title: assembloid, mutant microglia, rep2

city: Carlsbad

first: Tom

last: Chen

state: CA

address: 6155 Corte Del Cedro

department: R&D

institute: Universal Sequencing Technology Corp.

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryonic stem cell

growth_protocol: Oligodendrocyte-containing cortical neural organoids were generated from the H9 human embryonic stem cell (hESC) line. Human ESCs were differentiated with mTeSR1 Plus medium supplemented with 10ul Rho kinase inhibitor and centrifugated to capture cell in microwells. Spheroids consisting of about 10,000 cells were collected 24 hours later and cltured into ultra-low attachment 6-well plate. Neural differentiation was induced by supplementation with 2.5uM dorsomorphin and 10uM SB431542 in mTeSR1 Plus medium for 5 days. Organoids were maintained on an orbital shaker inside a CO2 incubator at 95 rpm. On day 4, 5uM of the Wnt inhibitor IWP-2 was supplemented until day 24. On day 6, mTeSR1 Plus medium was replaced with differentiation and maintenance medium (DMM) consisting of DMEM/F12 containing B27 without Vitamin A, N2 NeuroPlex supplement, non-essential amino acids, penicillin/streptomycin, GlutaMAX, and 0.1mM beta-mercaptoethanol. Media was supplemented with the following growth factors until day 24: 20 ng/mL EGF and 20 ng/mL bFGF. On day 12 until day 24, 1uM smoothened agonist SAG was added to the media. On day 25 until day 36, DMM was supplemented with the following cocktail of factors: 25 ug/mL insulin, 60 ng/mL T3, 100 ng/mL biotin, 20 ng/mL NT-3, 20 ng/mL BDNF, 1 µM cAMP, 5 ng/mL hepatocyte growth factor, 10 ng/mL IGF-1, and 10 ng/mL PDGF-AA. On day 37 until endpoint, DMM was supplemented with the following cocktail of factors: 25 ug/mL insulin, 60 ng/mL T3, 100 ng/mL biotin, 1 uM cAMP, and 20 ug/mL ascorbic acid. On Day 37, organoids were prepared for co-culture with microglia. Individual organoids were placed into wells of ultra-low attachment u-bottom 96-well plates. Microglia precursor cells were resuspended in DMM supplemented with the day 37 organoid cocktail of supplements plus 50 ng/mL M-CSF and 50 ng/mL IL-34 and 100,000 cells were added per well of the 96-well plate on top of the organoid to a total volume of 200 uL of media. Organoids and microglia were kept in the 96-well plate for 1 week prior to transferring to a 6-well plate and continuing to culture under orbital rotation.

extract_protocol:
Freshly collected assembloids were dissociated to a single-cell suspension via a combination of mechanical dissociation and enzymatic digestion. First, assembloids were mechanically broken apart using pipette tips in a 6-well plate. Immediately after, a combination of Accutase (Thermo Fisher Scientific) and Papain supplemented with DNase (Worthington) were added to the plate and incubated under orbital rotation. Clumps were dissociated every 10 minutes by pipetting up and down for a total of 30 minutes. Dissociated cells were pelleted (3 min, 100 × g) and resuspended in PBS. Cells were counted and viability was checked using an automated cell counter (Bio-Rad). Cells were then fixed and processed with AmpliDrop. AmpliDrop is a droplet-based technology that co-encapsulates barcodes and single cells. After RT, tagmentation, and adapter PCR, single-cell containing droplets were dissociated and amplicons were size selected and isolated.
Library were generated according to manufacture's instructions (3' Amplidrop scRNA-seq). Single cells and reagents were partitioned in an oild emulsion. PolyA-based RNA was captured and retrotranscribed to cDNA. Illumina's P5 and P7 primers were used for library preparation. OligodT is sided with P7 primers, and AmpliDrop barcodes are sided with P5 primers, and a sample index was also added. Barcode are in R1; inserts is R2.

value: embryonic stem cell

value: H9 ESC

value: microglia-cortical neural assembloid

value: TREX1 mutant

value: 100-day culture


title: RKO_WT

status: Public on Oct 08 2024

type: SRA

city: nanjing

first: xian

last: luo

address: xianlin

country: China

institute: NJUCM

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal cancer cell

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

tag: cell type

value: Homo colorectal cancer cell

value: wildtype

value: RKO


title: RKO_OE

value: overexpression


title: HT29_OE


title: assembloid, mutant microglia, rep1

country: USA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: escherichia coli, BL21(DE3)-3

city: Nanjing

first: Jinyuan

last: Xu

address: No. 138, Xianlin Street, Qixia District, Nanjing City, Jiangsu Province

institute: Nanjing University of Traditional Chinese Medicine

description: fpkm all samples(Due_3)

data_processing:
Illumina NovaSeq6000 reads were trimmed and clipped for quality control in Fastp v0.22.0
High quality reads in each sample were mapped to the reference genome Escherichia coli BL21(DE3)  GCF_000022665.1 using analysis tool: Hisat2
rRNA contamination assessment using Blast
Expression analysis Quantify gene and transcript abundances from paired-end RNA-Seq data using RSEM
Differential expression analysis was performed using the DESeq2 v1.4.5
Assembly: BL21(DE3)(https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000022665.1/)
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text files include FPKM values for each sample

organism: Escherichia coli

growth_protocol: BL21 (DE3) cells grown on LB-agar plates containing 50 μg/mL kanamycin overnight at 37 ˚C.

extract_protocol:
When the OD600 reached 0.1-0.2, the cells were induced with 0.2 mM IPTG, and the AcK group was supplied with 5 mM AcK. Subsequently, the cells were moved to 30 ˚C and harvested when the OD600 reached 0.5-0.6.
RNA was harvested using FreeZol Reagent (vazyme, catalog no. R711) and Bacteria RNA Enhancement Reagent (vazyme, catalog no. R412-C5) .

treatment_protocol: The resulting colonies were inoculated into seed cultures, which were then diluted 1:100 into LB media containing 50 μg/mL kanamycin and incubated at 37 ˚C.

tag: strain

tag: transformed with

value: negative control


title: H26 strain, 0.1mM-2

city: Shenzhen

first: Jinquan

last: Li

state: Guangdong

address: 3688 Nanhai Avenue

institute: Shenzhen University

data_processing:
Raw reads were quality filtered and adapter trimmed with fastp.
Trimmed reads were then mapped to the genome of H. volcanii DS2 using Bowtie2.
Assembly: GCF_000025685.1
Supplementary files format and content: tab-delimited text files include TPM values for each sample

organism: Haloferax volcanii DS2

source_name: cell culture

growth_protocol: Strains were grown in Hv-YPC medium at 45°C until OD600 reach 0.5.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep Kits (Zymo) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations.

treatment_protocol: Sodium bisulfite was added to the final concentration of 0.1 or 0.5 mM and continuously cultured for 48 h.

value: cell culture

value: H26 strian

value: 0.1mM sodium bisulfite


title: escherichia coli, BL21(DE3), 5mM AcK-3

description: fpkm all samples(Kac_3)

value: 5mM AcK


title: H26 strain, 0.5mM-1

value: 0.5mM sodium bisulfite


title: assembloid, wild-type microglia, rep3

description: 10x Genomics

value: wild-type


title: HT29_WT


title: BM_251_Rep1_tHMGA2-GFP

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

description: TRACE

library_source: genomic

data_processing:
For computational analyses, unless otherwise stated default parameters are used for all commands. All code for the below initial TRACE processing is provided on github (https://github.com/ensoma/andrelieber-trace-isa-wf). Briefly, fastq trimming using cutadapt [https://doi.org/10.14806/ej.17.1.200] (v4.4) was performed in four steps to ensure proper read structure: 1) R1 and R2 adapter trimming (-g ”^NNNNCGAGTTTTAATGACTCCAACT” -G ”^AGTGGCACAGCAGTTAGGNNNNNNNNAGATGTGTATAAGAGACAG” -m20 –e5), 2) IR trimming (-g ”^TAAGTGTATGTAAACTTCCGACTTCAACTG” -m20 -e4), 3) R1 and R2 adapter readthrough trimming (-a ”CTGTCTCTTATACACATCTNNNNNNNNCCTAACTGCTGTGCCACT” -A ”AGTTGGAGTCATTAAAACTCGNNNN” -m20 -e4), and IR readthrough trimming (-A ”CAGTTGAAGTCGGAAGTTTACATACACTTA” -m20 –e3). FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/] (v0.12.1) is then used for read QC before and after each processing step
The ENSEMBL mouse GRCm39 hard-masked assembly (https://ftp.ensembl.org/pub/release-111/fasta/mus musculus/dna/Mus musculus.GRCm39.dna rm.primary assembly.fa.gz) and v111 annotation (https://ftp.ensembl.org/pub/release-111/gtf/mus musculus/Mus musculus.GRCm39.111.chr.gtf.gz) were concatenated to the payload sequence, indexed with bwa [https://doi.org/10.48550/arXiv.1303.3997] (0.7.17), and the previously trimmed and filtered reads aligned to the index with bwa-mem.
There are three samtools [PMID: 19505943] (v1.17) alignment filtering steps to ensure accurate insertion sites: 1) Flag and quality score filtering (samtools view –q30 –F 3852 –f3; samtools sort –n; samtools fixmate –m; samtools view –f2; samtools sort), 2) Removal of PCR duplicates (samtools sort –n; samtools fixmate –m; samtools sort; samtools markdup –r), 3) Removing read-pairs with more than 5 soflcip reads on the 5’ end of R1 (a custom python (v3.10.13) and pysam [https://github.com/pysam-developers/pysam] (v0.21.0) script; samtools sort –n; samtools fixmate; samtools view –f3; samtools sort). Samtools flagstat and idstat are used before and after each filtering step to collect various metrics about the alignments.
Insertion sites are called using a custom Python and Pysam script that finds the genomic coordinate of the 5’-most non-sofclipped base on the R1 read. Insertion sites within 5 bases are summed and the new location set at the position with the largest read number, or given equal read numbers for multiple positions the median position of those sites. Insertion sites with a score ≥ 2 in 2 or more samples are removed using bedtools [PMID: 20110278] (2.31.0) due to their likely status of being artifacts of the TRACE method. Insertion sites are annotated to the nearest gene using a custom R (4.3.1) script that utilizes ChIPseeker [PMID: 25765347] (v1.36.0) with the settings: tssRegion=c(-2000, 200), level=”transcript”, sameStrand=TRUE. Insertion sites were retained if present in at least 2 of 3 technical replicates.
Assembly: GRCm39
Supplementary files format and content: HDAd_tHMGA2_GFP.fasta contains the sequence of the tHMGA2-containing vector.
Supplementary files format and content: annotated_insertion_sites.tsv is a table containing the post-filtering integration sites for all samples, as well as their summed scores and annotations to the nearest gene and transcript.
Library strategy: TRACE Insertion Site Analysis

molecule: genomic DNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Genomic DNA (gDNA) from week 44 bone marrow cells were extracted using the Quick-DNA miniprep kit (Zymo Research).
TRACE sequencing was performed as previously described [PMID: 35705805] with the following modifications. Tagmentation was done in an 80 µL reaction by incubating 500 ng of genomic DNA (gDNA) with 3 µL of Tn5 transposase (Diagenode; C01070010) and 4.8 µL of annealed Tn5 adapter top and bottom oligos at 45 µM in 5X TAPs buffer (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2) with 8 µL DMF for 10 mins at 55°C. The reaction was quenched with 160 µL RLT buffer (Qiagen; 79216) followed by a 0.7X SPRI bead cleanup (Beckman Coulter; B23318). Tagmented DNA was eluted with 30 µL of nuclease-free water and 20 µL was used in the first round of PCR at 20 cycles with the Tn1c and LCI primers and Q5 High-Fidelity DNA Polymerase (NEB; M0494S), and the product was cleaned with 0.7X SPRI beads and eluted into 20 µL of nuclease-free water. 12 µL was then used for nested PCR at 20 cycles with primers MA-F and MA-LCII, and the product was purified with 0.7X SPRI-beads and eluted into 20 µL of nuclease-free water. 2 µL was used as input to indexing PCR with the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) (NEB; E7600S) followed by a 0.7X SPRI bead cleanup. Final libraries were sequenced paired-end 150 x 2 (MiSeq Reagent Kit v2 300-cycles; Ms-102-2002) on an Illumina MiSeq.

value: Bone Marrow

value: Mononuclear Cells

tag: time

value: Week 44


title: H26 strain, 0.1mM-1


title: knockout strain, control-2

value: HVO_RS06830 gene knockout

value: no treatment


title: BM_251_Rep2_tHMGA2-GFP

description: TRACE


title: escherichia coli, BL21(DE3)-1

description: fpkm all samples(Due_1)


title: assembloid, wild-type microglia, rep2

description: 10x Genomics

value: embryonic stem cell

value: H9 ESC

value: microglia-cortical neural assembloid

value: 100-day culture


title: H26 strain, control-2


title: BHK-21, Fetal bovine serum

city: Salt Lake City

first: Justin

last: English

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

data_processing:
Barcodes were obtained by collecting the first 24 nucleotides of each read from demultiplexed fastq files.
Paired-end reads were trimmed using TrimGalore and joined using FastQ-Join.
Barcodes were clustered within each sample via Starcode using a Levenshtein distance of one.
Assembly: Custom barcode dictionary.
Supplementary files format and content: finalBarcodeMap.csv contains the barcode sequences and associated candidate transcriptional response elements
Supplementary files format and content: rpms.csv contains the barcode reads per million for each treatment and plasmid library

organism: Mesocricetus auratus

source_name: Kidney

growth_protocol: Cell lines were maintained in maintenance media (typically DMEM supplemented with 10% FBS and antibiotics) in a 37C humidified incubator with 5% carbon dioxide.

extract_protocol:
RNA was isolated from cell pellets using the AllPrep DNA/RNA Mini Kit (Qiagen) with QIAshredder columns (Qiagen).
RNA libraries were prepared using the Superscript IV One-Step RT-PCR System (Invitrogen) with custom primers. DNA libraries from plasmid inputs were prepared using the Platinum SuperFI II Green PCR Master Mix (Invitrogen) with custom primers.

treatment_protocol: Cells on 10 cm dishes were transfected with 10 micrograms of the TRE-MPRA plasmid library when subconfluent.Six hours after transfection, the maintenance media was replaced with serum-free media. The following day, cells were treated for six hours. Cells were then trypsinied and pellets were frozen at -80 C until processing.

value: Kidney

value: Fibroblast

tag: age

value: neonate (1 day)

tag: Sex

value: Missing

value: 10% fetal bovine serum


title: escherichia coli, BL21(DE3)-2

description: fpkm all samples(Due_2)

value: negative control


title: assembloid, wild-type microglia, rep1

description: 10x Genomics


title: H26 strain, control-1

value: cell culture

value: H26 strian


title: BHK-21, Serum free


title: MDC1_Ino80cKO_pachytene_rep1

status: Public on Oct 07 2024

city: Chapel Hill

first: Prabuddha

last: Chakraborty

state: NC

address: 120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
CUT&RUN reads were aligned to the reference genome mm10 using Bowtie2 with very-sensitive setting allowing dovetail alignment.
Duplicates were marked by Picard and replicates were merged using Samtools.
Bigwig files were prepared from merged files with 1X normalization using Deeptools.
Assembly: mm10
Supplementary files format and content: Bigwig files for genomic tracks.
Library strategy: CUT&Run

source_name: Testis

extract_protocol:
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were prepared for CUT&RUN library by previously published protocol (Skene et al., 2018; Meers et al., 2019).
Libraries were generated using Kapa hyperprep DNA library kit for Illumina sequencing with modifications from CUT&RUN protocol (Skene et al., 2018; Meers et al., 2019).

value: Testis

value: Spermatogenic cells


title: MDC1_Ino80cKO_pachytene_rep2


title: MDC1_Ino80WT_pachytene_rep2


title: MDC1_Ino80WT_pachytene_rep1


title: escherichia coli, BL21(DE3), 5mM AcK-1

description: fpkm all samples(Kac_1)

value: 5mM AcK


title: IgG_Ino80WT_pachytene_rep2


title: IgG_Ino80WT_pachytene_rep1


title: ET_ESA_Me_Fer_1

city: Minneapolis

first: Lei

middle: Justan

last: Zhang

state: MN

address: 312 Church Street SE

department: Department of Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

data_processing:
Quality control on raw sequence data for each sample was performed with FastQC
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (GRCm38) as reference.
Gene quantification was done via Feature Counts for raw read counts.
Differentially expressed genes (DEGs) were identified using the R package edgeR.
Assembly: GRCm38
Supplementary files format and content: Processed_raw_counts_ESA.xlsx

source_name: MEFs

growth_protocol: MEFs were grown at a 1:1 ratio of Dulbecco’s Modification of Eagles Medium (supplemented with 4.5 g/L glucose and L-glutamine) and Ham’s F10 medium, supplemented with 10% fetal bovine serum, penicillin, streptomycin and non-essential amino acid. WT MEFs were induced senescence by treating with hydrogen peroxide H2O2 (200 μM) or etoposide (2 μM) for 24 h, followed by 5 days in normal culture media.

extract_protocol:
Trizol RNA extraction
Illumina TruSeq Stranded Total RNA Library Prep kit

treatment_protocol: Cells were treated with α-ESA (10 μg/mL) or α-ESA-me (20 μg/mL) for 12 hours with or without a 1-hour pretreatment with Fer-1 (2 μM).

value: MEFs

value: WT

tag: senescence induced_by

value: Etoposide

value: ESA-Me (2 µg/mL) +Fer-1 (2 µM)


title: ET_ESA_Me_2

value: ESA-Me (2 µg/mL)


title: ET_ESA_Me_Fer_3


title: ET_ESA_3

value: ESA (2 µg/mL)


title: ET_ESA_2


title: ET_EtOH_2

value: EtOH


title: ET_ESA_Me_3


title: ET_ESA_Fer_2

value: ESA (2 µg/mL) +Fer-1 (2 µM)


title: ET_ESA_Me_1


title: ET_ESA_Fer_3


title: ET_EtOH_3


title: ET_ESA_Fer_1


title: H2O2_ESA_Me_Fer_3


title: ET_ESA_1


title: H2O2_ESA_Fer_3


title: H2O2_ESA_Me_3


title: ET_EtOH_1


title: H2O2_ESA_Me_2


title: H2O2_EtOH_3


title: H2O2_ESA_Me_Fer_2


title: ET_ESA_Me_Fer_2


title: H2O2_ESA_2


title: H2O2_ESA_Me_Fer_1


title: H2O2_ESA_1


title: H2O2_ESA_Fer_2


title: H2O2_ESA_Fer_1


title: H2O2_EtOH_2


title: H2O2_ESA_Me_1


title: H2O2_EtOH_1


title: H2O2_ESA_3


title: WT_ESA_Me_3

value: no inducer


title: WT_ESA_Fer_3


title: WT_ESA_3


title: CNA PpHOX32 induced biol rep 3

city: Philadelphia

first: Aman

last: Husbands

email: aman.husbands@gmail.com, ayh@upenn.edu

state: Pennsylvania

address: 103B Caroline Lynch Bldg, 433 S University Ave

institute: University of Pennsylvania

description: 24hrs post induction

data_processing:
Sequences were trimmed with trimmomatic using an initial ILLUMINA CLIP for TruSeq3 singled ended adaptors, and performing sliding window trimming averaging across 4 bp with an average score of 20.
Sequences were trimmed with trimmomatic using an initial ILLUMINA CLIP for custom sequence polyA20 tail, and performing sliding window trimming averaging across 4 bp with an average score of 20.
Reads were aligned to the TAIR10 genome using RNA STAR
Read counts were obtained using featureCounts
Differential expression was analyed using DEseq2
Assembly: TAIR10
Supplementary files format and content: Tab delimited counted files including raw counts for each sample

organism: Arabidopsis thaliana

source_name: 10 day seedlings

growth_protocol: seedlings were grown at 22°C under long-day conditions on soil or 1% agarose Murashige and Skoog medium plates (pH 5.7).

extract_protocol:
Trizol
Lexogen QuantSeq 3'

treatment_protocol: Inductions were performed by spraying 9 day old T2 seedlings on agarose plates 10 times with a 50uM β-Estradiol, 1% DMSO, and 0.005% Silwet L-77 solution. Mock induction control samples were sprayed with a 1% DMSO and 0.005% Silwet L-77 solution.

value: 10 day seedlings

value: whole seedling

value: Estradiol


title: CNA PpHOX32 mock biol rep 2

description: 24hrs post mock induction

value: Mock


title: WT_ESA_Me_Fer_3


title: CNA PpHOX32 mock biol rep 1

description: 24hrs post mock induction


title: WT_ESA_Fer_2


title: WT_ESA_Me_2


title: CNA PpHOX32 induced biol rep 2

description: 24hrs post induction


title: WT_EtOH_3


title: WT_ESA_Me_Fer_2


title: CNA PpHOX32 induced biol rep 1

description: 24hrs post induction


title: WT_ESA_Me_Fer_1


title: WT_ESA_2


title: CNA SmHOX32 mock biol rep 3

description: 24hrs post mock induction


title: WT_EtOH_2


title: CNA PpHOX32 mock biol rep 3

description: 24hrs post mock induction


title: CNA SmHOX32 mock biol rep 2

description: 24hrs post mock induction


title: WT_ESA_1


title: WT_ESA_Me_1


title: CNA SmHOX32 mock biol rep 1

description: 24hrs post mock induction


title: CNA SmHOX32 induced biol rep 2

description: 24hrs post induction


title: CNA SmHOX32 induced biol rep 1

description: 24hrs post induction


title: IR_D2, scRNA

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

description: 10X Genomics

data_processing:
Cellranger 7.0.1
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: Bone marrow

extract_protocol:
To perform 10X Genomics single-cell sequencing on mouse bone marrow LSK cells, begin by euthanizing the mouse following ethical guidelines and extracting the femurs and tibias. Flush the bone marrow with  PBS with 2% FBS, to obtain a single-cell suspension. Filter this suspension through a 40 µm cell strainer to remove debris and clumps. Next, enrich the LSK (Lineage^-, Sca-1^+, c-Kit^+) cells using magnetic-activated cell sorting (MACS) or fluorescence-activated cell sorting (FACS). Count the cells and assess viability using trypan blue staining or a similar method. Adjust the concentration of LSK cells to the required density, typically 700-1200 cells/µL
Load the single-cell suspension, reagents, and gel beads into the appropriate wells of a 10X Genomics Single Cell 3' Chip and run the chip in the Chromium Controller to encapsulate single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs). Perform reverse transcription within the GEMs to generate barcoded cDNA from the mRNA of individual cells, then break the emulsion and clean up the barcoded cDNA. Amplify the cDNA via PCR and assess the quality and quantity using an Agilent Bioanalyzer or similar instrument. Construct sequencing libraries from the amplified cDNA, following the 10X Genomics protocol. Sequence the libraries on  Illumina 3000 platform.

value: Bone marrow

value: LSK phenotype HSCs

value: Day 2 after recovery from radiation damage.


title: MousePlaque_LL_female, HTO

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description:
hashtag-derived oligonucleotide (HTO)
MousePlaque_LL_female_matrix.mtx.gz
MousePlaque_LL_female_barcodes.tsv.gz
MousePlaque_LL_female_features.tsv.gz

library_source: other

data_processing:
Cell Ranger (10x Genomics, v6.0.1) was used to performalignment (GRCm38, Ensembl 84), filtering, barcode counting and UMI counting of sequencing reads from fastq files
Assembly: GRCm38
Supplementary files format and content: Tab -separated values files and matrix files

molecule: protein

source_name: carotid plaque

extract_protocol:
Digested tissue was filtered through a 70-µm strainer, washed with cold PBS, centrifuged at 500 g for 5 min. at 4 °C and resuspended in PBS supplemented with 1% vol/vol BSA. Single-cell suspensions were placed on ice and stained with eFluor 780 Fixable Viability Dye (eBioscience, 65-0865-14) for 30 min., washed, blocked with TruStain FcX (anti-mouse CD16/32) Antibody (Biolegend, 101319) for 5 min. and then stained with PerCP/Cyanine5.5 anti-mouse CD45 Antibody (Biolegend, 103132) for 30 min. Live, CD45+ cells were purified by fluorescence-activated cell sorting using a BD FACSAria II instrument at the Cytometry and Cell Sorting Laboratory at the NYU Grossman School of Medicine at NYU Langone Health. For sorting, specimens were pooled by experimental group. The sorter was equipped with a 100 µm nozzle.
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively) according to the manufacturer’s instructions.

value: carotid plaque

value: lipid lowering

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0301-anti-mouse, TotalSeq-B0302-anti-mouse, TotalSeq-B0303-anti-mouse, TotalSeq-B0304-anti-mouse, TotalSeq-B0305-anti-mouse


title: CNA KnC3 HDZ_8m mock biol rep 3

description: 24hrs post mock induction


title: CNA KnC3 HDZ_8m mock biol rep 2

description: 24hrs post mock induction


title: WT_ESA_Fer_1

value: MEFs

value: WT


title: MousePlaque_LL_male, HTO

description:
hashtag-derived oligonucleotide (HTO)
MousePlaque_LL_male_matrix.mtx.gz
MousePlaque_LL_male_barcodes.tsv.gz
MousePlaque_LL_male_features.tsv.gz


title: MousePlaque_LL_male, mRNA

description:
polyA-RNA
MousePlaque_LL_male_matrix.mtx.gz
MousePlaque_LL_male_barcodes.tsv.gz
MousePlaque_LL_male_features.tsv.gz

value: mRNA


title: CNA SmHOX32 induced biol rep 3

description: 24hrs post induction


title: CNA KnC3 HDZ_8m induced biol rep 3

description: 24hrs post induction


title: MousePlaque_LL_female, mRNA

description:
polyA-RNA
MousePlaque_LL_female_matrix.mtx.gz
MousePlaque_LL_female_barcodes.tsv.gz
MousePlaque_LL_female_features.tsv.gz


title: CNA KnC3 HDZ_8m mock biol rep 1

description: 24hrs post mock induction


title: G34R_control_V5_rep1

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
CUT&RUN data was processed using GenPipes (v4.3.2) ChIP Sequencing Pipeline.
Briefly, this includes adapter removal and trimming with Trimmomatic (v0.39), alignment to mm10 with BWA (v0.7.17), removal of duplicated reads with Picard (v2.26.6)
BigWig tracks were generated usiing Homer (v4.11)
Peak calling was done using MACS2 (v2.2.7.1)
Assembly: mm10
Supplementary files format and content: BigWig files: compressed, binary format for genome-wide signal data
Supplementary files format and content: narrowPeak files: peaks with signal enrichment info
Library strategy: CUT&RUN

source_name: cell line from IUE mouse models

extract_protocol:
5x105 cells per sample were dissociated, washed and bound to CUTANA Concanavalin A coated Paramagnetic Beads (EpiCypher). V5-Tag antibody (D3H8Q, CST 13202, RRID:AB_2687461) was bound to cells overnight at a 1:50 dilution. Digestion of target chromatin used CUTANA pAG-MNase, followed by DNA collection.
Libraries were generated using Kapa HTP Illumina library preparation reagents using 9-12 cycles of PCR, followed by dual 0.6-0.8x size selection using AMPure XP magnetic beads

treatment_protocol: Cross-linking was performed in suspension with 0.1% formaldehyde for 1 minute, followed by reverse cross-linking with glycine, according to the Epicypher CUTANA cross-linking protocol. Reagents and protocol were based on the Epicypher cleavage under targets and release under nuclease (CUT&RUN) commercial protocol.

value: cell line from IUE mouse models

tag: antibody

value: IUE


title: FOXR2_P53LoF_V5_rep2

value: FOXR2 P53LoF


title: FOXR2_p53LoF_02

data_processing:
Adapter sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic(v0.39). Reads were scanned from the 5′ end and truncated when the average quality of a four-nucleotide sliding window fell below a threshold (phred33 < 30). Short reads after trimming (<30 base pairs) were discarded.
High-quality reads were aligned to the reference genome mm10 (GRCm38) with STAR (v2.7.9a) using default parameters.
To generate BigWig files, a bedgraph file was created using the genomeCoverageBed function from bedtools (v2.30.0) using the split and bg parameters. Then the coverage was normalized by dividing the bedgraph coverage by a factor equals to the number of mapped reads divided by 100 million. The bedGraphToBigWig function from UCSC tools (v387) was used to create BigWig files.
Assembly: mm10
Supplementary files format and content: BigWig files: compressed, binary format for genome-wide signal data

extract_protocol:
Total RNA was extracted from cell pellets using the Maxwell RSC simplyRNA Cells Kit (AS1390, Promega) according to instructions from the manufacturer
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (New England Biolabs)

tag: passage number

value: FOXR2 p53LoF


title: FOXR2_p53LoF_03


title: CNA KnC3 HDZ_8m induced biol rep 2

description: 24hrs post induction

value: 10 day seedlings

value: whole seedling


title: CNA KnC3HDZ mock biol rep 3

description: 24hrs post mock induction

value: Mock


title: M_Cst7_KO_Day21pi (CellPlex Multiplex Capture)

first: Amber

last: Syage

state: Utah

address: 2000 Circle of Hope

department: Pathology

description: 10x Genomics, 3'

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 6.1.2 to create I1 and I2 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-6.1.2 reference from 10X Genomics.
Barcodes and UMIs were counted using cellranger count with expected-cells=6,000
refdata-gex-mm10-2020-A
Assembly: Filtered feature-barcode matrices in TSV and MTX format from cellranger count.
Supplementary files format and content: CellPlex labeles were demultiplexed using Seurat to create the four experimental groups: WT_Uninfected, KO_Uninfected, WT_Day21pi, and KO_Day21pi

source_name: Spinal cord

extract_protocol: Tissue was extracted from isofluorine euthanized mice after saline cardiac perfusion. Single cell suspensions were generated from tissue samples by grinding with frosted microscope slides. Immune cells were then enriched via a 2-step Percoll cushion (90% and 63%) and cells were collected at the interface of the two Percoll layers. These cells were then FACS sorted for CD45+DAPI- using CD45-APC conjugated Flow antibodies.

value: CD45+ cells

value: Spinal cord

value: JHMV infected

value: 6-8 weeks old

value: CellPlex Multiplex Capture


title: FOXR2_P53LoF_V5_rep1


title: CNA KnC3HDZ mock biol rep 2

description: 24hrs post mock induction


title: CNA KnC3 HDZ_8m induced biol rep 1

description: 24hrs post induction

value: Estradiol


title: G34R_control_V5_rep2


title: CNA KnC3HDZ induced biol rep 1

description: 24hrs post induction


title: C_Cst7_WT_Day21pi (CellPlex Multiplex Capture)

description: 10x Genomics, 3'


title: CNA KnC3HDZ induced biol rep 3

description: 24hrs post induction


title: M_Cst7_KO_Day21pi (GEX)

description: 10x Genomics, 3'

value: GEX


title: WT_EtOH_1

value: MEFs

value: no inducer

value: EtOH


title: CNA KnC3HDZ induced biol rep 2

description: 24hrs post induction


title: CNA KnC3HDZ mock biol rep 1

description: 24hrs post mock induction


title: FOXR2_p53LoF_01

value: cell line from IUE mouse models


title: C_Cst7_WT_Day21pi (GEX)

description: 10x Genomics, 3'


title: Uninfected_Cst7_WT and KO (CellPlex Multiplex Capture)

description: 10x Genomics, 3'

value: C57BL/6J_Cst7+/+ and Cst7-/-

value: Noninfected


title: Foxr2_r1_multiome_ATAC

description:
10x Genomics
Foxr2_r1_barcodes.tsv.gz
Foxr2_r1_features.tsv.gz
Foxr2_r1_matrix.mtx.gz

data_processing:
Cell Ranger ARC v2.0.0 (10x Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for the multiome samples.
Sequencing reads were aligned to a custom mm10 reference integrating the different vectors added to the mouse genome. A custom GTF file was created to count the reads mapping to these added sequences coupled with the Gencode vM23 (Ensembl 98) gene annotation.
Assembly: mm10
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes and peaks), barcodes and expression matrices generated by Cell Ranger.

source_name: brain

extract_protocol:
scMultiome nuclei were prepared using the extended nuclei protocol. Nuclei were isolated using the Nuclei Isolation kit and Singulator S100 instrument from S2 Genomics. After nuclei prep, nuclei were centrifuged and washed twice in Diluted Nuclei Buffer (10x Genomics) and counted with the ReadyProbes Cell Viability Blue/Green kit (ThermoFisher Scientific).
Library preparation was prepared following the manufacturer’s instructions (Next GEM Single Cell Multiome).
single-cell multiome (snRNA-seq + ATAC-seq)

value: brain

tag: disease state

value: brain tumor

value: Foxr2 overexpression


title: PHBdelta mock biol rep 1

description: 24hrs post mock induction

value: 10 day seedlings

value: whole seedling

value: PHB-SDdelta

value: Mock


title: PHBdelta induced biol rep 3

description: 24hrs post induction


title: PHBdelta induced biol rep 2

description: 24hrs post induction


title: Foxr2_r2_multiome_ATAC

description:
10x Genomics
Foxr2_r2_barcodes.tsv.gz
Foxr2_r2_features.tsv.gz
Foxr2_r2_matrix.mtx.gz


title: Foxr2_p53_r1_multiome_snRNAseq

description:
10x Genomics
Foxr2_p53_r1_barcodes.tsv.gz
Foxr2_p53_r1_features.tsv.gz
Foxr2_p53_r1_matrix.mtx.gz

value: Foxr2 overexpression and p53 LoF


title: PHB mock biol rep 3

description: 24hrs post mock induction

value: PHB


title: Foxr2_r1_multiome_snRNAseq


title: PHBdelta mock biol rep 3

description: 24hrs post mock induction


title: PHB mock biol rep 2

description: 24hrs post mock induction


title: PHB mock biol rep 1

description: 24hrs post mock induction


title: PHB induced biol rep 1

description: 24hrs post induction

value: Estradiol


title: lncap_MEG3 overexpression vector [M_3]

city: Wuhan

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: prostate

extract_protocol:
Total RNAs were extracted  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: prostate

value: lncap

value: Hormone-dependent prostate cancer cell

value: MEG3 overexpression


title: PHB induced biol rep 3

description: 24hrs post induction


title: PHBdelta mock biol rep 2

description: 24hrs post mock induction


title: PHB induced biol rep 2

description: 24hrs post induction


title: Foxr2_r2_multiome_snRNAseq


title: lncap_MEG3 overexpression vector [M_2]


title: HealthyDonor19 (snRNA-seq)

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

description: 10X Genomics

data_processing:
The demultiplexing, gene counting and alignment processes were performed using CellRanger software (v 7.0).
Doublets were removed for each sample. Normalization was performed with help of Seurat (v4.4.1) R package and integration of all sequenced samples was performed using Harmony (v0.1) R package.
Each cell cluster identified was annotated by canonical cell surface markers.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Infrapatellar Fat pad

extract_protocol:
Nuclei were isolated from frozen human fats pads (n=21, weighing approximately 50 mg) by physical dissociation using a glass dounce homogenizer and were sorted using fluorescence-activated cell sorting (FACS) based on DAPI-positive fluorescence to obtain a single nuclei population. Nuclei concentration was manually determined using DAPI staining and hemocytometer and adjusted to 1000 nuclei/uL.
Single nuclei RNA sequencing libraries were generated using the 10X Genomics Chromium Instrument andChromium Next GEM Single Cell 3’ Reagent Kits (v3.1) from approximately 4000 nuclei.Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).

value: Infrapatellar Fat pad

tag: condition

value: control

value: male

tag: bmi

tag: bmi category

value: Overweight

tag: procedure

value: Post-mortem with no history of musculoskeletal disease


title: HealthyDonor20 (snRNA-seq)

description: 10X Genomics

tag: tissue

value: female


title: CNAdelta mock biol rep 3

description: 24hrs post mock induction

value: 10 day seedlings

tag: cell line

tag: cell type

tag: genotype

value: CNA-SDdelta

tag: treatment


title: HealthyDonor21 (snRNA-seq)

description: 10X Genomics

tag: age


title: Foxr2_p53_r1_multiome_ATAC

value: brain

tag: strain

value: brain tumor


title: HealthyDonor18 (snRNA-seq)

description: 10X Genomics

tag: Sex

value: Normal


title: CNAdelta mock biol rep 2

description: 24hrs post mock induction

value: whole seedling

value: Mock


title: lncap_MEG3 overexpression vector [M_1]

value: prostate


title: HealthyDonor17 (snRNA-seq)

description: 10X Genomics


title: Uninfected_Cst7_WT and KO (GEX)

description: 10x Genomics, 3'

value: CD45+ cells

value: Spinal cord

value: C57BL/6J_Cst7+/+ and Cst7-/-

value: Noninfected

value: 6-8 weeks old

tag: library type

value: GEX


title: HealthyDonor16 (snRNA-seq)

description: 10X Genomics

value: Infrapatellar Fat pad

value: control

value: male


title: lncap_empty_vector [NC3]

value: lncap

value: Hormone-dependent prostate cancer cell

value: WT


title: CNAdelta mock biol rep 1

description: 24hrs post mock induction

value: 10 day seedlings

value: CNA-SDdelta


title: PHBdelta induced biol rep 1

description: 24hrs post induction

value: whole seedling

value: PHB-SDdelta

value: Estradiol


title: KneeOA_ObeseBMI13 (snRNA-seq)

description: 10X Genomics

value: OA

value: female

value: Obese

value: Total Knee Replacement


title: KneeOA_ObeseBMI15 (snRNA-seq)

description: 10X Genomics


title: CNAdelta induced biol rep 3

description: 24hrs post induction


title: KneeOA_ObeseBMI14 (snRNA-seq)

description: 10X Genomics


title: KneeOA_ObeseBMI12 (snRNA-seq)

description: 10X Genomics


title: KneeOA_ObeseBMI9 (snRNA-seq)

description: 10X Genomics


title: lncap_empty_vector [NC1]

value: prostate


title: CNAdelta induced biol rep 2

description: 24hrs post induction


title: CNAdelta induced biol rep 1

description: 24hrs post induction


title: KneeOA_ObeseBMI10 (snRNA-seq)

description: 10X Genomics


title: EK81.8, cultuted at 37 C 5% CO2 (T=6 hours staurosporine addition) R3

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

data_processing:
Raw reads were mapped using STAR v2.7.1with the standard parameters employed by the rsem-calculate-expression pipeline
rsem-calculate-expression (RSEM v1.3.1) was used to compute the  expected counts at the gene level from the BAM files
edgeR v4.2.0 was used to perform Differential Gene Expression analysis
Low expressed genes (cpm < 1in at least 16 replicates) were excluded from the analysis
Library size and composition normalizations were performed with the calcNormFactors (TMM method) and estimateDisp (TagWise method) functions respectively.
DE tests between sample pairs were performed with the exactTest function. Significant DE genes were called when FDR <= 0.01
Assembly: hs1/T2T - RefSeq Gene Annotation downloaded from the UCSC Genome Browser db on 2023-05-29
Supplementary files format and content: tsv - genes.results output from rsem-calculate-expression
Supplementary files format and content: xlsx - DGE analysis results for all tested sample pairs

growth_protocol: Culturing in DMEM High Glucose GlutaMAX (GibcoTM) supplemented with 10% heat inactivated-fetal bovine serum, 0.5% Sodium Pyruvate (Lonza™ BioWhittaker), 1% Penicillin/Streptomycin (Gibco™), and 0,1% Plasmocin® prophylactic (InvivoGen), at 37 °C in humified atmosfere at 5% CO2

extract_protocol:
RNeasy Mini Kit (QIAGEN)
Library prepared with TruSeq Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina), according to manufacturer’s instructions

treatment_protocol: Incubation of 6 hours after addition of 1 µM staurosporine (samples 4,5,6)

value: epithelial-like

value: staurosporine


title: CNA mock biol rep 3

description: 24hrs post mock induction

value: CNA

value: Mock


title: KneeOA_ObeseBMI11 (snRNA-seq)

description: 10X Genomics

value: Infrapatellar Fat pad


title: KneeOA_NormalBMI7 (snRNA-seq)

description: 10X Genomics

value: Normal


title: KneeOA_ObeseBMI8 (snRNA-seq)

description: 10X Genomics

value: male


title: KneeOA_NormalBMI6 (snRNA-seq)

description: 10X Genomics


title: KneeOA_NormalBMI5 (snRNA-seq)

description: 10X Genomics


title: KneeOA_NormalBMI3 (snRNA-seq)

description: 10X Genomics


title: EK81, cultuted at 37 C 5% CO2 (T=6 hours after staurosporine addition) R3

value: 293T with NM_033109.5 (PNPT1):c.1424A>G:p.Glu475Gly (heterozygous).


title: CNA mock biol rep 1

description: 24hrs post mock induction

value: 10 day seedlings


title: CNA mock biol rep 2

description: 24hrs post mock induction

value: whole seedling


title: KneeOA_NormalBMI4 (snRNA-seq)

description: 10X Genomics


title: KneeOA_NormalBMI2 (snRNA-seq)

description: 10X Genomics


title: EK81, cultuted at 37 C 5% CO2 (T=6 hours after staurosporine addition) R2


title: EK81, cultuted at 37 C 5% CO2 (T=6 hours after staurosporine addition) R1


title: EK81.8, cultuted at 37 C 5% CO2 (T=6 hours staurosporine addition) R2


title: CNA induced biol rep 3

description: 24hrs post induction


title: CNA induced biol rep 1

description: 24hrs post induction


title: Tea plant root, scRNA-seq

city: Hefei

first: Shijia

last: Lin

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultral University

description: 10x genomics

data_processing:
The raw files were analyzed by Cell Ranger 5.0.0 (10x Genomics). The tea plant genome and GTF annotation files, which excluded the organelle genomes, were downloaded from the Tea plants Information Archive (TPIA) website (http://tpia.teaplants.cn) (Xia et al., 2019). Running ‘cellranger mkref’ with ‘‘–genome, –fasta and –genes’’ inputs was employed to build the reference. Then ‘cellranger count’ with ‘‘–id, –transcriptome, –fastqs, –sample” was run. Some 79.8% of the reads in all of the samples were aligned to the tea plant genome by the aligner STAR (v.2.5.1b). Mean reads per cell were 26,411. Median genes per cell was in the range of 680.
Assembly: shuchazao_V2.genome.fas.gz, Tea plants Information Archive (TPIA) website (http://tpia.teaplants.cn)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Camellia sinensis

source_name: Tea plant

extract_protocol:
The root tip regions (~2 cm in length from root tip) were cut, longitudinally, into 3 - 4 small strips and then processed for protoplast isolation. Here, the root strips were transferred immediately and gently into the prepared enzyme solution (0.1 moluL-1 KCl, 0.08 moluL-1 MES, 0.02 moluL-1 CaCl2, 1.5% cellulase R10 (Yakult, Japan), 1% Pectolyase (Yakult, Japan), 0.4 moluL-1 mannitol, and 0.1% BSA), and digested at 25°C, with shaking (40 rpm), in the dark for the indicated period. An equal volume of washing buffer (WB) solution (0.1 moluL-1 KCl, 0.08 moluL-1 MES, 0.4 moluL-1 mannitol and 0.1% BSA) was added in the enzyme solution and the mixture was then filtered using nylon mesh (200 mesh/inch). The flow-through was centrifuged at 200 x g for 2 min to pellet protoplasts. To evaluate protoplast yield, under different isolation conditions, protoplasts were re-suspended with suitable WB solution and counted with a hemocytometer. Protoplast viability was determined by trypan blue staining, with the ratio of viable cells being more than 85%. The concentration of protoplasts was adjusted to 700–1200 cells/μL and cells were then processed with the 10x Genomics Single Cell Protocol (CG00052, RevC).
The libraries were constructed using 10× Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1(1000268). In brief, cell suspensions in a chip were loaded on a Chromium Controller (10xGenomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in emulsion). The scRNA-seq libraries were then prepared, according to the manufacturer’s protocol. Qualitative analysis of the DNA library was performed on an Agilent 2100 Bioanalyzer. The concentration of DNA library was measured by Qubit (Invitrogen).

value: Root

value: Root cell


title: WT, cultuted at 37 C 5% CO2 (T=6 hours after staurosporine addition) R2


title: NIPBL-D7-DMSO_PDS5_ChIP

city: La Jolla

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

data_processing:
ChIP-seq data was aligned to the hg38 reference genome using BWA-MEM.
Aligned data was de-duplicated using Picard MarkDuplicates.
Low quality and supplementary reads, and improper pairs were filtered out using samtools.
Reads aligning only to the primary chromosomes (chr1-22/X/Y) were captured using samtools. If required, hg38-aligned reads were also separated out from mm10-aligned reads.
Blacklisted regions were removed using bedtools intersect.
deepTools bamCoverage was used to generate BigWig files.
MACS2 was used to call peaks from the ChIP sample, using the input sample as a control.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeak

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin, and grown at 37°C with 5% CO2. NIH/3T3 cells (for spike-in) DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
For HA ChIP-seq, cells were fixed with 2 mM DSG for 45 minutes, washed with DPBS, then fixed further 1% formaldehyde for 10 minutes. Formaldehyde was quenched with 125mM glycine for 10 minutes. For other ChIP-seq experiments, cells were fixed with 1% formaldehyde for 10 minutes, then quenched with 125mM glycine for 10 minutes. All cells were lysed using formaldehyde lysis buffer (FALB; 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) supplemented with 1% SDS and 1X PIC, and sonicated for 9 minutes (10 seconds on/10 seconds off) at 25% power using an Active Motif Epishear Probe Sonicator. Antibodies were pre-bound to blocked Protein A Dynabeads for 6-8 hours at 4°C before being added to chromatin that had been diluted out 1:10 with FALB (no SDS), incuating overnight at 4°C. The following day, beads were washed as described above, then eluted for 1 hour at 65°C in 50 mM Tris pH 8, 1 mM EDTA, 1% SDS. Supernatant was transferred to a new tube, supplemented with 200 mM NaCl and proteinase K, then incubated for 30 minutes at 55°C followed by overnight at 65°C. The following day, samples were treated with RNAse for 2 hours at 37°C, before DNA was purified using Zymo ChIP DNA Clean & Concentrator kit (#D5205).
For CTCF input and ChIP, samples were size-selected using AMPure beads and libraries prepared using 2S Plus DNA Library Kit (IDT #10009878). Otherwise, libraries were prepared using Diagenode Microplex v3 (#C05010001) and UDIs (Set I: # C05010008; Set 2: #C05010009).

treatment_protocol: Asynchronous cells were actively cycling when treated with DMSO or dTAGV-1 for the stated times.

value: hTERT RPE-1

tag: clone name

value: DMSO 24hr

tag: spike-in


title: WT, cultuted at 37 C 5% CO2 (T=6 hours after staurosporine addition) R1


title: brain, Input, 37C, rep1, 797

city: Seattle

first: Karol

last: Bomsztyk

state: WA

address: 850 Republican St

department: Medicine

institute: University of Washington

description: 09-01-23 ChIP797MeDIP-Seq

data_processing:
Fastqs were processed using Fastp all-in-one processing tool.
Files were then converted to BAM using Bowtie2 tool, and into bigwig format using Bamcompare tool (treatment = 5mC, control = input).
Read counts were obtained from the BAM files using featureCounts, and then heatmaps and normalized count tables were generated using the Limma tool.
Gene Ontology analysis was performed on the normalized count tables by identifying the greatest differential expression between MGMT positive and MGMT negative samples
Assembly: hg38
Supplementary files format and content: tabular - normalized read counts

extract_protocol:
DNA was isolated using PIXUL ultrasonication method and proteinase K
library was constructed using xGen ssDNA library kit from IDT with immunoprecipitated (5mC) and input dsDNA

treatment_protocol: Glioma specimen collection was performed at the Houston Methodist Research Institute, Houston, TX and at the University of Washington, Seattle, WA. Frozen samples were stored at -80oC. FFPE samples were fixed for either 24hrs or 72 hrs. Ex-vivo ischemia was performed on some samples for 4hrs at either 4oC (Cold Ischemia) or 37oC (Warm Ischemia). Some samples were thawed and re-frozen 3x (Frozen-Thawed-3x)

value: brain

tag: nucleic acid

value: ssDNA

tag: medip antibody

value: Input

value: Frozen - Warm Ischemia


title: brain, 5mC, 37C, rep2, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: brain, Input, 0h, rep2, 797

description: 09-01-23 ChIP797MeDIP-Seq

value: Frozen


title: brain, 5mC, 4C, rep2, 797

description: 09-01-23 ChIP797MeDIP-Seq

value: Frozen - Cold Ischemia


title: brain, Input, 4C, rep2, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: brain, 5mC, 0h, rep2, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: brain, 5mC, 37C, rep1, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: brain, Input, 4C, rep1, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: RPE-1_WT_WAPL_input

value: wild-type

tag: antibody

value: WAPL (Proteintech #16370-1-AP)


title: EK81.8, cultuted at 37 C 5% CO2 (T=0) R3

value: epithelial-like


title: KneeOA_NormalBMI1 (snRNA-seq)

description: 10X Genomics

value: Infrapatellar Fat pad

tag: condition

value: OA

value: male

tag: bmi

value: Normal

value: Total Knee Replacement


title: brain, 5mC, 4C, rep1, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: brain, Input, 0h, rep1, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: EK81.8, cultuted at 37 C 5% CO2 (T=0) R2


title: NIPBL-D7-dTAG-24hr_RAD21_ChIP

value: dTAGV-1 24hr

value: RAD21 (Abcam #ab992)


title: brain, Input, 37C, rep2, 797

description: 09-01-23 ChIP797MeDIP-Seq


title: CNA induced biol rep 2

description: 24hrs post induction

value: 10 day seedlings

value: whole seedling

value: CNA

value: Estradiol


title: brain, Input, warm ischemia, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq

value: brain

value: ssDNA

value: Input

value: Frozen-Warm Ischemia


title: WT, cultuted at 37 C 5% CO2 (T=6 hours after staurosporine addition) R3

value: staurosporine


title: NIPBL-D7-dTAG-4hr_RAD21_ChIP

value: hTERT RPE-1

value: dTAGV-1 4hr


title: brain, 5mC, 0h, rep1, 797

description: 09-01-23 ChIP797MeDIP-Seq

value: Frozen


title: brain, Input, frozen, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: EK81, cultuted at 37 C 5% CO2 (T=0) R3

value: epithelial-like

value: 293T with NM_033109.5 (PNPT1):c.1424A>G:p.Glu475Gly (heterozygous).


title: NIPBL-D7-DMSO_RAD21_ChIP

value: DMSO 24hr


title: brain, 5mC, warm ischemia, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: brain, 5mC, frozen, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: brain, 5mC, 37C, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: RPE-1_WT_WAPL_ChIP

value: wild-type

value: WAPL (Proteintech #16370-1-AP)


title: brain, Input, 37C, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: EK81, cultuted at 37 C 5% CO2 (T=0) R2


title: NIPBL-A2-dTAG-4hr_RAD21_ChIP

value: RAD21 (Abcam #ab992)


title: WT, cultuted at 37 C 5% CO2 (T=0) R2


title: brain, 5mC, warm ischemia, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: WT, cultuted at 37 C 5% CO2 (T=0) R3


title: EK81.8, cultuted at 37 C 5% CO2 (T=0) R1


title: brain, Input, warm ischemia, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: NIPBL-D7-dTAG-24hr_RAD21_input

value: dTAGV-1 24hr

value: input


title: brain, Input, 0h, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: lncap_empty_vector [NC2]

value: prostate

value: lncap

value: Hormone-dependent prostate cancer cell

value: WT


title: brain, Input, frozen, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq

value: brain

value: ssDNA

value: Input


title: EK81, cultuted at 37 C 5% CO2 (T=0) R1


title: brain, 5mC, 0h, rep2, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: brain, Input, 37C, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq

value: Frozen-Warm Ischemia


title: WT, cultured at 37 C 5% CO2 (T=0) R1


title: brain, 5mC, frozen, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq

value: Frozen


title: NIPBL-D7-dTAG-4hr_RAD21_input

value: hTERT RPE-1

value: dTAGV-1 4hr


title: NIPBL-A2-DMSO_RAD21_ChIP

value: DMSO 24hr


title: brain, Input, 0h, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: NIPBL-A2-dTAG-24hr_RAD21_ChIP


title: rh3033, Group_1, D7

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

data_processing:
Sequenced reads were trimmed with Trim galore using default parameters version 0.6.10
Globin and rRNA reads filtered out with bowtie2 version 2.5.1
Reads aligned and quantified using STAR v 2.7.10b to Mmul_10
Ensembl annotation version 109
Assembly: Mmul_10
Supplementary files format and content: Comma separated value file of raw counts provided in count_matrix.csv

organism: Macaca mulatta

source_name: Whole blood PAXgene

extract_protocol:
Whole blood was collected from cynomolgus macaques in PAXgene RNA tubes (PreAnaytiX) to manufacturers instrucruction. RNA was isolated using RNAdvance Blood Kit with the manufacter's instructions
RNA was extracted using the PAXgene Blood miRNA Kit 96, enriched for mRNA with Thermofisher Dynabeads, and libraries prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin depletion kit.

treatment_protocol: Indian rhesus macaques were unvaccinated or received heterologous prime-boost of recombinant vectors expressing SIVmac239 Vif and Nef (rAd5-Vif and rAD5-Nef; rVSV-Nef-Tat-Vif; rRRV-Rev-Tat-Nef, rRRV-Nef, rRRV-Vif), then challenged with a minimal dose of SIVmac239 until productive infection was measured. D0 samples represent baseline prior to the qualifying challenge, with samples then collected at days 3,7,10 and 14 after qualifying challenge dose.

value: Whole blood PAXgene

tag: animal id

value: male

value: Vaccinated

tag: time

tag: outcome

tag: num challenges

tag: final virus_dose


title: rh2995, Group_3, D7

tag: tissue

tag: genotype

tag: treatment

value: Unvaccinated


title: brain, 5mC, 0h, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: brain, 5mC, frozen, rep4, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: rh3053, Group_1, D0

tag: Sex


title: NIPBL-A2-dTAG-24hr_RAD21_input

tag: cell line

value: dTAGV-1 24hr

value: input


title: NIPBL-A2-dTAG-4hr_RAD21_input

tag: clone name


title: brain, Input, frozen, rep3, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: brain, 5mC, 37C, rep1, 793

description: 06-01-23 ChIP793MeDIP-Seq


title: rh3053, Group_1, D10


title: NIPBL-A2-DMSO_RAD21_input

tag: spike-in


title: NIPBL-D7-STAG2_ChIP

value: STAG2 (Cell Signaling #5882)


title: rh3053, Group_1, D7


title: brain, 5mC, 72h, rep3, 791

description: 05-04-23 ChIP791MeDIP-Seq

tag: nucleic acid


title: brain, 5mC, frozen, rep2, 791

description: 05-04-23 ChIP791MeDIP-Seq

tag: medip antibody


title: brain, Input, 72h, rep3, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: NIPBL-D7-STAG1_ChIP

tag: antibody

value: STAG1 (Invitrogen #PA5-57115)


title: brain, Input, frozen, rep2, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: NIPBL-D7-STAG1/2_input


title: brain, Input, 72h, rep2, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: NIPBL-D7-DMSO_RAD21/PDS5_input


title: rh3053, Group_1, D3


title: brain, 5mC, 72h, rep2, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: brain, Input, frozen, rep4, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: brain, Input, frozen, rep1, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: brain, Input, 72h, rep4, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: brain, 5mC, frozen, rep1, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: rh3048, Group_1, D14

value: female


title: rh3053, Group_1, D14


title: brain, Input, 72h, rep1, 791

description: 05-04-23 ChIP791MeDIP-Seq

value: brain


title: brain, 5mC, 72h, rep4, 791

description: 05-04-23 ChIP791MeDIP-Seq

value: ssDNA


title: RAD21-B3_dTAG_24hr_HiC

data_processing:
HiC data was first aligned to the hg38 reference genome using BWA-MEM and processed with in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Aligned data was de-duplicated using Picard MarkDuplicates.
Contact files were generated from bam files using in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Juicer was used to create .hic files from contact files, while cooler was used to create multi-resolution cool (mcool) files.
Assembly: hg38
Supplementary files format and content: Multi-resolution cool file
Supplementary files format and content: hic file

growth_protocol: hTERT RPE-1 were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin, and grown at 37°C with 5% CO2.

extract_protocol:
Cells were fixed and processed according to the Arima Genomics HiC+ Kit protocol. For HiC of the RAD21 degron cell lines, cells were fixed and processed as-normal until prior to decrosslinking. At this stage, samples were stained with propidium iodide, and the G1/2N population was sorted in bulk. G1/2N sorted cells then reentered the HiC protocol.
Proximity-ligated DNA was first sonicated to ~400 bp using a Covaris M220 with 50 W power, 10% duty factor and 200 cycles per burst for 78 seconds, and then size-selected using AMPure beads. For high-input HiC samples, library preparation was performed using KAPA HyperPrep (Roche #KK8502) according to instructions provided with the Arima Genomics HiC+ Kit, with library preparation done on streptavidin beads. For low-input HiC samples, library preparation was performed using 2S Plus DNA Library Kit (IDT #10009878), with pre-PCR library preparation done in solution before biotin enrichment using Dynabeads MyOne Streptavidin T1 beads, and PCR on bead-bound DNA.

treatment_protocol: Asynchronous cells were actively cycling when treated with DMSO or dTAGV-1 for the stated times. For synchronization using a double thymidine block/nocodazole, engineered hTERT RPE-1 cells were treated with 2 mM thymidine for 14 hours, released for 10 hours, treated again with 2 mM thymidine for 14 hours, then released for 8 hours. Cells were then treated with 20 ng/ml nocodazole simultaneous with DMSO or dTAGV-1 for 120 minutes. Following this time, mitotic shake-off was used to enrich for cells synchronized to prometaphase, before being released into DMSO or dTAGV-1-containing media for the stated times.

tag: synchronization

value: Asynchronous

tag: facs

value: Propidium iodide stained, G1/2N sorted


title: rh3048, Group_1, D10

tag: animal id


title: RAD21-B1_dTAG_24hr_HiC


title: brain, 5mC, frozen, rep3, 791

description: 05-04-23 ChIP791MeDIP-Seq

value: Frozen


title: brain, 5mC, 72h, rep1, 791

description: 05-04-23 ChIP791MeDIP-Seq


title: rh3048, Group_1, D7

tag: time


title: RAD21-B3_dTAG_4hr_HiC

value: hTERT RPE-1


title: brain, Input, frozen, rep4, 784

description: 02-21-23 ChIP784MeDIP-Seq

value: Input


title: brain, Input, thawed, rep4, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: rh3048, Group_1, D3

tag: outcome


title: brain, 5mC, thawed, rep4, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: rh3048, Group_1, D0

tag: num challenges


title: RAD21-B1_dTAG_4hr_HiC

value: dTAGV-1 4hr


title: brain, 5mC, frozen, rep4, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: brain, Input, frozen, rep3, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: brain, Input, thawed, rep3, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: rh3045, Group_1, D14

value: Whole blood PAXgene

tag: final virus_dose


title: brain, 5mC, thawed, rep3, 784

description: 02-21-23 ChIP784MeDIP-Seq

tag: tissue


title: RAD21-B1_DMSO_24hr_HiC

tag: genotype

value: DMSO 24hr


title: rh3045, Group_1, D10

value: male

tag: treatment

value: Vaccinated


title: brain, Input, thawed, rep2, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: brain, 5mC, frozen, rep3, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: brain, Input, frozen, rep2, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: rh3045, Group_1, D7

tag: Sex


title: brain, 5mC, thawed, rep2, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: brain, 5mC, frozen, rep2, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: rh3045, Group_1, D3


title: brain, Input, frozen, rep1, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: brain, Input, thawed, rep1, 784

description: 02-21-23 ChIP784MeDIP-Seq


title: NIPBL-D7_dTAG_8hr_4sU_15min_R2_SLAM

data_processing:
Alignment was performed using HISAT-3N with a HISAT-3N index built to account for T>C conversions and with RPE-1 SNPs substituted with N. For alignment purposes, read2 was treated as read1, and read1 was treated as read2.
Aligned data was de-duplicated using Picard MarkDuplicates.
A custom HTSeq Python script (SLAM_HTSeq.py) was used count read pairs that align to a gencode.v25 gene. Read pairs that HISAT-3N determine contain a T>C conversion (Yf>0) are counted as nascent, while all nascent and non-converted read pairs are counted as total.
Assembly: hg38
Supplementary files format and content: Nascent and total gene (gencode.v25) counts in .txt format
Library strategy: SLAM-seq

extract_protocol:
RNA was extracted using TRIzol and purified using Direct-zol RNA Miniprep Kit (Zymo #R2052). Iodoacetamide conversion was performed using SLAMseq Kinetics Kit – Anabolic Kinetics Module (Lexogen #061), with subsequent purification using either ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo #R1013).
Sequencing libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Zymo #R3003), according to manufacturer’s instructions.

treatment_protocol: Asynchronous cells were actively cycling when treated with DMSO or dTAGV-1 for the stated times. For synchronization using a double thymidine block/nocodazole, engineered hTERT RPE-1 cells were treated with 2 mM thymidine for 14 hours, released for 10 hours, treated again with 2 mM thymidine for 14 hours, then released for 8 hours. Cells were then treated with 20 ng/ml nocodazole simultaneous with DMSO or dTAGV-1 for 120 minutes. Following this time, mitotic shake-off was used to enrich for cells synchronized to prometaphase, before being released into DMSO or dTAGV-1-containing media for the stated times. Four-thiouridine (4sU) was added to cells to a final concentration of 100 μM. Labeling periods are stated, and are included in the treatment time (e.g. DMSO/dTAG 4 hr would be DMSO/dTAG-only for 3:15 hr, then DMSO/dTAG + 4sU for an additional 45 minutes)

tag: cell line

value: dTAGV-1 120min + 8hr

tag: 4su labeling_period

value: 15 minutes


title: rh3045, Group_1, D0


title: NIPBL-D7_DMSO_8hr_4sU_15min_R2_SLAM

tag: clone name

value: DMSO 120min + 8hr


title: brain, 5mC, thawed, rep1, 784

description: 02-21-23 ChIP784MeDIP-Seq

tag: nucleic acid


title: rh3037, Group_1, D14


title: brain, 5mC, frozen, rep1, 784

description: 02-21-23 ChIP784MeDIP-Seq

tag: medip antibody


title: XS12C, Control

city: University Park

first: Maurice

last: Byukusenge

state: PA

address: 131 Pastureview Rd

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

description: RNA collected 12 hr post transfection

data_processing:
The Illumina NextSeq 2000 was used to sequence the prepared libraries.
The quality of reads was checked via FASTQC, and then mapped to the human reference genome (GRCh38.p14) using HISAT2 with default parameters.
The mapped reads were counted using featureCounts, and the results were analyzed via DESeq2 using the default Benjamini-Hochberg correction of the P-values from the Wald test
A 0.05 False Discovery Rate (FDR) cut off was considered to classify genes as differentially expressed.
The clusterProfiler R package was used for gene ontology enrichment analysis using the biological process ontology.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Comma-separated table contain raw count data. The first column lists the genes from the Human genome (GRCh38). All the the culmns are the raw counts for each sample obtained by HISAT2.

growth_protocol: A549 cells were maintained in Dulbecco's Modified Eagle Media (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and 1% antibiotics in humidified atmosphere with 5% Carbon dioxide at 37° C

extract_protocol:
Transfected  cells were lysed using RIPA buffer (Cat.# 89900, Thermofischer) and RNA was extracted using RNeasy Plus Mini Kit (Cat.# 74134, Qiagen) was used for RNA extraction, while the NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat.# E7490L, NEB)  was used to enrich mRNA from the extracted RNA.  IDT, USA,
RNA libraries were then prepared using the xGenTM RNA Lib Prep 96rxn xGen RNA Library Prep Kit (Cat.# 10009814, IDT), and normalized using the xGenTM NormalaseTM Module (Cat.# 10009793, IDT).

treatment_protocol: A539 cells were transfected with mRNA [2.5 µg of VEEV replicase mRNA or an unrelated (Xenopus elongation factor (Xef)) mRNA  & 0.05 µg  of SARS-CoV-2 spike mRNA], using Lipofectamine MessengerMAX reagent

value: Wt

value: 2.5 ug Xef mRNA + 0.05 ug SARS-CoV-2 Spike mRNA


title: NIPBL-D7_dTAG_4hr_4sU_15min_R2_SLAM

state: CA

value: dTAGV-1 120min + 4hr


title: RAD21-B3_DMSO_24hr_HiC


title: XS12B, Control

description: RNA collected 12 hr post transfection


title: NIPBL-D7_DMSO_6hr_4sU_15min_R2_SLAM

value: DMSO 120min + 6hr


title: XS12A, Control

description: RNA collected 12 hr post transfection


title: XS4C, Control

description: RNA collected 4 hr post transfection


title: rh3037, Group_1, D7

value: female


title: NIPBL-D7_DMSO_4hr_4sU_15min_R2_SLAM

value: DMSO 120min + 4hr


title: XS4B, Control

description: RNA collected 4 hr post transfection


title: NIPBL-D7_dTAG_8hr_4sU_15min_R1_SLAM


title: RS12C, Treatment

description: RNA collected 12 hr post transfection

value: 2.5 ug VEEV replicase mRNA + 0.05 ug SARS-CoV-2 Spike mRNA


title: rh3037, Group_1, D3


title: XS4A, Control

description: RNA collected 4 hr post transfection


title: RS12B, Treatment

description: RNA collected 12 hr post transfection


title: NIPBL-D7_dTAG_6hr_4sU_15min_R2_SLAM

value: hTERT RPE-1

value: dTAGV-1 120min + 6hr


title: rh3037, Group_1, D0


title: RS12A, Treatment

description: RNA collected 12 hr post transfection


title: RS4C, Treatment

description: RNA collected 4 hr post transfection


title: EK81.8, cultuted at 37 C 5% CO2 (T=6 hours staurosporine addition) R1

tag: cell type

value: epithelial-like

value: staurosporine


title: rh3036, Group_1, D14

value: Whole blood PAXgene


title: NIPBL-D7_dTAG_6hr_4sU_15min_R1_SLAM

tag: synchronization


title: RS4A, Treatment

description: RNA collected 4 hr post transfection


title: RS4B, Treatment

description: RNA collected 4 hr post transfection


title: rh3036, Group_1, D10


title: NIPBL-D7_dTAG_4hr_4sU_15min_R1_SLAM


title: NIPBL-A2_HA_input

tag: antibody

value: input

tag: spike-in


title: rh3037, Group_1, D10

tag: animal id

value: Vaccinated

tag: time


title: rh3036, Group_1, D7

tag: outcome

tag: num challenges


title: RPE-1_WT_CTCF_ChIP

value: wild-type

value: CTCF (Active Motif #91285)


title: NIPBL-A2_HA_ChIP

value: HA C29F4 (Cell Signaling #3724)


title: NIPBL-D7_DMSO_6hr_4sU_15min_R1_SLAM

value: 15 minutes


title: RPE-1_WT_CTCF_input


title: 4 Prior to Treatment

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 whole genome using STAR
Counts per million (CPM) were quantified using the Partek E/M model
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include CPM values for each Sample.

source_name: tumors

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: tumors

value: Prior to Treatment

value: Human plexiform neurofibroma


title: 5 Prior to Treatment


title: rh3036, Group_1, D3

value: female

tag: genotype

tag: final virus_dose


title: NIPBL-D7_release_dTAG_120min_4sU_120min_R3_SLAM

tag: treatment

value: dTAGV-1 120min

value: 120 minutes


title: 11 Prior to Treatment2


title: rh3033, Group_1, D14

tag: Sex

value: male


title: rh3036, Group_1, D0


title: NIPBL-D7_release_DMSO_120min_4sU_120min_R3_SLAM

tag: cell line

value: hTERT RPE-1

value: DMSO 120min

tag: 4su labeling_period


title: 04 On Treatment

value: On treatment


title: NIPBL-D7_DMSO_8hr_4sU_15min_R1_SLAM

tag: clone name

value: DMSO 120min + 8hr


title: NIPBL-D7_release_dTAG_120min_4sU_120min_R2_SLAM


title: 32 On Treatment


title: 02 Prior to Treatment


title: 34 On Treatment


title: 34 Prior to Treatment


title: 07 Progression


title: rh3032, Group_1, D7

value: Whole blood PAXgene


title: rh3033, Group_1, D10

value: Vaccinated


title: NIPBL-D7_release_DMSO_120min_4sU_120min_R2_SLAM


title: NIPBL-D7_release_dTAG_120min_4sU_120min_R1_SLAM


title: NIPBL-D7_DMSO_4hr_4sU_15min_R1_SLAM

value: DMSO 120min + 4hr


title: 29 On Treatment


title: rh3032, Group_1, D14


title: rh3032, Group_1, D10


title: 27 On Treatment


title: 27 Prior to Treatment


title: NIPBL-D7_release_DMSO_120min_4sU_120min_R1_SLAM


title: NIPBL-D7_release_dTAG_120min_4sU_15min_R3_SLAM


title: rh3013, Group_3, D14

value: Unvaccinated


title: rh3013, Group_3, D10


title: NIPBL-D7_release_DMSO_120min_4sU_15min_R3_SLAM


title: 26 Prior to Treatment


title: 25 Prior to Treatment


title: 25 On Treatment


title: rh3013, Group_3, D7


title: 24 On Treatment


title: NIPBL-D7_release_dTAG_90min_4sU_15min_R3_SLAM

value: dTAGV-1 90min


title: rh3013, Group_3, D0


title: 24 Prior to Treatment


title: 23 On Treatment


title: NIPBL-D7_release_DMSO_90min_4sU_15min_R3_SLAM

value: DMSO 90min

value: 15 minutes


title: 23 Prior to Treatment

value: tumors

value: Prior to Treatment


title: NIPBL-D7_release_dTAG_60min_4sU_15min_R3_SLAM

value: dTAGV-1 60min


title: rh3011, Group_1, D14

value: female


title: 22 On Treatment

value: Human plexiform neurofibroma


title: 30 Prior to Treatment


title: 21 Prior to Treatment


title: 29 Prior to Treatment


title: NIPBL-D7_release_DMSO_60min_4sU_15min_R3_SLAM

value: DMSO 60min


title: rh3011, Group_1, D10


title: NIPBL-D7_release_dTAG_30min_4sU_15min_R3_SLAM

value: hTERT RPE-1

value: dTAGV-1 30min


title: 21 On Treatment

value: On treatment


title: 19 On Treatment


title: rh3011, Group_1, D3


title: 19 Prior to Treatment


title: NIPBL-D7_release_DMSO_30min_4sU_15min_R3_SLAM

value: DMSO 30min


title: NIPBL-D7_release_dTAG_120min_4sU_15min_R2_SLAM

value: dTAGV-1 120min


title: rh3011, Group_1, D7

value: Whole blood PAXgene

value: Vaccinated


title: 15 On Treatment


title: 17 Prior to Treatment


title: 16 On Treatment


title: rh3011, Group_1, D0


title: 16 Prior to Treatment


title: 15 Prior to TreatmentPNR


title: 14 On Treatment


title: rh3006, Group_1, D14


title: NIPBL-D7_release_dTAG_90min_4sU_15min_R2_SLAM


title: 18 Prior to Treatment


title: 15 Prior to TreatmentDNL


title: rh3006, Group_1, D7


title: 14 Prior to Treatment


title: rh3006, Group_1, D10


title: rh2995, Group_3, D14

value: male

value: Unvaccinated


title: NIPBL-D7_release_dTAG_30min_4sU_15min_R2_SLAM


title: 20 Prior to Treatment


title: Batch2; sorted H2b-mCherry+ nuclei from the ARC

city: Charlottesville

first: John

middle: N

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

department: Biology

institute: University of Virginia

data_processing:
The 10X Genomics Cell Ranger pipeline (version 5.0) was used to map reads to the mouse reference transcriptome (mm10-2020-A) and quantify Unique Molecular Identifier (UMI)-corrected, gene-level expression values. Introns were included using the Cell Ranger include- introns parameter.
Assembly: mm10
Supplementary files format and content: CellRanger output .h5 files
Supplementary files format and content: Cell Ranger output files for HTO are found in supplementary files with filenames starting with 701, 702, 703

source_name: hypothalamus

growth_protocol: not applicable

extract_protocol:
Once all samples for each batch were collected, tissue samples were thawed on ice and pooled by region and feeding condition. Tissue was dounce homogenized and purified by density gradient centrifugation into a single-nuclei suspension as previously described 26,94, but with the following modifications: in batch 2, TruSeq anti-Nuclear Pore Complex Proteins Hashtags were applied to track the brain region of origin for each cell nuclei (BioLegend, catalog # 682205, 682207, 682209). We counterstained nuclei with a far-red DNA fluorescent intercalator, DRAQ5 (Thermo Fisher, catalog # 62251, 1:500 dilution in sample) and kept them chilled on ice until sorting. We sorted single, DRAQ5+/mCherry+ nuclei using the Becton Dickenson FACS Aria Fusion (sample batch 1) or Becton Dickenson Influx (sample batch 2) cell sorters. All sorts were performed with SCYM (ASCP) certified technical assistance at the University of Virginia Flow Cytometry Core, using an 85 μm nozzle and set to purity mode. To separate nuclei from non-nucleated debris, we gated for events with high relative intensity of DRAQ5 fluorescence, using a 640 nm excitation and a 670/30 nm collection filter. We then gated the nuclei by forward scatter area vs. side scatter area to eliminate large aggregates, followed by forward scatter area vs. forward scatter height to select for singlets. Finally, from the single nuclei, we selected mCherry+ nuclei based on their high relative fluorescence, excitation 561 nm and 610/20 nm collection filter. We sorted mCherry+ nuclei into 18.8 μL of RT Reagent B from the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1
We added the remainder of the kit Step 1 master mix reagents to the capture tube, plus enough resuspension buffer to reach a total volume of 75 μL. We then processed the sample into complementary DNA (cDNA) sequencing libraries according to the manufacturer's instructions (10X Genomics, CG000204 Rev D). Hashtag oligonucleotide (HTO) libraries were prepared according to a previously published protocol, with the following modification: double-sided SPRI (solid phase reversible immobilization) was repeated for a total of two times to cleanly separate HTO libraries from cDNA libraries after amplification and, if needed, just prior to pooling libraries for sequencing. Libraries were sequenced at a concentration of 1.85 pM and with a 75-cycle, high-output kit on the Illumina NextSeq 550 according to the manufacturer's instructions..

treatment_protocol: Mice were rapidly decapitated without anesthesia for brain extraction to avoid stress and anesthesia-related changes in nuclear mRNA. Brains were immediately extracted and coronally sectioned at 500 μm intervals through the hypothalamus (Bregma +0.14 mm to –2.92 mm) using a Compresstome (VF-200-0Z Legacy Compresstome; Precisionary Instruments). Brain sections were immediately immersed in ice-cold RNAprotect reagent (Qiagen, catalog # 76106) to preserve RNA. Brain sections remained in RNAprotect in the dark overnight at 4 °C. The following day, brain sections were visualized under a fluorescence stereomicroscope (Zeiss Discovery V8) and regions of interest visibly containing H2b-mCherry+ nuclei were microdissected into chilled microcentrifuge tubes. Tissue samples were then stored at –80 °C for no longer than 2 weeks.

value: hypothalamus

value: neural

value: AgRP-Cre


title: Batch 2; sorted Rabies + nuclei from ARC/DMH/PVH; condition FED


title: NIPBL-D7_release_dTAG_60min_4sU_15min_R2_SLAM

value: 15 minutes


title: 10 Prior to Treatment

value: tumors

value: Prior to Treatment


title: 9 On Treatment

value: Human plexiform neurofibroma


title: 11 On Treatment


title: Batch 1; sorted Rabies+ nuclei from ARC/DMH/PVH


title: 9 Prior to Treatment


title: NIPBL-D7_release_dTAG_120min_4sU_15min_R1_SLAM


title: rh2995, Group_3, D3


title: rh2995, Group_3, D10


title: rh3006, Group_1, D3

value: female


title: Batch 2; sorted Rabies + nuclei from ARC/DMH/PVH; condition RF


title: NIPBL-D7_release_DMSO_60min_4sU_15min_R2_SLAM

value: hTERT RPE-1

value: DMSO 60min


title: 11 Prior to Treatment1


title: NIPBL-D7_release_DMSO_120min_4sU_15min_R1_SLAM

value: DMSO 120min


title: rh2995, Group_3, D0


title: rh3006, Group_1, D0


title: NIPBL-D7_release_DMSO_120min_4sU_15min_R2_SLAM


title: 8 Prior to Treatment


title: Batch 2; sorted Rabies + nuclei from ARC/DMH/PVH; condition FASTED


title: Riboseq_U2OS_G3BP2B_Thaps_Rep1

city: San Francisco

first: José

middle: M.

last: Liboy-Lugo

address: 513 Parnassus Ave.

institute: UCSF

description: Ribosomal footprint RNA

data_processing:
FASTQ files were converted to FASTA format. Ribo-seq footprint reads were trimmed of adapter sequences with cutadapt and filtered based on a 32 nt cutoff. UMI sequences were collapsed and removed. Reads were aligned with bowtie2 2.4.1 and filtered against a collection of repeat RNAs like tRNA, rRNA, snRNA, scRNA, srpRNA, among others (RMSK). Filtered reads were mapped to the hg38 version of the human genome using STAR 2.7.5a with --sjdbOverhang set to 29. Quality control of mapped footprint reads was performed with R package Ribo-seQC (doi: doi:10.1101/601468) and MultiQC tool (doi: 10.1093/bioinformatics/btw354).
We used bamCoverage from deeptools to convert Ribo-seq pre-processed .bam files to .bigwig files. Raw counts of sequencing reads from exons were stored in a .csv file.
Assembly: hg38
Supplementary files format and content: Coverage tracks were stored in .bw files.
Supplementary files format and content: Raw counts of sequencing reads from exons were stored in .csv files.
Library strategy: Ribo-seq

source_name: Bone

growth_protocol: Cells were grown in Dubelcco’s Modified Eagle Medium/Ham’s F-12 media, supplemented with 10% Fetal Bovine Serum and 1x of a penicillin streptomycin solution (100x, 10,000 I.U. penicillin (per mL), 10,000 mg/mL streptomycin)  at 37°C, 5% CO2.

extract_protocol:
Cells at 80-90% confluency were harvested from a 15 cm dish. Cells were incubated with 1 µM thapsigargin for 2hrs, and then treated with 50 µg/mL cyclohexamide (CHX) for 1 minute. Then, cells were washed gently with PBS containing 50 µg/mL CHX and lysed in ice-cold lysis buffer (20mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% v/v Triton x-100, 1mM DTT, 20-25 U/mL TURBO DNAse (Thermo Fisher Scientific, AM2238), 100 µg/mL CHX). Cells were triturated with a 26-gauge needle. Lysate was recovered after spinning for 10 min, 20,000g, at 4°C. Lysates were treated with RNAse I (Ambion, 100 U/µL) at room temperature for 45 minutes in slow agitation. Then, treated with SUPERase Inhibitor (Ambion, 20 U/µL) on ice. Monosomes were recovered by size exclusion chromatography (Illustra MicroSpin Columns, S-400 HR, VWR, 95017-619), and footprint RNA fragments were extracted from the flow-through using a Direct-zol kit (Zymo Research).
Gel slices of RNA fragments with sizes between 26-34 nt were excised from a 15% polyacrylamide TBE-Urea gel (Thermo Fisher Scientific, EC68855BOX). Eluted RNA was treated with T4 PNK and preadenylated linker was ligated to the 3’ end using T4 RNA ligase 2 truncated KQ (NEB, M0373L). Linker-ligated RNA was reverse transcribed with Protoscript II (NEB, M0368L) for 30 minutes at 50°C. Template RNA was hydrolyzed with 1M NaOH for 20 minutes at 70°C. Gel slices of reverse transcribed cDNA around 105 nt long, were excised from 15% polyacrylamide TBE-Urea gel. Eluted cDNA was circularized with CircLigase II ssDNA ligase (Lucigen, CL9021K) for 1 hr at 60°C. rRNA was depleted with biotinylated oligos18. cDNA libraries were amplified with different reverse indexing primers per sample.

value: Bone

value: epithelial

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B

value: Thapsigargin for 2 hours


title: NIPBL-D7_release_DMSO_90min_4sU_15min_R2_SLAM

value: DMSO 90min


title: rh2943, Group_1, D14

value: Whole blood PAXgene

value: Vaccinated


title: Riboseq_U2OS_G3BP2B_Thaps_Rep2

description: Ribosomal footprint RNA


title: 8 On Treatment

value: On treatment


title: rh2943, Group_1, D7


title: NIPBL-D7_release_DMSO_30min_4sU_15min_R2_SLAM

value: DMSO 30min


title: NIPBL-D7_release_DMSO_60min_4sU_15min_R1_SLAM

value: 15 minutes


title: NIPBL-D7_release_DMSO_90min_4sU_15min_R1_SLAM


title: 7 On Treatment

value: tumors


title: Riboseq_U2OS_G3BP2A_Thaps_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2A


title: NIPBL-D7_release_dTAG_60min_4sU_15min_R1_SLAM

value: dTAGV-1 60min


title: 7 Prior to Treatment

value: Prior to Treatment

value: Human plexiform neurofibroma


title: Riboseq_U2OS_G3BP1wt_Thaps_Rep2

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1


title: 6 Prior to Treatment


title: NIPBL-D7_release_dTAG_90min_4sU_15min_R1_SLAM

value: hTERT RPE-1

value: dTAGV-1 90min


title: ES17,SLE,H3K27ac

city: Heidelberg

first: Nila

middle: Hendrika

last: Servaas

address: Meyerhofstrasse 1

department: Structural and Computational Biology

country: Germany

institute: EMBL

data_processing:
Reads were trimmed using Trimmomatic v0.36 for illumina TruSeq3-SE adaptors. FASTQC was performed on samples before and after trimming and those samples which passed quality control were used for alignment.
The ChIP-seq reads were then aligned to human genome assembly hg38 using Bowtie2 with default parameters in “—very-sensitive” mode.
Aligned reads mapping to ChrM, other unassembled contigs and also reads with minimum mapping quality score < 10 were filtered out using SAMtools v1.5. Additionally, duplicates were removed using Picard tool v2.17.6 using the “MarkDuplicates” function.
Peak calling was done per sample using MACS292 v.2.0.1 using default parameters and “--keep-dup all”.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (excluding Input samples)

source_name: Peripheral blood

extract_protocol:
30mL of peripheral blood was collected in EDTA tubes from patients with SLE (n=11) and psoriasis (n=15) and from age- and sex-matched healthy donors (n=11 and n=15 respectively) from The University of Tartu, Estonia. PBMCs were obtained by Ficoll Paque (GE Healthcare) density gradient centrifugation. CD4+ T cells were collected by magnetic isolation using CD4 MicroBeads (Miltenyi) on the AutoMACs (Miltenyi) according to the manufacturer's instructions. 1 million isolated CD4+ T cells were cross-linked with an 11% formaldehyde buffer, lysed and subjected to sonication using a Bioruptor sonicator UCD-200 (Diagenode) to obtain chromatin fragments of 100–500 bp. Sheared chromatin was immunoprecipitated with 2 μL of anti-H3K27ac antibody (Abcam, ab4729) and 2 μL of Dynabeads M-280 magnetic beads (Sheep Anti-Mouse IgG, Sheep Anti-Rabbit IgG, Invitrogen) using the SX-8G IP-Star Automated System (Diagenode). ChIP samples were decrosslinked at 65°C for 4 hours. After incubation, the samples were treated with 0.2 mg/mL RNaseA (RNase Cocktail Enzyme Mix, Ambion, Life Technologies) and 0.4 mg/mL Proteinase K (Thermo Scientific). DNA was purified with the MinElute PCR Purification Kit (Qiagen) according to the manufacturer's protocol.
ChIP-Seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions. Library quality and concentration were determined using an Agilent Bioanalyzer DNA1000 chip. Libraries were sequenced on an Illumina NextSeq 500 Sequencer (75-bp single-end mode).

value: Peripheral blood

value: CD4 T cell

value: Female

tag: age

tag: condition

value: SLE


title: 6 On Treatment

tag: cell type


title: rh2943, Group_1, D10

value: Whole blood PAXgene

value: female


title: ES16,SLE,H3K27ac


title: NIPBL-D7_DMSO_120min_4sU_120min_R3_SLAM

value: DMSO 120min + 120min

tag: synchronization

value: 120 minutes


title: rh2943, Group_1, D3

value: Vaccinated


title: Riboseq_U2OSwt_Thaps_Rep2

description: Ribosomal footprint RNA

value: Bone

value: epithelial

value: wild type

value: Thapsigargin for 2 hours


title: Riboseq_U2OS_G3BPKO_Thaps_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: ES9,SLE,H3K27ac


title: rh2932, Group_1, D7


title: Riboseq_U2OS_G3BP1wt_Thaps_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1


title: NIPBL-D7_release_dTAG_30min_4sU_15min_R1_SLAM

value: hTERT RPE-1

value: dTAGV-1 30min

value: 15 minutes


title: ES8,SLE,H3K27ac

value: Peripheral blood

value: CD4 T cell


title: Riboseq_U2OSwt_Thaps_Rep1

description: Ribosomal footprint RNA


title: rh2943, Group_1, D0


title: rh2932, Group_1, D3


title: Riboseq_U2OS_G3BPKO_Thaps_Rep2

description: Ribosomal footprint RNA


title: rh2932, Group_1, D14


title: NIPBL-D7_release_DMSO_30min_4sU_15min_R1_SLAM

value: DMSO 30min


title: NIPBL-D7_DMSO_120min_4sU_120min_R2_SLAM


title: NIPBL-D7_dTAG_120min_4sU_120min_R1_SLAM

value: dTAGV-1 120min + 120min


title: NIPBL-D7_dTAG_120min_4sU_120min_R3_SLAM


title: Riboseq_U2OS_G3BP2A_Thaps_Rep2

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2A


title: Riboseq_U2OS_G3BP2B_DMSO_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B

value: DMSO for 2 hours


title: ES3,SLE,Input

value: Female

value: SLE


title: rh2861, Group_3, D14

value: Whole blood PAXgene

value: male

value: Unvaccinated


title: NIPBL-D7_DMSO_120min_4sU_120min_R1_SLAM

value: DMSO 120min + 120min

value: 120 minutes


title: rh2932, Group_1, D10

value: female

value: Vaccinated


title: ES3,SLE,H3K27ac


title: NIPBL-D7_dTAG_120min_4sU_15min_R4_SLAM

value: hTERT RPE-1

value: 15 minutes


title: Riboseq_U2OS_G3BP2B_DMSO_Rep2

description: Ribosomal footprint RNA

value: Bone

value: epithelial


title: Riboseq_U2OS_G3BP1wt_DMSO_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1


title: rh2932, Group_1, D0


title: ES7,SLE,H3K27ac

value: Peripheral blood

value: CD4 T cell


title: NIPBL-D7_dTAG_120min_4sU_120min_R2_SLAM

value: dTAGV-1 120min + 120min


title: ES12,SLE,H3K27ac

value: Female


title: rh2848, Group_3, D14


title: Riboseq_U2OS_G3BP2A_DMSO_Rep2

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2A

value: DMSO for 2 hours


title: Riboseq_U2OS_G3BPKO_DMSO_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: NIPBL-D7_dTAG_60min_4sU_15min_R4_SLAM

value: dTAGV-1 120min + 60min


title: ES11,SLE,H3K27ac

value: SLE


title: EP9,Psoriasis,H3K27ac

value: Male

value: Psoriasis


title: rh2848, Group_3, D7

value: Whole blood PAXgene

value: male

value: Unvaccinated


title: Riboseq_U2OS_G3BP2A_DMSO_Rep1

description: Ribosomal footprint RNA

value: Bone


title: ES2,SLE,H3K27ac


title: rh2861, Group_3, D7


title: Riboseq_U2OS_G3BP1wt_DMSO_Rep2

description: Ribosomal footprint RNA

value: epithelial


title: ES15,SLE,H3K27ac


title: NIPBL-D7_dTAG_0min_4sU_15min_R4_SLAM

value: hTERT RPE-1

value: dTAGV-1 120min + 0min

value: 15 minutes


title: rh2861, Group_3, D3


title: NIPBL-D7_dTAG_90min_4sU_15min_R4_SLAM

value: dTAGV-1 120min + 90min


title: ES13,SLE,H3K27ac

value: Peripheral blood

value: CD4 T cell

value: Female


title: rh2861, Group_3, D0


title: rh2848, Group_3, D0


title: NIPBL-D7_DMSO_0min_4sU_15min_R4_SLAM

value: DMSO 120min + 0min


title: Riboseq_U2OS_G3BPKO_DMSO_Rep2

description: Ribosomal footprint RNA

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)

value: DMSO for 2 hours


title: NIPBL-D7_DMSO_90min_4sU_15min_R4_SLAM

value: DMSO 120min + 90min


title: rh2848, Group_3, D10


title: NIPBL-D7_DMSO_120min_4sU_15min_R3_SLAM

value: DMSO 120min + 120min


title: rh2861, Group_3, D10

value: Whole blood PAXgene


title: rh2848, Group_3, D3

value: male


title: EP19,Psoriasis,H3K27ac

value: Psoriasis


title: rh2527, Group_2, D7

value: female

value: Unvaccinated


title: NIPBL-D7_DMSO_120min_4sU_15min_R4_SLAM

value: hTERT RPE-1


title: Riboseq_U2OSwt_DMSO_Rep1

description: Ribosomal footprint RNA

value: Bone

value: epithelial

value: wild type


title: NIPBL-D7_DMSO_30min_4sU_15min_R4_SLAM

value: DMSO 120min + 30min

value: 15 minutes


title: EP8,Psoriasis,H3K27ac

value: Peripheral blood

value: CD4 T cell

value: Male


title: rh2527, Group_2, D3


title: NIPBL-D7_dTAG_60min_4sU_15min_R3_SLAM

value: dTAGV-1 120min + 60min


title: RNAseq_U2OS_G3BP2B_Thaps_Rep2

data_processing:
FASTQ files were converted to FASTA format. Reads were aligned with bowtie2 2.4.1 and filtered against a collection of repeat RNAs like tRNA, rRNA, snRNA, scRNA, srpRNA, among others (RMSK). Filtered reads were mapped to the hg38 version of the human genome using STAR 2.7.5a with --sjdbOverhang set to 64. Quality control of mapped reads was performed with MultiQC tool (doi: 10.1093/bioinformatics/btw354).
We used bamCoverage from deeptools to convert RNA-seq pre-processed .bam files to .bigwig files. Raw counts of sequencing reads from exons were stored in a .csv file.
Assembly: hg38
Supplementary files format and content: Coverage tracks were stored in .bw files.
Supplementary files format and content: Raw counts of sequencing reads from exons were stored in .csv files.

extract_protocol:
Cells at 80-90% confluency were harvested from a 15 cm dish. Cells were incubated with 1 µM thapsigargin for 2hrs, and then treated with 50 µg/mL cyclohexamide (CHX) for 1 minute. Then, cells were washed gently with PBS containing 50 µg/mL CHX and lysed in ice-cold lysis buffer (20mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% v/v Triton x-100, 1mM DTT, 20-25 U/mL TURBO DNAse (Thermo Fisher Scientific, AM2238), 100 µg/mL CHX). Cells were triturated with a 26-gauge needle. Lysate was recovered after spinning for 10 min, 20,000g, at 4°C. Total RNA was extracted from 25 µL of lysate with a Direct-zol kit.
rRNA was depleted with a NEBNext rRNA Depletion Kit (NEB, E7400), and following manufacturer’s instructions. Libraries were prepared with a NEBNext Ultra II Directional RNA Library Prep Kit of Illumina (E7760), and following manufacturer’s instructions. cDNA libraries were amplified with multiplex oligos for Illumina sequencing (NEB, E6609S).

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B

value: Thapsigargin for 2 hours


title: Riboseq_U2OSwt_DMSO_Rep2

description: Ribosomal footprint RNA

value: DMSO for 2 hours


title: EP5,Psoriasis,H3K27ac


title: NIPBL-D7_DMSO_60min_4sU_15min_R4_SLAM

value: DMSO 120min + 60min


title: EP4,Psoriasis,H3K27ac

value: Psoriasis


title: rh2527, Group_2, D14

value: Whole blood PAXgene

value: female


title: rh2504, Group_2, D14

value: male

value: Unvaccinated


title: EP16,Psoriasis,H3K27ac


title: RNAseq_U2OS_G3BP1wt_Thaps_Rep2

value: Bone

value: epithelial

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1


title: RNAseq_U2OS_G3BP2A_Thaps_Rep2

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2A


title: RNAseq_U2OS_G3BPKO_Thaps_Rep1

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: EP15,Psoriasis,Input

value: Peripheral blood

value: CD4 T cell

value: Female


title: RNAseq_U2OSwt_Thaps_Rep2

value: wild type


title: NIPBL-D7_DMSO_30min_4sU_15min_R3_SLAM

value: hTERT RPE-1

value: DMSO 120min + 30min

value: 15 minutes


title: rh2527, Group_2, D10


title: EP20,Psoriasis,H3K27ac

value: Male

value: Psoriasis


title: RNAseq_U2OS_G3BP2A_Thaps_Rep1

value: Thapsigargin for 2 hours


title: rh2504, Group_2, D7

value: Whole blood PAXgene

value: male


title: NIPBL-D7_dTAG_90min_4sU_15min_R3_SLAM

value: dTAGV-1 120min + 90min


title: RNAseq_U2OSwt_Thaps_Rep1

value: Bone

value: epithelial


title: NIPBL-D7_DMSO_90min_4sU_15min_R3_SLAM

value: DMSO 120min + 90min


title: RNAseq_U2OS_G3BP2B_Thaps_Rep1

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B


title: EP14,Psoriasis,H3K27ac

value: Peripheral blood


title: EP13,Psoriasis,H3K27ac

value: CD4 T cell


title: EP18,Psoriasis,H3K27ac

value: Female


title: RNAseq_U2OS_G3BP1wt_Thaps_Rep1

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1


title: NIPBL-D7_dTAG_120min_4sU_15min_R2_SLAM

value: hTERT RPE-1

value: dTAGV-1 120min + 120min


title: EP12,Psoriasis,H3K27ac


title: rh2494, Group_2, D14

value: Unvaccinated


title: NIPBL-D7_DMSO_120min_4sU_15min_R2_SLAM

value: DMSO 120min + 120min

value: 15 minutes


title: RNAseq_U2OS_G3BP2A_DMSO_Rep1

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2A

value: DMSO for 2 hours