title: spLHiChIP-RAD21-OHT-DRB

first: Martin

last: Eilers

address: Am Hubland

description: spLHiChIP-seq

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For pLHi-C, pLHiChIP and spLHiChIP sequencing reads, the program HiC-Pro v2.11.4 was used to trim linker sequences, align to hg19, filter by DpnII restriction fragments and carry out qualtiy controls. HiC-Pro was also used to generate valid pairs outputs (bedpe files). For pLHi-C, the program HiC-Pro was further used to build contact maps and to transform those into HIC format (hic files).
For spLHiChIP, a spike-in (mouse; mm10) normalization was done. The number of spike-in normalized reads per sample was calculated by dividing the number of reads mapping exclusively to hg19 by the number of reads mapping exclusively to mm10 and multiplying this number with the smallest number of reads mapping to mm10 of all samples. For spLHiChIP and pLHiChIP valid pairs, DNA loops were called using the program hichipper v0.7.7.
Assembly: hg19 (GRCh37) and mm10
Supplementary files format and content: For pLHi-C, the provided processed files are hic files for display and further analysis of contact maps. For pLHiChIP and spLHiChIP sequencing experiments, the provided processed files are bedpe files used to describe pairs of genomic regions.

source_name: SH-EP NMYC-ER

extract_protocol:
For phosphorylated linker Hi-C (pLHi-C), phosphorylated linker HiChIP (pLHiChIP) and spike-in phosphorylated linker HiChIP (spLHiChIP), cells were cross-linked with 1% formaldehyde for 5 min and stopped by adding 125 mM glycine for 10 min at room temperature. Nuclei were isolated and a one-step in situ digestion and dephosphorylation took place by using DpnII and rSAP enzymes. During the nuclei isolation step, only for the spLHiChIP samples, murine NHO2A cells were added as exogenous control (spike-in) at a 1:20 cell ratio. Next, biotinylated oligos with 5’ end phosphate were used with T4 ligase for the ligation step.
Chromatin fragmentation was performed using the Covaris Focused Ultrasonicator M220 for 30 min per ml lysate. Samples were de-crosslinked overnight and Protein and RNA were digested with proteinase K and RNase A. DNA was isolated using ChIP DNA Clean & Concentrator (Zymo Research). Biotin pull-down was performed with MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to manufacturer’s instructions.
Only for pLHiChIP and spLHiChIP samples, the chromatin fragmentation was followed by an immunoprecipitation of the target protein. To this end, Dynabeads Protein A and Protein G were pre-incubated overnight with 10-15 µg antibody in the presence of 5 mg/ml BSA. Next, chromatin was added to the pre-incubated beads for at least 6h at 4°C with rotation. Beads were then washed with different TRIS buffers containing distinct salt-concentrations, EDTA and detergents, followed by wahsing with only TE-buffer.
The immunoprecipitated chromatin of the pLHiChIP and spLHiChIP samples was eluted with 100mM NaHCO3 and 1% SDS for 15 min. Eluted samples were de-crosslinked overnight. DNA was isolated using ChIP DNA Clean & Concentrator (Zymo Research). Biotin pull-down was performed with MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to manufacturer’s instructions.
Library preparation was the same for all samples and was done on beads using the NEBNext ChIP-Sequencing Library Prep Master Mix Set for Illumina (NEB) according to manufacturer's instrcutions. The only deviation from the instructions was an additional washing step between each module using a Tris-buffer with 0.5 mM EDTA, 1 M NaCl and 0.05% Tween followed by a washing step with only TE buffer. Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
pLHi-C sequencing (Illumina NextSeq500) and (s)pLHiChIP sequencing (Illumina NextSeq500 or NextSeq2000)

value: SH-EP NMYC-ER

value: Neuroblastoma

tag: cell cycle_synchronization

value: unsynchronized

tag: dox-treatment (shrna-tf3c5)

value: not applicable

tag: 4-oht treatment_(nmyc_expresion)

value: induced (NMYC expression)

tag: treatment with_inhibitor

value: DRB (Benzimidazole; RNAPII CTD kinase inhibitor)

tag: spike-in

value: murine cells

tag: chip antibody

value: RAD21 (A300-080A; Bethyl Laboratories)


title: CD8-Virtual-Mem_Y_3

status: Public on Jul 15 2024

type: SRA

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

library_source: genomic

data_processing:
ATAC-seq data processing and alignment were completed using the Harvard pipeline (https://informatics.fas.harvard.edu/atac-seq-guidelines.html). The GRCm38.p6/mm10 genome primary assembly build used for alignment was obtained from the ensemble database (http://asia/ensembl.org/Musc_musculus/Info/Index; ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa)
All fastq files were trimmed to remove the Illumina Nextera Transposase adapter sequence using Cutadapt v.2.4 with “-m 20” parameter (Martin, 2011). After trimming, FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check overall sequence quality and evaluate proper adapter trimming. Bowtie2 (Langmead and Salzberg, 2012) was used to align reads to the GRCm38.p6/mm10 mouse reference genome using “-p 8, –very-sensitive” options. Picard tools (http://broadinstitute.githyb.io/picard/) were used to mark and remove duplicates using the MarkDuplicates tool with default options. All subsequent analyses were performed on deduplicated reads. Samtools (Li et al., 2009) was used to sort and obtain uniquely mapped reads using “-b -q 10” options. Samtools were also used to remove reads from the mitochondrial chromosome.
Finally, for visualization purposes, BAM files were converted to an index binary format bigWig using bedtools (Quinlan, 2014).
Peak calling was produced in accordance with Corces et al. 2018 to ensure reproducible high-quality fixed-with peaks with a minimal bias due to change in read depth (ranged from 12,870,021 to 121,543,847 ) and data quality (FROT ranged from 5.1 to 39.7).
First, peak calling per sample was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” (Zhang et al., 2008; Feng et al., 2012). Next, peak summits were extended by 250 bp on both sides to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions (Amemiya et al., 2019)(https://www.encodeproject.org/annotations/ENCSR636HFF/).    To avoid overlapping peaks within sample because of the 250bp peak summit extension, we performed an iterative removal approach as in Corces et al. 2018. During this process non overlapping peaks are kept as well as the most significant peaks within an overlap, whereas direct overlapping peaks are disregarded. The process is performed in an iterative manner to avoid the removal of indirect peak overlap. This yielded resulted a set of fixed-width peaks per sample.   Next, we normalized MACS2 “[−log10 (p-value)]” peak significance scores converting them to a score per million values (scpm). In brief, each individual peak score was divided by the sum of all the peak scores in the given sample divided by 1 million. This scpm value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield a higher number of peaks and higher significance scores using MACS2. Thus, scores per million allow the direct comparison of peaks across biological replicates.   Next, we sought to generate a cell-type specific peak set containing all reproducible peaks within a cell-type and aging stage. For that, we generated a cumulative peak set by combining all previous fixed-width peaks from a given cell-type and ageing stage and performed the previous iterative approach as performed per sample. Only peaks with a scpm >=1 in at least two samples (min. overlap 50%) were further considered, at the exception of Adipocytes and Neurons, where scpm >=3 was selected to increase signal-to-noise ratio due to some of their samples presented lower quality (I.e. FROT <=10). Next, we wanted to identify reproducible peaks within a cell-type and across ageing status. Therefore, we re-normalized the score per million per cell-type and ageing status and performed a cumulative peak which was again trimmed for overlap following the iterative approach mentioned above. This resulted in a set of reproducible, fixed-width per cell type () which we refer as cell-type specific.   Lastly, we wanted to obtain a universal peak set across cell-types and ageing status to perform a pan-somatic ageing analysis. For that, we re-normalized the scpms per cell-type specific peak sets. Then, the 23 peak sets ere combined and again, we performed the iterative approach to remove overlapping peak sets across conditions. This resulted in a universal peak set of 460K, each of 501 bp in width.
Assembly: mm10
Supplementary files format and content: bigWig (.bw), narrowPeak, summits.bed, bed format with score per million score (scpm.bed), bed format and gtf format as well as the counts within the unviersal peak set.

molecule: genomic DNA

organism: Mus musculus

source_name: CD8 Virtual Memory

extract_protocol:
The tissues of 5 healthy animals were pooled per-replicate for cell isolation, with 3-5 replicates (totalling 15-25 animals) collected per cell type/condition. Multi-omic bulk profiling (OMNI-ATAC-seq assay and RNA-seq) was performed on purified populations collected via fluorescence activated cell sorting (FACS).
 OMNI-ATACseq libraries were generated from FACS purified cells according to the standard protocol (Corces et al., 2017). Afterward, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations. Library fragments ranging from 150 to 700 bp were enriched and the final elution volume was 21 ul.

tag: cell type

value: CD8 Virtual Memory

tag: genotype

value: C57/Bl6 background

tag: time

value: 2 months


title: Fbp1△Hep  B6

city: Chongqing

first: Yahui

last: Zhu

address: ACampus, Chongqing University,Shapingba District, Chongqing, China

country: China

institute: Chongqing University

library_source: transcriptomic

data_processing:
The clustering of index-coded samples was performed on an Illumina Novaseq sequencer 6000 according to the manufacturer’s instructions.
After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated.
Assembly: RNA-seq reads were aligned to the mouse genome (GRCm38/mm10) using STAR. Biological and technical replicates were used in all experiments.
Supplementary files format and content: Transcript quantification was performed with HOMER (v.4.11). Principal component analysis (PCA) was done using fragments per kilobase million (FPKM) on all genes from all the samples
Supplementary files format and content: Expression value for each transcript was calculated using the analyzeRepeat Pl tool of HOMER.

molecule: total RNA

source_name: Liver

growth_protocol: Mice were maintained in filter-topped cages on autoclaved food and water with a 12 h light /dark cycle. Experiments were performed according to UCSD Institutional Animal Care and Use Committee (protocol S00218) and NIH guidelines and regulations.

extract_protocol:
Total RNA was isolated as above together with RNase-Free DNase kit (Qiagen, #79254) to obtain pure RNA. RNA degradation and contamination were monitored on 1% agarose gels and RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed with the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For library preparation, a total of 1 μg RNA per sample was used as input for RNA sample preparations. Sequencing libraries were generated with NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s protocols and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was performed with DNA polymerase Ⅰ and RNase H. Remaining overhangs were converted into blunt ends by exonuclease/polymerase activities. After 3’ end adenylation of DNA fragments, NEBNext adaptors with hairpin loop structures were ligated to prepare for hybridization. Library fragments were then purified with AMPpure XP system (Beckman Coulter, Beverly, USA) and 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNAs at 37℃ for 15 min followed by 5 min at 95℃. PCR was then performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For HCC induction by hydrodynamic injection, Fbp1ΔHep or  Nfe2l2Act-Hep mice were intravenously(i.v.) injected with NRASG12V (12.5 μg/ml) and Sleeping Beauty transposase (SB13) (2.5 μg/ml) plasmids diluted in Ringer’s solution at 0.1 ml/g body weight in 5-7 seconds.

tag: tissue

value: Liver

tag: cell line

value: No

value: hepatocyte

tag: treatment

value: Ctrl


title: Fbp1F/F B3


title: CD8-Virtual-Mem_O_1

value: 22-24 months


title: HEL_AF9shRNA1_AF9KD_Polll_rep2

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
For CUT&Tag, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
hg38
BigWig files contains normalized read count (CPM, in 50-bp bins)

organism: Homo sapiens

source_name: HEL

growth_protocol: Human cells HEL and THP1 were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
DNA was extracted by Phenol-Chloroform-Isoamylol and amplified by PCR
Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation.  DNA was extracted and amplified by PCR. The product was purified by AMpure XP beads. After size seletion of purified production, library will be analyzed by Illumina NovaSeq 6000.

value: HEL

value: Human erythroblast

tag: cut and_tag_antibody

value: Pol ll (Santa, SC-47701)


title: spLHiChIP-RAD21-EtOH-DRB

city: Wuerzburg

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description: spLHiChIP-seq

growth_protocol: Human neuroblastoma derived SH-EP cells expressing an exogenous and 4-OHT inducible NMYC allele (SH-EP-NMYC-ER), were grown in RPMI-1640 medium supplemented with with 10% horse serum and 1% penicillin/ streptomycin. Cells were cultured at 37C at 5% CO2.

treatment_protocol:
The indcution of NMYC in the SH-EP-NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours. Where indicated, SH-EP-NMYC-ER cells were treated with MLN8237 (1 µM) or DRB (100 µM) for 2 hours.
For spike-in phosphorylated linker HiChIP (spLHiChIP) samples, an exogenous control (spike-in) was used. For that purpose, murine NHO2A cells were added at a 1:20 cell ratio to the samples during the nuclei isolation step.

value: SH-EP NMYC-ER

value: Neuroblastoma

value: unsynchronized

value: uninduced (no NMYC expression)


title: HK2_Arid5a_1_IL17

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

country: USA

institute: University of Pittsburgh

data_processing:
The raw sequence reads were mapped to GrCH38/hg38 using default parameters in STAR (v2.7.9) and quantified using RSEM (v1.3.1)
Read count extraction and normalization were performed using DESeq2 (v1.36.0) in R(v4.2.0)
Assembly: hg38
Supplementary files format and content: comma-separated values file include FPKM and count values for each Sample

source_name: human kidney epithelial

growth_protocol: HK2 were plated in 150mm tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator overnight.

extract_protocol:
Cells were trypsinized and extracts were isolated with lysis buffer with RNase Inhibitor (40 U/μl; Thermo Scientific). Buffers included protease inhibitor cocktail (Sigma-Aldrich). Lysates were immunoprecipitated with Abs against FLAG or mouse IgG1. Beads were washed with NT2 buffer and digested with DNase I (Roche Applied Science) and protease K (Sigma-Aldrich). Total RNA was extracted with acid phenol or TRIzol.
RIP-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA kit

treatment_protocol: Cells were transfected with 10ug FLAG-hArid5a encoding plasmid by using FuGeneHD transfection reagent (Promega Cat#E2311). Cells were stimulated with IL-17 (200 ng/mL) or medium control for 3 hours .

value: human kidney epithelial

value: human kidney epithelial cell line

tag: rip antibody

value: FLAG; Cat# F3165; Sigma-Aldrich Lot SLCG2330


title: CD8-Virtual-Mem_Y_2

value: CD8 Virtual Memory

value: C57/Bl6 background


title: spLHiChIP-RAD21-OHT-DMSO

description: spLHiChIP-seq

value: not applicable

value: induced (NMYC expression)

value: DMSO

value: murine cells

value: RAD21 (A300-080A; Bethyl Laboratories)


title: HEL_AF9shRNA1_AF9KD_Polll_rep1

value: HEL


title: Fbp1F/F B2

value: Liver

value: No

value: hepatocyte

value: Ctrl


title: HK2_IgG_1_IL17

value: Mouse IgG1; Cat# 5415S; CST Lot 10


title: spLHiChIP-RAD21-EtOH-DMSO

description: spLHiChIP-seq

value: SH-EP NMYC-ER

value: Neuroblastoma

value: unsynchronized

value: uninduced (no NMYC expression)


title: HEL_AF9shRNA1_Ctrl_Polll_rep2

value: Human erythroblast

value: Pol ll (Santa, SC-47701)


title: CD8-Naive_Y_4

source_name: CD8 Naive

value: CD8 Naive

value: C57/Bl6 background

value: 2 months


title: Fbp1F/F B1


title: CD8-Naive_Y_3


title: spLHiChIP-TF3C5-OHT-DRB

description: spLHiChIP-seq

value: not applicable

value: induced (NMYC expression)

value: DRB (Benzimidazole; RNAPII CTD kinase inhibitor)

value: murine cells

value: TFIIIC5 (A301-242A; Bethyl Laboratories)


title: HEL_AF9shRNA1_Ctrl_Polll_rep1

value: HEL


title: CD8-Naive_Y_2


title: HEL_AF9shRNA1_AF9KD_MLL1_rep2

value: MLL1 (468, thanks to E. Canaani lab)


title: Fbp1△Hep  B7

value: Liver

value: No

value: hepatocyte

value: Ctrl


title: CD8-Naive_Y_1


title: HEL_AF9shRNA1_Ctrl_TBP_rep1

value: TBP (Santa, SC-56795)


title: spLHiChIP-TF3C5-EtOH-DRB

description: spLHiChIP-seq

value: SH-EP NMYC-ER

value: Neuroblastoma

value: unsynchronized

value: uninduced (no NMYC expression)


title: Nrf2Act-Hep + HD A15

description: Nrf2Act-Hep + HD


title: spLHiChIP-TF3C5-OHT-DMSO

description: spLHiChIP-seq

value: DMSO


title: CD8-Virtual-Mem_O_2

value: CD8 Virtual Memory

value: C57/Bl6 background

value: 22-24 months


title: HEL_AF9shRNA1_AF9KD_MLL1_rep1

value: Human erythroblast


title: CD8-Naive_O_4

value: CD8 Naive


title: Nrf2Tg/Tg + HD A13

description: Nrf2Tg/Tg + HD


title: Nrf2Act-Hep + HD A14

description: Nrf2Act-Hep + HD


title: spLHiChIP-TF3C5-EtOH-DMSO

description: spLHiChIP-seq

value: not applicable

value: murine cells

value: TFIIIC5 (A301-242A; Bethyl Laboratories)


title: CD8-Naive_O_3


title: HEL_AF9shRNA1_Ctrl_MLL1_rep1

value: HEL

value: MLL1 (468, thanks to E. Canaani lab)


title: HEL_AF9shRNA1_Ctrl_MLL1_rep2


title: CD8-Naive_O_2


title: spLHiChIP-MYCN-Sphase-OHT-MLN

description: spLHiChIP-seq

value: S-phase synchronized

value: uninduced (no shRNA expression)

value: induced (NMYC expression)

value: MLN8327 (Alisertib; Aurora A kinase inhibitor)

value: MYCN (B8.4.B) (sc-53993; Santa Cruz)


title: spLHiChIP-MYCN-Sphase-OHT-DMSO

description: spLHiChIP-seq

value: SH-EP NMYC-ER

value: Neuroblastoma


title: Nrf2Tg/Tg + HD A12

description: Nrf2Tg/Tg + HD

value: Liver

value: No

value: hepatocyte


title: HEL_AF9shRNA1_AF9KD_CDK9_rep2

value: Human erythroblast

value: CDK9 (ABconal, A0886)


title: CD8-Naive_O_1

value: CD8 Naive

value: C57/Bl6 background

value: 22-24 months


title: Nrf2Act-Hep + HD A16

description: Nrf2Act-Hep + HD


title: HEL_AF9shRNA1_AF9KD_CDK9_rep1

value: HEL


title: pLHiC-MYCN-Input-OHT

description: pLHiC-seq

value: unsynchronized

value: not applicable


title: pLHiChIP-MYCN-OHT

description: pLHiChIP-seq


title: HEL_AF9shRNA1_Ctrl_CDK9_rep2


title: CD8-Memory_Y_4

source_name: CD8 Memory

value: CD8 Memory

value: 2 months


title: Nrf2Act-Hep A7

value: Ctrl


title: HEL_AF9shRNA1_Ctrl_CDK9_rep1


title: CD8-Memory_Y_3


title: CD8-Memory_Y_2


title: Nrf2Act-Hep A6


title: HEL_AF9shRNA1_AF9KD_AF9_rep2


title: CD8-Memory_Y_1


title: Nrf2Tg/Tg A3


title: ChIPRx-RNAPII-Merged-Input

description: ChIP-Rx-seq

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For Cut&Run sequencing, ChIP-seq and ChIP-Rx sequencing, reads were aligned to the human genome (hg19/GRCh37) using Bowtie2 v2.3.5.1 with default parameters. Normalization by aligned read number was performed on the input and on all correspondent IP samples. Where applicable, the number of spike-in normalized reads per sample was calculated by dividing the number of reads mapping exclusively to hg19 by the number of reads mapping exclusively to mm10 and multiplying this number with the smallest number of reads mapping to mm10 of all samples.
Following read-normalization, files were converted to bedGraph with bedtools genomecov v2.26 and visualized in a genome browser using the package plotgardener v1.012 in R v4.1.1. MACS2 v2.1.2 was used for peak calling for MYCN, TF3C5 and RAD21. H3K4me1, H3K4me3 and H3K27ac peaks were called with SICER v1.1.
Assembly: hg19
Supplementary files format and content: For CUT&RUN-seq, ChIP-seq and ChIP-Rx sequencing, the provided processed files are bedGraph files for data display in a genome browser.

extract_protocol:
For Cut&Run sequencing, cells were harvested with Accutase, washed and then coupled to ConA-coated magentic beads (Polysciences Europe). Cells were then permeabilized and incubated with the primary antibody (EXOSC5 #NBP2-14952; 1:100 diluted; Novus Biologicals) in antibody binding buffer over night at 4°C. Cells were then washed in the presence of digitonin and 700 ng/ml MNase was added per sample for 1 hour at 4°C.
For Cut&Run sequencing samples, the MNase treated cells were washed with low-salt rinse buffer. Incubation buffer, containing CaCl2 and digitonin, was added for 30 min at 4°C. The Mnase activity was stoped in the presence of 20 µg/ml Rnase A. DNA fragments were released at 37°C for 30 min and the decrosslinking was done for 1 hour at 50°C by adding 0.01% SDS and 10 mg/ml Proteinase K. DNA was extracted wit phenol-chloroform and resuspended in TE buffer.
For ChIP-seq and ChIP-Rx sequencing, cells were fixed for 5 min at RT with 1% formaldehyde and harvested in cold PBS contianing protease and phosphatase inhibitors. For ChIP-Rx samples, murine NHO2A or NIH3T3 cells were added at a 1:10 cell ratio during cell lysis to serve as an exogenous control (spike-in). Cell lysis was done for 20 min in PIPES buffer containing 85 mM KCl and 0.5% NP-40, followed by collection of nuclei by centrifugation.
For ChIP-seq and ChIP-Rx sequencing, the crosslinked chromatin was extracted from the nuclei in TRIS buffer with 150 mMCaCl, 1 mM EDTA and 1% NP-40, 1% sodium deoxycholate and 0.1% SDS. The chromatin was fragmented using the Covaris Focused Ultrasonicator M220 for 50 min. Dynabeads Protein A and Protein G were pre-incubated overnight with 10-15 µg antibody in the presence of 5 mg/ml BSA.
For ChIP-seq and ChIP-Rx sequencing, chromatin was added to the pre-incubated beads for at least 6h at 4°C with rotation. Beads were then washed with different TRIS buffers containing distinct salt-concentrations, EDTA and detergents, followed by wahsing with only TE-buffer. Chromatin was eluted with 100mM NaHCO3 and 1% SDS for 15 min. Protein and RNA were digested with proteinase K and RNase A. DNA was isolated by phenol-chloroform extraction followed by an ethanol precipitation. DNA was quantified using the Quant-IT PicoGreen dsDNA assay.
The DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Pre-PCR samples were purified and/or size-selected using AMPureXP beads. The libraries were PCR-amplified with the NEBNext Multiplex Oligos for Illumina Kit and again purified using Agencourt AMPure XP beads (Beckman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
ChIP, ChIP-Rx and CUT&RUN followed by sequencing.

treatment_protocol:
The indcution of NMYC in the SH-EP NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours. Where indicated, SH-EP NMYC-ER cells were treated with DRB (100 µM) for 2 hours.
For ChIP-Rx samples, an exogenous control (spike-in) was used. For that purpose, murine NHO2A or NIH3T3 cells were added at a 1:10 cell ratio to the samples during the cell lysis step.

value: merge of samples

value: murine cells


title: HEL_AF9shRNA1_AF9KD_AF9_rep1


title: Nrf2Tg/Tg + HD A11

description: Nrf2Tg/Tg + HD


title: Nrf2Tg/Tg A1


title: CD8-Memory_O_4


title: Nrf2Tg/Tg A2


title: HEL_AF9shRNA1_Ctrl_AF9_rep1


title: Nrf2Act-Hep A8


title: ChIPRx-RNAPII-pS2-EtOH-EtOH

description: ChIP-Rx-seq

value: SH-EP NMYC-ER

value: Neuroblastoma

value: uninduced (no shRNA expression)

value: uninduced (no NMYC expression)

value: RNAPII pSer2 (ab5095; Abcam)


title: ChIPRx-RNAPII-pS2-EtOH-OHT

description: ChIP-Rx-seq

value: induced (NMYC expression)


title: CD8-Memory_O_3


title: HEL_AF9shRNA1_Ctrl_AF9_rep2

value: Human erythroblast


title: ChIPRx-RNAPII-pS2-DOX-OHT

description: ChIP-Rx-seq

value: induced (shRNA expression)


title: HFD, Liver, KO 1-5 pooled

city: Kansas City

first: Andrew

last: Lutkewitte

state: Kansas

address: 3901 Rainbow Blvd

institute: The University of Kansas Medical Center

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

extract_protocol:
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0.
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: Liver

value: Adipocyte Lpin1 Knockout

value: 16 weeks, 60 %HFD


title: HEL_MLL1shRNA1_MLL1KD_CDK9_rep1

value: HEL

value: CDK9 (ABconal, A0886)


title: CD8-Memory_O_2

value: CD8 Memory

value: C57/Bl6 background

value: 22-24 months


title: HEL_MLL1shRNA1_MLL1KD_CDK9_rep2


title: HFD, Liver, KO 5


title: CD8-Memory_O_1


title: ChIPRx-RNAPII-pS2-DOX-EtOH

description: ChIP-Rx-seq

value: unsynchronized

value: not applicable

value: murine cells


title: HFD, Liver, KO 4


title: ChIPRx-RNAPII-A10-EtOH-OHT

description: ChIP-Rx-seq

value: SH-EP NMYC-ER

value: Neuroblastoma

value: uninduced (no shRNA expression)

value: RNAPII (A-10) (sc-17798; Santa Cruz)


title: CD4-Naive_Y_3

source_name: CD4 Naive

value: CD4 Naive

value: 2 months


title: CD4-Naive_Y_4


title: HFD, Liver, KO 3

value: Liver


title: HEL_MLL1shRNA1_Ctrl_CDK9_rep1

value: Human erythroblast


title: CD4-Naive_Y_2


title: ChIPseq-Histones-Merged-Input

description: ChIP-seq

value: merge of samples


title: HFD, Liver, KO 2

value: Adipocyte Lpin1 Knockout

value: 16 weeks, 60 %HFD


title: ChIPseq-H3K4me3

description: ChIP-seq

value: uninduced (no NMYC expression)

value: H3K4me3 (ab8580; Abcam)


title: HEL_MLL1shRNA1_MLL1KD_AF9_rep2

value: HEL


title: CD4-Naive_Y_1

value: C57/Bl6 background


title: HFD, Liver, KO 1


title: HEL_MLL1shRNA1_MLL1KD_AF9_rep1


title: ChIPseq-H3K4me1

description: ChIP-seq

value: unsynchronized

value: not applicable

value: H3K4me1 (ab8895; Abcam)


title: CD4-Naive_O_3

value: 22-24 months


title: HEL_MLL1shRNA1_Ctrl_AF9_rep2


title: HFD, Liver, Control 1-5 pooled

value: Wildtype Control


title: CD4-Naive_O_2


title: HFD, Liver, Control 5


title: HEL_MLL1shRNA1_Ctrl_CDK9_rep2

value: CDK9 (ABconal, A0886)


title: H3 ChIP seq HSVd 20 dpi bioreplicate 1

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: H3 control for ChIP sequencing

data_processing:
Adapter and quality trimming of the raw reads were conducted using BBDuk from de BBTools suite (v38.90), applying the following parameters: qtrim=rl, trimq=20, ref=adapters, ktrim=r, k=23, mink=11, hdist=1, minlen=60, tpe, tbo. Optical duplicates were removed from the cleaned data using clumpify.sh from BBTools with the parametes dedupe, spany and adjacent set to true.
Sequences were aligned to the Arabidopsis Cucumis sativus "Chinese long" version 3 genome using bowtie2 with default parameters.
Genome coverage was calculated as the log2 fold change of the ratio between the coverage of H3K9me2 or H3K27me3 to the coverage of H3 using deeptools2 (Ramirez et al., 2016). For genome-wide profile images, the RPKM-normalized value of H3 was substracted to the RPKM value of either H3K9me2 or H3K27me3. Values for specific regions and quantitative analysis were retrieved using mapbed from bedtools (Quinlan & Hall, 2010).
Peak calling was performed using Sicer2 each sample to its respective H3 control with the parameters window size 200, fragment size 150, effective genome fraction 0.74, false discovery rate 0.01, false discovery rate of 0.01 and a gap size of 600bp. Peak location and overlap was compared using the intersect tool from bedtools with a minimum overlap of 1bp. Only peaks shared between the two replicates were considered as true peaks for that specific treatment. Shared peaks were compared between samples using the intersect tool from bedtools to determine gain and loss peaks.
Assembly: Cucumis sativus "Chinese long" version 3
Supplementary files format and content: RPKM-normalized value of H3 was subtracted from the RPKM value of either H3K9me2 or H3K27me3 for the generation of bigwig files
Supplementary files format and content: Peak location identified with Sicer2 is included in bed format (.txt file)

organism: Cucumis sativus

source_name: Systemic leaves

growth_protocol: Cucumis sativus (variety Marketer) seeds were sown into potting soil (P-Jord, Hasselfors Garden, Örebro, Sweden) into plastic pots (9 × 9 × 7 cm) with one plant per pot at a temperature of approximately 30°C and 60% relative humidity. Plants were grown under a 16 h: 8 h, light : dark photoperiod. The light was provided by FQ, 80 W, Hoconstant lumix (Osram, Munich, Germany) with a light intensity of 220 μmol photons m−2 s−1. HSVd infection was performed at the two-cotyledon stage. Seedlings were agroinfiltrated with an infectious HSVd clone or an empty vector (mock plants). Samples were collected at 10 (T1) and 24 (T2) dpi.

extract_protocol:
Immunoprecipitated DNA was extracted using the GeneJET PCR Purification Kit (Thermo Fisher), following the manufacturer’s instructions.
500 mg of systemic leaves were chemically cross-linked using 1% formaldehyde. Then, nuclei were isolated from cross-linked material following a standard nuclei isolation protocol based on sucrose gradients as previously described (Moreno-Romero et al., 2016). The resuspended nuclei pellets were sonicated for 9 cycles of 20 s On and 45 s Off at 4 °C and high power to obtain the chromatin. Afterward, the Immunoprecipitation (IP) was performed following a standard IP protocol and using the following antibodies: H3 (Reference: 07-690, Merck), H3K9me2 (Reference: pAb-060-050, Diagenode) and H3K27me3 (Reference: 07-449, Merck).
DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) and each individual library was barcoded using the NEBNext® Multiplex Oligos for Illumina® kit (New England Biolabs).

value: Systemic leaves

value: Marketer

tag: infection

value: HSVd-infected

value: 20 dpi


title: HFD, Liver, Control 4

value: Liver


title: H3 ChIP seq HSVd 20 dpi bioreplicate 2

description: H3 control for ChIP sequencing

treatment_protocol: HSVd infection was performed at the two-cotyledon stage. Seedlings were agroinfiltrated with an infectious HSVd clone or an empty vector (mock plants).


title: HEL_MLL1shRNA1_Ctrl_AF9_rep1

value: Human erythroblast


title: CD4-Memory_Y_3

source_name: CD4  Memory

value: CD4  Memory

value: 2 months


title: HFD, Liver, Control 2

value: 16 weeks, 60 %HFD


title: HEL_MLL1shRNA1_MLL1KD_MLL1_rep2

value: HEL

value: MLL1 (468, thanks to E. Canaani lab)


title: H3 ChIP seq Mock 20 dpi bioreplicate 1

description: H3 control for ChIP sequencing

value: Mock


title: CD4-Memory_Y_4

value: C57/Bl6 background


title: HFD, Liver, Control 3


title: HEL_MLL1shRNA1_Ctrl_MLL1_rep2


title: HEL_MLL1shRNA1_MLL1KD_MLL1_rep1


title: CD4-Memory_Y_2


title: HFD, Liver, Control 1


title: H3 ChIP seq HSVd 10 dpi bioreplicate 2

description: H3 control for ChIP sequencing

value: 10 dpi


title: ChIPseq-H3K27ac

description: ChIP-seq

value: SH-EP NMYC-ER

value: Neuroblastoma

value: unsynchronized

value: not applicable

value: uninduced (no NMYC expression)

value: H3K27ac (ab4729; Abcam)


title: HEL_MLL1shRNA1_Ctrl_MLL1_rep1


title: CD4-Memory_Y_1


title: H3 ChIP seq HSVd 10 dpi bioreplicate 1

description: H3 control for ChIP sequencing

value: Systemic leaves

value: Marketer

value: HSVd-infected


title: E-micA714-35h_1

city: Hangzhou

first: Yilong

last: Wang

state: Zhejiang

address: NO.3333 binsheng Road

department: Department of Neurology

institute: Children’s Hospital, Zhejiang University School of Medicine

description:
sample40-HC10
A714-35h

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
The miRNAs expressions were normalized corrected according to  UMI counts and normalized to transcript per millioncounts per million (TPM)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: plasma samples

extract_protocol:
Total RNA samples were extracted and purified from sEVs by the miRNeasy Mini kit
For small RNA libraries, a total of 1–  500 ng of RNA per sample was prepared as the input  material. Sequencing libraries were constructed using QIAseq  miRNA Library Kit

value: plasma

tag: diagnosis

value: healthy control


title: LFD, Liver, KO 1-5 pooled

value: Liver

value: Adipocyte Lpin1 Knockout

value: 16 weeks, 10% LFD


title: CD4-Naive_O_1

value: CD4 Naive

value: 22-24 months


title: H3 ChIP seq Mock 20 dpi bioreplicate 2

description: H3 control for ChIP sequencing

value: Mock

value: 20 dpi


title: LFD, Liver, KO 5


title: CD4-Memory_O_3

value: CD4  Memory

value: C57/Bl6 background


title: H3 ChIP seq Mock 10 dpi bioreplicate 1

description: H3 control for ChIP sequencing

value: 10 dpi


title: LFD, Liver, KO 4


title: E-micA714-33h_1

description:
sample38-HC8
A714-33h


title: LFD, Liver, KO 3


title: H3 ChIP seq Mock 10 dpi bioreplicate 2

description: H3 control for ChIP sequencing


title: H3K27me3 ChIP seq HSVd 20 dpi bioreplicate 2

description:
ChIP sequencing H3K27me3
K27_HSVd_T2_RPKM_subst.bigwig
Peaks_K27_HSVd_T2.txt


title: CD4-Memory_O_2


title: LFD, Liver, KO 1


title: E-micA714-32h_1

description:
sample37-HC7
A714-32h


title: E-micA714-34h_1

description:
sample39-HC9
A714-34h


title: CD4-Memory_O_1


title: LFD, Liver, KO 2


title: H3K27me3 ChIP seq Mock 20 dpi bioreplicate 2

description:
ChIP sequencing H3K27me3
K27_Mock_T2_RPKM_subst.bigwig
Peaks_K27_Mock_T2.txt


title: E-micA323-49h_1

description:
sample35-HC5
A323-49h


title: E-micA323-50h_1

description:
sample36-HC6
A323-50h


title: LFD, Liver, Control 1-5 pooled

value: Wildtype Control


title: H3K27me3 ChIP seq HSVd 20 dpi bioreplicate 1


title: E-micA323-48h_1

description:
sample34-HC4
A323-48h


title: H3K27me3 ChIP seq Mock 20 dpi bioreplicate 1


title: CD4-Memory_O_4


title: LFD, Liver, Control 5


title: Brain-endothelial_Y_2

source_name: Brain endothelial

value: Brain endothelial

value: 2 months


title: Brain-endothelial_Y_4


title: H3K27me3 ChIP seq HSVd 10 dpi bioreplicate 2

description:
ChIP sequencing H3K27me3
K27_HSVd_T1_RPKM_subst.bigwig
Peaks_K27_HSVd_T1.txt

value: Systemic leaves

value: Marketer


title: Brain-endothelial_Y_1


title: E-micA323-47h_1

description:
sample33-HC3
A323-47h

value: plasma


title: LFD, Liver, Control 4


title: E-micA323-46h_1

description:
sample32-HC2
A323-46h

value: healthy control


title: H3K27me3 ChIP seq HSVd 10 dpi bioreplicate 1

value: HSVd-infected


title: Brain-endothelial_O_4


title: H3K27me3 ChIP seq Mock 10 dpi bioreplicate 2

description:
ChIP sequencing H3K27me3
K27_Mock_T1_RPKM_subst.bigwig
Peaks_K27_Mock_T1.txt


title: E-micA323-45h_1

description:
sample31-HC1
A323-45h


title: LFD, Liver, Control 3

value: Liver


title: LFD, Liver, Control 2

value: 16 weeks, 10% LFD


title: Brain-endothelial_Y_3


title: LFD, Liver, Control 1


title: E-micA714-31h_1

description:
sample30-TS-10
A714-31h

value: Tourette Syndrome


title: Brain-endothelial_O_3

value: 22-24 months


title: E-micA714-30h_1

description:
sample29-TS-9
A714-30h


title: E-micA714-29h_1

description:
sample28-TS-8
A714-29h


title: Brain-endothelial_O_1


title: H3K9me2 ChIP seq HSVd 20 dpi bioreplicate 1

description:
ChIP sequencing H3K9me2
K9_HSVd_T2_RPKM_subst.bigwig
Peaks_K9_HSVd_T2.txt


title: Beta-cells_Y_5

source_name: Beta cells

value: Beta cells


title: Beta-cells_Y_4


title: Osteoclasts Acod1 KO_4OI3

city: Erlangen

first: Katerina

last: Kachler

address: Glueckstraße 6

department: Medicine 3 - Rheumatology and Immunology

institute: University Clinic Erlangen

data_processing:
Raw reads of FASTQ format were processed through fastp. Clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality. Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were aligned to the reference genome using theSTAR (v2.5) software. STAR used the method of Maximal Mappable Prefix (MMP), which can generate a precise maping result forjunction reads.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Assembly: mm10
Supplementary files format and content: Excel file (xlsx) contains raw counts for each sample

source_name: In vitro differentiated osteoclasts

growth_protocol: Total bone marrow cells from WT and Acod1-deficient (KO) mice were isolated by flushing femur and tibia. The cells were plated overnight at 37°C, 5.5 % CO2 in αMEM medium supplemented with 10 % fetal calf serum (FCS), 1 % penicillin and streptomycin (PS) as well as with 5 ng/ml Macrophage colony-stimulating factor (M-CSF). The next day, non-adherent bone marrow monocytes (BMMs) were collected, washed and plated at 37°C, 5.5 % CO2 in αMEM medium with 10 % FCS, 1% PS, 20 ng/ml M-CSF and 10 ng/ml Receptor Activator of NF-κB Ligand (RANKL). Osteoclasts were fully differentiated on day 3 of cell culture. Cells were washed with PBS and harvested for RNA extraction.

extract_protocol:
Total RNA was extracted on day 3 of osteoclast cell culture and purified with the RNeasy Mini Kit (Qiagen). A total amount of 1µg RNA per sample was used as input material for sample preparation.
Sequencing libraries were generated using  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina).

treatment_protocol: On day 1 of osteoclast cell culture, cells were either stimulated with 50µM of 4-octyl-itaconate (4-OI) or left unstimulated as a control condition.

value: In vitro differentiated osteoclasts

tag: cell source

value: Bone marrow

value: Acod1 KO


title: Osteoclasts Acod1 KO_4OI1


title: E-micA714-28h_1

description:
sample27-TS-7
A714-28h


title: H3K27me3 ChIP seq Mock 10 dpi bioreplicate 1

value: Mock

value: 10 dpi


title: H3K9me2 ChIP seq Mock 20 dpi bioreplicate 1

description:
ChIP sequencing H3K9me2
K9_Mock_T2_RPKM_subst.bigwig
Peaks_K9_Mock_T2.txt

value: 20 dpi


title: E-micA714-27h_1

description:
sample26-TS-6
A714-27h


title: H3K9me2 ChIP seq Mock 20 dpi bioreplicate 2


title: H3K9me2 ChIP seq HSVd 20 dpi bioreplicate 2


title: Osteoclasts Acod1 KO_CTR3

value: untreated


title: Beta-cells_Y_3

value: C57/Bl6 background

value: 2 months


title: Brain-endothelial_O_2

value: Brain endothelial


title: E-micA714-26h_1

description:
sample25-TS-5
A714-26h

value: plasma


title: H3K9me2 ChIP seq HSVd 10 dpi bioreplicate 2

description:
ChIP sequencing H3K9me2
K9_HSVd_T1_RPKM_subst.bigwig
Peaks_K9_HSVd_T1.txt

value: Systemic leaves

value: Marketer

value: HSVd-infected


title: Beta-cells_Y_2


title: E-micA714-25h_1

description:
sample24-TS-4
A714-25h

value: Tourette Syndrome


title: Osteoclasts Acod1 KO_CTR2


title: Osteoclasts Acod1 KO_4OI2


title: Osteoclasts Acod1 KO_CTR1


title: H3K9me2 ChIP seq HSVd 10 dpi bioreplicate 1


title: E-micA714-24h_1

description:
sample23-TS-3
A714-24h


title: Beta-cells_Y_1


title: Osteoclasts WT_CTR3

value: WT


title: E-micA714-23h_1

description:
sample22-TS-2
A714-23h


title: H3K9me2 ChIP seq Mock 10 dpi bioreplicate 2

description:
ChIP sequencing H3K9me2
K9_Mock_T1_RPKM_subst.bigwig
Peaks_K9_Mock_T1.txt


title: H3K9me2 ChIP seq Mock 10 dpi bioreplicate 1


title: TEAD4KO_bBL_rep6

first: Bingjie

last: Hu

address: Yuhangtang Rd, Hangzhou, Zhejiang , China

institute: Zhejiang University

data_processing:
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to ARS-UCD1.2  by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized  by DESeq2
Differentially expressed genes were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >2 or <0.5
Assembly: ARS-UCD1.2 , mm10
Supplementary files format and content: text files include normalized counts calculated by DESeq2 for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: embryo

extract_protocol:
Polyadenylated RNAs were captured and reverse transcribed with an Oligo(dT) primer
The RNA-seq libraries were constructed according to a Smart-seq2 procedures. Briefly, mRNA was fragmented and reverse transcribed. The cDNA library was subject to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

tag: developmental stage

value: Blastocyst

tag: age

value: 7.0 day after fertilization

value: embryos were injected with BE3 mRNA and TEAD4 sgRNAs mix at zygote stage


title: Beta-cells_O_2

value: Beta cells

value: 22-24 months


title: Osteoclasts WT_CTR2

value: In vitro differentiated osteoclasts

value: Bone marrow


title: E-micA714-22h_1

description:
sample21-TS-1
A714-22h


title: Osteoclasts WT_CTR1

value: untreated


title: TEAD4KO_bBL_rep4


title: E-micA714-21h_1

description:
sample20-CTD-10
A714-21h

value: chronic motor or vocal tic disorder


title: Tead4_mMO_rep2

value: Morula

value: 3.25 day after fertilization

value: embryos were injected with BE3 mRNA and Tead4 sgRNAs mix at zygote stage


title: E-micA714-20h_1

description:
sample19-CTD-9
A714-20h

value: plasma


title: Beta-cells_O_3

value: C57/Bl6 background


title: TEAD4KO_bBL_rep5


title: Beta-cells_O_1


title: B-cells_Y_4

source_name: B-cells

value: B-cells

value: 2 months


title: Tead4_mMO_rep1


title: B-cells_Y_3


title: B-cells_Y_2


title: E-micA714-19h_1

description:
sample18-CTD-8
A714-19h


title: TEAD4KO_bBL_rep3


title: NC_mMO_rep2

value: embryos were injected with BE3 mRNA at zygote stage


title: TEAD4KO_bBL_rep2

value: Blastocyst


title: E-micA714-18h_1

description:
sample17-CTD-7
A714-18h


title: TEAD4KO_bBL_rep1

value: 7.0 day after fertilization


title: E-micA714-17h_1

description:
sample16-CTD-6
A714-17h


title: B-cells_Y_1


title: U251-1813-3

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

data_processing:
Bcl2fastq (v2.17.1.14) software was used for base-calling
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
All transcripts as the result of Cuffmerge, were filtered by known non-lincRNA annotation, non- lincRNA characters, ORFs and protein-coding potential methods. Known non-lincRNA includes known protein-coding RNA, miRNA, tRNA, snoRNA, rRNA and pseudogenes. There are three characters of non-lincRNA, such as transcripts of non-lincRNA contain more than one exon; their length must be longer than 200bp; and the coverage of each transcript must be more than 3. ORFs were predicted by software HMMER (v3.1b1). CPC (Coding Potential Calculator) was used to do protein-coding potential prediction. CNCI (Coding-Non-Coding Index), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. Transcriptional regulation by lncRNAs could work either in cis or in trans, and could negatively or positively control pc gene expression. lncRNAs work in cis when their effects are restricted to the chromosome from which they are transcribed, and work in trans when they affect genes on other chromosomes. The cis regulation by lncRNAs can be predicted by software Bedtools (v2.17.0). And regulation in trans was analyzed via Pearson correlation coefficient.
Assembly: ENSEMBLE GRCh38.14
Supplementary files format and content: xls file includes FPKM values for each sample

extract_protocol:
The total RNA of each sample was extracted from the stable transfected glioma cell lines U87 and U251 by using TRIzol reagent (Life Technologies, USA)/RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s protocol. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The rRNA was depleted from total RNA using rRNA removal Kit. The ribosomal depleted RNA was then fragmented and reverse-transcribed. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix (include dACG-TP/dUTP). The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. The dUTP-marked second strand was digested with Uracil-Specific Excision Reagent enzyme. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P5/P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA,USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA) or a MGI2000 instrument according to manufacturer’s instructions (MGI, Shenzhen, China) . Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline- 1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.

value: glioma cell line

value: LAMP2A knockdown


title: NC_bBL_rep6


title: E-micA714-16h_1

description:
sample15-CTD-5
A714-16h


title: U251-1813-2


title: NC_bBL_rep5


title: E-micA714-15h_1

description:
sample14-CTD-4
A714-15h


title: U251-1812-3


title: B-cells_O_1

value: 22-24 months


title: E-micA714-14h_1

description:
sample13-CTD-3
A714-14h


title: NC_bBL_rep3


title: Adipocytes_Y_3

source_name: Adipocytes

value: Adipocytes


title: NC_bBL_rep2


title: U251-1813-1


title: U251-1812-2


title: E-micA714-13h_1

description:
sample12-CTD-2
A714-13h


title: U251-1812-1


title: Adipocytes_Y_2


title: E-micA714-11h_1

description:
sample10-TTD-10
A714-11h

value: transient tic disorder


title: E-micA714-12h_1

description:
sample11-CTD-1
A714-12h


title: NC_bBL_rep1


title: B-cells_O_4


title: NC_mMO_rep1


title: Adipocytes_Y_1


title: Drosophila_Neuroblast lineage_Fer2LCH RNAi_rep3

city: Nanjing

first: Su

state: Jiangsu

address: 2 Sipailou Road

department: School of Life Science and Technology

institute: Southeast University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads. (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is Paired-End (PE) sequence, both of the reads must be removed ) (fqtools_plus2.1)
Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads)
Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15%. If either one of the PE Reads defined as low quality, we will remove both ends of the reads)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Assembly: Drosophila_melanogaster.r6.14
Supplementary files format and content: tab-delimited text file includes counts for  each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for  each sample

organism: Drosophila melanogaster

source_name: Neuroblast lineage

extract_protocol:
Cells were lysed using ribonuclease inhibitor and lysis component, and cDNA was synthesised by Oligo-dT primer. In summary, cDNA was amplified by the Smart Seq2 method and 40 ng cDNA was used for the construction of sequencing libraries.
The qualified cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification, and library validation.

value: Neuroblast lineage

value: repo>Fer2LCH RNAi


title: U251-3

value: WT


title: E-micA714-10h_1

description:
sample9-TTD-9
A714-10h


title: B-cells_O_3


title: Drosophila_Neuroblast lineage_Fer2LCH RNAi_rep2


title: NC_bBL_rep4


title: B-cells_O_2


title: Adipocytes_O_4


title: E-micA714-09h_1

description:
sample8-TTD-8
A714-09h


title: Adipocytes_O_3


title: U251-1


title: Drosophila_Neuroblast lineage_Fer2LCH RNAi_rep1


title: U87-1812-3


title: E-micA714-08h_1

description:
sample7-TTD-7
A714-08h


title: U87-1812-2


title: Drosophila_Neuroblast lineage_Fer1HCH RNAi_rep2

value: repo>Fer1HCH RNAi


title: E-micA714-07h_1

description:
sample6-TTD-6
A714-07h


title: U87-1812-1


title: Drosophila_Neuroblast lineage_Fer1HCH RNAi_rep1


title: E-micA714-05h_1

description:
sample4-TTD-4
A714-05h


title: E-micA714-04h_1

description:
sample3-TTD-3
A714-04h


title: Drosophila_Neuroblast lineage_Control_rep3

value: repo>mCherry RNAi


title: U87-3


title: Drosophila_Neuroblast lineage_Control_rep2


title: U87-2


title: E-micA714-03h_1

description:
sample2-TTD-2
A714-03h

value: plasma


title: U251-2


title: U87-1


title: Drosophila_Neuroblast lineage_Control_rep1


title: E-micA714-02h_1

description:
sample1-TTD-1
A714-02h


title: merged_187_0S56837

status: Public on Jul 14 2024

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

data_processing:
HiSeq Control Software (HCS, HD 3.4.0.38) and Real-Time Analysis Software (RTA, 2.7.7) were used for raw data acquisition and base calling, respectively.
STAR was used for read mapping to hg38.
DESeq2 was used to test for differential gene expression.
Assembly: hg38
Supplementary files format and content: Read count table

source_name: fibroblast-like synoviocytes

extract_protocol:
Total RNA was extracted using Qiagen´s Rneasy kit
QuantSeq 3’ mRNA-Seq FWD library preparation protocol (Lexogen GmbH, Vienna, Austria)

value: fibroblast-like synoviocytes

value: wt

value: TNF, DMEM without threonine


title: merged_189_0S56835

value: TNF, DMEM without tyrosine


title: merged_188_0S56838

value: TNF, DMEM without tryptophane


title: merged_190_0S56836

value: TNF, DMEM without valine


title: Adipocytes_O_2

value: C57/Bl6 background


title: Drosophila_Neuroblast lineage_Fer1HCH RNAi_rep3


title: merged_185_0S56818

value: TNF, DMEM without phenylalanine


title: E-micA714-06h_1

description:
sample5-TTD-5
A714-06h


title: merged_184_0S56815

value: TNF, DMEM without methionine


title: merged_182_0S56813

value: TNF, DMEM without leucine


title: merged_183_0S56816

value: TNF, DMEM without lysine


title: merged_177_0S56810

value: TNF, DMEM without glutamine


title: merged_178_0S56809

value: TNF, DMEM without arginine


title: merged_179_0S56812

value: TNF, DMEN without cystine


title: merged_176_0S56807

value: TNF, DMEM without glycine


title: merged_175_0S56808

value: TNF, DMEM


title: merged_173_0S56806

value: CTRL, DMEM


title: merged_174_0S56805

value: fibroblast-like synoviocytes

value: TNF, DMEM without AA


title: merged_180_0S56811

value: wt

value: TNF, DMEM without histidine


title: merged_170_0S56834

value: TNF, DMEM without tyrosine


title: merged_169_0S56833

value: TNF, DMEM without tryptophane


title: merged_167_0S56831

value: TNF, DMEM without serine


title: merged_165_0S56829


title: merged_186_0S56817


title: merged_164_0S56828


title: merged_172_0S56803

value: CTRL, DMEM without AA


title: merged_171_0S56804

value: TNF, DMEM without valine


title: merged_163_0S56827

value: TNF, DMEM without leucine


title: merged_168_0S56832

value: TNF, DMEM without threonine


title: merged_160_0S56824


title: merged_159_0S56823


title: merged_181_0S56814

value: TNF, DMEM without isoleucine


title: merged_155_0S56819


title: merged_158_0S56822

value: TNF, DMEM without glutamine


title: merged_161_0S56825


title: merged_156_0S56820


title: merged_162_0S56826


title: merged_154_0S56772


title: merged_157_0S56821


title: merged_133_0S56774


title: merged_153_0S56771


title: M_full_0h_D

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to GRCm38 using STAR
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38
Supplementary files format and content: Read counts

source_name: bone marrow derived cells

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, #12034977) and Monarch RNA Clean-up kit (NEB, #T2030L).
NGS libraries were prepared using the QuantSeq 3’ mRNA-Seq FWD library preparation protocol

value: bone marrow derived cells


title: merged_131_0S56776


title: merged_166_0S56830

value: TNF, DMEM without phenylalanine


title: M_full_0h_B


title: merged_128_0S56777


title: M_R_full_6_h_D


title: merged_129_0S56778


title: merged_130_0S56775


title: merged_127_0S56780

value: TNF, DMEM without methionine


title: M_R_full_6_h_C


title: M_R_full_48h_3


title: merged_126_0S56779

value: TNF, DMEM without lysine


title: M_R_full_48h_1


title: M_R_full_6_h_B


title: M_R_full_48h_2


title: M_R_full_3_h_D


title: merged_123_0S56784

value: fibroblast-like synoviocytes


title: M_R_full_3_h_C


title: M_R_full_3_h_B


title: merged_119_0S56787

value: TNF, DMEM without glycine


title: merged_121_0S56786

value: wt

value: TNF, DMEM without arginine


title: M_R_full_24_h_C


title: merged_132_0S56773

value: TNF, DMEM without tyrosine


title: M_full_0h_C


title: M_R_full_24_h_D


title: M_R_full_1_1_2_h_D


title: merged_117_0S56789

value: TNF, DMEM without AA


title: merged_116_0S56790

value: CTRL, DMEM


title: M_R_full_24_h_B


title: M_R_full_1_1_2_h_C


title: M_R_full_1_1_2_h_B


title: merged_115_0S56791

value: CTRL, DMEM without AA


title: M_R_Gluc_48h_3


title: merged_125_0S56782


title: merged_124_0S56781


title: merged_95_0S56792

value: TNF, DMEM without valine


title: M_R_Gluc_48h_2


title: merged_122_0S56783

value: TNF, DMEN without cystine


title: merged_94_0S56793


title: merged_92_0S56795

value: TNF, DMEM without threonine


title: merged_120_0S56785


title: M_R_Gluc_48h_1


title: merged_93_0S56794

value: TNF, DMEM without tryptophane


title: M_R_Gln_48h_2


title: merged_91_0S56796

value: TNF, DMEM without serine


title: M_R_Gln_48h_3

value: bone marrow derived cells


title: merged_118_0S56788

value: TNF, DMEM


title: merged_88_0S56799


title: merged_89_0S56798

value: TNF, DMEM without methionine


title: merged_90_0S56797

value: TNF, DMEM without phenylalanine


title: M_R_Gln_48h_1


title: merged_87_0S56800

value: fibroblast-like synoviocytes

value: TNF, DMEM without leucine


title: merged_86_0S56801

value: wt

value: TNF, DMEM without isoleucine


title: merged_85_0S56802

value: TNF, DMEM without histidine


title: HESCs, OE_4

city: Shanghai

first: Xueqing

last: Liu

state: Shanghai

address: 910 Hengshan

institute: International Peace Maternity and Child Health Hospital

data_processing:
Raw reads of fastq format were firstly processed using fastp (Version 0.20.1) and the low quality reads were removed to obtain the cleanreads using fastqc (Version 0.11.9).
The clean reads were mapped to the reference genome using HISAT2 (Version 2.1.0).
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count (Version 0.11.2).
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 (Version 1.22.2). Hierarchical cluster analysis of DEGs was performed using R (Version 3.2.0).
Assembly: hg38
Supplementary files format and content: tab delimited text file include FPKM values for each sample

source_name: HESCs

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: HESCs

value: endometrial strmoal cells

value: CBLL1 overexpressed


title: merged_84_0S56747


title: merged_83_0S56746

value: TNF, DMEM without arginine


title: HESCs, OE_2


title: HESCs, OE_3


title: HESCs, OE_1


title: merged_82_0S56745

value: TNF, DMEM without glutamine


title: merged_80_0S56751


title: merged_81_0S56744

value: TNF, DMEM without glycine


title: merged_79_0S56750

value: TNF, DMEM without AA


title: merged_78_0S56749

value: CTRL, DMEM


title: HESCs, control_3

value: WT


title: HESCs, control_2


title: merged_57_0S56755

value: TNF, DMEM without valine


title: sk-T2, senescence escaped SKBR3 ,re2

city: Tianjin

first: Xiao

middle: Yu

last: Chen

state: None Selected

address: Tianjin Medical University Cancer Institute and Hospital

department: Department of Diagnostic and Therapeutic Ultrasonography

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1. fastq -p out2. fastq in1. fastq in2. fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome. gtf -o output. gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged. gtf -o samples. gtf samples.bam).
Assembly: Homo sapiens Ensembl v96
Supplementary files format and content: Supplementary_files_format_and_content:4_genes_fpkm_expression.xlsx

source_name: breast

growth_protocol: SKBR3 cells were cultured in DMEM medium with 10% fetal bovine serum at 37 ℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent(Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Senescent SKBR3 cells(SKBR3 cells were treated with 250 nM lapatinib for two weeks,referred to as SK-S or SK-la) and senescence escaped SKBR3 cells(The senescent SKBR3 cells were then cultured in the absence of lapatinib and the cells began to actively proliferate.The reproliferating cells were identified as senescence escape cells and were referred as SK-T. )

value: breast

value: HER2+ breast cancer cells

value: 250 nM lapatinib for two weeks,then cultured in the absence of lapatinib for 21-28 days


title: sk-T3, senescence escaped SKBR3 ,re3

institute: Tianjin Medical University Cancer Institute and Hospital


title: merged_77_0S56748

value: fibroblast-like synoviocytes

value: CTRL, DMEM without AA


title: pcFLAG-expressed Huh7 cells 1

type: RNA

city: Miki-cho

first: Yasunori

last: Sugiyama

state: kagawa

address: ikenobe 2393

department: Department of Life Science

country: Japan

institute: Kagawa University

description: Gene expression data from pcFLAG-expressed Huh7 cells

hyb_protocol: Following fragmentaion, single-stranded cDNA were hybridized for 20 hours at 48 ℃ with HuGene2.1ST Array Strip (Affymetrix)  and GeneChip Expression 3'-Amplification Reagents Hybridization Control kit (Affymetrix).

scan_protocol: The array was scanned using Imaging Station (Affymetrix) according to the manufacture's instructions.

data_processing: Arrays were summarized and normalized with Transcriptome Analysis Console.

label: Biotin

source_name: pcFLAG-expressed Huh7 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification Kit Module 1(Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from Huh7 cells transfected with pcFLAG or pcFLAG-hSTYK1 using RNeasy kit (QIAGEN).

treatment_protocol: Huh7 cells were transfected with pcFLAG or pcFLAG-hSTYK1

value: hepatocellular carcinoma

value: pcFLAG-expressed


title: merged_56_0S56754

value: wt

value: TNF, DMEM without tyrosine


title: merged_55_0S56753

value: TNF, DMEM without tryptophane


title: sk-T1, senescence escaped SKBR3 ,re1


title: pcFLAG-hSTYK1 expressed Huh7 cells 1

description: Gene expression data from pcFLAG-hSTYK1-expressed Huh7 cells

source_name: pcFLAG-hSTYK1 expressed Huh7 cells

value: pcFLAG-hSTYK1 expressed


title: pcFLAG-hSTYK1 expressed Huh7 cells 2


title: sk-la3,senescent SKBR3 ,re3

value: 250 nM lapatinib for two weeks


title: sk-la2, senescent SKBR3,re2


title: merged_54_0S56752

value: TNF, DMEM without threonine


title: merged_53_0S56759

value: TNF, DMEM without serine


title: sk-la1,senescent SKBR3, re1


title: Prss56_E12

city: lyon

first: valérie

last: CASTELLANI

address: 8 Avenue Rockefeller

country: France

institute: MeLiS | CNRS UMR 5284 | INSERM U1314

library_source: transcriptomic single cell

data_processing:
Reads were aligned and counted using CellRanger 7.0 (10x Genomics) using standard parameters
Assembly: mm39
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix files

source_name: meninges

extract_protocol:
E11.5 and 12.5 Egr2Cre/+,Rosa26RTom and Prss56Cre/+,Rosa26RTom embryos were identified on the basis of Tomato expression under fluorescent stereomicroscope (Leica, Nussloch, Germany). Meninge and DRG was dissected and then digested with collagenase/dispase type I (Merck/Roche) for 15 min at 37°C. Digestion was stopped by addition of 0.1 ml of fetal calf serum. Samples were slowly mechanically dissociated and the cell suspension was filtered. Dissociated cells were then resuspended in PBS, 1% BSA, and subjected to FACS. Tomato-positive cells were isolated, while dead cells and doublets were excluded by gating on a forward-scatter and side-scatter area versus width. Log RFP fluorescence was acquired through a 530/30 nm band pass. Internal Tomato-negative cells served as negative controls for FACS gating. Tomato-positive cells were sorted directly into PBS, 0.04% BSA for scRNA-seq experiments.
Libraries were prepared according to 10x 3'expression V2 kit  & Illumina protocols

value: meninges

value: boundary cap cells


title: Egr2_E12


title: sk3, SKBR3,re3

value: WT


title: Egr2_E11


title: HESCs, control_1

value: HESCs

value: endometrial strmoal cells


title: pcFLAG-expressed Huh7 cells 2


title: merged_51_0S56757

value: TNF, DMEM without methionine


title: HESCs, control_4


title: MGG152-GSKJ4+Bel 2

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description:
m4_2_i22_R1
genes.tsv

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

source_name: Brain tumor

growth_protocol: A172 cells were cultured in DMEM with 10% FBS and 1% Pen/Strep in a 37oC incubator with 5% CO2. MGG152 IDH mutant cell lines were established with patient-derived xenograft model, and were cultured as neurospheres in GBM/EF medium consisting of neurobasal medium with 7.5 ml L-Glutamine, 1X B-27 supplement, 0.5X N-2 supplement, 0.5 ml heparin solution, 0.5% Pen/Strep, FGF (20 ng/ml), and EGF (20 ng/ml).

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: A172 WT and IDH mutant cells were treated with GSK-864 for 4 days, and pellets from treated or untreated cells were collected. MGG152 cells were treated with GSK-J4 and Belinostat individually or in combination. After 48h of treatments, pellets were collected.

value: IDH MUT

tag: cell-line


title: MGG152-GSKJ4+Bel 1

description:
m4_1_i21_R1
genes.tsv


title: sk2, SKBR3,re2

value: breast

value: HER2+ breast cancer cells


title: MGG152-GSKJ4 2

description:
m2_2_i18_R1
genes.tsv


title: MGG152-Bel 1

description:
m3_1_i19_R1
genes.tsv

value: Bel


title: MGG152-Bel 2

description:
m3_2_i20_R1
genes.tsv


title: merged_50_0S56756

value: fibroblast-like synoviocytes

value: wt

value: TNF, DMEM without lysine


title: ZII_T_mRNA-seq

city: Beijing

first: Zhenyuan

last: Han

address: No.22, Zhongguancun South Avenue Haidian District

institute: Peking University School of Stomatology

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Genome_build: hg19
Supplementary_files_format_and_content: filtered mRNA expression files

source_name: pleomorphic adenoma tissue

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: pleomorphic adenoma tissue

tag: treatment type

value: Surgery

tag: vital status

value: Alive


title: ZII_G_mRNA-seq

source_name: normal salivary gland

value: normal salivary gland


title: merged_49_0S56762

value: TNF, DMEM without leucine


title: sk1,SKBR3, re1


title: MGG152-Ctrl 2

description:
m1_2_i16_R1
genes.tsv

value: DMSO


title: MGG152-GSKJ4 1

description:
m2_1_i17_R1
genes.tsv


title: A172 IDH MUT 2

description:
a9_2_i31_R1
genes.tsv


title: merged_47_0S56760

value: TNF, DMEM without histidine


title: merged_52_0S56758

value: TNF, DMEM without phenylalanine


title: ZAY_T_mRNA-seq


title: MGG152-Ctrl 1

description:
m1_1_i15_R1
genes.tsv


title: merged_48_0S56763

value: TNF, DMEM without isoleucine


title: A172 IDH MUT 1

description:
a9_1_i7_R1
genes.tsv


title: merged_46_0S56761

value: TNF, DMEN without cystine


title: A172 WT 1

description:
a1_1_i39_R1
genes.tsv

value: IDH WT


title: merged_44_0S56767

value: TNF, DMEM without glutamine


title: ZAY_G_mRNA-seq


title: OAR_G_mRNA-seq


title: A172 IDH MUT-GSK864 1

description:
a13_1_i11_R1
genes.tsv

value: IDH MUT


title: A172 WT 2

description:
a1_2_i23_R1
genes.tsv


title: merged_45_0S56766

value: TNF, DMEM without arginine


title: ChIP PE RARα Input

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq v2.17 software.
Sequencing adapters and low-quality bases were trimmed using the Trimmomatic v0.39 software with parameters ILLUMINACLIP:/path/to/adapter:2:30:10:1:true SLIDINGWINDOW:20:15 MINLEN:36.
Preprocessed reads were then aligned to hg38 genome using Bowtie2 v2.3.4.1 with parameters --wrapper basic-0 --fr -X 2000.
Aligned reads were filtered using SAMtools v1.11 to keep only concordant primary alignments having a minimum mapping quality of 30. PCR or optical duplicates were marked using Picard v2.25.1 tool and removed. Reads mapping to mitochondrial DNA and to unplaced contigs were filtered out. Reads falling in ENCODE Blacklist regions were removed using BEDTools v2.30.0 pairToBed tool.
The HOMER makeTagDirectory and findPeaks tools were employed to call peaks for each IP sample, comparing them with the corresponding input samples, setting the findPeaks style parameter to factor and keeping only peaks with peak score >= 20.
Assembly: hg38
Supplementary files format and content: BED files with peaks called by HOMER. Column 5: findPeaks Score (integer); Column 7: Fold Change vs Control; Column 8: findPeaks Score (float); Column 9: Normalized Tag Count; Column 10: Peak center.

source_name: Pharyngeal Endoderm (PE, d5 +RA)

growth_protocol: H9 hESCs were routinely propagated feeder-free in mTeSR1 on cell culture plates previously coated with Matrigel following the manufacturer instructions. Undifferentiated hESCs were propagated and passed at least 3 times after thawing and plated for the differentiation when at 80% of confluence. Cells were maintained in culture and expanded at high quality with particular care to avoid any spontaneous differentiation, which would confound downstream differentiation. The day before the induction of the differentiation, hESCs were washed twice in PBS, dissociated with Accutase, plated in mTeSR1 + Rock Inhibitor (Y27632, 5uM) to promote cell survival and incubated for 12 hours at 37 °C, 5% CO2 for 12 hours. The day after, 30% confluent hESCs were induced to differentiate into definitive endoderm, by incubation with Medium A (Gibco cat. n. A30621-01) for 24 hours and with Medium B (Gibco cat. n. 30624-01) for the following 24 hours at 37 °C, 5% CO2. The third day DE was patterned into AFG by the addition of CDM2 medium with A-83-01, 1uM and DM3189, 250nM. The composition of CDM2 basal medium was as follows: 50% IMDM (+GlutaMAX, +HEPES, +Sodium Bicarbonate; Gibco, 31980-097) + 50% F12 (+GlutaMAX; Gibco, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v concentrated lipids (Gibco, 11905-031) + 450 µM monothioglycerol (Sigma, M6145) + 0.7 µg/mL insulin (Roche, 1376497) + 15 µg/mL transferrin (Roche, 652202) and incubated at 37 °C, 5% CO2. From day four to day 5, Retinoic Acid 200 nM was added at the CDM2 medium with A-83-01, 1 uM and DM3189, 250 nM and medium was changed every 24 hours.

extract_protocol:
ChIP experiments were performed on chromatin extracts according to the manufacturer's protocol (MAGnify ChIP, Life Technologies Cat. n. 492024). For the immunoprecipitation reaction of RARα, 60µg of sheared chromatin from AFE (d5) and PE (d5 +RA) differentiated cells was used. Sheared chromatin was incubated O.N. with 5μg of anti-RARα (Diagenode Cat. n. C15310155) antibodies.
Immunoprecipitated (IP) and input DNA samples were quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and the DNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). NEBNext Ultra DNA Library Preparation kit was used following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). Briefly, the ChIP DNA was end-repaired and adapters were ligated after adenylation of the 3’ ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA).

value: Pharyngeal Endoderm (PE, d5 +RA)

tag: chip antibody

value: RARalpha (Diagenode Cat. n. C15310155)

value: Day 5 + RA


title: OAR_T_mRNA-seq

value: pleomorphic adenoma tissue


title: ChIP PE RARα IP

tag: cell type


title: merged_42_0S56765

value: fibroblast-like synoviocytes

tag: genotype

value: wt

value: TNF, DMEM


title: A172 IDH MUT-GSK864 2

description:
a13_2_i35_R1
genes.tsv


title: merged_43_0S56764

value: TNF, DMEM without glycine


title: Rpl22 WT-Replicate3

city: PHILADELPHIA

first: David

middle: Lynn

last: Wiest

address: 333 COTTMAN AVENUE, REIMANN BUILDING, LAB  R364

department: Nuclear Dynamics and Cancer Program

institute: FOX CHASE CANCER CENTER

data_processing:
Paired-end FASTQ files were aligned to mm10 genome using Tophat2 (v2.1.1)
Aligned BAM files were sorted by read name & quantified with htseq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing htseq-count gene counts for 6 samples

source_name: Bone marrow

extract_protocol:
Lineage - CD48-CD150+ HSC  were  sorted  directly  into  500µL  TriReagent  (Sigma-Aldrich),  following  which  RNA  was  isolated  according  to  the  manufacturer’s protocol
RNA-Seq  libraries  were  prepared  using  TruSeq  RNA  sample  kit  (polyA+) according  to  the  manufacturer protocols

value: Bone marrow

value: CD48-CD150+ hematopoietic stem cells

value: Rpl22 WT


title: ANK_T_mRNA-seq

value: Surgery

value: Alive


title: Rpl22 WT-Replicate1


title: A172 WT-GSK864 1

description:
a5_1_i3_R1
genes.tsv


title: ANK_G_mRNA-seq

value: normal salivary gland


title: Rpl22 KO-Replicate3

value: Rpl22 KO


title: merged_41_0S56769

value: TNF, DMEM without AA


title: ChIP AFE RARα IP

source_name: Anterior Foregut Endoderm (AFE, d5)

value: Anterior Foregut Endoderm (AFE, d5)

tag: time

value: Day 5


title: Rpl22 KO-Replicate1

tag: tissue


title: A172 WT-GSK864 2

description:
a5_2_i27_R1
genes.tsv

value: IDH MUT


title: Rpl22 WT-Replicate2


title: AKG_G_mRNA-seq


title: merged_40_0S56770

value: CTRL, DMEM


title: Rpl22 KO-Replicate2


title: Prog-Tg mouse, >25 weeks, microRNA, replicate 2

status: Public on Jul 13 2024

city: Vienna

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

department: Center for Medical Biochemistry

institute: Max Perutz Labs, Medical University of Vienna

description:
59992
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Plasma_Pr_pl_vs_WT_pl.xlsx

library_source: other

data_processing:
Sequencing reads were aligned against the mus musculus reference genome (GRCm38 release) (https://doi.org/10.1093/nar/gkx1098) with STAR (https://doi.org/10.1093/bioinformatics/bts635), version 2.5.1b using 2-pass alignment mode. Gencode v4 annotation was used in the alignment. TMM normalisation method of the edgeR (https://doi.org/10.1093/bioinformatics/btp616), R/Bioconductor package (R version 3.3.2, Bioconductor version 2.12) was applied.
The short sequencing reads were aligned against the reference genome using Gencode v4 annotation with 2-pass alignment mode of STAR v2.5.1b.
After alignment, the short reads were associated with known genes, and the number of reads aligned within each gene was counted using HTSeq v0.5.4p3.
The data was normalised to remove variation between samples caused by non-biological reasons and to make the values comparable across the sample set using the TMM normalisation method of the edgeR.
For differential expression analyses, the data were further log transformed using the voom approach, and the R package limma was used to perform the statistical testing.
Assembly: mus musculus reference genome (GRCm38 release)  (https://doi.org/10.1093/nar/gkx1098)
Supplementary files format and content: Excel files starting with Counts contains the number of raw counts for each gene for each sample.
Supplementary files format and content: The rest of the Excel files (which do not start with Counts) contain differential expression results between each comparison pair using 3 replicates of each sample versus Wild Type.

molecule: other

source_name: Plasma (>25 weeks)

growth_protocol: Endothelial cells were cultured in DMEM supplemented with 20% FCS, EC growth supplement (CellBiologics Catalog No 1166), 25 mM HEPES, 50 U/ml penicillin, 50 μg/ml streptomycin, 2 mM L-glutamine, 1 mM nonessential amino acids, 1 mM sodium pyruvate, and 139 μg/ml heparin (complete culture medium) and were used at passage 3 forpreparation of RNA extracts.

extract_protocol:
RNA extracts were prepared using miRNeasy Mini Kit (Qiagen 217084)
For mRNA (with parallel isolation of microRNA libraries) from endothelial cells polyA enrichment was performed for mRNAs from 100 ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions. Library preparation of polyA+ enriched RNA was performed with the NEBNext UltraII Directional RNA library Kit from Illumina. microRNA libraries from endothelial cells were prepared from 100 ng total RNA with the QIAseq miRNA library Kit according to the manufacturer's instructions small RNA libraries from supernatants of endothelial cells and mouse plasma were prepared using CleanTag™ Small RNA Library Preparation Kit Catalog # L-3206.

treatment_protocol: no treatment

value: Plasma (>25 weeks)

value: Prog-Tg

value: Cdh5TA+TetOp-LAG608G minigene

tag: molecule subtype

value: small RNA


title: AKG_T_mRNA-seq

value: pleomorphic adenoma tissue


title: LA-Tg mouse, >25 weeks, microRNA, replicate 1

description:
59988
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Plasma_LaTg_pl_vs_WT_pl.xlsx

value: LA-Tg

tag: treatment

value: Cdh5TA+TetOp-LA minigene


title: merged_39_0S56768

value: fibroblast-like synoviocytes

value: wt

value: CTRL, DMEM without AA


title: Prog-Tg mouse, >25 weeks, microRNA, replicate 3

description:
59993
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Plasma_Pr_pl_vs_WT_pl.xlsx


title: ChIP AFE RARα Input

value: RARalpha (Diagenode Cat. n. C15310155)


title: Prog-Tg mouse, >25 weeks, microRNA, replicate 1

description:
59991
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Plasma_Pr_pl_vs_WT_pl.xlsx


title: Wt mouse, >25 weeks, microRNA, replicate 3

description:
59987
Counts_miRNA_Plasma_Supernatant.xlsx

value: WT

value: wild-type


title: LA-Tg mouse, >25 weeks, microRNA, replicate 2

description:
59989
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Plasma_LaTg_pl_vs_WT_pl.xlsx


title: LA-Tg mouse, >25 weeks, microRNA, replicate 3

description:
59990
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Plasma_LaTg_pl_vs_WT_pl.xlsx


title: Wt mouse, >25 weeks, microRNA, replicate 2

description:
59986
Counts_miRNA_Plasma_Supernatant.xlsx


title: Prog-Tg endothelial supernatant, microRNA, replicate 3

description:
59984
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Supernatant_Pr_sn_vs_WT_sn.xlsx

source_name: Lung, (age 10-15 days)

value: Lung, (age 10-15 days)

tag: cell line

value: primary endothelial cells

value: endothelial cells


title: LA-Tg endothelial supernatant, microRNA, replicate 3

description:
59983
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Supernatant_LaTg_sn_vs_WT_sn.xlsx


title: LA-Tg endothelial supernatant, microRNA, replicate 2

description:
59980
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Supernatant_LaTg_sn_vs_WT_sn.xlsx


title: Prog-Tg endothelial supernatant, microRNA, replicate 1

description:
59978
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Supernatant_Pr_sn_vs_WT_sn.xlsx


title: LA-Tg endothelial supernatant, microRNA, replicate 1

description:
59977
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Supernatant_LaTg_sn_vs_WT_sn.xlsx


title: WT endothelial cell supernatant, microRNA, replicate 3

description:
59976
Counts_miRNA_Plasma_Supernatant.xlsx


title: WT endothelial cell supernatant, microRNA, replicate 2

description:
59979
Counts_miRNA_Plasma_Supernatant.xlsx


title: WT endothelial cell supernatant, microRNA, replicate 1

description:
59982
Counts_miRNA_Plasma_Supernatant.xlsx


title: Prog-Tg endothelial cells, microRNA, replicate 1

description:
54377
Counts_miRNA.xlsx
miRNA_Pr_vs_WT.xlsx


title: LA-Tg endothelial cells, microRNA, replicate 1

description:
54376
Counts_miRNA.xlsx
miRNA_LaTg_vs_WT.xlsx


title: Wt mouse, >25 weeks, microRNA, replicate 1

description:
59985
Counts_miRNA_Plasma_Supernatant.xlsx


title: LA-Tg endothelial cells, microRNA, replicate 3

description:
54392
Counts_miRNA.xlsx
miRNA_LaTg_vs_WT.xlsx


title: Prog-Tg endothelial cells, microRNA, replicate 3

description:
54374
Counts_miRNA.xlsx
miRNA_Pr_vs_WT.xlsx


title: WT endothelial cells, microRNA, replicate 2

description:
54388
Counts_miRNA.xlsx


title: LA-Tg endothelial cells, microRNA, replicate 2

description:
54389
Counts_miRNA.xlsx
miRNA_LaTg_vs_WT.xlsx


title: Prog-Tg endothelial cells, replicate 3

description:
54396
Counts_mRNA.xlsx
mRNA_Pr_vs_WT.xlsx

value: mRNA


title: WT endothelial cells, microRNA, replicate 1

description:
54375
Counts_miRNA.xlsx


title: Prog-Tg endothelial cells, replicate 1

description:
54371
Counts_mRNA.xlsx
mRNA_Pr_vs_WT.xlsx


title: LA-Tg endothelial cells, replicate 2

description:
54373
Counts_mRNA.xlsx
mRNA_LaTg_vs_WT.xlsx


title: LA-Tg endothelial cells, replicate 3

description:
54395
Counts_mRNA.xlsx
mRNA_LaTg_vs_WT.xlsx


title: Prog-Tg endothelial cells, replicate 2

description:
54393
Counts_mRNA.xlsx
mRNA_Pr_vs_WT.xlsx


title: LA-Tg endothelial cells, replicate 1

description:
54370
Counts_mRNA.xlsx
mRNA_LaTg_vs_WT.xlsx


title: WT endothelial cells, replicate 3

description:
54394
Counts_mRNA.xlsx


title: Prog-Tg endothelial supernatant, microRNA, replicate 2

description:
59981
Counts_miRNA_Plasma_Supernatant.xlsx
miRNA_Supernatant_Pr_sn_vs_WT_sn.xlsx


title: WT endothelial cells, replicate 1

description:
54369
Counts_mRNA.xlsx


title: DICER-E1564Q pri-mir-30a-WT replicate 2

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The sequencing reads of mRNA were also adapter-trimmed by cutadapt (Martin 2011) (-a AGATCGGAAGAGCACACGTCT for Read 1 and -a GATCGTCGGACTGTAGAACTCTGAAC for Read 2).
Processed pair-end reads were then joined by using fastq-join (Aronesty 2013), and low-quality reads were then discarded by using fastq_quality_filter (-q 30 -p 90) (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13).
Reads are then mapped to human genome reference (GRCh38) using bowtie2 (bowtie2 --local --score-min L,-4,2 --ma 2 -k 5) (Langmead and Salzberg, 2012).
miRNA genomic coordination file was obtained from miRBase v22 (Kozomara et al., 2019), and annotation of the mapped reads was done by using bedtools intersect (Quinlan A.R. and Hall I. M., 2010).
Assembly: home-made reference shRNA sequences
Supplementary files format and content: Bed files of control samples contain the raw read count of each shRNA in the control library.
Supplementary files format and content: Bed files of the single cleavage and double cleavage samples contains the assigned cleavage sites, cleavage accuracy, positional cleavage efficiency, global cleavage efficiency.

source_name: HCT116 DICER-KO

growth_protocol: The HCT116 DICER-KO cells were cultured in McCoyʼs 5A medium (Gibco, 16600082) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10270106) and 1% of  Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
The total RNAs were isolated from the cells by using TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
Transfected cells were harvested 48 h post-transfection and total RNA was extracted using Trizol (Ambion, #15596018). Small RNA fractions were obtained from 10 µg of total RNA by using 12% urea-gel and IPA precipitation. The small RNA sequencing libraries were constructed by using the TruSeq Small RNA Library Prep Kits (Illumina). The DNA libraries of small RNAs were sequenced by Illumina Nextseq 6000. The concentration and size distribution of the DNA libraries were examined by Qubit dsDNA HS Assay Kit (Invitrogen, #Q32854) and Fragment Analyzer system, respectively. Finally, the examined DNA libraries were subjected to the next-generation sequencing (NGS).

treatment_protocol: Cells were transfected with pXG-DICER-WT, pXG-DICER mutant and construct expressing pri-miRNAs or shRNAs using Lipofectamine 3000.

value: HCT116 DICER-KO

value: culture cells

value: pXG-DICER-E1564Q and pcDNA3-pri-mir-30a-WT plasmid


title: DICER-E1564Q pri-mir-30a-MT replicate 1

value: pXG-DICER-E1564Q and pcDNA3-pri-mir-30a-MT plasmid


title: WT endothelial cells, microRNA, replicate 3

description:
54391
Counts_miRNA.xlsx

value: small RNA


title: DICER-E1564A pri-mir-30a-MT replicate 1

value: pXG-DICER-E1564A and pcDNA3-pri-mir-30a-MT plasmid


title: DICER-WT pri-mir-30a-WT replicate 1

value: pXG-DICER-WT and pcDNA3-pri-mir-30a-WT plasmid


title: DICER-D1709N sh21bp replicate 1

value: pXG-DICER-D1709N and pU6-sh21bp plasmid


title: DICER-WT pri-mir-30a-MT replicate 2

value: pXG-DICER-WT and pcDNA3-pri-mir-30a-MT plasmid


title: DICER--D1709N sh21bp replicate 2


title: DICER-E1564A pri-mir-30a-WT replicate 1

value: pXG-DICER-E1564A and pcDNA3-pri-mir-30a-WT plasmid


title: DICER--D1709A sh22bp replicate 2

value: pXG-DICER-D1709A and pU6-sh22bp plasmid


title: DICER-E1564A pri-mir-30a-WT replicate 2


title: DICER-WT sh2122bp replicate 2

value: pXG-DICER-WT and pU6-sh2122bp plasmid


title: DICER--D1709A sh21bp replicate 2

value: pXG-DICER-D1709A and pU6-sh21bp plasmid


title: DICER--D1709N sh2122bp replicate 1

value: pXG-DICER-D1709N and pU6-sh2122bp plasmid


title: DICER-E1564A pri-mir-30a-MT replicate 2


title: DICER-WT pri-mir-30a-WT replicate 2


title: DICER--D1709N sh22bp replicate 1

value: pXG-DICER-D1709N and pU6-sh22bp plasmid


title: DICER--D1709N sh2122bp replicate 2


title: DICER-E1564Q pri-mir-30a-WT replicate 1


title: DICER-WT pri-mir-30a-MT replicate 1


title: Prog-Tg endothelial cells, microRNA, replicate 2

description:
54390
Counts_miRNA.xlsx
miRNA_Pr_vs_WT.xlsx

value: Lung, (age 10-15 days)

value: primary endothelial cells

value: endothelial cells

value: Prog-Tg

value: Cdh5TA+TetOp-LAG608G minigene


title: DICER-E1564Q pri-mir-30a-MT replicate 2

value: HCT116 DICER-KO

value: culture cells

value: pXG-DICER-E1564Q and pcDNA3-pri-mir-30a-MT plasmid


title: DICER-D1709A sh21bp replicate 1


title: WT endothelial cells, replicate 2

description:
54372
Counts_mRNA.xlsx

value: WT

value: wild-type

value: mRNA


title: DICER-WT sh2122bp replicate 1


title: DICER--D1709A sh2122bp replicate 1

value: pXG-DICER-D1709A and pU6-sh2122bp plasmid


title: DICER--D1709A sh22bp replicate 1

value: pXG-DICER-D1709A and pU6-sh22bp plasmid


title: DICER--D1709N sh22bp replicate 2


title: DICER-WT sh22bp replicate 1

value: pXG-DICER-WT and pU6-sh22bp plasmid


title: DICER-WT sh21bp replicate 2

value: pXG-DICER-WT and pU6-sh21bp plasmid


title: DICER-WT sh21bp replicate 1


title: SKOV3 1_1

city: Dalian

first: lingxi

last: tian

state: liaoning

address: lingshui street

institute: Dalian University of Technology

data_processing:
Illumina Casava software used for basecalling
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired_x0002_end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice
Quantification of gene expression level:The raw counts were first normalized using TPM (Zhou et al., 2010 ) Normalized expression level = ( readCount* 1,000,000 ) / libsize (libsize is the sum of circRNA readcount) .
http://circbase.org/
Assembly: GRCh38
Supplementary files format and content: Readcount_TPM text file include TPM values for each sample
Supplementary files format and content: TPM_interval text file include FPKM_Interval for each sample

source_name: SKOV3 1_1

extract_protocol:
RNA was collected using RNeasy mini plus kit (Qiagen). A total amount of 2 μ g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed and rRNA free residue was cleaned up by ethanol precipitation. the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA, and then used for the construction of sequencing libraries.
The sequencing libraries for RNA-Seq were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’ s recommendations.

value: SKOV3 1_1

value: Ovarian cancer cell


title: T293 3_1

value: normal cell


title: T293 2_1


title: NIHOVCAR3 1_1

source_name: NIHOVCAR3 1_1

value: NIHOVCAR3 1_1


title: SKOV3 3_1

source_name: SKOV3 3_1

value: SKOV3 3_1


title: RL95-2 2_1

value: Endometrial cancer cell


title: MCF-7 3

value: Breast cancer cell


title: RL95-2 3_1


title: MCF-7 1


title: SKOV3 2_1

source_name: SKOV3 2_1

value: SKOV3 2_1


title: MCF-7 2


title: Hela 2

source_name: Hela 2_1

value: Hela 2_1

value: Cervical cancer cell