembly: GRCm38
Supplementary files format and content: RSEM TPM for 28 samples
Supplementary files format and content: STAR counts for 28 samples

source_name: Liver

growth_protocol: Mice were fed with a regular diet (Altromin). The study started at 4-6 weeks of age and the end point was 8 weeks later

extract_protocol:
Total RNA from the liver was extracted using the RNeasy Mini Kit (No. 74106, Qiagen).
Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific)

treatment_protocol: WT mice treated with empty nanoparticles (WT+Blank), LAL-/- were injected with either empty nanoparticles (LAL-/-+Blank) or with the mRNA-LNP treatment (LAL-/-+F23)

value: Liver

value: LAL-/-


title: NC1-8.1_2


title: Myocardian fibroblast, cultured, subject tp300


title: 0629 LAL KO hLAL mRNA

value: F23 at later age


title: C2

value: brain

value: male

value: db/db


title: Myocardian fibroblast, cultured, subject tp308, PF supernatant and TGFbR1i treated

value: myocardial fibroblast

value: percardial fluid supernatant + TGFbR1i


title: IP_RING1A-in-al24567_FLAG_rep2

value: Arabidopsis seedlings

value: SIGMA, F1804

value: 1305-RING1A-FLAG transformed plants (in al2/4/5/6/7)


title: 0695 LAL KO hLAL mRNA


title: al24567_ATACseq rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
ATAC-enriched peaks were called uing MACS2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
The nuclei of 11-day-old Arabidopsis wild type and four mutants were extracted in a nuclear extraction buffer (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 0.3% [v/v] Triton X-100, and 0.1% cocktail, Roche) and resuspended in a nuclear purification buffer (20 mM MOPS pH 7.0, 90 mM KCl, 40 mM NaCl, 2 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.5 mM spermidine, 0.2 mM spermine, and 0.1% cocktail, Roche). The quality of the nuclei was determined under a microscope, followed by Tn5 fragmentation and DNA fragment purification.
Libraries were built for ATAC-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)


title: H3K27ac HiChIP: HS68 HCMV-infected Replicate 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Pooled samples were created by combining the fastq files for the three replicates.
HiC-Pro (version 2.11.4) was used to align and filter read pairs and identify the contact map (Servant et al. 2015). MboI restriction sites and default parameters were used to align the reads to the hg19 genome.
Loops were called using FitHiChIP (version 11.0) (Bhattacharyya et al. 2019). The overlap conservative peaks generated by the ENCODE pipeline for the H3K27ac ChIP-seq data were used as the input peaks. The parameters for FitHiChIP were the following: interaction type of “peak to all”; bin size of 10 kb; lower loop distance of 20 kb; upper loop distance of 20 mb; background model of loose; bias correction of coverage bias regression; merge filtering was enabled; and FDR of 0.01.
We identified differential looping events using the DiffAnalysisHiChIP.r script included in the FitHiChIP software (Bhattacharyya et al. 2019) with a default bcv parameter value of 0.4 and cutoffs of > 2 fold change and FDR < 0.01.
Assembly: hg19
Supplementary files format and content: allValidPair files created by HiC-Pro. Files are in tsv format and contain the standard HiC-Pro output.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10
Supplementary files format and content: KR normalized hic files were generated using the hicpro2juicebox.sh script from HiC-Pro (Servant et al. 2015) and KR normalized using Juicer Tools (https://github.com/aidenlab/juicer/wiki/Juicer-Tools-Quick-Start)
Supplementary files format and content: Loop files created by FitHiChIP. Files are in tsv format and contain the standard FitHiChIP output.
Supplementary files format and content: Loops identified as differential by the DiffAnalysisHiChIP.r script. Files are in tsv format and contain the standard DiffAnalysisHiChIP.r output.
Library strategy: HiChIP

growth_protocol: HS68 cells were maintained in DMEM supplemented with 10% HyClone FetalClone III serum (FC-III) and antiobiotics in a humidified incubator with 5% CO2 at 37 C.

extract_protocol:
10 million cells were cross-linked with 1% formaldehyde, followed by a cell lysis with Hi-C lysis buffer, following Mumbach et al. (Mumbach et al. 2016).
HiChIP libraries were prepared following Mumbach et al. (Mumbach et al. 2016).

treatment_protocol: HS68 cells were infected with the TB40/E clinical isolate of HCMV at a multiplicity of infection (MOI) of 5. Cells were harvested 48 hours post infection.

value: Foreskin fibroblast

tag: infection

value: TB40/E HCMV


title: C1


title: H3K27ac HiChIP: HS68 HCMV-infected Replicate 1


title: ff_3

city: Shanghai

first: Yanhao

last: Yu

address: Yueyang Street

institute: Center of Excellence in Molecular Cell Science

data_processing:
First, the raw paired-end RNA-seq FASTQ data were trimmed to remove low-quality bases and adaptor sequences by Trim Galore (v0.5.0) with default settings. Then, the clean RNA-seq FASTQ data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were reserved for downstream analysis. Count matrixes were calculated by featureCounts (v1.6.4) with the parameters -p -M -O. DEG analysis was performed using DESeq2 package with the raw count. Only genes with P value less than 0.05 and at least two-fold change were considered to be differentially expressed. DEGs were submitted to the Database for Annotation, Visualization and Integrated Discovery (DAVID) 6.7 (https://david.ncifcrf.gov) for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Gene set enrichment analysis(GSEA) was conducted using clusterProfiler package.
Assembly: mm10
Supplementary files format and content: comma-separated values file, raw counts for gene expression.

source_name: lung tissue

growth_protocol: All animal experiments were performed under strict compliance with the Institutional Animal Care and Use Committee (IACUC) of CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Chinese Academy of Sciences. All animal studies were performed according to protocols approved by the IACUC (Protocols: SIBCB-NAF-15-003-s202-013) and in accordance with the guidelines and ethical regulations of the IACUC.

extract_protocol:
Approximately 500 premalignant cells were lysed, and the reverse-transcribed RNA was preamplified to obtain enough cDNA by a modified SMART-Seq2 protocol.
Approximately 500 premalignant cells were lysed, and the reverse-transcribed RNA was preamplified to obtain enough cDNA by a modified SMART-Seq2 protocol. cDNA was quantified by Qubit 4 (Invitrogen), and then 1 ng cDNA was used for DNA library construction with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503).

value: lung tissue

value: APE1 flox/flox

value: 12 wk Cre-adenoviral infection


title: Col-0_ATACseq rep2

value: wild type


title: IP_RING1A-in-al24567_FLAG_rep1


title: fN_3

value: APE1 flox/N211A


title: Input-RING1A-in-al24567_FLAG


title: Myocardian fibroblast, cultured, subject tp320, PF supernatant and TGFbR1i treated

value: subject tp320


title: H3K27ac HiChIP: HS68 Uninfected Replicate 2


title: ff_1


title: fN_2


title: H3K27ac HiChIP: HS68 HCMV-infected Replicate 3


title: TEAD1 ChIP-seq: HS68 HCMV-infected Replicate 2

data_processing:
We performed quality control of raw sequencing reads using the ChIP-seq transcription factor Pipeline v2.2.0 from the ENCODE Project (https://www.encodeproject.org/pipelines/).
ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2. Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using the default parameters of MACS2.
The ENCODE blacklist region was removed upon establishing the final peak set.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each condition and used for downstream analyses.
DiffBind was used to find differential and non-differential ("shared") peaks using the conservative overlap peaksets. Peaks were considered significantly differential if the FDR was less than 0.01 and the fold change was at least 2-fold.
Assembly: hg19
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10
Supplementary files format and content: Peaks identified as either differential or shared by DiffBind. Files are in tsv format and contain the standard DiffBind output.

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared using the NEBNext Ultra II kit (NEB #E7645S) as per the instructions provided by the manufacturer.

value: ActiveMotif 61643, lot 34614001


title: 0665 LAL KO hLAL mRNA

value: Liver

value: LAL-/-


title: al24567_ATACseq rep1


title: fN_1


title: C3

value: brain

value: male

value: db/db

value: control


title: H3K27ac HiChIP: HS68 Uninfected Replicate 3


title: 0722 LAL KO hLAL mRNA


title: 0673 LAL KO hLAL mRNA


title: fWT_2

value: APE1 flox/+


title: ff_2


title: Col-0_H2A.Z rep1

value: Arabidopsis seedlings

value: our lab


title: 0708 LAL KO hLAL mRNA


title: 0669 WT empty

value: WT

value: Blank


title: TEAD1 ChIP-seq: HS68 Uninfected Replicate 1

value: Foreskin fibroblast


title: Map1-GFP_FE_Rep1

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of either Fold Enrichment (FE) vs Input-normalized Untagged control, or raw pileups (Input)

organism: Schizosaccharomyces pombe

growth_protocol: YEA, 30°C and 18°C, 2hrs

extract_protocol:
Cells were crosslinked using 3% PFA at 18°C for 30 min and cells were spun at 2,000g for 5 min, washed with PBS and treated with DMA at room temperature for 45min. Cells pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

tag: strain

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Map1-GFP::KanMX6

value: Abcam anti-GFP (cat# ab290)

tag: growth

value: Growth in YEA 30°C and 18°C/2hrs

tag: fixation

value: 3% PFA and DMA


title: al24567_H2A.Z rep1


title: fWT_3

value: lung tissue

value: 12 wk Cre-adenoviral infection


title: 0642 LAL KO hLAL mRNA

value: Liver

value: LAL-/-


title: 0654 LAL KO hLAL mRNA


title: Col-0_H2A.Z rep2

value: wild type


title: TEAD1 ChIP-seq: HS68 HCMV-infected Replicate 1

value: TB40/E HCMV

value: ActiveMotif 61643, lot 34614001


title: al24567_H2A.Z rep2


title: H3K27ac HiChIP: HS68 Uninfected Replicate 1


title: al24567_H3K27me3 rep2

value: millipore, 07-449


title: TEAD1 ChIP-seq: HS68 Uninfected Replicate 2


title: fWT_1

value: APE1 flox/+


title: 0632 LAL KO hLAL mRNA


title: CTCF ChIP-seq: HS68 HCMV-infected Replicate 2

value: ActiveMotif 61311, lot 17118005


title: 0677 WT empty

value: WT


title: 0681 WT empty

value: Blank


title: fWT_4


title: Col-0_H3K27me3 rep2

value: Arabidopsis seedlings


title: CTCF ChIP-seq: HS68 Uninfected Replicate 2

value: Foreskin fibroblast


title: minu12_H2Aub rep2


title: al24567_H3K27me3 rep1


title: Col-0_ATACseq rep1


title: RNAPII_8WG16_RNAPII_clr4Dphp2D_FE_Rep1

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: S. pombeV2 reference (Wood et al. 2002) with the sequence of the full 40 kbmatregion provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of either Fold Enrichment (FE) vs Input-normalized Untagged control, or raw pileups (Input)

growth_protocol: Cells were grown in YEA at 30°C and then shifted to 18°C for 2hrs

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php2delta::NatMX6 clr4delta::KanMX6

value: Santa Cruz Biotechnology, anti-Pol II (8WG16) Cat#sc56767

value: Growth in YEA 30 C and 18 C/2hrs


title: H3K27ac ChIP-seq: HS68 HCMV-infected Replicate 2


title: Col-0_H2Aub rep4


title: 0754 WT empty


title: Mca1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Mca1-GFP::KanMX6

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30°C and 18°C/2hrs

value: 3% PFA and DMA


title: ring1a1b_H2Aub rep2

value: ring1a-/- ring1b-/-


title: 0683  LAL KO empty

value: Liver

value: LAL-/-


title: CTCF ChIP-seq: HS68 HCMV-infected Replicate 1

value: TB40/E HCMV


title: 0671 WT empty


title: RNAPII_8WG16_RNAPII_WT_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E


title: Col-0_H3K27me3 rep1

value: millipore, 07-449

value: wild type


title: 0707 WT empty

value: WT

value: Blank


title: RNA-seq: HS68 HCMV-infected Replicate 2

data_processing:
RNA-seq reads were mapped to the hg19 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates generated by Salmon
DESeq2 was used to find differential gene expression. Gene expression was considered significantly differential if the FDR was less than 0.01 and the fold change was at least 2-fold.
Assembly: hg19 genome augmented with the HCMV TB40-BAC4 sequence (GenBank EF999921.1)
Supplementary files format and content: quant.sf file generated by Salmon: tab-delimited txt file containing TPM results for reads aligned to the hg19 genome augmented with the HCMV TB40-BAC4 sequence (GenBank EF999921.1). Quantification is done on the transcript level.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. Only the reads aligning to the human chromosomes are included in the file.
Supplementary files format and content: Differential genes identified by DESeq2. Files are in csv format and contain the standard DESeq2 output.

extract_protocol:
Total RNA was extracted from 5x10^6 cells using the Rneasy mini kit (Qiagen # 74104) according to the manufacturer's protocol. 500 ng of ribosomal-RNA depleted total RNA was used for library preparation.
Sequencing libraries were generated from the rRNA-depleted RNA using the Directional RNA Library Prep Kit

value: Foreskin fibroblast


title: CTCF ChIP-seq: HS68 Uninfected Replicate 1

value: ActiveMotif 61311, lot 17118005


title: 0692 WT empty


title: RNAPII_8WG16_RNAPII_clr4Dphp3D_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php3delta::KanMX6 clr4delta::KanMX6

value: Santa Cruz Biotechnology, anti-Pol II (8WG16) Cat#sc56767


title: al24567_H2Aub rep2

value: Arabidopsis seedlings


title: RNAPII_8WG16_RNAPII_clr4D_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 clr4delta::KanMX6 otr1R(Spn1)::ura4

value: Growth in YEA 30 C and 18 C/2hrs


title: 0635 LAL KO empty


title: 0724 WT empty


title: Col-0_H2Aub rep3


title: minu12_H2Aub rep1


title: ring1a1b_H2Aub rep1


title: H3K27ac ChIP-seq: HS68 Uninfected Replicate 1


title: Moc3-GFP_nda3KM311_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E Moc3-GFP::KanMX6 nda3-KM311

value: Abcam anti-GFP (cat# ab290)

value: 3% PFA and DMA


title: al24567_H2Aub rep1


title: RNAPII_8WG16_RNAPII_php2D_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php2delta::NatMX6 otr1R(Spn1)::ura4


title: Col-0_H2Aub rep2


title: RNAPII_8WG16_RNAPII_clr4Dmoc3D_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E moc3delta::KanMX6 clr4delta::KanMX6 otr1R(Spn1)::ura4


title: 0697 LAL KO empty

value: Liver

value: LAL-/-


title: RNAPII_8WG16_RNAPII_WT_Input_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E


title: Moc3-GFP_clr4∆_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Moc3-GFP::KanMX6 clr4delta::NatMX6


title: 0706 WT empty

value: WT

value: Blank


title: Col-0_H2Aub rep1

value: wild type


title: H3K27ac ChIP-seq: HS68 HCMV-infected Replicate 1

value: Foreskin fibroblast

value: TB40/E HCMV


title: 0718 LAL KO empty


title: RNA-seq: HS68 Uninfected Replicate 2


title: 0639 LAL KO empty


title: Php3-GFP_nda3KM311_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php3-GFP::KanMX6 nda3-KM311


title: Input_RING1A-in-WT_FLAG

value: Arabidopsis seedlings

value: SIGMA, F1804

value: 1305-RING1A-FLAG transformed plants (in Col-0)


title: Php3-GFP_cenH CCAATATGAC_FE_Rep1

description: Php3-GFP_cenH CCAATATGAC_FE_Rep1

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ cenH CCAATATGAC Php3-GFP::KanMX6

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs


title: RNAPII_8WG16_RNAPII_clr4Dphp5D_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E php5delta::KanMX6 clr4delta::KanMX6 otr1R(Spn1)::ura4

value: Santa Cruz Biotechnology, anti-Pol II (8WG16) Cat#sc56767

value: 3% PFA and DMA


title: H3K27ac ChIP-seq: HS68 Uninfected Replicate 2


title: Brd7_sh4, ATAC

city: Houston

first: Junfeng

last: Zhang

state: TX

address: 2130 W. Holcombe Blvd

department: Department of Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
All sequencing reads were mapped to the reference genome using the Bowtie 2 (v2.2.4), and duplicate reads were removed using Picard tools (v.1.126; http://broadinstitute.github.io/picard/). Low-quality mapped reads (MQ < 20) were removed from the analysis. Normalized BigWig files were generated using BEDTools (v.2.17.0) and the bedGraphToBigWig tool (v.4). Peak calling was performed using MACS (v1.4.2) and peak count tables were created using BEDTools.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: ATACseq

growth_protocol: 4T07-TGL cells were cultured in Dulbecco's Modified Eagle Medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) at 37 °C in 5% CO2. All cell lines used in this study were confirmed Mycoplasma-negative using the Universal Mycoplasma Detection Kit (ATCC 30-1012K).

extract_protocol:
ATACseq was performed in the mouse 4T07 cell line with or without Brd7 KO using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003 ,Cell Signaling Technologies) following the manufacturer's instructions, employing the  H3K27Ac Rabbit mAb (8173, Cell Signaling Technologies).
ChIP DNA was purified and sent to the MD Anderson Advanced Technology Genomics Core for library construction and sequencing.

value: 4T07-TGL cells

value: breast cancer cells


title: ATAC-seq: HS68 HCMV-infected Replicate 2

data_processing:
Quality control of raw sequencing reads was performed using the DNA Accessibility Pipeline v2.2.0 from the ENCODE Project.
ATAC-seq reads were aligned to the human genome (hg19) using Bowtie2. Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89)
Peaks were called using the default parameters of MACS2.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each cell type and condition and used for downstream analyses.
DiffBind was used to find differential and non-differential ("shared") peaks using the conservative overlap peaksets. Peaks were considered significantly differential if the FDR was less than 0.01 and the fold change was at least 2-fold.
Assembly: hg19
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format. Peaks are filtered based on q-value and contain only those with a q-value < 0.01
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10
Supplementary files format and content: Peaks identified as either differential or shared by DiffBind. Files are in tsv format and contain the standard DiffBind output.

growth_protocol: HS68 cells were maintained in DMEM supplemented with 10% HyClone FetalClone III serum (FC-III) and antibiotics in a humidified incubator with 5% CO2 at 37 C. ARPE19 cells were maintained in DMEM/F-12 supplemented with 10% Fetal bovine serum (FBS) and antibiotics in a humidified incubator with 5% CO2 at 37 C.

extract_protocol:
Transposase Tn5 with sequencing adapter sequences was used to cut the accessible DNA as detailed in Buenrostro et al. 2015.
The resulting accessible DNA sequences were isolated, and libraries were prepared using the OMNI ATAC protocol as detailed in Corces et al 2017.

treatment_protocol: HS68 and ARPE cells were infected with the TB40/E clinical isolate of HCMV. HS68 cells were infected at a multiplicity of infection (MOI) of 5 and ARPE cells at an MOI of 10. Cells were harvested 48 hours post infection.


title: RNA-seq: HS68 Uninfected Replicate 1


title: IP_AL2-PHD-M2_FLAG rep1

value: 1305-AL2-PHD-M2-FLAG transformed plants (in Col-0)


title: 0675 LAL KO empty

value: Liver

value: LAL-/-

value: Blank


title: ATAC-seq: ARPE-19 HCMV-infected Replicate 2

value: Retinal epithelial

value: TB40/E HCMV


title: RNA-seq: HS68 HCMV-infected Replicate 1

value: Foreskin fibroblast


title: Php3-GFP_clr4∆_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php3-GFP::KanMX6 clr4delta::KanMX6


title: 0634 LAL KO empty


title: Input_AL2-PHD-M2_FLAG

value: Arabidopsis seedlings

value: SIGMA, F1804


title: ATAC-seq: ARPE-19 HCMV-infected Replicate 1


title: IP_RING1A-in-WT_FLAG rep2

value: 1305-RING1A-FLAG transformed plants (in Col-0)


title: IP_RING1A-in-WT_FLAG rep1


title: shNTC, ATAC

value: control


title: 0638 LAL KO empty


title: ATAC-seq: ARPE-19 Uninfected Replicate 1


title: ATAC-seq: ARPE-19 Uninfected Replicate 2


title: CD45+cells, 4T07-BRD7KO_lung

library_source: transcriptomic single cell

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger (v.3.0.2). Quality control was then performed on the cells to calculate the number of genes, UMIs, and the proportion of mitochondrial genes for each cell using Seurat R package V3 (https://satijalab.org/seurat/), and  cells with a low number of covered genes (gene count < 500) and high mitochondrial counts (mt-genes > 0.1) were excluded. Gene expression matrices were normalized by the NormalizeData function and 2,000 features with high cell-to-cell variation were calculated using the FindVariableFeatures function.
Assembly: mm10
Supplementary files format and content: RAR file including sparse data matrices processed using CellRanger v3 for each sample

source_name: tissue

extract_protocol:
Mouse lung tissues were harvested and dissociated to single cells. Live CD45-positive immune cells were sorted  and resuspended at a concentration of 1 × 106 per ml in 1× PBS with 0.4% BSA for 10x genomics processing. Cell suspensions were then loaded onto a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEM). Approximately 10,000 cells per sample were loaded.
scRNA-seq libraries were prepared using the following Single Cell 3′ Reagent Kits: Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237), Single Cell 3′ Chip Kit v2 (PN-120236), and i7 Multiplex Kit (PN-120262; 10x Genomics), as directed by the Single Cell 3′ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A).
Libraries were run on an Illumina HiSeq 4000 system (SY-401-4001, Illumina) with 2 × 150 paired-end reads for approximately >90% sequencing saturation. cDNA integrity, libraries quality , number of cells sequenced, and mean number of reads per cell were confirmed before further processing.

value: tissue

value: Cd45+ cells sorted by FACS


title: IP_AL2-DEL-PHD_FLAG rep2

value: 1305-AL2-DEL-PHD-FLAG transformed plants (in Col-0)


title: 0644 LAL KO empty


title: CD45+cells, 4T07-TGL_lung


title: Php3-GFP_moc3∆_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php3-GFP::KanMX6 moc3delta::KanMX6

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs

value: 3% PFA and DMA


title: Php3-GFP_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php3-GFP::KanMX6 otr1R(Spn1)::ura4


title: Moc3-GFP_php2∆_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E Moc3-GFP::KanMX6 php2delta::KanMX6


title: SW480 cells, siYTHDC1_3, rep2

city: shenzhen

first: jiadong

last: liu

address: 1088 Xueyuan Avenue

institute: Southern university of science and and technology

data_processing:
The reference transcriptome index was produced with RSEM using the reference genome hg38 and ensemble Homo_sapiens.GRCh38.109.
Sequence resds were trimmed for adaptor sequence/low-quality sequence using Trimgalore
The reads were mapped to the reference transcriptome using RSEM and bowtie 2 (with options ‘rsem-calculate-expression -p 12–bowtie2–no-bamout’)
The reads were normalized using EDASeq
Assembly: hg38
Supplementary files format and content: CSV file includes raw counts for each sample

growth_protocol: Colorectal cancer cell lines HCT116 and SW480 were cultured in DMEM supplemented with 10% fetal bovine serum , 1% NEAA, Gluta-MAX, and penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
RNA was extracted from the cells according to the instructions of Total RNA Kit I (Omega, R6834).
RNA-seq library was constructed as the instruction of VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-02).

value: Colorectal cancer cell lines

value: YTHDC1 knockdown #3


title: IP_AL2-PHD-M2_FLAG rep2

value: 1305-AL2-PHD-M2-FLAG transformed plants (in Col-0)


title: Php3-GFP_php2∆_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E Php3-GFP::KanMX6 php2delta::KanMX6


title: ATAC-seq: HS68 HCMV-infected Replicate 1

value: Foreskin fibroblast

value: TB40/E HCMV


title: ATAC-seq: HS68 Uninfected Replicate 2


title: Brd7_sh1, ATAC

value: 4T07-TGL cells

value: breast cancer cells


title: Input_AL2-DEL-PHD_FLAG

value: Arabidopsis seedlings

value: SIGMA, F1804


title: Gaf1-GFP_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Gaf1-GFP::KanMX6


title: ATAC-seq: HS68 Uninfected Replicate 1


title: Php2-GFP_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php2-GFP::KanMX6 otr1R(Spn1)::ura4


title: SW480 cells, siYTHDC1_3, rep1


title: IP_AL2-PAL-M7_FLAG rep2

value: 1305-AL2-PAL-M7-FLAG transformed plants (in Col-0)


title: SW480 cells, siYTHDC1_2, rep2

value: YTHDC1 knockdown #2


title: Input_AL2-PAL-M7_FLAG


title: Php3-GFP_FE_Rep1

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs

value: 3% PFA and DMA


title: Moc3-GFP_cenH CCAATATGAC_FE_Rep1

description: Moc3-GFP_cenH CCAATATGAC_FE_Rep1

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ cenH CCAATATGAC Moc3-GFP::KanMX6


title: Brd7-KO2, input, rep2

source_name: 4T07-TGL cells

extract_protocol:
ChIP was performed in the mouse 4T07 cell line with or without Brd7 KO using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003 ,Cell Signaling Technologies) following the manufacturer's instructions, employing the  H3K27Ac Rabbit mAb (8173, Cell Signaling Technologies).
ChIP DNA was purified and sent to the MD Anderson Advanced Technology Genomics Core for library construction and sequencing.

tag: antibody


title: IP_AL2-DEL-PHD_FLAG rep1

value: 1305-AL2-DEL-PHD-FLAG transformed plants (in Col-0)


title: Brd7-KO1, input, rep1


title: IP_AL2-DEL-PAL_FLAG rep2

value: 1305-AL2-DEL-PAL-FLAG transformed plants (in Col-0)


title: Pcr1-FLAG_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Pcr1-FLAG::KanMX6


title: IP_AL2-DEL-PAL_FLAG rep1


title: SW480 cells, siYTHDC1_2, rep1

value: Colorectal cancer cell lines


title: IP_AL2-PAL-M7_FLAG rep1


title: SW480 cells, siNC, rep1

value: knockdown negetive control


title: Atf1-FLAG_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Atf1-FLAG::KanMX6


title: sgControl, input, rep1

value: 4T07-TGL cells

value: breast cancer cells

value: sgControl


title: Moc3-GFP_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Moc3-GFP::KanMX6


title: HCT116 cells, siYTHDC1_3, rep2

value: YTHDC1 knockdown #3


title: Php5-GFP_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php5-GFP::KanMX6 otr1R(Spn1)::ura4


title: Input_AL2-DEL-PAL_FLAG

value: Arabidopsis seedlings

value: SIGMA, F1804


title: Brd7-KO1, ChIP, rep1


title: CD45+cells, untreated_lung

value: tissue

value: Cd45+ cells sorted by FACS


title: Brd7-KO2, ChIP, rep2


title: Php2-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php2-GFP::KanMX6 otr1R(Spn1)::ura4

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs

value: 3% PFA and DMA


title: IP_AL2-WT_FLAG rep2

value: 1305-AL2-FLAG transformed plants (in Col-0)


title: HCT116 cells, siYTHDC1_3, rep1

value: Colorectal cancer cell lines


title: HCT116 cells, siYTHDC1_2, rep2

value: YTHDC1 knockdown #2


title: Untag_Input_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E


title: sgControl, ChIP, rep2

value: 4T07-TGL cells

value: breast cancer cells


title: Pcr1-FLAG_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Pcr1-FLAG::KanMX6


title: sgControl, input, rep2

value: sgControl


title: cx3cr1-cKO_brain_O4+ cell

data_processing:
The single-end, 76-bp raw sequencing reads for each sample were aligned to the mouse reference genome and transcriptome (GRCm39) using STAR (v 2.7.10)
The expected read counts of each gene were estimated by RSEM (v1.3.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes the raw read count for each sample

extract_protocol:
Total RNA was extracted utilizing the RNeasy Mini Kit (Qiagen; Cat# 74104) and its concentration was determined using a Nanodrop 2000 spectrophotometer and a Qubit fluorometer (both from ThermoFisher Scientific). The quality of the extracted RNA was evaluated using a 2100 Bioanalyzer (Agilent).
For O4+ cell-specific transcriptomics, library preparation was performed using the SMART-Seq Stranded Kit (Takara Bio; Cat# 634442) following the manufacturer’s protocols. Sequencing was carried out on a NextSeq 500 system (Illumina) with the NextSeq 500/550 High Output Kit v2.5 (Illumina; Cat#20024906).

value: brain

value: O4+ cell

value: oligodendrocytes


title: IP_AL2-WT_FLAG rep1

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: Arabidopsis seedlings

value: SIGMA, F1804


title: IP_AL6_GFP rep2

value: 1305-AL6-GFP transformed plants (in Col-0)


title: sgControl, ChIP, rep1


title: HCT116 cells, siNC, rep1

value: knockdown negetive control


title: SW480 cells, siNC, rep2


title: HCT116 cells, siYTHDC1_2, rep1


title: Atf1-FLAG_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Atf1-FLAG::KanMX6

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs


title: Input_AL2-WT_FLAG

value: 1305-AL2-FLAG transformed plants (in Col-0)


title: cx3cr1-control_brain_O4+ cell


title: cspg4-cKO_brain_O4+ cell_2


title: H1944 AKO1

data_processing:
First, the raw paired-end RNA-seq FASTQ data were trimmed to remove low-quality bases and adaptor sequences by Trim Galore (v0.5.0) with default settings. Then, the clean RNA-seq FASTQ data were mapped to human reference genome hg38 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were reserved for downstream analysis. Count matrixes were calculated by featureCounts (v1.6.4) with the parameters -p -M -O. DEG analysis was performed using DESeq2 package with the raw count. Only genes with P value less than 0.05 and at least two-fold change were considered to be differentially expressed. DEGs were submitted to the Database for Annotation, Visualization and Integrated Discovery (DAVID) 6.7 (https://david.ncifcrf.gov) for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Gene set enrichment analysis(GSEA) was conducted using clusterProfiler package.
Assembly: hg38
Supplementary files format and content: comma-separated values file, raw counts for gene expression.

growth_protocol: A549 cell lines were cultured in DMEM (Gibco, 11965-118) media supplemented with 10% FBS (ExCell, FSP500). H1944 cell line was cultured in RPMI1640 (Gibco, 11875-119) supplemented with 10% FBS and 1 mM sodium pyruvate (Gibco, 11360070). All media were supplemented with penicillin and streptomycin (Gibco, 15140-122). Cells were cultured at 37°C with 5% CO2, and were periodically tested and shown to be mycoplasma negative.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for the following library preparation. RNAseq libraries were prepared with VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 platform.

value: LUAD

value: APE1 knockout


title: IP_AL6_GFP rep1


title: IP_AL4_GFP rep2

value: 1305-AL4-GFP transformed plants (in Col-0)


title: H1944 AKO2


title: cspg4-cKO_spinalcord_O4+ cell_2

value: spinal cord


title: Untag_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E

value: 3% PFA and DMA


title: Input_AL6_GFP


title: Klf1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Klf1-GFP::KanMX6


title: Cuf1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Cuf1-GFP::KanMX6


title: H1944 WT2

value: WT


title: Zip1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Zip1-GFP::KanMX6


title: H1944 WT1


title: Moc3-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Moc3-GFP::KanMX6


title: Input_AL4_GFP

value: Arabidopsis seedlings


title: Gaf1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Gaf1-GFP::KanMX6


title: A549 AKO1


title: IP_AL4_GFP rep1


title: Gsf1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Gsf1-GFP::KanMX6


title: HCT116 cells, siNC, rep2

value: Colorectal cancer cell lines

value: knockdown negetive control


title: Phx1-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Phx1-GFP::KanMX6

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs


title: A549 AKO3

value: LUAD

value: APE1 knockout


title: IP_AL3_FLAG rep1

value: SIGMA, F1804

value: 1305-AL3-FLAG transformed plants (in Col-0)


title: A549 AKO2


title: cspg4-control_spinalcord_O4+ cell

value: spinal cord

value: O4+ cell

value: oligodendrocytes


title: cspg4-cKO_spinalcord_O4+ cell_1


title: IP_AL3_FLAG rep2


title: pdgfra-cKO_brain_O4+ cell

value: brain

value: pdgfra-cKO


title: cspg4-control_brain_O4+ cell


title: Input_AL3_FLAG

value: Arabidopsis seedlings


title: A549 WT3

value: WT


title: cspg4-cKO_brain_O4+ cell_1


title: Php5-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php5-GFP::KanMX6 otr1R(Spn1)::ura4

value: 3% PFA and DMA


title: A549 WT2


title: IP_AL2_GFP rep2

value: 1305-AL2-GFP transformed plants (in Col-0)


title: Input_AL2_GFP


title: A549 WT1


title: pdgfra-control_brain_O4+ cell

value: pdgfra-control


title: IP_AL2_GFP rep1


title: IP_AL1_FLAG rep2

value: 1305-AL1-FLAG transformed plants (in Col-0)


title: pdgfra-cKO_spinalcord_O4+ cell


title: Rsv2-GFP_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-216 ura4 D18 or DS/E Rsv2-GFP::KanMX6

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs


title: H3K9me3_WT_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E

value: Growth in YEA 30 C

value: 3% PFA


title: AKO_2

data_processing:
The CUT&Tag reads were mapped to the human genome (UCSC hg38) with Bowtie2. The duplicated reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per genome coverage, RPGC) with the bamCoverage command from deepTools 3.3.0.
Assembly: hg38
Supplementary files format and content: bigwig files for BG4/H3K4me3 enrichment
Library strategy: CUT&Tag

extract_protocol:
WT, G4 sequences mutated and APE1 KO A549/H1944 cells (1 × 106) were used for the CUT&Tag experiment, and cell counting was performed using a Luna II (Logos Biosystems, Korea).
CUT&Tag was performed essentially as described (68), with minor modifications according to the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).

value: Melanoma

value: APE1 knockout


title: MP_S13

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Sequencing data was analyzed on the Galaxy web platform (usegalaxy.eu). Quality control was performed with FastQC (Galaxy Version 0.73, http://www. bioinformatics.babraham.ac.uk/projects/fastqc/, last access on 6th November 2022).
Reads were mapped to the human reference genome (Gencode, GRCh38.p13, all regions, release 42) with RNA STAR (Galaxy Version 2.7.8a, default parameters).
Reads mapped to the human reference genome were counted by featureCounts (Galaxy Version 2.0.1, default parameters).
The output of featureCounts was imported to RStudio (version 1.4.1103, R Version 4.0.3). Gene symbols and gene types were determined based on Ensembl (Release 108, download on 5 November 2022). Principal component analysis (PCA) was applied to check for potential outlier and batch effects.
Normalized reads and differential gene expression were calculated using the R package DESeq2 (version 1.34) with default parameters (Benjamini-Hochberg adjusted p-values). Transcripts with log2 fold change (log2FC) >2 or <-2 and adjusted p-value <0.05 were considered as differentially expressed genes (DEG).
Assembly: Gencode GRCh38.p13, all regions, release 42
Supplementary files format and content: csv, normalized reads (DESeq2)

source_name: hyalocytes

extract_protocol:
Vitreous tissue samples were collected in vitrectomy bags during surgery and processed for cell isolation within two hours of resection, according to a previously published protocol (11) adapted for the specificities of diabetic vitreous. For half of the samples in the preliminary analysis (see Table 1) and for diabetic samples, 1 ml of RBC Lysis Buffer (Thermo Fisher Scientific) was added for erythrocyte lysis. Samples were stained for cluster of differentiation (CD) 45 (BV421, anti-human, 1:100, BioLegend), CD11b (FITC, anti-human, 1:100, BioLegend), CX3C motif chemokine receptor 1 (CX3CR1, PE-Cy7, anti-human, 1:200, BioLegend) and Anti-Human Mature Macrophages (MatMac) Antibody, an ED2-like (ectodermal dysplasia 2) marker for resident macrophages (eFluor660, anti-human, 1:100, eBioscience). Finally, cells were processed for sorting on the MoFlo Asrios EQ Cytometer (Beckman Coulter). Hyalocytes were isolated as CD45+CD11b+CX3CR1+MatMac+ cells.
RNA extraction, library preparation and RNA-Seq were conducted at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Germany), according to previously published protocols (11,16).

value: hyalocytes


title: PDR_S12


title: H3K9me3_WT_Input_Rep1


title: Input_AL1_FLAG

value: SIGMA, F1804


title: PAT_TAC_12_wks, rep 7

city: Munich

first: Sabine

last: Steffens

address: Pettenkoferstrasse 9b

department: Clinical Pathobiochemistry

institute: Institute for Cardiovascular Prevention-LMU Klinikum

description: Library name: TTAGCACACCTT

data_processing:
The reads were demultiplexed using deML and then filtered.
The reads were mapped to the mouse genome (mm10, GRCm38), and counted using zUMIs (version 2.5.5) with STAR.
Differential gene expression analysis was performed using DESeq2.
The characterization of enriched the molecular functions or pathways of differentially expressed genes (DEGs) was performed by using Gene Ontology in clusterProfiler.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw counts for each sample matrix file

source_name: Pericardial adipose tissue

extract_protocol:
PAT was excised at the respective study endpoint and lysed with 27.8 µl Quiagen RLT Plus lysis buffer (#1053393) + 1% β-mercaptoethanol per mg PAT via bead homogenisation to yield an RNA concentration of 2-20 ng/µl following the RNA extraction with Zymo Direct-zol RNA MicroPrep (#R2062).
Libraries were then constructed with the NEB Next Ultra II FS kit (E6177S, NEB) using the prime-seq specifications

value: Pericardial adipose tissue

value: male


title: WT_1

value: WT


title: IP_AL1_FLAG rep1

value: Arabidopsis seedlings


title: WT_2


title: pdgfra-control_spinalcord_O4+ cell

value: spinal cord

value: O4+ cell

value: oligodendrocytes


title: SK-N-BE stable cell line with doxy inducible FUS-WT, Doxycyclin, Arsenite treated, SG-enriched, Rep2

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
DOXY+_ARS+_FUS-WT_REP2_SGenr_S16
SK-N-BE stable cell line with doxycyclin inducible FUS-WT, Doxycyclin, Arsenite treated, SG-enriched sample, Replicate2

data_processing:
Trimmomatic (v0.39; Bolger et al., 2014) and Cutadapt (v3.2; Martin, 2011) were used to remove adapter sequences and poor quality bases; minimum read length after trimming was set to 35.
Reads aligning to rRNAs were filtered out; this first alignment was performed using Bowtie2 software (v2.4.2, https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
STAR software (v2.7.7a, Dolbin et al., 2013) was used to align reads to GRCh38 genome.
PCR duplicates were removed from all samples using MarkDuplicates command from Picard suite (v2.24.1; https://broadinstitute.github.io/picard/).
Uniquely mapping fragments were counted for each annotated gene (ensembl release 99) using htseq-counts software (v0.13.5; Anders et al., 2015). See Material and Methods section for further explanation.
Assembly: GRCh38
Supplementary files format and content: counts_table.tsv contains fragment counts for each gene. Counts were performed using htseq-counts algorithm (v0.13.5; Anders et al., 2015).
Supplementary files format and content: gene_quantification_table.FPKM_withoutTMM.tsv contains FPKMs gene quantifications

source_name: SK-N-BE

growth_protocol: Cells were grown in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10%FBS, 1mM sodium pyruvate, 1x GlutaMAX (Thermo Fisher Scientific), 100U/mL penicillin and 100mg/mL streptomycin.

extract_protocol:
Total RNA was purified using Direct-zol RNA Miniprep (Zymo Research) kit according to the manufacturer’s specifications.
RNA libraries for RNA-seq were prepared using Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) following manufacturer's protocols, with minor adjustments for low-input samples.

treatment_protocol: FUS expression was induced with 50 ng/mL doxycycline in growth medium 24 hours before harvesting. Sodium arsenite was added to a final concentration of 0.5 mM to the ARS+ samples, and cells were incubated for 1 hour to induce Stress Granules formation. Cells were then harvested by scraping in growth medium.

value: SK-N-BE

value: Neuroblastoma

value: Doxycyclin,Arsenite


title: Untag_FE_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E

value: Abcam anti-GFP (cat# ab290)

value: Growth in YEA 30 C and 18 C/2hrs

value: 3% PFA and DMA


title: PAT_TAC_12_wks, rep 6

description: Library name: TCACGACGACAG


title: PDR_S10


title: PAT_TAC_12_wks, rep 5

description: Library name: GTCACCAAGCCA


title: ob200129_R_12

city: Tokyo

first: Kenji

last: Uno

address: 2-11-1 Kaga, Itabashi-ku

country: Japan

institute: Teikyo University

description: Library name: Sample 12

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

extract_protocol:
The total RNA was isolated from liver tissues using miRNeasy  system (QIAGEN) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set according protocols

value: Liver

value: ob/ob

value: administer adenovirus expressing Rspo3


title: ob200129_R_8

description: Library name: Sample 11


title: MH_S17

value: hyalocytes


title: Untag_Input_Rep1


title: ob200129_R_4

description: Library name: Sample 10


title: SK-N-BE stable cell line with doxy inducible FUS-WT, Doxycyclin, Arsenite treated, SG-enriched, Rep1

description:
DOXY+_ARS+_FUS-WT_REP1_SGenr_S8
SK-N-BE stable cell line with doxycyclin inducible FUS-WT, Doxycyclin, Arsenite treated, SG-enriched sample, Replicate1


title: AKO_1

value: Melanoma

value: APE1 knockout


title: PAT_TAC_12_wks, rep 4

description: Library name: CACCGTGGATCA

value: Pericardial adipose tissue

value: male

value: WT


title: PAT_TAC_12_wks, rep 3

description: Library name: CTTCTCGCTACA


title: PDR_S8


title: ob200129_R_2

description: Library name: Sample 9


title: PDR_S7


title: PDR_S11


title: PAT_TAC_12_wks, rep 2

description: Library name: CGCGGTCAAGAA


title: SK-N-BE stable cell line with doxy inducible FUS-WT, Doxycyclin, Arsenite treated, Input, Rep1

description:
DOXY+_ARS+_FUS-WT_REP1_INP_S4
SK-N-BE stable cell line with doxycyclin inducible FUS-WT, Doxycyclin, Arsenite treated, Input, Replicate1


title: SK-N-BE stable cell line with doxy inducible FUS-P525L, Doxycyclin, Arsenite treated, SG-enriched, Rep2

description:
DOXY+_ARS+_FUS-P525L_REP2_SGenr_S32
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L, Doxycyclin, Arsenite treated, SG-enriched sample, Replicate2


title: ob200129_Z_9

description: Library name: Sample 8

value: administer control adenovirus


title: PAT_TAC_12_wks, rep 1

description: Library name: CCTCTATGGTCC


title: SK-N-BE stable cell line with doxy inducible FUS-P525L, Doxycyclin, Arsenite treated, Input, Rep2

description:
DOXY+_ARS+_FUS-P525L_REP2_INP_S28
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L, Doxycyclin , Arsenite treated, Input, Replicate2

value: SK-N-BE


title: PDR_S6


title: ob200129_Z_7

description: Library name: Sample 7


title: PAT_TAC_1_wk, rep 6

description: Library name: TAGCGGTCTGCA


title: PDR_S5


title: SK-N-BE stable cell line with doxy inducible FUS-WT, Doxycyclin, Arsenite treated, Input, Rep2

description:
DOXY+_ARS+_FUS-WT_REP2_INP_S12
SK-N-BE stable cell line with doxycyclin inducible FUS-WT, Doxycyclin, Arsenite treated, Input, Replicate2

value: Neuroblastoma


title: ob200129_Z_3

description: Library name: Sample 6


title: ob200129_Z_1

description: Library name: Sample 5


title: PAT_TAC_1_wk, rep 5

description: Library name: GATTCATTCGGA


title: SK-N-BE stable cell line with doxy inducible FUS-P525L, Doxycyclin, Arsenite treated, SG-enriched, Rep1

description:
DOXY+_ARS+_FUS-P525L_REP1_SGenr_S24
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L, Doxycyclin, Arsenite treated, SG-enriched sample, Replicate1

value: Doxycyclin,Arsenite


title: SK-N-BE stable cell line with doxy inducible FUS-P525L, Doxycyclin, Arsenite treated, Input, Rep1

description:
DOXY+_ARS+_FUS-P525L_REP1_INP_S20
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L, Doxycyclin , Arsenite treated, Input, Replicate1


title: WT_Ctrl_DMSO

city: Daejeon

first: Doyeong

last: Kim

country: South Korea

institute: Chungnam Natl' University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: human indiced pluripotent stem cell

growth_protocol: All iPSCs were maintained in mTeSR plus medium (STEMCELL TECH). iPSCs were differentiated toward myoblast under special differentiation medium (AMSBIO).

extract_protocol:
Cellular RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Total RNA was isolated from tumor tissues using TRIzol (Invitrogen) following the manufacturer’s protocol. The RNA quality was assessed using a Bioanalyzer 2100 System (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was measured using a NanoDrop ND-2000 (Thermo Fisher Scientific). The cDNA libraries were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Inc., Vienna, Austria) and sequenced on a NextSeq 500 (Illumina Inc., San Diego, CA, USA) to generate single-end 75 bp reads according to the manufacturer’s instructions.

treatment_protocol: The 40 µM AMOs (GENE TOOLS) were transfected into hiPSCs. And, Cells were exposed to 0.2 µM doxorubicin (SIGMA).

value: human indiced pluripotent stem cell

value: AMO control-DMSO


title: PAT_TAC_1_wk, rep 4

description: Library name: CTTCCAGAGGCA


title: WT_Ctrl_DOXO

value: AMO control-Doxorubicin


title: WT_AMO_DOXO

value: AMO-Doxorubicin


title: SK-N-BE stable cell line with doxy inducible FUS-WT,CONTROL (w/x doxycyclin), Arsenite treated, Input, Rep2

description:
DOXY-_ARS+_FUS-WT_REP2_INP_S10
SK-N-BE stable cell line with doxycyclin inducible FUS-WT,CONTROL (without doxycyclin induction), Arsenite treated, Input, Replicate2

value: Arsenite


title: PAT_TAC_1_wk, rep 2

description: Library name: CAGCGGAACTTA


title: NC210623_Z_5

description: Library name: Sample 3

value: Liver

value: wt


title: SK-N-BE stable cell line with doxy inducible FUS-WT,CONTROL (w/x doxycyclin), Arsenite treated, SG-enriched, Rep1

description:
DOXY-_ARS+_FUS-WT_REP1_SGenr_S6
SK-N-BE stable cell line with doxycyclin inducible FUS-WT,CONTROL (without doxycyclin induction), Arsenite treated, SG-enriched sample, Replicate1


title: PAT_TAC_1_wk, rep 1

description: Library name: AGCATAGCCACA


title: PAT_TAC_1_wk, rep 3

description: Library name: CCACGTAAGAGG


title: NC210623_Z_1

description: Library name: Sample 1


title: MT_Ctrl_DOXO

value: TP53 c/359A>G mutation


title: NC210623_Z_11

description: Library name: Sample 4


title: WT_AMO_DMSO

value: AMO-DMSO


title: NC210623_Z_3

description: Library name: Sample 2


title: Brain microvessel, RNA_seq_BCAS_3

first: Zengyu

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

data_processing:
Raw data were first evaluated by FastQC for quality control to determine whether the sequencing data were suitable for subsequent analyses.
Adapter sequences, low-quality reads, and too short reads were removed from raw data with Trim-galore to obtain clean data.
Sequencing reads were aligned to annotated RefSeq genes in the mouse reference genome (NCBI, GCF_000001635.26_GRCm38.p6) with HISAT2. And Samtools v1.9 was used to sort and build the alignment file index.A gene count matrix that contained raw transcript counts for each annotated gene were generated using the featureCounts v1.6.3.
BamCoverage from Deeptools was used to generate normalized bigwig files, which were then visualized on IGV. Use the Integrated Genomics Viewer (IGV) for visual browsing.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: bw

source_name: microvessels isolated from the right brain

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water

extract_protocol:
RNA was harvested using the TRIzol Reagent (Life technologies, California, USA). Total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The control group was exposed to sham operation. The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

value: brain

tag: time

value: 14 weeks


title: SK-N-BE stable cell line with doxy inducible FUS-P525L,CONTROL (w/x doxycyclin), Arsenite treated, SG-enriched, Rep2

description:
DOXY-_ARS+_FUS-P525L_REP2_SGenr_S30
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L,CONTROL (without doxycyclin induction), Arsenite treated, SG-enriched sample, Replicate2


title: MT_AMO_DMSO


title: MT_AMO_DOXO


title: Brain microvessel, RNA_seq_BCAS_1

value: microvessels isolated from the right brain

value: bilateral carotid artery stenosis (BCAS) operation


title: PAT_Sham_1_wk, rep 4

description: Library name: GTAGGCGCATGA

value: Pericardial adipose tissue

value: male

value: WT


title: SK-N-BE stable cell line with doxy inducible FUS-P525L,CONTROL (w/x doxycyclin), Arsenite treated, SG-enriched, Rep1

description:
DOXY-_ARS+_FUS-P525L_REP1_SGenr_S22
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L,CONTROL (without doxycyclin induction), Arsenite treated, SG-enriched sample, Replicate1

value: SK-N-BE

value: Neuroblastoma


title: PAT_Sham_1_wk, rep 3

description: Library name: CCTAACCTACAA


title: SK-N-BE stable cell line with doxy inducible FUS-WT,CONTROL (w/x doxycyclin), Arsenite treated, SG-enriched, Rep2

description:
DOXY-_ARS+_FUS-WT_REP2_SGenr_S14
SK-N-BE stable cell line with doxycyclin inducible FUS-WT,CONTROL (without doxycyclin induction), Arsenite treated, SG-enriched sample, Replicate2


title: Brain microvessel, RNA_seq_BCAS_2


title: SK-N-BE stable cell line with doxy inducible FUS-P525L,CONTROL (w/x doxycyclin), Arsenite treated, Input, Rep2

description:
DOXY-_ARS+_FUS-P525L_REP2_INP_S26
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L,CONTROL (without doxycyclin induction), Arsenite treated, Input, Replicate2


title: Brain microvessel, RNA_seq_Sham_3

value: Sham operation


title: PAT_Sham_1_wk, rep 2

description: Library name: CATCAACTCGAA


title: SK-N-BE stable cell line with doxy inducible FUS-P525L,CONTROL (w/x doxycyclin), Arsenite treated, Input, Rep1

description:
DOXY-_ARS+_FUS-P525L_REP1_INP_S18
SK-N-BE stable cell line with doxycyclin inducible FUS-P525L,CONTROL (without doxycyclin induction), Arsenite treated, Input, Replicate1


title: MDS_targeted (31 months after diagnosis of AA)

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Targeted

data_processing:
Demultiplexing of raw reads using cellranger mkfastq (v 5.0.0).
Alignment against GRCh38 and generation of count matrices using cellranger count (v 5.0.0).
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list and feature list in csv file format.

source_name: bone marrow

extract_protocol:
Ficoll-based extraction of fresh bone marrow mononuclear cells and immediate processing for single-cell RNA-sequencing.
Single-cell 3' and U2AF1S34Y locus-enriched library construction according to manufacturer's specifications (10x Genomics) and as outlined in the publication.

value: bone marrow

tag: disease state

value: aplastic anemia


title: Brain microvessel, RNA_seq_Sham_2


title: SK-N-BE stable cell line with doxy inducible FUS-WT,CONTROL (w/x doxycyclin), Arsenite treated, Input, Rep1

description:
DOXY-_ARS+_FUS-WT_REP1_INP_S2
SK-N-BE stable cell line with doxycyclin inducible FUS-WT,CONTROL (without doxycyclin induction), Arsenite treated, Input, Replicate1

value: Arsenite


title: MDS_additionalPCR (31 months after diagnosis of AA)


title: MT_Ctrl_DMSO

value: human indiced pluripotent stem cell

value: AMO control-DMSO


title: PAT_Sham_1_wk, rep 6

description: Library name: TGTTATGGCCAA


title: PAT_Sham_1_wk, rep 5

description: Library name: TCCATACGCGAA


title: PAT_Sham_1_wk, rep 1

description: Library name: ACGTATTGTCCA


title: MDS (31 months after diagnosis of AA)

description: MDS


title: MDS_prog (33 months after diagnosis of AA)


title: zhaoqinFu_2y

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

description: mRNA Expression Profiling

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.1)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: blood

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp paired-end reads were generated.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

tag: sample preparation

value: scRNA-seq


title: Brain microvessel, RNA_seq_Sham_1

tag: tissue


title: INTS4K/A, PRO-seq, Rep1

status: Public on Dec 05 2024

first: Varun

last: Sood

state: Maryland

address: 41 Medlars Drive

department: Laboratory of receptor biology and gene expression

institute: National Institues of Health, National Cancer Institute, Center for Cancer Research

description: Library name: PRO-seq_INTS4_K/A-rep1

data_processing:
Dual 6 nt molecular identifiers from read pairs were detected using UMI tools and trimmed using cutadapt 1.14. Reads from HBEC and spike-in were aligned to the genome sequence of concatenated human (hg38) and spike-in Drosophila (dm6) genomes using Bowtie 2 and mapped reads were deduplicated using UMI-tools. Reads to the reference genome was sorted based on their origin as R1 or R2 reads using SAMTools 1.3.1.
Each read was counted once at the 3’ end of nascent RNA and the + and – strands were swapped to generate bedGraph files representing 3’ end position at single-nucleotide resolution using the published script (bowtie2stdBedGraph.pl, https://github.com/AdelmanLab/NIH_scripts). Differential expression was performed on the TSS to TES counts from the merged replicates using DEseq2’s and normalized with both the spike-in and copy number differences between replicates and samples, respectively.
For pausing analysis, the 3’ PRO-seq count from the replicate merged, normalized and binned data was assigned to the promoter and gene-body as defined by TSS/+150 and +250/+2250, respectively
The polymerase density was calculated as counts per kb and pseudocount was added to calculate the pause index. = (promoter density +1) / (body density +1). The gene-body window was truncated if TES was shorter than 2250 bp and omitted if shorter than 400 bp or if the promoter had fewer that 8 reads
Assembly: Hg38 and dm6
Supplementary files format and content: bedGraph
Library strategy: PRO-Seq

molecule: nuclear RNA

source_name: HBEC

growth_protocol: Human bronchial epithelial cells (HBECs) were grown in Keratinocyte-SFM medium (Gibco, 17005-042) supplemented with Penicillin/Strep (100units/mL Penicillin, 100micrograms/mL Streptomycin)

extract_protocol:
For permeabilization, a 80% confluent plate of HBEC was washed with PBS to remove media before lightly trypsinization and transfer to cold PBS. Cells were maintained at 4°C for the rest of the permeabilization steps. Cells were spun at 200 g for 3 min and suspended in 10 ml PBS for counting. Cells were re-spun at 200 g for 3 min and suspended in 250l of Buffer W (10 mM Tris-Cl, pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 10 % (v/v) Glycerol, 0.5mM DTT,  0.2l /mL SUPERase-in RNase inhibitor) before 10 ml of Buffer P (Buffer W + 0.05 % (v/v) Tween-20, 10 % (v/v)) was slowly added from the side of the tube and incubated for 5 min. Thereafter cells were spun down at 300 g for 3 min for wash with 10ml of Buffer W and re-spun for final suspension in 400 of Buffer F (50 mM Tris-Cl, pH 8.0, 40 % (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, DTT to 0.5mM + SUPERase-IN RNase inhibitor to 1 L/mL final) before final counting.  For run-on, the volume of cell suspension was adjusted to 1 million cells in 45 l of Buffer F and 50,000 drosophila S2 cells in 5 l of Buffer F were added as spike-in. 25 L of sarkosyl was mixed with preheated 25 L of 4x run-on mix ( 20 mM Tris-Cl pH 8, 20 mM MgCl2, 2 mM DTT, 600 mM KCl, 40 M of biotin-11-NTP and 11 L nuclear free water) at 37°C. The permeabilized cells were incubated at 37°C before incubating with the complete run-on mix for 5 min at 37°C. Run-on was stopped by vortexing with Buffer RL (Norgen Biotek # 37500) for 10 min. 240 L of ethanol was further added for RNA purification with Norgen column (Norgen Biotek # 37500) using the manufacturer’s protocol. Briefly, the run-on lysate was passed through the column and eluted in 50 L of water after washing thrice with solution A (Norgen Biotek # 37500). The sample was incubated with 25 L of ice-cold fragmentation buffer (375 mM Tris·Cl, pH 8.3, 562.5 mM KCl, 22.5 mM MgCl2) at 95°C for 5 min and reaction stopped with 125 L of 0.1 M EDTA before incubating on ice.  For adding 3’ adapter, RNA binding beads were prepared as follows: 20 l MyOne Streptavidin C1 DynaBeads (Thermo # 65001) per samples were prepared by resuspending and rotating 2 min for three times in Decon buffer (0.1 M NaOH, 100 mM NaCl) before washing twice in succession with 100 mM NaCl and Binding buffer (10 mM 1 M Tris-Cl, pH 7.4 , 300 mM NaCl, 0.1% Triton X-100, 1 mM EDTA and 0.2 µl SUPERase⋅In per ml) and finally suspended in 100 l of Binding buffer. 50 µl these beads were added to the sample and washed as follows: 2× high-salt buffer (low-salt + 2M NaCl), 2× binding buffer and 2× low-salt buffer (5 mM Tris-Cl, pH 7.4, 0.1% Triton X-100, 1 mM EDTA) before resuspending in 500 µl TRIzol. The sample was incubated at 65°C for 5 min with intermitted vortexing. The RNA was extracted from the aqueous layer by chloroform extraction and ethanol precipitation. The pellet was washed with 75% ethanol and air dried. This pellet was suspended in 5 l of 2.5mM 3’ adapter (App-VRA3-6N) and incubated for 30 s at 65°C. 15 l of ligation master mix (6 µl 50% PEG 8000, 2 µl 10× T4 RNA ligase buffer, 0.5 µl SUPERase⋅In, 1 µl T4 RNA ligase 2, truncated KQ, and 5.5 µl water) was added and incubated overnight at 16°C.  For 5’ end processing, 180 ml of betaine buffer (1.25 M in Binding buffer) was added to the ligated mix and incubated for 5 min at 65°C before adding the remaining beads for rotation at room temperature for 20 min. Beads were washed as follows: 2× binding buffer, 2× high-salt buffer and 2× low-salt buffer. Decaping was done by incubating in MDE master mix for 30 min at 37°C after washing once with MDE buffer (New England Biolabs #M0608S). Subsequent 5’ hydroxyl repair was done by washing the beads as follows: 2× high-salt buffer, 2× low-salt buffer and 2× PNK buffer (New England Biolabs M0201) before incubating with PNK master mix (13 µl water, 2 µl 10× PNK buffer, 2 µl 10 mM ATP, 1 µl of T4 PNK and 1 µl SUPERase) for 1 h at 37°C. For 5’ adapter ligation, beads were washed as follows: 2× high-salt buffer, 2× binding buffer, 2× low-salt buffer and 1× with 0.25X SSIV buffer (Invitrogen, cat. no. 18090200) before incubating with 7.5 µl RT mix (3 µl 5× SSIV buffer, 0.75 µl 0.1 M DTT, 0.75 µl, 12.5 mM dNTP mix, 0.75 µl SUPERase⋅In, 1 µl SSIV RTase, 1.25 µl water) in a thermocycler following the temperature program: 10 min at 48°C, 15 min at 54°C, hold at 4°C).
PRO-seq libraries were generated using Ultra II Q5 Master Mix (New England Biolabs # M0544) following the manufacturer’s protocol.

treatment_protocol: Overexpressing ectopic INTS4 mutants at lysine 26 and 27 that are changed to either glutamine (acetylation-mimic) or alanine (acetylation-null)

value: HBEC

value: Human Bronchial epithelial cell

value: Wild-type

value: ectopic INTS4 K/A


title: INTS4K/A, PRO-seq, Rep2

description: Library name: PRO-seq_INTS4_K/A-rep2


title: INTS4K/Q, PRO-seq, Rep2

description: Library name: PRO-seq_INTS4_K/Q-rep2

value: ectopic INTS4 K/Q


title: INTS4K/Q, PRO-seq, Rep1

description: Library name: PRO-seq_INTS4_K/Q-rep1


title: Reads obtained from sequencing of sample PG35

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human stool

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose >Log_di_cutadapt.txt
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 276 --p-trunc-len-r 169 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
bowtie2 -x GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV.fasta -S bowtie2_SAM_output.txt -f -p 4 2> percentuals_aligned_bowtie2.txt
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads clean_rep-seqs.qza --o-classification taxonomy.qza
The R scripts are available at https://github.com/LeandroD94/Papers/tree/main/2024_ADM_microbiota_gut_retina_axis
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence (excluding the human off-target related ASVs)
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundances of ASVs in each sample and the related taxonomic assignments
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

organism: human feces metagenome

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
OTHER: paired-end (2x300) amplicon sequencing

value: Stool

tag: sample id

tag: condition

value: AMD

tag: treatment time

tag: kit dna_extraction

value: QIAmp PowerFecal Pro DNA Kit


title: Reads obtained from sequencing of sample PG34


title: Reads obtained from sequencing of sample PG33


title: Reads obtained from sequencing of sample PG32


title: Reads obtained from sequencing of sample PG36


title: Reads obtained from sequencing of sample PG31


title: Reads obtained from sequencing of sample FL15

value: Healthy


title: Chipseq_Pdef_Mre11_rep2

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Cells were cultured using McCoy’s 5A media with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100ug/ml streptomycin. Cells were grown at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Chipseq: Cultured cells were fixed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. Twenty million fixed cells were washed with PBS, snap-frozen and stored at -80°C until further processing. Before use, the cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and freshly added Complete Mini EDTA free proteinase inhibitor. Sonication was performed using Branson sonicator at amplitude 35%, 12 cycles of 20 sec sonication followed by 30 sec of pause or using Covaris ME220 sonicator at duty factor 20%, peak incident power 75, cycle/burst 1000 for 6 min at 4°C. The antibody-protein solution was then incubated with 40 ml of Dynabeads Protein A for 40 min at room temperature under agitation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% NaDOC), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column.
Chipseq: Ovation Ultralow Library System V2 kit , Hi-C library were amplified directly from of the beads with 4-6 cycles of PCR, using Illumina primers (Bioo Scientific) and Q5 Hi-Fidelity DNA polymerase

treatment_protocol: HCT116-Rad21-mAID-clover cells were grown for 3 days before addition of media containing 750uM indole-3-acetic acid (IAA). For AsiSI induction, HCT-116 cells containing the nAsiSI-T2A-BFP construct show efficient induction of breaks 4-8 hours following treatment with 1M 4OHT. In experiments where DNA damage was induced for 72h, fresh 4OHT was added every 24h. Inhibition of ATM was achieved by incubating cells with 1M KU-55933 for 1 hour prior to induction of DSBs

tag: chip antibody

value: Mre11 (Novus Biologicals NB100-142)

tag: cell type

value: Human colorectal carcinoma cell

tag: genotype

value: Rad21_AIDdegron, SMC1AS957AHz/S966AHz

tag: treatment


title: Chipseq_Pdef_Rad21_UTR_rep2

value: Rad21 (abcam, Ab992)

tag: cell line


title: Reads obtained from sequencing of sample FL3


title: Reads obtained from sequencing of sample FL5


title: Reads obtained from sequencing of sample EN47


title: Reads obtained from sequencing of sample FL7


title: Reads obtained from sequencing of sample EN46


title: Chipseq_Pdef_Rad21_DSB_rep2


title: Reads obtained from sequencing of sample FL13


title: Reads obtained from sequencing of sample EN32


title: Reads obtained from sequencing of sample EN17


title: Reads obtained from sequencing of sample EN24


title: Reads obtained from sequencing of sample EN29


title: Reads obtained from sequencing of sample EN13


title: Reads obtained from sequencing of sample EN12


title: Reads obtained from sequencing of sample EN26


title: Reads obtained from sequencing of sample PG26


title: Reads obtained from sequencing of sample PG30


title: Reads obtained from sequencing of sample PG28


title: Reads obtained from sequencing of sample PG27


title: Reads obtained from sequencing of sample PG25


title: Reads obtained from sequencing of sample PG23


title: Reads obtained from sequencing of sample PG19


title: Reads obtained from sequencing of sample PG20


title: Reads obtained from sequencing of sample PG21


title: Reads obtained from sequencing of sample PG24


title: Reads obtained from sequencing of sample PG22


title: Reads obtained from sequencing of sample PG18


title: Reads obtained from sequencing of sample PG14


title: Reads obtained from sequencing of sample PG11


title: Reads obtained from sequencing of sample PG16


title: Reads obtained from sequencing of sample PG13


title: Reads obtained from sequencing of sample PG17


title: Reads obtained from sequencing of sample EN39


title: Reads obtained from sequencing of sample PG9


title: Reads obtained from sequencing of sample PG10


title: Reads obtained from sequencing of sample PG7


title: Reads obtained from sequencing of sample PG8


title: Reads obtained from sequencing of sample PG15


title: Reads obtained from sequencing of sample PG29


title: Reads obtained from sequencing of sample PG6


title: Reads obtained from sequencing of sample PG12


title: Reads obtained from sequencing of sample PG3


title: Reads obtained from sequencing of sample PG5


title: Reads obtained from sequencing of sample PG4


title: Reads obtained from sequencing of sample PG2


title: Reads obtained from sequencing of sample PG1


title: Reads obtained from sequencing of sample PG45


title: Reads obtained from sequencing of sample PG44


title: Reads obtained from sequencing of sample PG42


title: Reads obtained from sequencing of sample PG43


title: PDR_S9

value: hyalocytes


title: Reads obtained from sequencing of sample PG40


title: Reads obtained from sequencing of sample PG38


title: Reads obtained from sequencing of sample PG39


title: Reads obtained from sequencing of sample PG37


title: Anti-Nanog, ESCs

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

data_processing:
The quality of the generated fastq files was examined with the FASTQC software. FASTQ files were aligned against mm10 mouse genome with Bowtie2 aligner. The output file was filtered for low quality reads, duplicates, blacklist regions and mitochondrial genome entries with custom-made pipeline from Bedtools  and Samtools packages. Peak calling was performed with MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: The bed file Nanog_ESCs_peaks.bed contains the peaks generared with MACS2 compared to the respective Input file.

growth_protocol: Bruce-4 ESCs were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378).

extract_protocol:
ESCs were cultured under optimum conditions and were fixed at a high‐confluence stage at room temperature for 15 min using 1% formaldehyde in fixing buffer, followed by quenching with 0.125 M glycine at room temperature for 7 min. Cells were resuspended in lysis buffer [50 mM Hepes (pH 7.9), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP‐40, 0.25% Triton X‐100] and then in sonication buffer [0.1% SDS, 1 mM EDTA, 10 mM Tris (pH 8.1)]. Chromatin shearing was carried out in the Covaris S2 sonicator using the Covaris TC12 × 12 mm tubes (Tube AFA Fiber and Cap, Covaris) for 12 min (duty factor: 75, peak power: 25, cycles per burst: 200) allowing the shearing of chromatin within a range of 250–500 base pairs DNA fragments. Triton X‐100 and NaCl were then added in the sheared chromatin to final concentrations of 1% and 150 mM, respectively. ChIPs were carried out by incubating 100 μg of chromatin with the proper dilution of the anti-Nanog antibody (1:100) per ChIP reaction [anti‐Nanog, D1G10 Rabbit mAb ChIP Formulated #8785, Cell Signalling]. Next, protein G‐Dynabeads (10004D, Thermo Fisher Scientific) pre‐equilibrated in IP buffer [0.1% SDS, 1 mM EDTA, 10 mM Tris (pH 8.1), 1% Triton X‐100, 150 mM NaCl] were incubated with the chromatin‐antibody solution in an orbital mixer at 4°C for 4 hours. The recovered resin was subsequently washed with 150mM NaCl buffer (1%Triton, 0.1%SDS, 2mM EDTA, 20mM Tris pH 8.0, 150mM NaCl), 250 mM  NaCl buffer (1%Triton, 0.1%SDS, 2mM EDTA, 20mM Tris pH 8.0, 250mM NaCl), once with LiCl buffer (0.25M LiCl, 1% NP-40, 1% DOC, 1mM EDTA, 10mM Tris pH 8.0) and once with TE (1mM EDTA, 10mM Tris pH 8.0). The captured chromatin fragments were subjected to 30ug RnaseA for 1 hr at 37°C , then 40ug/ml PK for 1 hr at 50°C  and finally 0.3M NaCl at 65°C overnight for reverse crosslinking. All DNA present in each sample was purified with Nucleomag DNA purification beads (Macherey-Nagel) and eluted in TE buffer.
Libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, according to the manufacturer’s guidelines.

value: Embryonic Stem Cells

value: Anti-Nanog (D1G10 Rabbit mAb ChIP Formulated #8785, Cell Signalling)


title: TMEM88 KD time course, HTO

city: St Lucia

first: Sophie

last: Shen

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: The University of Queensland

data_processing:
Raw BCL files generated by Illumina sequencers were demultiplexed into FASTQ files using cellranger mkfastq, which wraps Illumina's bcl2fastq software (cellranger version 3.0.2 and bcl2fastq v2.19.0.316). The cellranger count pipeline was used to align, filter and count barcodes and UMIs from the fastq files to generate feature-barcode (raw count) matrices.
For barcoded samples, barcode sequences were both appended to the GrCh38 reference genome with "BC01-18" identifiers to allow their expression to be recognised as custom "gene" expression, as well as sequenced as independent libraries with exclusively the barcode sequences as the reference. For HTO libraries, CITE-seq-Count was used to generate a count matrix for the hashing reads from the fastq files.
Cellranger aggr was used in the analysis for comparing the three time course datasets.
For sample demultiplexing, 'HTODemux' from the Seurat package in R was used for both HTO and barcode (BC) demultiplexing. Doublets identified from 'HTODemux' and the scds doublet detection package were removed. The Seurat package was also used for cell filtering and count normalisation. Where relevant, the R package RISC was used for dataset integration. See methods for further details and downstream analysis.
Assembly: GrCh38, BC reference file
Supplementary files format and content: All files containing 'raw_count' and 'raw_barcode' in the name are direct output from cellranger count, which provides three files: cell barcodes (*barcodes.tsv.gz), gene names (*features.tsv.gz) and the count matrix (*matrix.mtx.gz).
Supplementary files format and content: Files containing "raw_hto" in the name are direct output from CITE-seq-count, which provides three files: cell barcodes (*barcodes.tsv.gz), HTO barcode sequence (*features.tsv.gz) and the HTO count matrix (*matrix.mtz.gz)
Supplementary files format and content: Supplemental files containing "integrated_sig_time" are from RISC integration of raw counts from the three signalling dataset libraries and the control time course dataset after cell filtering as detailed in the methods. The .mtx file contains batch-corrected (integrated) and normalised values. The metadata file additionally contains cell type annotations with reference to three in vivo datasets (columns "PijuanSala_LabelTransfer", "Hutchins_CTDomains" and "Tyser_GastrulaLT". See methods for more details), as well as final clusters, annotations, and anchor genes presented in the accompanying manuscript.
Supplementary files format and content: Supplemental files containing "integrated_tm88" are from RISC integration of raw counts from cellranger aggr processing of the three time course datasets and cell quality filtering as detailed in the methods. The .mtx file contains batch-corrected (integrated) and normalised values. The metadata additionally contains label transfer results against one in vivo dataset (column: "LT_PijuanSala2019"), initial cell clusters, filtered cell clusters, as well as final cell type annotations, marker genes, and anchor genes presented in the accompanying manuscript.
Supplementary files format and content: Supplemental files "barcode.fa" and "barcode.gtf" are the fasta and gtf files added to the GrCh38 genome reference for the samples utilising the barcoded iPSC lines for sample multiplexing. The barcode.fa file contains more sequence flanking each of the unique 15bp barcodes in each cell line for better mapping.

source_name: WTC CRISPRi TMEM88-g2.3 hiPSCs (WTC CRISPRi GCaMP background/RRID: CVCL_VM38)

growth_protocol: Mesendoderm directed iPSC differentiation protocol (used as the control in this study) was adapted from a small molecule-directed cardiomyoycte differentiation protocol (https://doi.org/10.1038/nmeth.2999). In brief, undifferentiated cells are cultured in mTeSR+ pluripotency media and seeded onto vitronectin-coated plates the day prior to differentiation (day -1) with ROCK inhibitor to promote survival. The following day, once cells have formed an ~80% confluent monolayer, differentiation is induced (day 0) by changing culture media to RPMI containing 3uM CHIR99021 (small molecule Wnt agonist), 500mg/mL bovine serum albumin (BSA), and 213mg/mL ascorbic acid (AA). Media is changed every second day, maintaining the RPMI, BSA and AA backbone until day 7 and onwards where the BSA and AA are replaced with 1x B27 supplement plus insulin.

extract_protocol:
Cells were dissociated with EDTA/Trypsin. For hashtagged samples, 1e6 cells were stained with their corresponding TotalSeq-A anti-human Hashtag antibody (see HTO antibody details above). Cells were sorted for viability using propidium iodide before being pooled for 10X Genomics Chromium Single Cell 3' V3 capture, targeting 2e4 cells.
mRNA libraries were constructed according to manufacturer's instructions (Chromium Single Cell 3' V3). The barcoding (BC) libraries were generated from a portion of the cleaned up full length amplified cDNA from each mRNA sample pool. In brief, the cDNA regions containing the barcode cassette were amplified and partial P5 and P7 sequencing adaptors were appended in one round of PCR. After clean-up to remove primers, additional PCR was performed as per the SI-PCR protocol in the Chromium gene expression library construction workflow  with a unique i7 indexed R primer from Chromium i7 Multiplex Kit for a total of 14 cycles. For more details, see methods. The HTO libraries were generated following additional methods from Stoeckius et al., (2018) to capture the fraction of droplets containg HTO-derived cDNA and generate the hashing libraries.

treatment_protocol: Treatments in the signalling dataset were each added to the differentiation media on day 3 and removed on day 5 of differentiation. Likewise, the XAV treatment for the XAV-treated time course dataset was also added to the differentiation backbone media on day 3 and removed on day 5. For the TMEM88 knockdown sample, doxycycline was added from day 0 of differentiation for the entire duration to induce the tetracycline-inducible CRISPRi-mediated TMEM88 knockdown of expression.

value: WTC CRISPRi TMEM88-g2.3 hiPSCs (WTC CRISPRi GCaMP background/RRID:CVCL_VM38)

value: mesendoderm derivatives

value: TMEM88 knockdown

tag: library type

value: HTO


title: hfCas13d_Cd47-1

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description: Library name: 12_1

data_processing:
FASTQ files were aligned to the mouse reference genome GRCm39 (version Ensembl 112) by STAR 2.7.10b . Reads mapped to each gene were counted using STAR --quantMode.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Mus

extract_protocol:
RNA was  extracted by TRIZOL.
The RNA sequencing library was prepared using the NEBNext polyA mRNA isolation kit and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

value: Breast cancer

tag: batch


title: Control time course, HTO

value: Control


title: hfCas13d_Cd47-3

description: Library name: 12_3


title: hfCas13d_Lgals3-3

description: Library name: 11_3


title: hfCas13d_Lgals3-2

description: Library name: 11_2


title: hfCas13d_Lgals3-1

description: Library name: 11_1


title: hfCas13d_Cd274-3

description: Library name: 9_3


title: hfCas13d_Lgals9-2

description: Library name: 10_2


title: hfCas13d_Cd274-1

description: Library name: 9_1


title: hfCas13d_Cd274-2

description: Library name: 9_2


title: hfCas13d_Lgals9-3

description: Library name: 10_3


title: hfCas13d_Scramble-1

description: Library name: 8_1

value: Scramble


title: hfCas13d_Scramble-3

description: Library name: 8_3


title: hfCas13d_Lgals9-1

description: Library name: 10_1


title: hfCas13d_Vec-2

description: Library name: 7_2

value: Vector


title: hfCas13d_Vec-1

description: Library name: 7_1


title: Cas13d_Cd47-3

description: Library name: 6_3


title: Cas13d_Cd47-2

description: Library name: 6_2


title: Reads obtained from sequencing of sample PG41

value: Stool

value: AMD

value: QIAmp PowerFecal Pro DNA Kit


title: hfCas13d_Scramble-2

description: Library name: 8_2


title: Cas13d_Cd47-1

description: Library name: 6_1


title: hfCas13d_Vec-3

description: Library name: 7_3


title: Cas13d_Lgals3-3

description: Library name: 5_3


title: Cas13d_Lgals3-1

description: Library name: 5_1


title: Cas13d_Lgals9-3

description: Library name: 4_3


title: Cas13d_Lgals9-2

description: Library name: 4_2


title: XAV-treated time course, HTO

value: 5uM XAV-939 treatment


title: hfCas13d_Cd47-2

description: Library name: 12_2


title: Cas13d_Cd274-2

description: Library name: 3_2


title: Cas13d_Lgals9-1

description: Library name: 4_1


title: Cas13d_Cd274-3

description: Library name: 3_3


title: BALF2_GEX

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

institute: University of Missouri

data_processing:
The gene matrix data was obtained using Cell Ranger (v8.0.0).
Assembly: Sscrofa 11.1
Supplementary files format and content: matrix files, and fasta files

organism: Sus scrofa

source_name: Lung

extract_protocol:
Approximately 1 g of tissue collected from the left cranial, middle, and caudal lung lobes, were combined, and then digested with 2.5 mg/mL of Liberase TL (Roche, Indianapolis, IN) in Dulbecco’s Modified Eagle Medium (Thermo Fisher, Waltham, MA) at 37oC for 45 minutes. The digested tissue was dispersed into single cells as previously described30, and then passed through a 70 um cell strainer (Thermo Fisher, Waltham, MA). Cells were immediately cryopreserved in freezing media (90% FBS 10% dimethylsulfoxide (DMSO)) in temperature-controlled freezing containers at 3 x 107 cells per/mL and stored at -80oC until use. To obtain T cells from lung washes, lavage fluid was filtered first through a 70 m cell strainer (Thermo Fisher, Waltham, MA) and then a 40 um pipette tip cell strainer, washed in RPMI medium with 10 % FBS, counted, stained with PE-Cy7-conjugated anti-porcine CD3 antibody. live CD3 positive cells were sorted.
All samples underwent cDNA amplification upon which cDNA concentration and quality were assessed using a Fragment Analyzer 5200 (Agilent, Santa Clara, CA). V(D)J libraries were constructed using pig-specific primers for two successive enrichments of TCR and BCR transcripts.
scRNA-seq, scTCR-seq, and scBCR-seq

value: Lung

value: leucocytes