title: RR057e_00480_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00480


title: RR057e_00333_Peds

status: Public on Jul 19 2021

type: SRA

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

country: USA

institute: University of California San Francisco

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00333

library_source: transcriptomic

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv files with genecounts

molecule: total RNA

organism: Homo sapiens

source_name: NP/OP swab

growth_protocol: Clinical naso/pharyngeal swab specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

treatment_protocol: DNAse

tag: gender

value: M

tag: age

tag: infection

tag: sample type

value: naso/pharyngeal swab


title: RR057e_00326_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00326

value: F


title: RR057e_00197_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00197


title: RR057e_00230_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00230


title: DKO.Treg.Ad2.13 [ATAC-seq]

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

library_source: genomic

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
ATAC-seq FASTQ files were quality and adapter trimmed using Trim Galore (v0.4.2) prior to mapping to the UCSC mouse genome mm9 using Bowtie2 (v2.2.6) with default parameters.
Mapped SAM files were converted to BAM and putative PCR duplicates were marked with Samtools (v1.7).
Regions of chromatin accessibility were determined using MACS2 (v2.1.0.20151222) with the following settings “-g mm -q 0.01”.
The union of accessible regions in all samples were determined using the ‘GenomicRanges’ package (v1.36.1) in R and data was normalized to reads in peaks per million (RPPM) as previously described.
Genome_build: mm9
Supplementary_files_format_and_content: MACS2_q_0.05.union.annot.clean.cts.gz: Raw counts, each column represent a sample
Supplementary_files_format_and_content: MACS2_q_0.05.union.annot.clean.rppm.cov.gz: RPPM normalized counts, each column represent a sample

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
50,000 cells were sorted and directly used for the library preparation
50,000 cells were washed once with 120 μl ice-cold 1 X PBS and spin down at 500g for 10mins at 4°C. Cell pellets were resuspended in 50 μl cold lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) and immediately spin down at 500g for 15mins at 4°C. The supernatant was discarded and the nuclei pellets was resuspended in 25 μl of transposition mix (12.5 μl 2 X Nextera Tagment DNA Buffer, 1.25 μl Nextera Tagment DNA Enzyme, 11.25 μl H2O), incubated at 37°C for 30mins. DNA was purified using Zymo DNA Clean and Concentrator Kit (Zymo Research). Samples were then amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) for 11 cycles and purified using Ampure XP Beads (Beckman Coulter).

treatment_protocol: Cells were sorted directly from the mice or differentiated from CD4+ naïve T cells into Th0 cells or iTreg cells under the indicated conditions

tag: strain

value: 3 weeks

tag: genotype/variation

value: Tet2fl/fl Tet3fl/fl Foxp3-eGFP CD4-Cre

tag: tissue

value: Spleen and lymph nodes

tag: sorting/differentiation strategy

value: CD4+eGFP+ Treg cells


title: DKO.Treg.Ad2.14 [ATAC-seq]


title: RR057e_00162_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00162


title: RR057i_00116_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00116


title: RR057e_00146_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00146


title: RR057e_00053_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00053


title: RR057e_00574_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00574


title: RR057i_00067_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00067


title: organoid-day 11

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

description: >200 bp RNA

data_processing:
Qualiy control using FASTQC
alignment was performed with HISAT2
Reads were counted with featurecounts
Differential expression analysis was performed with EdgeR
Genome_build: hg38
Supplementary_files_format_and_content: Excel files containing counts per million

growth_protocol: Specific differentiation protocol conditions can be found in Israeli et al., 2020

extract_protocol:
Qiagen RNAeasy Kit
Libraries were prepared according to Illumina Truseq protocols

treatment_protocol: Each sample represents a mean pool of 3 6-wells of a 6-well plate for monolayer samples, and 5-8 organoids for organoid samples

tag: cell line

tag: cell type

value: human induced pluripotent stem cells derived from a healthy patient

tag: experimental condition

value: cells differentiated using heart organoid protocol


title: RR057e_00728_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00728


title: RR057e_00731_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00731


title: RR057e_00564_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00564


title: Th0.Ad2.10 [ATAC-seq]

value: 5-6 weeks

value: Foxp3-eGFP reporter mice

value: Th0 cells differentiated with anti-CD3/CD28


title: RA+vitC.Ad2.4 [ATAC-seq]

value: iTregs differentiated in the presence of TGFβ+RA+VitC


title: organoid-day 13

description: >200 bp RNA


title: RR057e_00719_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00719


title: TGF.Ad2.1 [ATAC-seq]

value: iTregs differentiated in the presence of TGFβ


title: WT.Treg.Ad2.11 [ATAC-seq]

value: Tet2fl/fl Tet3fl/fl Foxp3-eGFP


title: RR057i_00158_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00158


title: RR057i_00137_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00137


title: vitC.Ad2.2 [ATAC-seq]

value: iTregs differentiated in the presence of TGFβ+VitC


title: organoid-day 7

description: >200 bp RNA


title: RR057i_00138_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00138


title: RR057i_00136_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00136


title: TGF.3.day6 [RNA-seq]

description:
processed data file:
2019_Restimulation_counts.csv.gz
2019_Restimulation_FPKM.csv.gz

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
FASTQ files were quality and adapter trimmed using Trim Galore (v0.4.2)
Reads were mapped to the UCSC mouse genome mm9 using Tophat2 (v2.1.1) with the following parameters “-p 8 –N2” and the UCSC mm9 KnownGenes gtf transcript file
BAM files from Tophat where sorted with Samtools (v1.7) and duplicates were marked with PICARD (v2.5.0; http://broadinstitute.github.io/picard).
Quantification of gene expression used exons defined by the ‘TxDb.Mmusculus.UCSC.mm9.knownGene’ transcript database (v3.2.2) and the summarizeOverlaps function in mode "IntersectionNotEmpty" from the GenomicAlignments package (v1.20.1) in R (v3.6.1).
Fragments per kilobase per million reads (FPKM) normalization was performed in R based on the number of mapped autosomal reads. Differentially expressed genes (DEGs) were determined using EdgeR (v3.26.6) where a maximum FDR of 0.05 and minimum fold-change of 2 were enforced to determine significance.
Genome_build: mm9
Supplementary_files_format_and_content: 201903geneCts.exon.csv.gz: Raw counts, each column represent a sample
Supplementary_files_format_and_content: 201903geneFpkm.exon.csv.gz: FPKM normalized counts, each column represent a sample
Supplementary_files_format_and_content: 201903geneRpm.exon.csv.gz: RPM normalized counts, each column represent a sample
Supplementary_files_format_and_content: 2019_Restimulation_FPKM.csv.gz: FPKM normalized counts, each column represent a sample
Supplementary_files_format_and_content: 2019_Restimulation_counts.csv.gz: Raw counts, each column represent a sample

extract_protocol:
Total RNAs were extracted using RNeasy plus mini or micro kit (Qiagen)
Truseq stranded mRNA kit (Illumina)

treatment_protocol: Cells were sorted directly from the mice; differentiated from CD4+ naïve T cells into Th0 cells or iTreg cells under the indicated conditions; or collected after anti-CD3/CD28 restimulation

tag: strain background

value: 12-14 weeks

value: iTregs differentiated in the presence of TGFβ and sorted for Foxp3+ cells on day6


title: organoid-day 5

description: >200 bp RNA


title: RR057i_00108_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00108

value: M

value: naso/pharyngeal swab


title: RR057i_00109_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00109


title: RR057i_00110_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00110

value: F


title: organoid-day 3

description: >200 bp RNA


title: RR057i_00112_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00112


title: TGF.2.day6 [RNA-seq]


title: TGF.1.day6 [RNA-seq]


title: RR057i_00114_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00114


title: RR057i_00141_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00141


title: organoid-day 1

description: >200 bp RNA


title: RE.3.NEG [RNA-seq]

value: TGFβ iTregs after anti-CD3/CD28 restimulation, Foxp3- cells were sorted on day6 after restimulation


title: RR057i_00163_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00163


title: RE.2.NEG [RNA-seq]

value: Spleen and lymph nodes


title: WT.Treg.Ad2.12 [ATAC-seq]

value: 3 weeks

value: CD4+eGFP+ Treg cells


title: organoid-day 0

description: >200 bp RNA

value: human induced pluripotent stem cells derived from a healthy patient

value: cells differentiated using heart organoid protocol


title: RR057e_00104_Peds

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00104


title: Patient-3_DSRSF1_CyT

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

country: Italy

institute: National Research Council of Italy (CNR)

data_processing:
RNASeq reads were QC and trimmed and post processing of read  data including removal of  low-quality bases and sequencing  adapters
After alignment, quantification of the transcripts abundance was done using aligned the aligned .bam files with the RSEM, a methods to accurately quantify transcripts from RNA-Seq data with or without a reference genome (Li, B & Dewey, CN, 2011). Transcripts counts were then analysed with EdgeR (Robinson et al., 2009), to normalise the data and to perform Differential Expression. Data normalisation was performed using the relative log expression (RLE) implemented in EdgeR. After normalisation, transcripts abundance was filtered for low and no reads, we retained those transcripts with which counts per million (cmp) was greater or equal than 2 in at least two samples. Transcripts sequenced in each group were compared to one another to evaluate transcriptome coverage across our experimental conditions. For each comparison we evaluated the biological variation using the maximisation of the negative binomial dispersion using the empirical Bayes likelihood function, as implemented in EdgeR. Differentially-expressed transcript isoforms were computed for fold change FC>2 and p-value p<0.05, which were evaluated using the quasi-likelihood (QL) methods with empirical-Bayes Test in EdgeR. Differentially expressed transcripts were annotated using BioMart (Kasprzyk, 2011) based on their Ensembl transcript Id to recover gene symbol, gene description and biotype.
For the splicing analysis, sequencing reads were aligned to the GRCh38.79 genome build through STAR two-pass mode (v2.5.4b) (Dobin et al. 2013). The DEXSeq module of Bioconductor was used to identify differential exon usage (Anders et al. 2012). We used the python scripts provided by the package to annotate the genome and to count the reads overlapping the exons. The significance thresholds for differential exon usage were set at a Benjamini–Hochberg false discovery rate of 5%.
Genome_build: Human Genome GRCh38
Supplementary_files_format_and_content: two tab-delimited text files: 1) RPKM values of transcripts for each sample and 2) exon counts for each sample

source_name: Patient SFRSF1RNAi CyT

growth_protocol: Human induced pluripotent stem cells iPSCs were maintained in Matrigel-coated plates according to the manufacturer’s recommendations in complete mTeSR™-Plus™ Medium. Cultures were replenished with fresh medium every day. Cells were passaged every four to six days as clumps using ReLeSR™ an enzyme-free reagent for dissociation according to the manufacturer’s recommendations. For all the experiments in this study, iPSCs were used between passage 20 and 35, all iPSCs were cultured in 5% O2, 5% CO2 at 37°C. Neural differentiation of iPSCs was performed using the modified version dual SMAD inhibition protocol (Du et al., 2015).

extract_protocol:
Total sample extracts were added to PureZOL™ to extract the RNA. Briefly, lysates was cleared by centrifugation for 10 min at 12,000 g at 4 °C. One fifth the volume of chloroform was added and tubes were vigorously shaken for 15 s. After 10 min incubation at room temperature, tubes were centrifuged 12,000 g, 10 min, 4 °C and supernatants collected. RNA was precipitated for 30 min at room temperature with equal volume isopropanol and 2 μl Glycogen and subsequently pelleted at 12,000 g, 20 min, 4 °C. Pellets were washed with 70% DEPC ethanol and re-suspended in DEPC water. All PureZol™ extracted RNA samples were treated with DNaseI and quantified using a Nanodrop (NanoDropTechnologies).  Fractionated extracts were subjected to RNA extraction using Direct-zol™ RNA microprep kits following the manufacturer’s protocol, including the recommended in-column DNase I treatment and quantified using a Nanodrop.  RNA quality was then assessed using a eukaryote total RNA Nano 6000 Kit prior to high depth RNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols
Preparation of dual-indexed,  strand-specific RNASeq library  from submitted total RNA, using  RiboZero rRNA depletion and the  NEBNext Ultra Directional RNA  library preparation kits

treatment_protocol: In order to evaluate the neuroprotective potential of NS6180 (NS), a potent calcium-activated potassium channel blocker, motor neurons derived from iPSC cells from unaffected controls and C9ORF72 patients were exposed to  NS (0.3-10 µM) diluted in neuronal medium for 72 hours. Cells treated with dimethyl sulfoxide (DMSO), the vehicle of dilution of the NS, was used as an untreated control.

value: iPs derived neurons

tag: group

value: C9ORF72-ALS (C9) patient

tag: fraction

value: Cytoplasm - CyT


title: organoid-day 9

description: >200 bp RNA


title: RR057i_00175_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00175


title: RR057i_00133_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00133


title: Patient-3_DSRSF1_WCT

source_name: Patient SFRSF1RNAi WCT

value: Total - WCT


title: RR057i_00117_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00117


title: naive-2   [RNA-seq]

description:
processed data file:
201903geneCts.exon.csv
201903geneFpkm.exon.csv
201903geneRpm.exon.csv

value: 5-6 weeks

value: Foxp3-eGFP reporter mice

value: CD4+eGFP-CD25-CD62LhiCD44lo naïve T cells


title: RR057i_00070_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00070


title: RR057i_00071_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00071


title: naive-1  [RNA-seq]


title: RR057i_00122_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00122


title: Patient-3_C-RNAi_CyT

source_name: Patient CtrlRNAi CYT


title: Patient-3_C-RNAi_WCT

source_name: Patient CtrlRNAi WCT


title: RR057i_00090_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00090


title: RR057e_00746_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00746


title: VC-2 [RNA-seq]

value: iTregs differentiated in the presence of TGFβ+VitC


title: Patient-2_DSRSF1_CyT


title: RR057i_00082_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00082


title: RR057i_00118_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00118

value: M


title: RR057i_00134_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00134

value: naso/pharyngeal swab


title: RE.1.NEG [RNA-seq]

description:
processed data file:
2019_Restimulation_counts.csv.gz
2019_Restimulation_FPKM.csv.gz

value: 12-14 weeks


title: Patient-2_DSRSF1_WCT


title: RR057i_00062_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00062


title: TH0-2  [RNA-seq]

value: Th0 cells differentiated with anti-CD3/CD28


title: RR057i_00115_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00115


title: RR057i_00074_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00074


title: RR057e_00733_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00733


title: TH0-1 [RNA-seq]

value: Spleen and lymph nodes


title: Patient-2_C-RNAi_WCT


title: TGF-2  [RNA-seq]

value: iTregs differentiated in the presence of TGFβ


title: RR057e_00261_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00261


title: RR057i_00068_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00068

value: F


title: Patient-1_DSRSF1_CyT


title: RR057e_00130_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00130


title: TGF-1 [RNA-seq]

description:
processed data file:
201903geneCts.exon.csv
201903geneFpkm.exon.csv
201903geneRpm.exon.csv


title: Patient-1_DSRSF1_WCT


title: RR057e_00039_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00039


title: RR057e_00058_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00058


title: RR057e_00759_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00759


title: RR057i_00081_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00081


title: VC-1  [RNA-seq]


title: RA-VC-1 [RNA-seq]

value: iTregs differentiated in the presence of TGFβ+RA+VitC


title: RR057e_00456_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00456


title: RR057e_00431_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00431


title: Patient-1_C-RNAi_WCT


title: Patient-2_C-RNAi_CyT


title: RA-2  [RNA-seq]

value: iTregs differentiated in the presence of TGFβ+RA


title: RR057e_00534_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00534


title: RR057e_00401_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00401


title: Healthy3_DSRSF1_CyT

source_name: Heathy SFRSF1RNAi CyT

value: iPs derived neurons

value: Healthy


title: Healthy3_DSRSF1_WCT

source_name: Heathy SFRSF1RNAi WCT


title: RA-1 [RNA-seq]


title: RR057e_00761_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00761


title: RR057e_00223_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00223


title: RR057e_00173_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00173


title: HIV_LN3 chronic Lymph Node nonTfh ADA1

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Normalized expression values were generated through the TMM and  voom methods using the limma and edgeR Libraries in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as TMM normalized voom expression values.

molecule: polyA RNA

source_name: Lymph Node

growth_protocol: in vivo

extract_protocol:
Cells were sorted directly into RLT lysis buffer with beta mercaptoethanol added and then flash frozen on dry ice. RNA was isolated using Qiagen's RNeasy Micro kit (cat# 74004). 300 pg of total RNA was used to generate cDNA with Takara's SMARTSeq v4 Ultra Low Input RNA Kit for Seuencing (cat# 634892). Illumina's Nextera XT DNA kit (cat# FC-131-1096) was used with 1 ng of unsheared cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on a NextSeq 550 instrument in a Paired-End 75 bp configuration.

treatment_protocol: CoCulture Protocol: Five days after co-culture of the sorted CFSE-labeled GC-Tfh and autologous GC-B cells from HIVneg and HIVpos LNs, the cells were harvested and re-sorted as described above, based on their proliferation status. Proliferating cells were CFSEneg while non-proliferating cells were CFSEpos.

value: Lymph Node

tag: patient diagnosis

value: HIV+

tag: hiv status

value: chronic

tag: donorid

tag: coculture

value: nonTfh


title: HIV_LN3 chronic Lymph Node preTfh ADA1

value: preTfh


title: RR057e_00586_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00586

tag: gender

tag: age


title: RR057e_00259_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00259

tag: infection

tag: sample type


title: Healthy3_C-RNAi_CyT

source_name: Healthy CtrlRNAi CyT

value: Cytoplasm - CyT


title: Healthy3_C-RNAi_WCT

source_name: Healthy CtrlRNAi WCT

value: Total - WCT


title: RR057e_00168_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00168

value: M

value: naso/pharyngeal swab


title: RA-VC-2 [RNA-seq]

value: 5-6 weeks

tag: genotype/variation

value: Foxp3-eGFP reporter mice


title: Patient-1_C-RNAi_CyT

value: C9ORF72-ALS (C9) patient


title: RR057e_00752_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00752


title: HIV_LN3 chronic Lymph Node GCTfh ADA1

tag: tissue

value: GCTfh


title: RR057e_00540_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00540

value: F


title: Healthy2_DSRSF1_CyT


title: HIV_LN3 chronic Lymph Node nonTfh SEB

value: SEB


title: RR057e_00093_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00093


title: Healthy2_DSRSF1_WCT

value: iPs derived neurons


title: HIV_LN3 chronic Lymph Node preTfh SEB


title: RR057e_00088_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00088


title: RR057e_00206_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00206


title: Healthy2_C-RNAi_CyT

value: Healthy


title: RR057i_00171_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00171


title: HIV_LN3 chronic Lymph Node GCTfh SEB

value: Lymph Node


title: RR057e_00187_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00187


title: RR057e_00231_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00231


title: Healthy2_C-RNAi_WCT


title: RR057i_00084_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00084


title: HIV_LN2 chronic Lymph Node preTfh ADA1

value: HIV+


title: RR057e_00427_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00427


title: RR057e_00037_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00037


title: RR057i_00119_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00119


title: Healthy1_DSRSF1_CyT


title: Healthy1_DSRSF1_WCT


title: HIV_LN2 chronic Lymph Node GCTfh ADA1

value: chronic


title: RR057e_00449_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00449


title: HIV_LN2 chronic Lymph Node nonTfh SEB

value: nonTfh


title: RR057e_00736_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00736


title: HIV_LN2 chronic Lymph Node preTfh SEB

value: preTfh


title: Healthy1_C-RNAi_WCT


title: RR057i_00139_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00139


title: TIR1_wt_ctrl_XInput_rep3

city: Oxford

first: Paula

last: Dobrinić

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Paired-end reads were aligned to the concatenated mouse (mm10) and spike-in (dm6 for native, hg19 for cross-linked cChIP-seq) genome sequences using Bowtie 2 (“–no-mixed” and “–no-discordant” options). Only uniquely mapped reads were kept for downstream analysis, after removal of PCR duplicates with Sambamba.
To internally calibrate cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells for native cChIP-seq and human HEK293T cells for cross-linked cChIP-seq) to each experimental sample
For visualization of cChIP-seq sequencing data and annotation of genomic regions with read counts, uniquely mapped mouse reads were normalized using dm6 or hg19 spike-in as described previously (Furosva et al., 2019). Briefly, mouse reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. Additionally, to account for possible minor variations in spike-in cell mixing between cChIP-seq replicates, we corrected the subsampling factors by using the ratio of spike-in to mouse total read counts in the corresponding input samples. Prior to merging normalized replicates for visualization and analysis, read coverage across regions of interest (RING1B peaks for RING1B, SUZ12, H2AK119ub1 and H3K27me3, or TSS ± 2.5 kb for total Pol II, Ser5P-Pol II and H3K4me3, or gene bodies for Ser2P) was analyzed using multiBamSummary and plotCorrelation functions from deepTools , confirming a high correlation between replicates (Pearson's correlation coefficient > 0.9). Genome coverage tracks for cChIP-seq were generated using the pileup function from MACS2.
To identify genomic regions bound by PRC1 we performed peak calling using MACS2 (“BAMPE” and “–broad” options) on the RING1B cChIP-seq data with corresponding input samples for background normalization. A set of peaks identified in all biological replicates of untreated PRC1deg cells was used for further analysis, after filtering out several peaks identified following 4 hours of auxin treatment (i.e. following loss of RING1B) and manually removing sequencing artefacts. In total, 7240 stringent RING1B peaks were identified.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq
Supplementary_files_format_and_content: bed file for a set of enrichment peaks for RING1B

organism:
Homo sapiens
Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control

growth_protocol: Mouse ESCs were grown on gelatin-coated plates, in Dulbecco’s Modified Eagle Medium (DMEM, Life Technologies) supplemented with 15% fetal bovine serum (FBS, Labtech), 0.5 mM beta-mercaptoethanol (Life Technologies), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin (Life Technologies), 1x non-essential amino acids (Life Technologies) and 10 ng/mL leukemia inhibitory factor. Cells were cultured at 37°C with 5% CO2. For calibration of genomic experiments, we used either Drosophila S2 (SG4) cells, cultured at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 10% heat-inactivated FBS and 1x penicillin-streptomycin, or human HEK293T cells, cultured at 37°C with 5% CO2, in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 1x penicillin-streptomycin and 0.5 mM beta-mercaptoethanol.

extract_protocol:
For RING1B and SUZ12 cChIP-seq, 5x107 mouse ESCs were first crosslinked with 2 mM disuccinimidyl glutarate (DSG, Thermo Scientific) while rotating for 45 min at 25°C, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for further 15 min. Reactions were quenched by addition of 125 mM glycine. Mouse ESCs were then mixed with 2x106 double-crosslinked HEK293T cells and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x PIC) for 10 min at 4°C. The released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x PIC) for 5 min at 4°C. Chromatin was then resuspended in 1 mL of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC) and sonicated for 30 min using the BioRuptor Pico (Diagenode). Following sonication, Triton X-100 was added to a final concentration of 1%. The supernatant was collected after centrifugation at 20,000 g for 10 min at 4°C. For ChIP, chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton X-100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl, 1x PIC) and pre-cleared for 1 h with either protein A agarose beads (Repligen, for RING1B ChIP) or protein A magnetic Dynabeads (Invitrogen, for SUZ12 ChIP) blocked with 1 mg/mL bovine serum albumin (BSA) and 1 mg/mL yeast tRNA. For each ChIP reaction, 1 mL of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, either anti-RING1B (CST, D22F2, 3 μl), or anti-SUZ12 (CST, D39F6, 3 μl). Antibody-bound chromatin was captured using blocked protein A beads (agarose for RING1B, magnetic Dynabeads for SUZ12) for at least 2 h at 4°C and collected by centrifugation/on a magnetic rack. ChIP washes were performed as described previously (Farcas et al. 2013). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-linking was reversed overnight at 65°C with 200 mM NaCl and 2 μL RNase A (Sigma). A matched input sample (1/10 of original ChIP reaction) was treated identically. The following day, ChIP samples and inputs were incubated with Proteinase K (Sigma) for 1.5 h at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For Pol II cChIP-seq, 5x107 mouse ESCs were crosslinked in 1% formaldehyde for 10 min at 25°C and then quenched with 125 mM glycine. Mouse ECSs were mixed with 2x106 single-crosslinked HEK293T cells and incubated in FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% sodium deoxycholate, 0.1% SDS, 10 mM NaF, 1 mM AEBSF, 1x PIC) for 10 min. Chromatin was sonicated for 30 min using the BioRuptor Pico, centrifuged at 20,000 g for 10 min at 4°C, and supernatant taken as chromatin. For ChIP, 300 ug of chromatin was diluted to 1 ml in FA-lysis buffer and pre-cleared for 1 h with protein A agarose beads blocked with 1 mg/mL BSA and 1 mg/mL yeast tRNA. For each ChIP reaction, diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-Rbp1-NTD (CST, D8L4Y, 15 μl) to detect total Pol II, anti-Rbp1-CTD-Ser5P (CST, D9N5I, 12.5 μl), or anti-Rbp1-CTD-Ser2P (CST, E1Z3G, 12.5 μl). Antibody-bound chromatin was isolated using blocked protein A agarose beads for 3 h at 4°C. Washes were performed with FA-Lysis buffer, FA-Lysis buffer containing 500 mM NaCl, DOC buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2 mM EDTA, 10 mM Tris–HCl pH 8), followed by two washes with TE buffer pH 8. ChIP DNA was eluted, de-crosslinked and purified as described above, along with the matched input samples. For H2AK119ub1, H3K27me3 and H3K4me3 cChIP-seq, 5x107 mouse ESCs were mixed with 2x107 Drosophila SG4 cells in PBS. The cells were pelleted and nuclei were released by resuspending in ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 5 mM NEM). Nuclei were then washed, and resuspended in 1 mL of MNase digestion buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.25 M sucrose, 3 mM CaCl2, 10 mM NEM, 1x PIC). Samples were digested with 150 units of MNase (Fermentas) for 5 min at 37°C, stopped by 4 mM EDTA. The supernatant (S1) was collected following centrifugation at 1500 g for 5 min at 4°C. The remaining pellet was incubated with 300 μl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 10 mM NEM, 1x PIC) at 4°C for 1 h, passed five times through a 27G needle, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 supernatant, and stored at -80°C until use. Digestion to predominantly mono-nucleosomal fragments was confirmed by agarose gel electrophoresis of purified DNA. Native chromatin was diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris–HCl pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% TritonX-100, 10 mM NEM, 1x PIC). For each ChIP reaction, 1 ml of diluted nucleosomes was incubated overnight at 4°C with the appropriate antibody, anti-H2AK119ub1 (CST, D27C4, 5 μL), anti-H3K27me3 (in-house, 5 μL) or anti-H3K4me3 (in-house, 3 μL). Antibody-bound nucleosomes were captured by incubation for 1 h at 4°C with protein A agarose beads, pre-blocked overnight in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA. The beads were then washed four times with native ChIP wash buffer (20 mM Tris–HCl pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% TritonX-100) and once with TE buffer pH 8. Immunoprecipitated DNA was eluted using 100 μl of elution buffer (1% SDS, 0.1 M NaHCO3) and purified using ChIP DNA Clean and Concentrator Kit. DNA from a matched input sample (corresponding to 10% of the original ChIP reaction) purified in the same way.
cChIP-seq libraries for both ChIP and input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (double-crosslinked and native ChIP-seq) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Pol II ChIP-seq), following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on the Illumina NextSeq 500.

treatment_protocol: To induce AID-RING1B degradation, water-dissolved auxin (indole-3-acetic acid (IAA), Sigma) was mixed with cell medium to the final concentration of 500 µM and added to PRC1deg cells at designated times before harvesting by trypsinisation. To induce dTAG-SUZ12 degradation, PRC2deg cells were treated with 100 nM dTAG-13 compound for 2 hours.

value: Mouse embryonic stem cells

value: E14 Rosa26::Tir1

tag: replicate

tag: treatment

tag: treatment duration

value: 0 hours

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: chip antibody

tag: antibody info


title: HIV_LN2 chronic Lymph Node GCTfh SEB

tag: patient diagnosis

tag: cell type


title: RR057e_00066_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00066

value: naso/pharyngeal swab


title: TIR1_wt_ctrl_XInput_rep2


title: HIV_LN1 chronic Lymph Node nonTfh ADA1

tag: hiv status

tag: donorid


title: RR057e_00494_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00494

tag: gender

value: M


title: HIV_LN2 chronic Lymph Node nonTfh ADA1

tag: coculture


title: TIR1_wt_ctrl_XInput_rep1


title: HIV_LN1 chronic Lymph Node preTfh ADA1


title: RR057e_00750_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00750

tag: age

tag: infection


title: RR057i_00154_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00154

tag: sample type


title: RR057e_00105_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00105


title: TIR1_wt_ctrl_RING1B_rep3

tag: genotype/variation

value: Cell Signaling Technology (#D22F2 )


title: RR057e_00454_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00454


title: RR057e_00116_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00116


title: HIV_LN1 chronic Lymph Node nonTfh SEB

tag: tissue


title: TIR1_wt_ctrl_RING1B_rep2

tag: replicate

tag: treatment


title: Healthy1_C-RNAi_CyT

tag: group

tag: fraction

value: Cytoplasm - CyT


title: RR057e_00086_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00086


title: RR057e_00052_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00052

value: F


title: RR057e_00250_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00250


title: TIR1_wt_ctrl_RING1B_rep1

tag: treatment duration

tag: spike-in reference organism

tag: spike-in cell line

tag: chip antibody


title: RR057i_00165_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00165


title: RR057e_00516_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00516


title: RR057e_00491_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00491


title: HIV_LN1 chronic Lymph Node preTfh SEB

tag: patient diagnosis

tag: hiv status

value: SEB

tag: cell type


title: RR057e_00131_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00131

tag: gender


title: HIV_LN1 chronic Lymph Node GCTfh SEB

tag: donorid

tag: coculture

value: GCTfh


title: RR057e_00272_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00272

tag: age

tag: infection

tag: sample type


title: RR057e_00549_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00549


title: ST39 treated PBMC noncTfh ADA1

source_name: PBMC

tag: tissue

value: PBMC

value: treated

value: noncTfh


title: RING1AKO.RING1BAID_PolII_XInput_IAA_8h_rep3

description: RING1AKO_RING1BAID_Pol2_Input_rep4_AUX_8h_S19

data_processing:
Paired-end reads were aligned to the concatenated mouse (mm10) and spike-in (dm6 for native, hg19 for cross-linked cChIP-seq) genome sequences using Bowtie 2 (“–no-mixed” and “–no-discordant” options). Only uniquely mapped reads were kept for downstream analysis, after removal of PCR duplicates with Sambamba.
To internally calibrate cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells for native cChIP-seq and human HEK293T cells for cross-linked cChIP-seq) to each experimental sample
For visualization of cChIP-seq sequencing data and annotation of genomic regions with read counts, uniquely mapped mouse reads were normalized using dm6 or hg19 spike-in as described previously (Furosva et al., 2019). Briefly, mouse reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. Additionally, to account for possible minor variations in spike-in cell mixing between cChIP-seq replicates, we corrected the subsampling factors by using the ratio of spike-in to mouse total read counts in the corresponding input samples. Prior to merging normalized replicates for visualization and analysis, read coverage across regions of interest (RING1B peaks for RING1B, SUZ12, H2AK119ub1 and H3K27me3, or TSS ± 2.5 kb for total Pol II, Ser5P-Pol II and H3K4me3, or gene bodies for Ser2P) was analyzed using multiBamSummary and plotCorrelation functions from deepTools , confirming a high correlation between replicates (Pearson's correlation coefficient > 0.9). Genome coverage tracks for cChIP-seq were generated using the pileup function from MACS2.
To identify genomic regions bound by PRC1 we performed peak calling using MACS2 (“BAMPE” and “–broad” options) on the RING1B cChIP-seq data with corresponding input samples for background normalization. A set of peaks identified in all biological replicates of untreated PRC1deg cells was used for further analysis, after filtering out several peaks identified following 4 hours of auxin treatment (i.e. following loss of RING1B) and manually removing sequencing artefacts. In total, 7240 stringent RING1B peaks were identified.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq.
Supplementary_files_format_and_content: bed file for a set of enrichment peaks for RING1B

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (8h IAA)

extract_protocol:
For RING1B and SUZ12 cChIP-seq, 5x107 mouse ESCs were first crosslinked with 2 mM disuccinimidyl glutarate (DSG, Thermo Scientific) while rotating for 45 min at 25°C, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for further 15 min. Reactions were quenched by addition of 125 mM glycine. Mouse ESCs were then mixed with 2x106 double-crosslinked HEK293T cells and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x PIC) for 10 min at 4°C. The released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x PIC) for 5 min at 4°C. Chromatin was then resuspended in 1 mL of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC) and sonicated for 30 min using the BioRuptor Pico (Diagenode). Following sonication, Triton X-100 was added to a final concentration of 1%. The supernatant was collected after centrifugation at 20,000 g for 10 min at 4°C. For ChIP, chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton X-100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl, 1x PIC) and pre-cleared for 1 h with either protein A agarose beads (Repligen, for RING1B ChIP) or protein A magnetic Dynabeads (Invitrogen, for SUZ12 ChIP) blocked with 1 mg/mL bovine serum albumin (BSA) and 1 mg/mL yeast tRNA. For each ChIP reaction, 1 mL of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, either anti-RING1B (CST, D22F2, 3 μl), or anti-SUZ12 (CST, D39F6, 3 μl). Antibody-bound chromatin was captured using blocked protein A beads (agarose for RING1B, magnetic Dynabeads for SUZ12) for at least 2 h at 4°C and collected by centrifugation/on a magnetic rack. ChIP washes were performed as described previously (Farcas et al. 2013). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-linking was reversed overnight at 65°C with 200 mM NaCl and 2 μL RNase A (Sigma). A matched input sample (1/10 of original ChIP reaction) was treated identically. The following day, ChIP samples and inputs were incubated with Proteinase K (Sigma) for 1.5 h at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For Pol II cChIP-seq, 5x107 mouse ESCs were crosslinked in 1% formaldehyde for 10 min at 25°C and then quenched with 125 mM glycine. Mouse ECSs were mixed with 2x106 single-crosslinked HEK293T cells and incubated in FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% sodium deoxycholate, 0.1% SDS, 10 mM NaF, 1 mM AEBSF, 1x PIC) for 10 min. Chromatin was sonicated for 30 min using the BioRuptor Pico, centrifuged at 20,000 g for 10 min at 4°C, and supernatant taken as chromatin. For ChIP, 300 ug of chromatin was diluted to 1 ml in FA-lysis buffer and pre-cleared for 1 h with protein A agarose beads blocked with 1 mg/mL BSA and 1 mg/mL yeast tRNA. For each ChIP reaction, diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-Rbp1-NTD (CST, D8L4Y, 15 μl) to detect total Pol II, anti-Rbp1-CTD-Ser5P (CST, D9N5I, 12.5 μl), or anti-Rbp1-CTD-Ser2P (CST, E1Z3G, 12.5 μl). Antibody-bound chromatin was isolated using blocked protein A agarose beads for 3 h at 4°C. Washes were performed with FA-Lysis buffer, FA-Lysis buffer containing 500 mM NaCl, DOC buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2 mM EDTA, 10 mM Tris–HCl pH 8), followed by two washes with TE buffer pH 8. ChIP DNA was eluted, de-crosslinked and purified as described above, along with the matched input samples. For H2AK119ub1, H3K27me3 and H3K4me3 cChIP-seq, 5x107 mouse ESCs were mixed with 2x107 Drosophila SG4 cells in PBS. The cells were pelleted and nuclei were released by resuspending in ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 5 mM NEM). Nuclei were then washed, and resuspended in 1 mL of MNase digestion buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.25 M sucrose, 3 mM CaCl2, 10 mM NEM, 1x PIC). Samples were digested with 150 units of MNase (Fermentas) for 5 min at 37°C, stopped by 4 mM EDTA. The supernatant (S1) was collected following centrifugation at 1500 g for 5 min at 4°C. The remaining pellet was incubated with 300 μl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 10 mM NEM, 1x PIC) at 4°C for 1 h, passed five times through a 27G needle, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 supernatant, and stored at -80°C until use. Digestion to predominantly mono-nucleosomal fragments was confirmed by agarose gel electrophoresies of purified DNA. Native chromatin was diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris–HCl pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% TritonX-100, 10 mM NEM, 1x PIC). For each ChIP reaction, 1 ml of diluted nucleosomes was incubated overnight at 4°C with the appropriate antibody, anti-H2AK119ub1 (CST, D27C4, 5 μL), anti-H3K27me3 (in-house, 5 μL) or anti-H3K4me3 (in-house, 3 μL). Antibody-bound nucleosomes were captured by incubation for 1 h at 4°C with protein A agarose beads, pre-blocked overnight in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA. The beads were then washed four times with native ChIP wash buffer (20 mM Tris–HCl pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% TritonX-100) and once with TE buffer pH 8. Immunoprecipitated DNA was eluted using 100 μl of elution buffer (1% SDS, 0.1 M NaHCO3) and purified using ChIP DNA Clean and Concentrator Kit. DNA from a matched input sample (corresponding to 10% of the original ChIP reaction) purified in the same way.
cChIP-seq libraries for both ChIP and input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (double-crosslinked and native ChIP-seq) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Pol II ChIP-seq), following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on the Illumina NextSeq 500.

tag: genotype/variation

value: E14 Rosa26::Tir1; Ring1A-/-; AID-Ring1B

tag: replicate

tag: treatment

value: auxin (IAA)

value: 8 hours

tag: antibody info.


title: RING1AKO.RING1BAID_PolII_XInput_IAA_8h_rep2

description: RING1AKO_RING1BAID_Pol2_Input_rep3_AUX_8h_S19

value: Mouse embryonic stem cells

tag: treatment duration

tag: spike-in reference organism


title: RR057e_00763_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00763


title: RR057e_00508_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00508


title: RR057e_00290_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00290


title: RR057e_00107_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00107


title: ST39 treated PBMC cTfh1 ADA1

value: HIV+


title: HIV_LN1 chronic Lymph Node GCTfh ADA1

value: Lymph Node

value: chronic


title: RING1AKO.RING1BAID_PolII_XInput_IAA_8h_rep1

description: RING1AKO_RING1BAID_Pol2_Input_rep2_8h_S19

value: Homo sapiens

tag: spike-in cell line

tag: chip antibody


title: RR057e_00442_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00442

value: naso/pharyngeal swab


title: RING1AKO.RING1BAID_PolII_XInput_IAA_4h_rep3

description: RING1AKO_RING1BAID_Pol2_Input_rep4_AUX_4h_S18

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (4h IAA)

value: 4 hours


title: ST39 treated PBMC cTfh2_17 ADA1

tag: patient diagnosis

tag: hiv status


title: RR057e_00232_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00232

tag: gender


title: ST39 treated PBMC noncTfh SEB

tag: donorid

tag: cell type


title: RR057e_00246_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00246

value: M

tag: age


title: RR057e_00184_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00184

tag: infection


title: RR057e_00577_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00577

value: F

tag: sample type


title: RING1AKO.RING1BAID_PolII_XInput_IAA_4h_rep1

description: RING1AKO_RING1BAID_Pol2_Input_rep2_4h_S18


title: RING1AKO.RING1BAID_PolII_XInput_IAA_4h_rep2

description: RING1AKO_RING1BAID_Pol2_Input_rep3_AUX_4h_S18


title: RR057e_00222_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00222


title: ST39 treated PBMC cTfh1 SEB

tag: tissue

tag: coculture

value: SEB


title: RR057e_00273_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00273


title: RR057e_00410_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00410


title: RING1AKO.RING1BAID_PolII_XInput_IAA_2h_rep3

description: RING1AKO_RING1BAID_Pol2_Input_rep4_AUX_2h_S17

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (2h IAA)

tag: genotype/variation

tag: replicate

value: 2 hours


title: ST39 treated PBMC cTfh2_17 SEB

value: PBMC


title: RR057e_00268_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00268


title: ST18 treated PBMC noncTfh ADA1

value: treated


title: RR057e_00515_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00515


title: RR057e_00757_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00757


title: ST18 treated PBMC cTfh1 ADA1


title: RR057e_00198_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00198


title: ST18 treated PBMC cTfh2_17 ADA1


title: RING1AKO.RING1BAID_PolII_XInput_UNT_rep3

description: RING1AKO_RING1BAID_Pol2_Input_rep4_UNT_S16

tag: treatment

value: 0 hours

tag: antibody info.


title: RR057e_00423_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00423


title: RR057e_00727_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00727


title: ST18 treated PBMC noncTfh SEB

value: noncTfh


title: RING1AKO.RING1BAID_PolII_XInput_IAA_2h_rep1

description: RING1AKO_RING1BAID_Pol2_Input_rep2_2h_S17

value: E14 Rosa26::Tir1; Ring1A-/-; AID-Ring1B

value: auxin (IAA)

tag: treatment duration

tag: spike-in reference organism


title: RR057e_00119_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00119


title: RR057e_00140_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00140


title: RING1AKO.RING1BAID_PolII_XInput_UNT_rep1

description: RING1AKO_RING1BAID_Pol2_Input_rep2_UNT_S16

value: Mouse embryonic stem cells

tag: spike-in cell line

tag: chip antibody


title: RING1AKO.RING1BAID_PolII_Ser2P_IAA_2h_rep3

description: RING1AKO_RING1BAID_Ser2P_rep4_AUX_2h_S12

value: Cell Signaling Technology (#E1Z3G)


title: RR057e_00765_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00765


title: ST18 treated PBMC cTfh2_17 SEB

tag: patient diagnosis

value: HIV+

tag: hiv status


title: RR057e_00485_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00485

tag: gender


title: RING1AKO.RING1BAID_PolII_XInput_IAA_2h_rep2

description: RING1AKO_RING1BAID_Pol2_Input_rep3_AUX_2h_S17

tag: cell type


title: RR057e_00079_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00079

tag: age


title: RR057e_00291_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00291

tag: infection


title: RING1AKO.RING1BAID_PolII_Ser2P_IAA_2h_rep2


title: RR057e_00295_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00295

tag: sample type


title: RING1AKO.RING1BAID_PolII_Ser2P_UNT_rep3


title: RING1AKO.RING1BAID_PolII_Ser2P_IAA_2h_rep1


title: ST37 treated PBMC cTfh1 ADA1

tag: tissue

tag: donorid


title: RR057e_00581_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00581


title: RR057e_00051_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00051


title: RING1AKO.RING1BAID_PolII_XInput_UNT_rep2

description: RING1AKO_RING1BAID_Pol2_Input_rep3_UNT_S16

tag: genotype/variation


title: RR057e_00754_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00754


title: RR057e_00169_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00169


title: ST37 treated PBMC noncTfh ADA1

tag: coculture


title: ST37 treated PBMC cTfh2_17 ADA1


title: RR057e_00171_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00171


title: RR057e_00340_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00340


title: RING1AKO.RING1BAID_PolII_Ser2P_UNT_rep2

tag: replicate

tag: treatment


title: ST37 treated PBMC noncTfh SEB


title: RING1AKO.RING1BAID_PolII_Ser2P_UNT_rep1

tag: treatment duration

tag: antibody info.


title: RR057e_00049_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00049


title: ST18 treated PBMC cTfh1 SEB


title: ST37 treated PBMC cTfh1 SEB


title: RING1AKO.RING1BAID_PolII_Ser5P_IAA_2h_rep3

description: RING1AKO_RING1BAID_Ser5P_rep4_AUX_2h_S12

tag: spike-in reference organism

tag: spike-in cell line

value: Cell Signaling Technology (#D9N5I)


title: RR057e_00138_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00138


title: RR057e_00216_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00216


title: ST37 treated PBMC cTfh2_17 SEB

tag: patient diagnosis


title: RING1AKO.RING1BAID_PolII_Ser5P_IAA_2h_rep2

value: Homo sapiens

tag: chip antibody


title: ST3 treated PBMC noncTfh ADA1

tag: hiv status


title: RR057e_00224_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00224

tag: gender

value: naso/pharyngeal swab


title: RR057e_00567_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00567

tag: age


title: RING1AKO.RING1BAID_PolII_Ser5P_IAA_2h_rep1

tag: cell type


title: RR057e_00074_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00074

tag: infection

tag: sample type


title: RR057i_00173_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00173


title: RR057e_00145_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00145


title: RR057e_00475_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00475


title: RR057e_00280_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00280


title: RING1AKO.RING1BAID_PolII_Ser5P_UNT_rep2


title: RR057e_00239_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00239


title: RR057e_00590_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00590


title: RR057e_00489_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00489


title: RR057e_00302_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00302


title: RR057e_00142_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00142


title: RR057e_00309_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00309


title: RR057e_00460_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00460


title: RR057e_00437_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00437


title: RING1AKO.RING1BAID_PolII_NTD_IAA_8h_rep3

value: 8 hours

value: Cell Signaling Technology (#D8L4Y )


title: RING1AKO.RING1BAID_PolII_NTD_IAA_8h_rep2


title: RING1AKO.RING1BAID_PolII_Ser5P_UNT_rep1


title: RING1AKO.RING1BAID_PolII_NTD_IAA_8h_rep1


title: ST3 treated PBMC cTfh1 SEB

tag: tissue

tag: donorid


title: ST3 treated PBMC noncTfh SEB

tag: coculture


title: ST5 treated PBMC noncTfh ADA1


title: RR057e_00436_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00436

value: M


title: ST3 treated PBMC cTfh2_17 ADA1


title: ST3 treated PBMC cTfh2_17 SEB

value: SEB


title: ST3 treated PBMC cTfh1 ADA1


title: RING1AKO.RING1BAID_PolII_Ser5P_UNT_rep3

tag: genotype/variation

tag: replicate


title: ST5 treated PBMC cTfh1 ADA1


title: RR057e_00047_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00047


title: ST5 treated PBMC cTfh2_17 ADA1


title: RR057e_00412_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00412


title: RR057e_00253_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00253


title: ST5 treated PBMC noncTfh SEB


title: RING1AKO.RING1BAID_PolII_NTD_IAA_4h_rep2

tag: treatment

tag: treatment duration

value: 4 hours


title: RR057e_00440_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00440

value: F


title: RR057e_00749_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00749


title: RING1AKO.RING1BAID_PolII_NTD_IAA_4h_rep1

tag: spike-in reference organism

tag: antibody info.


title: RR057i_00167_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00167


title: RR057e_00414_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00414


title: RING1AKO.RING1BAID_PolII_NTD_IAA_2h_rep3

value: 2 hours

tag: spike-in cell line


title: RING1AKO.RING1BAID_PolII_NTD_IAA_4h_rep3

tag: chip antibody


title: ST5 treated PBMC cTfh2_17 SEB

value: PBMC

tag: patient diagnosis

tag: hiv status

value: treated


title: RING1AKO.RING1BAID_PolII_NTD_UNT_rep2

value: E14 Rosa26::Tir1; Ring1A-/-; AID-Ring1B

value: 0 hours


title: RR057e_00399_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00399

tag: gender

tag: age


title: RR057e_00165_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00165

tag: infection


title: RING1AKO.RING1BAID_PolII_NTD_UNT_rep3

tag: cell type

value: Mouse embryonic stem cells


title: RR057e_00451_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00451

tag: sample type


title: RR057e_00254_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00254


title: RR057e_00060_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00060


title: RR057e_00285_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00285


title: RR057e_00726_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00726


title: RING1AKO.RING1BAID_PolII_NTD_UNT_rep1


title: RR057e_00560_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00560


title: RING1AKO.RING1BAID_PolII_NTD_IAA_2h_rep1

value: auxin (IAA)


title: RR057i_00083_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00083


title: RR057e_00520_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00520


title: RR057e_00505_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00505


title: RR057e_00294_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00294


title: RR057e_00764_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00764


title: RING1AKO.RING1BAID_XInput_IAA_24h_rep2

description: RING1AKO_RING1BAID_Xinput_AUX_24h_rep3_S10

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (24h IAA)

value: 24 hours


title: RING1AKO.RING1BAID_XInput_IAA_24h_rep3

description: RING1AKO_RING1BAID_Xinput_AUX_24h_rep4_S15


title: ST5 treated PBMC cTfh1 SEB

tag: tissue

value: HIV+

tag: donorid


title: RR057e_00751_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00751


title: RR057e_00287_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00287


title: RR057e_00080_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00080


title: RR057i_00157_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057i_00157


title: RR057e_00202_Adult

description:
all_adult_and_ped_samples_combined_counts_unfiltered.csv
RR057e_00202


title: RING1AKO.RING1BAID_XInput_IAA_24h_rep1

description: RING1AKO_RING1BAID_Xinput_AUX_24h_rep1_S5

tag: genotype/variation

value: Homo sapiens


title: RING1AKO.RING1BAID_XInput_IAA_8h_rep3

description: RING1AKO_RING1BAID_Xinput_AUX_8h_rep4_S14

tag: replicate


title: RING1AKO.RING1BAID_PolII_NTD_IAA_2h_rep2

tag: treatment


title: CUT-Tag-BG4-rep2

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

country: China

institute: Wuhan University

description: G4 CUT&Tag analysis with Flag-BG4 antibody

data_processing:
Library strategy: CUT&Tag
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads.The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0 (Ramírez et al. 2014). Peaks were called using MACS (model-based analysis of ChIP-Seq) version 2.1.2 using default parameters and a q-value cutoff of 1E-5. The distribution of G4 peaks were annotated with ChIPpeakAnno. Heatmap  and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deepTools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmaps were generated with the indicated regions with ngs.plot or the computeMatrix command from deepTools 3.3.0.
Genome_build: Homo sapiens .hg38
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

extract_protocol:
PRO-seq was performed as described previously ( K. Lianget al. 2018; H. Kwak et al. 2013). Briefly, all four biotinylated nucleotides (PerkinElmer) were used at 25 mM for the nuclear run-on reaction. RNA 5′ pyrophosphohydrolase (NEB, M0356S) was used to remove the RNA cap to facilitate the downstream library preparation.
Cleavage Under Targets and Tagmentation (CUT&Tag) was performed as described before (Kaya-Okur et al. 2019; Wang et al. 2019) with some modifications. Briefly, half million cells were washed twice in 1.5 mL wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) by gentle pipetting. 10 μL concanavalin A coated magnetic beads (Smart-Lifesciences) were activated, and added to these cells with a 10 minutes’ incubation at room temperature. The supernatant was removed and bead-bound cells were resuspended in 100 μL dig-wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors,0.05% digitonin, 0.01% NP-40) containing 2mM EDTA and a 1:10 dilution of the 0.1 mg/mL BG4 primary antibody. Primary antibody incubation was performed on a rotating platform overnight at 4°C and then the liquid was removed. The Anti-Flag M2 antibody (Sigma-Aldrich) was diluted to 1:100 in 100 μL of dig-wash buffer with 2 mM EDTA, and was incubated with the cells at room temperature for 30 minutes followed by removing the liquid. The rabbit anti-mouse IgG antibody was diluted 100 folds and incubated with the cells for another 1 hour and washed with dig-wash buffer three times. A 1:200 dilution of pA-Tn5 adapter complex (~0.2 μM) was prepared in dig-300 buffer (0.05% digitonin, 20 mM HEPES at pH 7.5, 300 mM KCl, 0.5 mM spermidine, 1× protease 36inhibitors, 0.01% NP-40). 100 μL pA-Tn5 adapter complex was added to the cells with gentle vertexing, and was incubated at room temperature for 1 hour. Cells were washed three times in 200 μL dig-300 buffer to remove unbound pA-Tn5 proteins. Next, bead-bound cells were resuspended in 40 μL tagmentation buffer (10 mM TAPS-NaOH at pH 8.5, 10 mM MgCl 2 , 7.5% DMF) and incubated at 37°C for 1 hour. To stop tagmentation reaction, 1.5 μL 0.5 M EDTA, 0.5 μL 10% SDS and 0.5 μL 20 mg/mL proteinase K were added and incubated at 55°C for 1 hour and then for 15 minutes at 75°C. The DNA was extracted with Sera-Mag carboxylate-modified magnetic beads (GE Healthcare) for library preparation.21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high-fidelity 2× master mix. The libraries were purified with 1.1× volume of Sera-Mag carboxylate-modified magnetic beads, and subjected to LabChip DNA analysis and Illumina sequencing.

tag: cell line

value: embryonic kidney cell line HEK293T

tag: antibody


title: RING1AKO.RING1BAID_XInput_IAA_8h_rep2

description: RING1AKO_RING1BAID_Xinput_AUX_8h_rep3_S9

tag: treatment duration

value: 8 hours

tag: spike-in reference organism

tag: antibody info.


title: RING1AKO.RING1BAID_XInput_IAA_4h_rep3

description: RING1AKO_RING1BAID_Xinput_AUX_4h_rep4_S13

tag: spike-in cell line

tag: chip antibody


title: RING1AKO.RING1BAID_XInput_IAA_4h_rep1

description: RING1AKO_RING1BAID_Xinput_AUX_4h_rep1_S3


title: DAA-13

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

institute: USC

data_processing:
Illumina BCL files were de-multiplexed and converted to FASTQs using Cell Ranger mkfastq (version 5.0.1, 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest).
FASTQs were then used to quantify gene expression using Cell Ranger count (version 5.0.1) and the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference.
Genome_build: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary_files_format_and_content: gene expression counts in 10X format (separate barcodes, features, and matrix files for each sample).

source_name: CD3 cells from subject 6 BEFORE DAA therapy

extract_protocol: Cells resuspended in the reaction mix were loaded into the Chromium Single Cell Chip B, as well as the 10x Barcoded Gel Beads and the partitioning oil. The Chip B was placed into the 10x Chromium controller for cell partitioning, targeting a final number of 10 thousand cells per sample. After partition was concluded, the GEMs (Gel Bead-In EMulsions) were transferred to the C1000 Touch Thermal Cycler for the first phase of reverse transcription and samples proceed to library preparation following manufacturer’s instructions.

tag: subject

tag: time point

tag: disease

value: HCV

value: T cells

tag: Sex

value: male


title: DAA-12

source_name: CD3 cells from subject 5 AFTER DAA therapy

tag: cell type


title: DAA-16

source_name: CD3 cells from subject 7 - healthy normal control

value: Normal

value: Healthy


title: DAA-15

source_name: CD3 cells from subject 6 AFTER DAA therapy


title: DAA-11

source_name: CD3 cells from subject 5 DURING (Week 4) DAA therapy


title: DAA-09

source_name: CD3 cells from subject 4 AFTER DAA therapy


title: RING1AKO.RING1BAID_XInput_IAA_8h_rep1

description: RING1AKO_RING1BAID_Xinput_AUX_8h_rep1_S4


title: DAA-14

source_name: CD3 cells from subject 6 DURING (Week 4) DAA therapy


title: DAA-07

source_name: CD3 cells from subject 4 BEFORE DAA therapy


title: RING1AKO.RING1BAID_XInput_IAA_2h_rep2

description: RING1AKO_RING1BAID_Xinput_AUX_2h_rep3_S7

value: 2 hours


title: DAA-08

source_name: CD3 cells from subject 4 DURING (Week 4) DAA therapy


title: Untreated_nonFTO_m7GIP-rep1

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

description: cap-m7G RNA immunoprecipitation

data_processing:
Trim_galore (version0.6.6 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the reads length is 25~60nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end.
Processed reads were mapped to hg19 (UCSC refseq hg19).
The gene expression level was quantified as FPKM by Cufflinks.
Genome_build: hg19, UCSC Genome Browser
Supplementary_files_format_and_content: bigWig files, csv files

extract_protocol:
Total RNA was extracted from tissues using TRIzol reagent (Invitrogen,15596018), followed by DNase I (NEB, M0303L) treatment to remove DNA contamination.
Additional phenol-chloroform isolation and ethanol precipitation treatment was performed to remove enzyme contamination. Total RNA was fragmented into ~130-nucleotide-long fragments by magnesium RNA fragmentation buffer (NEB, E6150S). The fragmentation was stopped by adding RNA fragmentation stop solution followed by ethanol precipitation. 8ng of fragmented total RNA was used as input and remained RNA was used to do the m6A-seq. The libraries were sequenced on Illumina Hiseq X10 with paired-end 150 bp read length.

value: human embryonic kidney


title: HEK293T_CAGE_seq

description: CAGE-seq

value: CAGE


title: DAA-18

source_name: CD3 cells from subject 9 - healthy normal control


title: DAA-10

source_name: CD3 cells from subject 5 BEFORE DAA therapy


title: RING1AKO.RING1BAID_XInput_IAA_2h_rep3

description: RING1AKO_RING1BAID_Xinput_AUX_2h_rep4_S12

value: E14 Rosa26::Tir1; Ring1A-/-; AID-Ring1B


title: Untreated_nonFTO_m7GIP-rep2

description: cap-m7G RNA immunoprecipitation


title: DAA-06

source_name: CD3 cells from subject 3 AFTER DAA therapy


title: Untreated_nonFTO_m6AIP-rep2

description: m6A RNA immunoprecipitation


title: PROseq-293T

description: Pro-seq analysis with 293T

data_processing:
Library strategy: PRO-seq
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads.The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0 (Ramírez et al. 2014). Peaks were called using MACS (model-based analysis of ChIP-Seq) version 2.1.2 using default parameters and a q-value cutoff of 1E-5. The distribution of G4 peaks were annotated with ChIPpeakAnno. Heatmap  and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deepTools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmaps were generated with the indicated regions with ngs.plot or the computeMatrix command from deepTools 3.3.0.
Genome_build: Homo sapiens .hg38
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples


title: DAA-04

source_name: CD3 cells from subject 3 BEFORE DAA therapy


title: DAA-17

source_name: CD3 cells from subject 8 - healthy normal control


title: RING1AKO.RING1BAID_XInput_IAA_4h_rep2

description: RING1AKO_RING1BAID_Xinput_AUX_4h_rep3_S8

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (4h IAA)

value: 4 hours


title: DAA-03

source_name: CD3 cells from subject 2 AFTER DAA therapy


title: DAA-05

source_name: CD3 cells from subject 3 DURING (Week 4) DAA therapy


title: DAA-02

source_name: CD3 cells from subject 2 DURING (Week 4) DAA therapy


title: Untreated_nonFTO_m6AIP-rep1

description: m6A RNA immunoprecipitation


title: RING1AKO.RING1BAID_XInput_IAA_2h_rep1

description: RING1AKO_RING1BAID_Xinput_AUX_2h_rep1_S2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (2h IAA)

value: Mouse embryonic stem cells


title: Untreated_input

description: RNA-seq


title: DAA-01

source_name: CD3 cells from subject 2 BEFORE DAA therapy


title: Untreated_FTO_m6AIP-rep2

description: In vitro demethylation treatment


title: DAA-A3

source_name: CD3 cells from subject 1 AFTER DAA therapy


title: DAA-A2

source_name: CD3 cells from subject 1 DURING (Week 4) DAA therapy


title: RING1AKO.RING1BAID_XInput_UNT_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control

value: 0 hours


title: DAA-A1

source_name: CD3 cells from subject 1 BEFORE DAA therapy


title: RING1AKO.RING1BAID_XInput_UNT_rep3


title: TMPyP4-ChIP-Rx-TFIIB-DMSO

description: ChIP-seq analysis with TFIIB

data_processing:
G4 ChIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie  version 1.1.2 (Langmead et al. 2009), allowing only uniquely mapping reads with up to three  mismatches within the 150 bp reads. The resulting reads were extended to 200 bp toward the interior  35of the sequenced fragments and normalized to the total reads using for alignment (reads per million,  r.p.m.). Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 (Zhang  et al. 2008) with default parameters and a q-value cutoff of 0.001. To perform the motif analysis, the  summits of the called G4 ChIP-seq peaks were extended to 50 bp to fetch the DNA sequences, and  MEME-ChIP (Bailey et al. 2009) was used.
ChIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 150 bp reads (Langmead et al. 2009). The resulting reads were extended to 200 bp toward the interior of the sequenced fragments and normalized to the total reads used for aligning (reads per million, r.p.m.).The aligned human BAM files were normalized to the total aligned reads and converted to bigwig files for visualization in the UCSC genome browser. Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008) and were annotated with ChIPseeker (Yu et al. 2015). Heatmap and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
ChIP signals were normalized by the normalization factors as previous reported (Orlando et al. 2014).
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads.The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0 (Ramírez et al. 2014). Peaks were called using MACS (model-based analysis of ChIP-Seq) version 2.1.2 using default parameters and a q-value cutoff of 1E-5. The distribution of G4 peaks were annotated with ChIPpeakAnno. Heatmap  and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
ATAC-seq reads were aligned to human genome hg38 and E. coli genome. Alignments were processed with Bowtie with command option of –m 1 –v2,  allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. E. coli reads were used as spike-in controls for normalization of the ATAC-seq signals.
KAS-seq reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp reads (Langmead et al. 2009). The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
TT-seq reads were aligned to the human genome(UCSC hg38) and Drosophila dm6 genome, respectively. Alignments were processed with HISAT2,allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads. The 42resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m) for each strand. The read counts across each gene were counted with HT-seq with the union mode, and DESeq2 were used to perform the differentially gene expression analysis (Love et al. 2014). To estimate the fold changes based on the Drosophila spike-in RNA, size factors were calculated on the counts of the Drosophila genes and applied to the human gene counts prior to fold change estimation with DESeq2. The heatmap was generated by R package 3.4.3 with normalized counts from DESeq2.
qPRO-seq reads were aligned to the human hg38 genome. The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows using the average coverage (r.p.m.).
WGS reads were aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with the following parameters: --local  --sensitive-local. The resulting reads were extended to 200 bp toward the interior 35 of the sequenced fragments and normalized to the total reads using for alignment (reads per million,r.p.m.).
Genome_build: Homo sapiens .hg38
Genome_build: Mus musculus.mm10
Genome_build: Escherichia coli K-12 substr. MG1655
Genome_build: Drosophila melanogaster.dm6
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

growth_protocol: HEK293T, HeLa, U937 and SW1271 cells were obtained from ATCC and cultured at 37°C with 5% CO 2 . HEK293T and HeLa cells were maintained in DMEM (Life Technologies) supplemented with 10% fetal bovine serum (FBS; LONSERA). U937 and SW1271 cells were maintained in RPMI-1640 and DMEM-F12 medium (Life Technologies), respectively. MDA-231-LM2 (LM2) cells were cultured in DMEM supplemented with 10% FBS.Drosophila S2 cells were obtained from Invitrogen and maintained in Schneider's medium. Mouse embryonic fibroblasts (MEF) cells were maintained in DMEM with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol.
G4 ChIP-seq was performed according to a previously published protocol (Hansel-Hertsch et al.2018) with minor modifications. After fixation and chromatin shearing, 0.25% Triton X-100 was added to the chromatin and centrifuged at 20,000 g for 10 minutes to remove the insoluble debris.12.5 μl chromatin was immunoprecipitated with 800 ng BG4 antibodies and pre-blocked 5μl Anti-DYKDDDDK affinity beads (Smart-Lifesciences) sequentially. The beads were washed with 200 μl wash buffer (10 mM Tris-HCl at pH 7.4, 100 mM KCl, 0.1% Tween-20) at a 37°C rotating incubator (1,400 rpm) for 10 minutes. The captured DNA was eluted and reverse-crosslinked with 75 μl TE buffer and 1 μl 200 mg/mL proteinase K by incubation under rotation (1,400 rpm) for 1 hour at 37°C and then for 2 hours at 65°C. The DNA was further purified with phenol-chloroform extraction and ethanol precipitation. The G4 ChIP-seq libraries were prepared with the NEBNext ultra II DNA library prep kit for Illumina. The libraries were analyzed on an Agilent bioanalyzer and sequenced on a NovaSeq 6000.
Chromatin immunoprecipitation sequencing (ChIP-seq) was performed as previously described (Liang et al., 2015). Briefly, 1×107 cells were fixed with 1% paraformaldehyde in PBS for 10 minutes and then quenched with 0.125 M glycine for 5 minutes at room temperature. Fixed cells were sequentially lysed with 10 mL lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) and 10 mL lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitors). The cells were then resuspended in 300 μl lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1× protease inhibitors), and were sheared using the Diagenode Bruptor Plus with the high power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). After sonication, 1% Triton X-100 was added to the chromatin and centrifuged at 20,000 g for 10 minutes to remove the insoluble debris. The chromatin was immunoprecipitated with 10 μg individual antibodies and 15 μl pre-blocked Protein A/G beads (Smart-Lifesciences). The beads were washed three times with 1 mL lysis buffer 3, and three times with wash buffer (50 mM HEPES-KOH, pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate). The immunoprecipitated DNA was eluted with 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS, 200 μg/mL proteinase K) at 55°C overnight, and purified by phenol-chloroform extraction and ethanol precipitation. Library preparation was done using the NEBNext ultra II DNA library prep kit for Illumina, followed by sequencing on a NovaSeq 6000.
sonicated human chromatin was spiked-in with 10%-30% mouse chromatin toquantitatively normalize across experiments.
Cleavage Under Targets and Tagmentation (CUT&Tag) was performed as described before (Kaya-Okur et al. 2019; Wang et al. 2019) with some modifications. Briefly, half million cells were washed twice in 1.5 mL wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) by gentle pipetting. 10 μL concanavalin A coated magnetic beads (Smart-Lifesciences) were activated, and added to these cells with a 10 minutes’ incubation at room temperature. The supernatant was removed and bead-bound cells were resuspended in 100 μL dig-wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors,0.05% digitonin, 0.01% NP-40) containing 2mM EDTA and a 1:10 dilution of the 0.1 mg/mL BG4 primary antibody. Primary antibody incubation was performed on a rotating platform overnight at 4°C and then the liquid was removed. The Anti-Flag M2 antibody (Sigma-Aldrich) was diluted to 1:100 in 100 μL of dig-wash buffer with 2 mM EDTA, and was incubated with the cells at room temperature for 30 minutes followed by removing the liquid. The rabbit anti-mouse IgG antibody was diluted 100 folds and incubated with the cells for another 1 hour and washed with dig-wash buffer three times. A 1:200 dilution of pA-Tn5 adapter complex (~0.2 μM) was prepared in dig-300 buffer (0.05% digitonin, 20 mM HEPES at pH 7.5, 300 mM KCl, 0.5 mM spermidine, 1× protease 36inhibitors, 0.01% NP-40). 100 μL pA-Tn5 adapter complex was added to the cells with gentle vertexing, and was incubated at room temperature for 1 hour. Cells were washed three times in 200 μL dig-300 buffer to remove unbound pA-Tn5 proteins. Next, bead-bound cells were resuspended in 40 μL tagmentation buffer (10 mM TAPS-NaOH at pH 8.5, 10 mM MgCl 2 , 7.5% DMF) and incubated at 37°C for 1 hour. To stop tagmentation reaction, 1.5 μL 0.5 M EDTA, 0.5 μL 10% SDS and 0.5 μL 20 mg/mL proteinase K were added and incubated at 55°C for 1 hour and then for 15 minutes at 75°C. The DNA was extracted with Sera-Mag carboxylate-modified magnetic beads (GE Healthcare) for library preparation.21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high-fidelity 2× master mix. The libraries were purified with 1.1× volume of Sera-Mag carboxylate-modified magnetic beads, and subjected to LabChip DNA analysis and Illumina sequencing.
ATAC-seq was performed as previously described (Corces et al. 2017). Briefly, 2.5×10 4 cells were washed with cold PBS and centrifuged at 600 g for 5 minutes. The cells were resuspended with 50μL cold lysis buffer (10 mM Tris-HCl at pH 7.5, 10 mM NaCl, 3 mM MgCl 2 , 0.1% NP-40, 0.1% Tween-20 and 0.02% digitonin) and incubated on ice for 3 minutes. The cells were furthered added with 200 μL cold resuspension buffer (10 mM Tris-HCl at pH 7.5, 10 mM NaCl and 3 mM MgCl 2 ) and centrifuged at 600 g for 5 minutes. The pellet was resuspended with 12.5 μL resuspension buffer. 10 μL 5× tagmentation buffer (50 mM TAPS-NaOH at pH 8.5 and 25 mM MgCl 2 ), 16.5 μL PBS, 0.5 μL 10% Tween-20, 0.5 μL 1% digitonin, 0.75 μL 37.5 μM pA-Tn5 transposome and 9.5 μLnuclease-free H2O were mixed with 12.5 μL cell suspension. The transposition reaction was performed at 37°C for 60 minutes with mixing at 1,000 rpm. The reaction was stopped by adding 1.5μL 0.5 M EDTA and 0.5 μL 10% SDS, and digested with 1 μL 20 mg/mL proteinase K (Roche) at 65°C for 6 hours. The DNA was further purified with 1× Sera-Mag carboxylate-modified magnetic beads and eluted with 20 μL H 2 O with 0.1% Tween-20. The purified transposed DNA was amplified with NEBNext high-fidelity 2× PCR master mix, Ad1_noMX primer and Ad2.indexing primers. The DNA libraries were size-selected with Sera-Mag carboxylate-modified magnetic beads and sequenced on the NovaSeq 6000 platform.
KAS-seq was performed as reported (Wu et al. 2020a) with minor modifications. Briefly, after drug treatment, HEK293T cells were labeled with 2.5 mM N 3 -kethoxal for 10 minutes. The cells were collected for genomic DNA purification. The extracted genomic DNA was biotinylated with DBCO-PEG 4 -biotin (Sigma-Aldrich) and sonicated with a Diagenode Bruptor Plus with a high power mode for 40 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). The fragmented N 3 -kethoxal- modified DNA was enriched with the Dynabeads Myone Streptavidin C1 beads (Thermo Fisher) and eluted with nuclease-free water at 95 ̊C for 15 minutes. The elutes were then repaired with the phi29 DNA polymerase (NEB) and random hexamers, and purified with the Sera-Mag carboxylate-modified magnetic beads. The libraries were prepared with the NEBNext ultra II DNA library prep kit. Indexed libraries were pooled and sequenced on an Illumina platform.
TT-seq was performed as described previously (Schwalb et al. 2016; Liang et al. 2018) with minor modifications. 1×10 7 cells were labeled with 400 μM 4-thiouridine (4sU, Sigma-Aldrich) in a CO 2 incubator at 37°C for 10 minutes and were quickly lysed with 4 mL Trizol (Invitrogen). RN

treatment_protocol: 4SU labeling was performed for TT-seq

tag: tissue

value: embryonic kidney

value: DMSO

value: TFIIB


title: RING1AKO.RING1BAID_XInput_UNT_rep1

value: Homo sapiens


title: TMPyP4-ChIP-Rx-TFIIB-TMPYP4

description: ChIP-seq analysis with TFIIB and TMPyP4


title: Untreated_FTO_m6AIP-rep1

description: In vitro demethylation treatment


title: TMPyP4-ChIP-Rx-TBP-TMPYP4

description: ChIP-seq analysis with TBP and TMPyP4

value: TBP


title: Hypoxia_nonFTO_m7GIP-rep2

description: cap-m7G RNA immunoprecipitation


title: RING1AKO.RING1BAID_SUZ12_IAA_24h_rep3

description: RING1AKO_RING1BAID_SUZ12_AUX_24h_rep4_S15

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, auxin-treated (24h IAA)

value: auxin (IAA)

value: 24 hours

value: Cell Signaling Technology (#D39F6 )


title: TMPyP4-ChIP-Rx-TAF1-TMPYP4

description: ChIP-seq analysis with TAF1 and TMPyP4


title: TMPyP4-ChIP-Rx-TBP-DMSO

description: ChIP-seq analysis with TBP


title: RING1AKO.RING1BAID_SUZ12_IAA_24h_rep2

description: RING1AKO_RING1BAID_SUZ12_AUX_24h_rep3_S10


title: TMPyP4-ChIP-Rx-TAF1-DMSO

description: ChIP-seq analysis with TAF1


title: RING1AKO.RING1BAID_SUZ12_IAA_24h_rep1

description: RING1AKO_RING1BAID_SUZ12_AUX_24h_rep1_S5


title: TMPyP4-qPRO-seq-TMPYP4

description: qPRO-seq  analysis with 293T TMPyP4 treatment

data_processing:
Library strategy: qPRO-seq
G4 ChIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie  version 1.1.2 (Langmead et al. 2009), allowing only uniquely mapping reads with up to three  mismatches within the 150 bp reads. The resulting reads were extended to 200 bp toward the interior  35of the sequenced fragments and normalized to the total reads using for alignment (reads per million,  r.p.m.). Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 (Zhang  et al. 2008) with default parameters and a q-value cutoff of 0.001. To perform the motif analysis, the  summits of the called G4 ChIP-seq peaks were extended to 50 bp to fetch the DNA sequences, and  MEME-ChIP (Bailey et al. 2009) was used.
ChIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 150 bp reads (Langmead et al. 2009). The resulting reads were extended to 200 bp toward the interior of the sequenced fragments and normalized to the total reads used for aligning (reads per million, r.p.m.).The aligned human BAM files were normalized to the total aligned reads and converted to bigwig files for visualization in the UCSC genome browser. Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008) and were annotated with ChIPseeker (Yu et al. 2015). Heatmap and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
ChIP signals were normalized by the normalization factors as previous reported (Orlando et al. 2014).
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads.The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0 (Ramírez et al. 2014). Peaks were called using MACS (model-based analysis of ChIP-Seq) version 2.1.2 using default parameters and a q-value cutoff of 1E-5. The distribution of G4 peaks were annotated with ChIPpeakAnno. Heatmap  and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
ATAC-seq reads were aligned to human genome hg38 and E. coli genome. Alignments were processed with Bowtie with command option of –m 1 –v2,  allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. E. coli reads were used as spike-in controls for normalization of the ATAC-seq signals.
KAS-seq reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp reads (Langmead et al. 2009). The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.).
TT-seq reads were aligned to the human genome(UCSC hg38) and Drosophila dm6 genome, respectively. Alignments were processed with HISAT2,allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads. The 42resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m) for each strand. The read counts across each gene were counted with HT-seq with the union mode, and DESeq2 were used to perform the differentially gene expression analysis (Love et al. 2014). To estimate the fold changes based on the Drosophila spike-in RNA, size factors were calculated on the counts of the Drosophila genes and applied to the human gene counts prior to fold change estimation with DESeq2. The heatmap was generated by R package 3.4.3 with normalized counts from DESeq2.
qPRO-seq reads were aligned to the human hg38 genome. The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows using the average coverage (r.p.m.).
WGS reads were aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with the following parameters: --local  --sensitive-local. The resulting reads were extended to 200 bp toward the interior 35 of the sequenced fragments and normalized to the total reads using for alignment (reads per million,r.p.m.).
Genome_build: Homo sapiens .hg38
Genome_build: Mus musculus.mm10
Genome_build: Escherichia coli K-12 substr. MG1655
Genome_build: Drosophila melanogaster.dm6
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples


title: Hypoxia_nonFTO_m6AIP-rep1

description: m6A RNA immunoprecipitation


title: TMPyP4-qPRO-seq-DMSO

description: qPRO-seq  analysis with 293T