title: Arabidopsis thaliana col-0 Yb Shoots replicate 2

city: Vandoeuvre-les-Nancy

first: Nicolas

last: Grosjean

address: Faculté des Sciences et Technologies

country: France

institute: LIEC UMR 7360 CNRS-Université de Lorraine

data_processing:
Galaxy
Raw data sequences were trimmed for their adaptor (TruSeq3) using Trimmomatic v0.36.1
Sorted reads were mapped to the Arabidopsis thaliana Col-0 genome (version TAIR10) using TopHat v2.1.1. Reads mapped to multiple locations were discarded.
Numbers of reads in genes were counted by the HTSeq-count v0.6.1p1 tool using corresponding Arabidopsis thaliana gene annotations (available from https://www.arabidopsis.org/)
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Arabidopsis thaliana

source_name: Shoots

growth_protocol: Arabidopsis thaliana Col-0 were grown hydroponically according to the protocol of Conn et al. (2013). Seeds were sown on lids of black micro-centrifuge tubes containing agar germination medium (GM), dipping in liquid GM (0.75 mM CaCl2, 1 mM KCl, 0.25 mM Ca(NO3)2∙4H2O, 1 mM MgSO4∙7H2O, 0.2 mM KH2PO4, 50 µM NaFe(III)-EDTA, 50 µM H3BO3, 5 µM MnCl2∙4H2O, 10 µM ZnSO4∙7H2O, 0.5 µM CuSO4∙5H2O, 0.1 µM Na2MoO3, pH 5.6, 0.7% (m/v) agar). Seeds were then vernalized at 4°C for three days in the dark and further transferred in a growth chamber (18/23°C, 16/8 h dark/light cycles (260 µmol/m2/s)). After 10 days of growth, seedlings were transferred into BNS medium (2 mM NH4NO3, 3 mM KNO3, 2 mM KCl, 2 mM Ca(NO3)2∙4H2O, 2 mM MgSO4∙7H2O, 1.5 mM NaCl, 600 µM KH2PO4, 100 µM CaCl2, 50 μM NaFe(III)-EDTA, 50 μM H3BO3, 5 μM MnCl2∙4H2O, 10 µM ZnSO4∙7H2O, 0.5 μM CuSO4∙5H2O, 0.1 μM Na2MoO3, pH 5.6). Three-week-old seedlings were subsequently transferred individually into bottomless 50 mL centrifuge tubes, so that roots could dip into 10 L BNS medium in a black container. The solution was continuously aerated.

extract_protocol:
Total RNAs were extracted and purified from the roots and the shoots using the RNeasy Plant Mini Kit (Qiagen), following the manufacturer’s instructions. Genomic DNA was removed using DNAse I (Sigma Aldrich). Total RNAs were quantified spectrophotometrically using a Nanodrop ND-1000 (NanoDrop Technologies), and RNA integrity assessed using a Bioanalyzer 2100 (Agilent, CA, USA).
Stranded cDNA libraries (TruSeq-3 library kit) were made using at least 2 µg RNA, and RNA selection using polyA selection. RNA-sequencing was performed using an Illumina HiSeq 2500 instrument, with 2x 125 bp paired-end sequencing.

treatment_protocol: Six-week-old Arabidopsis plants were then exposed to 5 µM of either La or Yb (provided as LaCl3 and YbCl3, respectively) or not exposed (control condition), into 2 L black containers of BNS medium lacking phosphate, for 72 h before harvesting. Roots and shoots were then separated and snapped frozen. Three plants were pooled to form a single replicate, and three replicates were performed per treatment. Plants were ground into powder with liquid nitrogen using a mortar and a pestle, and kept at -80°C.

value: Shoots

tag: ecotype

value: Ytterbium


title: Arabidopsis thaliana col-0 Yb Roots replicate 3

status: Public on Jul 23 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

source_name: Roots

tag: tissue

value: Roots

tag: genotype

value: WT

tag: treatment


title: hapa1-6 cell WT  by HieffNGS kit repeat1

city: wuhan

first: zaiqiao

last: sun

country: China

institute: wuhan university

data_processing:
Raw reads from sequencing were firstly subjected to Trimmomatic (v0.39) for quality control and adaptor trimming
reads were mapped to genome using STAR (v2.7.10a)
gene counts was statisticed with featurecount
Genes with FPKM >0.5 were considered to be expressed
Assembly: Homo_sapiens.GRCh38, Mus_musculus.GRCm39, Mycobacterium_smegmatis.NZ_CP054795.1
Supplementary files format and content: tab-delimited text file includes raw counts for each
Supplementary files format and content: Sampletab-delimited text files include FPKM values for each Sample mRNA Fragmentation and cDNA synthesis.

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: HEK293T cells and Hepa1-6 cells were maintained in DMEM medium (Gibco, Cat #11965092) + 10% FBS (Gibco, Cat#16000044) and 1% penicillin/streptomycin (Gibco, Cat#15140122) at 37°C with 5%CO2, Mycobacterium smegmatis was maintained in Middlebrook 7H9 broth base medium

extract_protocol:
Total RNA was extracted from mouse tissue with TRIzol, Total RNA from Cell line or bacterium was extracted by MolPure® Cell/Tissue Total RNA Kit
RNA libraries for RNA-seq were prepared using DADCSeq, HieffNGS kit and SHERRY following manufacturer's protocols

treatment_protocol: No special treatment

value: liver

tag: cell line

tag: cell type

value: live cancel

value: hapa1-6 cell WT  by HieffNGS kit


title: COVIRS_14_V0_Monocytes_ATACSeq

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: ATAC Seq on human classical monocytes from participant COVIRS_14 pre-vaccination

library_source: genomic

data_processing:
Reads were aligned to the hg38 human genome using Bowtie2.
Peaks were called using Genrich v0.6.
Counts per peak were generated using FeatureCounts v1.53p.
Assembly: hg38
Supplementary files format and content: FeatureCounts output; Tab-delimited text files with raw peak counts for every peak for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: Monocytes

extract_protocol:
Cryopreserved PBMC were thawed and stained and classical monocytes (CD3-CD19-CD56-CD14+CD16-; 50,000 per sample) were sorted via flow cytometry. Transposed DNA samples were purified using DNA Clean and Concentrator 5 columns (Zymo Research).
Libraries were prepared from transposed DNA with custom primers and subjected to double-sided cleanup with SPRI beads to enrich for fragments in the 200-700bp range. Samples were sequenced on an illumina NovaSeq using paired end (2x150pb) sequencing.

value: Monocytes

tag: batch

tag: vaccine

tag: timepoint

tag: participant id


title: Arabidopsis thaliana col-0 Yb Shoots replicate 1


title: hapa1-6 cell Raf_knockdown by HieffNGS kit repeat3


title: Arabidopsis thaliana col-0 Yb Shoots replicate 3


title: hapa1-6 cell Raf_knockdown by HieffNGS kit repeat2


title: Arabidopsis thaliana col-0 Yb Roots replicate 2


title: DTHT96hRep1 [ChIP-seq]

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

country: USA

institute: Purdue University

description: Robert Nobel Foundation

data_processing:
The libraries were sequenced on Illumina HiSeq 2500 platform with 101 bp paired-end reads.
Read quality was assessed using FastQC (v 0.11.2) for all samples and quality trimming was done using cutadapt (v 1.13)
Histone modification peaks were detected using SICER (v 1.1)
Genome_build: The quality trimmed reads were mapped against the bowtie2-indexed Panicum virgatum reference genome (v4.1) using bowtie2 (v 2.3.1)
Supplementary_files_format_and_content: BigWig files were generated using deeptools

organism: Panicum virgatum

source_name: leaf tissue

growth_protocol: The ramets of lowland ecotype Alamo, AP13 genotype of switcghrass were transplanted in 3GP nursery pots and later transferred to the green house for optimum conditions at the Samuel Roberts Noble Foundation in Ardmore, Oklahoma.

extract_protocol:
ChIP-DNA was extracted from Proteinase-K digested samples by phenol-chloroform extraction and ethanol precipitation using glycogen.
100 ng of purified DNA was used to generate the ChIP-Seq library using Illumina HiSeq using manusfacturer instructions

treatment_protocol: The control and drought treated plants were arranged in one growth chamber and palnts with drought and heat treatment in a separate chamber

tag: developmental stage

value: leaf

value: drought and heat


title: hapa1-6 cell Raf_knockdown by HieffNGS kit repeat1


title: DTHT72hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 Yb Roots replicate 1


title: COVIRS_29_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_29 post-vaccination


title: DTHT72hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 La Shoots replicate 3

value: Lanthanum


title: COVIRS_29_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_29 pre-vaccination


title: Day2, Veh, Exp1

city: Stockholm

first: Kaisa

last: Hofwimmer

address: Blickagången 16

country: Sweden

institute: Karolinska Institutet

description:
Day2_Veh_Exp1
raw_counts.txt
normalized_counts.txt

data_processing:
BCL conversion and demultiplexing of raw data was performed using bcl2fastq (v2.20.0)
Read quality was assessed using FastQC (v0.11.8)
Reads were aligned to the Ensembl GRCh38 reference genome using STAR (v2.6.1d)
Counts for each gene were obtained using featureCounts (v1.5.1)
Bioconductor package DESEq2 (v1.22.2) was used for normalization
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for ech sample

source_name: White adipose tissue

growth_protocol: Human adipose-derived stem cells were expanded in proliferation media, consisting of low-glucose DMEM (#31885-023, Gibco) supplemented with 10% fetal bovine serum (FBS), 0.01 M HEPES buffer, 50 U/ml Penicillin, 50 ug/ml Streptomycin, and 2.5 ng/ml fibroblast growth factor 2 (FGF2).

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel)
Libraries were constructed using the Illumina TruSeq Stranded mRNA sample preparation protocol, with 200 ng total RNA.

treatment_protocol: When proliferating cells reached confluence, FGF2 was removed from the proliferation media. The day after, cells were seeded to plates at a density of 65 000 cells/cm2 in proliferation media –FGF2. The following day (day 0), cells were washed twice with PBS and adipogenesis was induced by adding differentiation media, consisting of the proliferation media –FGF2/–FBS and Ham's F-12 Nutrient mix (#21765-029, Gibco) in equal volumes, along with the following adipogenic stimulators: 860 nM insulin, 10 ug/ml transferrin, 0.2 nM triiodothyronine, 10 uM rosiglitazone, 100 uM 3-isobutyl-1-methylxanthine (IBMX), and 1 uM dexamethasone. Media was changed on day 2, 5, and 7 of differentiation. Differentiation media –IBMX/–dexamethasone was used from day 5. Human recombinant IL-1b (10 ng/ml, #I9401, Sigma-Aldrich) or vehicle (water, 1:1000) was added to the differentiation media prior to all media changes starting from day 0.

value: White adipose tissue

value: Mesenchymal stem cells

value: Adipogenic differentiation, vehicle

tag: time

value: Day 2


title: DTHT72hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 La Shoots replicate 2


title: stomach_MUT2_rep2

city: CHAPEL HILL

first: Gang

middle: Greg

last: Wang

state: North Carolina

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: UNC chapel hill

description: total RNA, rRNA depletion

data_processing:
The fastq files were aligned to the mm10 mouse genome by using STAR v2.4.2 with the following parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Then, transcript abundance for each sample was estimated with salmon V1.4.0 to quantify the transcriptome defined by Gencode v22. QC was performed using the Picard 2.22.4 CollectRnaSeqMetric and FastQC 0.11.9. Gene level counts were summed across isoforms, and genes with low counts (maximum expression < 10) were filtered out from the downstream analyses. We tested genes for differential expression in DESeq2 v1.38.2 in R and gene set enrichment analysis (GSEA) on Molecular Signatures Database (MsigDB) C2 curated genesets was conducted with GSVA v1.30.1 in R.  We used SalmonTE to calculate the TE abundance in the mouse samples. By performing a read mapping against the TE sequences, SalmonTE reassigns multi-mapping reads using the expectation-maximization algorithm before determining the read count of each sequence. From the counts table the differentially expressed TEs were identified and the statistical analysis function of salmonTE generated the summary of each class and clade through the generalized linear model.
Assembly: mm10
Supplementary files format and content: normalized abundance measurements

source_name: stomach

extract_protocol: For RNA-seq, total RNA was extracted using the RNeasy Mini Kit (Qiagen #74106). Total RNA was first subjected for the on-column digestion by DNase (Qiagen #79254) for 0.5 hours and next prepared by using the NEBNext rRNA Depletion Kit (NEB #E6310L). The multiplexed RNA-seq libraries were then constructed for deep sequencing.

value: stomach

value: Tnrc18 BAH mutant, W2745A/Y2747A


title: DTHT168hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_32_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_32 post-vaccination


title: Arabidopsis thaliana col-0 La Shoots replicate 1

value: Shoots


title: Arabidopsis thaliana col-0 La Roots replicate 3


title: DTHT168hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_13_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_13 post-vaccination


title: stomach_MUT3_rep1

description: total RNA, rRNA depletion


title: COVIRS_13_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_13 pre-vaccination


title: Arabidopsis thaliana col-0 La Roots replicate 2


title: stomach_MUT1_rep2

description: total RNA, rRNA depletion


title: stomach_MUT3_rep2

description: total RNA, rRNA depletion


title: stomach_WT2_rep2

description: total RNA, rRNA depletion


title: DTHT144Rep3 [ChIP-seq]

description: Robert Nobel Foundation


title: DTHT144Rep2 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_6_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_6 pre-vaccination


title: stomach_MUT1_rep1

description: total RNA, rRNA depletion


title: COVIRS_6_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_6 post-vaccination


title: DTHT144Rep1 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 Ctrl Shoots replicate 3

value: Control


title: stomach_WT1_rep2

description: total RNA, rRNA depletion


title: COVIRS_27_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_27 post-vaccination


title: Arabidopsis thaliana col-0 Ctrl Shoots replicate 2


title: stomach_MUT2_rep1

description: total RNA, rRNA depletion


title: DTHT120Rep3 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_27_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_27 pre-vaccination


title: COVIRS_32_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_32 pre-vaccination


title: stomach_WT1_rep1

description: total RNA, rRNA depletion


title: DTHT120Rep2 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 La Roots replicate 1

value: Roots


title: DTHT168hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 Ctrl Roots replicate 3

value: WT


title: COVIRS_28_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_28 pre-vaccination


title: lung_MUT3_rep2

description: total RNA, rRNA depletion

source_name: lung

value: lung


title: lung_MUT2_rep2

description: total RNA, rRNA depletion


title: DTHT0hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 Ctrl Roots replicate 1


title: stomach_WT2_rep1

description: total RNA, rRNA depletion


title: Arabidopsis thaliana col-0 Ctrl Roots replicate 2


title: COVIRS_1_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_1 pre-vaccination


title: COVIRS_28_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_28 post-vaccination


title: lung_MUT3_rep1

description: total RNA, rRNA depletion


title: COVIRS_1_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_1 post-vaccination


title: DTHT120Rep1 [ChIP-seq]

description: Robert Nobel Foundation


title: lung_MUT2_rep1

description: total RNA, rRNA depletion


title: COVIRS_17_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_17 pre-vaccination


title: DT96hRep3 [ChIP-seq]

description: Robert Nobel Foundation

value: drought


title: DTHT0hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: Arabidopsis thaliana col-0 Ctrl Shoots replicate 1


title: lung_MUT1_rep1

description: total RNA, rRNA depletion


title: SK-MEL-2 cells, 5 min plasma treatment, Day 2

city: Seoul

first: Nagendra

middle: Kumar

last: Kaushik

state: Nowon-Gu

address: 20 Kwangwoongil, Wolgye Dong 447-1

department: Biophysics

country: South Korea

institute: Kwangwoon University

description:
5min
5 min plasma-treated cells

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to hsa (miRBase) whole genome using Bowtie2.
Read count extraction using bedtools.
Quantile normalization was performed by EdgeR.
Assembly: hsa miRBase version 22
Supplementary files format and content: *.txt: Tab-delimited text files include normalized values for each Sample.

growth_protocol: Cells were cultured in RPMI-1640 media supplemented in 10% FBS with antibiotics.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: Cells were exposed/treated with plasma jet for 3 and 5 min and incubated for two additional days for the analysis.

value: Melanoma cells

value: 5 min plasma jet treatment

tag: time point


title: SK-MEL-2 cells, 3 min plasma treatment, Day 2

description:
3min
3 min plasma-treated cells

value: 3 min plasma jet treatment


title: DT96hRep2 [ChIP-seq]

description: Robert Nobel Foundation

value: leaf


title: DTHT0hRep1 [ChIP-seq]

description: Robert Nobel Foundation

value: drought and heat


title: HEK293_SETDB1_KO_TNRC18

data_processing:
Fastq files were mapped to the reference genome (hg19) using bowtie2.3.4.1.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was performed using MACS2 (v2.2.7.1) (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1 -q 1e-5 –c IgG.control.bam).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of CUT&RUN signals.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: HEK293, CRISPR-Cas9 edited, SETDB1-KO

growth_protocol: HEK293 and HeLa cells were cultured and maintained in the DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). K562 cells were maintained in the RPMI-1640 base medium supplemented with 10% of FBS, 1% of antibiotics, and GlutaMAX.

extract_protocol:
1 million of cells was collected, washed and bound to ConA beads. Cell:bead sample was incubated with indicated antibodies overnight and then washed and treated with pAG-MNase, followed by adding 2mM of CaCl2 to activate pAG-MNase. Solubilized chromatin was then released using the CUT&RUN stop buffer.
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030).
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L) with 20ng CUT&RUN DNA as input.

treatment_protocol: HEK293 cells used in this work included parental cells and those with stable expression of GFP-tagged TNRC18 or the CRISPR-cas9-based KI mutation (W2858A) at TNRC18’s H3K9me3-binding BAH domain. HEK293 cells with the SETDB1 KO versus WT were also used.

value: HEK293, CRISPR-Cas9 edited, SETDB1-KO

value: Human embryonic kidney

tag: cut&run antibody

value: TNRC18 antibody,Sigma HPA024251


title: SK-MEL-2 cells, Control, Day 2

description:
Con
Control SK-MEL-2 cells

value: No treatment

value: Day 2


title: lung_WT2_rep2

description: total RNA, rRNA depletion


title: DT96hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_38_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_38 pre-vaccination

value: Monocytes


title: DT72hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_37_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_37 post-vaccination


title: CAGEseq_HEK293_TNRC18_MUT_W2858A_2

data_processing:
For CAGE-seq data analysis, raw reads (CAGE tags) were mapped to the human hg19 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5). CAGE tag clustering, detection of differentially expressed genes (DEGs) and motif discovery were performed by pipeline RECLU. Tag count data were clustered using the modified Paraclu program. Clusters with count per million (CPM) < 0.1 were discarded. Regions that have 90% overlap between replicates were extracted by BEDtools (version 2.12.0). The clusters with irreproducible discovery rate (IDR) over the value of 0.1 and clusters longer than 200 bp were discarded. Differentially expressed genes were detected using the edgeR package (version 3.22.5).
Assembly: HEK293 cells were mapped to hg19; MEF cells were mapped to mm10
Supplementary files format and content: CAGEseq: bw files

growth_protocol: HEK293 cells were cultured and maintained in the DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). A routine examination of cell lines in culture for any possible mycoplasma contamination was performed every month with MycoAlert PLUS Mycoplasma Detection Kit (Lonza, #LT27-286). Cells at a passage of less than ten were used in this study.

extract_protocol: For CAGE-seq experiment, qualities of total RNA were first assessed by Bioanalyzer (Agilent) to ensure that RNA integrity number (RIN) is over 7.0. The cDNA synthesis was conducted by using the total RNA and random primers. The ribose diols in the 5? cap structures of RNAs were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE-seq libraries) were constructed.

treatment_protocol: HEK293 cells used in this work included parental cells and those with stable expression of GFP-tagged TNRC18 or the CRISPR-cas9-based KI mutation (W2858A) at TNRC18?s H3K9me3-binding BAH domain.The Alt-R CRISPR-Cas9 System (IDT) in combination with a single-stranded oligodeoxynucleotide donor (ssODN) was used to introduce a point mutation of TNRC18. For the Alt-R CRISPR?Cas9 system, the trans-activating CRISPR RNA (tracrRNA) with ATTO 550, crRNA targeting the site to be mutated, the S.p. HiFi Cas9 Nuclease V3 and electroporation enhancer were all purchased from IDT. The ssODN was custom designed and then ordered from commercial sources (IDT). Preparation and delivery of a CRISPR?Cas9 ribonucleoprotein (RNP) complex (Alt-R CRISPR-Cas9 crRNA:tracrRNA and S.p. HiFi Cas9 Nuclease), electroporation enhancer and ssODN into cells were performed according to the manufacturer?s user guide. In brief, crRNA and tracrRNA were mixed in equimolar concentrations, followed by heating at 95?°C for 5?min. Then the mixture was cooled to RT (15-25?°C) on the bench top, allowing the crRNA:tracrRNA duplex to form. The RNP complex was made by diluting the crRNA:tracrRNA duplex and Cas9 enzyme components in PBS, followed by incubation at RT for 10-20?min. The RNP complex mixed with electroporation enhancer and ssODN was delivered to cells using electroporation with Amaxa Cell Line Nucleofector Kit V (Lonza). 18 hours after electroporation, ATTO 550 positive cells were sorted out by FACS and split into 96-well plates to establish clonal lines for PCR and sequencing-based genotyping. After genotyping, lines with homozygous mutation were further validated at both DNA and RNA levels by Sanger sequencing of PCR products that covered the mutation site.

value: TNRC18 BAH mutant, W2858A

value: CRISPR-Cas9 knock-in, TNRC18 W2858A


title: COVIRS_17_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_17 post-vaccination


title: lung_WT1_rep2

description: total RNA, rRNA depletion


title: lung_WT2_rep1

description: total RNA, rRNA depletion


title: lung_MUT1_rep2

description: total RNA, rRNA depletion

value: Tnrc18 BAH mutant, W2745A/Y2747A


title: COVIRS_37_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_37 pre-vaccination


title: COVIRS_25_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_25 post-vaccination


title: CAGEseq_HEK293_TNRC18_WT_2

value: WT

value: CRISPR-Cas9 knock-in, TNRC18 WT


title: DT72hRep1 [ChIP-seq]

description: Robert Nobel Foundation

value: drought


title: CAGEseq_HEK293_TNRC18_WT_1


title: DT168hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: lung_WT1_rep1

description: total RNA, rRNA depletion

value: lung


title: HEK293_KIT18W2858AY2860A_2

description:
RNAseq_GENE_HEK293_KI_TNRC18.txt
RNAseq_TRANSPOSON_HEK293_KI_TNRC18.txt

data_processing:
RNA-seq raw sequencing reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Assembly: HEK293 cells were mapped to hg19; MEF cells were mapped to mm10
Supplementary files format and content: RNAseq: normalized abundance measurements.

growth_protocol: HEK293 cells were maintained in DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). MEF cells were derived from embryo of mice that carried either wildtype (WT) TNRC18 or homozygous H3K9me3-binding-defective mutations (MUT) at TNRC18?s BAH domain and maintained in DMEM supplemented with 20% of FBS and 1% of antibiotics. A routine examination of cell lines in culture for any possible mycoplasma contamination was performed every month with MycoAlert PLUS Mycoplasma Detection Kit (Lonza, #LT27-286). Cells at a passage of less than ten were used in this study.

extract_protocol: For RNA-seq, total RNA was extracted using the RNeasy Mini Kit (Qiagen #74106); in brief, RNA was first subjected for the on-column digestion by DNase (Qiagen #79254) for 0.5 hours and then prepared by using the NEBNext rRNA Depletion Kit (NEB #E6310L).

treatment_protocol: HEK293 cells were stably expressed with either scramble shRNA (shCtl) or TNRC18-targeting shRNA (shTNRC18), or were ones with the rescued re-expression of TNRC18 (shTNRC18-resistant) in cells with KD of endogenous TNRC18; in a separate experiment, CRISPR-cas9-based editing of TNRC18?s BAH domain was conducted in HEK293 cells. HEK293 cells used in this work included parental cells and those with stable expression of GFP-tagged TNRC18 or the CRISPR-cas9-based KI mutation (W2858A) at TNRC18?s H3K9me3-binding BAH domain.The Alt-R CRISPR-Cas9 System (IDT) in combination with a single-stranded oligodeoxynucleotide donor (ssODN) was used to introduce a point mutation of TNRC18. For the Alt-R CRISPR?Cas9 system, the trans-activating CRISPR RNA (tracrRNA) with ATTO 550, crRNA targeting the site to be mutated, the S.p. HiFi Cas9 Nuclease V3 and electroporation enhancer were all purchased from IDT. The ssODN was custom designed and then ordered from commercial sources (IDT). Preparation and delivery of a CRISPR?Cas9 ribonucleoprotein (RNP) complex (Alt-R CRISPR-Cas9 crRNA:tracrRNA and S.p. HiFi Cas9 Nuclease), electroporation enhancer and ssODN into cells were performed according to the manufacturer?s user guide. In brief, crRNA and tracrRNA were mixed in equimolar concentrations, followed by heating at 95?°C for 5?min. Then the mixture was cooled to RT (15-25?°C) on the bench top, allowing the crRNA:tracrRNA duplex to form. The RNP complex was made by diluting the crRNA:tracrRNA duplex and Cas9 enzyme components in PBS, followed by incubation at RT for 10-20?min. The RNP complex mixed with electroporation enhancer and ssODN was delivered to cells using electroporation with Amaxa Cell Line Nucleofector Kit V (Lonza). 18 hours after electroporation, ATTO 550 positive cells were sorted out by FACS and split into 96-well plates to establish clonal lines for PCR and sequencing-based genotyping. After genotyping, lines with homozygous mutation were further validated at both DNA and RNA levels by Sanger sequencing of PCR products that covered the mutation site.

value: CRISPR-Cas9 knock-in, TNRC18 W2858A/Y2860A


title: COVIRS_38_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_38 post-vaccination


title: COVIRS_2_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_2 post-vaccination


title: COVIRS_25_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_25 pre-vaccination


title: HEK293_KIT18W2858AY2860A_1


title: liver_MUT3_rep1

description: total RNA, rRNA depletion

value: liver


title: DT168hRep1 [ChIP-seq]

description: Robert Nobel Foundation

value: leaf


title: COVIRS_2_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_2 pre-vaccination


title: HEK293_TNRC18_K_BAH_W2858A_2

data_processing:
The fastq files of human cell and mouse cell RNA-seq data were aligned respectively to the GRCh38 human genome (GRCh38.d1.vd1.fa) and the mm10 mouse genome by using STAR v2.4.2 with the following parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Then, transcript abundance for each sample was estimated with salmon V1.4.0 to quantify the transcriptome defined by Gencode v22. QC was performed using the Picard 2.22.4 CollectRnaSeqMetric and FastQC 0.11.9. Gene level counts were summed across isoforms, and genes with low counts (maximum expression < 10) were filtered out from the downstream analyses. We tested genes for differential expression in DESeq2 v1.38.2 in R and gene set enrichment analysis (GSEA) on Molecular Signatures Database (MsigDB) C2 curated genesets was conducted with GSVA v1.30.1 in R.  To comprehensively quantify expression by all repetitive elements including transposable elements (TEs) in RNA-seq data, we used REdiscoverTE (v1.0.1) which annotates the genes defined in Gencode and all RepeatMasker sequences in the human genome down to the TE sub-family level after the repetitive element expression quantification by salmon. TE count matrix was appended to gene expression data matrix for differential expression analysis using DESeq2 and the TE showing significant differential expression is defined by the adjusted p-value less than 0.05 and a log2 value of fold-change greater than 1 in the experimental versus control group (with a basemean value greater than 10).  Since REdiscoverTE is specific to human, we then used SalmonTE to calculate the TE abundance in the mouse samples. By performing a read mapping against the TE sequences, salmonTE reassigns multi-mapping reads using the expectation-maximization algorithm before determining the read count of each sequence. From the counts table the differentially expressed TEs were identified and the statistical analysis function of salmonTE generated the summary of each class and clade through the generalized linear model.
Assembly: human cells were mapped to hg38 and mouse cells to mm10
Supplementary files format and content: normalized abundance measurements

growth_protocol: HEK293 cells were maintained in DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). MEF cells were derived from embryo of mice that carried either wildtype (WT) TNRC18 or homozygous H3K9me3-binding-defective mutations (MUT) at TNRC18’s BAH domain and maintained in DMEM supplemented with 20% of FBS and 1% of antibiotics.

treatment_protocol: HEK293 cells were stably expressed with either scramble shRNA (shCtl) or TNRC18-targeting shRNA (shTNRC18), or were ones with the rescued re-expression of TNRC18 (shTNRC18-resistant) in cells with KD of endogenous TNRC18; in a separate experiment, CRISPR-cas9-based editing of TNRC18’s BAH domain was conducted in HEK293 cells.


title: liver_MUT2_rep1

description: total RNA, rRNA depletion


title: CAGEseq_HEK293_TNRC18_MUT_W2858A_1


title: COVIRS_19_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_19 pre-vaccination


title: COVIRS_19_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_19 post-vaccination


title: DT72hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: DT144hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: liver_MUT3_rep2

description: total RNA, rRNA depletion


title: HEK293_TNRC18_KI_BAH_W2858A_1


title: DT144hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: liver_MUT1_rep1

description: total RNA, rRNA depletion


title: DT168hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: liver_MUT1_rep2

description: total RNA, rRNA depletion


title: DT120hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: HEK293_TNRC18_KD_rescue_2

description:
RNAseq_GENE_TNRC18_KDrescue.txt
RNAseq_TRANSPOSON_TNRC18_KDrescue.txt

value: TNRC18 rescue in cells with shTNRC18


title: COVIRS_24_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_24 pre-vaccination


title: liver_MUT2_rep2

description: total RNA, rRNA depletion


title: liver_WT2_rep1

description: total RNA, rRNA depletion


title: HEK293_TNRC18_WT_2

value: parental, TNRC18 WT


title: COVIRS_15_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_15 post-vaccination


title: HEK293_TNRC18_WT_1

value: Human embryonic kidney


title: DT120hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: liver_WT1_rep2

description: total RNA, rRNA depletion


title: COVIRS_15_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_15 pre-vaccination


title: HEK293_TNRC18_KD_rescue_1


title: DT120hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: liver_WT2_rep2

description: total RNA, rRNA depletion


title: HEK293_shTNRC18_2


title: DT144hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: DT0hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: liver_WT1_rep1

description: total RNA, rRNA depletion


title: HEK293_shTNRC18_1


title: heart_MUT3_rep2

description: total RNA, rRNA depletion

source_name: heart

value: heart


title: DT0hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_8_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_8 post-vaccination


title: COVIRS_8_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_8 pre-vaccination


title: HEK293_shCtrl_2

value: shScramble


title: COVIRS_24_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_24 post-vaccination


title: heart_MUT3_rep1

description: total RNA, rRNA depletion


title: heart_MUT2_rep2

description: total RNA, rRNA depletion


title: HEK293_shCtrl_1


title: DT0hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_31_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_31 pre-vaccination


title: heart_MUT2_rep1

description: total RNA, rRNA depletion


title: heart_MUT1_rep2

description: total RNA, rRNA depletion


title: C96hRep3 [ChIP-seq]

description: Robert Nobel Foundation

value: untreated


title: COVIRS_31_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_31 post-vaccination

value: Monocytes


title: HEK293_WT_H3ac

source_name: HEK293, CRISPR-Cas9 editing,TNRC18 wild type

value: HEK293, parental, with WT TNRC18

value: H3Kac antibody, Millipore 06-599


title: C96hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: C96hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: HEK293_TNRC18_KI_MUT_H3ac

source_name: HEK293, CRISPR-Cas9 editing,TNRC18 W2858A

value: HEK293, CRISPR-Cas9 edited,TNRC18 W2858A mutant


title: COVIRS_18_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_18 post-vaccination


title: COVIRS_18_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_18 pre-vaccination


title: C72hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_23_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_23 post-vaccination


title: heart_MUT1_rep1

description: total RNA, rRNA depletion

value: Tnrc18 BAH mutant, W2745A/Y2747A


title: C72hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: heart_WT2_rep2

description: total RNA, rRNA depletion

value: WT


title: HEK293_WT_H3K9me3

value: H3K9me3 antibody, Abcam ab8898


title: HEK293_TNRC18_KI_MUT_H3K9me3


title: COVIRS_23_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_23 pre-vaccination


title: C72hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_16_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_16 post-vaccination


title: C168hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: HEK293_TNRC18_KI_MUT_SETDB1

value: SETDB1 antibody, Proteintech, 11231-1-AP


title: heart_WT1_rep2

description: total RNA, rRNA depletion


title: COVIRS_16_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_16 pre-vaccination


title: HEK293_WT_SETDB1


title: heart_WT1_rep1

description: total RNA, rRNA depletion


title: HEK293_TNRC18_KI_MUT_TRIM28

value: TRIM28 antibody, Bethyl Laboratories A300-274A


title: COVIRS_4_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_4 post-vaccination


title: HEK293_TNRC18_KI_MUT_HDAC2

value: HDAC2 antibody, Abcam ab7029


title: brain_MUT3_rep1

description: total RNA, rRNA depletion

source_name: brain

value: brain


title: HEK293_WT_TRIM28


title: C144hRep3 [ChIP-seq]

description: Robert Nobel Foundation

value: leaf


title: COVIRS_36_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_36 post-vaccination


title: COVIRS_4_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_4 pre-vaccination


title: HEK293_WT_HDAC2

value: HEK293, parental, with wildtype (WT) TNRC18


title: C144hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: K562_TNRC18

value: Human embryonic kidney

value: TNRC18 antibody,Sigma HPA024251


title: brain_MUT2_rep1

description: total RNA, rRNA depletion


title: C144hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_36_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_36 pre-vaccination


title: COVIRS_26_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_26 post-vaccination


title: brain_MUT1_rep2

description: total RNA, rRNA depletion


title: heart_WT2_rep1

description: total RNA, rRNA depletion

value: heart


title: brain_MUT2_rep2

description: total RNA, rRNA depletion


title: C120hRep3 [ChIP-seq]

description: Robert Nobel Foundation

value: untreated


title: Hela_TNRC18

source_name: HeLa

value: HeLa


title: brain_MUT1_rep1

description: total RNA, rRNA depletion


title: C120hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: C168hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_35_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_35 pre-vaccination

value: Monocytes


title: HEK293_H3K9me3_ab2

value: H3K9me3 antibody, Active Motif 39161


title: COVIRS_35_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_35 post-vaccination


title: HEK293_H3K9me3_ab1


title: brain_WT2_rep2

description: total RNA, rRNA depletion


title: brain_MUT3_rep2

description: total RNA, rRNA depletion


title: C168hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: C120hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: brain_WT2_rep1

description: total RNA, rRNA depletion


title: HEK293_GFP_TNRC18

source_name: HEK293, GFP-TNRC18 overexpression

value: HEK293, stably expressed with GFP-TNRC18

value: Rabbit anti-GFP antibody, Abcam ab290


title: C0hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_30_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_30 pre-vaccination


title: HEK293_TNRC18


title: C0hRep2 [ChIP-seq]

description: Robert Nobel Foundation


title: brain_WT1_rep1

description: total RNA, rRNA depletion

value: WT


title: brain_WT1_rep2

description: total RNA, rRNA depletion


title: COVIRS_22_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_22 post-vaccination


title: C0hRep1 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_26_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_26 pre-vaccination


title: SOCS1-g1-Stim-2_sorted

status: Public on Jul 22 2023

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts

source_name: Healthy Donor PBMCs

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

value: Healthy Donor PBMCs

value: Macrophage

value: stimulation with IFNgamma


title: SOCS1-g1-Stim-1_sorted


title: IRF1-g1-Stim-2_sorted


title: IRF1-g1-Stim-1_sorted


title: Mock-Stim-1_sorted

value: Mock edited


title: SOCS1-g1-Unstim-2_sorted

value: Unstimulated


title: SOCS1-g1-Unstim-1_sorted


title: Mock-Stim-2_sorted


title: IRF1-g1-Unstim-1_sorted


title: COVIRS_30_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_30 post-vaccination


title: IRF1-g1-Unstim-2_sorted


title: Mock-Unstim-2_sorted


title: EGI1_TET_FOSL1sh10_3

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode v28 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: cholangiocarcinoma cell line

growth_protocol: EGI-1 cell were grown in 10% FBS DMEM using 10 cm plates

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9.
Low input RNA-seq (mars-seq)

treatment_protocol: Cells were treated with 2ug/ml doxycycline for 4 days and seeded for 24 h. Then cells were harvested and RNA isolated.

value: cholangiocarcinoma (CCA)


title: EGI1_TET_FOSL1sh3_2


title: EGI1_TET_FOSL1sh10_1


title: Mock-Unstim-1_sorted


title: EGI1_TET_FOSL1sh10_2


title: EGI1_TET_FOSL1sh3_1


title: EGI1_TET_GFPsh_3


title: EGI1_TET_FOSL1sh3_3


title: EGI1_TET_GFPsh_2


title: EGI-1 flag-tagged FOSL1 overexpressing cells

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using Bowtie2 v2.5.3a with default parameters.
MACS 2.1.0.20151222 was the peak calling algorithm used with default parameters.
SAM files were converted to BAM files and sorted with SAMtools v1.9-foss-2018b
BAM files were converted to bedGraph files with the bedtools suite v2.27.1
bedGraph files were converted to BigWig files using bedGraphToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files generated from bedGraph files.

extract_protocol: Library preparation was performed with the NEBNext® Ultra™ II DNA Library Prep Kit


title: EGI-1 Input


title: EGI1_TET_GFPsh_1


title: HEK293_IgG

value: Rabbit IgG,Cell Signaling Technology 2729S


title: P.aeruginosa_TBCF strain MTase ap KO, mid log phase, biol rep 3

city: Shenzhen

first: Yang

last: Liu

state: Guangdong

address: Liuxian

institute: Sustech Hospital

data_processing:
RSEM v1.3.1
Trimmed sequence reads were mapped to Pseudomonas aeruginosa TBCF using rsem-calculate-expression with unique mapping setting (--bowtie-m)
Read count extraction was performed using RSEM rsem-generate-data-matrix
Assembly: Pseudomonas aeruginosa TBCF
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

organism: Pseudomonas aeruginosa

source_name: P.aeruginosa_TBCF strain MTase ap KO

growth_protocol: P. aeruginosa TBCF and mutants were grown in Luria-Bertani (LB) liquid media at 37°C with constant shaking at 220 rpm with aeration.

extract_protocol:
Total RNA extraction and purification was performed for 3 biological replicates of each strain using RNeasy Mini Kit (QIAGEN) and RNase-Free DNase Set (QIAGEN) according to the manufacturer’s protocol. 1μg of total RNA was used for the construction of sequencing libraries.
RNA sequencing was performed on Illumina NovaSeq 6000 sequencing platform generating 150 bp paired-end reads.

treatment_protocol: The in-frame deletion mutagenesis of methyltransferase ap or cp was performed through two-step allelic exchange. P. aeruginosa TBCF and mutants were cultured to mid log phase.

tag: strain

value: P.aeruginosa_TBCF strain MTase ap KO

value: mid log stage

value: MTase ap KnockOut


title: P.aeruginosa_TBCF strain MTase ap KO, mid log phase, biol rep 2


title: P.aeruginosa_TBCF strain MTase ap KO, mid log phase, biol rep 1


title: POXKu70_35

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing wheat bran plus Avicel and cultivated for 36h

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol:
Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.

extract_protocol: Total RNA were extracted using TRIzol RNA Kit


title: POXKu70_34

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing wheat bran plus Avicel and cultivated for 24h


title: POXKu70_37


title: POXKu70_32


title: POXKu70_33


title: POXKu70_30

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing wheat bran plus Avicel and cultivated for 13h


title: POXKu70_26

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and cultivated for 36h


title: POXKu70_24

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and cultivated for 12h


title: POXKu70_29

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing wheat bran plus Avicel and cultivated for 12h


title: POXKu70_25


title: POXKu70_28


title: POXKu70_23


title: POXKu70_27


title: POXClrBWA_36hS

description: The deletion mutant of gene POXClrB, transferred from glucose medium to medium containing wheat bran plus Avicel medium and cultured for 36h

value: MuPOXClrB


title: POXClrBWA_24hT

description: The deletion mutant of gene POXClrB, transferred from glucose medium to medium containing wheat bran plus Avicel medium and cultured for 24h


title: POXClrBWA_36hF


title: POXClrBWA_24hF


title: POXClrBWA_24hS


title: POXClrBWA_12hT

description: The deletion mutant of gene POXClrB, transferred from glucose medium to medium containing wheat bran plus Avicel medium and cultured for 12h


title: POXClrBWA_12hS


title: POXClrBWA_12hF


title: POXClrBAV_36hT

description: The deletion mutant of gene POXClrB, transferred from glucose medium to medium containing Avicel medium and cultured for 36h


title: POXClrBAV_36hS


title: POXClrBAV_24hS

description: The deletion mutant of gene POXClrB, transferred from glucose medium to medium containing Avicel medium and cultured for 24h


title: POXClrBAV_36hF


title: POXKu70_36


title: POXClrBAV_24hT


title: POXClrBAV_12hT

description: The deletion mutant of gene POXClrB, transferred from glucose medium to medium containing Avicel medium and cultured for 12h


title: POX1167WA_36hS

description: The deletion mutant of gene POX01167, transferred from glucose medium to medium containing wheat bran plus Avicel medium and cultured for 36h


title: POXClrBAV_12hF


title: POXClrBAV_12hS


title: POX1167WA_36hT


title: POXKu70_31


title: POX1167WA_36hF


title: POXClrBWA_36hT


title: POX01167WA_24hS

description: The deletion mutant of gene POX01167, transferred from glucose medium to medium containing wheat bran plus Avicel medium and cultured for 24h


title: POX01167WA_12hS

description: The deletion mutant of gene POX01167, transferred from glucose medium to medium containing wheat bran plus Avicel medium and cultured for 12h


title: POX1167WA_24hT


title: POX01167WA_12hT


title: POX01167WA_24hF


title: POX01167WA_12hF


title: POX01167AV_36hF

description: The deletion mutant of gene POX01167, transferred from glucose medium to medium containing Avicel medium and cultured for 36h


title: POX01167AV_36hS


title: Leaf tissue, Intermediate leaf, Wild-type, biol rep 3, RNA-seq

city: Pohang

first: Sang-Yun

last: Han

state: Gyeongbuk

address: 77 Cheongam-Ro, Nam-Gu

department: Department of Life Sciences

institute: Pohang University of Science and Technology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Read count extraction was performed by RSEM on Trinity assembly.
The TPM data obtained from RSEM were normalized using TMM with NOISeq.
Assembly: We generated 9 paired-end raw reads of RNA-seq on leaf tissue development of Bienertia sinuspersici by Illumina HiSeq 2500 sequencer. From the raw reads, we obtained clean reads by Trimmomatic program and transcripts were then assembled by de novo transcriptome assembler Trinity.
Supplementary files format and content: TPMTMM (TMM-normalized TPM) matrix: gene expression data (.txt)

organism: Bienertia sinuspersici

source_name: Intermediate leaf

extract_protocol:
Total RNA of leaf tissue was extracted with CTAB extraction buffer, followed by TURBO DNA-free™ kit (Invitrogen) treatment.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina, CA, USA) was used for 100 bp paired-end sequencing and KAPA library quantification kit (Kapa Biosystems) was used for quantification of cDNA library. Quality control was performed with Agilent 2100 BioAnalyzer (Agilent).

value: Intermediate leaf

value: Wild type


title: POXClrBAV_24hF


title: Leaf tissue, Mature leaf, Wild-type, biol rep 1, RNA-seq

source_name: Mature leaf

value: Mature leaf


title: Leaf tissue, Mature leaf, Wild-type, biol rep 2, RNA-seq


title: Leaf tissue, Mature leaf, Wild-type, biol rep 3, RNA-seq


title: POX01167AV_12hT

description: The deletion mutant of gene POX01167, transferred from glucose medium to medium containing Avicel medium and cultured for 12h


title: POX01167AV_12hF


title: POX01167AV_12hS


title: CLD6

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi Road 44

institute: Shandong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (version 2.2.0) provided by 10 × Genomics was used to demultiplex cellular barcodes, align reads and generate the featurebarcode unique molecular identifier (UMI) matrices based on the human reference genome GRCh38.
We processed the unique molecular identifier (UMI) count matrix using the Seurat R package (v2.4.3)
Assembly: GRCh38
Supplementary files format and content: Expression matrices provided as CSV files

source_name: Liver

extract_protocol:
Each tissue sample was placed in a sterile Petri dish on ice. The tissue was subsequently minced to smaller pieces of less than 3 mm. Sample pieces were transferred to a gentle MACS C Tube (Miltenyi #130-093-237) containing 5 ml digestion enzyme mix. The C tube was then placed on a gentleMACS Octo Dissociator for mechanical dissociation. Upon run completion, the sample was incubated for 30 min at 37  C under continuous low shaking. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300 x 3 g and 4 C for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco). Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Single-cell RNA-seq libraries were prepared with Chromium Single cell 30 Reagent v2 Kits according to the manufacturer’s protocol. The Chromium Single Cell 30 Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 30 Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used. Briefly, single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10 × Genomics) to generate single cell gel beads in emulsions (GEMs). After generation of GEMs, reverse transcription reactions were engaged barcoded fulllength cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform (HiSeq X Ten), and 150 bp paired-end reads were generated.
10x Genomics Single Cell Transcriptome Sequencing

tag: disease state

value: cholestasis liver tissue

value: Liver


title: Leaf tissue, Intermediate leaf, Wild-type, biol rep 1, RNA-seq


title: POXKu70_9

description: The deletion mutant of POXKu70 gene is the control strain for differential transcriptome analysis, and cultured in induced carbon source


title: CLD7

description: 10x Genomics


title: CLD5

description: 10x Genomics


title: Leaf tissue, Young leaf, Wild-type, biol rep 3, RNA-seq

source_name: Young leaf

value: Young leaf


title: POXKu70_8


title: POXKu70_7


title: CLD4

description: 10x Genomics


title: SVL_12.5

city: Irvine

first: Yongsheng

last: Shi

address: 811 Health Sciences Rd, Med Sci B262

institute: University of California, Irvine

library_source: other

data_processing:
(1). MPIVA: All MPIVA read 1 and read 2 FASTQ files were merged using bbmerge V38 using option ` maxloose=t`.
(1). MPIVA: MPIVA Input samples were used establish the sequences of the full randomized PAS region contained in the IVT pool by clustering the 25 nt randomized region with starcode version 1.4. The expected cleaved lengths of the 25 nt consensus sequences for L3 and SVL backbones (13 nt and 12 nt, respectively) were used as unique identifiers of the full randomized region. If any of these identifiers were not unique within L3 and SVL libraries, respectively, then these sequences were not used in subsequent analyses.
(1). MPIVA: RNA-seq reads from DMSO and drug-treated libraries were locally aligned against the shared 5′ region of the reporter constructs to determine the beginning of the randomized region. The part of the RNA-seq read containing the randomized region and shared 3′ region was locally aligned against the list of consensus sequences from the Input libraries.
(1). MPIVA: Sequences with at least 50 reads in the DMSO libraries were kept to avoid noise from lowly abundant RNA sequences in the IVT pool.
(1). MPIVA: A pseudocount of 1 was added to variants in L3 2.5 µM, L3 12.5 µM, and SVL 12.5 µM due to drug-mediated drop out of high abundance variants in the DMSO libraries. This pseudocount avoids having undefined drug sensitivities in later steps that would be introduced by log(0).
(1). MPIVA: Each variant that passed these filters were counted and converted to a percentage within each RNA-seq library.
(1). MPIVA: Drug sensitivity for each variant in each dose of Compound 2 was defined as the log ratio of normalized reads from drug-treated RNA-seq divided by the normalized reads from DMSO-treated RNA-seq.
(2). 4sU-seq: Reads were mapped to human(hg19) genome using STAR. Multi-mapping was not allowed. Mapped reads were converted to bigwig files using deepTools.
(3). PAS-seq: Reads that lack a poly(A) tail (15 consecutive As) were removed with python script. The trimmed reads were mapped to human (hg19) genome using STAR.
(3). PAS-seq: Removed internal priming reads (reads that are mapped to genomic sequences that are immediately followed by 6-consecutive As, or seven As out of 10 nucleotides)
(3). PAS-seq: Reads were converted to BigWig files using deepTools
Assembly: hg19
Supplementary files format and content: (1). MPIVA: TSV file containing log ratio of different concentrations of Compound 2 vs DMSO in both L3 and SVL backbone and their sequences.
Supplementary files format and content: (2). 4sU-seq and (3). PAS-seq: BigWig files.

molecule: other

organism: synthetic construct

source_name: in vitro

extract_protocol:
(1). MPIVA: RNA from in vitro assay is phenol chloroform extracted and polyadenylated RNA is purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
(2). 4sU-seq and (3). PAS-seq: RNA is extracted by Trizol. For 4sU-seq, RNA is biotinylated and 4sU labeled RNA is enriched by strepavdin beads and further purified by phenol chloroform extraction
(1). MPIVA: Library is constructed by RT-PCR.
(2). 4sU-seq and (3). PAS-seq: RNA is fragmented and library is constructed following illumina's protocol

treatment_protocol:
(1). MPIVA: Libraries were cloned by gibson assembly and in vitro transcribed to RNA. The RNA pool was then used in in vitro cleavage and polyadenylation assay.
(2). 4sU-seq: HepG2 cells were treated with DMSO or 20µM JTE-607 for 3 hours at 37˚C followed by addition of 500µM 4sU. The cell containing JTE-607 and 4sU was incubated at 37˚C for another 1 hour prior to sample harvesting.
(3). PAS-seq: HepG2 cells were treated with DMSO or 20µM JTE-607 for 4 hours at 37˚C prior to sample harvesting

value: in vitro

value: 12.5 µM Compound 2

tag: sample type

value: library composed of in vitro synthesized random sequence

tag: library backbone

value: SVL


title: Leaf tissue, Young leaf, Wild-type, biol rep 1, RNA-seq

tag: tissue


title: SVL_0.5

value: 0.5 µM Compound 2


title: Leaf tissue, Young leaf, Wild-type, biol rep 2, RNA-seq

tag: genotype


title: POX01167AV_36hT


title: CLD2

description: 10x Genomics


title: POXKu70_6


title: SVL_2.5

tag: treatment

value: 2.5 µM Compound 2


title: POXKu70_10


title: CLD3

description: 10x Genomics


title: Leaf tissue, Intermediate leaf, Wild-type, biol rep 2, RNA-seq


title: CLD1

description: 10x Genomics


title: SVL_DMSO

value: DMSO


title: HL2

description: 10x Genomics

value: healthy liver  tissue


title: POXKu70_4


title: POX07277_oleic_24hS

description: The deletion mutant of the gene POX07277 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and added oleic acid, and cultivated for 24h

growth_protocol:
Mycelium of 1 gram Mutant POX07277 were cultured in 2% Avicel liquid medium and added  oleic acid for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POX07277_oleic_24hT


title: POXKu70_3


title: SVL_Input

value: no treatment


title: HL1

description: 10x Genomics


title: POX07277_oleic_24hF


title: L3_12.5


title: POXKu70_2


title: POX07277_linol_24hT

description: The deletion mutant of the gene POX07277 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and added linolenic acid, and cultivated for 24h

growth_protocol:
Mycelium of 1 gram Mutant POX07277 were cultured in 2% Avicel liquid medium and added linolenic acid for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: Socs1-Stim-R2_sorted

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (mm10)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: mm10
Supplementary files format and content: count file generated by featureCounts

source_name: Bone Marrow

value: Bone Marrow

value: Macrophage

value: stimulation with IFNgamma


title: Socs1-Stim-R1_sorted


title: POX07277_linol_24hS


title: POXKu70_1T


title: L3_2.5


title: POXKu70_1S


title: L3_0.5


title: Irf1-Stim-R2_sorted


title: POX07277_linol_24hF


title: L3_DMSO


title: POXKu70_1F


title: Irf1-Stim-R1_sorted


title: L3_Input


title: POX07277_ARA_24hT

description: The deletion mutant of the gene POX07277 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and added arochidonic acid oil, and cultivated for 24h

growth_protocol:
Mycelium of 1 gram Mutant POX07277 were cultured in 2% Avicel liquid medium and added arochidonic acid oil for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POXClrB_2T

description: The deletion mutant of POXClrB gene was cultured in induced carbon source

value: MuPOXClrB


title: Mock-Stim-R2_sorted

value: Mock edited


title: POX07277_ARA_24hS


title: POXKu70_5


title: POX07277_ARA_24hF


title: POXClrB_2S


title: Mock-Stim-R1_sorted


title: Hep3B, DNMT1-S878A, 25mM Glucose, Thiamet-G, Replicate 2

city: Duarte

first: Heon

last: Shin

address: 1500 E Duarte Rd, Gonda, 2132B

institute: City of Hope

data_processing:
Converting the signal data, indexing, and methylation call were performed using nanopolish version 0.11.1.
Indexing, Data aligned by minimap2 version 2.17.
Aligned reads were sorted using samtools version 1.10 in the hg19 genome.
UCSC genome browser tracks were established using bedGraphToBigWig.
Methylation percentage was averaged across CpG islands.
Assembly: Reads were aligned to hg19 genomes
Supplementary files format and content: bigWig

growth_protocol: DMEM or DMEM high glucose, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA was extracted using DNA mini kit with G-tip (Qiagen). 2 ug of genomic DNA was used for the construction of sequencing libraries.
DNA library for nanopore sequencing were constructed using Genomic DNA Ligation Kit following manufacturer's protocols.

treatment_protocol: Cells were induced by treatment of 96 hours post confluent cells with or without 25mM Thiamet-G (Cayman Chemical).

tag: cell line

value: Human epithelial liver

value: 25mM Glucose + Thiamet-G


title: POXClrB_2F


title: Hep3B, DNMT1-S878A, 25mM Glucose, Thiamet-G, Replicate 1

value: Liver

tag: cell type


title: Socs1-Unstim-R2_sorted

value: Unstimulated


title: POXClrB_1T

description: The deletion mutant of POXClrB gene was cultured in induced carbon source and was not transferred

growth_protocol:
1 ml of mutant POXClrB spore fluid were cultured in 2% Avicel liquid medium for 72 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: Socs1-Unstim-R1_sorted


title: Hep3B, DNMT1-S878A, 5mM Glucose, Replicate 1

value: 5mM Glucose


title: POXKu70_45

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and added oleic acid, and cultivated for 24h

growth_protocol:
Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium and added  oleic acid for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POXKu70_44


title: Hep3B, DNMT1-WT, 25mM Glucose, Thiamet-G, Replicate 1


title: POX04420T

description: The deletion mutant of POX04420 gene was cultured in induced carbon source


title: POXKu70_43

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and added linolenic acid, and cultivated for 24h

growth_protocol:
Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium and added linolenic acid for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POXClrB_1F


title: Irf1-Unstim-R1_sorted


title: Mock-Unstim-R2_sorted


title: POXKu70_42


title: POX04420S


title: POXKu70_41


title: Hep3B, DNMT1-WT, 5mM Glucose, Replicate 2


title: Hep3B, DNMT1-WT, 5mM Glucose, Replicate 1


title: POX01167T

description: The deletion mutant of POX01167 gene was cultured in induced carbon source and was not transferred

growth_protocol:
1 ml of mutant HP7-1 spore fluid were cultured in 2% Avicel liquid medium for 72 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POXKu70_39

description: The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and added arochidonic acid oil, and cultivated for 24h

growth_protocol:
Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium and added arochidonic acid oil for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: Hep3B, DNMT1-S878A, 5mM Glucose, Replicate 2


title: POX04420F


title: Mock-Unstim-R1_sorted


title: AT3_INPUT-2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were trimmed for adaptor sequence using Ngmerge, then mapped to the mm10 genome with bowtie2
Peaks were called with Macs2 with respective INPUT files
Assembly: mm10
Supplementary files format and content: Peak files called with macs2

extract_protocol:
Following stimulation, cross linked chromatin was sonicated followed by immunoprecipitation with anti-Irf1 antibody. Chromatin was reverse crosslinked and DNA isolated and sequenced.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.

value: Breast Cancer

value: IFNg stimulation, no immunoprecipitation


title: POXKu70_46


title: H9c2 cells, control 3

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

institute: University of Melbourne

data_processing:
Base calling was made with Illumina Real Time Analysis 3 (RTA3) Software
Reads first underwent adapter trimming and quality check with FastQC v0.11.7.
Raw read quality filtering and adapter trimming was conducted with fastp v0.14.1 (Chen et al., 2018) (auto detect of adapters, trim_tail=1, poly_g_min_len=1, min phred quality 20, min length 36, u 90).
Filtered reads were aligned to the rat reference genome (Rattus norvegicus, Ensembl version bn7.2.106) using STAR v2.5 (Dobin et al., 2013) in 2-pass mode and expression quantified at the gene level and collated into a counts matrix.
Assembly: Rattus norvegicus, Ensembl version bn7.2.106
Supplementary files format and content: Tab-delimited text file contains a counts matrix (raw gene counts for every gene and every sample)

organism: Rattus norvegicus

growth_protocol: H9c2 rat cardiomyoblasts (RRID: CVCL_ 0286) were sourced from CellBank Australia (Westmead, NSW, Australia). Cells were cultured at 37℃ with 5% CO2 in a humidified incubator in proliferation media consisting of Dulbecco’s Modified Eagle Medium (DMEM; Gibco #11995-065) supplemented with 1% v/v penicillin-streptomycin (Gibco #15140-122) and 10% v/v FBS (Gibco #A3161001). Cells were grown in T75 flasks to ~80% confluence then washed with sterile PBS wash and detached (Gibco TrypLE Express #LTS12604021) for passaging into 6- or 12-well plates. After 24 h in proliferation media, cells were differentiated for 5 days in media consisting of DMEM (Gibco #11995-065) supplemented with 1% v/v penicillin-streptomycin (Gibco #15140-122), 1% v/v FBS (Gibco #A3161001) and 1 µM retinoic acid (Sigma R2625) which was added to media daily, protected from light.

extract_protocol:
Media was aspirated then cells were immediately lysed in 900 µL TRI-reagent (#15599018 Ambion) with homogenisation achieved by pipette mixing. Lysates were then frozen at -80℃ until RNA isolation. TRI-reagent lysates were thawed on ice and centrifuged at 10,000 x g for 10 min at 4℃. An aliquot of the supernatant was transferred to a new tube and mixed with an equal volume of 96% ethanol, then transferred to a spin column for RNA purification with on-column DNase-I treatment, as per manufacturer’s directions (#R2052 Direct-Zol RNA Miniprep, Zymo Research). RNA concentration and purity (260:280 nm: >2.0) was determined with a spectrophotometer (NanoDrop 1000, Thermo Fisher Scientific).
Library construction was conducted by Macrogen Oceania. RNA concentration was confirmed fluorometrically (Qubit, Thermo Fisher) and RNA integrity number (≥9) was determined by electrophoresis (Tapestation, Agilent). Stranded libraries were prepared from 500 ng total RNA input with poly-A+ selection (TruSeq Stranded mRNA, Illumina). Final library size and concentration were assessed (Qubit, Thermo Fisher and TapeStation, Agilent).

treatment_protocol: The antisense locked nucleic acid (LNA) GapmeR (#339515, Qiagen) sequence for the Tug1 LNA was (5’-3’) ATTCAGTAGACAGCTA (Cat # LG00798122-DDA), and Negative control (NC) LNA was (5’-3’) GCTCCCTTCAATCCAA (cat # LG00000001-DDC). Lyophilised LNAs were first resuspended in nuclease free water to make a stock solution (50 µM). Lipofectamine® 2000 transfection reagent (Thermo Fisher Scientific) was diluted in serum-free DMEM (7% v/v) and in a separate tube, LNAs were diluted in serum-free DMEM. The diluted LNAs and diluted Lipofectamine were then mixed 1:1 and incubated at room temperature for 15 min to form a final transfection mix. Transfection mix was then added to each well to a final LNA concentration of 25 nM. LNA transfection was performed for 24 h prior to harvest.

value: cardiomyocyte

value: WT

value: negative control LNA


title: POXKu70_40


title: H9c2 cells, Tug1 knockdown 3

value: Tug1 knockdown LNA


title: POXClrB_1S


title: Irf1-Unstim-R2_sorted


title: Hep3B, DNMT1-WT, 25mM Glucose, Thiamet-G, Replicate 2


title: POXKu70_38


title: H9c2 cells, Tug1 knockdown 2


title: Mac_INPUT-2

source_name: Bone marrow

value: Bone marrow


title: POX01167S


title: POX01167F


title: Mac_INPUT-1


title: POXKu70_22


title: HP7-1_WB_SB

description: Wild-type strain HP7-1 under non-transferred wheat bran plus bagasse conditions

growth_protocol:
1 ml of mutant HP7-1 spore fluid were cultured in wheat bran plus bagasse liquid medium for 72 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: AT3_IRF-2

value: IFNg stimulation and immunoprecipitation with anti-Irf1


title: POXKu70_21


title: H9c2 cells, Tug1 knockdown 1


title: HP7-1_WB_RS

description: Wild-type strain HP7-1 under non-transferred wheat bran plus rice straw conditions

growth_protocol:
1 ml of mutant HP7-1 spore fluid were cultured in wheat bran plus rice straw liquid medium for 72 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: AT3_IRF-1


title: POXKu70_20


title: AT3_INPUT-1


title: H9c2 cells, control 1


title: HP7-1WB

description: Wild-type strain HP7-1 under non-transferred wheat bran conditions

growth_protocol:
1 ml of mutant HP7-1 spore fluid were cultured in 2% wheat bran liquid medium for 72 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: Mac_IRF1-2

value: Macrophage


title: POXKu70_19


title: Mac_IRF1-1


title: POXKu70_18


title: HP7-1GluS

description: Wild-type strain HP7-1 under non-transferred glucose conditions

growth_protocol:
1 ml of mutant HP7-1 spore fluid were cultured in 2% glucose liquid medium for 72 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POXKu70_17


title: HP7-1GluT


title: HP7-1GluF


title: POXKu70_16


title: T0-IH27_S34_R1_001

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were trimmed for adaptor sequences using Cutadapt
Guide enrichment was determined using MAGeck
Assembly: Brie/Gecko whole genome sgRNA libraries in lenti-Guide-Pro backbone
Supplementary files format and content: Peak files called with macs2

extract_protocol:
DNA was isolated from gene edited AT-3 breast cancer cells using the Qiagen Blood and Tissue kit. Guide sequences were amplified by PCR. Purified PCR product was sequenced.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.
CRISPR Sreen using Brie and Gecko whole genome libraries

value: HDR knockin of GFP into CXCL9

value: Time 0 control


title: Low-IH25_S36_R1_001

value: Sorted for bottom 15% GFP+ cells following 2.5ng/mL IFNg/TNF stimulation for 14 hours


title: POXKu70_15


title: H9c2 cells, control 2


title: POXKu70_14


title: POXKu70_13


title: High-IH24_S37_R1_001

value: Sorted for top 15% GFP+ cells following 2.5ng/mL IFNg/TNF stimulation for 14 hours


title: 3RNA-IHB18_sorted

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (mm10)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: mm10
Supplementary files format and content: count file generated by featureCounts

value: 14hr stimulation with IFNgamma and TNF


title: 3RNA-IHB17_sorted


title: Tend-IH26_S35_R1_001

value: Time endpoint control


title: 3RNA-IHB14_sorted


title: 3RNA-IHB13_sorted


title: SAT22

city: Los Angeles

first: Marcus

last: Alvarez

state: CA

address: 695 Charles E Young Dr South, Gonda 6335

department: Human Genetics

institute: UCLA

description: 10X Genomics 3' V2

data_processing:
Reads were aligned to the GRCh37 human genome reference with GENCODE v19 gene annotations [46] using STARsolo v2.7.5 a[34] with the GeneFull argument to account for unspliced mRNA.
Assembly: GRCh37
Supplementary files format and content: Matrix market format for gene counts
Supplementary files format and content: Tab-separated text file for meta data

source_name: Subcutaneous adipose

extract_protocol:
Frozen tissue was minced over dry ice and transferred into ice-cold lysis buffer consisting of 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2. After a 10-min incubation period, the lysate was gently homogenized using a dounce homogenizer and filtered through a 70-μm MACS smart strainer (Miltenyi Biotec #130-098-462) to remove debris. Nuclei were centrifuged at 500gfor 5 min at 4 °C and washed in 1 ml of resuspension buffer (RSB) consisting of 1× PBS, 1.0% BSA, and 0.2 U/μl RNase inhibitor. We further filtered nuclei using a 40-μm Flowmi cell strainer (Sigma Aldrich # BAH136800040) and centrifuged at 500gfor 5 min at 4 °C.
Pelleted nuclei were re-suspended in wash buffer and immediately processed with the 10X Chromium platform following the Single Cell 3' v2 protocol. After library generation with the 10X Genomics platform, libraries were sequenced on an Illumina NovaSeq S2 at a sequencing depth of 50,000 reads per cell.

value: Subcutaneous adipose


title: SAT21

description: 10X Genomics 3' V2


title: SAT8

description: 10X Genomics 3' V2


title: SAT7

description: 10X Genomics 3' V2


title: POX02968T

description: The deletion mutant of POX02968 gene was cultured in induced carbon source


title: MCF7 cells cultured in 30 mM glucose  (set 1)

type: RNA

city: Sheffield

first: Samrein

middle: BM

last: Ahmed

state: --- Select One ---

address: Owen building-731

country: United Kingdom

institute: Sheffield Hallam University

description: Gene expression after MCF7 cells clutured in 30 mM glucose after 72 hrs

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Human Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed

source_name: MCF7 breast cancer cell line cultured in 37C, humidified and  sterile incubator

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The MCF7 cell line was maintained in the Minimal essential medium (M2279) supplemented with 5.6 mM glucose medium from Sigma-Aldrich supplemented with 10% Fetal bovine serum, and penicillin (100 U/ml) / streptomycin (100 µg/ml) antibiotic mixture. The cells were left to grow in a humidified incubator provided with 5% CO2. When maintaining and seeding cells, 1x Trypsin/ EDTA was used. All the mammalian cell culturing was performed under aseptic conditions

extract_protocol: The RNA extracted from peeleted cells by RNeasy Kits-QIAGEN. The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000). The integrity of the extracted RNA was analysed on the Bioanalyzer (Agilent; 2100). We considered RNA to be of good quality based on the 260/280 values (Nanodrop), rRNA 28S/18S ratios and RNA integrity number (RIN) (Bioanalyzer).

treatment_protocol: Medium supplemented with 5.6 mM glucose was used to mimic normoglycemic conditions, while 30mM was used following previous studies to mimic hyperglycemia.  Insulin concentration that mimics hyperinsulinemia was decided based on a previous study by Mwe-Lin Wei and co-workers, in which they used 25 nM to mimic hyperinsulinemia. Treamnets were applied for 72 hrs.

value: Human Breast cancer cell line


title: K3P Med1 D3 rep2

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Sequencing reads were mapped to the human genome hg19 using Bowtie2 (2.3.5.1) with standard parameters only allowing uniquely aligned reads
Peaks were called against input using MACS2 (2.1.1.20160309)  for H3K27ac and Med1 using broadpeak settings, and CTCF, VDR, P63 using standard peak settings.
BedGraph files were created using HOMER (v4.10.3) using standard parameters.
Super-enhancers are analyzed by Rose software
Assembly: hg19
Supplementary files format and content: bedGraph to be displayed in the UCSC genome browser

source_name: Foreskin

growth_protocol: Primary human keratinocytes (NHK) were isolated from neonatal foreskin and maintained in defined Keratinocyte Serum Free Basal Medium (K-SFM) (Thermo Fisher) supplemented with the growth factors and 0.07 mM CaCl2 (Thermo Fisher). Keratinocytes in third or fourth passages were treated with 0.1% EtOH (vehicle) or 1,25D3 (1 x 10 -7 M) for 4 hr and used for Chip-seq studies

extract_protocol:
Dissected CLH or CLT tissues were homogenized and cross-linked with 1% paraformaldehyde for 8 min (H3K27ac) or for 15 min (MED1), sonicated using a ultrasonicator (Covaris) to obtain DNA fragments with an average length of 300±50 bp. Sheared chromatin was thereafter immunoprecipitated with Protein A-coated magnetic beads (Diagenode) preincubated with 4.5 microgram/IP MED1 antibody (Bethyl A300-793A) or 3 ug/IP H3K27ac antibody (ab4729, Abcam). Chromatin input samples were used as reference. Complexes were then washed and eluted from the beads with washing buffer and crosslinks were reversed by incubation at 65°C for 4 hours. Immunoprecipitated DNA along with genomic DNA (Inputs) were purified using the IPure v2 kit (Diagenode). IP efficiency was confirmed by qPCR using primers provided in the kits. Experiments were carried out in duplicates.
ChIP-Seq libraries were generated using the Accel-NGS 2S Plus DNA library kits (Swift Sciences) and amplified by PCR for 11-13 cycles. High molecular weight smear was removed in the library by right side size selection using SPRI beads (Beckman Coulter). The libraries were quantified by Agilent 2100 Bioanalyzer with the high sensitivity DNA assay and sequenced on an Illumina HiSeq 4000 (UCSF Center of advanced technology) in a single strand 50 bp run.

treatment_protocol: Cultured keratinocytes were treated with vehicle (EtOH) or 1,25D3 (1x 10 -7M) for 4hr

value: Foreskin

value: cultured keratinocyte

tag: chip antibody


title: K3P H3K27ac D3 rep1

value: H3K27ac Abcam ab 4729 lot GR3211959-1


title: MCF7 cells cultured in 5.6 mM glucose  (set 2)

description: Gene expression after MCF7 cells clutured in 5.6 mM glucose


title: MCF7 cells cultured in 5.6 mM glucose and 25 nM insulin (set 2)

description: Gene expression after MCF7 cells clutured in 5.6 mM glucose and 25 nM insulin ofr 72 hrs


title: MCF7 cells cultured in 30 mM glucose and 25 nM insulin (set 1)

description: Gene expression after MCF7 cells clutured in 30 mM glucose and 25 nM insulin


title: SAT24

description: 10X Genomics 3' V2


title: MCF7 cells cultured in 30 mM glucsoe  (set 2)


title: MCF7 cells cultured in 5.6 mM glucose  (set 1)


title: MCF7 cells cultured in 5.6 mM glucose and 25 nM insulin (set 1)


title: POX02968S

growth_protocol:
Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: SAT19

description: 10X Genomics 3' V2


title: SAT23

description: 10X Genomics 3' V2


title: POXKu70_12

description: The deletion mutant of POXKu70 gene is the control strain for differential transcriptome analysis, and cultured in induced carbon source


title: K3P Med1 D3 rep1


title: 3RNA-IHB11_sorted

value: Breast Cancer

value: 8hr stimulation with IFNgamma and TNF


title: POX02968F


title: MCF7 cells cultured in 30 mM glucose and 25 nM insulin (set 2)


title: K3P CTCF D3 rep2


title: POXKu70_11


title: 3RNA-IHB8_sorted


title: SAT18

description: 10X Genomics 3' V2


title: SAT20

description: 10X Genomics 3' V2


title: POXOES1167T

description: A mutant that overexpresses the POX01167 gene using its own promoter, and cultured under induced carbon.

growth_protocol:
Mycelium of 1 gram Mutant OES1167 were cultured in 2% Avicel liquid medium for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.


title: POXOES1167S


title: K3P p63 D3 rep2

value: p63 Cell signaling D2K8X lot 3


title: SAT17

description: 10X Genomics 3' V2


title: K3P CTCF D3 rep1


title: 3RNA-IHB12_sorted


title: 3RNA-IHB6_sorted

value: Unstimulated


title: K3P p63 D3 rep1


title: 3RNA-IHB7_sorted


title: SAT15

description: 10X Genomics 3' V2


title: POXOES1167F


title: 3RNA-IHB5_sorted


title: 3RNA-IHB2_sorted


title: 203 µM 1

city: Urbana

first: Hua

state: IL

address: 202 MSE Building, 1304 West Green Street

institute: University of Illinois at Urbana Champaign

data_processing:
Sequenced reads were pseudo-aligned to NCBI’s Mus musculus Annotation Release 109 transcripts  using Salmon (v1.10.0) and the GRCm39 genome as the decoy sequence and with the following options: --seqBias --gcBias  --numBootstraps=30 --validateMappings --recoverOrphans.
The transcript-levels counts were then read into R (v.4.3.0) and gene-level counts were calculated using the "lengthScaledTPM" method from the tximport package (v1.28.0)
Assembly: GRCm39, NCBI Annotation Release 109
Supplementary files format and content: Wang_Salmon_gene-level_counts.txt : gene level annotations and counts in tab-delimited text format

growth_protocol: Mouse bone marrow cells were maintained in RPMI 1640 supplemented with 10% FBS, 100 units/mL Penicillin/Streptomycin, 50 µM 2-mercaptoethanel, and 10 ng/mL GM-CSF with 5% CO2 at 37C

extract_protocol:
RNA was extracted with RNeasy Plus kit from Qiagen
RNA libraries for RNA-Seq were constructed with the Kapa Hyper Stranded mRNA Sample Prep kit

treatment_protocol: Mouse bone marrow-derived dendritic cells were placed in the culture medium with 200 µM Ac4ManNAz for 72 hours

value: Bone marrow

value: WT


title: K3P p63 Veh rep2

value: Vehicle


title: 202 µM 1

value: Mouse bone marrow-derived dendritic cells


title: SAT13

description: 10X Genomics 3' V2


title: SAT14

description: 10X Genomics 3' V2


title: 3RNA-IHB1_sorted


title: K3P p63 Veh rep1


title: SAT12

description: 10X Genomics 3' V2


title: SAT11

description: 10X Genomics 3' V2


title: K3P VDR D3 rep3

value: VDR Santa Cruz C-20 lot J2309


title: 200 µM 1


title: IRF1-SOCS1-KO-2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were trimmed for adaptor sequence using Ngmerge, then mapped to the mm10 genome with bowtie2
Peaks were called with Macs2
Assembly: mm10
Supplementary files format and content: Peak files called with macs2

extract_protocol:
Gene edited AT-3 breast cancer cells lysed using the ZYMO research DNA isolation kit. Tagmentation then purification was performed on DNA, and isolated chromatin was amplified.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.

value: IRF1 and SOCS1 KO

value: stimulation with IFNgamma and TNF


title: K3P VDR D3 rep2


title: 201 µM 1


title: IRF1-SOCS1-KO-1


title: SAT10

description: 10X Genomics 3' V2


title: Control 4

value: PBS


title: PAS-seq_HepG2_JTE-607_2

data_processing:
(1). MPIVA: All MPIVA read 1 and read 2 FASTQ files were merged using bbmerge V38 using option ` maxloose=t`.
(1). MPIVA: MPIVA Input samples were used establish the sequences of the full randomized PAS region contained in the IVT pool by clustering the 25 nt randomized region with starcode version 1.4. The expected cleaved lengths of the 25 nt consensus sequences for L3 and SVL backbones (13 nt and 12 nt, respectively) were used as unique identifiers of the full randomized region. If any of these identifiers were not unique within L3 and SVL libraries, respectively, then these sequences were not used in subsequent analyses.
(1). MPIVA: RNA-seq reads from DMSO and drug-treated libraries were locally aligned against the shared 5′ region of the reporter constructs to determine the beginning of the randomized region. The part of the RNA-seq read containing the randomized region and shared 3′ region was locally aligned against the list of consensus sequences from the Input libraries.
(1). MPIVA: Sequences with at least 50 reads in the DMSO libraries were kept to avoid noise from lowly abundant RNA sequences in the IVT pool.
(1). MPIVA: A pseudocount of 1 was added to variants in L3 2.5 µM, L3 12.5 µM, and SVL 12.5 µM due to drug-mediated drop out of high abundance variants in the DMSO libraries. This pseudocount avoids having undefined drug sensitivities in later steps that would be introduced by log(0).
(1). MPIVA: Each variant that passed these filters were counted and converted to a percentage within each RNA-seq library.
(1). MPIVA: Drug sensitivity for each variant in each dose of Compound 2 was defined as the log ratio of normalized reads from drug-treated RNA-seq divided by the normalized reads from DMSO-treated RNA-seq.
(2). 4sU-seq: Reads were mapped to human(hg19) genome using STAR. Multi-mapping was not allowed. Mapped reads were converted to bigwig files using deepTools.
(3). PAS-seq: Reads that lack a poly(A) tail (15 consecutive As) were removed with python script. The trimmed reads were mapped to human (hg19) genome using STAR.
(3). PAS-seq: Removed internal priming reads (reads that are mapped to genomic sequences that are immediately followed by 6-consecutive As, or seven As out of 10 nucleotides)
(3). PAS-seq: Reads were converted to BigWig files using deepTools
Assembly: hg19
Supplementary files format and content: (1). MPIVA: TSV file containing log ratio of different concentrations of Compound 2 vs DMSO in both L3 and SVL backbone and their sequences.
Supplementary files format and content: (2). 4sU-seq and (3). PAS-seq: BigWig files.
Library strategy: PAS-seq

source_name: liver

value: liver

value: human liver carcinoma cell

value: mRNA


title: Control 3


title: K3P VDR Veh rep3

value: Foreskin

value: cultured keratinocyte


title: PAS-seq_HepG2_JTE-607_1


title: K3P VDR D3 rep1


title: Control 2


title: K3P VDR Veh rep2

value: VDR Santa Cruz C-20 Lot J2309


title: PAS-seq_HepG2_DMSO_2

value: DMSO


title: SOCS1-KO-1

value: Breast Cancer


title: Control 1


title: IRF1-KO-2


title: K3P VDR Veh rep1


title: PAS-seq_HepG2_DMSO_1


title: IRF1-KO-1


title: Mock-2

value: Mock edited