title: HEK293, Treatment, rep2

description:
Results_TPM_counts_CCD841_Untreated_vs_Treatment.xlsx
Results_TPM_counts_HEK_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_HEK_Positive_ctrl_vs_Treatment.xlsx
HEK293_DHX40_2_S11

value: immortalized human embryonic kidney cells


title: wtglu20min+A 1

status: Public on Nov 08 2023

type: SRA

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

country: China

institute: the institute of microbiology chinese academy of sciences

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to H99 whole genome using STAR 2.7.7a with parameters  STAR --runMode genomeGenerate --runThreadN 8  --genomeDir index/  --genomeFastaFiles $king/1_data/fa/H99.fasta  --sjdbGTFfile $king/1_data/gtf/H99.gtf  --sjdbOverhang 134  --genomeSAindexNbases 11;  STAR --runThreadN 8  --genomeDir index/   --outFileNamePrefix ./ --readFilesIn $king/${a}_R1.paired.fq.gz $king/${a}_R2.paired.fq.gz --readFilesCommand zcat    --outFilterTy --alignMatesGapMax 1000000pe BySJout  --outFilterMultimapNmax 10  --alignSJoverhangMin 5 --alignSJDBoverhangMin 3  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --outSAMtype SAM --outSAMattributes NH HI AS nM NM XS --quantMode GeneCounts; STAR --runThreadN 8   --genomeDir index/ --outFileNamePrefix ./ --readFilesIn $king/${a}_R1.paired.fq.gz $king/${a}_R2.paired.fq.gz --readFilesCommand zcat  --sjdbFileChrStartEnd $sjFileList  --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 5  --alignSJDBoverhangMin 3  --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --outSAMtype SAM --outSAMattributes NH HI AS nM NM XS --quantMode GeneCounts
Gene  were calculated using htseq 0.6.0 with parameters htseq-count -s reverse ./${a}_filtered.sam  ../1_data/gtf/H99.gtf > ./${a}_2.count
Assembly: H99

molecule: total RNA

organism: Cryptococcus neoformans H99

source_name: wild type

growth_protocol: 50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 OD600, transferred into YPD, YPG liquid medium with or without AmB treatment (10xMIC), cultured in 37℃ 5% CO2 for 10, 20 30min.

extract_protocol:
Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.
Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.

tag: strain

tag: age

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C

tag: genotype

value: wild type


title: mig1gal20min-A 1

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C


title: shoot-N_K4me3, Rep1

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

country: USA

institute: Purdue University

library_source: genomic

data_processing:
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were converted to fragments and dynamic islands were called using SICER-df.
RNA-Seq data was trimmed using CutAdapt and aligned using TopHat2. The gene counts were generated from mapped reads using htseq and counts were normalized with EDAseq, while differentially expressed genes were determined using DESeq2.
Genome_build: SL4.0
Supplementary_files_format_and_content: raw_counts.txt, SICER-df output files

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: shoot

growth_protocol: Plants were germinated on 1/2 strength MS plates and then transferred to a hydroponic system under greenhouse conditions.

extract_protocol:
Two grams of tissues were fixed with 1% formaldehyde by applying vacuum at 700 mmHg for 25 min. Fixation was terminated by adding 2M glycine to a final concentration of 0.125M and vacuum application for 5 minutes. Formaldehyde-fixed tissues were ground in liquid nitrogen and nuclei were isolated. Isolated nuclei were sonicated using Bioruptor to prepare chromatin samples with single nucleosomes.
Chromatin immunoprecipitated using Protein A dynabeads with antibodies against histone marks or input chromatin was recovered and reverse-crosslinked. Libraries were prepared using NEBNext dual index library kit.

treatment_protocol: Twenty-two day old plants were transferred to nitrogen free media for four days and then either replenished with fresh nitrogen free media (-N condition) or resupply of media containing nitrate (+N condition). After 6 hours of treatment, -N and +N samples were harvested.

tag: cultivar

tag: tissue

value: shoot

tag: treatment

value: -N

tag: chip antibody


title: mig1glu20min-A 3


title: HEK293, Treatment, rep1

city: Helsinki

first: Alisa

last: Olkinuora

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Results_TPM_counts_CCD841_Untreated_vs_Treatment.xlsx
Results_TPM_counts_HEK_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_HEK_Positive_ctrl_vs_Treatment.xlsx
HEK293_DHX40_1_S10

data_processing:
RNAseq data was quantified and aligned by using Salmon and STAR.
Differential transcript and gene expression data generated using the Fishpond R pacakge.
Novel splice events were called using ASGAL.
Assembly: GRCh38
Supplementary files format and content: Fishpond-generated differential experssion analysis results are given in accompanying tab-delimited Excel-tables.

organism: Homo sapiens

source_name: immortalized human embryonic kidney cells

extract_protocol:
RNA was extracted using NucleoSpin® RNA extraction kit with DNAse(Macherey-Nagel, Düren, Germany). 300ng of RNA was used for library prep.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit

tag: cell line

tag: cell type

value: normal

value: DHX40 knockdown

value: Treatment

tag: replicate


title: HEK293, Negative_ctrl, rep3

description:
Results_TPM_counts_HEK_Negative_ctrl_vs_Positive_ctrl.xlsx
HEK293_nonT3_S9

value: Non-Target knockdown


title: mig1glu20min-A 2


title: root+N_K4me3, Rep2

source_name: root

value: root

value: +N


title: Head_RNA_BD10-3

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Parental photoperiod: White-light: darkness = 12 h: 12h; Parental age after eclosion: 3 days

data_processing:
After removing adaptors and low-quality bases by fastp (version 0.20.1), the resulting reads no less than 50 bp were mapped to the Drosophila melanogaster reference genome (FB2021_02) released by FlyBase database (http://flybase.org/).
The featureCounts program within SourceForge Subread package (version 2.0.2) was used for counting the reads that mapped to genes.
The genes with an average read count less than 10 in any group or lacking read count in any replicate were primarily filtered.
R package DESeq2 (version 1.30.0) was used for the identification of differentially expressed genes (DEGs) by setting false discovery rate corrected P-value (FDR) < 0.05 and fold change >= 2 as the thresholds of significance (Supplementary Table S2), and the read count normalization across samples by size factors.
t-SNE dimension reduction analysis was performed using R (version 4.0.3) package Rtsne (version 0.15); heatmap was generated using R package pheatmap (version 1.0.12); common and unique DEGs were visualized in a Venn diagram generated using R package VennDiagram; volcano plot was generated using R package ggplot2; GO (Gene Ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the DEGs were performed using either Metascape (version 3.5) (https://metascape.org/) or R package clusterProfiler (version 3.18.1);  Gene set enrichment analysis (GSEA) software (version 4.2.0) was used for determining the statistical significance of priori defined gene sets.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data of w1118 male adult heads.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Male adult heads

growth_protocol: We collected the eggs oviposited by 3-day-old Drosophila melanogaster w1118 adults which were colonized under the photoperiodic cycles of 12 h white fluorescent light: 12 h darkness (LD) after eclosion. These eggs were grown on standard mediums (comprised of 80 g cornmeal, 125 g sucrose, 16 g yeast, and 5 g agar/L) under the photoperiodic cycles of LD until one day after eclosion.

extract_protocol:
Total RNAs were isolated and dissolved in RNase-free water after the bulk samples had been homogenized in 0.5–1 mL TRIzol AG RNAex Pro Reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) with glass beads using a homogenizer.
Poly-A RNAs were purified from the extracted total RNAs using Dynabeads™ Oligo(dT)25 (#61002, Invitrogen, CA, USA) and were further fragmented as ~350 nt fragments using NEBNext® Second Strand Synthesis (dNTP-Free) Reaction Buffer (#B6117S, New England BioLabs, MA, USA). Strand-specific sequencing libraries were conducted using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, New England BioLabs) according to the manufacturer's protocols including first- and second-strand cDNA synthesis, adaptor ligation, and library amplification with index sequences.

treatment_protocol: We transferred these 1-day-old adults to a climatic chamber under the photoperiodic cycles of BD and DD, respectively. We collected the bulk 10- and 25-day-old male adult heads (BD10, BD25, DD10, and DD25) for poly-A RNA-seq.

tag: photoperiod

value: Blue-light:darkness = 12 h:12h

tag: age after eclosion

value: 10 days


title: root+N_K4me3, Rep3


title: HEK293, Negative_ctrl, rep2

description:
Results_TPM_counts_HEK_Negative_ctrl_vs_Positive_ctrl.xlsx
HEK293_nonT2_S8


title: Head_RNA_BD10-1


title: mig1glu20min-A 1


title: Head_RNA_BD10-2


title: HEK293, Negative_ctrl, rep1

description:
Results_TPM_counts_HEK_Negative_ctrl_vs_Positive_ctrl.xlsx
HEK293_nonT1_S7


title: root+N_K4me3, Rep1


title: HEK293, Positive_ctrl, rep3

description:
Results_TPM_counts_HEK_Untreated_vs_Positive_ctrl.xlsx
HEK293_GAPDH3_S6

value: GAPDH knockdown


title: FecB ++ sheep in the luteal phase-3

city: Yangzhou

first: Weihao

last: Chen

address: 88 Daxuenan Rd.

institute: Yangzhou University

data_processing:
The raw reads in FASTQ format were filtered using fastp  to remove low-quality reads containing poly-N, adapters, or poly A, T, C, or G sequences. The obtained clean reads were mapped to the Ovis aries reference genome (Oar_v3.1) using HISAT2.
Coding and non-coding RNAs transcripts were distinguished using Coding-Non-Coding Index (CNCI) , Coding Potential Calculator 2 (CPC2) , and Protein Families database (Pfam)  software. StringTie was used to assemble the mRNA transcripts.
The fragments per kilobase per million mapped reads (FPKM) method was used to estimate the expression levels of lncRNA and mRNA transcripts.
Assembly: Oar_v3.1
Supplementary files format and content: text file include FPKM values for each samole

organism: Ovis aries

source_name: oviduct

extract_protocol:
Total RNA was extracted from the stored oviduct tissues with TRIzol reagent. 1.3ug of extracted RNA was used for library construction.
RNA libraries were constructed using an NEBNext® Ultra™ RNA Library Prep Kit (NEB, Ipswich, MA, USA) for Illumina® according to the manufacturer’s recommendations.

tag: phase

value: luteal

value: oviduct

value: WT


title: wtgal20min-A 2


title: wtgal20min-A 3


title: FecB ++ sheep in the luteal phase-2


title: HEK293, Positive_ctrl, rep2

description:
Results_TPM_counts_HEK_Untreated_vs_Positive_ctrl.xlsx
HEK293_GAPDH2_S5

value: immortalized human embryonic kidney cells


title: Head_RNA_BD25-1

value: 25 days


title: root-N_K4me3, Rep2


title: FecB ++ sheep in the luteal phase-1


title: root-N_K4me3, Rep3


title: HEK293, Positive_ctrl, rep1

description:
Results_TPM_counts_HEK_Untreated_vs_Positive_ctrl.xlsx
HEK293_GAPDH1_S4


title: shoot+N_K36me3, Rep3


title: root-N_K4me3, Rep1


title: wtgal20min-A 1

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C

value: wild type


title: FecB ++ sheep in the follicular phase-3

value: follicular


title: wtglu20min-A 3

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: FecB ++ sheep in the follicular phase-2


title: shoot+N_K36me3, Rep2

value: shoot


title: wtglu20min-A 2


title: wtglu20min-A 1


title: FecB ++ sheep in the follicular phase-1


title: shoot+N_K36me3, Rep1


title: HEK293, Untreated, rep2

description:
Results_TPM_counts_HEK_Untreated_vs_Negative_ctrl.xlsx
HEK293_UT2_S2

value: normal

value: Untreated


title: HEK293, Untreated, rep1

description:
Results_TPM_counts_HEK_Untreated_vs_Negative_ctrl.xlsx
HEK293_UT1_S1


title: FecB BB sheep in the luteal phase-3

value: MUT


title: mig1gal10min+A 3


title: HCC_T_4HT1

city: Bethesda

first: Amanda

last: Craig

state: Maryland

address: 37 Convent Dr. Bld.37/Rm.3044

institute: National Institutes of Health

description: 10x Genomics

library_source: genomic single cell

data_processing:
Data processing was performed in concordance with the published Satpathy & Granja et al. pipeline, (https://github.com/GreenleafLab/10x-scATAC-2019). Beginning with the fragment files generated from the cellranger pipeline, cells with less than 1,000 unique fragments were removed. Transcription start site (TSS) enrichment scores were calculated at previously described. TSS sites were acquired from the Bioconductor package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’. Cells with a TSS enrichment score lower than 8 were also excluded from further analysis. Next, overlaps of Tn5 insertions with 2.5kb windows were found to create a cell by window sparse matrix. This matrix was binarized and filtered to include only the 20,000 most accessible sites. Normalization and dimension reduction (retaining top 50 dimensions) as performed using Latent Semantic Indexing (LSI), which includes calculating the term frequency-inverse document frequency (TF-IDF) transformation followed by singular value decomposition (SVD) using the Seurat R package v3.1.430. Initial graph-based clustering was also done using the Seurat package, including dimensions 2 to 25 and a resolution of .8x N, with N representing the number of iterations needed to create clusters of a minimum size of 200 cells. Dimension 1 was omitted as it reflected cell read depth.
ATAC peaks were next called from the grouped cells from each cluster using the MACS2 callpeak command with parameters ‘–shift -75–extsize 150–nomodel–call-summits–nolambda–keep-dup all -q 0.05’. The peak summits were then extended by 150bp on either, filtered by the ENCODE hg38 blacklist (https://sites.google.com/site/anshulkundaje/projects/blacklists) and then filtered to remove peaks that extended beyond the ends of chromosomes. To create a union peak set across all cells from all samples, an iterative process of finding overlapping peaks and discarding all but the most significant peak coordinates was performed, first across all cells within each cluster, and then across all cells from all samples.
Gene activity scores were calculated using the Signac R package v1.0.0 using the GeneActivity function.
Transcription factor (TF) motif activity scores were calculated using the ChromVAR R package.
Assembly: GRCh38
Supplementary files format and content: comma-separated values files and matrix files

source_name: Liver

extract_protocol:
Nuclei isolation was performed following the 10x Genomics protocol (Nuclei isolation for single cell ATAC sequencing, revision D). Cells were briefly thawed in a 37 °C water bath and resuspended in 10ml RPMI media supplemented with 10% FBS. After centrifugation at 300 rcf for 5 minutes, the supernatant was removed, and the cell pellet was resuspended in 1ml PBS supplemented with 0.04% BSA and passed through a 40 mm cell strainer. Sample concentration and viability were assessed using the LunaFL fluorescent cell counter. Cells were again centrifuged at 300 rcf for 5 minutes at 4 °C and resuspended in 50ml PBS + 0.04% BSA. After an additional spin at 300 rcf for 5 minutes at 4 °C, 45ml of the supernatant was removed and 45ml of chilled lysis buffer was added to the cell pellet. Cells were incubated in lysis buffer for 20 minutes on ice, after which 50ml of chilled wash buffer was added, and cells were centrifuged at 500 rcf for 5 minutes at 4 °C. 95ml of the supernatant was removed, and nuclei were resuspended in 45ml of chilled 10x Genomics diluted nuclei buffer. After a final centrifugation at 500 rcf for 5 minutes at 4 °C the supernatant was removed, and nuclei were resuspended in a final volume of 7ml of chilled 10x Genomics diluted nuclei buffer.
Nuclei were loaded according to the 10x ATAC User guide with a single capture lane per sample. Transposition and nuclei partitioning were completed successfully with uniform emulsion consistency and the GEM incubation PCR was run overnight. All subsequent steps of library preparation and quality control were performed as described in the 10X Genomics ATAC User Guide.

value: Tumor

value: Liver

value: Male


title: mig1gal10min+A 2


title: shoot-N_K36me3, Rep3

value: -N


title: FecB BB sheep in the luteal phase-2

value: luteal


title: mig1gal10min+A 1


title: FecB BB sheep in the luteal phase-1

value: oviduct


title: shoot-N_K36me3, Rep1


title: HEK293, Untreated, rep3

description:
Results_TPM_counts_HEK_Untreated_vs_Negative_ctrl.xlsx
HEK293_UT3_S3

value: WT


title: FecB BB sheep in the follicular phase-3


title: HCC_T_H77

description: 10x Genomics


title: HCC_T_2HT1

description: 10x Genomics

value: Female


title: shoot-N_K36me3, Rep2


title: HCC_T_1HT1

description: 10x Genomics


title: root+N_K36me3, Rep3

value: root

value: +N


title: HCC_T_H70

description: 10x Genomics


title: mig1glu10min+A 3


title: root+N_K36me3, Rep2


title: mig1glu10min+A 2


title: FecB BB sheep in the follicular phase-2


title: HCC_T_H69

description: 10x Genomics


title: wtgal10min+A 3

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C

value: wild type


title: mig1glu10min+A 1

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: root-N_K36me3, Rep2


title: wtgal10min+A 2


title: sorted splenic Ikzf1 KO NK cells, rep 3

city: Monash University

first: Harrison

last: Sudholz

state: VIC

address: 15 Innovation walk

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Single-end 75bp reads were aligned to mm10 Gencode version M16 (Ensembl 91) using the STAR aligner.
Genewise counts were obtained using featureCounts. Genes with counts-per-million (CPM) greater than 0.5 in at least three biological replicates were retained in the downstream analysis.
The gene expression values were TMM normalized.
Differentially expressed genes were determined by voom-limma using voomWithQualityWeight() function. Genes were called differentially expressed if they achieved an adjusted-value of less than 0.05.
Pathway enrichments and gene set tests were carried out using limma package (v. 3.34.9), and sample scoring was performed using the singscore method (v.1.14)
Assembly: mm10
Supplementary files format and content: RPKM file
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA from sorted NK cells was extracted using a RNeasy Plus Mini Kit (QIAGEN), according to the manufacturer’s protocol. RNA samples were quantified using the Agilent 2200 TapeStation System (Agilent).
Next-generation sequencing libraries were prepared with quality-controlled RNA samples (RIN > 7.0) from at least three biological replicates per genotype using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). cDNA libraries were pooled and subjected to 75 bp single end sequencing at the WEHI Genomics Laboratory on a NextSeq 500 next-generation sequencer (Illumina) to obtain approximately 20 million reads per sample.

value: spleen

value: Ikzf1 KO

value: NK cells were sorted and RNA isolated prior to processing for sequencing


title: wtgal10min+A 1


title: sorted splenic Ikzf1 KO NK cells, rep 2


title: HCC_T_H63

description: 10x Genomics


title: HCC_T_H62

description: 10x Genomics


title: sorted splenic Ikzf1 KO NK cells, rep 1


title: sorted splenic Cre only NK cells, rep 3

value: Cre only


title: HCC_T_H58

description: 10x Genomics

value: Tumor


title: wtglu10min+A 3


title: sorted splenic Cre only NK cells, rep 2


title: wtglu10min+A 2


title: wtglu10min+A 1


title: root-N_K36me3, Rep3


title: sorted splenic Cre only NK cells, rep 1


title: HCC_T_H30

description: 10x Genomics

value: Liver


title: shoot+N_K27me3, Rep2

value: shoot


title: HCC_T_H38

description: 10x Genomics

value: Male


title: shoot-N_K27me3, Rep3

value: -N


title: shoot+N_K27me3, Rep3


title: shoot+N_K27me3, Rep1


title: root+N_K36me3, Rep1


title: HCC_T_H23

description: 10x Genomics


title: sorted splenic Cre only NK cells, cultured, rep 4

value: NK cells were sorted and maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM GlutaMAX (GIBCO), 50 mM b-mercaptoethanol (b-ME, Sigma-Aldrich), 50 ng/ml recombinant hIL-15 (rhIL-15; Miltenyi Biotec), 100 mg/ml streptomycin and 100 IU/ml penicillin (Sigma-Aldrich)


title: HCC_T_H65

description: 10x Genomics


title: FecB BB sheep in the follicular phase-1

value: follicular

value: oviduct

value: MUT


title: mig1gal10min-A 2


title: sorted splenic Cre only NK cells, cultured, rep 3


title: root-N_K36me3, Rep1

value: root


title: CCA_T_C60

description: 10x Genomics

source_name: Bile Duct

value: Bile Duct

value: Female


title: shoot-N_K27me3, Rep2


title: sorted splenic Cre only NK cells, cultured, rep 2


title: mig1gal10min-A 1

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C


title: CCA_T_C56

description: 10x Genomics


title: mig1gal10min-A 3


title: mig1glu10min-A 3

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: CCA_T_C39

description: 10x Genomics


title: root+N_K27me3, Rep3

value: +N


title: root+N_K27me3, Rep2


title: mig1glu10min-A 2


title: sorted splenic Ikzf1 KO NK cells, cultured, rep 4

value: spleen

value: Ikzf1 KO


title: root+N_K27me3, Rep1


title: mig1glu10min-A 1


title: wtgal10min-A 3

value: wild type


title: sorted splenic Ikzf1 KO NK cells, cultured, rep 2


title: root-N_K27me3, Rep2


title: sorted splenic Ikzf1 KO NK cells, cultured, rep 1


title: PRO-seq data for MEDOE in MED30 overexpression Mia PaCa-2 cells, no Dox replicate #2

city: La Jolla

first: Guofeng

last: Zhao

address: 9500 Gilman Dr.

department: Medicine

institute: UCSD

description: nascent RNA

data_processing: Data were aligned to human genome hg38 and drosophila genome dm3 by Bowtie2. Normalized signal was calculated by Bamcoverage with separation of forward and reverse strand, and setting “1” as “offset inside each alignment to use for the signal location”. For calculating MED30 bound or non-bound promoters, -2000bp to TSS region BED file (~170 000 regions) was generated by ncbiRefSeq from UCSC genome browser, and overlapped with MED30 ChIP-seq peaks, resulting in 58801 overlapped regions out of ~170000 regions total. The rest ~110000 TSS regions were seen as non-bound. 1/50 random TSS for these two groups were selected for further heatmap analysis to reduce the file size. Gene expression counts were calculated by analyzeRepeats.pl (http://homer.ucsd.edu/homer/ngs/analyzeRNA.html), and subjected to Deseq2 analysis for identifying different expressed genes and size factor. For heatmap, PRO-seq signal density from -3000bp to +10000bp region relative to TSS was calculated by scaling of drosophila spike-in size factor.

source_name: Mia PaCa-2 cell

extract_protocol: For nuclei isolation, cells were incubated with swelling buffer (10 mM Tris-Cl pH 7.5, 2 mM MgCl2 and 3 mM CaCl2) for 5 min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100 μl of freezing buffer (50 mM Tris-Cl pH 8.0, 40% glycerol, 5 mM MgCl2 and 0.1 mM EDTA). For the run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM dithiothreitol, 20 units of SUPERase•In, 1% sarkosyl, and 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30 °C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (10296010, Invitrogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (88816, Thermo Fisher). Purified RNA was treated with PNK before being used for complementary DNA synthesis by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina Kit (E7300S, NEB). Obtained complementary DNA template was amplified by PCR using the Phusion High-Fidelity enzyme (M0530L, NEB) for deep sequencing.

value: Mia PaCa-2 cell


title: PRO-seq data for Ctrl in MED30 overexpression Mia PaCa-2 cells, no Dox replicate #1

description: nascent RNA


title: root-N_K27me3, Rep3


title: PRO-seq data for MED30 OE in MED30 overexpression Mia PaCa-2 cells, no Dox replicate #1

description: nascent RNA


title: wtgal10min-A 2


title: PRO-seq data for Ctrl in MED30 overexpression Mia PaCa-2 cells, no Dox replicate #2

description: nascent RNA


title: root-N_K27me3, Rep1


title: wtgal10min-A 1


title: wtglu10min-A 3


title: shoot-N_K27me3, Rep1

value: shoot


title: sorted splenic Ikzf1/Ikzf3 DKO NK cells, cultured, rep 3

value: Ikzf1/Ikzf3 KO


title: sorted splenic Cre only NK cells, cultured, rep 1

value: Cre only


title: shoot+N_K27ac, Rep3


title: RNAseq data in teton MED30 overexpression Mia PaCa-2 cells, +Dox replicate #1

data_processing: Following sequencing, quality control with FastQC and trimming of adaptor sequence and poly-A tails with Trim Galore, reads were mapped and assigned to the human transcripts using HISAT2. The counts file was generated by “featureCounts” on Galaxy (usegalaxy.org) with build-in genome hg38. Differential expression gene (DEG) analysis was performed using the DESeq2 package in Galaxy.

extract_protocol: RNA was extracted by Trizol (Life Technologies) RNA concentration and quality was quantified by Qubit and Agilent 2100 Bioanalyzer system, respectively. Libraries were generated using NEBNext Ultra II RNA Kits (NEB) and sequenced on the NovaSeq 6000 with 100 bp paired-end reads.


title: sorted splenic Ikzf1/Ikzf3 DKO NK cells, cultured, rep 2

value: NK cells were sorted and maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM GlutaMAX (GIBCO), 50 mM b-mercaptoethanol (b-ME, Sigma-Aldrich), 50 ng/ml recombinant hIL-15 (rhIL-15; Miltenyi Biotec), 100 mg/ml streptomycin and 100 IU/ml penicillin (Sigma-Aldrich)


title: wtglu10min-A 2


title: RNAseq data in teton MED30 overexpression Mia PaCa-2 cells, no Dox replicate #2


title: sorted splenic Ikzf1 KO NK cells, cultured, rep 3


title: sorted splenic Ikzf1/Ikzf3 DKO NK cells, cultured, rep 1


title: shoot+N_K27ac, Rep2


title: wtglu10min-A 1


title: sorted splenic Ikzf3 KO NK cells, cultured, rep 4

value: Ikzf3 KO


title: RNAseq data in teton MED30 overexpression Mia PaCa-2 cells, no Dox replicate #1


title: sorted splenic Ikzf3 KO NK cells, cultured, rep 3


title: shoot-N_K27ac, Rep3

value: -N


title: RNAseq data in teton shMED30 Mia PaCa-2 cells, +Dox replicate #2


title: WT_22DPA_IP_ Rep1

city: Beijing

first: Xiaojing

last: Li

state: Beijing

address: No.20 Nanxincun, Xiangshan, Beijing

department: Institute of Botany

institute: Chinese Academy of Sciences

description: grown in a standard greenhouse

data_processing:
The quality of raw sequencing reads in DAP-seq was assessed using FastQC tool (version 0.11.5). The remaining reads were analyzed by using FastQC tool once again to ensure sufficient quality assessment.
Reads alignment was performed with BWA (version 0.7.15-r1140) by using the strawberry Fragaria_vesca genome_v4.0.a1 as a reference genome.
DAP-seq peaks were identified by MACS2 (version 2.1.1) using default parameters (q-value < 0.05). Only peaks present in both two biological replicates were selected as confident peaks for further analysis.
Assembly: Fragaria_vesca genome_v4.0.a1
Library strategy: DAP-seq

organism: Fragaria vesca

source_name: genomic DNA from  22 DPA WT fruits

extract_protocol:
Total DNA was extracted from fruits of 22 DPA WT fruits using the Hi-DNAsecure Plant Kit (TIANGEN, China). Genomic DNA library was prepared using NEBNext®DNA Library Prep Master Mix Set Kit for Illumina®. FvRIF-HaloTag recombinant protein was purified with HaloTag Beads, and the FvRIF-HaloTag beads mixtures or HaloTag beads (input negative control) were directly used to incubate with the genomic DNA library. After washing five times with PBS buffer, the DNA fragments were eluted from the FvRIF-HaloTag beads by the elution buffer.
DAP-seq library was constructed using KAPA Library Quantification Kit (KAPA, USA) and then subjected to high-throughput sequencing analysis on Illumina Nova S4 (Illumina, USA).

value: Rugen

value: fruits

tag: developmental stage

value: 22 DPA


title: sorted splenic Ikzf3 KO NK cells, cultured, rep 2


title: shoot-N_K27ac, Rep2


title: WT_22DPA_Input

description: grown in a standard greenhouse


title: shoot-N_K27ac, Rep1


title: RNAseq data in teton MED30 overexpression Mia PaCa-2 cells, +Dox replicate #2


title: RNAseq data in teton shMED30 Mia PaCa-2 cells, +Dox replicate #1


title: FvRIF-cr-13_28DPA_Rep3

description: grown in a standard greenhouse

data_processing:
The quality of raw sequencing reads in RNA-seq was assessed using fastp tool. Reads containing ambiguous nucleotides or with a length < 20 nt were filtered out by fastp.
RNA-seq raw reads were mapped to the F. vesca reference genome 4.0 a1 annotation (https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a1) using HISAT2.
Gene expression was shown as fragments per kilobase of exon per million mapped fragments (FPKM) by using featureCounts.
The differentially expressed genes were analyzed using DESeq2 (version 1.22.1) with the P value being corrected by the Benjamini & Hochberg method. Genes with FDR < 0.05 and fold change > 2 were considered as differentially expressed genes.
Assembly: Fragaria_vesca genome_v4.0.a1

source_name: Total RNA from 28 DPA FvRIF-cr-13 fruits

extract_protocol:
Total RNA was extracted from fruits of 28 DPA WT fruits and 28 DPA FvRIF mutants (FvRIF-cr-6 and FvRIF-cr-13 at 28-day postanthesis using the E.Z.N.A. Total RNA Kit (Omega, Bienne, Switzerland).
For library construction, 1 μg RNA was used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the Illumina Nova seq 6000 sequencer with a paired-end read length of 150 bp according to the standard protocols.

value: Ruegen

value: 28 DPA


title: RNAseq data in teton shMED30 Mia PaCa-2 cells, no Dox replicate #2


title: ex vivo expanded splenic Ikzf1 KO NK cells, Ikzf1 ChIP, rep 3

data_processing:
Single-End, 75 bp read in FASTQ files were aligned to mm10 using subread (v ≥ 1.6.3).
Duplicate reads in the resulting BAM files were marked using picard tools (v ≥ 2.18). The aligned reads were sorted and indexed in samtools (v ≥ 1.9). A list of genomic coordinates corresponding to tandom repeats and microsatellite regions was downloaded from ENCODE.
MACS2 (v ≥ 2.1.1) was used to perform peak calling. De-novo bindings were detected using csaw (v. 1.12.0) using a window-based strategy.
Differential binding analysis was done in edgeR (v. 3.20.0) using the Quasilikelihood model to identify genes with differential IKZF1 binding in mutant compared to WT.
BigWig files were generated using Galaxy
Assembly: mm10
Supplementary files format and content: narrow peak files
Supplementary files format and content: BigWig files

growth_protocol: NK cells were expanded in culture (complete IMDM + 50 ng/ml IL-15) to obtain at least 15 x 106 cells per replicate

extract_protocol:
Cells were cross-linked in PBS containing 2% (v/v) formaldehyde and 10% FBS (v/v) for 10 min at room temperature before quenching with 0.65 M glycine. After washing with ice-cold PBS containing 5% (w/v) bovine serum albumin (BSA), cells were lysed in nuclear extraction buffer (50 mM Tris-HCl [pH7.5], 150 mM NaCl, 5 mM EDTA [pH8], 0.5% NP-40, 1% Triton X-100 in H2O) for 5 min at 4ºC. The released nuclear contents were pelleted and resuspended in sonication buffer (20 mM Tris-HCl [pH7.5], 150 mM NaCl, 2 mM EDTA [pH8], 1% NP-40, 0.3% SDS in H2O). Nuclear fractions were sonicated (peak power: 105 W; duty factor: 20%; cycles per burst: 200) for 10 minutes at 4ºC with a Covaris ultrasonicator (Covaris) to obtain DNA fragments of 100-200 bp. Nuclear debris was removed by centrifugation and the cleared supernatant was collected. 1% (v/v) supernatant was set aside as input control and the remaining supernatant was used for ChIP. ChIP was performed with 2 μg anti-IKZF1 (Santa Cruz Biotechnology) in ChIP dilution buffer (20 mM Tris-HCl [pH8], 150 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 1X cOmplete Mini EDTA-free Protease Inhibitor Cocktail (PIC; Roche Diagnostics) for at least 12 hr at 4°C. Immunoprecipitated lysates were incubated with DynaBeads Protein A/G (Thermo Fisher Scientific) for 2 h at 4°C. Bead/antibody/DNA complexes were washed successively in low salt wash buffer (20 mM Tris-HCl [pH8], 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.15% SDS in H2O), high salt wash buffer (20 mM Tris-HCl [pH8], 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.10% SDS in H2O), LiCl Wash Buffer (20 mM Tris-HCl [pH8], 250 mM LiCl, 2 mM EDTA, 1% Triton X-100, 0.10% (w/v) sodium deoxycholate in H2O) and TE Buffer. ChIP DNA elution was achieved by incubating the washed bead/antibody/DNA complexes in elution buffer (100mM NaHCO3 and 1% SDS in H2O) for 45 min at 45°C and harvesting the supernatant after separation with a DynaMag-2 magnet (Thermo Fisher Scientific). Reverse cross-linking of antibody/DNA complexes in the supernatant was achieved after two successive incubations; first with 5M NaCl for at least 12 h at 65°C then with reverse cross-linking buffer (100 mM NaHCO3, 200 mM NaCl, 1% SDS, 0.3 mg/ml Proteinase K in H2O) for 1 h at 55°C. Free DNA obtained after reverse cross-linking was purified using a ChIP DNA Clean and Concentrator Kit (Zymo Research) according to the manufacturer’s protocol.
Libraries were constructed using the TruSeq ChIP Library Preparation Kit according to the manufacturer's guidelines

value: anti-Ikzf1 antibody (sc-13039, Santa Cruz)


title: sorted splenic Ikzf3 KO NK cells, cultured, rep 1


title: root+N_K27ac, Rep3

value: root

value: +N


title: FvRIF-cr-13_28DPA_Rep2

description: grown in a standard greenhouse


title: root+N_K27ac, Rep2


title: RNAseq data in teton shMED30 Mia PaCa-2 cells, no Dox replicate #1


title: ex vivo expanded splenic Ikzf1 KO NK cells, Ikzf1 ChIP, rep 2

value: spleen

value: Ikzf1 KO


title: ChIP-seq data for Myc in teton shMED30 Mia PaCa-2 cells, +dox

data_processing: The sequence tag returned by the Illumina Pipeline was adapter trimmed by Trim Galore and aligned to the hg38 assembly by Bowtie2. For subsequent visualization of ChIP-Seq signal, bigwig files were generated using the DeepTools “bamCoverage” script integrated in Galaxy server using “Normalized to reads per kilobase per million(RPKM)”. DeepTools “computeMatrix”, “plotHeatmap”, and “plotProfile” functions were used to generate heatmaps and profile plots. The data were visualized by preparing custom tracks on the University of California, Santa Cruz (UCSC) genome browser. Peaks were identified by MACS2. Peak file was uploaded to UCSC genome browser aligned with BamCoverage (bigwig) to check the reliability of peak calling. Myc ChIP for Dox-induced shMED30 was called by q<0.1 in MACS2; others were called in default parameters.

extract_protocol: The ChIP-seq DNA library construction was performed using Illumina’s ChIP-seq Sample prep kit or ABclonal’s the Rapid DNA Lib Prep Kit (ABclonal, #RK20200). Library was usually amplified by 14 cycles of qPCR. Constructed libraries were further double size selected between 150-600 bp with AMPure XP (Beckman, #A63881) and sequenced on NovaSeq 6000 with 100 bp paired-end reads at the UCSD IGM Genomics Center.

value: Mia PaCa-2 cell


title: shoot+N_K27ac, Rep1

value: shoot


title: FvRIF-cr-13_28DPA_Rep1

description: grown in a standard greenhouse


title: ex vivo expanded splenic Ikzf1 KO NK cells, Ikzf1 ChIP, rep 1


title: WT_22DPA_IP_ Rep2

description: grown in a standard greenhouse


title: FvRIF-cr-6_28DPA_Rep3

description: grown in a standard greenhouse

source_name: Total RNA from 28 DPA FvRIF-cr-6 fruits


title: root+N_K27ac, Rep1


title: root-N_K27ac, Rep3


title: ex vivo expanded splenic WT NK cells, Ikzf1 ChIP, rep 3

value: WT


title: FvRIF-cr-6_28DPA_Rep2

description: grown in a standard greenhouse


title: ChIP-seq data for Myc in Mia PaCa-2 cells


title: FvRIF-cr-6_28DPA_Rep1

description: grown in a standard greenhouse


title: root-N_K27ac, Rep2


title: ChIP-seq data for MED30 in Mia PaCa-2 cells


title: ex vivo expanded splenic WT NK cells, Ikzf1 ChIP, rep 1


title: WT_28DPA_ Rep3

description: grown in a standard greenhouse

source_name: Total RNA from 28 DPA WT fruits


title: root-N_K27ac, Rep1


title: WT_28DPA_ Rep2

description: grown in a standard greenhouse


title: Cut&Tag  data for H3K4me3 in teton shMED30  Mia PaCa2 cells ,+dox

data_processing: Because the sequencing is deep, the signal is not sparse. Data processing steps are same as ChIP-seq: The sequence tag returned by the Illumina Pipeline was adapter trimmed by Trim Galore and aligned to the hg38 assembly by Bowtie2. For subsequent visualization of ChIP-Seq signal, bigwig files were generated using the DeepTools “bamCoverage” script integrated in Galaxy server using “Normalized to reads per kilobase per million(RPKM)”. DeepTools “computeMatrix”, “plotHeatmap”, and “plotProfile” functions were used to generate heatmaps and profile plots. The data were visualized by preparing custom tracks on the University of California, Santa Cruz (UCSC) genome browser. Peaks were identified by MACS2. Peak file was uploaded to UCSC genome browser aligned with BamCoverage (bigwig) to check the reliability of peak calling. Myc ChIP for Dox-induced shMED30 was called by q<0.1 in MACS2; others were called in default parameters.

extract_protocol:
cells were seeded in 24-well plate at 30-50% confluency, and treated with indicated doxycycline concentration for two days to allow the induction of shRNAs or cDNA plasmid, and the attachment to the well’s bottom. On the day of experiment, cells in culture media were lightly fixed (0.1 % formaldehyde for 2 minutes) for non-histone epitopes or without fixation for histone marks, and quenched glycine of >twice molar concentration of formaldehyde. Next, the cells were washed with PEX buffer (PBS, 2mM EDTA, 0.1% Triton X-100) for 5min thrice, in order to complete remove Mg2+ and permeabilize the cell. Then the cells were blocked by antibody buffer (0.1%BSA, 2mMEDTA) for 10-30min at room temperature, and subjected to primary antibody incubation overnight at 4°C. The antibodies were used as 1:1000 dilution in antibody buffer if not specified. The next day the primary antibody was removed and wash with wash buffer (20mMTrisCl pH7.4, 150mMNaCl, 0.05%Triton X-100) for 5min, and then incubated with secondary antibody 1:2000 diluted in wash buffer for 1h. The secondary antibody contains fluorophore (Alexa FluorTM) so the signal can be checked under microscope. After secondary antibody incubation, cells were washed three times with wash buffer, and then add adapter loaded pAG-Tn5 (purified in-house [3]) in Dig-300 buffer (20mMTrisCl pH7.4, 300mMNaCl, 0.05%Triton X-100) for 1h, followed by three time wash in Dig-300 buffer. Then cells were subjected to tagmentation buffer (10mMMgCl2 in Dig-300 buffer) at 37°C for 1-3h, and terminated and de-crosslinked by adding 7.5ul 0.5MEDTA, 8ul 10%SDS, 0.25ul 20mg/ml proteinase K per 150ul tagmentation buffer in one well and incubated at 65 °C for 30 min, and transferred into Eppendorf tube to avoid evaporation and continue de-crosslinking overnight, followed by DNA purification with DNA purification Kit (Qiagen).
The DNA was eluted and utilized as template for PCR reaction with i7 and i5 dual-index for library construction and sequenced on the NovaSeq 6000 with 100 bp paired-end reads at the UCSD IGM Genomics Center.


title: Limbus_Mouse_L003

city: Houston

first: Isabel

middle: Yi

last: Moreno

state: Texas

address: 4901 Calhoun Rd., Room 2195

department: College of Optometry

institute: University of Houston

data_processing:
RNA-seq fastq data was processed using CLC Genomics Workbench 20 (Qiagen).
Illumina sequencing adaptors were trimmed, and reads were mapped to the Mus musculus reference genome GRCm38 (mm10).
Normalization of RNA-seq data was performed using trimmed mean of M-values.
Top under and overexpressed genes were selected by differential expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each gene, negative values correspond to expression in the limbus

source_name: Limbal Rim

extract_protocol:
Murine corneal buttons and limbal rims were dissected and mRNA was extracted using RNeasy micro kit (Qiagen).
Total RNA libraries were prepared with the QIAseq Stranded Total RNA kit (Qiagen) using 100 ng input RNA.

value: Limbal Rim

value: Wild type


title: Limbus_Mouse_L004


title: ChIP-seq data for MED17 in Mia PaCa-2 cells


title: shoot+N_INPUT, Rep1


title: shoot+N_INPUT, Rep2


title: Cut&Tag  data for H3K4me3 in teton shMED30  Mia PaCa2 cells ,no dox


title: WT_28DPA_ Rep1

description: grown in a standard greenhouse


title: ChIP-seq data for Myc in teton shMED30 Mia PaCa-2 cells, no dox


title: Cut&Tag  data for H3K27Ac in teton shMED30  Mia PaCa2 cells ,+dox


title: Limbus_Mouse_L001


title: shoot-N_INPUT, Rep3


title: Cut&Tag  data for H3K27Ac in teton shMED30  Mia PaCa2 cells ,no dox


title: shoot-N_INPUT, Rep2


title: Cornea_Mouse_L004

source_name: Corneal Button

value: Corneal Button


title: HEV-infected HepaRG (SAMPLE 12), D100 plaque 1

type: RNA

city: Maisons-Alfort

first: Virginie

last: Doceul

address: 7 avenue du Général de Gaulle

country: France

institute: UMR VIROLOGIE INRAE-ANSES-ENVA

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package "GeneGlobe Data Analysis Center" : https://geneglobe.qiagen.com/fr/analyze
For the normalization it uses the average of four housekeeping genes: ACTB, GAPDH, HSP90AB1 and GUSB
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ave Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., HEV-3f/Mock) ratios.

label: SYBR Green

source_name: HepaRG

label_protocol: PCR assays were performed using the Human Type I Interferon Response PCR array (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (Light Cycler 96, Roche) with 45 cycles at 95 oC for 15 seconds and 60 oC for 30 seconds.

growth_protocol: HepaRG were seeded into 6- well plates and cultured in proliferation medium for 2 weeks. Medium was then replaced for 2 extra weeks by “differentiation medium” supplemented with 1.2% DMSO (Sigma-Aldrich).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit including a DNase I treatment step.

treatment_protocol: Two days before infection, differentiation medium was replaced by proliferation medium. Cells were infected overnight with an HEV-3f inoculum diluted in proliferation medium to a final volume of 1ml. The viral suspension was then removed and cells were washed three times in PBS before adding 2 ml of proliferation medium. Every 2 to 3 days, one-half (1 ml) of the culture medium was replaced with fresh growth medium and infection maintained for 100 days. A HEV-3f strain originating from a French patient suffering from acute autochthonous hepatitis E was used (GenBank under accession number JN906974)

value: HepaRG

tag: time

value: 100 days

tag: moi

value: MOI 100

tag: experiment


title: Cut&Tag  data for MED23 in teton shMED30  Mia PaCa2 cells ,+dox


title: ex vivo expanded splenic WT NK cells, Ikzf1 ChIP, rep 2


title: Non-treated HepaRG (SAMPLE 9), D100 plaque 1

description: Control

value: Mock


title: Cornea_Mouse_L003


title: shoot+N_INPUT, Rep3


title: Cut&Tag  data for MED23 in teton shMED30  Mia PaCa2 cells ,no dox


title: root+N_INPUT, Rep3


title: Cornea_Mouse_L002


title: Cut&Tag  data for MED17  in teton shMED30  Mia PaCa2 cells ,+dox


title: Limbus_Mouse_L002


title: Non-treated HepaRG (SAMPLE 8), D100 plaque 1

description: Control


title: root+N_INPUT, Rep2


title: Cornea_Mouse_L001


title: HEV-infected HepaRG (SAMPLE 11), D100 plaque 1

description: Test


title: Cut&Tag  data for MED1 7 in teton shMED30  Mia PaCa2 cells ,no dox


title: root+N_INPUT, Rep1


title: HEV-infected HepaRG (SAMPLE 6), D100 plaque 1

description: Test


title: Cut&Tag  data for MED1 in teton shMED30  Mia PaCa2 cells ,+dox


title: root-N_INPUT, Rep3

value: -N


title: RNA_rWT_M_707-3

city: St. Louis

first: Diana

middle: Christian

last: Beard

state: Missouri

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
Sequence reads were trimmed for adaptors using Trim Galore and filtered for rRNA sequences with Bowtie.
Remaining reads were aligned to the mm9 genome with STAR. Only uniquely mapping reads were converted to BED files and separated by intronic and exonic reads.
Bedtools coverage -counts paramter was used to assess read coverage in genes.
Assembly: mm9

source_name: Cortex

extract_protocol:
RNA was harvested using Allprep DNA/RNA Mini Kit (Qiagen). 250ng of total RNA was used for the construction of sequencing libraries.
RNA was rRNA depleted using NEBNext rRNA Depletion Kit (NEB). RNA libraries for RNA-seq were subsequently prepared using NEBNext Ultra Directional RNA Library Prep Kit with NEBNext Mulitplex Oligos for Illumina (NEB) following manufacturer's protocols.

value: Cortex

tag: strain

tag: Sex

value: Male


title: HEV-infected HepaRG (SAMPLE 5), D100 plaque 1

description: Test


title: Cut&Tag  data for MED1 in teton shMED30  Mia PaCa2 cells ,no dox


title: HEV-infected HepaRG (SAMPLE 10), D100 plaque 1

description: Test


title: root-N_INPUT, Rep2

value: root


title: RNA_rWT_M_696-2

tag: genotype

tag: age


title: shoot-N_INPUT, Rep1

source_name: shoot

tag: cultivar

tag: tissue


title: HEV-infected HepaRG (SAMPLE 4), D100 plaque 1

description: Test

tag: treatment


title: RNA_rWT_M_44921


title: Cut&Tag  data for MED30 in teton MED30 expression Mia PaCa2 cells ,+dox, replicate #1

tag: cell line


title: spleen, ReUL23c_infected, Day5

city: Zhengzhou

first: ZHU Xiaojing

middle: Xiaojing

last: ZHU

state: Henan

address: 15 Longzihu University Park, Zhengdong New District

institute: Henan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Supplementary files format and content: tab-delimited text files include fpkm and count values for each Sample

organism: Gallus gallus

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols.

treatment_protocol: One-day-old chickens were wing-banded at hatch, randomly sorted into six experimental groups, and maintained in modified HorsfallBauer isolators for the duration of animal experiment. One group of chickens was remained as the uninoculated control.  The rest of five groups were inoculated subcutaneously with 2,000 PFUs Md5BAC, or Md5BAC ΔLORF9 or Md5BAC ΔLORF9-Re, or Md5BAC ΔUL23, or Md5BAC ΔUL23-Re virus. 3 chickens from each group were euthanatized at 5-days post infection (dpi). Spleen tissues were collected for splenocytes isolation followed by RNA extraction


title: Non-treated HepaRG (SAMPLE 3), D100 plaque 1

description: Control


title: RNA_rWT_F_697-3

value: Female


title: Non-treated HepaRG (SAMPLE 7), D100 plaque 1

description: Control


title: Non-treated HepaRG (SAMPLE 2), D100 plaque 1

description: Control


title: Cut&Tag  data for MED30 in teton MED30 expression Mia PaCa2 cells ,no dox, replicate #2


title: RNA_rWT_F_697-2


title: Non-treated HepaRG (SAMPLE 1), D100 plaque 1

description: Control


title: Cut&Tag  data for MED30 in teton MED30 expression Mia PaCa2 cells ,no dox, replicate #1


title: RNA_rWT_M_698-3


title: spleen, ReLORF9c_infected, Day5

value: spleen


title: RNA_rWT_F_44930


title: spleen, ReUL23b_infected, Day5


title: spleen, ReUL23a_infected, Day5


title: RNA_R878H_M_698-4


title: root-N_INPUT, Rep1

data_processing:
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were converted to fragments and dynamic islands were called using SICER-df.
RNA-Seq data was trimmed using CutAdapt and aligned using TopHat2. The gene counts were generated from mapped reads using htseq and counts were normalized with EDAseq, while differentially expressed genes were determined using DESeq2.
Genome_build: SL4.0
Supplementary_files_format_and_content: raw_counts.txt, SICER-df output files

extract_protocol:
Two grams of tissues were fixed with 1% formaldehyde by applying vacuum at 700 mmHg for 25 min. Fixation was terminated by adding 2M glycine to a final concentration of 0.125M and vacuum application for 5 minutes. Formaldehyde-fixed tissues were ground in liquid nitrogen and nuclei were isolated. Isolated nuclei were sonicated using Bioruptor to prepare chromatin samples with single nucleosomes.
Chromatin immunoprecipitated using Protein A dynabeads with antibodies against histone marks or input chromatin was recovered and reverse-crosslinked. Libraries were prepared using NEBNext dual index library kit.

tag: chip antibody


title: RNA_R878H_M_707-4


title: Cut&Tag  data for MED1 in teton MED30 expression Mia PaCa2 cells ,+dox, replicate #1


title: spleen, ReLORF9b_infected, Day5


title: HEV-infected HepaRG (SAMPLE 20)

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package GeneGlobe Data Analysis Center : https://geneglobe.qiagen.com/fr/analyze
For the normalization it uses the average of four housekeeping genes: ACTB, GAPDH, HSP90AB1 and GUSB
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ave Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., HEV-3f/Mock) ratios.

treatment_protocol:
Two days before IFN treatment, differentiation medium was replaced by proliferation medium. Cells were then treated overnight with 200 IU/ml of IFN-β1a (PBL Interferon Source, Piscataway, NJ, USA).
Two days before infection, differentiation medium was replaced by proliferation medium. Cells were infected overnight with an HEV-3f inoculum diluted in proliferation medium to a final volume of 1ml. The viral suspension was then removed and cells were washed three times in PBS before adding 2 ml of proliferation medium. Every 2 to 3 days, one-half (1 ml) of the culture medium was replaced with fresh growth medium and infection maintained for up to 100 days. A HEV-3f strain originating from a French patient suffering from acute autochthonous hepatitis E was used (GenBank under accession number JN906974)


title: Cut&Tag  data for MED30 in teton MED30 expression Mia PaCa2 cells ,+dox, replicate #2


title: spleen, ReLORF9a_infected, Day5


title: RNA_R878H_M_696-1


title: Uninfected HepaRG (SAMPLE 19)

description: Control


title: Cut&Tag  data for MED1 in teton MED30 expression Mia PaCa2 cells ,no dox, replicate #2


title: spleen, DeUL23c_infected, Day5


title: RNA_R878H_M_44922


title: Cut&Tag  data for MED1 in teton MED30 expression Mia PaCa2 cells ,no dox, replicate #1


title: Cut&Tag data for IgG in teton MED30 expression Mia PaCa2 cells  (negative control), +dox 5day


title: HEV-infected HepaRG (SAMPLE 18)

description: Test

value: 72 days


title: RNA_R878H_F_697-4


title: HEV-infected HepaRG (SAMPLE 16)

description: Test

value: 21 days


title: Cut&Tag  data for MED1 in teton MED30 expression Mia PaCa2 cells ,+dox, replicate #2

value: Mia PaCa-2 cell


title: Uninfected HepaRG (SAMPLE 17)

description: Control


title: spleen, DeUL23b_infected, Day5


title: Cut&Tag data for IgG in teton MED30 expression Mia PaCa2 cells  (negative control), +dox 1day


title: spleen, DeUL23a_infected, Day5


title: Uninfected HepaRG (SAMPLE 15)

description: Control


title: Cut&Tag data for IgG in teton MED30 expression Mia PaCa2 cells  (negative control), no dox


title: RNA_R878H_F_697-1


title: RNA_R878H_F_44931


title: HEV-infected HepaRG (SAMPLE 14)

description: Test

value: MOI 10


title: RNA_pWT_M_753-2


title: Cut&Tag data for Myc in teton MED30 expression Mia PaCa2 cells ,+dox 5day


title: spleen, DeLORF9b_infected, Day5


title: spleen, DeLORF9a_infected, Day5


title: spleen, DeLORF9c_infected, Day5


title: RNA_pWT_M_706-6


title: Cut&Tag data for Myc in teton MED30 expression Mia PaCa2 cells , +dox 1day


title: RNA_pWT_M_701-1


title: spleen, Md5BACc_infected, Day5


title: Cut&Tag data for Myc in teton MED30 expression Mia PaCa2 cells,no dox


title: Uninfected HepaRG (SAMPLE 13)

description: Control


title: HEV-infected HepaRG (SAMPLE 12)

description: Test

value: 40 days


title: Uninfected HepaRG (SAMPLE 11)

description: Control


title: primary Uveal Melanoma T5

city: Wenzhou

first: Meng

last: Zhou

address: 270 Xueyuan Xi Road

institute: Wenzhou Medical University

data_processing:
Clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
RNA-seq reads were aligned to an index of human genome (hg38) using HISAT2.
Use StringTie to assemble and quantify the reads on the alignment.
Assembly: GRCh38(hg38)
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: primary Uveal Melanoma

extract_protocol:
RNA concentration and purity was measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: disease state

value: Uveal Melanoma (eye)

value: primary Uveal Melanoma


title: spleen, Md5BACb_infected, Day5


title: HEV-infected HepaRG (SAMPLE 10)

description: Test

value: HepaRG

value: 26 days


title: RNA_pWT_M_602-2


title: spleen, Md5BACa_infected, Day5


title: primary Uveal Melanoma T4


title: primary Uveal Melanoma T3


title: spleen, Negative c, Day5

description: CEFc

value: uninfected


title: RNA_pWT_F_483-6


title: Uninfected HepaRG (SAMPLE 9)

description: Control

value: Mock


title: RNA_pWT_F_306-1


title: spleen, Negative b, Day5

description: CEFb


title: RNA_P900L_M_753-1


title: primary Uveal Melanoma T2


title: adjacent tissues N4

source_name: adjacent tissues

value: adjacent tissues


title: RNA_P900L_M_706-5

value: Cortex


title: adjacent tissues N3


title: HEV-infected HepaRG (SAMPLE 8)

description: Test

value: 14 days


title: P8-Irr_H3K27ac

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
ChIP-seq reads were trimmed using fastx_trimmer to remove adapters and low quality bases.
ChIP-seq reads were aligned to the hg38 genome using Bowtie2 v2.3.3.1.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using Deeptools. narrowPeak files were generated using MACS v2.2.7.1 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: NHC

growth_protocol: Cells were grown in H69 media  (DMEM/F12 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, adenine, insulin, epinephrine, T3-T, hydrocortisone, and epidermal growth factor).

extract_protocol:
Cells were fixed with 1% formaldehyde and quenched with glycine. Chromatin input was prepared and incubated with H3K27ac antibody. DNA was isolated from the enriched chromatin-DNA complexes.
ChIP-seq libraries were prepared by the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions.

treatment_protocol: Senescence was induced by exposing the cells to X-ray irradiation (10GY) and maintaining in culture for 5 days, with media change at 48 hours.

value: NHC

tag: cell type

value: cholangiocytes

value: Irradiation


title: RNA_pWT_F_483-2

value: Female


title: P8-Irr_Input

value: input


title: HEV-infected HepaRG (SAMPLE 6)

description: Test

value: 7 days


title: Uninfected HepaRG (SAMPLE 7)

description: Control


title: adjacent tissues N2


title: P7-Irr_H3K27ac


title: RNA_P900L_M_602-1

value: Male


title: Uninfected HepaRG (SAMPLE 5)

description: Control


title: HEV-infected HepaRG (SAMPLE 4)

description: Test

value: 1 day

value: MOI 10


title: RNA_P900L_M_701-2


title: adjacent tissues N1

value: Uveal Melanoma (eye)


title: hMDMs_ pLV-RFX1_ FLAG

city: Changsha

first: Shuang

last: Yang

address: No.139，Renmin Road Central Changsha-Hunan-China

institute: The Second Xiangya Hospital of central south university

data_processing:
Before data analysis, the original sequencing data were processed to remove the low-quality and splitter sequences using Skewer software.
The filtered sequencing data were compared with the reference genome (GRCh37/hg19) by Bowtie to obtain alignment information of ChIP-seq.
Alignment peak position and alignment intensity information were found using MACS by comparing position information of reads on the genome.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: human CD14+ monocyte derived macrophage induced by M-CSF

growth_protocol: hMDMs maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
hMDMs were infected with lentivirus carrying control or Rfx1-3×Flag plasmid and stimulated with LPS for 24 hours.  Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.Before data analysis, the original sequencing data were processed to remove the low-quality and splitter sequences using Skewer software. The Fastqc software was used to perform quality control of the treated sequences. The filtered sequencing data were compared with the reference genome (hg38) by Bowtie to obtain alignment information of ChIP-seq.
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina

value: macrophage

value: Flag


title: RNA_P900L_F_483-4


title: primary Uveal Melanoma T1

value: primary Uveal Melanoma


title: Uninfected HepaRG (SAMPLE 3)

description: Control

value: HepaRG

value: Mock


title: spleen, Negative a, Day5

description: CEFa

value: spleen

value: uninfected


title: RNA_P900L_F_483-1

value: Cortex


title: P5-Irr_H3K27ac

value: NHC

value: cholangiocytes


title: Non-treated HepaRG (SAMPLE 1)

description: Control

value: Non-treated


title: IFN-treated HepaRG (SAMPLE 2)

description: Test

value: IFN


title: LPS_h_pLV_RFX1_3

data_processing:
The Skewer software was used for dynamically remove the joint sequence and poor-quality fragment.
The STAR software was used to compare the preprocessed sequence with the reference genome sequence of the sequenced species.
The StringTie software was used to count the original sequence of known genes, and FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was used to calculate the expression.
Using DESeq2 software to screen differently expressed genes between two groups according to the experimental design
Assembly: mm10 or hg38
Supplementary files format and content: h_RFX1_RNA-seq worksheet: counts for RNA-seq of ontrol and Rfx1-overexpressed hMDMs
Supplementary files format and content: m_Rfx1_RNA-seq worksheet:counts.txt for RNA-seq of ontrol and Rfx1-overexpressed PMAs
Supplementary files format and content: m_CKO_RNA-seq worksheet:counts.txt for RNA-seq of WT and CKO PMAs

source_name: hMDMs

growth_protocol: PMAs and hMDMs maintained in DMEM  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina

treatment_protocol: Macrophage with RFX1 overexpression or Rfx1 deficiency were treated by LPS  for 24h.

value: hMDMs

value: RFX1 overexpression

value: LPS treatment

value: 24 hours


title: P5-Irr_Input

value: input

value: Irradiation


title: RNA_P900L_F_306-2

value: Female


title: LPS_h_pLV_RFX1_2

value: macrophage


title: ∆topAPZntopA[pLSROMtopARA] strain, S medium, +NOV, rep2

city: Madrid

first: Pablo

last: Hernandez

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Centro de Investigaciones Biologicas (CSIC)

data_processing:
Analysis of RNA-Seq data was carried out using the web-based platform Galaxy (European server UseGalaxy.eu).
Quality of raw sequence data from Illumina NovaSeq 6000 was analysed with FastQC tool. Trimming for quality control was conducted with Trimmomatic (Galaxy Version 0.38.1).
Sequencing reads were mapped against the S. pneumoniae R6 genome (ASM704v1) using BWA software package (Galaxy version 0.7.17.4) in simple Illumina mode.
BAM files from BWA were analyzed to obtain the number of reads overlapping each protein-coding gene using program featureCount (Galaxy Version 2.0.1+galaxy2).
Assembly: ASM704v1 RefSeq GCF_000007045.1
Supplementary files format and content: Tab-delimited text files obtained from featureCounts (protein-coding genes), including Reference assembly, Gene ID, Gene name, Start, End and Counts.

organism: Streptococcus pneumoniae

source_name: Bacterial cell

growth_protocol: S. pneumoniae was grown as static cultures at 37ºC in a casein hydrolysate-based liquid medium (AGCH) containing 0.2% yeast extract and 0.8% sucrose (C+Y).

extract_protocol:
RNA (about 5 µg) was obtained from samples containing 2-4E8 cells using the RNeasy mini kit (Quiagen). RNA was depleted of ribosomal RNA using the Ribo-Zero (Bacteria) Magnetic Kit (Illumina).
Libraries for RNA-Seq were prepared from 1 µg RNA using the ScriptSeq v2 RNA-Seq system (Illumina).

treatment_protocol: Overnight cultures grown in the medium described above were diluted 1000-fold in medium with 0.8% sucrose (noninducing medium) or 0.4% sucrose plus 0.4% maltose (inducing medium) and grown to OD=0.4. To analyze the effect of novobiocin, the antibiotic at 10 x MIC was added to the cultures and they were grown for 30 additional minutes.

value: deltatopAPZntopA[pLSROMtopARA]  from R6

value: Bacterial cell

value: S medium, 10xMIC NOV


title: ∆topAPZntopA[pLSROMtopARA] strain, SM medium, +NOV, rep2

value: SM medium, 10xMIC NOV


title: P8-Ctrl_H3K27ac

value: Control


title: LPS_h_pLV_RFX1_1


title: K27ac_rWT_M_791-2

data_processing:
ChIP-seq reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
Assembly: mm9
Supplementary files format and content: bed

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the S220 Ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material. Libraries were amplified using 11-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D1000 Screentape Assay Kit.

value: Cortex

value: Male

value: H3K27ac:Abcam ab4729


title: P7-Irr_Input

value: NHC

value: cholangiocytes


title: K27ac_R878H_M_791-7


title: ∆topAPZntopA[pLSROMtopAWT] strain, SM medium, +NOV, rep2

value: deltatopAPZntopA[pLSROMtopAWT]  from R6


title: K27ac_R878H_F_677-6


title: LPS_h_pLV_NC2

value: hMDMs

value: Negetive control

value: LPS treatment


title: ∆topAPZntopA[pLSROMtopARA] strain, SM medium, +NOV, rep1


title: P8-Ctrl_Input

value: input


title: P7-Ctrl_H3K27ac


title: LPS_h_pLV_NC3

value: 24 hours


title: LPS_h_pLV_NC1

value: macrophage


title: P5-Ctrl_H3K27ac


title: K27ac_rWT_F_677-7

value: Female


title: ∆topAPZntopA[pLSROMtopARA] strain, S medium, +NOV, rep1

value: deltatopAPZntopA[pLSROMtopARA]  from R6

value: Bacterial cell


title: IP_KO_Tal_III

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
BSSE_QGF_132507_H2JC5BGXF_1_IP_KO_Tal_3_CCGTCC_S8_R*_001_MM
BSSE_QGF_132507_H3MGGBGXF_1_IP_KO_Tal_3_CCGTCC_S8_R*_001_MM
processed data file: SSB_KO_Tal.txt.gz

data_processing:
library strategy: Single-Strand Break (SSB)-Seq
Reads where aligned to the mouse genome (mm10 UCSC version) with bowtie2 (version 2.3.4.2) and extra options "--maxins 2000 --no-mixed --no-discordant --local --mm". Duplicates where marked with picard tools (version 2.9.2)
BAM files where filtered by removing reads falling into ENCODE blacklist regions (version 2014 + manual removal of high coverage regions) using Rsamtools (R version 3.6, Bioconductor version 3.10)
Peaks were called across all replicates of a sample group using HOMER (version 4.11) and “findPeaks”  with  specifying commands “-style histone -o auto” with the corresponding input as a control.
Genome_build: mm10
Supplementary_files_format_and_content: HOMER output files of detected SSB peaks called over the three replicates; columns: chrom, start, end, name, score, strand, signal value, -log10(p-value), -log10(q-value), peak ID

growth_protocol: ESCs were cultured on gelatin-coated dishes under a controlled atmosphere (37°C, 5% CO2, 95% humidity) in serum-free 2i medium with 1000 U/ml LIF and without antibiotics. The 4-OHT to excise Tdg minigene (Sigma-Aldrich H7904) was dissolved in DMSO (stock 10 mM) and administered at 5 uM for 2 h before each experiment.

extract_protocol:
~20 mio cells were harvested from a 15 cm dish and genomic DNA was extracted with the genomic tips kit 100 (Qiagen). 50 ug of DNA were subjected to SSB-seq protocol. Briefly: Nick-translation was performed with E-coli Pol I at 16°C for 1 min, including DIG-dUTPs and ddNTPs to prevent exceeding polymerization. The labelled DNA was precipitated, purified and subsequently sonicated and digested with restriction enzymes to get rid of high-molecular DNA. The fragmented DNA was purified again and subjected to immunoprecipitation using an anti-DIG antibody (Roche 11333089001) and Protein G Dynabeads (Life Technologies). Immunoprecipitated DNA was purified with the ChIP DNA clean & concentrator kit (Zymo).
10 ng of each immunoprecipitated DNA and Input DNA were subjected to library construction with a KAPA HyperPrep Kit (Roche) using 8 cycles of amplification.

treatment_protocol: ESCs were treated with 5 nM Talazoparib (Selleckchem, S7048) for 24 h prior to extraction.

value: mouse embryonic stem cells

value: KO; Tdg-depleted

value: 5 nM Talazoparib for 24 h


title: P5-Ctrl_Input

value: Control


title: ∆topAPZntopA[pLSROMtopAWT] strain, S medium, +NOV, rep2

value: S medium, 10xMIC NOV


title: P7-Ctrl_Input

value: NHC


title: MKN74 siYWHAG TGFβ 2

city: Singapore

first: Nguan Soon

last: Tan

address: 11 Mandalay Rd

country: Singapore

institute: Lee Kong Chian School of Medicine

data_processing:
Alignment by HISAT2
Raw counts using featurecounts
DEGs determined using DESeq2 with cutoff of log2fc >±1
Assembly: GRCh38

source_name: Cell line

growth_protocol: MKN74 cells were maintained in Roswell Park Memorial Institute 1640 (RPMI) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Thermo Fisher Scientific, USA) followed by Pure NA. Fastspin Total RNA Extraction Kit (Research Instruments, USA).
Illumina library preparation done by NovogeneAIT.

value: Cell line

value: human gastric adenocarcinoma

value: YWHAG knockdown

value: TGFβ


title: MKN74 siYWHAG TGFβ 1


title: ∆topAPZntopA[pLSROMtopAWT] strain, S medium, +NOV, rep1

value: deltatopAPZntopA[pLSROMtopAWT]  from R6


title: ∆topAPZntopA[pLSROMtopAWT] strain, SM medium, +NOV, rep1

value: SM medium, 10xMIC NOV


title: IP_KO_Tal_I

description:
BSSE_QGF_132505_H2JC5BGXF_1_IP_KO_Tal_1_AGTTCC_S6_R*_001_MM
BSSE_QGF_132505_H3MGGBGXF_1_IP_KO_Tal_1_AGTTCC_S6_R*_001_MM
processed data file: SSB_KO_Tal.txt.gz


title: MKN74 siYWHAG DMOG 2

value: DMOG


title: ∆topAPZntopA[pLSROMtopARA] strain, S medium, -NOV, rep2

value: S medium


title: Input_KO_Tal

description:
BSSE_QGF_132504_H2JC5BGXF_1_Input_KO_Tal_AGTCAA_S5_R*_001_MM
BSSE_QGF_132504_H3MGGBGXF_1_Input_KO_Tal_AGTCAA_S5_R*_001_MM
processed data file: SSB_KO_Tal.txt.gz


title: MKN74 siYWHAG DMOG 1


title: Exosomes derived from HCT116 Cell line treated by ETBF for 6 hours-replicate 3

city: Shanghai

first: Haoyan

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
single-end reads were filtered and trimmed using software Trimmomatic
Quality control before and after raw reads preprocessing was done using software FastQC
Count files of the aligned sequencing reads were generated by the  featurecount, using the GFF annotation file from miRBase-v20
Genome_build: GRCh37.p5
Supplementary_files_format_and_content: Tab-separated matrices with read counts,

source_name: Exosomes derived from HCT116 cells

growth_protocol: HCT116 cells were routinely cultured adherently in the petri dish with 1640 medium

extract_protocol:
Exosomes from conditioned media were collected through standard centrifugation steps, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100 ng of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 Cells were co-cultured with ETBF for 6h. Multiplicity of infection (MOI) was 500. The normal control samples were treated with the bacteria medium without ETBF.

value: human colorectal cancer cells

tag: passage


title: ∆topAPZntopA[pLSROMtopARA] strain, S medium, -NOV, rep1

value: deltatopAPZntopA[pLSROMtopARA]  from R6


title: Exosomes derived from HCT116 Cell line treated by ETBF for 6 hours-replicate 1


title: Exosomes derived from HCT116 Cell line treated by ETBF for 6 hours-replicate 2


title: IP_KO_III

description:
BSSE_QGF_132503_H2JC5BGXF_1_IP_KO_III_CTTGTA_S4_R*_001_MM
BSSE_QGF_132503_H3MGGBGXF_1_IP_KO_III_CTTGTA_S4_R*_001_MM
processed data file: SSB_KO_DMSO.txt.gz

value: DMSO


title: MKN74 siYWHAG Control 4


title: ∆topAPZntopA[pLSROMtopAWT] strain, S medium, -NOV, rep2

value: Bacterial cell


title: IP_KO_II

description:
BSSE_QGF_132502_H3MGGBGXF_1_IP_KO_II_GGCTAC_S3_R*_001_MM
BSSE_QGF_132502_H2JC5BGXF_1_IP_KO_II_GGCTAC_S3_R*_001_MM
processed data file: SSB_KO_DMSO.txt.gz

value: mouse embryonic stem cells

value: KO; Tdg-depleted


title: IP_KO_I

description:
BSSE_QGF_132501_H2JC5BGXF_1_IP_KO_I_TAGCTT_S2_R*_001_MM
BSSE_QGF_132501_H3MGGBGXF_1_IP_KO_I_TAGCTT_S2_R*_001_MM
processed data file: SSB_KO_DMSO.txt.gz


title: ∆topAPZntopA[pLSROMtopAWT] strain, S medium, -NOV, rep1


title: Exosomes derived from HCT116 Cell line untreated-replicate 2


title: MKN74 siYWHAG Control 2

value: Control


title: Exosomes derived from HCT116 Cell line untreated-replicate 1


title: IP_KO_Tal_II

description:
BSSE_QGF_132506_H3MGGBGXF_1_IP_KO_Tal_2_ATGTCA_S7_R*_001_MM
BSSE_QGF_132506_H2JC5BGXF_1_IP_KO_Tal_2_ATGTCA_S7_R*_001_MM
processed data file: SSB_KO_Tal.txt.gz

value: 5 nM Talazoparib for 24 h


title: Exosomes derived from HCT116 Cell line untreated-replicate 3


title: Input_KO

description:
BSSE_QGF_132500_H2JC5BGXF_1_Input_KO_GATCAG_S1_R*_001_MM
BSSE_QGF_132500_H3MGGBGXF_1_Input_KO_GATCAG_S1_R*_001_MM
processed data file: SSB_KO_DMSO.txt.gz


title: ∆topAPZntopA[pLSROMtopARA] strain, SM medium, -NOV, rep2

value: SM medium


title: MKN74 siYWHAG Control 1

value: Cell line


title: HCT116 Cell line untreated-replicate 4

source_name: HCT116 cells

growth_protocol: HCT116 cells were routinely cultured adherently in the six hole plate in the concertration of 5*10e7 per hole with 1640 medium

extract_protocol: miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 Cells were co-cultured with ETBF  for 6h. Multiplicity of infection (MOI) was 500. The normal control samples were treated with the bacteria medium without ETBF.


title: ∆topAPZntopA[pLSROMtopARA] strain, SM medium, -NOV, rep1


title: IP_WT_Tal_III

description:
BSSE_QGF_132498_HTVWKBGXC_1_IP_WT_Tal_III_ACTTGA_S8_R*_001_MM
BSSE_QGF_132498_HWNKLBGXC_1_IP_WT_Tal_III_ACTTGA_S8_R*_001_MM
processed data file: SSB_WT_Tal.txt.gz

value: wild type


title: MKN74 TGFβ 2

value: human gastric adenocarcinoma

value: WT


title: HCT116 Cell line untreated-replicate 3


title: IP_WT_Tal_II

description:
BSSE_QGF_132497_HTVWKBGXC_1_IP_WT_Tal_II_CAGATC_S7_R*_001_MM
BSSE_QGF_132497_HWNKLBGXC_1_IP_WT_Tal_II_CAGATC_S7_R*_001_MM
processed data file: SSB_WT_Tal.txt.gz


title: ∆topAPZntopA[pLSROMtopAWT] strain, SM medium, -NOV, rep2

value: deltatopAPZntopA[pLSROMtopAWT]  from R6


title: MKN74 TGFβ 1

value: TGFβ


title: ∆topAPZntopA[pLSROMtopAWT] strain, SM medium, -NOV, rep1


title: HCT116 Cell line untreated-replicate 2


title: IP_WT_Tal_I

description:
BSSE_QGF_132496_HTVWKBGXC_1_IP_WT_Tal_I_GCCAAT_S6_R*_001_MM
BSSE_QGF_132496_HWNKLBGXC_1_IP_WT_Tal_I_GCCAAT_S6_R*_001_MM
processed data file: SSB_WT_Tal.txt.gz


title: Input_WT_Tal

description:
BSSE_QGF_132495_HTVWKBGXC_1_Input_WT_Tal_ACAGTG_S5_R*_001_MM
BSSE_QGF_132495_HWNKLBGXC_1_Input_WT_Tal_ACAGTG_S5_R*_001_MM
processed data file: SSB_WT_Tal.txt.gz


title: MKN74 DMOG 2

value: DMOG


title: HCT116 Cell line untreated-replicate 1


title: MKN74 siYWHAG Control 3

value: YWHAG knockdown


title: IP_WT_III

description:
BSSE_QGF_132494_HTVWKBGXC_1_IP_WT_III_TGACCA_S4_R*_001_MM
BSSE_QGF_132494_HWNKLBGXC_1_IP_WT_III_TGACCA_S4_R*_001_MM
processed data file: SSB_WT_DMSO.txt.gz


title: IP_WT_II

description:
BSSE_QGF_132493_HTVWKBGXC_1_IP_WT_II_TTAGGC_S3_R*_001_MM
BSSE_QGF_132493_HWNKLBGXC_1_IP_WT_II_TTAGGC_S3_R*_001_MM
processed data file: SSB_WT_DMSO.txt.gz


title: HCT116 Cell line treated by ETBF for 6 hours-replicate 3

value: human colorectal cancer cells


title: MKN74 Control 4


title: HCT116 Cell line treated by ETBF for 6 hours-replicate 4


title: MKN74 Control 3


title: HCT116 Cell line treated by ETBF for 6 hours-replicate 1


title: MKN74 DMOG 1


title: HCT116 Cell line treated by ETBF for 6 hours-replicate 2


title: MKN74 Control 2


title: IP_WT_I

description:
BSSE_QGF_132492_HTVWKBGXC_1_IP_WT_I_CGATGT_S2_R*_001_MM
BSSE_QGF_132492_HWNKLBGXC_1_IP_WT_I_CGATGT_S2_R*_001_MM
processed data file: SSB_WT_DMSO.txt.gz


title: MKN74 Control 1


title: Input_WT

description:
BSSE_QGF_132491_HTVWKBGXC_1_Input_WT_ATCACG_S1_R*_001_MM
BSSE_QGF_132491_HWNKLBGXC_1_Input_WT_ATCACG_S1_R*_001_MM
processed data file: SSB_WT_DMSO.txt.gz


title: Sedentary_rep3

city: Nagoya

first: Tomoki

last: Hirunagi

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Neurology

country: Japan

institute: Nagoya University GraduateSchool of Medicine

description: Gene expression in the quadriceps of AR97Q mice in the sedentary group

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Quadriceps, sedentary, replicate 3

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Hilden, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA was isolated from tissues homogenized in TRIzol Reagent (Thermo Scientific, Waltham, MA) using a PureLink Genomic DNA Mini Kit (Thermo Scientific) according to the protocol supplied by the manufacturer.The quality of total RNA was assessed with Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA), and and the RNA integrity number values showed sufficiently high quality (ranging from 8.4 to 9.2).

tag: gender

value: male

value: 9 weeks


title: Sedentary_rep2

source_name: Quadriceps, sedentary, replicate 2


title: HCT116,USP51,rep2

status: Public on Nov 07 2023

city: Xi'an

first: mingchao

last: mu

address: 277 West Yanta Road

department: Department of General Surgery

institute: the First Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Dr Tom II
The sequencing data was filtered with SOAPnuke (v1.5.2)
Aligning against the reference genome was performed using Tophat for the set of high-quality reads.
Statistical modeling was carried out utilizing the DESeq 1.32.0 package from the Bioconductor platform.
Assembly: hg38
Supplementary files format and content: tab-delimited text file for FPMK values

growth_protocol: HCT116,SW480 cells were all routinely cultured in DMEM supplemented with 10% fetal bovine serum at 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using TRIzol Reagent
RNA libraries were prepared for sequencing using standard BGISEQ500

treatment_protocol: Untreated

value: humancolon cancercell line


title: HCT116,USP51,rep1


title: HCT116,NC,rep2

value: NC

value: Vector


title: FTO3

type: protein

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

description: Culture medium were collected after treated for three days

hyb_protocol: Each sample was incubated in 96-well plates embedded with microbeads for 30 min, and then incubated with detection antibody for 30 min. Furthermore, streptavidin-PE was filled in each well for 10 min, and values were read on the Bio-Plex 200 Systemm（Luminex Corporation, Austin, TX, USA）

scan_protocol: use luminex 200 system Calculate fitted cytokine concentrations

data_processing: For indicators with OOR<, assign a value that is half of the lowest concentration of the indicator.

label: PE

molecule: protein

source_name: HUVEC

label_protocol: Use the matching detection antibody to identify the antigen and finally use PE fluorescence to identify it.

growth_protocol: culture mediums were collected from all samples

extract_protocol: Use cell supernatant directly

treatment_protocol: FTO teams were transfected with lentivirus containing coding sequence of human FTO, Flg teams were transfected with empty lentiviral plasmid with FLAG tag

value: HUVEC cell line

value: FTO


title: SW480,NC,rep2


title: Exercise_rep3

description: Gene expression in the quadriceps of AR97Q mice in the exercise group

source_name: Quadriceps, exercise, replicate 3


title: FTO2


title: Exercise_rep2

source_name: Quadriceps, exercise, replicate 2


title: HCT116,USP51,rep3


title: Flg2

value: flag control


title: Flg1


title: HCT116,NC,rep3


title: N5

city: Jinan

first: Gongqiang

last: Yuan

address: No. 372, Jingsi Road

institute: Eye Institute of Shandong First Medical University

data_processing:
Total RNA was isolatTotal RNA was isolated using TRIzol reagent from samples. RNA-sequencing was performed based on DNBseq platform (PE150 strategy).ed using TRIzol reagent from samples.
To obtain the clean reads from RNA-sequencing results, sequence with low quality including adapter sequences, sequences with quality score < 20, sequences with N base rate of raw reads > 10% and sequence less than 25bp were removed.
HISAT2 (version 2.1.0) was used to align the clean reads with the human reference genome GRCh38.
DEseq2 was applied to obtain DEmRNAs and DElncRNAs with p <0.05 and |log2foldchange| >1.
Assembly: hg18
Supplementary files format and content: explevel_analysis_lnc_salmon_fpkm.csv
Supplementary files format and content: explevel_analysis_mRNA_salmon_fpkm.csv

source_name: whole blood

extract_protocol:
Nine patients with neovascular AMD were included in the study. Control group comprised seven patients with epiretinal membranes. Peripheral whole blood (2.5 ml) drawn from each individual was used for RNA extraction.
RNA sequencing and identification of DEmRNAs and DElncRNAs Total RNA was isolated using TRIzol reagent from samples. RNA-sequencing was performed based on DNBseq platform (PE150 strategy).

value: whole blood

value: control, epiretinal membranes


title: N6


title: SW480,USP51,rep3


title: N3


title: N1


title: Sedentary_rep1

source_name: Quadriceps, sedentary, replicate 1


title: SW480,USP51,rep1


title: Exercise_rep1

source_name: Quadriceps, exercise, replicate 1


title: SW480,NC,rep3


title: HCT116,NC,rep1


title: SW480,NC,rep1


title: SW480,USP51,rep2


title: N7


title: T6

value: neovascular AMD


title: T5


title: T4


title: FTO1


title: N4


title: Flg3


title: T3


title: T9


title: T2


title: T7


title: T1


title: T8


title: N2


title: 22Rv1_RNA_ENZ3w_siARV7_Dex_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: 22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the 22Rv1 cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. 22Rv1 cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for 18 h before the start of RNA extraction.

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

tag: enz treatment

value: 3 weeks

tag: sirna treatment

value: Custom AR-V7 siRNA (Dharmacon)

tag: hormone treatment

value: dexamethasone

tag: hormone concentration


title: 22Rv1_RNA_ENZ3w_siARV7_Dex_rep3


title: 22Rv1_RNA_ENZ3w_siARV7_EtOH_rep3

value: EtOH vehicle


title: 22Rv1_RNA_ENZ3w_siARV7_Dex_rep1


title: PATC148 PDAC cell line

city: Tampa

first: Karen

middle: M

last: Mann

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

hyb_protocol: Following fragmentation, 5 ug of biotinylated amplified cDNA was hybridized for 16 hr at 45C to the Affymetrix Calriom D arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip  Scanner 3000 7G

data_processing: CEL files were processed using Affymetrix TAC 4.0 software, normalized with SST-RMA, with DABG background estimates enabled for analyses.  The Affymetrix-provided Clariom_D_Human.r1.na36.hg38.a1.transcript.csv file was used for genomic annotation.

label: biotin

source_name: RBFOX2 wild type

label_protocol: RNA samples underwent two cycles of cDNA synthesis using the GeneChip WT Amplification Kit, and the second cycle cDNA was enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Thermo)

growth_protocol: All cell lines were grown under recommended conditions by ATCC.

extract_protocol: RNA was isolated from cell lines and snap frozen mouse pancreas tumors and related liver metastases using Qiagen Rneasy mini kits

value: cell line

value: cell line expressing endogenous RBFOX2 levels; no modification


title: PATC153 PDAC cell line


title: mouse liver metastasis paired with G3147 PAN

source_name: RBFOX2 depleted

value: murine liver metastasis

value: liver metastasis derived from orthotopic pancreas tumor G3147 PAN


title: mouse pancreas tumor generated from Panc1 cell line with stable RBFOX2 depletion 2

value: murine pancreas

value: orthotopic pancreas tumor generated from Panc1 cell line with stable RBFOX2 depletion


title: mouse pancreas tumor generated from 4039 cell line with RBFOX2 expression 1

value: orthotopic pancreas tumor generated from 4039 cell line with non-targeting shRNA (NTC)


title: mouse liver metastasis paired with 1679 PAN

value: liver metastasis derived from orthotopic pancreas tumor 1679 PAN


title: 22Rv1_RNA_ENZ3w_siARV7_EtOH_rep2


title: mouse liver metastasis paired with 1681 PAN

value: liver metastasis derived from orthotopic pancreas tumor 1681 PAN


title: mouse liver metastasis paired with G3151 PAN

value: liver metastasis derived from orthotopic pancreas tumor G3151 PAN


title: mouse_50

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

data_processing:
RNA preparation, library construction and sequencing on DNBSEQ platform was performed at Beijing Genomics Institute.
Reads were aligned to the mouse genome (GRCm39.104) using STAR  (-runThreadN 2 --genomeDir --readFilesIn  --readFilesCommand gunzip -c --outFileNamePrefix  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Mus_musculus.GRCm39.104.gtf --quantMode TranscriptomeSAM
Reads were quantified using Htseq
Genome_build: Mus_musculus.GRCm39.104
Supplementary_files_format_and_content: Raw counts using HTSeq

source_name: proximal small intestine scraping

extract_protocol:
21 days old mice were stratified by body weight and divided into the two dietary groups. The galactose group received a pelleted diet containing 16 en% in galactose + 16 en% in glucose, the glucose group was fed with a pelleted diet containing 32 en% in glucose. The two diets were otherwise identical. The mice were fed for 3 weeks with the intervention diet and sacrificed on day PN42. The RNA used for the analysis was obtained from the scraping of the proximal part of the small intestine. Collected tissue was snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was isolated with RNeasy columns (Qiagen, Venlo, TheNetherlands). RNA integrity was checked on an Agilent 2200 Tapestation according to the manufacturer's instructions (Agilent Technologies Inc., Santa Clara, CA, USA).
RNA preparation, library construction and sequencing on DNBSEQ platform was performed at Beijing Genomics Institute.

value: female

tag: strain

tag: diet

value: 42 days

value: proximal small intestine scraping


title: mouse pancreas tumor generated from Panc1 cell line with RBFOX2 expression 2

tag: genotype

value: orthotopic pancreas tumor generated from Panc1 cell line with non-targeting shRNA (NTC)


title: mouse liver metastasis paired with G3144 PAN

value: liver metastasis derived from orthotopic pancreas tumor G3144 PAN


title: mouse pancreas tumor generated from 4039 cell line with RBFOX2 expression 2


title: Panc1 cell line with shRBFOX2 depletion

value: stable depletion of RBFOX2 by shRNA


title: mouse pancreas tumor generated from Panc1 cell line with RBFOX2 expression 1


title: mouse_43

tag: Sex

tag: age


title: mouse liver metastasis paired with 1603 PAN

tag: tissue

value: liver metastasis derived from orthotopic pancreas tumor 1603 PAN


title: 22Rv1_RNA_siARV7_Dex_rep3

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

value: Custom AR-V7 siRNA (Dharmacon)

value: dexamethasone


title: 22Rv1_RNA_ENZ3w_siARV7_EtOH_rep1

value: 3 weeks

value: EtOH vehicle


title: 22Rv1_RNA_siARV7_Dex_rep2


title: 22Rv1_RNA_siARV7_Dex_rep1


title: mouse pancreas tumor generated from Panc1 cell line with stable RBFOX2 depletion 1

value: murine pancreas

value: orthotopic pancreas tumor generated from Panc1 cell line with stable RBFOX2 depletion


title: 4039 cell line with RBFOX2 expression

value: cell line

value: stable expression of non-targeting shRNA (NTC)


title: 4039 cell line with RBFOX2 depletion


title: MiaPaCa2 cell line with RBFOX2 expression


title: mouse pancreas tumor generated from 4039 cell line with stable RBFOX2 depletion 1

value: orthotopic pancreas tumor generated from 4039 cell line with stable RBFOX2 depletion


title: mouse pancreas tumor generated from 4039 cell line with stable RBFOX2 depletion 2


title: mouse liver metastasis paired with G3152 PAN

value: murine liver metastasis

value: liver metastasis derived from orthotopic pancreas tumor G3152 PAN


title: mouse_42

value: female

value: 42 days

value: proximal small intestine scraping


title: MiaPaCa2 cell line with shRBFOX2 depletion

value: stable depletion of RBFOX2 by shRNA


title: mouse_38


title: mouse liver metastasis paired with 1614 PAN

value: liver metastasis derived from orthotopic pancreas tumor 1614 PAN


title: Panc1 cell line with RBFOX2 expression


title: mouse_37


title: 22Rv1_RNA_siARV7_EtOH_rep3

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line


title: 22Rv1_RNA_siARV7_EtOH_rep1

value: Custom AR-V7 siRNA (Dharmacon)


title: 22Rv1_RNA_siARV7_EtOH_rep2


title: mouse_36


title: 22Rv1_RNA_ENZ3w_siNON_EtOH_rep3

value: Non-targeting control siRNA (Dharmacon, D-001810-10)


title: 22Rv1_RNA_ENZ3w_siNON_Dex_rep3

value: 3 weeks

value: dexamethasone


title: mouse_34


title: 22Rv1_RNA_ENZ3w_siNON_Dex_rep2


title: mouse_25


title: mouse_23


title: mouse_33


title: 22Rv1_RNA_siNON_Dex_rep3


title: mouse_28


title: mouse_21


title: 22Rv1_RNA_ENZ3w_siNON_Dex_rep1


title: mouse_29


title: 22Rv1_RNA_siNON_Dex_rep2


title: mouse_27


title: mouse_12


title: 22Rv1_RNA_siNON_EtOH_rep2

value: EtOH vehicle


title: mouse_8


title: 22Rv1_RNA_ENZ3w_siNON_EtOH_rep1


title: 22Rv1_RNA_siNON_EtOH_rep1


title: 22Rv1_RNA_siNON_Dex_rep1


title: mouse_6


title: 22Rv1_GR_ENZ3w-siARV7_Dex_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding EtOH sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the 22Rv1 cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. 22Rv1 cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for 1 h before the start of ChIPs.

value: GR (Cell Signaling, 12041)


title: mouse_13


title: 22Rv1_RNA_ENZ3w_siNON_EtOH_rep2


title: 22Rv1_GR_ENZ3w-siARV7_Dex_rep1


title: mouse_3


title: 22Rv1_GR_ENZ3w-siARV7_EtOH_rep2


title: 22Rv1_GR_ENZ3w-siARV7_EtOH_rep1