title: NCI-H23_replicate01


title: NCI-H2405_replicate01

status: Public on Apr 20 2021

type: SRA

city: Freiburg im Breisgau

first: Jagriti

last: Pal

state: Baden Wurttemburg

address: Breisacher Str. 115

department: ZTZ

country: Germany

institute: Universitatsklinikum, Freiburg

library_source: transcriptomic

data_processing:
Quality assessment of the reads was performed using the pipeline EvalRSeq. This checks for rRNA contamination and computes quality metrics.
The adapter sequence was removed and the reads were sorted for a length between 50 and 126 bp.
The reads were uniquely aligned to the human genome GRCh38, allowing for up to two mismatches, using STAR mapper.
Gene expression was determined by calculating FPKM using easyRNASeq and Ensembl version 75.
Genome_build: GRCh38
Supplementary_files_format_and_content: NSCLC_panel_RNAseq_FPKM_all.csv

molecule: total RNA

organism: Homo sapiens

growth_protocol: All cell lines were grown in RPMI-1640 medium containing 10% Fetal Calf Serum and maintained in a humidified chamber at 37°C and 5% CO2.

extract_protocol:
Whole-cell RNA was isolated using RNeasy Mini columns (Qiagen).
Total RNA (5 μg) from each sample were depleted of rRNA using the Ribo-Zero Gold rRNA Removal Kit for human, mouse and rat RNA (Illumina). 20 ng of RNA input was used to generate the RNA-seq libraries using the Agilent Sure Select Strand Specific RNA Library Prep for Illumina Multiplex Sequencing Version C.0 (Illumina).
The single-stranded RNA library was sequenced on a HiSeq 2000 V4 (Illumina) with 150 bp paired-end reads.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: Adenocarcinoma


title: NCI-H2347_replicate03


title: NCI-H23_replicate02


title: NCI-H2347_replicate01


title: NCI-H838_replicate02


title: NCI-H2342_replicate02


title: NCI-H2342_replicate03


title: NCI-H3122_replicate02


title: NCI-H2291_replicate01


title: NCI-H2405_replicate02


title: NCI-H2291_replicate02


title: NCI-H2291_replicate03


title: NCI-H2405_replicate03


title: NCI-H2228_replicate03


title: NCI-H2122_replicate02


title: NCI-H2122_replicate03


title: NCI-H2228_replicate01


title: NCI-H2087_replicate03


title: NCI-H2126_replicate02


title: NCI-H2126_replicate01


title: NCI-H2085_replicate02


title: NCI-H2122_replicate01


title: NCI-H2073_replicate02


title: NCI-H2085_replicate01


title: NCI-H2087_replicate01


title: NCI-H2087_replicate02


title: NCI-H2126_replicate03


title: NCI-H2073_replicate01


title: NCI-H2073_replicate03


title: NCI-H2347_replicate02


title: NCI-H2030_replicate03


title: NCI-H2342_replicate01


title: NCI-H2030_replicate02


title: NCI-H2030_replicate01


title: NCI-H2023_replicate01


title: NCI-H2228_replicate02


title: NCI-H2023_replicate03


title: NCI-H2009_replicate02


title: NCI-H2085_replicate03


title: NCI-H2009_replicate03


title: NCI-H2009_replicate01


title: NCI-H1993_replicate03


title: NCI-H1993_replicate01


title: NCI-H1838_replicate03


title: NCI-H1793_replicate03


title: NCI-H1975_replicate03


title: NCI-H1793_replicate01


title: NCI-H1975_replicate01


title: NCI-H1944_replicate03


title: NCI-H1792_replicate03


title: NCI-H1793_replicate02


title: NCI-H1838_replicate01


title: NCI-H1755_replicate02


title: NCI-H1975_replicate02


title: NCI-H1944_replicate02


title: NCI-H1781_replicate02


title: NCI-H1792_replicate02


title: NCI-H1944_replicate01


title: NCI-H1792_replicate01


title: NCI-H1781_replicate01


title: NCI-H1838_replicate02


title: NCI-H1781_replicate03


title: NCI-H2023_replicate02


title: NCI-H1755_replicate01


title: NCI-H1734_replicate03


title: NCI-H1755_replicate03


title: NCI-H1993_replicate02


title: NCI-H1703_replicate01

value: NSCLC


title: NCI-H1693_replicate03


title: NCI-H1734_replicate02


title: NCI-H1734_replicate01


title: NCI-H1693_replicate02


title: NCI-H1693_replicate01


title: NCI-H1666_replicate01


title: NCI-H1651_replicate03


title: NCI-H1651_replicate02


title: NCI-H1650_replicate02


title: NCI-H1666_replicate03


title: NCI-H1648_replicate03


title: NCI-H1666_replicate02


title: NCI-H1650_replicate03


title: NCI-H1650_replicate01


title: NCI-H1623_replicate03


title: NCI-H1623_replicate01


title: NCI-H1648_replicate02


title: NCI-H1623_replicate02


title: Hi-C data of Rat replicate 2 sequenced by NovaSeq-6000

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Juicer
TADs were identified using DomainCaller
Genome_build: Rnor_6.0, OryCun2.0, Sscrofa11.1, Oar_v3.1, Felis_catus_6.2 and CanFam3.1
Supplementary_files_format_and_content: valid read pairs text files
Supplementary_files_format_and_content: binned raw and normalized 2D contact matrices text files
Supplementary_files_format_and_content: TAD text files

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Adipose tissue

extract_protocol:
1 g adipose tissue were pulverized, and 37% formaldehyde was added to obtain a final concentration of 4% for chromatin cross-linking. Mixture were incubated at room temperature (20–25℃) for 30 minutes, then glycine was added to obtain a final concentration of 0.25 mol/L to quench the formaldehyde. The mixture was then centrifuge at 1,500×g for 10 min at room temperature, and sediment was added the lysis buffer and homogenized. Homogenate was centrifuge at 5,000×g for adipocytes sediment. Nuclei of formaldehyde-fixed adipose tissue were permeabilized and DNA was digested with 200 units of MboI (a 4-cutter restriction enzyme) for one hour at 37 ℃. The restriction fragment overhangs were filled and labbled by biotinylated nucleotides, then ligated in a small volume.
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina NovaSeq 6000 sequencing.

tag: strain

value: SD rat

value: Inguinal white adipose

tag: age

tag: developmental stage

value: Adult

tag: Sex

value: female


title: Hi-C data of Rat replicate 1 sequenced by NovaSeq-6000


title: NCI-H1573_replicate02


title: NCI-H1568_replicate02


title: NCI-H1568_replicate03


title: NCI-H1568_replicate01


title: NCI-H1651_replicate01


title: NCI-H1648_replicate01


title: NCI-H1563_replicate02


title: NCI-H1563_replicate01


title: siTRMT2A replicate 3

type: RNA

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

description:
Gene expression after siTRMT2A transfection
US45102846_257236320006_siTRMT2AR3

hyb_protocol: RNA sample preparation, labeling, hybridization, microarray wash, scanning and feature extraction were performed according to the manufacturer’s protocol: “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labeling” version 6.9.1 from Agilent Technologies”.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HeLa cells transfected with a siTRMT2A

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Cat.11965084), supplemented with 10% of Fetal Bovine Serum (FBS) (Sigma, Cat.F1051) and 1% of Pen-Strep-Glut (Gibco, Cat.15070063). Cells were maintained in culture in an incubator at 37°C with 5% of CO2 and 95% of humidity.

extract_protocol: The total RNA was extracted using the mirVanaTM miRNA Isolation kit (Ambion) or TRIsure™ (Bioline) according to manufacturer´s instructions. The integrity and quantity of each RNA sample were assessed using a Denovix spectrophotometer.

treatment_protocol: A siGenome SMARTpool human siRNA targeting the tRNA-modifying enzyme TRMT2A (siTRMT2A) and a negative control siGenome SMARTpoll human siRNA (siCtrl) were obtained from Dharmacon (ThermoScientific) and reversely transfected into HeLa cells in 24 well plates. SMARTpools are a mixture of 4 siRNAs against the gene of interest provided as a single reagent, increasing potency and specificity. Briefly, 12 µL of 500 nM siRNA duplex in 88 µL of Opti-MEM (Alfagene, Cat.31985062) was added to each well, followed by the addition of 1 µL/well of lipofectamine RNAimax (Invitrogen, Cat.13778075) mix. After an incubation for 30 minutes, 4x104 cells/mL were added to each well in complete growth medium without antibiotics. Finally, cells were incubated for 72 hours at 37°C in a CO2 incubator.

value: HeLa

value: cervical cancer cell


title: siTRMT2A replicate 1

description:
Gene expression after siTRMT2A transfection
US45102846_257236320005_siTRMT2AR1

scan_protocol: RNA sample preparation, labeling, hybridization, microarray wash, scanning and feature extraction were performed according to the manufacturer’s protocol: “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labeling” version 6.9.1 from Agilent Technologies”.


title: at-aerial_part.BSseq.F2.pol4.replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F2 aerial part of nrpd1-3 (Columbia-0)

data_processing:
Bisulfite-seq: The 150 bp long pair-end reads were first quality trimmed by removing the first 5 bases from the 5' end and the last 20 bases from the 3' end. Reads were mapped to the TAIR10 reference genome using Bismark (Version: v0.16.3) in PE mode (--score_min L,0,-0.6). Mapped reads were deduplicated and cytosine methylation values calculated using the Bismark Methylation Extractor.
ChIP-seq: Reads passing a quality control were mapped to the Arabidopsis (TAIR10) genome using Bowtie (Langmead, 2010) in single-end mode allowing for up to two mismatches. Mapped reads were deduplicated and extended to the estimated average length of the genomic fragments (270 bp). Coverage was estimated and normalized to 10 million of reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: ChIP-seq: BedGraph files representing average values of Read per Ten Million Mapped reads for each 50 bp across the genome. Format:  <chromosme><bin_start><bin_end><read_per_ten_million>

organism: Arabidopsis thaliana

source_name: AT aerial part nrpd1-3

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 days and grown under long day conditions.

extract_protocol:
Genomic DNA was extracted using MagJET Plant Genomic DNA Kit (K2764)
Libraries  were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift)

treatment_protocol: no treatment

value: aerial parts

tag: genotype

value: nrpd1-3 (Col-0)


title: siCtrl replicate 2

description:
Gene expression after siCtrl transfection
US45102846_257236320006_siCtrlR2

source_name: HeLa cells transfected with a siCtrl

label_protocol: RNA sample preparation, labeling, hybridization, microarray wash, scanning and feature extraction were performed according to the manufacturer’s protocol: “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labeling” version 6.9.1 from Agilent Technologies”.


title: siTRMT2A replicate 2

description:
Gene expression after siTRMT2A transfection
US45102846_257236320005_siTRMT2AR2


title: NCI-H1573_replicate03


title: NCI-H1437_replicate03


title: at-aerial_part.BSseq.F2.pol4.replicate1

extract_protocol:
Genomic DNA was extracted using MagJET Plant Genomic DNA Kit (K2763)
Libraries  were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift)


title: at-aerial_part.BSseq.wt.replicate2

description: Arabidopsis thaliana aerial part of wt (Columbia-0)

source_name: AT aerial part wt

extract_protocol:
Genomic DNA was extracted using MagJET Plant Genomic DNA Kit (K2762)
Libraries  were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift)

value: wt (Col-0)


title: siCtrl replicate 3

description:
Gene expression after siCtrl transfection
US45102846_257236320005_siCtrlR3


title: NCI-H1437_replicate02


title: at-aerial_part.BSseq.wt.replicate1

extract_protocol:
Genomic DNA was extracted using MagJET Plant Genomic DNA Kit (K2761)
Libraries  were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift)


title: RNA-seq data of Rat replicate 2 sequenced by HiSeq X-ten

description:
TPM.rat.txt
SDC-iwat-pool-2-lnc

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Rnor_6.0, Sscrofa11.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform.

tag: breed


title: NCI-H1437_replicate01


title: NCI-H1573_replicate01


title: RNA-seq data of Rat replicate 1 sequenced by HiSeq X-ten

description:
TPM.rat.txt
SDC-iwat-pool-1-lnc


title: siCtrl replicate 1

description:
Gene expression after siCtrl transfection
US45102846_257236320006_siCtrlR1


title: NCI-H1435_replicate01


title: RNA sequencing Rat-Skeletal-muscle biological replicate 1

description:
Rat-Skeletal-muscle
rat_exp.txt

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Felis_catus_6.2, Gallus_gallus-5.0, CanFam3.1, Cavpor3.0, Mmul_8.0.1, GRCm38.p5, OryCun2.0, Rnor_6.0, Oar_v3.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

source_name: Skeletal muscle

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

value: Skeletal muscle


title: RNA sequencing Rat-Spleen biological replicate 1

description:
Rat-Spleen
rat_exp.txt

source_name: Spleen

value: Spleen


title: NCI-H1435_replicate02


title: NCI-H1563_replicate03


title: NCI-H1395_replicate02


title: at-aerial_part.BSseq.Fi.pol4.replicate1

description: Arabidopsis thaliana Fi aerial part of nrpd1-3 (Columbia-0)

extract_protocol:
Genomic DNA was extracted using MagJET Plant Genomic DNA Kit (K2765)
Libraries  were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift)


title: at-aerial_part.BSseq.Fi.pol4.replicate2

extract_protocol:
Genomic DNA was extracted using MagJET Plant Genomic DNA Kit (K2766)
Libraries  were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift)


title: RNA sequencing Rat-Lung biological replicate 1

description:
Rat-Lung
rat_exp.txt

source_name: Lung


title: NCI-H1435_replicate03


title: RNA sequencing Rat-Liver biological replicate 1

description:
Rat-Liver
rat_exp.txt

source_name: Liver

value: Liver


title: NCI-H1395_replicate03


title: RNA sequencing Rat-Heart biological replicate 1

description:
Rat-Heart
rat_exp.txt

source_name: Heart

value: Heart


title: NCI-H1373_replicate03


title: NCI-H1373_replicate02


title: RNA sequencing Rat-Kidney biological replicate 1

description:
Rat-Kidney
rat_exp.txt

source_name: Kidney

value: Kidney


title: RNA sequencing Rat-Adipose biological replicate 1

description:
Rat-Adipose
rat_exp.txt

source_name: Adipose

value: Adipose


title: NCI-H1373_replicate01

value: Lung

value: Adenocarcinoma


title: NCI-H1299_replicate03

value: NSCLC


title: patient8

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description: bulk RNA sequencing

data_processing:
For bulk RNAseq, the adaptor sequences were first trimmed from sequencing reads by using Trim Galore! with parameters --clip_R1 3, the remaining parameters default. Trimmed reads mapped to ribosomal RNA were removed using Bowtie2 (version 2.3.5). All remaining reads were mapped to the mouse genome mm9 using STAR (version 2.7.0f). Uniquely mapped reads were selected using SAMtools (version 1.9) with mapping quality ≥ 20.
For colon cancer RNAseq, single-end RNA-seq data were mapped to the human genome hg19 using STAR. The gene expression raw counts were calculated using htseq-count in Python.
Genome_build: hg19

source_name: tumor infiltrating stromal cells

extract_protocol:
For RNA seq, total RNA was extracted using Trizol. For m6A seq, total RNA in macrophage was extracted using Trizol and polyadenylated RNA was purified using the Dynabeads mRNA Purification Kit (Invitrogen). Fragment the RNAs into ~100-nucleotide-long fragments by 10X Fragmentation Reagent(Invitrogen) at 94℃ for 45s and stop it using the 10X Stop Solution(Invitrogen). EpiMark N6-methyladenosine enrichment kit (NEB E1610S) was used for m6A immunoprecipitation (m6A-IP) to enrich the m6A marked RNAs followed by RNA extraction by Trizol.
For RNA seq and m6A seq, the library construction was performed with SMARTer Stranded Total RNA-Seq Kit (Takara). For single cell RNA seq, the library was performed using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1(1000128) purchased from 10X Genomics according to the protocols provided by manufactures.

value: tumor infiltrating stromal cells

tag: tumor type

value: colon cancer

tag: gender

value: Male

tag: tumor location

value: Proximal/Right Colon

tag: histologic type of tumor

tag: pathologic staging (ptnm)

value: pT2, N0,pM = not applicable

tag: technology

value: bulk RNA sequencing


title: patient7

description: bulk RNA sequencing

value: Female

value: Distal/Left Colon

value: pT3, N0, pM = not applicable


title: HCC827_replicate03


title: patient6

description: bulk RNA sequencing

value: pT2(Tumor invades muscularis propria),N0,Mx = not specified


title: patient10

description: bulk RNA sequencing

value: adenocarcinoma

value: pT3 (m), N2a


title: NCI-H1299_replicate01


title: patient5

description: bulk RNA sequencing

value: pT2(tumor invades muscularis propria),N0,Mx a


title: HCC827_replicate02


title: HCC827_replicate01


title: HCC4006_replicate02


title: HCC4006_replicate03


title: patient2

description: bulk RNA sequencing

value: pT4b (tumor directly invades or is adherent to other ); pN0:No regional lymph node metastasis


title: HCC4006_replicate01

value: Lung


title: patient4

description: bulk RNA sequencing

value: Adenocarcinoma

value: ypT4b,N0 (No regional lymph node metastasis),MX,R1


title: HCC2935_replicate03


title: SG0029M_post

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated. Batch correction was applied using R package limma.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each sample

source_name: tumour-associated macrophages

growth_protocol: FITC-HLA-DR+CD14+ cells were sorted using a FACSAria II cell sorter (BD Bioscience), lysed in RLT buffer (1015750, Qiagen) with 1% β-mecaptoethanol (M-6250, Sigma-Aldrich) and stored at -80˚C. 0.25-2x106 cells were sorted per sample.

extract_protocol:
Human macrophage RNA was extracted from the FACS-sorted TAM population using the micro RNAEasy kit (74004, Qiagen) according to manufacturer instructions
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

value: high-grade serous ovarian cancer omental metastasis

tag: tumour stage

value: Stage 3-4

tag: neoadjuvant chemotherapy

value: post

tag: batch description

value: sequencing batch2


title: NCI-H1395_replicate01

tag: tissue

tag: cell line


title: patient9

description: bulk RNA sequencing

tag: cell type

value: tumor infiltrating stromal cells

value: colon cancer

value: pT2, N1a


title: HCC2935_replicate01


title: patient1

description: bulk RNA sequencing

value: Female

tag: age

value: Proximal/Right Colon

value: pT3, N1a, Mx

value: bulk RNA sequencing


title: SG0026M_pre

value: pre


title: SG0024M_pre


title: Calu6_replicate02

value: NSCLC


title: HCC2935_replicate02


title: Calu6_replicate01


title: SG0021M_pre


title: SG0028M_post


title: Calu3_replicate02


title: patient3

description: bulk RNA sequencing

value: pT3 (tumor invades into pericolic tissues); pN0 (no regional lymph node metastasis)


title: Calu3_replicate01

value: Lung


title: A549_replicate03

value: Adenocarcinoma


title: SG0020M_post


title: A549_replicate02


title: Calu1_replicate01


title: SG0005M_post

value: sequencing batch1


title: SG0013M_pre

value: high-grade serous ovarian cancer omental metastasis


title: SG0004M_post

value: Stage 3-4


title: SG0012M_pre


title: A427_replicate03


title: SG0011M_post

value: post


title: Calu6_replicate03


title: A549_replicate01


title: RNAseq_WT_UV_rep3

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description:
poly-A RNA (RNA-seq)
genome used for mapping:
Hg19

data_processing:
ChIP-seq, BrU-seq and ATAC-seq data analyses: For RNAPII-Ser2 ChIP-seq, low-quality sequence reads and adapters were filtered out by Trimmomatic (v3.36) (A. M. Bolger et al, 2014). The trimmed reads were aligned to the human reference genome (GRC h37/hg19) with the Burrows-Wheeler Aligner (BWA-v0.7.12-r1039) (H. Li et al, 2013). Biobambam2 (v2.0.72) (G. Tischler et al, 2014) was used to remove duplicate reads from the aligned reads. Sequence reads were locally realigned and base-quality scores were recalibrated with the IndelRealigner and BaseRecalibrator programs in Genome Analysis Toolkit (GATK-v3.5) (McKenna et al, 2010).
For pan-RNAPII ChIP-seq, BrU-seq and ATAC-seq, reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (BWA (Version 0.7.16a) or STAR (Version 2.5.3a)) (H. Li et al, 2013; Dobin et al, 2013). Only high-quality reads (> q30) were included in the analyses and duplicates were removed using Samtools (Version 1.6) with fixmate -m and markdup -r settings (Table S7). Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (S. Heinz et al, 2010). A list of 49,948 genes was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the knownCanonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes should be non-overlapping with at least 2 kb between genes. Subsequent selection of sets of genes is described per analysis.
For ChIP-seq, binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Read densities in input samples were subtracted from individual ChIP-seq datasets to background-correct our data in which negative values were converted to 0, to prevent the use of impossible negative read densities in further calculations. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 3.5.3) (R. Core Team, R, 2019). ChIP-seq binding and metagene profiles were averaged per set of genes and profiles were normalized to area under the curve to allow proper comparison of the profiles without effects of overall differences in read density.
ATAC-seq and BrU-seq heatmaps were generated as described for ChIP-seq analyses, except for the input subtraction and removal of negative values. BrU-seq aggregated profiles, were defined using the AnnotatePeaks.pl tool or makeMetaGeneProfile.pl tool of HOMER using the default normalization to 10mln reads, as for ChIP-sequencing. Genes were selected on size and strongest binding of RNAPII at the TSS in undamaged condition, as for ChIP-sequencing. Averaged binding profiles were subsequently normalized to nascent transcript levels, as quantified by 5-EU labelling, relative to the control in their specific cell type. For example, WT cells 3 h after UV irradiation showed 35% RNA relative to WT control cells, so we multiplied the expression of the bins by 0.35.  RNA-seq analyses: Obtained sequencing reads were cleaned by 5'-end quality trimming and Illumina-adapter clipping by Trimmomatic (A. M. Bolger et al, 2014). Pre-alignment quality control of the cleaned sequencing reads was done with FastQC. The alignment to reference genome hg19 of trimmed sequencing reads was done with Hisat2, guided by gene annotation in the refGene UCSC table (D. Kim et al, 2015). The generated SAM files were converted to the binary counterpart BAM, followed by BAM sorting and indexing with SAMtools (H. Li et al, 2009).  Counting reads to the UCSC's genomic features hg19 was performed by Subread/featureCounts (Y. Liao et al, 2014). Differential expression analysis was carried out, using edgeR (M. D. Robinson et al, 2010). Only genes indicating at least 2 counts per million in at least 20% of samples were included in the analysis. Data were normalized for sample specific effects by the trimmed mean of M-values. This was followed by estimating the dispersion and determining the differentially expressed genes using the general linear model (GLM). FDR-adjusted p-values < 0.05 were considered significant.
Genome_build: hg19 or hg38 as indicated per sample
Supplementary_files_format_and_content: excel tables providing stranded metagene profiles for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

molecule: polyA RNA

source_name: RPE1-iCas9 WT

growth_protocol: DMEM GlutaMAX +10% Fetal Calf Serum + antibiotics

extract_protocol:
ATAC-seq: For each experimental condition 50.000 cells were harvested and washed with cold PBS containing protease inhibitors (Roche). The cells were resuspended in 50  l Transposase mixture, containing 1x Tagment DNA buffer Illumina Kit, #20034197), 0.5  l Tagment DNA enzyme (Illumina Kit, #20034197) and 0,2  g/ l Digitonin (Promega, #G9441), and incubated at 37  C for 30 min. Fragmented DNA was purified using a Qiagen MinElute kit (#28204).  BrU-seq: For BrU(DRB)-seq, cells were pre-treated with 100  M DRB for 1-3hrs (as indicated per sample) after which cells were washed with PBS and immdeidately, or 30 min later, incubated with 2 mM bromouridine (Bru) at 37 C for 15 or 30 min. For regular BrU-seq, cells were either mock-treated or irradiated with UV-C light (9 J/m2). Cells were then incubated in conditioned media for different periods of time before being incubated with 2 mM bromouridine (Bru) at 37 C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015). ChIP-seq: Cells were mock treated or UV-irradiated with 9 J/m2 and incubated in conditioned media for different periods of time (1, 4, 8, 16 h). Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1% PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4 C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3  g antibody (Antibodies are listed in Table S3) overnight at 4 C, followed by a 1.5 h protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65 C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.  RNA-seq: Cells were UV-irradiated (254 nm, 9 J/m2) or mock-treated and harvested 24 h later. Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. Up to 5   106 cells per sample were lysed in RLT buffer. For quantification purposes, 24 ng of the eight ArrayControl(tm) RNA Spikes (Thermo Fisher Scientific) were added to each sample (3 ng/spike).
ATAC-seq: Libraries were prepared by PCR using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) and Nextera XT index Kit v2 (Illumina). Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Indicated is whether single-end or paired-end sequencing data was used for downstream analyses ChIP-seq: For RNAPII-Ser2 ChIP-seq sample libraries were prepared from 1 ng ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) and index primer sets (NEB, E7335S). Strand-biased library amplification was performed using high-fidelity KAPA HiFi Enzyme (Roche, KK2102). The prepared libraries were sequenced on an Illumina HiSeq 2500 system (Illumina), resulting in 150 bp paired-end reads. For the remaining ChIP-seq samples, libraries were prepared using kapa hyper prep kit (Roche) and A-T mediated ligation of full Y-shaped IDT adapters. Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. RNA-seq: Samples were purified using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's instructions, and sequenced in a single lane on an Illumina HiSeq4000.

treatment_protocol: DNA damage was induced by irradiating cells with varying doses of UV-C as indicated per sample; samples were assayed at different time-periods after UV treatment as indicated per sample.

value: WT

tag: uv-c dose

tag: time after uv-c

value: 24 hours

tag: chip-antibody

value: not applicable


title: RNAseq_WT_UV_rep2

tag: genotype


title: A427_replicate01


title: A427_replicate02


title: RNAseq_WT_UV_rep1


title: RNAseq_WT_Mock_rep3

value: mock


title: RNAseq_WT_Mock_rep2


title: Calu3_replicate03


title: RNAseq_WT_Mock_rep1


title: RNAseq_ELOFKO_UV_rep3

source_name: RPE1-iCas9 ELOF1-KO


title: RNAseq_ELOFKO_UV_rep2


title: RNAseq_ELOFKO_UV_rep1


title: RNAseq_ELOFKO_Mock_rep3


title: RNAseq_ELOFKO_Mock_rep1


title: RNAseq_ELOFKO_Mock_rep2


title: RNAseq_CSBKO_UV_rep3

source_name: RPE1-iCas9 CSB-KO

value: CSB-KO


title: RNAseq_CSBKO_UV_rep2


title: RNAseq_CSBKO_UV_rep1


title: RNAseq_CSBKO_Mock_rep2


title: RNAseq_CSBKO_Mock_rep3


title: RNAseq_CSBKO_Mock_rep1


title: C3H mouse, 0 ppm (control) for 27 weeks, biological rep3

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description: gene expression data from liver of C3H mouse fed diets containing 0 ppm (control) for 27 weeks

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, mixtures were hybridized to SurePrint G3 Rat Gene Expression 8x60K Microarrays, SurePrint G3 Mouse GE 8x60K Microarrays or SurePrint G3 Human GE v2 8x60K Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent) using one color scan setting for 8x60K array slides. The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: The processed signal intensities were log2-transformed and normalized to the 75th percentile using GeneSpring software (version 14.9.1) (Agilent).

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop 2000/2000c Spectrophotometer.

growth_protocol: The animals were housed in a barrier maintained animal room. The environmental conditions in the animal room were set to maintain a temperature range of 22 - 26°C and a relative humidity range of 40 - 70%, and a 12 hour light (8:00 - 20:00)/ 12 hour dark (20:00 - 8:00) illumination cycle. A commercially available pulverized diet and filtered tap water were provided ad libitum.

extract_protocol: The livers were stored in RNAlater RNA Stabilization Reagent (Life Technologies Corporation, Carlsbad, CA) at -20°C. Total RNA was prepared using Isogen solution (Nippon Gene) and RNeasy Mini Kits (Qiagen) following the manufacturer's instructions. Total RNA was quantified using a NanoDrop 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male CD-1 mice (4 animals/dose) were fed diets containing 0 (control) or 1500 ppm PB for 7 days. Male hCAR/hPXR mice (7 animals/dose) were fed diets containing 0 (control) or 1000 ppm PB for 7 days. Male C3H/HeNCrlCrlj  mice (3 animals/dose) were fed diets containing 0 (control) or 500 ppm PB for 27 weeks after a single intraperitoneal injection of 90 mg/kg diethylnitrosamine.

value: male

value: liver


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep7

description: gene expression data from liver of hCAR/hPXR mouse fed diets containing 1000 ppm PB for 7 days


title: T-PLL_P5_H3K27ac

city: ROCHESTER

first: Shulan

last: Tian

state: Minnesota

address: 200 1st street SW

department: Health Science Research

institute: Mayo Clinic

data_processing:
Data were analyzed by the HiChIP pipeline (PMID: 25128017)
Reads were mapped to the hg19 reference genome using BWA v0.7.10). After excluding read pairs with both ends being mapped uniquely or mapped to multiple locations, the remaining reads were re-mapped with GSNAP (gmap_2015_0723). BWA and GSNAP alignments were then combined and uniquely mapped pairs of reads with mapping quality ≥ 20 were extracted.
Duplicates were removed using Picard (https://broadinstitute.github.io/picard/).
Peaks were identified using MACS v2.0.10. Peaks overlapping the blacklisted regions were excluded.
Reads-per-million signal tracks (bigwig files) were generated using deeptools v1.5.12 with parameters "-bs 10 --smoothLength 150".
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited encodePeak files include peaks; bigwig (bw) files include count-per-million signals

source_name: Peripheral blood

extract_protocol:
ChIP was performed with PBMCs, as described (PMID: 29268714). The chromatin was then incubated with anti-H3K27ac antibody (Abcam, Cat. # ab4729) or in-house generated anti-H3K4me3 antibody. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA).
ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI)

value: Peripheral blood

value: Leukemia T cells

tag: antibody


title: T-PLL_P6_H3K27ac


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep5

source_name: liver of hCAR/hPXR mouse fed diets containing 1000 ppm PB for 7 days

tag: gender


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep4


title: T-PLL_P3_H3K27ac


title: T-PLL_P4_H3K27ac


title: T-PLL_P2_H3K27ac


title: C3H mouse, 0 ppm (control) for 27 weeks, biological rep1

source_name: liver of C3H mouse fed diets containing 0 ppm (control) for 27 weeks


title: C3H mouse, 0 ppm (control) for 27 weeks, biological rep2


title: C3H mouse, 500 ppm PB for 27 weeks, biological rep1

description: gene expression data from liver of C3H mouse fed diets containing 500 ppm PB for 27 weeks


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep3


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep4

description: gene expression data from liver of hCAR/hPXR mouse fed diets containing 0 ppm (control) for 7 days


title: C3H mouse, 500 ppm PB for 27 weeks, biological rep2

source_name: liver of C3H mouse fed diets containing 500 ppm PB for 27 weeks


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep6


title: C3H mouse, 500 ppm PB for 27 weeks, biological rep3


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep6

source_name: liver of hCAR/hPXR mouse fed diets containing 0 ppm (control) for 7 days


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep1


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep3


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep5


title: T-PLL_P1_H3K27ac


title: hCAR/hPXR mouse, 1000 ppm PB for 7 days, biological rep2


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep7


title: Normal_N3_H3K27ac

value: CD3+ T cell


title: Normal_N2_H3K27ac


title: T-PLL_P5_H3K4me3


title: T-PLL_P6_H3K4me3


title: T-PLL_P4_H3K4me3


title: T-PLL_P3_H3K4me3


title: CD-1 mouse, 1500 ppm PB for 7 days, biological rep4

description: gene expression data from liver of CD-1 mouse fed diets containing 1500 ppm PB for 7 days


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep1


title: T-PLL_P2_H3K4me3


title: CD-1 mouse, 1500 ppm PB for 7 days, biological rep2

source_name: liver of CD-1 mouse fed diets containing 1500 ppm PB for 7 days


title: T-PLL_P1_H3K4me3


title: Normal_N1_H3K27ac


title: Normal_N3_H3K4me3


title: Normal_N2_H3K4me3


title: CD-1 mouse, 1500 ppm PB for 7 days, biological rep3


title: CD-1 mouse, 0 ppm (control) for 7 days, biological rep2

description: gene expression data from liver of CD-1 mouse fed diets containing 0 ppm (control) for 7 days


title: CD-1 mouse, 1500 ppm PB for 7 days, biological rep1


title: hCAR/hPXR mouse, 0 ppm (control) for 7 days, biological rep2


title: Utricl-P7

city: Baltimore

first: Seth

last: Ament

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
10x matrices were input to Seurat R package and normalized
We filtered cells with <50 or >20,000 unique molecular identifiers (UMIs) and with >20% of UMIs coming from mitochondrial genes.
Highly variable genes were identified using the FindVariableGenes function with the following parameters: dispersion formula = LogVMR, minimum = 0.0123, maximum = 3, y cutoff = 0.5.
Counts from variable genes were scaled, and we regressed out effects of cell cycle, percent of mitochondrial genes, and number of unique molecular identifiers
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 format raw gene expression matrix

source_name: Utricle

extract_protocol:
Cochlear ducts and the utricle were harvested and pooled into Thermolysin (Sigma-Aldrich) for 20 min at 37oC. The Thermolysin was then replaced with Accutase (Sigma-Aldrich) and the tissue incubated for 3 min at 37oC followed by mechanical dissociation, repeating this step 3 times. After inactivation of the Accutase with 5% fetal bovine serum, the cell suspension was filter through a 35µm nylon mesh to remove cell clumps.
Library were prepared using the Chromium Single Cell Gene Expression Solution from 10x Genomics

tag: strain

value: Post-natal day 7


title: CD-1 mouse, 0 ppm (control) for 7 days, biological rep3

source_name: liver of CD-1 mouse fed diets containing 0 ppm (control) for 7 days


title: CD-1 mouse, 0 ppm (control) for 7 days, biological rep1


title: Mouse_10xGenomics_E18.5VP_NoEnrichment_1

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

data_processing:
Sequencing data were processed using Cell Ranger (v2.0.2, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

source_name: Ventral pancreas

extract_protocol: The procedure was performed according to the manufacturer’s instructions using the Single cell 3’ Reagent Kit v2 from 10x Genomics.

value: Ventral pancreas

tag: cell source

value: No enrichment

tag: developmental time point


title: Mouse_10xGenomics_E18.5DP_NoEnrichment_1

source_name: Dorsal pancreas

value: Dorsal pancreas


title: Normal_N1_H3K4me3


title: Mouse_10xGenomics_E17.5VP_Ngn3Cre_1


title: Utricl-P2

value: Post-natal day 2


title: Mouse_10xGenomics_E17.5DP_Ngn3Cre_1


title: Coch-P7

source_name: Cochlea


title: Coch-P2


title: Mouse_10xGenomics_E16.5VP_Ngn3Cre_1


title: CD-1 mouse, 0 ppm (control) for 7 days, biological rep4


title: 197461

city: bethesda

first: abdalla

last: abdelmaksoud

state: maryland

address: 37 Convent Dr

institute: NCI

hyb_protocol: A total of 20 ug of biotinylated cRNA was then fragmented for hybridization on the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChip Operating Software Tool was used for data capture and quality

data_processing: Raw CEL files from the scan were analyzed using a microarray pipeline written in ‘R’.  Data were normalized using the Robust Multichip Average (RMA) method.  Linear modeling was performed using Limma’s lmFit function (LIMMA, RRID:SCR_010943, Limma powers differential expression analyses for RNA-sequencing and microarray studies), and differential gene expression was determined using the contrasts.fit and eBayes functions. Top pathways for each comparison (Non-responders, Responders, and Relapse;  normalized with control IgG treatment samples) were determined using (Gene Set Enrichment Analysis) GSEA (SeqGSEA, RRID:SCR_005724, http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Gsea_Citation). The top 10 up and down regulated pathways were generated from Reactome (Reactome diagram viewer: data structures and strategies to boost performance) based on NES scores if Q-value meets threshold of less than 0.1. The top genes from Reactome were then used to run GSVA (Gene Set Variation Analysis for microarray and RNA-seq data) to find enrichment for each sample. Heatmaps were generated for the GSVA analysis, columns (samples) were sorted by group and rows (pathways) were clustered by Euclidean distance. Individual sample differential expression heatmap was analyzed by computing the log fold-change between a sample against the mean expression of the IgG samples, upper and lower limits shown on the heat map are log values from -2 to 2. Gene expression data from this report is available through the Collaborative Bioinformatics Resource of NIH, Center for Cancer Research (CCR). https://zenodo.org/record/3770853#.X9PmhhNKg_N.

label: Biotin

source_name: Subcutaneous tumor

label_protocol: A total input of 800ng of isolated RNA was applied to the Message Amp II-Biotin Enhanced aRNA Amplification Kit according to manufacture protocol for first and second Strand cDNA synthesis followed by in-vitro transcription (IVT) reaction to synthesize the complementary RNA (cRNA) for transcriptional amplification and biotin labeling.

growth_protocol: See publication Materials and Methods: Melanoma allograft model

extract_protocol: Tumor samples were lysed and homogenized for RNA isolation using the RNeasy Mini Kit following manufacturer’s protocol for purification of total RNA with on-column DNase digestion (Qiagen). RNA purity and concentration were determined spectrophotometrically, and RNA quality was assessed using the Agilent Technology Tape Station RNA Screen Tape.

treatment_protocol: See publication Materials and Methods: Immunotherapy treatment

tag: disease

value: Melanoma

tag: mouse strain

tag: treatment

value: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: 189746

value: PBS 10ml/Kg


title: 197436

value: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A in PBS


title: 197429


title: 189747


title: 197446


title: SG0027M_post

value: high-grade serous ovarian cancer omental metastasis

tag: tumour stage

value: Stage 3-4

tag: neoadjuvant chemotherapy

value: post

tag: batch description

value: sequencing batch2


title: 197463


title: 197409


title: 189748


title: 197454

value: Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: NCI-H1299_replicate02

extract_protocol:
Whole-cell RNA was isolated using RNeasy Mini columns (Qiagen).
Total RNA (5 μg) from each sample were depleted of rRNA using the Ribo-Zero Gold rRNA Removal Kit for human, mouse and rat RNA (Illumina). 20 ng of RNA input was used to generate the RNA-seq libraries using the Agilent Sure Select Strand Specific RNA Library Prep for Illumina Multiplex Sequencing Version C.0 (Illumina).
The single-stranded RNA library was sequenced on a HiSeq 2000 V4 (Illumina) with 150 bp paired-end reads.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: NSCLC


title: 197456


title: 189749


title: Mouse_10xGenomics_E16.5DP_Ngn3Cre_1


title: female_ovary_2

city: Wuhan

first: Shaobo

last: Liang

address: BaYi Road

department: College of life science

institute: Wuhan University

data_processing:
FsatQC v0.11.5 and cutadapt v1.15 used for base calling
TopHat (v2.1.1) used for mapping to the Drosophila genome with 2-nt mismatches allowed and other parameters default
ce-TopHat (developed here) used for dealing with unmapped reads
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: female adult ovary

growth_protocol: Stocks and crosses of the wild-type w1118 isogenic Drosophila strain (BDSC 5905) were maintained and cultured on standard cornmeal agar medium

extract_protocol:
Heads and bodies of adults were dismembered using liquid nitrogen, the gonads were dissected in ice-cold PBS from fresh flies and collected respectively
construction of cDNA libraries and sequencing were performed using Illumina Hi-Seq 2000

value: BDSC 5905

tag: developmental stage

value: adult 24hrs

tag: Sex

value: female

value: ovary


title: female_ovary_1


title: 197442

tag: genotype


title: male_testis_2

source_name: male adult testis

value: male

value: testis


title: male_testis_1


title: female_head_2

source_name: female adult head

value: head


title: female_head_1


title: male_head_1

source_name: male adult head


title: male_head_2


title: female_body_2

source_name: female adult body

value: body


title: female_body_1


title: male_body_2

source_name: male adult body


title: male_body_1


title: whole_adult_2

source_name: adult individual

value: whole individual


title: larva_2

source_name: Larva L3


title: MG_Cx43_f_f_acute

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

institute: Kyushu University

description: Control sample from peak phase

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: Control, peak phase

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: Isolated microglial cells

value: Control

tag: Stage

value: peak phase


title: MG_Cx43_icKO_acute

description: Cx43 icKO sample from peak phase

source_name: Cx43 icKO, peak phase

value: Cx43 icKO


title: 197441

value: Melanoma

value: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A in PBS


title: embryo_2

source_name: embryo

value: embyro 18hrs


title: whole_adult_1


title: 197420


title: larva_1


title: embryo_1


title: 197437


title: MG_Cx43_f_f_pre

description: Control sample from pre-immunized stage

source_name: Control, pre-immunized stage

value: pre-immunized stage


title: 197462

value: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: 197438


title: 197404


title: Human naïve CD4+ T cells

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

institute: King's College London

description: fragmented gDNA

data_processing:
Data processing was undertaken within usegalaxy.org
Using 'groomer', the first 5 5' bases were timmed from all reads
Overrepresented adapter sequences were clipped
Sequences were aligned to hg19 using Bowtie 2
The resulted Bam file was converted to Bigwig in order to visualize using 25 bin size, normalizing with rpkm and using a frament size of 150bp (approximately 1 nucleosome).
Genome_build: hg19

source_name: Adult peripheral blood

growth_protocol: naïve CD4+ T cells were isolated by positive selection using CD4+ magnetic beads (invitrogen) followed by CD45RA negative selection (Beckton Dickinson)

extract_protocol:
NEB adapters were ligated to the ends of the DNA fragments. The library was barcoded using PCR
Chromatin Immunocleavage (Cut and Run)

treatment_protocol: Cells were incubted first with anti GATA3 antibody for  1hr,  cells  were centrifuged at 300Xg for 5' and the supernatant removed, cells were washed with PBS then incubated  with proteinA-Mnase. After 30' 1mMCaCl2 was added to the solution and 1 hr later the reaction was terminated using EGTA. Cells were centrifuged and the releaed chromatin present in the supernatant was harvested.

tag: antibody used in cut and run protocol

value: anti GATA3

value: resting cells


title: 197434


title: 197444


title: 200372

value: Normal IgG 10 mg/kg


title: 197432


title: MG_Cx43_icKO_pre

description: Cx43 icKO sample from pre-immunized stage

source_name: Cx43 icKO, pre-immunized stage


title: IIH_DT_20_Pre

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Campus

institute: University of Warwick

data_processing:
TrimGalore! V0.4.4 for adapter trimming
RNA-seq reads were mapped to the human genome (hg19, UCSC annotation) utilising STAR software v2.5.3a with default parameters
Counts per gene were calculated using custom scripts acting in a HTSeqcount compatible mode with the following parameters: --format=bam --minaqual=10 --stranded=reverse –mode=union
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: Tab separated genes counts for each sample

source_name: Adipose tissue

extract_protocol:
Subcutaneous adipose tissue was biopsied and placed immediately in RNAlater
Illumina TruSeq mRNA Stranded

tag: subject status

value: IIH

value: Adipose tissue (subcutaneous biopsy)


title: IIH_DT_17_Post

value: Drug


title: IIH_DT_19_Post


title: IIH_DT_17_Pre


title: IIH_DT_19_Pre


title: 197435


title: IIH_DT_14_Pre


title: 200381


title: IIH_DT_14_Post


title: IIH_DT_13_Pre


title: 200377


title: IIH_DT_13_Post

value: Placebo


title: IIH_DT_10_Pre


title: 197460


title: 200376


title: 197426


title: 200370


title: 197431


title: 197425


title: IIH_DT_10_Post


title: 223308

value: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: 223262

value: Growth Delay to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: IIH_WT_H5090


title: IIH_WT_822

value: Control


title: IIH_WT_H5041


title: IIH_DT_24_Pre


title: IIH_DT_24_Post


title: 223305


title: 223298

value: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: 223320


title: 223323


title: 200375


title: 223274


title: 223261


title: IIH_WT_819


title: 223256


title: IIH_WT_813


title: 223307


title: 223254


title: 223324


title: 223282


title: IIH_WT_811


title: IIH_WT_818


title: IIH_WT_816


title: IIH_WT_15


title: 223331


title: 200378


title: 200373


title: 223315


title: IIH_WT_009


title: IIH_WT_007


title: 197451


title: 197443


title: IIH_WT_003


title: 223290


title: IIH_DT_20_Post


title: RAM2-5_Rep3-NT-SCR

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description:
HUVECs transfected with scramble control for 48 hr (Biological Repeat 1)
merged_gene_counts__RAMP2-AS1.txt.gz

data_processing:
Basecalls performed using Illumina RTA version 1.18.64
Raw sequencing reads were processed with the nf-core/RNASeq pipeline version 1.4.2. Briefly, trimmed reads were mapped using STAR to the GRCh38 reference,  counted across genomic features encoded in the GENCODE v33 annotation using Subread featureCounts and merged into a matrix of counts per gene.
Each library was subjected to extensive quality control, including estimation of library complexity, gene body coverage, and duplication rates, among other metrics detailed in the nf-core/rnaseq pipeline repository on GitHub.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix of read counts per gene

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs (Cell Applications Inc., San Diego, CA) (Passages 4–8) from pooled donors were cultured in HUVEC growth medium containing endothelial cell growth supplements (Cell Applications Inc.), based on the manufacturer’s recommendations, at 37°C in an atmosphere of 95% air and 5% CO2.

extract_protocol:
RNA was extracted from cells and tissues using TRIzol (Invitrogen) following the manufacturer’s instructions as described previously (Miao et al., 2018; Tang et al., 2020)
500 ng of total RNA per sample was used and the libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche Diagnostics) following the manufacturer’s manual.

treatment_protocol: HUVECs were treated with atorvastatin (ATV) at 1 or 5 mM, or TNFalpha at 100 ng/ml for 24 hr. Antisense LNA GapmeRs specifically targeting two different regions of RAMP2-AS1 (LG00116686, LG00226723) and scramble control designed and purchased from Qiagen were transfected into ECs with Lipofectamine 3000 following the protocol provided by the manufacturer and as described previously (Miao et al., 2018).

value: RAMP2-AS1 scramble control

value: human umbilical vein endothelial cells


title: 223277

source_name: Subcutaneous tumor

value: Melanoma


title: AGO1-5_Rep1-NT-SCR


title: AGO1-6_Rep1-NT-LNA

description:
HUVECs transfected with LNA for 48 hr (Biological Repeat 1)
merged_gene_counts__RAMP2-AS1.txt.gz

value: RAMP2-AS1 knockdown


title: 223310


title: 223266


title: 223330


title: IIH_WT_820


title: 223296


title: ZC6_HUAEC TNFA

description:
HAOEC TNFa 100 ng/ml 24 h (HAOEC treated with TNAalpha at 100 ng/ml for 24 hours)
merged_gene_counts__SS.txt.gz

source_name: human aortic endothelial cells

value: TNFalpha at 100 ng/ml for 24 hours

value: human aortic endothelial cells


title: ZC5_HUAEC ATV

description:
HAOEC ATV 1 uM 24 h (HAOEC treated with Atorvastatin at 1 microM for 24 hours)
merged_gene_counts__SS.txt.gz

value: Atorvastatin at 1 microM for 24 hours


title: ZC4_HUAEC DMSO

description:
HAOEC Ctrl (human aortic endothelial ECs [HAOEC] treated with DMSO for 24 hr)
merged_gene_counts__SS.txt.gz

value: DMSO for 24 hr


title: 223294


title: RAM2-6_Rep3-NT-LNA


title: 223337

value: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: ZC2_HUVEC ATV

description:
HUVEC ATV 1 uM 24 h (HUVEC treated with Atorvastatin at 1 microM for 24 hours)
merged_gene_counts__SS.txt.gz


title: 223273


title: 223301


title: ZC1_HUVEC DMSO

description:
HUVEC Control (human umbilical vein ECs [HUVECs] treated with DMSO for 24 hr)
merged_gene_counts__SS.txt.gz


title: 223280


title: Long stimulation IL1-TNF rep3

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

description: Sample 24

data_processing:
Basecalling was preformed using bcl2fastq
Raw reads were trimmed from Adapters and polyA and polyT and low quality bases using cutadapt. Reads with length below 30 were discarded.
Processed reads were mapped to human genome, GRCh38, using STAR v2.4
Counts per gene were calculated using HTSeq-count v0.6.1 with intersection-strict mode on exons using Ensembel annotations release 83
Differential expression and normalized counts were created using Bioconductor Deseq package
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited raw counts matrix. Each row is a gene and each column is a sample.
Supplementary_files_format_and_content: Comma seperated file. Rows are genes and columns are samples. Values are normalized counts produced by Deseq.

source_name: Bone marrow

growth_protocol: Human primary BM-derived MSCs were kept in culture for up to 9 passages. The cells were grown in mesenchymal stem cells growth medium.

extract_protocol:
Total RNA was isolated using Qiagen miRNeasy Mini Kit
500ng of total RNA were fragmented followed by reverse transcription and second strand cDNA synthesis. The double strand cDNA was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries

treatment_protocol: Samples were treated with either IL1β, TNFa, IL1β+TNFa or remained untreated, for duration of 2 days or 14 days in MEM alpha medium

value: primary bone marrow-derived MSCs

value: Bone marrow

value: treated with IL1 and TNF for 14 days


title: Long stimulation TNF rep3

description: Sample 23

value: treated with TNF for 14 days


title: 223327


title: ZC3_HUVEC TNFA

description:
HUVEC TNFa 100 ng/ml 24 h (HUVEC treated with TNFalpha at 100 ng/ml for 24 hours
merged_gene_counts__SS.txt.gz


title: Long stimulation control rep3

description: Sample 21

value: untreated


title: 223267


title: Short stimulation IL1-TNF rep3

description: Sample 20

value: treated with IL1 and TNF for 2 days


title: 223326


title: Long stimulation IL1 rep3

description: Sample 22

value: treated with IL1 for 14 days


title: 223263


title: 223334


title: Short stimulation TNF rep3

description: Sample 19

value: treated with TNF for 2 days


title: 223312


title: Short stimulation IL1 rep3

description: Sample 18

value: treated with IL1 for 2 days


title: 223317


title: 223281


title: Short stimulation control rep3

description: Sample 17


title: 223299

value: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A in PBS


title: 223239

value: Melanoma

value: Normal IgG 10 mg/kg


title: 223234


title: 223251


title: 223252


title: Long stimulation TNF rep2

description: Sample 15


title: 223291


title: 223235


title: 223253


title: Long stimulation IL1 rep2

description: Sample 14


title: Short stimulation IL1-TNF rep2

description: Sample 12


title: 223237


title: 223241


title: 223240


title: BMDMs, Unstimulated, WT-3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
RNA-seq libraries were sequenced at The Centre for Applied Genomics at the Hospital for Sick Children in Toronto on a HiSeq 2500 using 50 bp x 25 bp paired-end sequencing.
Sequences for each sample were aligned to mm10 using the STAR aligner.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample with barcode annotations

source_name: BMDMs

growth_protocol: Bome marrow cells were prepared from 8- to 20-week-old mice and cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum (Hyclone), 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin (complete media; cRPMI) and mouse recombinant M-CSF (20 ng/mL, Peprotech, #315-02) for 7 days. M-CSF was replenished at the day 4 of the culture. After 7 days, bone marrow-derived macrophages were harvested and plated for stimulations.

extract_protocol:
mRNA was extracted from cell pellets using oligo-dT beads (Invitrogen).
Custom oligo-dT primers containing barcode and adaptor-linker sequences (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15) were used to for cDNA synthesis. Barcoded first-strand synthesis cDNAs for each sample were pooled together, and the RNA-DNA hybrid was degraded by acid-alkali treatment. A second sequencing adaptor (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI bead cleanup (Beckman-Coulter). The libraries were PCR amplified 12 cycles, followed by SPRI bead clean-up prior to sequencing.
3'end DGE
single-end demultiplexed

treatment_protocol: BMDMs were seeded at concentration 8×10e5-10e6 cells/mL in tissue culture plates of various formats. Cells were stimulated with LPS 100 ng/ml for 24h, then media was changed and cells were rested for 1h and then re-stimulated with LPS for 3h (tolerized; LPS 24h->LPS 3h). Control non-tolerized cells underwent the same procedure without first dose of LPS (non-tolerized; LPS 3h). Alternatively cells were left unstimulated (Unstim.) or stimulated with LPS for 24h and directly harvested (LPS 24h).

value: WT

value: Unstimulated

value: BMDMs


title: Long stimulation IL1-TNF rep1

description: Sample 8


title: Short stimulation control rep2

description: Sample 9


title: BMDMs, Mock/3h_LPS, WT-3


title: Long stimulation IL1-TNF rep2

description: Sample 16


title: BMDMs, Unstimulated, WT-2


title: Long stimulation TNF rep1

description: Sample 7


title: 223238


title: 223244


title: 223248


title: BMDMs, Unstimulated, Irg1_KO-3

value: Irg1 KO


title: Short stimulation TNF rep1

description: Sample 3


title: BMDMs, 24h_LPS, WT-3


title: BMDMs, 24h_LPS/3h_LPS, WT-3


title: BMDMs, Unstimulated, Irg1_KO-2


title: Short stimulation IL1-TNF rep1

description: Sample 4


title: 223246


title: Short stimulation IL1 rep1

description: Sample 2


title: 223228

value: PBS 10ml/Kg


title: 223226


title: 223232


title: 223245


title: BMDMs, Unstimulated, Irg1_KO-1


title: Short stimulation control rep1

description: Sample 1

value: primary bone marrow-derived MSCs


title: MSC treated with cytokynes rep2

description: Sample 5b

data_processing:
Basecalling was preformed using bcl2fastq
Raw reads were trimmed from Adapters and polyA and polyT and low quality bases using cutadapt v.1.8.3. Reads with length below 30 were discarded.
Processed reads were mapped to human genome, GRCh38, using TopHat v.0.6.1
Counts per gene were calculated using HTSeq-count v0.6.1 with intersection-strict mode on exons, using Ensembel annotations release 83
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited raw counts matrix. Each row is a gene and each column is a sample.

treatment_protocol: Samples were either treated with IL1 and TNFa or untreated controls

value: Bone marrow

value: treated with IL1 and TNF


title: Long stimulation IL1 rep1

description: Sample 6


title: MSC treated with cytokynes rep1

description: Sample 4b


title: MSC treated with cytokynes rep3

description: Sample 6b


title: MSC control rep2

description: Sample 5a


title: BMDMs, Mock/3h_LPS, Irg1_KO-3


title: BMDMs, 24h_LPS/3h_LPS, Irg1_KO-1


title: MSC control rep3

description: Sample 6a


title: BMDMs, Mock/3h_LPS, Irg1_KO-1


title: BMDMs, 24h_LPS/3h_LPS, WT-2


title: BMDMs, 24h_LPS, Irg1_KO-1


title: BMDMs, 24h_LPS, WT-2


title: BMDMs, Unstimulated, WT-1


title: MSC control rep1

description: Sample 4a


title: E_untreated_cho_3_15

data_processing:
Sequencing reads were aligned to the Homo sapiens reference genome (hg38) with TopHat (v2.1.0).
HTSeq (v0.6.0) was used to quantify the reads that mapped to each gene.
Gene expression levels were evaluated as transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: SmartSeq2.ReadCount.txt: Tab-delimited text file includes read count values for each sample.
Supplementary_files_format_and_content: SmartSeq2.TPM.txt: Tab-delimited text file includes TPM values for each sample.

source_name: Liver

growth_protocol: Human endoderm stem cells were generated from hPSCs and maintained in serum-free conditions as described previously (Cheng et al., 2012). For the hepatocyte differentiation, the EnSCs were dissociated into a single-cell suspension with 0.25% trypsin-EDTA, and then the cells were suspended in a 500 mL spinner flask at a density of 1×10e6 cells per milliliter in 300 mL hepatic specification medium, mixed with Matrigel at the final concentration of 4%, that contained ascorbic acid (Wako), MTG (Sigma), bFGF (10 ng/ml), TGF-α (20 ng/ml), EGF (10 ng/ml), VEGF (10 ng/ml), BMP4 (50 ng/ml), HGF (25 ng/ml), dexamethasone (Dex) (40 ng/ml, Sigma), and 1% DMSO (Sigma) (from day 0 to day 6, Stage I). From day 6 to day 12 (Stage II), the medium was replaced with hepatoblast formation medium containing ascorbic acid, MTG, bFGF (10 ng/ml), HGF (25 ng/ml), EGF (20 ng/ml), VEGF (10 ng/ml), oncostatin M (OSM) (20 ng/ml), Dex (40 ng/ml), 1% DMSO, Compound E (0.1 μM, Millipore), A83-01 (0.5 μM, Selleck), and Vitamin K1 (6 g/ml, Sangon). Then, the medium was changed to maturation medium, which contained ascorbic acid, MTG, HGF (25 ng/ml), OSM (20 ng/ml, PeproTech), Dex (40 ng/ml), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and erlotinib HCl (EGFi) (2 μM, Stemgent) (from day 12 to day 24, Stage 3H). The above differentiation medium was SFD-based (Cheng et al., 2012). From day 24, the hepatic spheres were cultured in hepatocyte culture medium (HCM, Lonza) that consisted of ascorbic acid, MTG, 8 bromo-cAMP (1 mM, Biolog), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and EGFi (2 μM) (from day 24 to day 30, Stage 4H). The medium was changed every 2 days. The cells were maintained in a 5% CO2, 5% O2, 90% N2 environment (from day 0 to day 18), and then in a 5% CO2/ambient air environment (from day 18 to day 30). The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise. For the cholangiocyte differentiation, the hepatoblasts were generated from EnSCs using the method as aforementioned. After hepatoblast formation, the hepatic spheres were cultured in SFD-based cholangiocyte specification medium containing ascorbic acid, MTG, FGF10 (50 ng/ml), Activin A (50 ng/ml), and retinoic acid (3 μM, Sigma) (from day 12 to day 15, Stage 3C). Then, the medium was changed to maturation medium, which contained HGF (25 ng/ml), EGF (50 ng/ml), TGF-β (5 ng/ml, PeproTech), Dex (40 ng/ml), and TPPB (0.5 μM, Calbiochem) (from day 16 to day 21, Stage 4C). The basic medium used for this final stage was biliary differentiation medium (BDM) (Sampaziotis et al., 2015). The cells were cultured in a 5% CO2, 5% O2, 90% N2 environment. The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise.

extract_protocol:
Single-cell RNA-seq was performed according to the Smart-seq2 protocol as reported previously (Picelli et al., 2014). After the cells were digested into a single-cell suspension, each single-cell sample was manually selected under a microscope with a mouth pipette and transferred into lysis buffer containing 1.9 µl of 0.2% Triton X-100 (Sigma), 1 µl of 10 µM oligo (dT) primer, 1 µl of 10 mM dNTP mix (New England Biolabs), 0.1 µl of 40 U/µl RNase inhibitor (New England Biolabs) and 0.05 µl of ERCC spike-in RNA (a dilution of 1:300,000, Life Technologies). After single-cell lysis, the sample was mixed with 0.29 µl H2O, 2 µl of 5× Superscript II first-strand buffer, 2 µl of 5 M Betaine (Sigma), 0.5 µl of 100 mM DTT, 0.06 µl of 1 M MgCl2, 0.1 µl of 100 µM TSO primer, 0.25 µl of 40 U/µl RNase inhibitor and 0.5 µl of 200 U/µl SuperScript II reverse transcriptase (Invitrogen). After reverse transcription was performed, 2.25 µl H2O, 12.5 µl KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and 0.25 µl of 10 µM IS PCR primer were added to the sample. Then, PCR preamplification was conducted for 18 cycles. Next, cDNA samples were purified with VAHTS DNA Clean Beads XP beads (Vazyme).
Purified cDNA (2 ng) was prepared for library construction using a TruePrep DNA Library Prep Kit (Vazyme) with a 0.4× standard reaction system, and PCR amplification was conducted for 8 cycles. Finally, the library was purified and size-selected, and fragments with a peak size of ~350 bp were analyzed with an Advanced Analytical Fragment Analyzer.


title: E_untreated_cho_3_16


title: BMDMs, 24h_LPS/3h_LPS, Irg1_KO-2


title: E_untreated_cho_3_14


title: BMDMs, Mock/3h_LPS, Irg1_KO-2


title: BMDMs, 24h_LPS, Irg1_KO-3


title: E_untreated_cho_3_13


title: E_untreated_cho_3_12


title: BMDMs, Mock/3h_LPS, WT-2


title: BMDMs, 24h_LPS/3h_LPS, WT-1


title: BMDMs, 24h_LPS, Irg1_KO-2


title: E_untreated_cho_3_10


title: E_untreated_cho_3_11


title: E_untreated_cho_3_09


title: E_untreated_cho_3_08


title: E_untreated_cho_3_07


title: BMDMs, 24h_LPS, WT-1


title: E17_FJW161014003_H10

city: Chuo-ku, Kobe

first: Hironobu

last: Fujiwara

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

institute: RIKEN

data_processing:
FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 42 -l 36 -k 4.0 -q 30' for HiSeq 1500, '-L 50 -l 36 -k 4.0 -q 30' for HiSeq 2500 and '-L 75 -l 36 -k 4.0 -q 30' for NextSeq. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '-p 4 --end-to-end'. Transcript levels were quantified as Transcripts Per Kilobase Million (TPM) with Sailfish (version 0.10.0) using GENCODE vM14 annotation file.
outside of the mean minus three standard deviations of the number of mapped reads to a sailfish index (Sailfish) or the number of assigned reads to gene regions (featureCounts, function of Subread version 1.5.0); over 10% reads assigning to mitochondrial RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
for count table, after convert Ensemble transcript_id to Gene_id, each isoform expression were summarized on gene level.
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: E17.0_whisker follicles cells

extract_protocol:
Single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa).
RamDA-seq sequencing libraries were prepared by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0).

value: whisker follicles cells

tag: data quality

value: ok


title: E17_FJW161014003_H12

value: low


title: E17_FJW161014003_H09


title: E17_FJW161014003_H11


title: BMDMs, Mock/3h_LPS, WT-1


title: Short stimulation TNF rep2

description: Sample 11


title: E_untreated_cho_3_06


title: BMDMs, 24h_LPS/3h_LPS, Irg1_KO-3


title: E_untreated_cho_3_05


title: E17_FJW161014003_H08


title: E17_FJW161014003_H07


title: E17_FJW161014003_H05


title: E17_FJW161014003_H06


title: E_untreated_cho_3_03


title: E_untreated_cho_2_32


title: E_untreated_cho_3_04


title: E_untreated_cho_3_01


title: E17_FJW161014003_H04


title: E_untreated_cho_2_31


title: E_untreated_cho_2_30


title: E17_FJW161014003_H03


title: E17_FJW161014003_H02


title: E17_FJW161014003_H01


title: E_untreated_cho_2_29


title: E_untreated_cho_3_02


title: E17_FJW161014003_G12


title: E17_FJW161014003_G11


title: E17_FJW161014003_G10


title: E_untreated_cho_2_26


title: E_untreated_cho_2_25


title: E_untreated_cho_2_27


title: E17_FJW161014003_G08


title: E17_FJW161014003_G07


title: E_untreated_cho_2_22


title: E_untreated_cho_2_23


title: E_untreated_cho_2_21


title: E17_FJW161014003_G04


title: E_untreated_cho_2_20


title: E17_FJW161014003_G06


title: E17_FJW161014003_G05


title: E17_FJW161014003_G03


title: E_untreated_cho_2_17


title: E17_FJW161014003_G02


title: E_untreated_cho_2_19


title: E_untreated_cho_2_28


title: E17_FJW161014003_G01


title: E_untreated_cho_2_18


title: E_untreated_cho_2_16


title: E_untreated_cho_2_15


title: E_untreated_cho_2_24


title: E17_FJW161014003_F12


title: Short stimulation IL1 rep2

description: Sample 10


title: E17_FJW161014003_G09


title: E_untreated_cho_2_14


title: E17_FJW161014003_F09


title: E_untreated_cho_2_12


title: E_untreated_cho_2_13


title: E17_FJW161014003_F08


title: E_untreated_cho_2_11


title: E_untreated_cho_2_09


title: E17_FJW161014003_F06


title: E17_FJW161014003_F05


title: E_untreated_cho_2_08


title: E17_FJW161014003_F11


title: E17_FJW161014003_F04


title: E_untreated_cho_2_07


title: E_untreated_cho_2_06


title: E17_FJW161014003_F03


title: E17_FJW161014003_F10


title: E17_FJW161014003_F02


title: E_untreated_cho_2_04


title: E_untreated_cho_2_05


title: E17_FJW161014003_F01


title: E_untreated_cho_2_03


title: E_untreated_cho_2_10


title: E17_FJW161014003_F07


title: E17_FJW161014003_E12


title: E17_FJW161014003_E09


title: E_untreated_cho_1_26


title: E_untreated_cho_1_27


title: E17_FJW161014003_E11


title: E_untreated_cho_2_02


title: E_untreated_cho_2_01


title: E17_FJW161014003_E10


title: E_untreated_cho_1_25


title: E17_FJW161014003_E07


title: E_untreated_cho_1_24


title: E17_FJW161014003_E08


title: Long stimulation control rep2

description: Sample 13

value: untreated


title: E17_FJW161014003_E06


title: E_untreated_cho_1_23


title: E17_FJW161014003_E04


title: E_untreated_cho_1_22


title: E17_FJW161014003_E01


title: E17_FJW161014003_E03


title: E17_FJW161014003_E02


title: E_untreated_cho_1_19


title: E_untreated_cho_1_20


title: E_untreated_cho_1_18


title: E_untreated_cho_1_21


title: E17_FJW161014003_D12


title: E17_FJW161014003_D10


title: E_untreated_cho_1_17


title: E_untreated_cho_1_15


title: Long stimulation control rep1

description: Sample 5


title: E_untreated_cho_1_16


title: E17_FJW161014003_D08


title: E17_FJW161014003_D07


title: E_untreated_cho_1_14


title: E_untreated_cho_1_13


title: E17_FJW161014003_D06


title: E_untreated_cho_1_11


title: E17_FJW161014003_D05


title: E_untreated_cho_1_12


title: E17_FJW161014003_D04


title: E17_FJW161014003_D03


title: E_untreated_cho_1_09


title: E_untreated_cho_1_10


title: E17_FJW161014003_D11


title: E17_FJW161014003_D09


title: E17_FJW161014003_D01


title: E17_FJW161014003_C12


title: E17_FJW161014003_C10


title: E_untreated_cho_1_08


title: E17_FJW161014003_C11


title: E_untreated_cho_1_07


title: E17_FJW161014003_C09


title: E_untreated_cho_1_06


title: E_untreated_cho_1_04


title: E_untreated_cho_1_03


title: E17_FJW161014003_C08


title: E_untreated_cho_1_02


title: E17_FJW161014003_C07


title: E_untreated_cho_1_01


title: E17_FJW161014003_D02


title: E17_FJW161014003_C04


title: E17_FJW161014003_C03


title: E_untreated_cho_1_05


title: E_untreated_hep_3_80

value: EnSC-derived EGFi-untreated hepatocyte


title: E_untreated_hep_3_79


title: E_untreated_hep_3_78


title: E_untreated_hep_3_77


title: E17_FJW161014003_C01


title: E_untreated_hep_3_76


title: E17_FJW161014003_B12


title: E_untreated_hep_3_75


title: E17_FJW161014003_C05


title: E17_FJW161014003_C06


title: E_untreated_hep_3_73


title: E17_FJW161014003_B09


title: E17_FJW161014003_B10


title: E17_FJW161014003_B11


title: E_untreated_hep_3_74


title: E_untreated_hep_3_72


title: E17_FJW161014003_B06


title: E_untreated_hep_3_70


title: E_untreated_hep_3_71


title: E17_FJW161014003_B05


title: E_untreated_hep_3_69


title: E_untreated_hep_3_68


title: E17_FJW161014003_C02


title: E17_FJW161014003_B04


title: E_untreated_hep_3_67


title: E_untreated_hep_3_66


title: E17_FJW161014003_B02


title: E17_FJW161014003_B01


title: E17_FJW161014003_A11


title: E17_FJW161014003_A10


title: E17_FJW161014003_B08


title: E17_FJW161014003_A09


title: E_untreated_hep_3_62


title: E_untreated_hep_3_61


title: E_untreated_hep_3_65


title: E_untreated_hep_3_63


title: E_untreated_hep_3_64


title: E17_FJW161014003_B07


title: E17_FJW161014003_A06


title: E17_FJW161014003_A08


title: E_untreated_hep_3_60


title: E17_FJW161014003_A07


title: E_untreated_hep_3_58


title: E_untreated_hep_3_59


title: E_untreated_hep_3_57


title: E17_FJW161014003_A05


title: E17_FJW161014003_A03


title: E17_FJW161014003_A04


title: E17_FJW161014003_B03


title: E_untreated_hep_3_56


title: E_untreated_hep_3_54


title: E17_FJW161014003_A02


title: E_untreated_hep_3_55


title: E17_FJW161014002_H12


title: E17_FJW161014003_A01


title: E17_FJW161014002_H11


title: E_untreated_hep_3_51


title: E17_FJW161014002_H09


title: E17_FJW161014002_H10


title: E17_FJW161014002_H07


title: E17_FJW161014002_H06


title: E_untreated_hep_3_50


title: E17_FJW161014002_H04


title: E_untreated_hep_3_53


title: E17_FJW161014002_H05


title: E17_FJW161014002_H02


title: E17_FJW161014002_G12


title: E17_FJW161014002_H01


title: E17_FJW161014002_G11


title: E17_FJW161014002_G10


title: E_untreated_hep_3_49


title: E_untreated_hep_3_47


title: E_untreated_hep_3_48


title: E_untreated_hep_3_44


title: E_untreated_hep_3_45


title: E_untreated_hep_3_46


title: E_untreated_hep_3_39


title: E_untreated_hep_3_43


title: E_untreated_hep_3_41


title: E_untreated_hep_3_37


title: E_untreated_hep_3_38


title: E_untreated_hep_3_42


title: E17_FJW161014002_H03


title: E_untreated_hep_3_52


title: E_untreated_hep_3_35


title: E_untreated_hep_3_36


title: E17_FJW161014002_G06


title: E17_FJW161014002_G08


title: E_untreated_hep_3_40


title: E_untreated_hep_3_34


title: E17_FJW161014002_G07


title: E17_FJW161014002_G05


title: E_untreated_hep_3_33


title: E_untreated_hep_3_32


title: E17_FJW161014002_G03


title: E17_FJW161014002_G04


title: E_untreated_hep_3_31


title: E_untreated_hep_3_30


title: E17_FJW161014002_G09


title: E_untreated_hep_3_29


title: E17_FJW161014002_F11


title: E17_FJW161014002_G02


title: E17_FJW161014002_G01


title: E17_FJW161014002_F10


title: E17_FJW161014002_F12


title: E_untreated_hep_3_28


title: E_untreated_hep_3_25


title: E_untreated_hep_3_27


title: E_untreated_hep_3_26


title: E17_FJW161014002_F09


title: E17_FJW161014002_F07


title: E_untreated_hep_3_23


title: E_untreated_hep_3_21


title: E17_FJW161014002_F06


title: E_untreated_hep_3_19


title: E_untreated_hep_3_22


title: E17_FJW161014002_F05


title: E17_FJW161014002_F03


title: E17_FJW161014002_F04


title: E17_FJW161014002_F02


title: E_untreated_hep_3_18


title: E17_FJW161014002_E12


title: E17_FJW161014002_F01


title: E_untreated_hep_3_24


title: E_untreated_hep_3_20


title: E17_FJW161014002_E10


title: E_untreated_hep_3_16


title: E17_FJW161014002_E11


title: E17_FJW161014002_E09


title: E_untreated_hep_3_13


title: E_untreated_hep_3_12


title: E17_FJW161014002_E06


title: E_untreated_hep_3_15


title: E_untreated_hep_3_14


title: E_untreated_hep_3_11


title: E_untreated_hep_3_09


title: E_untreated_hep_3_10


title: E17_FJW161014002_E07


title: E17_FJW161014002_E05


title: E_untreated_hep_3_08


title: E17_FJW161014002_E04


title: E_untreated_hep_3_07


title: E17_FJW161014002_F08


title: E17_FJW161014002_E03


title: E_untreated_hep_3_17


title: E_untreated_hep_3_06


title: E17_FJW161014002_E02


title: E17_FJW161014002_E01


title: E_untreated_hep_3_05


title: E17_FJW161014002_D12


title: E_untreated_hep_3_04


title: E17_FJW161014002_D11


title: E17_FJW161014002_E08


title: E_untreated_hep_3_03


title: E17_FJW161014002_D10


title: E_untreated_hep_3_01


title: E_untreated_hep_3_02


title: E_untreated_hep_2_29


title: E_untreated_hep_2_28


title: E17_FJW161014002_D06


title: E_untreated_hep_2_27


title: E17_FJW161014002_D05


title: E17_FJW161014002_D07


title: E_untreated_hep_2_26


title: E_untreated_hep_2_25


title: E_untreated_hep_2_24


title: E17_FJW161014002_D04


title: E17_FJW161014002_D02


title: E17_FJW161014002_D03


title: E_untreated_hep_2_22


title: E17_FJW161014002_D01


title: E_untreated_hep_2_23


title: E17_FJW161014002_H08


title: E17_FJW161014002_C11


title: E_untreated_hep_2_21


title: E17_FJW161014002_C12


title: E_untreated_hep_2_20


title: E_untreated_hep_2_18


title: E_untreated_hep_2_19


title: E17_FJW161014002_D09


title: E_untreated_hep_2_17


title: E_untreated_hep_2_16


title: E17_FJW161014002_C09


title: E17_FJW161014002_C08


title: E17_FJW161014002_D08


title: E17_FJW161014002_C10


title: E_untreated_hep_2_14


title: E17_FJW161014002_C05


title: E17_FJW161014002_C06


title: E17_FJW161014002_C04


title: E_untreated_hep_2_12


title: E_untreated_hep_2_15


title: E17_FJW161014002_C03


title: E_untreated_hep_2_11


title: E17_FJW161014002_C02


title: E17_FJW161014002_C01


title: E_untreated_hep_2_10


title: E_untreated_hep_2_09


title: E17_FJW161014002_B12


title: E17_FJW161014002_B11


title: E17_FJW161014002_B10


title: E_untreated_hep_2_06


title: E_untreated_hep_2_08


title: E17_FJW161014002_B09


title: E17_FJW161014002_B08


title: E_untreated_hep_2_04


title: E_untreated_hep_2_05


title: E17_FJW161014002_C07


title: E_untreated_hep_2_03


title: E17_FJW161014002_B06


title: E17_FJW161014002_B07


title: E_untreated_hep_2_13


title: E17_FJW161014002_B05


title: E_untreated_hep_2_02


title: E_untreated_hep_2_01


title: E17_FJW161014002_B04


title: E_untreated_hep_1_19


title: E_untreated_hep_1_18


title: E17_FJW161014002_B02


title: E17_FJW161014002_A11


title: E_untreated_hep_1_17


title: E_untreated_hep_1_15


title: E_untreated_hep_2_07


title: E17_FJW161014002_A10


title: E17_FJW161014002_A08


title: E_untreated_hep_1_14


title: E17_FJW161014002_A07


title: E_untreated_hep_1_12


title: E_untreated_hep_1_13


title: E17_FJW161014002_A06


title: E17_FJW161014002_A05


title: E_untreated_hep_1_10


title: E17_FJW161014002_A04


title: E_untreated_hep_1_09


title: E_untreated_hep_1_08


title: E17_FJW161014002_A03


title: E_untreated_hep_1_07


title: E17_FJW161014002_B03


title: E17_FJW161014002_A02


title: E17_FJW161014002_A01


title: E17_FJW161014001_H12


title: E17_FJW161014002_B01


title: E17_FJW161014001_H11


title: E_untreated_hep_1_05


title: E_untreated_hep_1_16


title: E17_FJW161014001_H10


title: E_untreated_hep_1_03


title: E_untreated_hep_1_02


title: E17_FJW161014001_H08


title: E_untreated_hep_1_01


title: E17_FJW161014001_H07


title: E17_FJW161014001_H06


title: E_untreated_hep_1_11


title: E17_FJW161014001_H05


title: E17_FJW161014001_H04


title: LNCaP cells, 15siNFYA_neg_S20

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

data_processing:
FastQC
Trimmomatic
FastQC
Kallisto
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Seperated Value files with RAWCOUNTS/TPM/FPKM values for each sample in two cell lines. This file is can directly be used for further differentially gene expression and pathway analyses

source_name: LNCaP

growth_protocol: Cells were maintened in RPMI 1640 supplemented with penicillin, streptomycin, sodium pyruvate, and 10% fetal bovine serum

extract_protocol:
RNA were purified using the RNeasy plus purification kit from QIAGEN.
NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina

treatment_protocol: Cells were seeded in RPMI 1640 media cotaining 5% of charcola stripped serum for 48h to allow seroid deprivation. Medica was then changed, and fresh media with 10nM R1881 or vehicle (96% EtOH) was added. After 24h treatment cell, cells were harvested.

value: LNCaP

tag: transfection

value: siNFYA

value: 96 % Ethanol


title: LNCaP cells, 17siNFYA_pos_S22

value: Synthetic Androgen (R1881)


title: LNCaP cells, 18siNFYA_pos_S23


title: E17_FJW161014001_H03


title: LNCaP cells, 14siNFYA_neg_S19


title: E_untreated_hep_1_06


title: E17_FJW161014001_H02


title: E17_FJW161014001_G12


title: LNCaP cells, 13siNFYA_neg_S18


title: E17_FJW161014001_H09


title: E_untreated_hep_1_04


title: LNCaP cells, 12siKLF5_pos_S17


title: E17_FJW161014001_H01


title: LNCaP cells, 16siNFYA_pos_S21


title: LNCaP cells, 10siKLF5_pos_S15


title: LNCaP cells, 11siKLF5_pos_S16


title: E17_FJW161014001_G10


title: E17_FJW161014001_G11


title: E17_FJW161014001_G09


title: LNCaP cells, 9siKF5_neg_S14


title: LNCaP cells, 8siKF5_neg_S13


title: LNCaP cells, 7siKF5_neg_S12


title: E17_FJW161014001_G07


title: E17_FJW161014001_G06


title: E17_FJW161014001_G05


title: LNCaP cells, 3siC_neg_S8

value: Control siRNA


title: E17_FJW161014001_G04


title: LNCaP cells, 4siC_pos_S9


title: E17_FJW161014001_F12


title: E17_FJW161014001_G08


title: LNCaP cells, 6siC_pos_S11


title: LNCaP cells, 5siC_pos_S10


title: LNCaP cells, 2siC_neg_S7


title: ELOF1_UV_rep2_SPPE_TagDir

description:
genomic DNA (ChIP)
genome used for mapping:
Hg38

data_processing:
ChIP-seq, BrU-seq and ATAC-seq data analyses: For RNAPII-Ser2 ChIP-seq, low-quality sequence reads and adapters were filtered out by Trimmomatic (v3.36) (A. M. Bolger et al, 2014). The trimmed reads were aligned to the human reference genome (GRC h37/hg19) with the Burrows-Wheeler Aligner (BWA-v0.7.12-r1039) (H. Li et al, 2013). Biobambam2 (v2.0.72) (G. Tischler et al, 2014) was used to remove duplicate reads from the aligned reads. Sequence reads were locally realigned and base-quality scores were recalibrated with the IndelRealigner and BaseRecalibrator programs in Genome Analysis Toolkit (GATK-v3.5) (McKenna et al, 2010).
For pan-RNAPII ChIP-seq, BrU-seq and ATAC-seq, reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (BWA (Version 0.7.16a) or STAR (Version 2.5.3a)) (H. Li et al, 2013; Dobin et al, 2013). Only high-quality reads (> q30) were included in the analyses and duplicates were removed using Samtools (Version 1.6) with fixmate -m and markdup -r settings (Table S7). Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (S. Heinz et al, 2010). A list of 49,948 genes was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the knownCanonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes should be non-overlapping with at least 2 kb between genes. Subsequent selection of sets of genes is described per analysis.
For ChIP-seq, binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Read densities in input samples were subtracted from individual ChIP-seq datasets to background-correct our data in which negative values were converted to 0, to prevent the use of impossible negative read densities in further calculations. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 3.5.3) (R. Core Team, R, 2019). ChIP-seq binding and metagene profiles were averaged per set of genes and profiles were normalized to area under the curve to allow proper comparison of the profiles without effects of overall differences in read density.
ATAC-seq and BrU-seq heatmaps were generated as described for ChIP-seq analyses, except for the input subtraction and removal of negative values. BrU-seq aggregated profiles, were defined using the AnnotatePeaks.pl tool or makeMetaGeneProfile.pl tool of HOMER using the default normalization to 10mln reads, as for ChIP-sequencing. Genes were selected on size and strongest binding of RNAPII at the TSS in undamaged condition, as for ChIP-sequencing. Averaged binding profiles were subsequently normalized to nascent transcript levels, as quantified by 5-EU labelling, relative to the control in their specific cell type. For example, WT cells 3 h after UV irradiation showed 35% RNA relative to WT control cells, so we multiplied the expression of the bins by 0.35.  RNA-seq analyses: Obtained sequencing reads were cleaned by 5'-end quality trimming and Illumina-adapter clipping by Trimmomatic (A. M. Bolger et al, 2014). Pre-alignment quality control of the cleaned sequencing reads was done with FastQC. The alignment to reference genome hg19 of trimmed sequencing reads was done with Hisat2, guided by gene annotation in the refGene UCSC table (D. Kim et al, 2015). The generated SAM files were converted to the binary counterpart BAM, followed by BAM sorting and indexing with SAMtools (H. Li et al, 2009).  Counting reads to the UCSC's genomic features hg19 was performed by Subread/featureCounts (Y. Liao et al, 2014). Differential expression analysis was carried out, using edgeR (M. D. Robinson et al, 2010). Only genes indicating at least 2 counts per million in at least 20% of samples were included in the analysis. Data were normalized for sample specific effects by the trimmed mean of M-values. This was followed by estimating the dispersion and determining the differentially expressed genes using the general linear model (GLM). FDR-adjusted p-values < 0.05 were considered significant.
Genome_build: hg19 or hg38 as indicated per sample
Supplementary_files_format_and_content: excel tables providing stranded metagene profiles for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

source_name: RPE1-iCas9 ELOF1-KO

extract_protocol:
ATAC-seq: For each experimental condition 50.000 cells were harvested and washed with cold PBS containing protease inhibitors (Roche). The cells were resuspended in 50  l Transposase mixture, containing 1x Tagment DNA buffer Illumina Kit, #20034197), 0.5  l Tagment DNA enzyme (Illumina Kit, #20034197) and 0,2  g/ l Digitonin (Promega, #G9441), and incubated at 37  C for 30 min. Fragmented DNA was purified using a Qiagen MinElute kit (#28204).  BrU-seq: For BrU(DRB)-seq, cells were pre-treated with 100  M DRB for 1-3hrs (as indicated per sample) after which cells were washed with PBS and immdeidately, or 30 min later, incubated with 2 mM bromouridine (Bru) at 37 C for 15 or 30 min. For regular BrU-seq, cells were either mock-treated or irradiated with UV-C light (9 J/m2). Cells were then incubated in conditioned media for different periods of time before being incubated with 2 mM bromouridine (Bru) at 37 C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015). ChIP-seq: Cells were mock treated or UV-irradiated with 9 J/m2 and incubated in conditioned media for different periods of time (1, 4, 8, 16 h). Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1% PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4 C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3  g antibody (Antibodies are listed in Table S3) overnight at 4 C, followed by a 1.5 h protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65 C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.  RNA-seq: Cells were UV-irradiated (254 nm, 9 J/m2) or mock-treated and harvested 24 h later. Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. Up to 5   106 cells per sample were lysed in RLT buffer. For quantification purposes, 24 ng of the eight ArrayControl(tm) RNA Spikes (Thermo Fisher Scientific) were added to each sample (3 ng/spike).
ATAC-seq: Libraries were prepared by PCR using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) and Nextera XT index Kit v2 (Illumina). Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Indicated is whether single-end or paired-end sequencing data was used for downstream analyses ChIP-seq: For RNAPII-Ser2 ChIP-seq sample libraries were prepared from 1 ng ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) and index primer sets (NEB, E7335S). Strand-biased library amplification was performed using high-fidelity KAPA HiFi Enzyme (Roche, KK2102). The prepared libraries were sequenced on an Illumina HiSeq 2500 system (Illumina), resulting in 150 bp paired-end reads. For the remaining ChIP-seq samples, libraries were prepared using kapa hyper prep kit (Roche) and A-T mediated ligation of full Y-shaped IDT adapters. Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. RNA-seq: Samples were purified using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's instructions, and sequenced in a single lane on an Illumina HiSeq4000.

tag: uv-c dose

tag: time after uv-c

value: 8 hours

tag: chip-antibody

value: Pan-RNAPII (Bethyl; A304-405A)


title: E17_FJW161014001_F11


title: ELOF1_UV_rep1_SPPE_TagDir


title: E17_FJW161014001_F08


title: ELOF1_mock_rep2_SPPE_TagDir

value: mock

value: not applicable


title: ELOF1_UV1hrs_rep1_SPPE_TagDir

value: 1 hour


title: E17_FJW161014001_F09


title: ELOF1_UV1hrs_rep2_SPPE_TagDir


title: E17_FJW161014001_F07


title: E17_FJW161014001_F10


title: E17_FJW161014001_F06


title: ELOF1_mock_rep1_SPPE_TagDir


title: ELOF1_input_rep2_SSPE_TagDir


title: ELOF1_input_rep1_SPPE_TagDir


title: E17_FJW161014001_F03


title: E17_FJW161014001_F05


title: WT_UV_rep2_SPPE_TagDir

source_name: RPE1-iCas9 WT

value: WT


title: E17_FJW161014001_G03


title: E17_FJW161014001_F02


title: E17_FJW161014001_G01


title: LNCaP cells, 1siC_neg_S6

tag: treatment


title: E17_FJW161014001_F01


title: WT_UV1h_rep2_SSPE_TagDir


title: WT_UV1h_rep1_SSPE_TagDir


title: WT_UV_rep1_SPPE_TagDir


title: E17_FJW161014001_E12


title: WT_mock_rep1_SPPE_TagDir


title: WT_mock_rep2_SPPE_TagDir


title: WT_input_rep2_SSPE_TagDir


title: E17_FJW161014001_E10


title: WT_input_rep1_SPPE_TagDir


title: E17_FJW161014001_E08


title: E17_FJW161014001_E07