title: GX_0.25_dFnrG_3_1

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. Total RNA was prepared from the same culture of SAMPLE 9.


title: GX_0.50_dFnrG_3_1

status: Public on Jul 16 2021

type: RNA

city: Hanada-shi

first: Seiji

last: Watanabe

address: Nakamura-cho

department: Central Research Institute

country: Japan

institute: Mizkan Group Co. Ltd

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. Total RNA was prepared from the same culture of SAMPLE 13.

hyb_protocol: Hybridization was performed by Roche NimbleGen, Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen, Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Komagataeibacter medellinensis NBRC 3288

label_protocol: Labeling was performed by Roche NimbleGen, Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Gluconacetobacter xylinus NBRC 3288 delta-fnrG was grown to early-log phase (O.D.660nm 0.25) and mid-log phase (O.D.660nm 0.5) arobically shaking at 30°C in YPG media containing 1% (v/v) acetic acid and 3% (v/v) ethanol (Iida et al. J. Bacteriol. 190(7):2546). Cluture was statically incubated for 0 h and 3 h at 30°C.

extract_protocol: Total RNA was prepared by hot phenol method (Aiba et al. J. Biol. Chem. 256:11905). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at Roche Diagnostics Japan.

tag: genotype

value: disruptant mutant fnrG::Cat

tag: growth phase

value: mid-log phase (O.D.660nm 0.5)

tag: time

value: 3 hr


title: GX_0.50_WT_3_2

description: This sample is of wild-type Gluconacetobacter xylinus NBRC 3288. Total RNA was prepared from the same culture of SAMPLE 6.

source_name: Gluconacetobacter xylinus NBRC 3288 wild-type

growth_protocol: Gluconacetobacter xylinus NBRC 3288 was grown to early-log phase (O.D.660nm 0.25) and mid-log phase (O.D.660nm 0.5) arobically shaking at 30°C in YPG media containing 1% (v/v) acetic acid and 3% (v/v) ethanol (Iida et al. J. Bacteriol. 190(7):2546). Cluture was statically incubated for 0 h and 3 h at 30°C.

value: Wild-type


title: GX_0.25_dFnrG_0_2

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

value: early-log phase (O.D.660nm 0.25)

value: 0 hr


title: input_nBMDM_M1_6

type: SRA

city: Oxford

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Illumina NovaSeq Control Software" version 1.7.0 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real Time Analysis (RTA) version v3.4.4
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
BAM to fastQ conversion with bedtools2 (v.2.19.1) bamToFastQ
Read trimming and QC with Trim Galore! (v.0.3.3 with cutadapt v.1.8 and fastqc v0.11.3) using default parameters
Reads aligned to GRCm38/mm10 with bowtie2 (v.2.2.6) with --sensitive-local
Peak finding with MACS2 callpeak (v.2.2.7.1) for each ChIP vs matched input control
Reads were deduplicated with Picard Tools (v2.18.14-SNAPSHOT) MarkDuplicates
For profiles plots  replicate samples were merged with Picard MergeSamFiles
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: narrowPeak (http://genome.ucsc.edu/FAQ/FAQformat.html#format12)

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDM) were generated by flushing bone marrow from murine femurs and tibias and plating on non-tissue culture treated petri-dishes in complete 5 mmol/L glucose DMEM media (supplemented with 10% FBS, 2% penicillin -  streptomycin and 2 mmol/L glutamine) plus 20% L929 cell conditioned media for differentiation. After differentiation for 7 days, BMDM positively selected and plated at a density of 2 x105 cells/mL. HSCs were isolated using MagniSort Mouse Hematopoietic Lineage Depletion Kit (ThermoFisher Scientific, UK) by flushing bone marrow from murine femurs and tibias and incubating with markers to remove lineage committed cells (CD3, CD4, B220, Ter119 and Gr1) and enrich for HSCs.

extract_protocol:
1 x 10^6 cells/mL were fixed with 1% formaldehyde at room temperature for 10 minutes, washed with PBS and stored at -80oC. Cells were sheared using the Chromatin EasyShear Kit – Low SDS (Diagenode, Belgium) and sonicated using a Bioruptor® Pico sonication device (Cat# B01080010) (Diagenode, Belgium) according to the manufacture’s recommendations.
ChIP-seq libraries were prepared with the NEBNext Ultra II kit (New England Biolabs). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

treatment_protocol: BMDMs were stimulated in  5 mmol/L glucose DMEM media with either 10 ng/mL recombinant murine interferon-ɣ plus 100 ng/mL lipopolysaccharide or media only control for 16 hours.

tag: cell type

value: Bone marrow-derived macrophages

tag: strain

tag: chip antibody

tag: treatment

value: LPS + IFN-gamma

tag: disease state

value: Control


title: GX_0.25_dFnrG_0_1

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: GX_0.50_WT_0_2

description: This sample is of wild-type Gluconacetobacter xylinus NBRC 3288 harboring pTW201. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.


title: input_nBMDM_M1_5


title: input_nBMDM_M1_4


title: input_nBMDM_M1_3


title: GX_0.50_WT_3_1

description: This sample is of wild-type Gluconacetobacter xylinus NBRC 3288. Total RNA was prepared from the same culture of SAMPLE 5.


title: GX_0.50_WT_0_1

description: This sample is of wild-type Gluconacetobacter xylinus NBRC 3288 harboring pTW201. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Dis3 P17 KO2

city: Bethesda

first: Zhengpin

last: Wang

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

country: USA

institute: NIDDK, NIH

library_source: transcriptomic

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus genome sequence
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: featurecounts output

molecule: polyA RNA

source_name: P17 Testis

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P17 aged control and knockout mice.

extract_protocol:
Testes were isolated, total RNA was isolated using a RNeasy Micro Kit.
The libraries were constructed by using a Universal RNA-Seq Library Preparation Kit (TECAN) per the manufacturer’s protocol in which double-strand cDNA was generated using a mixture of random and poly(T) priming, followed by fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete, and PCR amplification to produce the final library.

value: B6D2F1 inbred

tag: tissue

value: Testis

value: Dis3 KO

tag: age

value: postnatal day 17 (P17)


title: GX_0.25_WT_3_1

description: This sample is of wild-type Gluconacetobacter xylinus NBRC 3288. Total RNA was prepared from the same culture of SAMPLE 1.


title: Dis3 P17 KO1


title: GX_0.25_WT_3_2

description: This sample is of wild-type Gluconacetobacter xylinus NBRC 3288. Total RNA was prepared from the same culture of SAMPLE 2.


title: input_nBMDM_M1_1


title: input_nBMDM_M1_2


title: Dis3 P17 WT2

value: Dis3 WT


title: GX_0.25_WT_0_1


title: input_dHSC_None_6

source_name: Haematopoietic stem cells

value: Haematopoietic stem cells

value: Unstimulated

value: Diabetic


title: Dis3 P17 WT1


title: input_dHSC_None_4


title: input_dHSC_None_1


title: input_dHSC_None_5


title: RPE cells, ERKi 250nM 24h Rep 2, S95

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

data_processing:
Reads were processed to counts using the bcbio-Nextgen toolkit (https://github.com/chapmanb/bcbio-nextgen).
Reads were trimmed and clipped for quality control in cutadapt v2.3
High-quality reads were then aligned to the human assembly and gene annotation GRCh38.97 using Hisat2 v2.1.0
Gene-level transcript-counts were calculated using HTseq-count v0.9.1. Only data from genes annotated as protein-coding according to annotation from GRCh38.97 were kept for further analysis.
Differential expression of genes was analysed using DESeq2.
Genome_build: GRCh38.97
Supplementary_files_format_and_content: raw_counts.csv.gz: CSV file of raw gene counts of all 96 samples with Ensembl gene IDs
Supplementary_files_format_and_content: normalized_counts.csv: CSV file of gene counts normalized for library size using DESeq2 size factors (normalized) and variance stabilized counts using the vsn R package (variance_stabilized)
Supplementary_files_format_and_content: deseq_pairwise_results.csv.gz: CSV file of the differential expression results from DESeq2 comparing all experimental conditions against the non-treated 0h condition

organism: Homo sapiens

source_name: Human Retinal Pigment Epithelial cells

growth_protocol: Human Retinal Pigment Epithelial (RPE) cells immortalized with human telomerase expression (RPE-hTERT, a kind gift from S.J. Elledge, Harvard Medical School) were grown in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), 2mM L-Glutamine, Antibiotic-Antimycotic (100U/ml penicillin, 100μg/ml streptomycin and 250ng/ml Amphotericin B), and 50μg/ml hygromycin B. BJ-5ta cells were obtained from ATCC and cultured in four parts DMEM and one part Medium 199 supplemented with 10% FBS, penicillin-streptomycin-glutamine (PSG), and 0.01 mg/ml hygromycin B.

extract_protocol:
Cells were lysed with 600µl Trizol per well and total RNA was prepared using Direct-zol-96 RNA Kits according to the manufacturer's protocol. Sample concentrations were determined by Nanodrop and RNA quality was assessed on a subset of samples by Bioanalyzer (Agilent); all samples scored RINs of > 9.0.
RNA sequencing library preparation was performed with the High Throughput TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol at half reaction volume. Input for each sample consisted of 300-500ng of RNA and 5ul of 1:500 diluted ERCC spike-in mix 1 (Ambion). Libraries were amplified for 12 cycles during the final amplification step. Libraries were quantified using the Qubit dsDNA HS assay (Thermo Fisher Scientific). Library size and quality were spot checked for a subset of samples by Bioanalyzer (Agilent). The average size of cDNA fragments in the libraries was 370 base pairs. Libraries were pooled at equimolar concentrations then the pool was quantitated using the KAPA library quantification kit (KAPA Biosystems). Libraries were sequenced single end 114 base pairs using NovaSeq_SP full flow cell (Illumina) at the Bauer Core Facility (Harvard University).

treatment_protocol: RPE/tet-BRafV600E-HA cells were plated in 6-well plates and allowed to grow for 48 hours till 50% confluency. Cells were then treated with various concentrations of ERK inhibitor (SCH772984) alone for 24h or in combination with DOX (250ng) for variable length of time as indicated by the experimental design. Each condition was performed twice on two different days for a total of two biological replicates.

value: Retinal Pigment Epithelial cells

value: ERKi 250nM

tag: doxycycline induction of brafv600e

value: 24h post-treatment


title: RPE cells, ERKi 62.5nM 24h Rep 2, S94

value: ERKi 62.5nM


title: input_dBMDM_ctrl_5


title: RPE cells, ERKi 3.9nM 24h Rep 2, S92

value: ERKi 3.9nM


title: input_dBMDM_ctrl_6


title: RPE cells, ERKi 1000nM 24h Rep 2, S96

value: ERKi 1000nM


title: RPE cells, ERKi 15.6nM 24h Rep 2, S93

value: ERKi 15.6nM


title: RPE cells, ERKi 250nM 24h Rep 1, S89


title: GX_0.25_WT_0_2

value: Wild-type

value: early-log phase (O.D.660nm 0.25)

value: 0 hr


title: RPE cells, ERKi 1000nM 24h Rep 1, S90


title: input_dBMDM_ctrl_4

value: Bone marrow-derived macrophages


title: RPE cells, ERKi 0nM 24h Rep 2, S91

value: ERKi 0nM


title: input_dBMDM_ctrl_2


title: input_dBMDM_ctrl_3


title: input_dBMDM_M1_6

value: LPS + IFN-gamma


title: input_dBMDM_ctrl_1


title: RPE cells, ERKi 15.6nM 24h Rep 1, S87


title: input_dBMDM_M1_5


title: RPE cells, ERKi 62.5nM 24h Rep 1, S88


title: RPE cells, ERKi 3.9nM 24h Rep 1, S86


title: input_dBMDM_M1_4


title: RPE cells, ERKi 0nM 24h Rep 1, S85


title: input_dBMDM_M1_3


title: input_dHSC_None_2


title: RPE cells, ERKi 250nM 24h DOX Rep 2, S83


title: input_dBMDM_M1_2


title: RPE cells, ERKi 1000nM 24h DOX Rep 2, S84


title: RPE cells, ERKi 62.5nM 24h DOX Rep 2, S82


title: input_dBMDM_M1_1


title: RPE cells, ERKi 3.9nM 24h DOX Rep 2, S80


title: H3K4me3_nHSC_None_6

value: H3K4me3 (abcam; ab8580)

value: Control


title: H3K4me3_nHSC_None_5

value: Haematopoietic stem cells

value: Unstimulated


title: H3K4me3_nHSC_None_3


title: RPE cells, ERKi 1000nM 24h DOX Rep 1, S78

value: Retinal Pigment Epithelial cells


title: H3K4me3_nHSC_None_2


title: RPE cells, ERKi 250nM 24h DOX Rep 1, S77

value: ERKi 250nM


title: RPE cells, ERKi 0nM 24h DOX Rep 2, S79

value: 24h post-treatment


title: H3K4me3_nHSC_None_1


title: H3K4me3_nBMDM_ctrl_6


title: RPE cells, ERKi 15.6nM 24h DOX Rep 1, S75


title: RPE cells, ERKi 3.9nM 24h DOX Rep 1, S74


title: A. flavus WT 72 h rep2

city: Qingdao

first: peng

last: wang

address: Ocean University of China, No.5 Yushan Road, Shinan District

country: China

institute: Ocean University of China

description: processed data file: Supplemental Dataset 3, WT and aflR gene knockout strains expressed genes significantly differently at 72 h

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp) with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Aspergillus flavus

source_name: A. flavus WT 72 h_mycelium

growth_protocol: Approximately 10^8 spores/mL of the WT and ΔaflR strains were inoculated in the PDB medium and incubated for 24 h at 30°C 180 rpm. Mycelia were collected through sterilized Miracloth and washed with sterile water. The water on the surface of the mycelia was blotted out. The mycelia were spread flat on PDA plates at 30°C and sampled at 0 h, 24 h, and 72 h.

extract_protocol:
Total RNA was extracted using the TRIzolTM kit (Thermo Fisher Scientific, USA) and DNA was removed using DNase I. RNA libraries were generated using the TruSeqTM RNA sample preparation kit (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: cultivation time


title: A. flavus WT 72 h rep3


title: A. flavus WT 24 h rep2

description: processed data file: Supplemental Dataset 2, WT and aflR gene knockout strains expressed genes significantly differently at 24 h

source_name: A. flavus WT 24 h_mycelium


title: A. flavus WT 24 h rep3


title: A. flavus WT 72 h rep1


title: H3K4me3_nBMDM_ctrl_5


title: A. flavus WT 0 h rep3

description: processed data file: Supplemental Dataset 1, WT and aflR gene knockout strains expressed genes significantly differently at 0 h

source_name: A. flavus WT 0 h_mycelium

value: 0 h


title: RPE cells, ERKi 0nM 24h DOX Rep 1, S73


title: A. flavus WT 0 h rep2


title: A. flavus WT 0 h rep1


title: H3K4me3_nBMDM_ctrl_4


title: input_dHSC_None_3

value: Diabetic


title: H3K4me3_nHSC_None_4


title: RPE cells, ERKi 1000nM 16h DOX Rep 2, S72

value: ERKi 1000nM

value: 16h post-treatment


title: A. flavus ΔaflR 72 h rep3

source_name: A. flavus ΔaflR 72 h_mycelium

value: {delta}aflR, {delta}Ku70, pyrG+


title: RPE cells, ERKi 62.5nM 24h DOX Rep 1, S76

value: ERKi 62.5nM


title: A. flavus ΔaflR 72 h rep2


title: H3K4me3_nBMDM_ctrl_3

value: Bone marrow-derived macrophages


title: RPE cells, ERKi 250nM 16h DOX Rep 2, S71


title: A. flavus ΔaflR 72 h rep1


title: A. flavus ΔaflR 24 h rep3

source_name: A. flavus ΔaflR 24 h_mycelium


title: RPE cells, ERKi 62.5nM 16h DOX Rep 2, S70


title: H3K4me3_nBMDM_ctrl_2


title: A. flavus ΔaflR 24 h rep2


title: RPE cells, ERKi 15.6nM 24h DOX Rep 2, S81

value: ERKi 15.6nM


title: A. flavus ΔaflR 24 h rep1


title: A. flavus ΔaflR 0 h rep2

source_name: A. flavus ΔaflR 0 h_mycelium


title: RPE cells, ERKi 15.6nM 16h DOX Rep 2, S69


title: H3K4me3_nBMDM_M1_6

value: LPS + IFN-gamma


title: A. flavus ΔaflR 0 h rep3


title: H3K4me3_nBMDM_M1_5

value: H3K4me3 (abcam; ab8580)


title: RPE cells, ERKi 3.9nM 16h DOX Rep 2, S68

value: ERKi 3.9nM


title: H3K4me3_nBMDM_ctrl_1

value: Control


title: A. flavus ΔaflR 0 h rep1


title: H3K4me3_nBMDM_M1_4


title: RPE cells, ERKi 0nM 16h DOX Rep 2, S67

value: ERKi 0nM


title: H3K4me3_nBMDM_M1_3


title: S2-Skin-Mut11

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was done using Hisat2
Cufflinks was used to assemble the transcripts
Cuffmerge was used to merged all the transcripts
Cuffdiff was for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each treatment group

source_name: Conditional knockout 100 days

extract_protocol:
Total RNA from skin was isolated using Rneasy kit (Qiagen)
rRNA removal was performed either by Ribo-Zero-Gold (Illumina) or Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible RNA-seq libraries using NEXTFLEX Rapid Directional RNA-Seq kit (Bioo Scientific).

value: total skin


title: S2-Skin-Mut6

source_name: Conditional knockout 300 days


title: S2-Skin-CO8

source_name: Control 100 days


title: RPE cells, ERKi 250nM 16h DOX Rep 1, S65

value: Retinal Pigment Epithelial cells

value: ERKi 250nM


title: S2-Skin-CO5


title: S2-Skin-Mut9


title: S2-Skin-Mut2


title: H3K4me3_nBMDM_M1_2


title: RPE cells, ERKi 62.5nM 16h DOX Rep 1, S64


title: S2-Skin-Mut4


title: H3K4me3_nBMDM_M1_1


title: S2-Skin-CO4

source_name: Control 300 days


title: RPE cells, ERKi 15.6nM 16h DOX Rep 1, S63


title: S2-Skin-CO3


title: H3K4me3_dHSC_None_6

value: Haematopoietic stem cells

value: Unstimulated


title: S2-Skin-Mut12


title: S2-Skin-CO1


title: RPE cells, ERKi 3.9nM 16h DOX Rep 1, S62


title: CO-Skin-O5

source_name: Chronologically Old Control 700days


title: RPE cells, ERKi 1000nM 16h DOX Rep 1, S66


title: RPE cells, ERKi 0nM 16h DOX Rep 1, S61


title: H3K4me3_dHSC_None_5

value: Diabetic


title: CO-Skin-O3


title: CO-Skin-O2


title: H3K4me3_dHSC_None_4


title: RPE cells, ERKi 1000nM 8h DOX Rep 2, S60

value: ERKi 1000nM

value: 8h post-treatment


title: CO-Skin-Y5

source_name: Young Control 50days


title: H3K4me3_dHSC_None_3


title: H3K4me3_dHSC_None_2


title: CO-Skin-Y3


title: CO-Skin-Y4


title: RPE cells, ERKi 250nM 8h DOX Rep 2, S59


title: RPE cells, ERKi 62.5nM 8h DOX Rep 2, S58


title: CO-Skin-Y2


title: H3K4me3_dHSC_None_1


title: H3K4me3_dBMDM_ctrl_6


title: RPE cells, ERKi 15.6nM 8h DOX Rep 2, S57


title: SENP6 depleted OCI-Ly1 cells #3

city: Berlin

first: Matthias

last: Wirth

address: Hindenburgdamm 30

institute: Charité Berlin

data_processing:
RNA-Seq reads were aligned to the reference index hg38 with Salmon (Release 0.8.1), salmon's estimate of the number of reads mapping to each transcript that was quantified.
Normalized output was generated using DeSeq2
Genome_build: hg38
Supplementary_files_format_and_content: Log normalized read counts in a tab delimeted text file

source_name: B cell lymphoma cell line

extract_protocol:
RNA was extracted using RNeasy MiniPrep Kit from Qiagen. RIN was determined using Agilent RNA 6000 Nano Kit (# 5067-1513, Agilent, Santa Clara, CA) and the Agilent 2100 Expert software (version B.02.10.SI764). Library preparation and paired-end sequencing was subsequently performed by Novogene (UK) (Cambridge, United Kingdom) on a HiSeq2500 (Illumina, San Diego, CA) with a sequencing depth of more than 20 M reads/sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: B cell lymphoma cell line

value: SENP6 knockdown


title: CO-Skin-O4


title: CO-Skin-Y1


title: RPE cells, ERKi 0nM 8h DOX Rep 2, S55


title: SENP6 depleted OCI-Ly1 cells #2


title: A. flavus WT 24 h rep1

value: wild type


title: RPE cells, ERKi 3.9nM 8h DOX Rep 2, S56


title: H3K4me3_dBMDM_ctrl_5

source_name: Bone marrow-derived macrophages

value: Bone marrow-derived macrophages


title: ATAC-seq_Conditional knockout 100 days

description: Sod2 mutant murine dermal fibroblasts

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was done using Bowtie2, followed by deduplicaiton by Picardtools MarkDuplicates
Bam to bed conversion was performed by bedtools bamtobed
MACS2 was used to find the peaks
Homer was used to annotate the peaks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include identified peaks by MACS2

source_name: Sod2 mutant murine dermal fibroblasts

extract_protocol: I50000 MDFs were lysed in Nuclei lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) for 2 min, followed by nuclei isolation using centrifugation (500 ´ g for 10 min at 4°C). Isolated nuclei were subjected to tagmentation reaction with Tn5 transposase (Illumina) for 30 min at 37°C. Tagmented DNA was then purified using MinElute kit (Qiagen) and used for PCR amplification to add the i5 and i7 dual barcodes. The PCR amplified products were purified by two times 1.8´ AMPure XP bead cleanup (Beckman Coulter). The purified library was then quality controlled by Qiaxcel advanced system (Qiagen) and Bioanalyzer (Agilent) and finally measured by Qubit fluorimeter (ThermoFisher Scientific). Thereafter, libraries were sequenced on Illumina NextSeq 500 platform (Microsynth GmbH) using NextSeq v2 chemistry (2 ´ 75 cycles).

value: Dermal fibroblast


title: H3K4me3_dBMDM_ctrl_4

value: H3K4me3 (abcam; ab8580)


title: RPE cells, ERKi 1000nM 8h DOX Rep 1, S54


title: ATAC-seq_Control 100 days_vehicle

description: control murine dermal fibroblasts treated with vehicle


title: RPE cells, ERKi 250nM 8h DOX Rep 1, S53


title: 7901_NC_transfected GC SGC7901 cells with NC_48hr

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

description: Gene expression after 48hr transfection with NC in SGC7901 cells.

hyb_protocol: Step 5 Hybridization  Kit and Instruments:  Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):  10X Blocking Agent  25X Fragmentation Buffer  2x GEx Hybridization Buffer HI-RPM  Hybridization Chamber, stainless (Agilent p/n G2534A)  Hybridization Chamber gasket slides (Agilent p/n G2534-60003)  Hybridization oven (Agilent p/n G2545A)  Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)    Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K  Volume Prepared 500ul 250ul 110ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: Step 7 Scanning  Instrument:  Agilent Microarray Scanner (Agilent p/n G2565BA)    Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Step 8 Extract data using Agilent Feature Extraction Software  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

label_protocol: Step 3 Prepare labeling reaction  Kit:  Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)    Procedure:  1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.     Step 4 Purify the labeled/amplified RNA and labeled cRNA QC  Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2. Add 350 μL of Buffer RLT and mix well by pipetting.  3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).   From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.   Blank the instrument with 1.5 μL of 1x labeling solution.   Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).   The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:  (Concentration of Cy3)  Specific Activity =——————————————— = pmol Cy3 per μg cRNA  (Concentration of cRNA) * 1000  * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: The cells were cultured with RPMI-1640 medium (HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS, Gibco) in a 37°C incubator containing 5% CO2.

extract_protocol: Step 1 Prepare the RNA Sample  Kits and Reagents:  TRIzol® Reagent (Invitrogen life technologies)  Biopulverizer(biospec)  Mini-Bead-Beater-16(biospec)    Procedure:  1. Homogenization  a. Tissues  a) Cryopulverization of tissue using the Biopulverizer   Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen.   Place prefrozen tissue in the well of the mortar.   Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS).   Empty the powdered contents for subsequent homogenization or extraction procedures.               b) Homogenization using the Mini-Bead-Beater-16   Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap.    Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten.   Set the timer depending on the type of sample. Start the machine.   b. Cells Grown in Monolayer  Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.   c. Cells Grown in Suspension  Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of animal, plant or yeast cells, or per 1 × 107 bacterial cells. Washing cells before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation. Disruption of some yeast and bacterial cells may require the use of a homogenizer.  2. Phase Separation  Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.  3. RNA Precipitation  Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.   4. RNA Wash  Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.  5. Redissolving the RNA  At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: GC SGC7901 cells was transfected with KIF26A siRNA 1 (siKIF26A 1) or NC for 48h.

value: gastric cancer

value: control


title: 7901_NC_transfected GC SGC7901 cells with siKIF26A 1_48hr

description: Gene expression after 48hr transfection with siKIF26A in SGC7901 cells.

value: KIF26A siRNA


title: SENP6 depleted OCI-Ly1 cells #1


title: H3K4me3_dBMDM_ctrl_1


title: RPE cells, ERKi 62.5nM 8h DOX Rep 1, S52

value: ERKi 62.5nM


title: parental OCI-Ly1 cells #2

value: parental


title: ATAC-seq_Control 100 days_rotenone

description: control murine dermal fibroblasts treated with rotenone 250µM


title: mESC_SLAM-seq_Degron_rep3

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

data_processing:
Library strategy: SLAM-Seq
Data from SLAM-seq experiments was processed using the SLAM-DUNK analysis pipeline as previously described (Neumann et al., 2019). Slamdunk v0.4.3 (https://github.com/t-neumann/slamdunk) was used for the mapping, filtering, variant calling, and T>C conversion rate quantification steps. Processed reads were mapped to the mouse mm10 genome using the T>C aware aligner NextGenMap (Sedlazeck et al., 2013) and uniquely mapped reads were retained. T>C SNPs were called with VarScan v2.4.1 (Koboldt et al., 2012) using default parameters. Then “slamdunk count” function was used to calculate all relevant numbers including nascent RNA-seq counts as indicated in Table S2. For total RNA-seq analysis, the single-end reads generated by the QuantSeq experiment were mapped to mouse mm10 genome using STAR v2.7 (https://github.com/alexdobin/STAR).
gene counts files were generated with DEseq2 v1.22.2 and contain the adjusted p-values and fold change for each transcript.
Genome_build: mm10

source_name: mouse embryonic stem cells

growth_protocol: dTAG-BRD4 cell line was generated by inserting FKBP12F36V tag into start codon of endogenoud Brd4 in mouse embryonic stem cell (ATCC #CRL-1934). They were maintained at 37°C in 20% O2 and 5% CO2 on gelatin-coated plates in knock-out DMEM (Gibco #10829018), 10% knockout serum replacement (Gibco #10828028), 1% FBS (Hyclone #SH30070.03), 1x non-essential amino acids (Gibco #11140050), 2 mM L-glutamine (Gibco #25030081), 1% ITS-X supplement (Gibco #51500056), 55 μM β-mercaptoethanol (Gibco #21985023), 1x103 units/ml recombinant mouse LIF (Millipore #ESG1107), 3 μM GSKβ inhibitor CHIR99021 (Reprocell #04-0004-02), 1 μM MEK inhibitor PD0325901 (Reprocell #04-0006-02), and 1% penicillin and streptomycin.

extract_protocol:
The SLAM-SEQ protocol was carried out as described in the SLAM-Seq Anabolic Kinetics Kit user guide (Lexogen #061.24) with modifications. Briefly, mESCs were seeded in 0.1% bovine gelatin (Sigma #G9391-500g) coated 6-well plates approximately two days prior to S4U labelling in order to attain an optimum confluency of around 70-80% (~2 x 106 cells). On the day of labelling, mESC media was aspirated and refreshed with pre-warmed mESC growth media containing either 500 nM dTAG-13 or DMSO to pre-establish acute degradation of BRD4. Time course for BRD4 degradation was set at 4.5 hours. Fifteen minutes into the time course, newly synthesized RNA was labelled via the addition of 4-thiouridine to all wells, including controls, at a final concentration of 500 µM/well and metabolic labelling was continued until the end of the time course. For the 4.5 hour time point, S4U medium was refreshed after 3 hours to continue efficient labelling. At the respective times points, media was aspirated and mESC cells were harvested following the addition of 400 µl of Accutase. The single cell suspension from each well was transferred into corresponding tubes and centrifuged at 2500 rpm for 5 minutes to pellet cells. The cell pellet was washed twice with ice cold 1x PBS and RNA extraction was carried out using the RNAeasy Plus kit (Qiagen #74134). Recommended amount of reducing agent (as indicated in the manufacturers’ protocol) was added to all extraction buffers to maintain a reducing environment during extraction. 8 µg of total RNA was alkylated via treatment with 10 mM iodoacetamide (IAA) at 50°C for 5 minutes under optimal reaction conditions and purified by ethanol precipitation. IAA fixed RNA concentrations were estimated using the Nanodrop and approximately ~300 ng/µl of alkylated RNA per sample was sent to Lexogen for downstream processing and sequencing.
Construction of SLAM-Seq libraries for sequencing on the Illumina NextSeq 500 platform was carried out using the Quant Seq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen #015) was carried out at Lexogen GmbH according to the manufacturers’ instructions.

treatment_protocol: Cells were treated with DMSO or 500 nM dTAG-13 for 4.5 hours

tag: knock-in line

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

tag: parental line

value: ES-D3 (ATCC CRL 1934)

value: Treated with 500nM of dTAG-13 for 4.5 hours

tag: technique

value: SLAM-Seq


title: mESC_SLAM-seq_Degron_rep2


title: RPE cells, ERKi 15.6nM 8h DOX Rep 1, S51

source_name: Human Retinal Pigment Epithelial cells

value: Retinal Pigment Epithelial cells

value: ERKi 15.6nM


title: mESC_SLAM-seq_Degron_rep1


title: RPE cells, ERKi 3.9nM 8h DOX Rep 1, S50

value: ERKi 3.9nM

value: 8h post-treatment


title: H3K4me3_dBMDM_M1_6

value: LPS + IFN-gamma

value: Diabetic


title: H3K4me3_dBMDM_M1_5

value: Bone marrow-derived macrophages


title: ATAC-seq_Control 100 days

description: control murine dermal fibroblasts

source_name: control murine dermal fibroblasts

value: Dermal fibroblast


title: H3K4me3_dBMDM_ctrl_2

value: H3K4me3 (abcam; ab8580)

value: Unstimulated


title: RPE cells, ERKi 0nM 8h DOX Rep 1, S49

value: ERKi 0nM


title: H3K4me3_dBMDM_M1_3


title: H3K4me3_dBMDM_M1_4


title: mESC_SLAM-seq_DMSO_rep3

value: Untreated control (DMSO added to a final concentration 0.1%)


title: mESC_SLAM-seq_DMSO_rep2


title: PHF5A knockdown

city: Shanghai

first: Alvin

last: Casper

address: RongJin

institute: Alvin

data_processing:
Paired-end sequencing was performed on cDNA library using HiSeq 2500 instrument (Illumina).
The qualified reads were mapped to human reference genome hg38 (GRCh38) using Hisat2 (version: 2.0.4) split mapping algorithm.
The expression level of genes was determined based on the value of FPKM which was calculated by cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: count and fpkm

source_name: PHF5A knockdown

extract_protocol:
Total RNA was harvested from the cells using Trizol reagent. TruSeq Stranded Total RNA Library Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were transfected with PHF5A siRNA or control siRNA.

value: CRC cells HCT116

value: PHF5A knockdown


title: Control

source_name: Control

value: control


title: mESC_SLAM-seq_DMSO_rep1

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: ES-D3 (ATCC CRL 1934)


title: parental OCI-Ly1 cells #3

value: B cell lymphoma cell line

value: parental


title: H3K4me3_dBMDM_M1_2


title: RPE cells, ERKi 1000nM 4h DOX Rep 2, S48

value: Retinal Pigment Epithelial cells

value: ERKi 1000nM

value: 4h post-treatment


title: mESC_CUT&RUN_Degron_RAD21_rep3

data_processing:
Library strategy: CUT&RUN
Processing of CUT&RUN data was done as previously described (Skene et al., 2018) with minor modifications. Raw pair-end reads were pre-processed using fastp v0.20.0 (Chen et al., 2018) with default parameters to filter low-quality reads, remove adapters, and trim read ends. Processed reads were then aligned to sacCer3/V64 and mouse mm10 genomes using Bowtie2 v1.2.2 with the following parameters: --local --very-sensitive-local --no-unal --no-discordant --no-mixed --phred33 --no-contain --no-overlap -N 1 -I 50 -X 1000 -p 40. Duplicates and poorly mapping reads were removed using Sambamba v0.7.0 as follows: sambamba view -t 8 -f bam -F "mapping_quality>=30 and not duplicate and ref_name =~ /^chr[0-9XY]/" file.bam. Coverage tracks were generated from mapped reads and normalized to counts per million (CPM) using: bamCoverage --bam reads.bam --outFileFormat bigwig -o coverage.bw --binSize 10 --normalizeUsing CPM --extendReads -p 10.
bigwig files were generated using Deeptools v3.1.3 on the pooled biological replicates., and normalized by CPM
Genome_build: mm10

extract_protocol:
The CUT&RUN protocol was carried out as previously described (Skene et al., 2018) with modifications. Cells were harvested via gentle agitation post the incubation with Accutase for 5 minutes and collected via centrifugation at 300 g for 3 minutes at 4°C. The cells were washed twice with ice-cold PBS and nuclei were isolated with Nuclear extraction buffer [20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM Spermidine (Sigma #05292-1ml-F), 0.1% Triton X-100, 20% Glycerol and 1x protease and phosphatase inhibitor (ThermoFisher #78442)]. To aid in nuclear capture, isolated nuclei were incubated with activated Concanavalin A beads (Bangs Laboratories #Bp531) for 15 minutes at room temperature followed by incubation with the desired primary antibody (1:100 dilution) overnight. Any unbound antibody was washed away using Wash Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x protease phosphatase inhibitor) for a total of two washes. Supernatant was discarded via bead liquid separation using a magnetic stand and pA-MNase was added at a final concentration of 700 ng/ml (Batch 6: Stock concentration: 143 μg/ml) and the complex was incubated for 1 hour at 4°C. Following incubation, the bound complexes were washed twice with Wash Buffer and placed in a 0°C metal block for 5 minutes to pre-chill the tubes. To activate pA-MNase, CaCl2 was added to the pre-chilled bound complexes at a final concentration of 2 mM and incubated in the 0°C metal block for 30 minutes. The digestion reaction was neutralized by the addition of an equal volume of 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A, 40 μg/mL glycogen and 100 pg/mL heterologous spike in DNA) followed by incubation at 37°C for 10 minutes to released cleaved fragments of DNA. The targeted protein-DNA complex was released via centrifugation at 16000 g for 5 minutes and supernatant was collected and transferred to freshly labelled 1.7 mL tubes. For H3K27ac, a spin column method (Macherey-Nagel #740609.250) of extraction was followed according to the manufacturer’s instructions to recover large DNA-protein complexes. To enrich for smaller fragments occupied by non-histone proteins (BRD4, NIPBL and RAD21), a phenol chloroform extraction protocol was followed as briefly described. The supernatant was decanted into a fresh tube to which 10% SDS (final concentration 0.1%) and proteinase K (final concentration of 20 mg/ml) was added and mixed by inversion followed by incubation for 10 minutes at 70°C. Post incubation, phenol-chloroform-isoamyl alcohol was added to the solution and vortexed at full speed to mix. The solution was transferred to a phase lock tube, centrifuged at 16000 g for 5 minutes and inverted 10 times post the addition of chloroform followed by another round of centrifugation at 16000 g for 5 minutes. The supernatant was transferred to a fresh tube containing glycogen (final concentration 20 µg/mL) and DNA was precipitated via the addition of 100% ethanol. The samples were incubated on ice for 10 minutes and subsequently centrifuged at 16000 g at 4°C. Excess liquid was carefully discarded and 1 ml of ethanol was added to the pellet and tubes were mixed by inverting. Samples were centrifuged once again at 16000 g at 4°C. The supernatant was carefully discarded, and the pellet was air dried for 10 minutes and resuspended in a desired amount of TE buffer (1 mM Tris-HCL pH 8, 0.1 mM EDTA).
Construction of the CUT&RUN DNA libraries for next generation sequencing was carried out with modifications using the KAPA Hyper Prep Kit (KAPA Biosystems #KK8502 07962347001), coupled with the NEBNext Multiplex Oligos for Illumina (New England Biolabs #E6440S). Briefly, the end repair and A-tailing temperature was dropped from the recommended 65°C to 58°C to avoid denaturation of small AT rich fragments and the reaction time for this step was increased to 60 minutes to compensate for lower enzymatic activity. Adapter ligation was performed using the NEB Adapter stock diluted down to the desired concentration. Post adapter ligation, the recommended volume of NEB USER enzyme was added to the reaction and incubated 37°C for 15 minutes ensuring digestion of the uracil bridge allowing successful pairing of the primers containing barcodes in the successive steps of the reaction. After adapter ligation and hairpin cleavage, 1.1x AgenCourt AMpure Beads (Beckman Coulter #A63880) were added to the reaction to ensure high recovery of short to medium sized fragments. For the amplification reaction, 10µl of the NEBNext Multiplex Oligos were added to the samples, replacing the KAPA Library Amplification Primer Mix (10X) and subjected to 14 cycles of amplification. Post amplification cleanup was carried out using 1.1x AgenCourt AMpure Beads. The libraries were quantified via qPCR using the KAPA Library Quantification Kit for Illumina Platforms (KAPA Biosystems #KK4835 07960204001) and quality control was carried out on the Agilent BioAnalyzer 2100 Expert (Agilent Technologies, USA) using the High Sensitivity DNA Kit (Agilent Technologies #5067-4626). 40 barcoded libraries were quantified and pooled together in equimolar ratio with a total of 20 libraries per pool. The pooled libraries were denatured according to the standard Illumina protocol.

value: Treated with 500nM of dTAG-13 for 4.5 hours

value: CUT&RUN

tag: antibody

value: RAD21 (Ab992, Abcam)


title: H3K4me3_dBMDM_M1_1

value: Bone marrow-derived macrophages

value: H3K4me3 (abcam; ab8580)

value: LPS + IFN-gamma

value: Diabetic


title: parental OCI-Ly1 cells #1

tag: genotype


title: RPE cells, ERKi 62.5nM 4h DOX Rep 2, S46

value: ERKi 62.5nM


title: PBMCs, S98

city: Zhengzhou

first: Youhua

last: Yuan

state: Henan

address: The People's Hospital, Zhengzhou University

department: Clinical Microbiology

institute: Henan Provincial People's Hospital

data_processing:
The raw sequencing data were evaluated by FAST-QC including quality distribution of nucleotides, position specific sequencing quality, GC content, the proportion of PCR duplication, Wmer frequency etc. Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
Reads were mapped to human genome assembly GRCh37 using Tophatv2.0.13 with default parameters.
HTSeq v0.5.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

source_name: Peripheral blood

growth_protocol: PBMC were maintained in RPMI medium supplemented with 10% heat-inactivated fetal bovin serum

extract_protocol:
RNA was extracted from PBMC using TRIzol reagent (Life Technologies, Grand Island, NY).
1 ug of total RNA for the construction of  RNA libraries. RNA libraries were prepared for sequencing using  Illumina TruSeq™ RNA sample preparation Kit (Illumina, San Diego, CA)  according to standard protocols.

treatment_protocol: After isolation, PBMC were cultured in RPMI treated with M. leprae whole cell sonicate antigen(10µg/ml) for 12h.

value: Peripheral blood

value: EC (endemic controls)

value: PBMC

value: stimulated with M. leprae whole cell sonicate antigen(10µg/ml)


title: PBMCs, S87


title: H3K27ac_nHSC_None_6

source_name: Haematopoietic stem cells

value: Haematopoietic stem cells

value: H3K27ac (abcam; ab4729)

value: Unstimulated

value: Control


title: RPE cells, ERKi 15.6nM 4h DOX Rep 2, S45

value: Retinal Pigment Epithelial cells

value: ERKi 15.6nM

value: 4h post-treatment


title: mESC_CUT&RUN_Degron_RAD21_rep1

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: ES-D3 (ATCC CRL 1934)

value: Treated with 500nM of dTAG-13 for 4.5 hours

value: CUT&RUN

value: RAD21 (Ab992, Abcam)


title: PBMCs, S83


title: mESC_CUT&RUN_DMSO_RAD21_rep3

value: Untreated control (DMSO added to a final concentration 0.1%)


title: RPE cells, ERKi 3.9nM 4h DOX Rep 2, S44

value: ERKi 3.9nM


title: H3K27ac_nHSC_None_4


title: PBMCs, S53

value: Peripheral blood

value: HHC (house hold contacts)


title: mESC_CUT&RUN_DMSO_RAD21_rep1


title: RPE cells, ERKi 250nM 4h DOX Rep 2, S47

value: ERKi 250nM


title: RPE cells, ERKi 0nM 4h DOX Rep 2, S43

value: ERKi 0nM


title: mESC_CUT&RUN_Degron_H3K27ac_rep3

value: H3K27ac (Ab4729, Abcam)


title: H3K27ac_nHSC_None_3

value: Haematopoietic stem cells

value: H3K27ac (abcam; ab4729)

value: Unstimulated


title: mESC_CUT&RUN_Degron_H3K27ac_rep2


title: H3K27ac_nHSC_None_1

value: Control


title: PBMCs, S95

value: EC (endemic controls)

value: PBMC

value: stimulated with M. leprae whole cell sonicate antigen(10µg/ml)


title: RPE cells, ERKi 250nM 4h DOX Rep 1, S41

value: Retinal Pigment Epithelial cells

value: 4h post-treatment


title: H3K27ac_nHSC_None_2


title: RPE cells, ERKi 1000nM 4h DOX Rep 1, S42

value: ERKi 1000nM


title: PBMCs, S35


title: mESC_CUT&RUN_DMSO_H3K27ac_rep3

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: ES-D3 (ATCC CRL 1934)

value: Untreated control (DMSO added to a final concentration 0.1%)

value: CUT&RUN


title: PBMCs, S33

value: Peripheral blood

value: HHC (house hold contacts)


title: RPE cells, ERKi 62.5nM 4h DOX Rep 1, S40

value: ERKi 62.5nM


title: PBMCs, S79

value: MB (multibacillary patients)


title: H3K27ac_nBMDM_ctrl_6

value: Bone marrow-derived macrophages

value: H3K27ac (abcam; ab4729)


title: PBMCs, S30


title: mESC_CUT&RUN_DMSO_H3K27ac_rep2

value: H3K27ac (Ab4729, Abcam)


title: H3K27ac_nHSC_None_5

value: Haematopoietic stem cells

value: Unstimulated

value: Control


title: RPE cells, ERKi 3.9nM 4h DOX Rep 1, S38

value: Retinal Pigment Epithelial cells

value: ERKi 3.9nM


title: mESC_CUT&RUN_Degron_NIPBL_rep3

value: Treated with 500nM of dTAG-13 for 4.5 hours

value: NIPBL (A301-779A (Lot 4), Bethyl Laboratories)


title: RPE cells, ERKi 15.6nM 4h DOX Rep 1, S39

value: ERKi 15.6nM

value: 4h post-treatment


title: H3K27ac_nBMDM_ctrl_5


title: PBMCs, S25

value: PBMC

value: stimulated with M. leprae whole cell sonicate antigen(10µg/ml)


title: H3K27ac_nBMDM_ctrl_4


title: mESC_CUT&RUN_Degron_NIPBL_rep2

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: ES-D3 (ATCC CRL 1934)

value: CUT&RUN


title: PBMCs, S59

value: Peripheral blood

value: MB (multibacillary patients)


title: PBMCs, S42

value: HHC (house hold contacts)


title: RPE cells, ERKi 0nM 4h DOX Rep 1, S37

value: ERKi 0nM


title: H3K27ac_nBMDM_ctrl_3

value: Bone marrow-derived macrophages

value: H3K27ac (abcam; ab4729)

value: Unstimulated


title: PBMCs, S54

value: PB (paucibacillary patients)


title: mESC_CUT&RUN_Degron_NIPBL_rep1

value: Treated with 500nM of dTAG-13 for 4.5 hours


title: RPE cells, ERKi 1000nM 2h DOX Rep 2, S36

value: Retinal Pigment Epithelial cells

value: ERKi 1000nM

value: 2h post-treatment


title: H3K27ac_nBMDM_ctrl_2

value: Control


title: RPE cells, ERKi 250nM 2h DOX Rep 2, S35

value: ERKi 250nM


title: mESC_CUT&RUN_DMSO_NIPBL_rep3

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: Untreated control (DMSO added to a final concentration 0.1%)

value: NIPBL (A301-779A (Lot 4), Bethyl Laboratories)


title: PBMCs, S52

value: Peripheral blood

value: PBMC

value: stimulated with M. leprae whole cell sonicate antigen(10µg/ml)


title: PBMCs, S26


title: H3K27ac_nBMDM_M1_6

value: LPS + IFN-gamma


title: mESC_CUT&RUN_DMSO_NIPBL_rep2

value: ES-D3 (ATCC CRL 1934)

value: CUT&RUN


title: mESC_CUT&RUN_DMSO_NIPBL_rep1


title: H3K27ac_nBMDM_M1_5

value: Bone marrow-derived macrophages

value: H3K27ac (abcam; ab4729)


title: H3K27ac_nBMDM_M1_4


title: RPE cells, ERKi 3.9nM 2h DOX Rep 2, S32

value: ERKi 3.9nM


title: H3K27ac_nBMDM_M1_3


title: mESC_CUT&RUN_Degron_BRD4_rep2

value: Treated with 500nM of dTAG-13 for 4.5 hours

value: BRD4 (A301-985A100 (Lot 7), Bethyl Laboratories)


title: mESC_CUT&RUN_Degron_BRD4_rep1


title: RPE cells, ERKi 250nM 2h DOX Rep 1, S29

value: Retinal Pigment Epithelial cells

value: 2h post-treatment


title: mESC_CUT&RUN_DMSO_BRD4_rep2


title: RPE cells, ERKi 1000nM 2h DOX Rep 1, S30

value: ERKi 1000nM


title: RPE cells, ERKi 0nM 2h DOX Rep 2, S31

value: ERKi 0nM


title: H3K27ac_nBMDM_M1_1

value: Control


title: RPE cells, ERKi 62.5nM 2h DOX Rep 1, S28

value: ERKi 62.5nM


title: H3K27ac_nBMDM_ctrl_1

value: Unstimulated


title: H3K27ac_dHSC_None_6

value: Haematopoietic stem cells

value: Diabetic


title: mESC_CUT&RUN_DMSO_BRD4_rep3

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: Untreated control (DMSO added to a final concentration 0.1%)


title: RPE cells, ERKi 62.5nM 2h DOX Rep 2, S34


title: mESC_CUT&RUN_DMSO_BRD4_rep1

value: ES-D3 (ATCC CRL 1934)

value: CUT&RUN


title: RPE cells, ERKi 3.9nM 2h DOX Rep 1, S26


title: H3K27ac_dHSC_None_4

value: H3K27ac (abcam; ab4729)


title: RPE cells, ERKi 15.6nM 2h DOX Rep 1, S27

value: ERKi 15.6nM


title: mESC_CUT&RUN_Degron_BRD4_rep3

value: Treated with 500nM of dTAG-13 for 4.5 hours


title: Naive-59-2

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Avenue South, Suite 276/11

institute: University of Alabama at Birmingham

data_processing:
Trimming: TrimGalore v.0.4.4 with settings: phred33 scores, paired, nextera adapters
Alignment: STAR aligner v.2.5.2a with settings: mm10, outputFilterMultimapNmax = 20, alignSJoverhangMin = 8, alignSJDBoverhangMin = 1, outFilterMismatchNmax = 999, alignIntronMin = 20, alignIntronMax = 1000000, alignMatesGapMax = 1000000
Counting: Htseq-count v0.6.1p1 with settings: unstranded and using mm10 annotations
edgeR for downstream analysis to find differentially expressed genes among the sample groups
Genome_build: mm10
Supplementary_files_format_and_content: Jenkins_2021_RNAseq_count_table.txt contains the raw count data for every sample

source_name: OTI cells

extract_protocol:
RNA was isolated using the Single Cell RNA Purification kit (Norgen)
RNA libraries were prepared for sequencing using standard Illumina protocols. All libraries were prepared at Genewiz.
Ultra-Low Input RNA-Seq

tag: mouse pool

value: OTI cells

tag: cell sorting

value: naive OTI cells


title: RPE cells, ERKi 15.6nM 2h DOX Rep 2, S33

tag: cell type

value: Retinal Pigment Epithelial cells

tag: time

value: 2h post-treatment


title: PBMCs, HJ

value: Peripheral blood

value: PB (paucibacillary patients)

value: PBMC

value: stimulated with M. leprae whole cell sonicate antigen(10µg/ml)


title: RPE cells, ERKi 1000nM 1h DOX Rep 2, S24

value: ERKi 1000nM

value: 1h post-treatment


title: H3K27ac_dHSC_None_3

value: Haematopoietic stem cells

tag: strain

tag: chip antibody

value: Unstimulated

value: Diabetic


title: H3K27ac_dHSC_None_2

tag: treatment

tag: disease state


title: H3K27ac_nBMDM_M1_2

value: Bone marrow-derived macrophages

value: LPS + IFN-gamma

value: Control


title: Naive-59-1


title: RPE cells, ERKi 250nM 1h DOX Rep 2, S23

value: ERKi 250nM


title: H3K27ac_dHSC_None_1

value: H3K27ac (abcam; ab4729)


title: SP-P-51

value: OTI cells

value: spleen primed OTI cells


title: SP-P-59


title: RPE cells, ERKi 62.5nM 1h DOX Rep 2, S22

value: Retinal Pigment Epithelial cells

value: ERKi 62.5nM


title: RPE cells, ERKi 15.6nM 1h DOX Rep 2, S21

value: ERKi 15.6nM


title: H3K27ac_dHSC_None_5


title: H3K27ac_dBMDM_ctrl_6


title: Naive-59-3

value: naive OTI cells


title: LN-P-51

value: mediastinal LN primed OTI cells


title: LN-P-59


title: H3K27ac_dBMDM_ctrl_5


title: RPE cells, ERKi 0nM 2h DOX Rep 1, S25

value: ERKi 0nM

value: 2h post-treatment


title: LN-P-40


title: H3K27ac_dBMDM_ctrl_2


title: RPE cells, ERKi 3.9nM 1h DOX Rep 2, S20

value: ERKi 3.9nM

value: 1h post-treatment


title: background_sham_rep2

city: Cambridge

first: Matthew

middle: C

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
Laser capture micro-dissection of GFP- background cells and RNA-seq
RS2

data_processing: mRNA reads were mapped to the mouse genome (mm10) using STAR [Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013)]. Differentially expressed genes were quantified using DESeq2 [Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014)].

source_name: Cardiac cells

extract_protocol: Pitx2cCreERT2/+;mTmGmouse heartswere collected at 10 days afterneonatalLAD-O or Sham surgery.Tissue were processed and embedded intotissue-plusO.C.T.without fixation. 10 micron sections wereprepared, slides dehydtratedand loadedonto a Zeiss laser capture microscope(PALM Micro Beam,ZEISS, Jena, Germany). GFP positive tissue were captured and collected into lysis buffer. Total RNA wasprepared using PicoPure RNA isolation kit (Applied Biosystems, Foster City, CA, US).RNA-Seq librarieswere prepared according to the manufacturer’s guidelines (Illumina, San Diego, CA, US).

value: Cardiac cells

tag: strain/genotype

tag: manipulation

value: Sham

tag: age


title: RPE cells, ERKi 0nM 1h DOX Rep 2, S19

tag: doxycycline induction of brafv600e


title: H3K27ac_dBMDM_M1_6

value: Bone marrow-derived macrophages

value: LPS + IFN-gamma

value: Diabetic


title: RPE cells, ERKi 1000nM 1h DOX Rep 1, S18

value: ERKi 1000nM


title: RPE cells, ERKi 250nM 1h DOX Rep 1, S17

value: ERKi 250nM


title: H3K27ac_dBMDM_ctrl_1

value: H3K27ac (abcam; ab4729)

value: Unstimulated


title: background_sham_rep1

description:
Laser capture micro-dissection of GFP- background cells and RNA-seq
RS1


title: H3K27ac_dBMDM_M1_5


title: RPE cells, ERKi 15.6nM 1h DOX Rep 1, S15

value: Retinal Pigment Epithelial cells


title: RPE cells, ERKi 62.5nM 1h DOX Rep 1, S16

value: ERKi 62.5nM


title: background_LAD_rep2

description:
Laser capture micro-dissection of GFP- background cells and RNA-seq
RL2

value: LAD


title: background_LAD_rep1

description:
Laser capture micro-dissection of GFP- background cells and RNA-seq
RL1


title: H3K27ac_dBMDM_M1_4


title: RPE cells, ERKi 3.9nM 1h DOX Rep 1, S14


title: H3K27ac_dBMDM_M1_3


title: SP-P-40

value: OTI cells

value: spleen primed OTI cells


title: CTRL_CTRL_IFNa_D4_3

city: Biberach a.d. Riß

first: Anna-Maria

last: Herzner

address: Birkendorfer Str 65

institute: Boehringer Ingelheim

description:
LIB1114370_SAM24343755
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

data_processing:
Reads were aligned to GrCH37 v13 using STAR (V2.5.4a) with the basic two-pass mode allowing for a maximum number of multiple alignments of 1000 and 999 mismatches per read (--outFilterMultimapNmax 1000 --outFilterMismatchNmax 999), however 10% mismatches per read pair using --outFilterMismatchNoverReadLmax 0.1 to increase the detection of A-to-I editing sites. In addition, we allowed introns to be 20-1000000 nt and a 1000000 nt distance between read pair mates.
Aligned reads were summarized to gene level using the R Rsubread package featureCounts function in paired end mode (isPairedEnd=TRUE) based on the GrCH37 gencode V19 GTF annotation, using the default exons as features for counting and genes as meta-features (GTF.featureType="exon" and GTF.attrType="gene_id"). We only allowed uniquely mapping reads by setting the read-quality filter to 255 (minMQS=255).
To quantify introns, we first extracted intron ranges from appris annotation based on https://davetang.org/muse/2013/01/18/defining-genomic-regions/ from the GrCH37 gencode V19 GTF file using awk to filter for appris annotated transcripts (awk ’BEGIN’{OFS=”\t”;} /appris/ {print}’). Exons were extracted from the appris annotated transcripts into bed format using awk ('BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5,$10,$3}'), sorted using bedtools2 sortBed and overlapping exons merged with bedtools2 mergeBed. Next, unique genes of appris-annotated transcripts were extracted using awk as described above, their annotations extracted from the original GTF file, sorted and the merged appris-annotated exons subtracted from genes using bedtools2 subtractBed to yield introns delineated from appris annotated transcripts, saved in bed format for later quantification.
Reads mapping to intron- and editing-cluster-rich-region- features were counted using the R Rsubread package featureCounts function after converting bed files to SAF format, as described for gene quantification, not using the meta-feature flag.
Editing sites were discovered using the SAILOR pipeline (https://github.com/YeoLab/sailor). Total or G counts (indicating adenosine-to-inosine editing) were extracted from *.sorted.rmdup.readfiltered.bam intermediate files generated by the SAILOR pipeline using flags -B -d10000000 -t DPR,INFO/DPR,DP4 -uf, using the -l flag with a bed annotation of the primary selection of editing sites. INFO/DPR counts were used to determine nucleotide counts. T and C counts for sense or A and G counts for antisense reads, respectively, were considered sequencing errors and added to reference counts.
Genome_build: GrCH37 v13
Supplementary_files_format_and_content: Raw gene counts, comma separated values
Supplementary_files_format_and_content: Raw intron counts, comma separated values
Supplementary_files_format_and_content: Raw counts of regions rich in RNA editing clusters (ECR), comma separated values
Supplementary_files_format_and_content: Raw G counts at unfiltered, putative editing sites, comma separated values
Supplementary_files_format_and_content: Raw total (G+H) counts at unfiltered, putative editing sites, comma separated values

growth_protocol: THP-1 were grown in RPMI, 10% FBS, 1x glutamax and 1x Pen/Strep at 37°C and 5% CO2

extract_protocol:
Cells were precipitated by centrifugation and either directly subjected to RNA extraction or separated into cytosolic vs nuclear/mitochondrial fractions as described in Baghirova et al, 2015 (PMID 26740924), using an increased digitonin concentration of 300 µg/mL. RNA extraction was performed using the Qiagen RNeasy Mini Kit including on-column DNase digest.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold kit (Illumina).

treatment_protocol: THP-1 were nucleofected with 2 ul of each gRNA (annealed crRNA:tracrRNA, idt) as described in Cuellar et al, 2017 (PMID 28887438).

value: monocytic cell line

tag: cell line

tag: background genotype

value: STING deficient, cas9 transgenic

tag: grna #1

tag: grna #2

value: IFN-alpha

tag: time point

value: day 4

tag: compartment

value: whole cell

tag: replicate


title: H3K27ac_dBMDM_ctrl_4

tag: cell type

value: Bone marrow-derived macrophages


title: Purkinje_sham_rep2

description:
Laser capture micro-dissection of GFP+ Purkinke cells and RNA-seq
PS2

source_name: Cardiac Purkinje cell

value: Cardiac Purkinje cell

value: Sham


title: CTRL_CTRL_IFNa_D4_2

description:
LIB1114369_SAM24343754
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: H3K27ac_dBMDM_M1_2

value: LPS + IFN-gamma

value: Diabetic


title: RPE cells, ERKi 0nM 0h Rep 2, S12

value: ERKi 0nM

tag: time

value: 0h post-treatment


title: Purkinje_sham_rep1

description:
Laser capture micro-dissection of GFP+ Purkinke cells and RNA-seq
PS1


title: CTRL_CTRL_IFNa_D4_1

description:
LIB1114368_SAM24343753
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv


title: H3K27ac_dBMDM_M1_1

tag: strain

value: H3K27ac (abcam; ab4729)


title: RPE cells, ERKi 0nM 0h Rep 2, S11

value: Retinal Pigment Epithelial cells


title: mESC_Hi-C_Degron_rep2

data_processing:
Paired-end reads were mapped and processed using HiC-Pro v2.11.1 as previously described (Servant et al., 2015) with standard parameters. Data was mapped to the mouse mm10 genome.
allValidPairs files were generated using HiC-Pro v2.11.1 for the individual and pooled samples with std parameters.
Genome_build: mm10

extract_protocol:
DNA extraction was carried out using standard protocol and samples were processed according to the manufacturers’ instructions using the Arima Hi-C Kit (Arima Genomics #A410030)
Illumina compatible libraries were prepared using a modified version of the KAPA Hyper Prep Kit (KAPA Biosystems #07962347001). Quality control steps were performed to assess the fraction of proximally ligated DNA labeled with biotin, and the optimal number of PCR reactions needed to make libraries. The libraries were loaded onto an Illumina S2 flow cell (Illumina, USA) and paired end sequencing (2 x 50bp).

tag: knock-in line

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

tag: parental line

value: ES-D3 (ATCC CRL 1934)

value: Treated with 500nM of dTAG-13 for 4.5 hours

tag: technique

value: In-Situ Hi-C


title: Purkinje_LAD_rep2

description:
Laser capture micro-dissection of GFP+ Purkinke cells and RNA-seq
PL2

tag: strain/genotype

value: LAD


title: GFP_CTRL_D5_3

description:
LIB1114367_SAM24343752
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

value: GFP

tag: treatment

value: medium

value: day 5


title: RA_Total5

city: Leeds

first: Julie

last: Aspden

address: Woodhouse

department: FBS

institute: University of Leeds

data_processing:
For polysome-associated RNA-seq and Ribo-seq (bed files): Adaptor sequences were trimmed using Cutadapt (v.2.8) with minimum read length of 25bp, and untrimmed outputs retained for RNA-seq reads.
Low-quality reads (score <20 for 10% or more of read) were discarded using FASTQ Quality Filter, FASTX-Toolkit (v.0.0.14).
Reads aligning to rRNA and tRNA sequences were discarded using Bowtie 2 (v2.3.5) and one base was removed from the 3' end of reads.
Unaligned Ribo-seq reads and RNA-seq reads were aligned to the Human reference genome (Gencode v30, GRCh38.p12) using the split-aware aligner STAR (v2.6.1b). The STAR genome index was built with an sjdbOverhang of 73.
Alignments flagged as secondary alignment were filtered out with samtools (v1.9), ensuring 1 genomic position per aligned read. "samtools view -b -F 0X100"
RiboTaper was applied to these data  to find ORFs and quantify the p-site positions per ORF (reported in score column of processed data bed file).
For total and polysome-associated RNA-seq: RNA-seq reads were trimmed with Cutadapt.
Low-quality reads (score <20 for 10% or more of read) were discarded using FASTQ Quality Filter, FASTX-Toolkit.
Filtered reads were mapped to the human reference genome (lncRNA GENCODE added to mRNA annotation from UCSC), assembly h19 with Rsubread and uniquely mapped reads reported.
BAM files were sorted and indexed with samtools.
Summarised read counts were caluclated using featureCounts, and RPKM calculated.
Differential expression analysis was carried out using DESeq2 between Control and RA Polysome associated RNA-seq, Control and RA Total RNA-seq, Control Total and Polysome associated RNA-seq, and RA Total and Polysome RNA-seq. The cut-offs  padj < 0.05 and the absolute value of log2FoldChange > 1 were used.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files of open reading frames determined by RiboTaper pipeline, xlsx file of DESeq2 results.

source_name: human neuroblastoma

growth_protocol: Human neuroblastoma SH-SY5Y cells, were cultured in Dulbecco’s Modified Eagle Medium (DMEM 4.5g/L Glucose with L-Glutamine) supplemented with 1% (v/v) Penicillin/Streptomycin and 10% Fetal Bovine Serum (FBS) at 37oC, 5% CO2.

extract_protocol:
RNA purification from RNaseI footprinted samples was performed by Trizol RNA extraction. RNA purification from polysome fractions  was  performed  by  isopropanol  precipitation,  followed  by  TURBO  DNase  treatment, acidic phenol/chloroform RNA purification and ethanol precipitation at -80oC overnight. RNA concentration was determined by Nano-drop 2000 software. Two rounds of polyA selection from polysome fractions were performed using oligo (dT) Dynabeads PolyA RNA  was  fragmented  by  alkaline  hydrolysis. 28–34  nt  ribosome  footprints  and  50–80  nt  mRNA fragments were gel purified in 10% (w/v) polyacrylamide-TBE-Urea gel. Ribosome footprints were subjected to rRNA depletion (Illumina RiboZero rRNA removal kit).
5’ stranded libraries were constructed using NEB Next Multiplex Small RNA Library Prep. Resulting cDNA was PCR amplified and gel purified prior to sequencing. Libraries were subjected to 75bp single end RNA Sequsing NextSeq 500 Illumina sequencer,High OutputKit v2.5 (75 Cycles)(Next Generation Sequencing Facility, Faculty of Medicine, University of Leeds).

treatment_protocol: Neuronal differentiation was performed using retinoic acid (RA) at passage 4. All trans Retinoic Acid (RA, Sigma) was added to cells 24h after plating, at final concentration of 30μM.

value: Retinoic acid (final conc. 30μM)


title: mESC_Hi-C_Degron_rep1


title: Purkinje_LAD_rep1

description:
Laser capture micro-dissection of GFP+ Purkinke cells and RNA-seq
PL1

value: Cardiac Purkinje cell

tag: manipulation

tag: age


title: RPE cells, ERKi 0nM 0h Rep 2, S10

tag: doxycycline induction of brafv600e


title: mESC_Hi-C_DMSO_rep2

value: Untreated control (DMSO added to a final concentration 0.1%)


title: RPE cells, ERKi 0nM 0h Rep 2, S9

value: ERKi 0nM


title: GFP_CTRL_D5_1

description:
LIB1114365_SAM24343750
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell line

tag: background genotype

value: whole cell


title: GFP_CTRL_D5_2

description:
LIB1114366_SAM24343751
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: grna #1

tag: grna #2


title: RA_Total4


title: RA_Total3


title: GFP_CTRL_D4_2

description:
LIB1114363_SAM24343748
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: time point

value: day 4

tag: compartment


title: GFP_CTRL_D4_3

description:
LIB1114364_SAM24343749
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell type

tag: replicate


title: RPE cells, ERKi 0nM 0h Rep 2, S8

value: Retinal Pigment Epithelial cells

tag: time

value: 0h post-treatment


title: mESC_Hi-C_DMSO_rep1

tag: knock-in line

value: FKBP12F36V tag knocked in at the BRD4 locus right after the ATG site

value: ES-D3 (ATCC CRL 1934)

tag: strain


title: RPE cells, ERKi 0nM 0h Rep 2, S7


title: RPE cells, ERKi 0nM 1h DOX Rep 1, S13

value: 1h post-treatment


title: RPE cells, ERKi 0nM 0h Rep 1, S6


title: Control_Total5

value: Control (DMSO)


title: 11601_BAT

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

data_processing:
The pool was sequenced for 35 million reads using an Illumina NovaSeq6000 instrument and a PE100 sequencing protocol.
Data was processed using the nf-core/rnaseq v1.4 pipeline.
Alignment to reference genome was done using STAR vSTAR_2.6.1d.
Gene abundance estimation was done using Salmon 0.14.1.
Differential gene expression analysis of IP/Input normalised gene counts was carried out using DESeq2 1.26.0.
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012.
Supplementary_files_format_and_content: almon_merged_gene_counts.csv: Comma-separated text file includes raw counts.
Supplementary_files_format_and_content: salmon_merged_gene_tpm.csv: Comma-separated text file includes TPM counts.
Supplementary_files_format_and_content: bat_deseq2_diff.xlsx: Excel spreadsheet containing mean expression levels per group, fold change and significance level for each annotated gene.

source_name: BAT

growth_protocol: Male mice were fed with a HFD since 4 to 18 wk old.

extract_protocol:
Tissue was frozen at -80°C until the RNA was extracted with DNase digestion using the RNeasyR Lipid Tissue Mini Kit and RNase-Free DNase Set (Qiagen), following the user’s manual. RNA integrity was detected with the Agilent RNA 6000 Nano Kit (5067-1511, Agilent Technologies) and the Agilent 2100 Bioanalyzer.
RNA libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

treatment_protocol: All mice were rapidly decapitated and tissue was taken between 14-16h at the end of hyperinsulinemic-euglycemic clamp experiments.

tag: genotype

tag: Sex

value: Male

tag: tissue

value: BAT

tag: diet

value: HFD


title: GFP_CTRL_D4_1

description:
LIB1114362_SAM24343747
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

value: GFP

tag: treatment

value: medium


title: GFP_CTRL_D3_3

description:
LIB1114361_SAM24343746
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: day 3


title: 11243_BAT


title: RPE cells, ERKi 0nM 0h Rep 1, S5

value: ERKi 0nM

tag: doxycycline induction of brafv600e


title: 11613_BAT


title: Control_Total3


title: HeLa_Rpb6_WT_rep3

city: Yokohama

first: Yuki

last: Yamaguchi

state: Kanagawa

address: 4259 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

data_processing:
The obtained reads were analyzed by using CLC Genomics Workbench version 11.0 (Qiagen).
Genome_build: GRCh38
Supplementary_files_format_and_content: These xlsx files include TPM values for each Sample.

source_name: cervix adenocarcinoma

extract_protocol:
Total RNA was extracted by using Sepasol-RNA I Super G (Nacalai Tesque) and further purified using an RNeasy Mini Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: HeLa

tag: genotype/variation

value: wild-type (WT) exogenous RPB6


title: RPE cells, ERKi 0nM 0h Rep 1, S4

data_processing:
Reads were processed to counts using the bcbio-Nextgen toolkit (https://github.com/chapmanb/bcbio-nextgen).
Reads were trimmed and clipped for quality control in cutadapt v2.3
High-quality reads were then aligned to the human assembly and gene annotation GRCh38.97 using Hisat2 v2.1.0
Gene-level transcript-counts were calculated using HTseq-count v0.9.1. Only data from genes annotated as protein-coding according to annotation from GRCh38.97 were kept for further analysis.
Differential expression of genes was analysed using DESeq2.
Genome_build: GRCh38.97
Supplementary_files_format_and_content: raw_counts.csv.gz: CSV file of raw gene counts of all 96 samples with Ensembl gene IDs
Supplementary_files_format_and_content: normalized_counts.csv: CSV file of gene counts normalized for library size using DESeq2 size factors (normalized) and variance stabilized counts using the vsn R package (variance_stabilized)
Supplementary_files_format_and_content: deseq_pairwise_results.csv.gz: CSV file of the differential expression results from DESeq2 comparing all experimental conditions against the non-treated 0h condition

extract_protocol:
Cells were lysed with 600µl Trizol per well and total RNA was prepared using Direct-zol-96 RNA Kits according to the manufacturer's protocol. Sample concentrations were determined by Nanodrop and RNA quality was assessed on a subset of samples by Bioanalyzer (Agilent); all samples scored RINs of > 9.0.
RNA sequencing library preparation was performed with the High Throughput TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol at half reaction volume. Input for each sample consisted of 300-500ng of RNA and 5ul of 1:500 diluted ERCC spike-in mix 1 (Ambion). Libraries were amplified for 12 cycles during the final amplification step. Libraries were quantified using the Qubit dsDNA HS assay (Thermo Fisher Scientific). Library size and quality were spot checked for a subset of samples by Bioanalyzer (Agilent). The average size of cDNA fragments in the libraries was 370 base pairs. Libraries were pooled at equimolar concentrations then the pool was quantitated using the KAPA library quantification kit (KAPA Biosystems). Libraries were sequenced single end 114 base pairs using NovaSeq_SP full flow cell (Illumina) at the Bauer Core Facility (Harvard University).

value: Retinal Pigment Epithelial cells


title: 11708_BAT


title: GFP_CTRL_D3_2

description:
LIB1114360_SAM24343745
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: background genotype

tag: grna #1

value: whole cell


title: 11560_BAT

value: CTRL


title: RPE cells, ERKi 0nM 0h Rep 1, S3

value: 0h post-treatment


title: HeLa_Rpb6_WT_rep2


title: 11563_BAT


title: HeLa_Rpb6_WT_rep1


title: RPE cells, ERKi 0nM 0h Rep 1, S2


title: GFP_CTRL_D3_1

description:
LIB1114359_SAM24343744
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: grna #2

tag: time point


title: hnRNPC_ADAR_D5_3

description:
LIB1114340_SAM24343725
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell type

value: hnRNPC

value: ADAR

value: day 5

tag: compartment


title: RPE cells, ERKi 0nM 0h Rep 1, S1

tag: time


title: 11253_BAT

value: Male

value: BAT


title: 10684_BAT

data_processing:
The pool was sequenced for 35 million reads using an Illumina NovaSeq6000 instrument and a PE100 sequencing protocol.
Data was processed using the nf-core/rnaseq v1.4 pipeline.
Alignment to reference genome was done using STAR vSTAR_2.6.1d.
Gene abundance estimation was done using Salmon 0.14.1.
Differential gene expression analysis of IP/Input normalised gene counts was carried out using DESeq2 1.26.0.
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012.
Supplementary_files_format_and_content: salmon_merged_gene_counts.csv: Comma-separated text file includes raw counts.
Supplementary_files_format_and_content: salmon_merged_gene_tpm.csv: Comma-separated text file includes TPM counts.
Supplementary_files_format_and_content: bat_deseq2_diff.xlsx: Excel spreadsheet containing mean expression levels per group, fold change and significance level for each annotated gene.

value: HFD


title: hnRNPC_ADAR_D5_2

description:
LIB1114339_SAM24343724
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

tag: replicate


title: hnRNPC_ADAR_D5_1

description:
LIB1114338_SAM24343723
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: medium


title: HeLa_Rpb6_F13A_rep3

value: F13A exogenous RPB6


title: Control_Total4

value: Control (DMSO)


title: HeLa_Rpb6_F13A_rep2

value: HeLa


title: HCT116-SH

city: WuHan

first: Meng

last: Xu

state: Hubei

address: No.115 Donghu Road, Wuchang District

institute: Wuhan university

description: HCT116-processed data files.txt

data_processing:
They were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/) using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs or FPKMs were calculated.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina).

value: colorectal cancer cells

value: AHNAK2 knock down


title: HCT116-SC

description: HCT116-processed data files.txt

value: control


title: HeLa_Rpb6_F13A_rep1


title: MDA-MB-231-SC

description: MDA-MB-231-processed data files.txt

value: breast cancer  cells


title: single-cell RNAseq data from 10-week-old C57BL/6 mice

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each cell

source_name: Testicular immune cells

extract_protocol:
Testicular immune cell were sorted CD45+ cells with BD FACS
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: Testicular immune cells from testis

tag: strain

tag: age


title: MDA-MB-231-SH

description: MDA-MB-231-processed data files.txt

tag: genotype


title: HeLa_Rpb6_F8A_F13A_rep3

value: F8A-F13A exogenous RPB6


title: mrc1D_rad9_IAA brdu rep2

city: New York

first: Xu

last: Hua

state: New York

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Library strategy: BrdU-Seq
Reads were mapped using bowtie2.
Read coverage in each bin was calculated using Deeptools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

organism: Saccharomyces cerevisiae

source_name: mrc1D_rad9_IAA brdu

growth_protocol: Yeast cells grown to OD600=0.4-0.5 in yeast extract peptone + 2% dextrose (YPD) were synchronized with a-factor (5 mg/ml, synthesized by EZBiolab) for 1.5 hr at 25°C, adding additional 5 mg/ml a-factor after 1.5 hr. G1-arrested cells were released into YPD medium at 30°C containing 400 mg/ml bromodeoxyuridine (BrdU, Sigma B5002) and 0.2M hydroxyurea (HU, Chem-Impex 24533). 45 minutes after release into S phase at 30°C, cell fixation was performed with 1% paraformaldehyde for 20 minutes at room temperature followed by the quenching with 0.125M glycine for 5 minutes at room temperature.

extract_protocol:
Input DNA obtained from the Chelex-100 extraction was used for BrdU immunoprecipitation. Briefly, DNA was denatured at 95°C for 5 minutes followed by incubation in an ice-water bath for 5 minutes. Samples were then diluted 10 fold with BrdU IP buffer solution (1XPBS, 0.0625% Triton X-100(v/v), 6.7 mg/mL Escherichia coli tRNA, 0.40mL/mL BrdU antibody (BD Bioscience)). After a 2 hr incubation at 4°C, 20 mL of protein G Sepharose beads (GE Healthcare) were added followed by an additional 1 hr incubation at 4°C. Protein G beads were extensively washed and DNA was eluted with 100 mL Tris-EDTA buffer containing 1% SDS at 65°C for 15 minutes.
The eluted DNA was purified with Minelute PCR kit (QIAGEN) and sequenced after  ssDNA library preparation using the Accel-NGS 1S Plus DNA library kit (Swift BioSciences). Samples were pooled and sequenced using paired-end sequencing on Illumina platforms at Columbia University Genome Center.

treatment_protocol: ChIP-ssSeq and BrdU-IP-ssSeq experiments were performed as described previously (Gan et al., 2017)

tag: experiment

value: BrdU

tag: condition

value: with IAA

value: mrc1D rad9

tag: chip antibody

value: BrdU antibody (BD Bioscience)


title: hnRNPC_ADAR_D4_2

description:
LIB1114336_SAM24343721
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: hnRNPC

value: ADAR

tag: treatment

value: day 4

value: whole cell


title: HeLa_Rpb6_F8A_F13A_rep2

tag: cell line


title: Hela-SH

description: Hela-processed data files.txt

source_name: Hela

value: Hela

value: cervical adenocarcinoma cells


title: hnRNPC_ADAR_D4_1

description:
LIB1114335_SAM24343720
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

value: medium


title: HeLa_Rpb6_F8A_F13A_rep1

value: HeLa

tag: genotype/variation


title: hnRNPC_ADAR_D3_3

description:
LIB1114334_SAM24343719
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: background genotype

value: day 3


title: hnRNPC_ADAR_D3_2

description:
LIB1114333_SAM24343718
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: grna #1


title: HeLa_Rpb6_dN20_rep3

value: dN20 exogenous RPB6


title: Hela-SC

description: Hela-processed data files.txt

value: control


title: rad9_AID_IAA brdu rep1

source_name: rad9_AID_IAA brdu

value: BrdU


title: rad9_AID_IAA brdu rep2

value: with IAA


title: hnRNPC_ADAR_D3_1

description:
LIB1114332_SAM24343717
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: grna #2


title: HeLa_Rpb6_dN20_rep2


title: hnRNPC_ADAR_D4_3

description:
LIB1114337_SAM24343722
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: time point


title: HeLa_Rpb6_dN20_rep1


title: mrc1D_rad9_IAA input rep1

source_name: mrc1D_rad9_IAA input

value: Input

value: mrc1D rad9


title: CTRL_ADAR_D5_3

description:
LIB1114331_SAM24343716
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

tag: cell type

value: day 5


title: human fetal skin-17w

city: Guangzhou

first: Yingping

state: Guangdong

address: LuJing Road

institute: Sourthern Medical University

data_processing:
10x cellrange pipeline
Supplementary_files_format_and_content: features
Supplementary_files_format_and_content: matrix
Supplementary_files_format_and_content: barcodes

source_name: Embryo

extract_protocol:
Human fetal skin was dissected and washed with phosphate-buffered saline (PBS; HyClone, Logan, UT, USA: SH30256.01) on ice after removing fat tissue. The skin was cut into small pieces in digestion medium composed of 1 mg/ml collagenase IV (Shanghai Yeasen Biotechnology Co, Shanghai, China; 40510ES60) in RPMI1640 medium (HyClone; C11875500BT), and incubated at 37°C for 40-60 min. The suspension was filtered through a 70-μm cell strainer (BD Biosciences; Franklin Lakes, NJ, USA; 352350) with gently grinding to release cells. After neutralizing the enzymes with FACS buffer (1 PBS with 2% fetal bovine serum), cells were pelleted at 2000 rpm for 7 min at 4°C and resuspended in FACS buffer, and labeled with specific antibodies in FACS buffer for 30 min on ice. After washing, the cells were resuspended in 1 PBS and were confirmed to be living cells by 4’, 6-diamidino-2-phenylindole (DAPI) staining for 5 min. CD45+ cells were sorted on a FACSAria III flow cytometer (BD Biosciences), and data analysis was performed using FlowJo v10 software (TreeStar, Ashland, OR, USA). Fetal skin was processed as described above and cell suspensions were labeled with appropriate antibodies against cell surface markers on ice for 30 min, followed by staining for 5 min with DAPI. Cells were obtained on a Celesta cytometer (BD Biosciences) and analyzed using FlowJo v10 (TreeStar).
Single cells were obtained as gel bead-in-emulsions (GEMs) using the 10× Genomics (Pleasanton, CA, USA) Chromium platform according to the manufacturer’s protocol. Briefly, skin cell suspensions were combined with reverse transcription master mix and loaded onto the 10× Genomics Single Cell 3’ chip, and partitioned into GEMs with gel beads precoated with oligonucleotides containing a poly-dT primer sequence to capture released mRNAs, a 16-bp 10× barcode for cell indexing, and a 10-bp unique molecular identifier (UMI) to distinguish between transcripts. After reverse transcription, barcoded cDNAs for each sample were amplified to generate a sufficient volume for library construction using the Single Cell 3’ Reagent Kit (v2 or v3 chemistry).
Libraries were subjected to 150-bp paired-end sequencing, which was performed by Novogene (Beijing, China) on a NovaSeq 6000 system (Illumina, San Diego, CA, USA).

tag: developmental stage

value: human fetal skin-17w


title: human fetal skin-15w

value: human fetal skin-15w


title: human fetal skin-13w

value: human fetal skin-13w


title: CTRL_ADAR_D5_2

description:
LIB1114330_SAM24343715
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: ADAR

tag: compartment

value: whole cell


title: mrc1D_rad9_IAA brdu rep1

value: BrdU antibody (BD Bioscience)


title: rad9_AID_IAA input rep2

source_name: rad9_AID_IAA input


title: CTRL_ADAR_D5_1

description:
LIB1114329_SAM24343714
part_1_genes_counts.csv
part_1_intron_counts.csv
part_1_ECR_counts.csv
part_1_editingsites_total_counts.csv
part_1_editingsites_G_counts.csv

value: monocytic cell line

value: STING deficient, cas9 transgenic

tag: replicate


title: rad9_AID_IAA input rep1


title: human fetal skin-12w

value: human fetal skin-12w