title: culture_RNA_MeCP2_KD_8

description: mixed (males and females)

data_processing:
Raw FASTQ files were trimmed with Trim Galore and rRNA sequences were filtered out using Bowtie and Mus Musculus rRNA sequences. The unaligned reads from this step were then aligned to mm9 using STAR. Uniquely mapped reads were converted to BED files. Intronic and exonic reads were then separated. Bedtools coverage -counts parameter was used to quantify read coverage in genes.
Assembly: mm9

extract_protocol:
At 12 days in vitro (DIV12), primary neuron cultures were harvested and total RNA was extracted using RLT buffer following RNeasy Mini Kit (Qiagen).
RNA was rRNA depleted using NEBNext rRNA Depletion Kit (NEB). RNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit with NEBNext Mulitplex Oligos for Illumina (NEB) following manufacturer's protocols.
Libraries were pooled to a final concentration of 4-10nM and reads were generated on the Illumina Nextseq 500 with the Center for Genome Science at Washington University in St. Louis, typically yielding 15-40 million single-end reads per sample.

value: primary neuron cultures

value: Embryonic day (E) 14.5

value: MeCP2 knockdown


title: culture_RNA_MeCP2_KD_7

status: Public on Nov 11 2023

type: SRA

city: St. Louis

first: Harrison

last: Gabel

state: MO

address: 4523 Clayton Ave

department: Neuroscience

country: USA

institute: Washington University in St. Louis

description: mixed (males and females)

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: primary neuron cultures

growth_protocol: Primary neurons were cultured in neurobasal medium with 5% fetal bovine serum, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic and maintained at 37oC with 5% CO2. Neurons were grown in vitro for 3 days. At DIV3 and DIV9, cells were fed with neurobasal medium with 4.84 ug/mL uridine 5’-triphosphate, 2.46 ug/mL 5-fluoro-2’-deoxyuridine, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic.

treatment_protocol: Primary neuron cultures were transduced with lentivirus at an MOI of 3 on days in vitro (DIV3).

tag: tissue

tag: age

tag: genotype


title: ATAC_exp1_sgBPTF-2_rep1

city: London

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

library_source: genomic

data_processing:
The sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.4.5), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in Picard Tools (v2.16.0).
The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized read density profiles, using a read extension of 0 bps.
A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), then merging all peaks within 500 bp, and counting reads with version 1.6.1 of featureCounts (http://subread.sourceforge.net). Comparison of intra vs inter-group clustering in principle component analysis was used to determine normalization strategy, using either the median ratio method of DESeq2 or a sequencing depth-based factor normalized to ten million uniquely mapped fragments.
Differential enrichment was scored using DESeq2 for all pairwise group contrasts. Peak-gene associations were created using linear genomic distance to the transcription start site.
Assembly: GRCh38/hg38
Supplementary files format and content: DESEq2 output table

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

growth_protocol: RPMI 1640, GlutaMAX supplement, sodium pyruvate medium containing 10% heat-inactivated FBS and 1x Penicillin/Streptomycin

extract_protocol: Corces MR, Trevino AE, Hamilton EG, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017;14(10):959-962. doi:10.1038/nmeth.4396

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for sequencing 4 days post-transduction

value: blood

tag: cell line

tag: cell type

value: monocyte

value: BPTF KO

tag: treatment

value: lentiviral transduction


title: culture_RNA_MeCP2_KD_6

description: mixed (males and females)


title: KD-A32B-CUT_Tag-1

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

country: China

institute: Zhejiang University

description:
KD-A32B-CUT_Tag-1
KD-A32B-CUT_Tag-peaks.bed
KD-A32B-CUT_Tag.bw

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the human genome (hg38) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed –nodiscordant --local --very-sensitive-local --phred33 -I 10 -X 700.
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 -f BAMPE --keep-dup all -g hs. For peak calling of histone modifications, --broad should be added.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
assembly: hg38
Supplementary files format and content:bigwig, peakfile text file
Library strategy: CUT&Tag

source_name: MEL1 hESC line

growth_protocol: hESCs were cultured in hESC medium: DMEM/F12 (Life Technologies), 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 0.055 mM 2-mercaptoethanol (Sigma), 1× Penicillin/Streptomycin, and 10 ng ml-1 bFGF (Peprotech). hESCs were maintained on CF1 feeder cells at 37°C and 5% CO2.

extract_protocol:
CUT&Tag assay was performed using NovoNGS_ CUT&Tag High- Sensitivity Kit (Novoprotein) according to the manufacturer’s recommendation.
We used TruePrep DNA Library Prep Kit V2 for library construction.

treatment_protocol: We performed shCTR or shNAT10 lentivirus transfection in hESCs.

value: MEL1 hESC line

value: Human embryonic stem cells

value: NAT10 KD

tag: chip antibody

value: ANP32B (ProteinTech, 10843-1-AP)


title: wild type, borrelidin, rep 17

city: Tempe

first: Blaise

middle: L

last: Mariner

state: AZ

address: 427 E Tyler Mall, LSC 356

department: School of Life Sciences and Center for Evolution and Medicine

institute: Arizona State University

data_processing:
fastqc
fastp
HISAT2
featurecounts
Assembly: R68
Supplementary files format and content: gene, counts

organism: Saccharomyces cerevisiae

source_name: Borrelidin

extract_protocol: Zymo RNA extraction

value: yeast cells

value: wild type

value: Borrelidin


title: culture_RNA_MeCP2_KD_5

description: mixed (males and females)


title: WT-H3K27me3-2

description:
WT-H3K27me3-2
WT-H3K27me3-peaks.bed
WT-H3K27me3.bw

value: WT


title: culture_RNA_MeCP2_KD_4

description: mixed (males and females)


title: WT-H3K27me3-1

description:
WT-H3K27me3-1
WT-H3K27me3-peaks.bed
WT-H3K27me3.bw


title: KD-H3K27me3-2

description:
KD-H3K27me3-2
KD-H3K27me3-peaks.bed
KD-H3K27me3.bw


title: KD-H3K27me3-1

description:
KD-H3K27me3-1
KD-H3K27me3-peaks.bed
KD-H3K27me3.bw


title: wild type, borrelidin, rep 15


title: A32B-WT-ATAC-2

description:
A32B-WT-ATAC-2
A32B-WT-ATAC-peaks.bed
A32B-WT-ATAC.bw

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the human genome (hg38) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed --no-discordant -X 2000 --local
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 -f BAMPE --keep-dup all -g hs.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
assembly: hg38
Supplementary files format and content:bigwig, peakfile text file

extract_protocol:
hESCs were lysed by lysis buffer (10 mM NaCl, 3 mM MgCl2, 10 mM Tris pH 7.4, and 0.1% NP-40) and the nuclei were resuspended in transposition reaction mix (50% DMF, 50 mM Tris pH 7.5, 20 ng/μl Tn5 transposome and 250 mM MgCl2) and incubated at 55 °C for 10 min.
We used transposed DNA, i5 primer, i7 primer and 2X HiFi polymerase mix to amplify library. PCR reaction was incubated at 72 °C for 5 min, and then 98 °C for 30 s, 14 cycles of 98 °C for 15 s and 60 °C for 30 s, followed by 72 °C for 5 min.

treatment_protocol: We performed shCTR, shNAT10 and shANP32B lentivirus transfection in hESCs.


title: wild type, borrelidin, rep 16


title: gcn4, borrelidin, rep 12


title: culture_RNA_MeCP2_KD_3

description: mixed (males and females)


title: WT-H3K4me3-1

description:
WT-H3K4me3-1
WT-H3K4me3-peaks.bed
WT-H3K4me3.bw


title: KD-H3K4me3-2

description:
KD-H3K4me3-2
KD-H3K4me3-peaks.bed
KD-H3K4me3.bw


title: A32B-KD-ATAC-2

description:
A32B-KD-ATAC-2
A32B-KD-ATAC-peaks.bed
A32B-KD-ATAC.bw


title: culture_RNA_MeCP2_KD_2

description: mixed (males and females)


title: wild type, borrelidin, rep 13


title: wild type, borrelidin, rep 14


title: A32B-WT-ATAC-1

description:
A32B-WT-ATAC-1
A32B-WT-ATAC-peaks.bed
A32B-WT-ATAC.bw


title: N10-WT-ATAC-2

description:
N10-WT-ATAC-2
N10-WT-ATAC-peaks.bed
N10-WT-ATAC.bw


title: culture_RNA_MeCP2_KD_1

description: mixed (males and females)


title: gcn4, borrelidin, rep 11


title: culture_RNA_MeCP2_OE_8

description: mixed (males and females)

value: MeCP2 overexpression


title: culture_RNA_MeCP2_OE_7

description: mixed (males and females)


title: N10-WT-ATAC-1

description:
N10-WT-ATAC-1
N10-WT-ATAC-peaks.bed
N10-WT-ATAC.bw


title: A32B-KD-ATAC-1

description:
A32B-KD-ATAC-1
A32B-KD-ATAC-peaks.bed
A32B-KD-ATAC.bw


title: gcn4, borrelidin, rep 10


title: culture_RNA_MeCP2_OE_6

description: mixed (males and females)


title: WT-H3K4me3-2

description:
WT-H3K4me3-2
WT-H3K4me3-peaks.bed
WT-H3K4me3.bw


title: N10-KD-ATAC-1

description:
N10-KD-ATAC-1
N10-KD-ATAC-peaks.bed
N10-KD-ATAC.bw


title: gcn4, borrelidin, rep 9


title: HiC_sgSMARCA5_rep1

data_processing:
Hi-C data was processed using HiC-Pro v2.11.1 1. The sequence reads were mapped onto the reference genome hg38 with a minimum mapping quality of 30 and binned at 10kb, 25kb and 40kb.
A genome coordinate file in Bed format on DpnII and HinfI restriction fragments was generated using the genome digestion tool from HiC-Pro. Other settings associated with HiC-Pro were kept as default. Uniquely mapped paired-end reads were retained and mapped to DpnII and HinfI-restricted fragments.
Replicates were pooled for each sample to obtain 267M/223M/431M validate interactions in sgBPTF KO/sgSMARCA5 KO/sgNegCtrl samples. The pooled interactions were subsequently rendered into the .hic format by the tool provided by HiC-Pro. The final Hi-C matrices were binned at 25kb, and the median counts per bin are ~ 2700 in the range of ~2600 – 2850.
Topologically associated domains (TADs) were called using hicFindTADs from HiCExplorer (3.4.3)
Assembly: GRCh38/hg38
Supplementary files format and content: Excel spreadsheet with TADs called by HiCExplorer

extract_protocol:
Hi-C was performed using the Arima Hi-C Kit according to the manufacturer’s protocol.
Hi-C was performed using the Arima Hi-C Kit according to the manufacturer’s protocol.

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for HiC analysis 4 days post-transduction

value: SMARCA5 KO


title: HiC_sgSMARCA5_rep2


title: KD-H3K4me3-1

description:
KD-H3K4me3-1
KD-H3K4me3-peaks.bed
KD-H3K4me3.bw


title: culture_RNA_MeCP2_OE_5

description: mixed (males and females)

value: primary neuron cultures


title: HiC_sgBPTF_rep2


title: HiC_sgBPTF_rep1


title: culture_RNA_MeCP2_OE_4

description: mixed (males and females)

value: Embryonic day (E) 14.5


title: gcn4, borrelidin, rep 8


title: gcn4, borrelidin, rep 6


title: culture_RNA_MeCP2_OE_2

description: mixed (males and females)


title: culture_RNA_MeCP2_OE_3

description: mixed (males and females)


title: HiC_sgNegCtrl_rep2


title: gcn4, borrelidin, rep 7


title: rMSA_INS_1

city: beijing

first: Anji

last: Ju

state: beijing

address: Tsinghua University,Beijing,China

institute: Tsinghua University

data_processing:
For each sample, a total of >20 M reads (single-end, 50 nt) were produced. Adapters were then deleted, and the reads were quality filtered utilizing Trimmomatic ver. 0.33, with the average base quality score cutoff threshold set at 20 over a three-base window. Reads with a post-trimming length of less than 20 bases were excluded.
Assembly: STAR version STAR 2.5.2b was used to map the cleaned reads to the Mus musculus genome reference (GRCm38). The featureCounts function of the subread package version 1.6.0 was used to calculate the number of reads aligned to the exon regions of each of the identified genes. Multiple mapped reads and reads overlapping with multiple features were excluded.
Supplementary files format and content: TPM

growth_protocol: Male B6.Cg-dock7m Leprdb/++/J (db/db) mice were housed in a sterile barrier environment at 23 °C with a 12-hour cycle of light and darkness, and fed with irradiation-sterilized JAX-standard breeder chow. Mouse hepatocytes AML12 were cultured with DMEM/F12 medium (Gibco) supplemented with 10% FBS, 10 μg/ml insulin, 5.5 mg/ml transferrin, 5 ng/ml selenium, 40 ng/ml dexamethasone, and 15 mM HEPES.

extract_protocol:
The mirVana RNA Isolation Kit (Life Technologies) was used to isolate total hepatic or cellular mRNAs.  Agilent 2200 TapeStation Nucleic Acid System was used to determine the RNA integrity number (RIN) and concentration of all RNA samples (Agilent, CA). For the construction of the cDNA library, RNA samples having a RIN greater than 8.5 were employed. rRNA was depleted using hybridization capture to facilitate the identification of protein-coding RNAs.
DNase I degrade double-stranded and single-stranded DNA contaminant in RNA samples. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription, then was followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were  ligated to the ends of these 3’ adenylated cDNA fragments. This process is to amplify the cDNA fragments with adaptors from previous step. PCR products are purified with the SPRI beads, and dissolved in EB solution. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was validating on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: Mice in the rMSA-treated group (n=3) were i.v. injected with rMSA in a dose of 1.5 mg per gram of body weight, while the control group mice were injected with isometric saline. The mice received one injection every 3 weeks, total 3 injections for 9 weeks. AML12 hepatocytes were washed twice with warm PBS and starved in serum-free DMEM overnight. Then the AML12 hepatocytes were respectively treated with vehicle, insulin (10 nM), rMSA (600 μM), or insulin+rMSA for 24h.

value: hepatocyte

value: rMSA+insulin


title: culture_RNA_MeCP2_OE_1

description: mixed (males and females)


title: HiC_sgNegCtrl_rep1

value: blood

value: monocyte


title: gcn4, borrelidin, rep 5


title: culture_RNA_WT_4

description: mixed (males and females)


title: rMSA_3

value: rMSA


title: gcn4, borrelidin, rep 4


title: N10-KD-ATAC-2

description:
N10-KD-ATAC-2
N10-KD-ATAC-peaks.bed
N10-KD-ATAC.bw

value: MEL1 hESC line


title: Decay, Total RNA from Hela with 4sU+UVA+Flavo, 2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
RNA-seq-spike in
decay_exon_4sU_UVA_Fla_vs_mock.txt
decay_intron_4sU_UVA_Fla_vs_mock.txt

data_processing:
Basic QC and mapping were performed using snakePipes v.2.5.1
Reads were trimmed using cutadapt2.8 and aligned to the hg38  genome assembly using STAR2.7.4a.
Counts for individual genes were obtained using featureCounts.
Differential expression analysis was performed using DESeq2 1.26.0.
For FLASH: Adapters were trimmed and libraries were demultiplexed using bctools (v.0.2.0) and Flexbar (v2.5). Reads were mapped to reference genome using bowtie2 (v.2.2.6).
Assembly: hg38
Supplementary files format and content: DESeq2 LFC output in tsv format, DHX9 peaks as bed files:
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing sgRNA from arsenite vs HS treatments)
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing sgRNA from arsenite vs NaCl treatments)
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing sgRNA from arsenite vs UV treatments)
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing sgRNA from HS vs NaCl treatments )
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing sgRNA from HS vs UV treatments )
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing sgRNA from NaCl vs UV )
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing totRNA from mock vs arsenite treatments )
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing totRNA from mock vs HS treatments )
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing totRNA from mock vs NaCl treatments )
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv (normalized DESeq output counts for comparing totRNA from mock vs UV treatments )
featureCounts_exon_counts.tsv (featureCounts matrix with counts summarized at exon level)
featureCounts_geneBody_counts.tsv (featureCounts matrix with counts summarized at gene level)
DHX9_WTpeaks.bed (DHX9 peaks from FLASH data in HeLa cells)
totalRNA_corrected_sampleSheet.tsv (the main sample sheet used for DESeq analysis)
decay_exon_4sU_UVA_Fla_vs_mock.txt (DESeq2 differential analysis of exon counts from 4sU + UVA treated cells between Flavopiridol and mock treatment)
decay_exon_untreated_Fla_vs_mock.txt (DESeq2 differential analysis of exon counts from untreated cells between Flavopiridol and mock treatment)
decay_intron_4sU_UVA_Fla_vs_mock.txt (DESeq2 differential analysis of intron counts from 4sU + UVA treated cells between Flavopiridol and mock treatment)
decay_intron_untreated_Fla_vs_mock.txt (DESeq2 differential analysis of intron counts from untreated cells between Flavopiridol and mock treatment)
Puroseq-Deseq2-low_vs_high.tsv (DESeq2 differential analysis of puro-low_vs_puro_high)
Puroseq-Deseq2-UVA_vs_mock.tsv (DESeq2 differential analysis of UVA_vs_puro_low)
Puroseq-Deseq2-4sU_vs_mock.tsv (DESeq2 differential analysis of 4sU_vs_puro_low)
Puroseq-Deseq2-high_vs_mock.tsv (DESeq2 differential analysis of puro-high_vs_mock)
Puroseq-Deseq2-low_vs_mock.tsv (DESeq2 differential analysis of puro-low_vs_puro_low)

source_name: Hela

extract_protocol:
Total RNA from cells was collected using Trizol and purified using Zymo Research DirectZol RNA Mini Prep Kit. Total RNA from FANCI was collected by Zymo Research Oligo Clean & Concentrator Kits. Standard FLASH protocol was followed for DHX9 (Ilik et al., 2019).
Libraries were prepared according to the instructions of Illumina's Stranded Total RNA with RiboZero Plus kit for total RNA-Seq and according to the previously published protocol for FLASH (Ilik et al., 2019).
RiboZero RNA-Seq, FLASH library using s-oligo

value: Hela

value: Wild Type

tag: library type

value: RNA-seq-spike in


title: gcn4, borrelidin, rep 3

value: yeast cells


title: rMSA_2


title: culture_RNA_WT_3

description: mixed (males and females)


title: gcn4, borrelidin, rep 2


title: Decay, Total RNA from Hela with 4sU+UVA+Flavo, 1


title: gcn4, borrelidin, rep 1


title: rMSA_1


title: rMSA_INS_3


title: culture_RNA_WT_2

description: mixed (males and females)


title: Decay, Total RNA from Hela with 4sU+UVA, 3


title: wild type, borrelidin, rep 11

value: wild type


title: Decay, Total RNA from Hela with 4sU+UVA, 1


title: rMSA_INS_2


title: Vehicle_3

value: Vehicle


title: INS_3

value: WT

value: Insulin


title: Decay, Total RNA from Hela with 4sU+UVA, 2


title: wild type, borrelidin, rep 12

value: Borrelidin


title: Vehicle_2


title: Decay, Total RNA from Hela with 4sU+UVA+Flavo, 3


title: INS_2


title: culture_ChIP_MeCP2_KD_TOP2b_A300-950A_IP_2

description: mixed (males and females)

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated. Bedtools coverage -counts parameter was used to quantify ChIP signal at transcriptional start site (TSS), promoter associated region, defined as 1kb upstream to 3kb downstream of the TSS, and at the gene body, defined as 3kb downstream of the TSS to the transcription end site (TES). edgeR was then used to determine differential ChIP-signal across conditions. Bigwig files were generated using bedtools genomecov to convert reads to bedgraph format. Bedgraphs were normalized to counts per million (cpm) and then converted to bigWigs.
Assembly: mm9
Supplementary files format and content: bigwig

extract_protocol:
At 12 days in vitro (DIV12), primary neuron cultures were fixed 1% formaldehyde for 10 minutes. After quenching and cell lysis, to fragment DNA, the lysates were sonicated with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). ChIP was performed with H3K27ac (Abcam ab4729) and TOP2B (Fortis Life Sciences, A300-950A).
ChIP libraries for H3K27ac were generated using Ovation Ultralow Library System V2 (NuGEN) and for TOP2B  using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences).
Libraries were pooled to a final concentration of 4-10nM and reads were generated on the Illumina Nextseq 500 with the Center for Genome Science at Washington University in St. Louis, typically yielding 15-40 million single-end reads per sample.

value: primary neuron cultures

tag: viral treatment

value: MeCP2 knockdown

tag: antibody

value: Topo II b (Fortis Life Sciences, A300-950A)


title: INS_1

value: hepatocyte


title: culture_ChIP_WT_TOP2b_A300-950A_IP_2

description: mixed (males and females)

value: Embryonic day (E) 14.5


title: Decay, Total RNA from Hela with Flavo, 3

description:
RNA-seq-spike in
decay_exon_untreated_Fla_vs_mock.txt
decay_intron_untreated_Fla_vs_mock.txt

value: Flavopiridol


title: Decay, Total RNA from Hela with Flavo, 1


title: culture_RNA_WT_1

description: mixed (males and females)


title: wild type, borrelidin, rep 10


title: Liver_rMSA_3

source_name: liver

value: liver

value: B6.Cg-dock7m Leprdb/++/J (db/db)

value: rMSA


title: culture_ChIP_WT_TOP2b_A300-950A_IP_1

description: mixed (males and females)


title: Decay, Total RNA from Hela, 2

value: Hela

value: untreated

value: Wild Type


title: wild type, borrelidin, rep 9

value: yeast cells

value: wild type


title: Decay, Total RNA from Hela with Flavo, 2

value: RNA-seq-spike in


title: Vehicle_1

value: WT

value: Vehicle


title: culture_ChIP_MeCP2_OE_TOP2b_A300-950A_IP_1

description: mixed (males and females)

value: primary neuron cultures

value: MeCP2 overexpression


title: Liver_rMSA_2


title: culture_ChIP_MeCP2_KD_TOP2b_A300-950A_IP_1

description: mixed (males and females)

value: MeCP2 knockdown

value: Topo II b (Fortis Life Sciences, A300-950A)


title: culture_ChIP_WT_H3K27ac_IP_2

description: mixed (males and females)

value: Embryonic day (E) 14.5

value: Histone H3 acetyl K27 (Abcam, ab4729)


title: Liver_rMSA_1

value: liver


title: Decay, Total RNA from Hela, 1


title: wild type, borrelidin, rep 5

value: Borrelidin


title: Decay, Total RNA from Hela, 3


title: wild type, borrelidin, rep 8


title: culture_ChIP_WT_Input_2

description: mixed (males and females)


title: wild type, borrelidin, rep 6


title: culture_ChIP_MeCP2_OE_TOP2b_A300-950A_IP_2

description: mixed (males and females)


title: wild type, borrelidin, rep 4


title: Puroseq, Total RNA from Hela with 4sU+UVA(4sU+UVA)-low, 3

description:
RNA-seq
Puroseq-Deseq2-low_vs_mock.tsv
Puroseq-Deseq2-low_vs_high.tsv

value: RNA-seq


title: Liver_Saline_3

value: B6.Cg-dock7m Leprdb/++/J (db/db)

value: saline


title: wild type, borrelidin, rep 7


title: cortex_eTIP_MeCP2_KO_500uM_ETOP_TOP2B_A300-950A_3

description: male

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated. Bedtools coverage -counts parameter was used to quantify eTIP signal at promoter associated region, defined as 1kb upstream to 3kb downstream of the transcription start site (TSS), and at the gene body, defined as 3kb downstream of the TSS to the transcription end site (TES). edgeR was then used to determine differential eTIP-signal across conditions. Bigwig files were generated using bedtools genomecov to convert reads to bedgraph format. Bedgraphs were normalized to counts per million (cpm) and then converted to bigWigs.
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: eTIP-Seq

extract_protocol:
Acute cortical slices were treated with 0.5mM etoposide (VP-16) for 15 minutes at 37oC. To fragment DNA, the lysates were sonicated with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). eTIP was performed with TOP2B (Fortis Life Sciences, A300-950A) or TOP2B (Santa Cruz, sc-13059).
At 12 days in vitro (DIV12), primary neuron cultures were treated with etoposide (VP-16) and incubated at 37oC. To fragment DNA, the lysates were sonicated with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). eTIP was performed with TOP2B (Fortis Life Sciences, A300-950A) or TOP2B (Santa Cruz, sc-13059).
eTIP libraries were generated using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences).
Libraries were pooled to a final concentration of 4-10nM and reads were generated on the Illumina HiSeq 3000 with the Genome Technology Access Center or generated on the Illumina Nextseq 500 with the Center for Genome Science at Washington University in St. Louis, typically yielding 15-40 million single-end reads per sample.

value: MeCP2 knockout

value: 8-10 weeks old

value: etoposide


title: NC_6

city: Guangzhou

first: Zhuohui

last: Luo

address: Jichang Road 12th

institute: Guangzhou University of Chinese Medicine

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp (v 0.11.5).
The low quality reads were removed to obtain the clean reads.
Then clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT2 (v 2.2.1.0). FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 (v 1.20.0).
Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drawn to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include FPKM and counts values for each Sample.

source_name: Lung tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Lung tissue

value: NC

tag: time


title: Liver_Saline_2


title: cortex_eTIP_MeCP2_KO_500uM_ETOP_TOP2B_A300-950A_1

description: male


title: Puroseq, Total RNA from Hela with 4sU+UVA(4sU+UVA)-low, 2

value: Hela

value: Wild Type


title: wild type, borrelidin, rep 3

value: yeast cells

value: wild type


title: culture_ChIP_WT_Input_1

description: mixed (males and females)

value: primary neuron cultures


title: Puroseq, Total RNA from Hela with 4sU+UVA(4sU+UVA)-low, 1


title: Puroseq, Total RNA from Hela with 4sU+UVA(4sU+UVA)-high, 3

description:
RNA-seq
Puroseq-Deseq2-high_vs_mock.tsv
Puroseq-Deseq2-low_vs_high.tsv


title: Liver_Saline_1


title: wild type, borrelidin, rep 1


title: NC_4

value: WT


title: wild type, borrelidin, rep 2


title: cortex_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_4

description: male

value: wildtype

value: Topo II b (Fortis Life Sciences, A300-950A)


title: culture_ChIP_WT_H3K27ac_IP_1

description: mixed (males and females)

value: Embryonic day (E) 14.5

value: Histone H3 acetyl K27 (Abcam, ab4729)


title: Puroseq, Total RNA from Hela with 4sU, 3

description:
RNA-seq
Puroseq-Deseq2-4sU_vs_mock.tsv

value: RNA-seq


title: Puroseq, Total RNA from Hela with 4sU+UVA(4sU+UVA)-high, 2


title: Puroseq, Total RNA from Hela with 4sU, 1

description:
RNA-seq
Puroseq-Deseq2-4sU_vs_mock.tsv


title: rpl31a, vehicle, rep 12

source_name: Vehicle

value: Vehicle


title: cortex_eTIP_MeCP2_KO_500uM_ETOP_TOP2B_A300-950A_2

description: male

value: MeCP2 knockout


title: Puroseq, Total RNA from Hela with 4sU+UVA(4sU+UVA)-high, 1


title: NC_5


title: rpl31a, vehicle, rep 10


title: rpl31a, vehicle, rep 11


title: cortex_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_5

description: male

value: 8-10 weeks old


title: Puroseq, Total RNA from Hela with 4sU, 2

description:
RNA-seq
Puroseq-Deseq2-4sU_vs_mock.tsv


title: NC_3


title: NC_1


title: Puroseq, Total RNA from Hela with UVA, 3

description:
RNA-seq
Puroseq-Deseq2-UVA_vs_mock.tsv

value: UVA


title: cortex_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_3

description: male

value: etoposide


title: rpl31a, vehicle, rep 9


title: cortex_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_2

description: male


title: rpl31a, vehicle, rep 7


title: LPS_4

description: Acute Lung Injury

value: Lung tissue

value: LPS


title: rpl31a, vehicle, rep 5


title: rpl31a, vehicle, rep 8


title: LPS_6

description: Acute Lung Injury


title: Puroseq, Total RNA from Hela with UVA, 2

description:
RNA-seq
Puroseq-Deseq2-UVA_vs_mock.tsv

value: Hela

value: Wild Type


title: rpl31a, vehicle, rep 6

value: yeast cells


title: cortex_eTIP_WT_500uM_ETOP_Input_2

description: male

value: primary neuron cultures


title: Puroseq, Total RNA from Hela with UVA, 1

description:
RNA-seq
Puroseq-Deseq2-UVA_vs_mock.tsv


title: NC_2

value: WT

value: NC


title: Puroseq, Total RNA from Hela, 2

description:
RNA-seq
Puroseq-Deseq2-low_vs_mock.tsv
Puroseq-Deseq2-high_vs_mock.tsv
Puroseq-Deseq2-4sU_vs_mock.tsv
Puroseq-Deseq2-UVA_vs_mock.tsv

value: untreated


title: Puroseq, Total RNA from Hela, 3


title: LPS_5

description: Acute Lung Injury


title: rpl31a, vehicle, rep 4


title: cortex_eTIP_WT_500uM_ETOP_Input_1

description: male

value: wildtype


title: rpl31a, vehicle, rep 3


title: LPS_3

description: Acute Lung Injury


title: rpl31a, vehicle, rep 2


title: Puroseq, Total RNA from Hela, 1


title: culture_eTIP_MeCP2_OE_500uM_ETOP_TOP2B_A300-950A_4

description: mixed (males and females)

value: Embryonic day (E) 14.5

value: MeCP2 overexpression

value: Topo II b (Fortis Life Sciences, A300-950A)


title: cortex_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_1

description: male


title: LPS_1

description: Acute Lung Injury


title: Gcn4rpl31a, vehicle, rep 12

value: Vehicle


title: CUS_DYM3

city: 南京

first: Xiaoyu

last: Yu

state: 选择所在的省份

address: 南京鼓楼丁家桥87号

institute: 东南大学

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: brain

growth_protocol: hippocampus tissue were obtained from brain of  C57BL/6J mice.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: mice were treated with the RVG-circDYM-EVs or RVG-Vector-EVs for 7 days continuously .

tag: strain

value: hippocampus


title: FANCI, Total RNA from SG with 4sU+UVA(4sU+UVA) stress, 3

description:
FANCI (During processing it is named as s27)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv

value: FANCI


title: rpl31a, vehicle, rep 1


title: culture_eTIP_MeCP2_OE_500uM_ETOP_TOP2B_A300-950A_2

description: mixed (males and females)

value: etoposide


title: cortex_eTIP_WT_500uM_ETOP_Input_3

description: male

value: 8-10 weeks old


title: FANCI, Total RNA from SG with 4sU+UVA(4sU+UVA) stress, 1

description:
FANCI (During processing it is named as s25)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv


title: CUS_DYM1


title: CUS_DYM2


title: FANCI, Total RNA from SG with osmosis(Os) stress, 2

description:
FANCI (During processing it is named as s23)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv

value: Os


title: Gcn4rpl31a, vehicle, rep 11


title: culture_eTIP_MeCP2_OE_500uM_ETOP_TOP2B_A300-950A_1

description: mixed (males and females)


title: FANCI, Total RNA from SG with 4sU+UVA(4sU+UVA) stress, 2

description:
FANCI (During processing it is named as s26)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv

value: Hela


title: culture_eTIP_MeCP2_KD_500uM_ETOP_TOP2B_A300-950A_4

description: mixed (males and females)

value: MeCP2 knockdown


title: FANCI, Total RNA from SG with osmosis(Os) stress, 3

description:
FANCI (During processing it is named as s24)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv


title: Gcn4rpl31a, vehicle, rep 10

value: yeast cells


title: CUS_Ctrl2


title: CUS_Ctrl3


title: Gcn4rpl31a, vehicle, rep 7


title: culture_eTIP_MeCP2_KD_500uM_ETOP_TOP2B_A300-950A_3

description: mixed (males and females)

value: primary neuron cultures


title: Ctrl_DYM3


title: LPS_2

description: Acute Lung Injury

value: Lung tissue

value: WT

value: LPS


title: Gcn4rpl31a, vehicle, rep 9


title: culture_eTIP_MeCP2_KD_500uM_ETOP_Input_1

description: mixed (males and females)

value: wildtype


title: FANCI, Total RNA from SG with heat shock(Hs) stress, 2

description:
FANCI (During processing it is named as s20)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv

value: Hs


title: culture_eTIP_MeCP2_OE_500uM_ETOP_TOP2B_A300-950A_3

description: mixed (males and females)

value: Embryonic day (E) 14.5

value: MeCP2 overexpression


title: Ctrl_DYM2


title: FANCI, Total RNA from SG with osmosis(Os) stress, 1

description:
FANCI (During processing it is named as s22)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_NaCl_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv


title: culture_eTIP_MeCP2_KD_500uM_ETOP_TOP2B_A300-950A_2

description: mixed (males and females)

value: Topo II b (Fortis Life Sciences, A300-950A)


title: Gcn4rpl31a, vehicle, rep 8

value: Vehicle


title: CUS_Ctrl1

value: hippocampus


title: culture_eTIP_WT_50uM_ETOP_A300-950A_2

description: mixed (males and females)

value: etoposide


title: culture_eTIP_MeCP2_KD_500uM_ETOP_TOP2B_A300-950A_1

description: mixed (males and females)


title: Ctrl_Ctrl2


title: FANCI, Total RNA from SG with heat shock(Hs) stress, 3

description:
FANCI (During processing it is named as s21)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv

value: FANCI


title: culture_eTIP_WT_500uM_ETOP_TOP2B_H286_2

description: mixed (males and females)

value: Topo II b (Santa Cruz Biotechnology, sc-13059)


title: Gcn4rpl31a, vehicle, rep 6


title: culture_eTIP_MeCP2_OE_500uM_ETOP_Input_1

description: mixed (males and females)


title: Ctrl_Ctrl1


title: Ctrl_DYM1


title: Gcn4rpl31a, vehicle, rep 2


title: culture_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_4

description: mixed (males and females)


title: T2-3(1-3)

city: Nanjing

first: Yun

middle: hui

last: Xia

address: 22 Hankou Road

institute: Nanjing university

data_processing:
bcl2fastq2 software used for basecalling.
HiSAT2 (Pertea M,et al.,2015) was used to compare and analyze the filtered RNA-seq data of each sample with the genome.
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: FPKM values for each sample

extract_protocol:
3μg total RNA from each sample was used as the starting amount to construct library.The samples were removed rRNA using RiBO-Zero ™ GoldKits.NEB Next Ultra Directional RNA LibraryPrep Kit for Illumina（NEB， Ispawich， USA ）was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Astrocyte

tag: treament

value: treated with 1 mM MBP for 24 hours


title: FANCI, Total RNA from SG with heat shock(Hs) stress, 1

description:
FANCI (During processing it is named as s19)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_HS_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_HS_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv

value: Hela


title: FANCI, Total RNA from Hela with 4sU+UVA(4sU+UVA) stress, 2

description:
FANCI (During processing it is named as s14)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv


title: FANCI, Total RNA from SG with arsenite(As) stress, 3

description:
FANCI (During processing it is named as s18)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv

value: As


title: Ctrl_Ctrl3


title: culture_eTIP_WT_50uM_ETOP_A300-950A_1

description: mixed (males and females)

value: primary neuron cultures


title: FANCI, Total RNA from SG with arsenite(As) stress, 2

description:
FANCI (During processing it is named as s17)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv


title: Gcn4rpl31a, vehicle, rep 3

value: yeast cells


title: culture_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_2

description: mixed (males and females)


title: FANCI, Total RNA from Hela with osmosis(Os) stress, 3

description:
FANCI (During processing it is named as s12)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv

value: Os


title: culture_eTIP_WT_500uM_ETOP_TOP2B_H286_1

description: mixed (males and females)

value: wildtype


title: UT-NTE 2.5 rep1

city: New York

first: Suresh

last: Cuddapah

state: NY

address: 341 E 25th St

department: Division of Environmental Medicine, Department of Medicine

institute: New York University School of Medicine

data_processing:
The fastq files were aligned against the human genome using Hisat2
Samtools and featureCounts were used to determine the number of reads that matched the different genes
Assembly: The genome sequence (GRCh38 primary assembly) and genome annotation were obtained from Ensembl (release 103)
Supplementary files format and content: CSV file containing raw read count matrix provided by featureCounts.

growth_protocol: Human lung epithelial BEAS-2B cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 1% Penicillin- Streptomycin and 10% Fetal Bovine Serum.

extract_protocol:
Total RNA was isolated using RNeasy kit according to manufacturer's instructions.
RNA-Seq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit according to manufacturer's protocol.

treatment_protocol: BEAS-2B cells were exposed to 100μM NiCl2 for 6 weeks. Following exposure, the cells were plated in a colony forming density and cultured in nickel-free medium. Individual colonies were then isolated and expanded in Ni-free medium for >6 months to obtain homogenous nickel-washed-out (NiW) cell populations. To examine the effects of nicotine exposure on the cells that were previously exposed to nickel, NiW cells were exposed to 1.25 µM or 2.5 µM nicotine for 3 weeks (NiW-NTE). To examine the effects of nicotine on the cells that were not previously exposed to nickel, untreated BEAS-2B cells (UT) were exposed to 1.25 µM or 2.5 µM nicotine for 3 weeks (UT-NTE).

value: lung epithelial cells

value: WT

value: Nicotine treatment


title: UT-NTE 2.5 rep2


title: C2

value: untreated


title: C3


title: culture_eTIP_WT_500uM_ETOP_Input_3

description: mixed (males and females)

value: Embryonic day (E) 14.5


title: FANCI, Total RNA from SG with arsenite(As) stress, 1

description:
FANCI (During processing it is named as s16)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_sgRNA_ars_UV_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_NaCl_counts_DESeq2.normalized.tsv
batch_sgRNA_ars_HS_counts_DESeq2.normalized.tsv


title: Gcn4rpl31a, vehicle, rep 4

value: Vehicle


title: Gcn4rpl31a, vehicle, rep 5


title: T2-1(1-1)


title: culture_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_3

description: mixed (males and females)

value: etoposide

value: Topo II b (Fortis Life Sciences, A300-950A)


title: FANCI, Total RNA from Hela with osmosis(Os) stress, 1

description:
FANCI (During processing it is named as s10)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv

value: FANCI


title: FANCI, Total RNA from Hela with 4sU+UVA(4sU+UVA) stress, 1

description:
FANCI (During processing it is named as s13)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv


title: UT rep2

value: Untreated


title: ORP4Lcko;LCK/R26Tax 2

first: Wenbin

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

data_processing:
bcl2fastq v2.20
Use the FANse3 ultra-high-precision sequence alignment algorithm to compare the reads which obtained by sequencing each sample with the reference sequence (reference library: Mouse RefSeq-RNA mm10 2017-03-25).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Primary T-cells

extract_protocol:
RNA was extracted following the Trizol reagent (Invitrogen) manual. RNA was precipitated in 1:1 isopropanol (v/v) and 1 μL glycogen at -20°C overnight.
mRNA library was constructed using VAHTS mRNA-seq V3 Library Prep Kit (Cellagen Technology, San Diego, CA) following the manufacturer’s instructions.

value: 15 months


title: FANCI, Total RNA from Hela with heat shock(Hs) stress, 3

description:
FANCI (During processing it is named as s9)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv

value: Hela

value: Hs


title: ORP4Lcko;LCK/R26Tax 1


title: UT rep1


title: UT-NTE 1.25 rep2


title: Gcn4rpl31a, vehicle, rep 1


title: NiW-NTE 2.5 rep2


title: UT-NTE 1.25 rep1


title: FANCI, Total RNA from Hela with osmosis(Os) stress, 2

description:
FANCI (During processing it is named as s11)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv


title: Macrophages form 18Day AML Spleen

city: Tianjin

first: Lina

last: Wang

address: 288 nanjing Road

institute: institute of blood disease

description:
LAMs form 18Day AML  Spleen
A-SP

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genes.
The clean reads of each sample were screened for sRNA within a certain length range for subsequent analysis.
The expressions of known and new miRNA in each sample were counted, and the expressions were normalized by TPM.Formula: Normalized expression =(readCount*1,000,000)/libsize (libsize: the sum of the sample miRNA readCount)
Supplementary_files_format_and_content: readcount and TPM

source_name: Macrophage

extract_protocol:
sorted Macrophages were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for MiRNA sequencing  using the Illumina HiSeq 2500

treatment_protocol: GFP+ leukemia cells were isolated from leukemia mice and transplanted into 6-8 weeks old C57BL/6J mice (1×106 cells/mouse) without irradiation. All mice suffered MLL-AF9 AML with a survival time of 35 to 40 days. Macrophages were sorted from BM and spleen of leukemia mice at 0d and 18d.

value: Spleen


title: AEW-DRG

city: Incheon

first: WOOK-JOO

last: LEE

address: 191, Hambangmoe-ro, Yeonsu-gu

department: College of Pharmacy

country: South Korea

institute: Gachon University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: dorsal root ganglia

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: dorsal root ganglia

value: neurons

value: Acetone/Ether/Water


title: FANCI, Total RNA from Hela with heat shock(Hs) stress, 2

description:
FANCI (During processing it is named as s8)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv


title: Macrophages form 18Day AML BM

description:
LAMs form 18Day AML BM
A-BM

value: BM


title: Con-DRG

value: WT

value: Water


title: NiW-NTE 2.5 rep1

value: lung epithelial cells

value: Nicotine treatment


title: LCK/R26Tax 3


title: Macrophages form Normal BM

description:
Macrophages form Normal BM
N-BM


title: FANCI, Total RNA from Hela with heat shock(Hs) stress, 1

description:
FANCI (During processing it is named as s7)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv


title: LCK/R26Tax 1


title: Macrophages from Normal Spleen

description:
Macrophages from Normal Spleen
N-SP


title: FANCI, Total RNA from Hela with arsenite(As) stress, 2

description:
FANCI (During processing it is named as s5)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv

value: As


title: NiW-NTE 1.25 rep1


title: Wild-type 3

value: Wild-type


title: FANCI, Total RNA from Hela with arsenite(As) stress, 3

description:
FANCI (During processing it is named as s6)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv


title: FANCI, Total RNA from Hela with arsenite(As) stress, 1

description:
FANCI (During processing it is named as s4)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv


title: LCK/R26Tax 2


title: ORP4Lcko;LCK/R26Tax 3


title: NiW-NTE 1.25 rep2


title: NiW rep2

value: Nickel treatment


title: Wild-type 2


title: FANCI, Total RNA from Hela, 3

description:
FANCI (During processing it is named as s3)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv

value: untreated

value: FANCI


title: NiW rep1


title: EMO9, collagen, day7

city: Sendai

first: Shun

last: Shibata

address: 2-1 Seiryo-chou

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

data_processing:
The sequenced data were first trimmed for quality control using the TrimGalore software (v0.6.7).
The reads were then aligned to the reference genome (UCSC hg38) using STAR (v2.7.10a)
The expression levels (transcript per million) of the Refseq genes were calculated using RSEM(v1.3.1)
Assembly: UCSC hg38
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file include TPM values for each sample

source_name: human decidua

extract_protocol:
Total RNA was extracted using the RNeasy Mini or Micro Kit (QIAGEN), and genomic DNA was removed by digestion with RNase-free DNase I (QIAGEN).
RNA libraries were prepared using the NEBNext UltraII Directional RNA Library Prep Kit (New England Biolabs)

value: human decidua

value: endometrial organoids

value: endometrial epithelial cells

tag: lot

tag: culture substrate

value: Type-I collagen (+30% Matrigel)


title: FANCI, Total RNA from Hela, 1

description:
FANCI (During processing it is named as s1)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv

value: Hela


title: Wild-type 1

value: 15 months


title: HeLaS3-TRIP12-IDR2

city: Toulouse

first: Claire

last: Vargas

address: 2 Avenue Hubert Curien

country: France

institute: Centre de Recherches en Cancérologie de Toulouse

description: 3_0E1F_0216Inserm_HeLaS3-ABC-G_ATAC_hs_i219

data_processing:
All analysis were performed by Active Motif company.
ATAC-seq reads were generated using Illumina sequencing (NextSeq 500) and were mapped to the hg38 human reference genome using BWA algorithm. MACS peak calling algorithm was used to identified the regions with high levels of tagging events. Only merged accessible regions with Max tag >50 were considered.
Assembly: hg38 human reference genome
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Cervical adenocarcinoma

growth_protocol: HelaS3 (ATCC CCL-2™) cells were grown in DMEM 4.5 g/L glucose medium were grown in advanced DMEM/F-12 4.5 g/L glucose medium both supplemented with 10% fetal calf serum (FCS), L-glutamine and antibiotics (Life Technologies) at 37°C in humid atmosphere with 5% CO2.

extract_protocol: After 24 h, GFP-expressing cells were sorting by cytometry using FACS Melody apparatus (BD Biosciences). 105 GFP-highly positive and GFP-negative (used as controls) cells were collected. Samples were frozen accordingly to the manufacturer’s instructions in an ice-cold cryopreservation solution and stored at -80°C until shipping.

treatment_protocol: HelaS3 cells were transfected with IDR-GFP construct using using jetPRIME® transfection reagent (Polyplus).

value: Cervical adenocarcinoma

value: transfected


title: HeLaS3-NT1

description: 1_0A4A_01J7INSERM_HeLaS3-NT-12_ATAC_hs_i229


title: HeLaS3-NT2

description: 1_0E1D_0216Inserm_HeLaS3-NT-19_ATAC_hs_i217


title: FANCI, Total RNA from Hela, 2

description:
FANCI (During processing it is named as s2)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_NaCl_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_HS_counts_DESeq2.normalized.tsv
batch_totalRNA_mock_ars_counts_DESeq2.normalized.tsv


title: EMO4, collagen, day7


title: EMO4, matrigel, day7

value: Matrigel


title: ORP4L KI 1

value: ORP4L KI


title: ORP4L KI 4


title: ORP4L KI 3


title: WT 3

value: WT


title: WT-a4-1

data_processing:
The clean reads were aligned to the human genome (hg38) using Bowtie2 (v2.2.5) with options: --local -k 1 --no-unal. Unmapped and duplicated reads were removed using sambamba (v0.6.6)
For peak calling, exomePeak2 with default parameter was used.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
For gene expression quantification, Hisat2 (v2.2.1) and Stringtie (v2.1.4) with default parameters were used.
Assembly: hg38
Supplementary files format and content: bigwig, peakfile text file, gene expression matirx

molecule: polyA RNA

extract_protocol:
Cells were havested and total RNA was isolated using Fast Pure Cell Total RNA Isolation Kit (Vazyme) and enrichment of polyadenylated RNA [poly(A) RNA] was further achieved through two rounds of selection with Oligo-(dT)25 Dynabeads (ThermoFisher Scientific).
We used SMARTer® Stranded Total RNA-Seq Kit v2 for library construction.
acRIP-seq

value: human embryonic stem cells (hESC)

tag: rip antibody

value: Rabbit anti-ac4C (Abcam,ab252215)


title: EMO9, matrigel, day7


title: Rice root tip_lad_3

city: Chongqing

first: yadi

last: xing

address: Beibei District

institute: Southwest University

description: lad mutant is also named sr1.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryza sativa

source_name: root tip

growth_protocol: The rice seedlings were cultured at 25°C and grown for six days. Take root tip 0.5cm for sequencing

extract_protocol:
Root tips were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprouting 6 days

value: mutant


title: WT-input-2

description: fpkm.matrix


title: RNA_sgBPTF-2_rep3

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and then aligned to human assembly hg38 with STAR v2.4 using default parameters.
Data quality and transcript coverage were assessed using the Picard tool CollectRNASeqMetrics (http://broadinstitute.github.io/picard/). Read count tables were generated with HTSeq v0.9.1.
Normalization and differential expression were evaluated with DESeq2 using the default parameters, and outliers were assessed by sample grouping in principal component analysis.
2 independent sgRNAs against BPTF were treated as biological replicates in the DESeq2 analysis
Assembly: GRCh38/hg38
Supplementary files format and content: DESeq2 output table

extract_protocol:
The total RNA was extracted using Qiagen Rneasy kit
Illumina Truseq v2 kit

value: blood

value: monocyte

value: BPTF KO

value: lentiviral transduction


title: RNA_sgBPTF-2_rep2


title: HeLaS3-TRIP12-IDR1

description: 3_0A4C_01J7INSERM_HeLaS3-ABC-G_ATAC_hs_i201


title: ORP4L KI 2


title: WT-input-1

description: fpkm.matrix


title: RNA_sgBPTF-2_rep1


title: RNA_sgBPTF-1_rep1


title: RNA_sgBPTF-1_rep3


title: Rice root tip_lad_2

description: lad mutant is also named sr1.


title: WT 2


title: RNA_sgBPTF-1_rep2


title: KD-a4-2

value: NAT10 KD


title: KD-input-2

description: fpkm.matrix


title: Rice root tip_lad_1

description: lad mutant is also named sr1.


title: WT 1


title: KD-input-1

description: fpkm.matrix


title: FLASH of endogenous DHX9, 1

description:
FLASH
DHX9_WTpeaks.bed

value: untreated

value: Wild Type

value: FLASH


title: FLASH of endogenous DHX9, 3

description:
FLASH
DHX9_WTpeaks.bed

value: Hela


title: Rice root tip_J10_3

description: J10 is wild type.

value: wild type


title: RNA_sgNegCtrl_rep2


title: RNA_sgNegCtrl_rep3


title: WT-a4-2


title: FLASH of endogenous DHX9, 2

description:
FLASH
DHX9_WTpeaks.bed


title: KD-a4-1


title: 2016S1215

status: Public on Nov 10 2023

type: genomic

city: Grand Rapids

first: Lena

last: Brundin

address: 333 Bostwick Ave NE

institute: Van Andel Institute

hyb_protocol: standard DNA methylation protocol from New York Genome Center

data_processing:
sesame
Differential DNA methylation analysis including sex and age as covariates was conducted by SeSAMe.

label: Cy3 and Cy5

source_name: brain tissue

tag: group

value: suicide


title: 2011S1154

scan_protocol: standard DNA methylation protocol from New York Genome Center

value: healthy


title: Rice root tip_J10_1

description: J10 is wild type.


title: 2011S1148

label_protocol: standard DNA methylation protocol from New York Genome Center


title: RNA_sgNegCtrl_rep1

tag: tissue


title: 2013S1194

extract_protocol: standard DNA methylation protocol from New York Genome Center


title: 2010S1104


title: 2010S1113


title: 2016S1214


title: Rice root tip_J10_2

description: J10 is wild type.

tag: age


title: 2014S1207


title: 2014S1202


title: 2012S1175


title: 2013S1182


title: 2009S1011


title: 2011S1132


title: 2010S1116


title: 2007S0962


title: 2010S1089


title: 2006S0935


title: 2006S0922


title: 2010S1082


title: 2010S1086


title: 2009S1042


title: 2010S1058


title: 2009S1039


title: 2005S0879


title: 2009S1020


title: 2009S1027


title: 2008S0997


title: 2004S0776


title: 2008S0977


title: 2006S0936


title: 2007S0945


title: 2006S0913


title: 2005S0899


title: 2005S0894


title: 2004S0761


title: 2005S0877


title: 2005S0875


title: 2003S0748


title: 2005S0866


title: 2005S0840


title: 2004S0808


title: 2002S0679


title: 2003S0696


title: FANCI, Total RNA from Hela with 4sU+UVA(4sU+UVA) stress, 3

description:
FANCI (During processing it is named as s15)
featureCounts_exon_counts.tsv
featureCounts_geneBody_counts.tsv
batch_totalRNA_mock_UV_counts_DESeq2.normalized.tsv

tag: genotype

value: FANCI


title: 2004S0797


title: 2004S0782


title: 2006S0926


title: 2004S0795


title: 2001S0577


title: 2004S0775


title: 2003S0744


title: 2003S0746


title: 2000S0545


title: 2000S0528


title: 2003S0724


title: 2005S0831


title: 2000S0520


title: 2000S0546


title: 2001S0579


title: 2000S0574


title: 1998S0461


title: eyeRiboRNA_nocteRNAi2

city: Baltimore

first: Weidong

state: MD

address: 251 Bayview Blvd BRC, Suite 100 Rm10B014

institute: National Institute of Aging

data_processing:
For RNA-seq of polyA RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function. Bam files and bed files are used to get bedgraph and raw counts. Raw counts are normalized to get RNA expression levels.
For RNA-seq of total RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index. Sorted bam files are used to generate bigwig graph and get raw counts in CDS regions by Htseq. Raw counts are normalized to get RNA expression levels.
For Ribo-seq fastq files, adaptors are removed by fastx_clipper, ribosomal RNA sequences are removed by bowtie2. Following steps are the same to the analysis of RNA-seq of total RNA samples.

organism: Drosophila melanogaster

source_name: eye discs

extract_protocol:
RNA was extracted byTRizol following the product manual. For Ribo-seq, total RNA was digested with Mnase S7 and run using 15% TBE-urea gel, followed by cutting the 28 nt RNA fragments.
Library was constructed by standard Illumina protocol. Ribo-seq library was generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs).

value: eye discs

value: ey-GAL4, UAS-nocte-RNAi

value: flies maintained at 25oC, eye discs with mouth hooks were dissected from late L3 larvae.


title: eyeRiboRNA_nocteRNAi3

description: RNA-seq

data_processing:
For RNA-seq of total RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index. Sorted bam files are used to generate bigwig graph and get raw counts in CDS regions by Htseq. Raw counts are normalized to get RNA expression levels.
Assembly: dm6
Supplementary files format and content: bw

extract_protocol:
RNA was extracted byTRizol following the product manual.
Library was constructed by standard Illumina protocol. Ribo-seq library was generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs).


title: 2004S0765


title: eyeRiboRNA_WT3

description: RNA-seq


title: eyeRiboRNA_WT1


title: eyeRiboRNA_WT2


title: eyeRibo_nocteRNAi1

data_processing:
library strategy: Ribo-seq
For RNA-seq of polyA RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function. Bam files and bed files are used to get bedgraph and raw counts. Raw counts are normalized to get RNA expression levels.
For RNA-seq of total RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index. Sorted bam files are used to generate bigwig graph and get raw counts in CDS regions by Htseq. Raw counts are normalized to get RNA expression levels.
For Ribo-seq fastq files, adaptors are removed by fastx_clipper, ribosomal RNA sequences are removed by bowtie2. Following steps are the same to the analysis of RNA-seq of total RNA samples.

tag: molecule subtype

value: ribosome bound RNA fragments


title: set2, AagrOXF 4week thalli, input, rep2

city: Ikoma

first: Tetsuya

last: Hisanaga

state: Nara

address: Takayama 8916-5

institute: Nara Institute of Science and Technology

data_processing:
Self-ligated adaptor sequences were removed by using catadapt with a option --minimum-length 1.
ChIP-seq reads were aligned to the Anthoceros agrestis Oxford genome using Bowtie2 version 2.3.4.2 with options --sensitive -p 8 -N 0 --trim5 0 --trim3 0. Reads with MAPQ less than ten were removed with Samtools v1.9 and duplicates were removed with Picard v2.18.27.
Bigwig files were generated using the bamCoverage function of deepTools v3.3.1 with options --normalizeUsing RPGC --effectiveGenomeSize 122905886 --binSize=10.
Bigwig files of log2 ratio of each mark to input sample were generated using the bamConpare function of deepTools v3.3.1 with options--scaleFactorsMethod readCount --binSize=10.
Peaks were called using MACS2 v2.2.5 with options --nomodel --nolambda -q 0.01 --broad --broad-cutoff 0.1.
Aligned BAM files of each replicate were merged using SAMtools v1.9. These merged BAM files were used to generate bigwig files and MACS2 peak files (used the same method described above)
Assembly: Anthoceros agrestis Oxford
Supplementary files format and content:
macs2 broadPeak (except for Input sample)
bigwig files for coverage of each mark.
bigwig files for log2 ratio of each mark normalized with input sample.
genome fasta file; Gene and TE annotations in gff3 format
log2r bigwig files of each mark made from merged bam files of each replicate
macs2 broadpeak files of each mark made from merged bam files of each replicate

organism: Anthoceros agrestis

source_name: thalli

growth_protocol: Plants were cultured on 0.5 Gamborg’s B5 medium solidified with 1% agar under continuous white light at 22°C.

extract_protocol:
Tissues were fixed with 1% paraformaldehyde for 10 minutes. After quenching and tissue lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the Ovation® Ultralow Library Systems V2. 1-10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12-15 cycles on the thermocycler. Libraries were validated using the fragment analyzer.

value: Oxford

value: thalli

value: 4 weeks


title: set2, AagrOXF 4week thalli, H3, rep2


title: eyeRibo_WT1


title: set2, AagrOXF 4week thalli, H3K27me1, rep2


title: eyeRNA_nocteRNAi2


title: eyeRNA_nocteRNAi1


title: set2, AagrOXF 4week thalli, H3K27me3, rep1


title: set2, AagrOXF 4week thalli, H3K27me1, rep1


title: eyeRNA_WT3


title: Embryoid, 21 days after induction with dox, CellPlex files

city: Pittsburgh

first: Mo

middle: Reza

last: Ebrahimkhani

state: PA

address: 3550 Terrace Street, Scaife Hall A804

department: Department of Pathology

institute: University of Pittsburgh

library_source: transcriptomic single cell

data_processing:
We used CellRanger (version 6.1.2) multi pipeline to demultiplex the libraries and quantify the gene expressions from raw fastq files. We first downloaded the FASTA file and GTF file of the human reference genome (GRCh38.84) and constructed the genome index by mkref command available in the Cell Ranger tool kit. This genome index was augmented by a few exogenous sequences (sequence names) to enable alignment against the exogenous sequences. We specified the number of expected cells in the config file as 24000 for the batch containing the day 21 scRNA-seq, and 30000 for the batch containing the day 5 and lower scRNA-seq. multi command in the Cell Ranger tool kit was then run to perform demultiplexing into GEX libraries and CellPlex libraries, and quantification of gene counts. Other than the number of expected cells specified above, we used the default parameters of the multi command. We used the filtered gene count output for our downstream analyses (located under the Cell Ranger output folder ‘outs/per_sample_output/sample_name/count/sample_feature_bc_matrix’).
Seurat V4 was used for downstream processing of the scRNA-seq data. Single cell data was excluded based on high mitochondrial genome transcript ratio and either high or low feature or UMI counts. Genes with UMI counts in fewer than 5 cells were removed from consideration. For scRNA-Seq data processing and cluster analysis using Seurat, we used the following general standardized pipeline for processing of the Cell Ranger output: SCTransform regressing percent mitochondrial genes, principal component analysis (PCA), and clustering. Jackstraw plots and permuted p-values were used to assist in determining the optimal number of principal components (PCs) needed to summarize the datasets without losing a significant amount of variation. The quality of a range of clustering resolution values was assessed using enrichment of cluster marker genes (genes differentially upregulated in a given cluster relative to all other clusters) with embryo cell type-specific genes. As a quality check, PC and resolution metrics were modulated to yield fewer or additional clusters to confirm that chosen parameters resulted in the most biologically relevant clustering. Visualization was achieved by the use of UMAP plots identifying cells, clusters, and selected gene expression in each cell, as well as heatmaps and violin plots showing the expression level of genes by cluster. Stacked violin plots were created using the scCustomize package in R. Stacked violin plots were created using the scCustomize package in R.
Subclustering the WT in the D3 and the endothelial cluster in the D21 dataset was achieved by subsetting the cluster of interest, then computing the distance between rows of the data matrix using Euclidean measurement (dist function in R). Hierarchical clustering was applied using this distance matrix (hclust in R), and used to create a dendrogram of the distance explained by different numbers of subclusters. The number of subclusters was selected based on the highest level of distance observed and applied to the data (clustercut in R). The cluster was then added back to the rest of the dataset and markers were determined.
Assembly: GRCh38.84
Supplementary files format and content: Rdata: R workspace file containing Seurat objects with the processed form of the data used in the manuscript.

source_name: Embryoid model system

growth_protocol: Samples were maintained in mTeSR-1 plus 1 μg/ml doxycycline with daily full media changes until day 5. After day 5, samples were maintained on IMDM, and half media changes were performed daily.

extract_protocol:
Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. iDiscoids of each day indicated were acquired in single cell suspension by incubation with Accutase for 20 minutes at 37°C. The cell suspension was passed through a 40μm strainer in order to remove aggregates. Each sample suspension was then centrifuged at 300g for 5 minutes at room temperature. The supernatant was manually aspirated from each of the samples using a P1000 pipette. The cell pellets were each resuspended in 1ml PBS+0.04% BSA, and the samples were centrifuged at 300g for 5 minutes at room temperature. The samples were then resuspended, targeting 1×106 cells/ml based on expected densities of cells at each day, and the cell suspension was passed through a 40um strainer again. Each cell suspension was counted using a hemocytometer, and a volume of cell suspension was removed as necessary to adjust the final cell count to 1×106 cells. The volumes were then adjusted to 1ml by adding additional PBS+0.04% BSA to replace the removed volumes. For Multiplexing Oligo Labeling: Samples were then centrifuged at 300g for 5 mins at room temperature. Supernatant was aspirated manually with a P1000 pipette. Samples were resuspended in 50μl of CellPlex Multiplexing Solution (10x Genomics), with unique multiplexing oligo solutions assigned to each sample. A maximum of 12 samples were labeled in parallel. Samples were incubated for 5 minutes, starting after the oligo solution was added to the last sample. Following labeling, 1.95ml 1x PBS + 1% BSA was added to each sample, and the solution was mixed thoroughly. Each sample was centrifuged at 300g for 5 minutes at 4°C. The supernatant was manually aspirated with a P1000 pipette, taking care to leave less than 10μl of supernatant remaining in each sample when possible. The samples were resuspended in 2ml 1x PBS + 1% BSA and were mixed thoroughly to wash. This wash and centrifugation step was repeated two additional times; at the last resuspension, enough wash buffer was added to reach a cell count of 1×106 cells/ml, assuming 50% cell loss from the count at the end of the first protocol. Labeled cell suspensions were then put on ice for transfer to the Pitt Single Cell Core for library creation.
Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3’ Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples.

treatment_protocol: Differentiation of samples was induced by 1 μg/ml doxycycline 24 hours after passaging.

value: Embryoid model system

tag: cell line

value: PGP1 iPSCs

tag: cell type

value: embryonic and extraembryonic tissues excluding trophoblast


title: set2, AagrOXF 4week thalli, input, rep1

tag: chip antibody


title: Embryoid, 21 days after induction with dox, GEX files


title: set2, AagrOXF 4week thalli, H3K4me3, rep1


title: eyeRiboRNA_nocteRNAi1

tag: treatment


title: set2, AagrOXF 4week thalli, H3K27me3, rep2


title: Embryoid, 5 days after induction with dox, GEX files


title: Embryoid, 5 days after induction with dox, CellPlex files


title: set1, AagrOXF 4week thalli, H3K9me1, rep2


title: Embryoid, 4 days after induction with dox, CellPlex files, biol rep 2


title: set2, AagrOXF 4week thalli, H3K4me3, rep2


title: set1, AagrOXF 4week thalli, H3, rep2


title: Embryoid, 4 days after induction with dox, GEX files, pt.2, biol rep 2


title: eyeRNA_nocteRNAi3


title: set1, AagrOXF 4week thalli, input, rep2


title: Embryoid, 4 days after induction with dox, GEX files, pt.2, biol rep 1


title: Embryoid, 4 days after induction with dox, CellPlex files, biol rep 1


title: set1, AagrOXF 4week thalli, H3K9me1, rep1


title: set1, AagrOXF 4week thalli, input, rep1


title: Embryoid, 3 days after induction with dox, CellPlex files


title: set2, AagrOXF 4week thalli, H3, rep1


title: Embryoid, 4 days after induction with dox, GEX files, pt.1, biol rep 1


title: set1, AagrOXF 4week thalli, H3, rep1


title: set1, AagrOXF 4week thalli, H3K36me3, rep2


title: AagrOXF 4 week thalli, EMseq, rep1

description:
TH_AaEM01
EM-seq

data_processing:
The bam files of EM-seq reads were sorted with SAMtools v1.9 and converted to fastq format using bamtofastq function of BEDTools v2.27.1, then trimmed with Trim Galore.
Bisulfite converted reference genome was prepared from A. agrestis Oxford strain genome sequence using Bismark.
Trimmed reads were mapped to the bisulfite genome using the Bowtie2 option of Bismark. Duplicates were removed using the deduplicate function in Bismark.
Cytosine methylation reports were created from deduplicated reads using the bismark_methylation_extractor function in Bismark.
Each cytosine which is covered by at least four reads was used for further analyses. Methylation ratio of each cytosine was calculated and summarized to a bed file.
Bam files of each replicate were merged using SAMtools v1.9 and processed using the same method described above.
Cytosines which are covered by at least ten reads was used to calculate methylation levels. Methylation levels of each cytosine context were summarized to bed files.
Assembly: Anthoceros agrestis Oxford
Supplementary files format and content: Cytosine methylation reports.
Supplementary files format and content: bedgraph files for methylation ratio of each cytosine per each context.

extract_protocol: Genomic DNA was extracted from 100 mg of 4-week-old gametophyte tissue of A. agrestis using Nucleon PhytoPure (cytiva). Sequencing libraries for genome-wide DNA methylation profiles were generated from 200 ng of genomic DNA using NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs). These libraries were sequenced on a Illumina NextSeq 2000 to generate 100 bp paired end reads.


title: Embryoid, 3 days after induction with dox, GEX files


title: AagrOXF 4 week thalli, EMseq, rep2

description:
TH_AaEM02
EM-seq


title: Embryoid, 48 hrs after induction with dox, GEX files


title: Embryoid, 48 hrs after induction with dox, CellPlex files


title: CT26 shmaurka-1

city: Tainan

first: Shiang-Jie

last: Yang

address: No.1, University Road, Tainan City 701, Taiwan (R.O.C)

department: Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng Kung University

data_processing:
Illumina's official basecalling program, thebcl2fastqconversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Adaptor clipping and sequence quality trimming were conducted using Trimmomatic v0.36, employing a sliding-window approach
HISAT2 was used for read alignment against the GRCm39 mouse reference genome.
Differential expression analysis was conducted using cuffdiff (part of Cufflinks v2.2.1) with genome bias detection and correction, in conjunction with Welgene Biotech's in-house pipeline.
Assembly: GRCm39
Supplementary files format and content: The provided tab-delimited text files contain read counts for each sample.
Supplementary files format and content: The provided tab-delimited text files contain FPKM values for each sample.

source_name: Colon

growth_protocol: CT26 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin, and maintained in a humidified atmosphere containing 5% CO2 at 37°C. MC38 cells were cultured in high glucose DMEM supplemented with 10 mM HEPES, 0.1 mM non-essential amino acids, 10% fetal bovine serum, and 1% Penicillin-Streptomycin, and were also maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the Trizol® Reagent (Invitrogen, USA) following the manufacturer's instructions
Library construction was performed by using Agilent's SureSelect Strand-Specific RNA Library Preparation Kit, followed by size selection with AMPure XP beads (Beckman Coulter, USA)

treatment_protocol: Aurora-A was knocked down in CT26 and MC38 cells using lentiviral-mediated short hairpin RNA (lenti-shmaurka-1). Cells transduced with lenti-shGFP served as the control group.

value: Colon

value: Fibroblast

value: WT


title: Embryoid, 36 hrs after induction with dox, GEX files


title: Embryoid, 24 hrs after induction with dox, CellPlex files


title: MC38 shGFP

value: Epithelial cell

value: lenti-shGFP


title: MC38 shmaurka-1


title: Embryoid, 36 hrs after induction with dox, CellPlex files


title: CT26 shGFP


title: Embryoid, 4 days after induction with dox, GEX files, pt.1, biol rep 2


title: set1, AagrOXF 4week thalli, H3K36me3, rep1

value: wild type


title: Embryoid, 24 hrs after induction with dox, GEX files


title: Embryoid, 12 hrs after induction with dox, GEX files


title: intestine, 6Gy+CBLB502, 24h, rep3

city: Beijing

first: wang

last: qiong

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

description:
mouse was treated with 6Gy IR and 0.2mg/kg CBLB502, then collected intestine at 24h
Six502_24h3

data_processing:
Illumina Casava1.7 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Intestine

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestine

tag: Sex

value: male

value: Wildtype

value: 6Gy+0.2mg/kg CBLB502 i.p.,sample at 24h


title: intestine, 6Gy, 24h, rep3

description:
mouse was treated with 6Gy IR, then collected intestine at 24h
Six24h3

value: 6Gy radiation, sample at 24h


title: Embryoid, 12 hrs after induction with dox, CellPlex files


title: iPSC, 24 hours after passage, CellPlex files

source_name: iPSC cells

value: iPSC cells

value: induced pluripotent stem cells


title: intestine, 6Gy+CBLB502, 24h, rep1

description:
mouse was treated with 6Gy IR and 0.2mg/kg CBLB502, then collected intestine at 24h
Six502_24h1


title: iPSC, 24 hours after passage, GEX files


title: intestine, 6Gy+CBLB502, 24h, rep2

description:
mouse was treated with 6Gy IR and 0.2mg/kg CBLB502, then collected intestine at 24h
Six502_24h2


title: intestine, 6Gy, 24h, rep1

description:
mouse was treated with 6Gy IR, then collected intestine at 24h
Six24h1


title: intestine, 15Gy+CBLB502, 24h, rep2

description:
mouse was treated with 15Gy IR and 0.2mg/kg CBLB502, then collected intestine at 24h
Ftn502_24h2

value: 15Gy+0.2mg/kg CBLB502 i.p.,sample at 24h


title: DIV 21 Dravet Patient iPSC neurons

city: Cambridge

first: Laura

last: Chipman

state: MA

address: 1 Portland St

institute: Pfizer

description: 10x Genomics

data_processing:
Raw sequence data (.bcl files) generated from Illumina was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequent UMI and cell barcode de-convolution was also performed prior to downstream analysis. Mapping to the respective genome and gene expression analysis was performed on Rosalind’s platform. Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Quality scores were assessed using FastQC (Andrews, 2010). Cell Ranger was used to align reads to the Homo sapiens genome build GRCh38, count UMIs, call cell barcodes, and perform default clustering. In R using the Matrix package, UMAP projection data and feature-barcode matrices outputs from cellranger were converted to csv format which included gene expression data and UMAP projection coordinates for each barcoded cell. Natural log of the expression counts of select genes were projected on UMAP plots to create heatmap plots using R’s ggplot2.
Assembly: Homo sapiens genome build GRCh38

source_name: GABAergic Cortical Neurons

growth_protocol: Neurons were thawed following the manufacturer’s protocol and plated in 24-well plate format at 300,000 live cells/well. Base media contained DMEM/F-12 media (0.5x, Gibco), Neurobasal media (0.5x, Gibco), B-27 supplement (1x, Gibco), N-2 supplement (1x, Gibco), GlutaMax (0.5 mM, Gibco), brain-derived neurotrophic factor (BDNF, 10 ng/mL, PeproTech), glial-derived neurotrophic factor (GDNF, 10 ng/mL, PeproTech), and TGF-β1 (1 ng/mL, PeproTech), for a total of 500 mL/well. For seeding media at DIV 0, GABA neuron seeding supplement (1x, BrainXell) was added. At DIV 4, base media plus Day 4 Supplement (1x, BrainXell) and Supplement K (1x, BrainXell) were added at 500 mL/well. Starting at DIV 7, a 50% media change 2x per week was performed using base media.

extract_protocol:
Cells were disassociated at DIV 21 following protocol for mature neuronal culture outlined (Julie Jerber, 2020). Live cell count was accessed using Nexcelom Cellaca Cell Counter along with Nuc blue for all cell nucleus staining and propidium iodide for dead cell nucleus staining. Sample with cell counts > 50,000 and viability > 70% was diluted and loaded onto the Chromium Controller. Loading was performed to target capture of ~3,000 GEMs per sample for downstream analysis. Sample was processed through the Chromium Controller following the standard manufacturer’s specifications.
Single cell RNA library was generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA). The sequencing library was evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Sample was also quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA) prior to loading onto an Illumina sequencing platform. The final library was sequenced at a configuration compatible with the recommended guidelines as outlined by 10X Genomics.

value: GABAergic Cortical Neurons

value: human iPSC neurons

value: Dravet syndrome patient with SCN1A Variant 1:1 base pair deletion of T; Nucleotide Position 4522' Codon Position:1508


title: intestine, CBLB502, 24h, rep3

description:
mouse was treated with 0.2mg/kg CBLB502, then collected intestine at 24h
NC502_3

value: 0.2mg/kg CBLB502 i.p.,sample at 24h


title: human articular chondrocytes-IL-β-Meloxicam - H3

city: Changsha

first: Wenxiang

last: Deng

address: 300 Bachelor's Road, Hanpu Science and Education Park, Yuelu District

institute: Hunan University of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).
We aligned reads of all samples to the reference genome using Tophat2 (2.0.4) package, remaining reads (unmapped reads) were still mapped to reference genome using tophat-fusion (2.1.0), which was subsequently used to identify circRNA.
CIRCExplorer2 (2.2.6, default) and CIRI (2.0.2, default) was used to denovo assemble the mapped reads to circular RNAs at first; Then, back-spliced junction reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2 or CIRI. All samples were generated unique circular RNAs.
We normalized the back-spliced reads (support for circRNA) by read length and number of mapped reads (spliced reads per billion mapping, denoted as SRPBM), which permits quantitative comparisons between back splicing from different RNA-seq. We counted the total number of reads mapped to the reference genome in each sample and normalized the number of reads spanning the back-spliced junction to the total number of mapped reads (units in billion) and read length. The SRPBM value of each sample circRNA was calculated by the Perl script and used as the expression abundance. SRPBM = number of circular reads/number of mapped reads (units in billion)/read length

source_name: human articular chondrocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (hermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) with RIN number > 7.0.
Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: human articular chondrocytes

value: IL-β-Meloxicam


title: intestine, 6Gy, 24h, rep2

description:
mouse was treated with 6Gy IR, then collected intestine at 24h
Six24h2


title: intestine, 15Gy+CBLB502, 24h, rep3

description:
mouse was treated with 15Gy IR and 0.2mg/kg CBLB502, then collected intestine at 24h
Ftn502_24h3


title: human articular chondrocytes-IL-β-Meloxicam - H2


title: intestine, 15Gy+CBLB502, 24h, rep1

description:
mouse was treated with 15Gy IR and 0.2mg/kg CBLB502, then collected intestine at 24h
Ftn502_24h1


title: intestine, CBLB502, 24h, rep1

description:
mouse was treated with 0.2mg/kg CBLB502, then collected intestine at 24h
NC502_1


title: human articular chondrocytes-IL-β-Curcumin - G2

value: IL-β-Curcumin


title: human articular chondrocytes-IL-β-Curcumin - G3


title: human articular chondrocytes-IL-β - F3

value: IL-β


title: intestine, 15Gy, 3d, rep1

description:
mouse was treated with 15Gy IR, then collected intestine at 3d
Ftn3d1

value: 15Gy radiation, sample at 3d


title: human articular chondrocytes-IL-β - F2


title: human articular chondrocytes-IL-β - F1


title: human articular chondrocytes-IL-β-Curcumin - G1


title: intestine, 15Gy, 24h, rep2

description:
mouse was treated with 15Gy IR, then collected intestine at 24h
Ftn24h2

value: Intestine

value: 15Gy radiation, sample at 24h


title: intestine, 15Gy, 24h, rep1

description:
mouse was treated with 15Gy IR, then collected intestine at 24h
Ftn24h1

value: male

value: Wildtype


title: human articular chondrocytes - E1


title: intestine, 15Gy, 24h, rep3

description:
mouse was treated with 15Gy IR, then collected intestine at 24h
Ftn24h3


title: human articular chondrocytes - E3


title: human articular chondrocytes - E2


title: human articular chondrocytes-IL-β-Meloxicam - H1


title: intestine, CBLB502, 24h, rep2

description:
mouse was treated with 0.2mg/kg CBLB502, then collected intestine at 24h
NC502_2


title: Rtt101-HA_ChIP_45minHU_rep1

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

data_processing:
After adapters removal using Trim Galore!, reads were aligned to the sacCer3 genome via Bowtie2 (Langmead and Salzberg, 2012) through the Galaxy server. BigWig density files were then produced using the bamCoverage function with the following options: a bin size of 250 smoothed by a rolling window of 1000bp, cpm normalization with the exclusion of the chrM, centering fragments after their artificial extension to 250bp and a minimal Phred quality score of 20. Differential densities between time points in S-phase and G1-phase were processed through the bigwigCompare function. Metagene plots were made using the computeMatrix and plotProfile commands. The list of ARS Consensus Sequences (ACSs) was retrieved from (Soudet et al., 2018) and their orientation was taken into account. The 40 early ARSs were defined through a k-means clustering based on the DNA Pol 2 signal 10kb around the ACSs. The median Z-score was finally calculated on the 30kb-window around ACSs.
Assembly: sacCer3
Supplementary files format and content: bigWig files

source_name: yeast cell

growth_protocol: Yeast cells were grown in YEPD until exponential phase, and synchronized in G1 phase by addition of α-factor (ref) for 2 hours. After two washes, cells were released into the cell cycle in fresh YEPD medium without drugs, or supplemented with 200 mM of HU.

extract_protocol:
Cells were crosslinked with 1 % formaldehyde for 15 min at room temperature, quenched with 250 mM glycine incubated for 5 min, followed by ice-cooling for at least 10min. Before freezing, pellets were washed twice with cold 1X Phosphate Buffer Saline (PBS) and transferred into 2 mL screw-cap tubes. All subsequent steps were performed at 4°C or on ice, if not mentioned otherwise. Frozen pellets were resuspended in 1 mL cold FA lysis buffer (50 mM HEPEs-KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 1 % Triton X-100; 0.1 % sodium deoxycholate; protease inhibitor cocktail) and lysed by MagNA Lyzer (6000 rpm; 5 cycles of 30 secs; 1 min on ice between runs). Extracts were recovered in a new tube and centrifuged at 13,000 x rpm for 30min. After resuspension with 1 mL of fresh FA lysis buffer, extracts were sonicated via Bioruptor Twin (Diagenode) at 4°C for 20 cycles of 30 secs. After centrifugation at 13,000 x rpm for 15 min, supernatant was transferred in a new tube and the amount of protein was determine by Bio-Rad protein assay (cat. 500-0006).  Each immunoprecipitation was carried out with 1 mg of protein (1/10 retained as the input) incubated overnight at 4°C under rotation, with 1 uL of anti-HA antibody. Protein G sepharose beads were then added for 3 hours, at 4°C under rotation.  After incubation, beads were washed 1x with 500 µL cold FA lysis buffer, 2x with 500 µL cold FA-500 buffer (FA lysis with 500 mM NaCl), 2x with 500 µL Buffer 3 (10 mM Tris-HCl pH 8; 1 mM EDTA; 250 mM LiCl, 1 % IGEPAL; 1 % sodium deoxycholate) and 1x with 500 µL 1X TE (50 mM Tris-HCl pH 7.5; 10 mM EDTA). Elution was then performed twice with 100 µL elution buffer (50 mM Tris-HCl pH 7.5; 1 % SDS; 10 mM EDTA) incubated at 65°C for 8 minutes. Eluted sample and input were treated with 0.75 mg/mL Proteinase K and incubated at 42°C for 2 hours, followed by de-crosslinking overnight at 65°C.  Both IP and input were purified with the MinElute PCR Purification kit (Qiagen, cat. 28006), following manufacturer’s recommendations and eluted from the column twice with 30 µL of elution buffer from the kit.
NEBnext Ultra DNA library prep kit for Illumina (NEB, cat. E7370L)

value: Rtt101-3HA-HIS3; Pol2-5Flag-KAN; bar1D::URA3; MATa

value: yeast cell

value: 45min after release fron G1-phase in HU-containing medium

value: anti-HA (BioLegend 901502)


title: Rtt101-HA_ChIP_30min_rep1

value: 30min after release from G1-phase


title: Rtt101-HA_ChIP_30min_rep2


title: Rtt101-HA_ChIP_G1_rep2

value: G1-phase arrested cells


title: intestine, 15Gy, 6h, rep3

description:
mouse was treated with 15Gy IR, then collected intestine at 6h
Ftn6h3

value: 15Gy radiation, sample at 6h


title: DNAPol2-Flag_ChIP_45minHU_rep2

value: anti-Flag (Sigma F3165-1MG)


title: Rtt101-HA_ChIP_G1_rep1