title: rdd_3h_RNAseq_rep3

value: seedlings

value: with 100 nm flg22 for 3 h


title: Control_lot1

status: Public on Jun 20 2022

type: SRA

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

library_source: transcriptomic

data_processing:
Library strategy: BRB-seq
Extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were trimmed using Cutadapt (M. Martin, 2011)  (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  -a GATCGTCGGACT. The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1).  UMIs were not used and mitochondrial genes are excluded in the following analysis.
Downstream analysis was conducted by DESeq2 software (M. I. Love et al., 2014) (1.28.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix, normalized count matrix, and TPM matrix.

molecule: total RNA

organism: Mus musculus

source_name: C2C12 cell line

growth_protocol: C2C12 cells were cultured in 6 well plates in Dulbecco’s modified Eagle’s medium (DMEM) (1g/L D-glucose) supplemented with 20% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin.

extract_protocol:
All samples were collected by adding lysis buffer to the cell culture plates followed by scraping (Control) and re-suspending cells. Total RNAs were extracted from lysate using NucleoSpin RNA XS (Takara).
Sequencing was performed using HiSeq PE Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2 (50 Cycles) on Illumina HiSeq 1500 sequencers, with 15 cycles for read 1 and 45 cycles for read 2.

treatment_protocol:
For time series analysis, cells were washed twice with PBS and treated with 200 µL of 0.25% trypsin for 30 sec, 3 min or 30 min at 37ºC.
For low trypsin level treatment, cells were washed twice with PBS, and treated with 200 µL of 0.25% trypsin. Trypsin was removed immediately and cells were incubated at 37 °C for 3 min.
For cold-active protease treatment, cells were washed twice with PBS followed by adding 200 µL of cold protease. Cells were incubated at 4 °C for 5 min with shaking.

tag: cell line

tag: cell type

value: myoblast


title: P1-PD1-19bbz

city: Shanghai

first: Jiqin

last: Zhang

address: No.500 Dongchuan Road

country: China

institute: East China Normal University

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

organism: Homo sapiens

source_name: T-cell product

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: treatment naive

value: Primary cells

tag: Sex

value: Male

tag: age

tag: agent


title: Time-series-30sec_lot3


title: siSTING4x_siAS_14

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression of STING-depleted fibroblasts

data_processing:
Raw reads were trimmed for adapters, polyA read through, and low-quality tails (quality <Q20) using BBDuk (version 37.02). Reads shorter than 35 bp were also removed resulting on average 27 M trimmed reads per sample.
Reads were subsequently aligned to the human reference genome using STAR (version 2.5.3a) and setting the STAR parameters as indicated in the Lexogen data analysis guidelines (see https://www.lexogen.com/quantseq-data-analysis/ for details).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (version 1.30.3) and the Gencode gene annotation for hg38 genome.
Gene counts were normalized to counts per million mapped reads (CPM) using the edgeR package; only genes with a CPM greater than 1 in at least 2 samples were further retained for differential analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with CPM values for each sample

source_name: WI-38 fibroblasts

growth_protocol: MEM medium, supplemented with 10% Fetal Bovine Serum (FBS), L-Glutamine and antibiotic.

extract_protocol:
RNA extraction was performed with NucleoSpin 8 RNA Core Kit (Macherey-Nagel) according to the manufacturer’s instructions, using an automated system (Freedom EVO, Tecan).
RNA-seq libraries were prepared with QuantSeq 3’mRNA-Seq Library Prep kit (LEXOGEN), according to manufacturer’s instructions.

treatment_protocol: siRNA transfections were carried out using Lipofectamine RNAi-MAX (Life Technologies, 56532) in antibiotics-free medium according to the manufacturer’s instructions.

value: WI-38 fibroblasts

tag: transfection

value: Control siRNA (siAS) + STING siRNA


title: rdd_flg22_24h_RNAseq_rep1

city: Wuhan

first: mengling

last: Huang

state: Hubei

address: shizisan

department: College of Plant Science and Technology

institute: Huazhong Agricultural Universityhuazong

data_processing:
RNA-seq library preparation and sequencing were performed on an Illunima HiSeq X-ten (Beijing, China). RNA-seq reads with low sequencing quality or reads with sequencing adaptors were filtered from the raw data. The resulting clean reads were then aligned to the Arabidopsis reference genome (TAIR10) using Hisat2  with default parameters. A GFF (general feature format) formatted gene model annotation file was provided for reads alignment. Following the alignments, transcriptome quantification based on gene level was performed by FeatureCounts  and then used DESeq2  to find the significant differential gene expression. Genes with expression fold change > 2 and Padj < 0.05 were considered as significantly different between samples with and without flg22 treatment.
Whole-Genome Bisulfite Sequencing were performed by BGI Genomics (Shenzhen, China). Sequencing was performed on an Illumina HiSeq 4000 instrument to generate paired-end reads.For data analysis, paired-end sequencing reads were first trimmed with Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for removal of Illumina adapters and low-quality bases (Phred score < 20). The cleaned reads were then aligned to TAIR10 genome using bsmap with default settings. Only uniquely mapped reads were retained for further analysis. PCR duplicates were marked by Picard (https://broadinstitute.github.io/picard/). Further processing was accomplished via SAMtools , BAMtools  and bamUtil (https://github.com/statgen/bamUtil/). Methylation ratio was extracted with BatMeth2 .
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample
Supplementary_files_format_and_content: wig files were generated using script

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in soil (Metro Mix 366)  in a growth room at 21°C, 45% humidity, and 75 μE m-2 s-1 light with a 12-h-light/12-h-dark photoperiod.Seedlings were germinated on half-strength Murashige and Skoog (½MS) plates containing 1% sucrose and 0.8% agar, and grown under the same conditions as above.

extract_protocol:
Total RNA was extracted from ten-day-old seedlings or leaves from 4-week-old soil-grown Arabidopsis plants by TRNzol reagent.                                                                                Genomic DNA was extracted from ten-day-old seedlings by CTAB
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings were treated  with or without 100 nM flg22 for 1 h, 3 h, 12 h; 4-week-old plants were hand-inoculated with water or 100 nM flg22 for 24 h; p1: Leaves from 4-week-old plants were hand-inoculated with or without 100 nM flg22, and 24 h later hand-inoculated with Pst DC3000 hrcC at 2*10e8 cfu/mL for 1 h.

tag: tissue

value: leaves

tag: genotype

value: rdd

tag: treatment

value: hand-inoculated with 100 nm flg22 for 24 h


title: Time-series-30sec_lot1


title: Time-series-30min_lot1


title: rdd_3h_RNAseq_rep2


title: Patient-3_IP

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38Ensembl91
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Infusion product

tag: individual

value: Primary cells (Infusion product)


title: rdd_H2O_24h_RNAseq_rep2

value: hand-inoculated with H2O for 24 h


title: Male double-hit 2

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefeller University

library_source: genomic

data_processing:
Illumina NovaSeq 6000
Paired-end sequencing was performed to a depth of 100X coverage of the genome to ensure adequate resolution.
Reads were aligned with the mm10 genome from the BSgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0), with Rsubread’s alignment method in paired-end mode, with fragments of 1 to 5,000 base pairs in length considered correctly paired.
Duplicated pairs were removed using Picard tools (version 2.25.4).
Normalized, fragment signal bigWigs were created with the rtracklayer package. Peak calls were made with MACS2 software in BAMPE mode.
Differentially accessible motifs were discovered using ChromVAR package (version 1.14.0) with the motif database JASPAR 2020.
Differential ATAC-seq signals were identified using the DESeq2 package, and assigned to genes using ChIPseeker (version 1.26.2), and the annotation TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Assembly: mm10
Supplementary files format and content: DESeq2 files contain the logFC values comparing control animals and animals which underwent acute stress (ARS, FSS, and double-hit).

molecule: genomic DNA

source_name: Ventral Hippocampus

growth_protocol: Animals were group housed (n=4–5) in standard cages (28.5x17x13cm), which were changed weekly, and were kept on a 12-h light-dark cycle (lights off 7:00pm) in a temperature-controlled room maintained at 21±2°C. A 2lux red light permitted animal maintenance in the dark phase. Food and water were available ad libitum.

extract_protocol:
After rapid decapitation, brains were immediately dissected to separate the ventral hippocampus, which was rapidly flash frozen and stored at -80 °C. Cell nuclei were extracted from the ventral hippocampal tissue using the omni-ATAC protocol.
Tagmented DNA fragments were isolated to generate paired-end libraries constructed for next generation sequencing. Libraries were amplified and quantified using the KAPA Library Quantification Kit (Roche, Pleasenton, CA, USA). Three biological replicates were used per experimental group. cDNA libraries were sequenced on an Illumina NovaSeq 6000 to obtain 2x50-bp paired-end reads at an approximate sequencing depth of 150 million reads per sample.

treatment_protocol: At 2.5 months of age, mice were randomly assigned to either ARS, FSS, double-hit stress, or control groups.

tag: strain

value: Wild Type

value: Double-hit


title: siSTING4x_siYT_15

description: Gene expression of YAP/TAZ-depleted and STING-depleted fibroblasts

value: YAP and TAZ siRNAs + STING siRNA


title: P1-Untreated

source_name: T-cell

value: Untreated


title: Male double-hit 1


title: siSTING4x_siYT_16


title: Female double-hit 3

value: Female


title: Control_lot2


title: sicGAS4x_siAS_8

description: Gene expression of cGAS-depleted fibroblasts

value: Control siRNA (siAS) + cGAS siRNA


title: rdd_1h_RNAseq_rep1

value: seedlings

value: with 100 nm flg22 for 1 h


title: Patient-2_IP


title: rdd_3h_RNAseq_rep1

value: with 100 nm flg22 for 3 h


title: Patient-3_D7

source_name: PBMC

value: Primary cells (PBMC)

value: Male


title: Male double-hit 3


title: siSTING4x_siAS_13

value: WI-38 fibroblasts

value: Control siRNA (siAS) + STING siRNA


title: Female double-hit 2


title: Patient-1_D29


title: sicGAS4x_siYT_10

description: Gene expression of YAP/TAZ-depleted and cGAS-depleted fibroblasts

value: YAP and TAZ siRNAs + cGAS siRNA


title: rdd_1h_RNAseq_rep3

value: rdd


title: Patient-2_D28


title: rdd_1h_RNAseq_rep2


title: sicGAS4x_siYT_9


title: Patient-1_D12


title: sicGAS4x_siAS_7


title: siAS_siYT_3

description: Gene expression of YAP/TAZ-depleted fibroblasts

value: Control siRNA (siAS) + YAP and TAZ siRNAs


title: siAS_siAS_2

description: Gene expression of control fibroblasts

value: Control siRNA (siAS)


title: siAS_siYT_4


title: rdd_0h_RNAseq_rep3

value: with 100 nm flg22 for 0 h


title: Patient-1_IP

value: Primary cells (Infusion product)


title: Patient-2_D12


title: Female double-hit 1

value: Wild Type

value: Double-hit


title: Male FSS 3

value: FSS


title: Male FSS 1


title: Male FSS 2


title: CHiC HH18 posterior trunks

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: Capture Hi-C

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
Raw reads were preprocessed with cutadapt version 1.16 (Martin 2011 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length=15 --pair-filter=any --quality-cutoff=30).
Then hicup version 0.6.1 (Dryden et al. 2014) with bowtie2 version 2.2.6 (Langmead et al. 2012) and samtools 1.2 (Danecek et al. 2021) were used with default parameters.
The pairs  with both mates MAPQ30 and in the capture region (chr2:72402000-77000000 (mm10) and chr7:15000000–17000000 (galGal6)) were then loaded to a 5kb (mouse) and 2.5kb (chicken) resolution matrices with cooler version 0.7.4 (Abdennur and Mirny 2020).
The matrices obtained were corrected with hicCorrectMatrix tool version 3.5.3  (Ramirez et al. 2018, Wolff et al. 2018 and Wolff et al. 2020) and cooler balance.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: validPairs_filtered.csort.gz: valid pairs in juicebox format: Each line is a pair: <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse). Only pairs with both mates MAPQ30 and in the capture region (chr2:72402000-77000000 (mm10) and chr7:15000000–17000000 (galGal6)).
Supplementary_files_format_and_content: raw.cool: raw matrices
Supplementary_files_format_and_content: iced.cool: matrices ICEd normalized
Supplementary_files_format_and_content: domains.bed: TAD calling on Captured region

organism: Gallus gallus

source_name: posterior trunk

extract_protocol:
Micro-dissected E9.5 posterior trunks and HH18 posterior trunks were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated into single cell by collagenase treatment (10 µl of collagenase 50mg/ml (Sigma C9697) at 37º for approximately 15 mn). Samples were cross-linked with 2% formaldehyde (ThermoFisher 28908) for 10 minutes at room temperature and washed three times with PBS containing proteinase inhibitor. After discarding the supernatant cells were stored at -80º. Further processing was performed as described in (Yakushiji-Kaminatsui et al., 2018)
Following the Hi-C protocol, ligated DNA fragments were processed through the Agilent SureSelectXT protocol to enrich for fragments coming from the probe regions chr2:72240000-76840000 (mm9) and chr7:14946000–17870000 (galGal5).

tag: developmental stage

value: White Leghorn

value: WT


title: WT_flg22_priming_RNAseq_rep1

value: leaves

value: wild type

value: hand-inoculated with 100 nm flg22,and 24 h later hand-inoculated with Pst DC3000 hrcC at 2*108 cfu/mL for 1 h.


title: rdd_0h_RNAseq_rep1

value: seedlings


title: WT_flg22_priming_RNAseq_rep2


title: ChIP_H3K27ac_HH35_DS_rep2

description: ChIP

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: bigwig: normalized coverage track, when multiple biological replicates were done, the average was done
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2

source_name: dorsal skin

extract_protocol:
ChIP-seq experiments were performed as described in (Rodríguez-Carballo et al 2017).
ChIP-seq libraries were prepared as described in (Rodríguez-Carballo et al 2017).

treatment_protocol: dissection: Embryonic skin was micro-dissected from four HH35 embryos, sampled in the area delimited by the posterior limit of the neck, the posterior limit of the forelimbs and the lateral limit of forelimbs.

tag: chip antibody

value: H3K27ac Diagenode #C15410196


title: Female FSS 3

value: Female


title: ChIP_H3K27ac_HH35_FB_rep1

description: ChIP

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: bigwig: normalized coverage track, when multiple biological replicates were done, the average was done
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Open H3K27ac peaks were obtained by the intersection of H3K27ac peaks with ATAC peak regions in matching tissues, using betdtools intersect.
Conserved non-coding open H3K27ac peaks were obtained by the intersection of open H3K27ac peaks with conserved non-coding elements using betdtools intersect.
processed data files format and content: "OL_ATAC" narrowPeak: open H3K27ac peaks
processed data files format and content: "OL_ATAC_OL_CNEs" narrowPeak: conserved, non-coding and open H3K27ac peaks

source_name: forebrain

treatment_protocol: dissection: Four telencephalons from HH35 embryos were micro-dissected.


title: rdd_0h_RNAseq_rep2


title: WT_H2O_priming_RNAseq_rep2

value: hand-inoculated with H2O,and 24 h later hand-inoculated with Pst DC3000 hrcC at 2*108 cfu/mL for 1 h.


title: ChIP_H3K27ac_HH18_PT_rep2

description: ChIP

treatment_protocol: dissection: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from approximately fifty HH18 embryos.


title: ChIP_H3K27ac_HH35_DS_rep1

description: ChIP


title: Female FSS 1


title: siAS_siAS_1

description: Gene expression of control fibroblasts

value: WI-38 fibroblasts


title: WT_H2O_priming_RNAseq_rep1


title: WT_flg22_24h_RNAseq_rep3

value: hand-inoculated with 100 nm flg22 for 24 h


title: Male ARS 3

value: Male

value: ARS


title: WT_flg22_24h_RNAseq_rep2


title: WT_flg22_24h_RNAseq_rep1


title: ChIP_H3K27ac_HH18_PT_rep1

description: ChIP


title: Male ARS 2


title: d3 AMI heart_4_05_07_12

type: RNA

city: Hannover

first: Marc

middle: R.

last: Reboll

state: NDS

address: Carl-Neuberg-Str. 1

department: Molecular and Translational Cardiology, Department of Cardiology and Angiology

country: Germany

institute: Hannover Medical School

description: Myeloid cells from the infarctd left ventricle

hyb_protocol: cRNA fragmentation, hybridization to Whole Mouse Genome Oligo Microarrays V2 (Agilent Technologies, Agilent MicroArray Design Identifier 026655), and washing were performed as recommended in the One-Color Microarray-Based Gene Expression Analysis Protocol V5.7, except that 300 ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned with an Agilent G2565CA microarray scanner system (pixel resolution 5 µm, bit depth 20).

data_processing: Data were extracted with Feature Extraction Software V10.7.3.1 using the extraction protocol file GE1_107_Sep09.xml. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS), to retrieve one resulting value per unique non-control probe. Single features were excluded from averaging, if they were (i) manually flagged, (ii) were identified as outliers by the Feature Extraction Software, (iii) lay outside the interval of ‘1.42x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or (iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5. Averaged gPS values were normalized by Quantile normalization first, followed by global linear scaling. For the latter approach all quantile normalized gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be finally normalized (‘Array I’ in the formula shown below). Accordingly, finally normalized gPS values for all samples (microarray data sets) were calculated by the following formula: finally normalized gPSArray i = quantile normalized gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 finally normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.  Finally, normalized processed data were imported into Qlucore Omics Explorer software under default import settings for Agilent One Color mRNA microarrays, except that any (further) normalization option during import was deselected. Accordingly, data processing steps during Omics Explorer import were (i) removal of control measurements, (ii) log2 transformation, and (iii) baseline transformation to the median.

label: Alexa Fluor 555

source_name: d3 AMI heart

label_protocol: Aminoallyl-UTP (aa-UTP)-modified cRNA was prepared from 10 ng total RNA using the Amino Allyl MessageAmp II kit (Thermo Fisher Scientific; catalogue number, AM1753) and applying one round of amplification as recommended by the company; aa-UTP-cRNA was labeled with Alexa Fluor 555 reactive dye (Thermo Fisher Scientific; catalogue number, A32756) as described in the Amino Allyl MessageAmp II kit. All reaction volumes were down-scaled by a factor of 2.

extract_protocol: Total RNA was purified using the PicoPure kit (Thermo Fisher Scientific; catalogue number, KIT0204).

treatment_protocol: CD45high CD11bhigh (CD45R/B220, CD90.2/Thy-1.2, NK‑1.1, CD49b/DX5, Ly6G)low myeloid cells were isolated by FACS from the infarcted left ventricle and spleen 3 days after AMI in C57BL/6N wild-type mice.

value: infarcted left ventricle


title: d3 AMI heart_2_28_06_12


title: Female FSS 2

value: Wild Type


title: WT_H2O_24h_RNAseq_rep3

value: hand-inoculated with H2O for 24 h


title: ChIP_CTCF_HH18_PT_rep1

description: ChIP

value: CTCF Active motif #61311


title: Female ARS 3


title: Male ARS 1


title: Cisplatin-treated sorted CSC-like MDA-MB-231, exosome (Replicate 3)

city: Semenyih

first: May Zie

last: Koh

state: Selangor

address: Jalan Broga

department: Faculty of Sciences and Engineering

country: Malaysia

institute: University of Nottingham Malaysia

data_processing:
Cutadapt, Fastx toolkit, for quality control using FastQC software.
Clean data were obtained by filtering out low-quality reads and bases with less than 17 and more than 27 nucleotides prior to mapping miRNA read sequences to the human genome.
Reads were aligned to Ensembl human database (Homo sapiens GRCh 37.57) and known miRBase-21 (Homo sapiens) database using CLC benchwork v20.
Statistical analysis: Baggerley's t-test.

growth_protocol: The parental and sorted CSC-like MDA-MB-231 were cultured with or without 56µM of cisplatin treatment for 48 hours. All cells were maintained in 5% CO2 humidified incubator in exosomes depleted serum.

extract_protocol:
Total RNA with retention of small RNAs from the cells were extracted using ExoRNeasy.
RNA libraries were prepared for sequencing using standard NEB-Next multiplex small RNA protocols.

treatment_protocol: Cells were treated with 56µM of cisplatin for 48 hours prior to exosomes for RNA extraction.

tag: cell source

value: Human Caucasian breast adenocarcinoma

value: cisplatin-treated


title: d3 AMI heart_1_28_06_12


title: Cisplatin-treated sorted CSC-like MDA-MB-231, exosome (Replicate 2)


title: Cisplatin-treated sorted CSC-like MDA-MB-231, exosome (Replicate 1)


title: siCTR_Rep3

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

data_processing:
Raw reads were assessed for Phred quality scores using FASTQC, and low bases and adaptor sequences were trimmed off using Fqtrim retaining only reads of 76 bass length. Then, clean reads were aligned against the human reference genome (GRCh38.p10) with Gencode v27 annotation using STAR v2.5.1b [58]. STAR was run in two-pass mode allowing alignments to the transcriptome coordinates by setting the option --quantMode to TranscriptomeSAM.
The expression levels in read counts, TPM, and FPKM units were then estimated at both genes and isoforms levels by running RSEM, on the alignment files in default parameters.
Differentially expressed genes and isoforms upon ESRP1/2 silencing were identified using the DESeq2 R package (v1.26.0) in default parameters. The expression at isoform level was summarized to gene-level using the tx-import bioconductor package and the resulting count matrices were provided to DESeq2. Prior to DE analysis, lowly expressed genes and isoforms were discarded from the analysis and only genes or isoforms with more than 10 normalized read counts in at least one condition (3 out of 6 samples) were considered for further downstream analysis. A gene or isoform was assigned as differentially expressed if its associated BH-adjusted p-value < 0.05.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include the normalized gene and isoform levels for each sample

molecule: polyA RNA

growth_protocol: MCF-7 cells were routinely grown in DMEM (Dulbecco’s Modified Eagle’s Medium) (Life Technologies, 31053–028, Waltham, MA, USA) supplemented with 10% heat-inactivated FBS (fetal bovine serum) (Euroclone S.p.A, ECS0180L, Milan, Italy) and 2 mM L-glutamine (ThermoFisher Scientific, 25030–024, Waltham, MA, USA). Cells were cultured at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated from MCF-7 cells using the RNeasy Mini Kit, according to the manufacturer’s protocol (Qiagen, 74104, Hilden, Germany). Experiments were performed in three biological replicates. First-strand cDNA synthesis was performed with the SensiFAST™ cDNA Synthesis Kit (Bioline, BIO-65054, London, UK). Qualitative PCR analysis was performed using MA038 EconoTaq 2xMaster Mix (Lucigen). PCR products were analyzed on a 3% agarose gel, stained with SYBR™ Safe DNA Gel Stain (S33102 ThermoFisher Scientific).
RNA quality check (RNA integrity number (RIN) > 8) was achieved with a Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, IA, USA) and quantified with Qubit (Qubit™ RNA HS Assay Kit, ThermoFisher Scientific, Waltham, MA, USA; Q32852). Total RNA, depleted of ribosomal RNAs fractions, was used to construct the RNA-Seq libraries using Illumina TruSeq RNA sample prep kit (TruSeq™ RNA Sample Prep Kit v2-Set B, Illumina, RS-122-2002, San Diego, CA, USA).

treatment_protocol: The cell transfection in suspension was performed by seeding one million cells along with a transfection mix composed of siRNAs (30 nM final concentration) and Lipofectamine3000 (ThermoFisher Scientific, L3000015, Waltham, MA, USA), as transfection reagents. Cells were left to attach overnight in the cell incubator and, subsequently, the medium was refreshed. Two custom-designed siRNAs were used to target ESRP1 and ESRP2 (siESRP1 5′-CAGCAGGUGCUGAAUCGUUCUCCU-3′, siESRP2 5′-GCACAUCACUAGAGGUGGCUCGUUU-3′); stealth RNAi™ siRNA Negative Control medium GC was used as a control (siCTRL). All the siRNAs were purchased from ThermoFisher Scientific (Waltham, MA, USA).

value: breast cancer cell line


title: WT_H2O_24h_RNAseq_rep2

value: leaves

value: wild type


title: Female ARS 2


title: siESRP12_Rep3


title: WT_H2O_24h_RNAseq_rep1


title: Female ARS 1


title: siESRP12_Rep2


title: Male Control 3

value: Control


title: d3 AMI spleen_4_05_07_12

description: Myeloid cells from the spleen

source_name: d3 AMI spleen

value: spleen


title: WT_3h_RNAseq_rep2

value: seedlings

value: with 100 nm flg22 for 3 h


title: WT_3h_RNAseq_rep3


title: Sorted CSC-like MDA-MB-231, exosome (Replicate 1)

source_name: Sorted CSC-like MDA-MB-231, exosome

value: Untreated


title: Male Control 2


title: siCTR_Rep1


title: Male Control 1


title: human-Ctrl_3-mRNA

city: Urumqi

first: xia

last: li

address: 567Shangde North Road

department: Department of Histology and Embryology ,School of Basic Medical Sciences

institute: Xinjiang Medical University

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

source_name: serum exosome

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

tag: sample type

value: serum exosome

tag: molecule subtype

value: exosome RNA

tag: subject status

value: uterine fibroid patient; ovarian normal control


title: siESRP12_Rep1

tag: cell line


title: d3 AMI spleen_2_28_06_12

description: Myeloid cells from the spleen


title: WT_1h_RNAseq_rep3

value: with 100 nm flg22 for 1 h


title: Female Control 3

value: Female

value: Wild Type


title: Cisplatin-treated MDA-MB-231 parental, exosome (Replicate 2)


title: WT_1h_RNAseq_rep2


title: siCTR_Rep2

tag: cell type


title: Sorted CSC-like MDA-MB-231, exosome (Replicate 3)


title: human-Ctrl_2-mRNA


title: human-Ctrl_1-mRNA


title: d3 AMI spleen_1_28_06_12

description: Myeloid cells from the spleen


title: Sorted CSC-like MDA-MB-231, exosome (Replicate 2)


title: Female Control 1

tag: Sex


title: WT_1h_RNAseq_rep1

tag: age


title: Cisplatin-treated MDA-MB-231 parental, exosome (Replicate 1)


title: WT_0h_RNAseq_rep3

value: with 100 nm flg22 for 0 h


title: MDA-MB-231 parental, exosome (Replicate 3)

source_name: MDA-MB-231 parental, exosome

value: Human Caucasian breast adenocarcinoma


title: WT_3h_RNAseq_rep1


title: human-CA_3-mRNA

value: ovarian cancer patient


title: MDA-MB-231 parental, exosome (Replicate 2)


title: Cisplatin-treated MDA-MB-231 parental, exosome (Replicate 3)

value: cisplatin-treated


title: Young_YTcKO

description: Single-cell profiling of young YAP/TAZ knockout mouse skin

data_processing:
The Cell Ranger Count pipeline (version 3.1.0) was used to align reads to the mouse reference transcriptome (mm10) and to calculate UMI counts from the mapped reads.
Expression data were imported in R and analyzed using Seurat R package (version 3.1.5).
Genome_build: mm10
Supplementary_files_format_and_content: Output files of Cell Ranger Count pipeline (contained in 'filtered_feature_bc_matrix' found in the outs folder)

source_name: Dorsal skin

extract_protocol:
Single cell suspension was obtained from mouse dorsal skin samples incubated in Collagenase I; cells were then washed with PBS and filtered repeatedly through a 70 µm cell strainer. Droplet-based single cell RNA-capture was performed with the Chromium Single Cell 3’ kit v3.1 (10x Genomics).
cDNA generation and library preparation were performed using the Chromium Single Cell 3’ kit v3.1 (10x Genomics).

treatment_protocol: Young mice were treated with one oral gavage of 0.11 mg/g body weight Tamoxifen (Sigma-Aldrich, T5648) per day, during 2 consecutive days every week for four weeks.

value: Dorsal skin

value: 2.5 months-old

tag: genetic background

value: R26-CAG-CreER; Yap1 fl/fl; Wwtr1 fl/fl

tag: experimental conditions

value: Tamoxifen-treated


title: WT_0h_RNAseq_rep2

tag: tissue

value: seedlings

value: wild type


title: human-CA_2-mRNA


title: MDA-MB-231 parental, exosome (Replicate 1)

value: Untreated


title: WT_0h_RNAseq_rep1

tag: genotype


title: Old_control

description: Single-cell profiling of old control mouse skin

value: 24 months-old

value: wild-type


title: Female Control 2

tag: treatment

value: Control


title: human-CA_1-mRNA

value: serum exosome

value: exosome RNA


title: OB-Con-3

status: Public on Jun 19 2022

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

data_processing:
Trimmed Reads were mapped to Mus musculus GRCm38 using STAR aligner v.2.5.2b
Assembly: GRCm38
Supplementary files format and content: counts

source_name: olfactory bulb

extract_protocol:
OBs (two for each mouse, from 3 mice each condition) were collected and homogenized in 500 mL TRIzol reagent (ThermoFisher). Samples were incubated for five minutes at 4°C and 100 mL chloroform was subsequently added. Samples were centrifuged for fifteen minutes at 12,000 x g at 4°C and the aqueous layer was collected and transferred to a 1.5 mL centrifuge tube. 250 mL of isopropanol was added to samples and incubated for ten minutes at 4°C. The samples were centrifuged for ten minutes at 12,000 x g at 4°C and the supernatant discarded. Pellets were resuspended in 500 mL 75% ethanol and vortexed before being centrifuged for five minutes at 7,500 x g at 4°C. Pellets were allowed to dry and rehydrated in 35 mL of RNase free ultrapure water. Samples were incubated at 60℃ for fifteen minutes to complete RNA isolation. RNA concentrations and purity were assessed using a NanoDrop Lite Spectrophotometer (Thermo Scientific). Sample quantity and RIN values were determined.
Libraries were prepared using NEBNext Ultra RNA Library Preparation Kit according to the manufacturer’s protocol (New England Biolabs).

treatment_protocol: Mice were injected with tamoxifen or not injected

value: olfactory bulb

value: Tsc2 mut/mut

value: CON


title: OB-Con-2


title: OB-TX-3

value: tamoxifen


title: OB-Con-1


title: OB-TX-2


title: OB-TX-1


title: zr2149_3

city: Munich

first: sharmilee

last: vetrivel

state: Bayern

address: ziemssenstraße 1, DG

institute: Ludwig Maximilian University of Munich (Universität München)

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and 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: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: E10.5 heads

extract_protocol:
ChIP pull-downs are prepared using snap-frozen mice embryo heads
ChIP-Seq libraries are quantified using 2200 Tape Station
Next-Gen Sequencing platform – HiSeq

value: E10.5 heads


title: control-HBP1-3

city: beijing

first: ZHANG

last: Tongjia

address: xueyuan Road 38

institute: peking university

data_processing:
HISAT2-2.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using HISAT2-2.0.4
Read count extraction and normalization were performed using sequence using HISAT2-2.0.4
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hela

growth_protocol: Hela cells were 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 Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® mRNA Isolation Master Kit following manufacturer's protocols.

treatment_protocol: Over expression HBP1 and HBP1R378A in Hela cells,respectively

value: Hela

value: cervical cancer cells


title: control-HBP1-2


title: control-HBP1-1


title: HBP1R378A3

value: HBP1 Mut


title: HBP1R378A2


title: 1231A3, MSC from NCC PN7, rep1

city: Fujisawa

first: Daisuke

last: Kamiya

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: CiRA

institute: Kyoto University

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent S5 XL sequencer (Torrent suite v5.16.1).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent S5 XL sequencer (Torrent suite v5.16.1).
RPM were calculated using plug-in software provided with the Ion Torrent S5 XL sequencer (ampliSeqRNA v5.6.0.3)
Assembly: hg19
Supplementary files format and content: Tab-delimited text file include gene symbol and gene expression in RPM for each sample

growth_protocol: 1231A3 human iPSC were cultured on an iMatrix-511 (Nippi, Tokyo, Japan)-coated cell culture plate or dish in StemFit AK03N (Ajinomoto, Tokyo, Japan). The medium was changed every 2 days

extract_protocol:
Total RNA was purified using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA)
10 ng of total RNA were reverse transcribed  to obtain single-stranded cDNA using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). cDNA libraries were  synthesised using the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel (Thermo Fisher Scientific) and the Ion Ampliseq Library Kit Plus (Thermo Fisher Scientific), according to the manufacturer’s protocol. Barcode-labeled cDNA libraries were analyzed using the Ion S5 XL System (Thermo Fisher Scientific) and the Ion 540 Chip Kit (Thermo Fisher Scientific).

treatment_protocol: For NCC induction, iPS cells were cultured in StemFit Basic03 (equivalent to AK03N without bFGF, Ajinomoto, Tokyo, Japan) with 10 μM SB431542 (FUJIFILM Wako) and 1 μM CHIR99021 (Axon Medchem, Reston, VA, USA) for 10 days.CD271high sorted NCCs were seeded onto fibronectin-coated plates in Basic03 supplemented with 10 μM SB431542, 20 ng/mL EGF (FUJIFILM Wako), and FGF2 (FUJIFILM Wako). MSCs were induced from NCCs by cultured in PRIME-XV MSC Expansion XSFM medium (IrvineScientific).

value: MSCs from iPSC-derived NCCs

value: WT

value: MSC differentiation

tag: time


title: 1231A3, MSC from NCC PN7, rep3


title: 1231A3, MSC from NCC PN7, rep2


title: 1231A3, MSC from NCC PN4, rep2


title: 1231A3, MSC from NCC PN7, rep4


title: 1231A3, MSC from NCC PN4, rep4


title: 1231A3, MSC from NCC PN4, rep3


title: 1231A3, MSC from NCC PN2, rep3


title: 1231A3, MSC from NCC PN2, rep1


title: 1231A3, MSC from NCC PN2, rep2


title: HBP1R378A1


title: 1231A3, NCC expansion PN7, rep1

value: NCCs from iPSCs

value: NCC expansion


title: 1231A3, NCC expansion PN7, rep2


title: 1231A3, NCC expansion PN4, rep2


title: 1231A3, NCC expansion PN4, rep1


title: 1231A3, NCC expansion PN4, rep3


title: Aba_100ug_4

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Primary fibroblast like synoviocyte

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Isolated synovial cells were cultured in DMEM with 10% FBS and cultured at 37°C containing 5% CO2 for overnight.

extract_protocol: RNA samples were extracted from cells using ReliaPrep RNA Tissue miniprep system (Promega).

treatment_protocol: Abatacept (100 mg/ml), human IgG (100 mg/ml), and vehicle (DMEM with 10% FBS as a control) added and incubated at 37°C with 5% CO2 for 48 h.

value: Inflamed joints

value: Primary fibroblast like synoviocyte

value: Abatacept


title: 1231A3, NCC expansion PN7, rep3


title: 1231A3, MSC from NCC PN2, rep4


title: Non treatment_7

value: Vehicle


title: 1231A3, MSC from NCC PN4, rep1


title: HSC-5 sgEZH2-2_3

city: Cold Spring Harbor

first: Seamus

last: Balinth

address: 1 Bungtown road

institute: Cold Spring Harbor Lab

data_processing:
Quality control using FastQC
Mapping reads to a reference genome with STAR
Differential expression gene analysis using DESeq
Assembly: hg38
Supplementary files format and content: Counts from DeSeq analysis were exported into a single file comparing control samples to sgEZH2-1 and sgEZH2-2 samples

source_name: skin

growth_protocol: Cells were grown in DMEM with 10% FBS

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit
Libraries were constructed following the Illumina TruSeq Stranded mRNA (LT) Protocol

tag: cell condition

value: EZH2-depleted (sgRNA)


title: HSC-5 sgEZH2-2_2


title: Syn_100ug_6

value: Human IgG


title: HSC-5 sgEZH2-1_3


title: HSC-5 sgEZH2-1_1


title: HSC-5 sgEZH2-2_1


title: HSC-5 sgEZH2-1_2


title: HSC-5 Control-2

value: Control (empty vector)


title: HSC-5 p63 IP 2

data_processing:
Quality control using FastQC
Trimmomatic
Bowtie Mapper
MACS14
Wig-to-bigWig
Assembly: hg19
Supplementary files format and content: Peaks from MACS14 analysis were exported as processed files

extract_protocol:
HSC-5 cells were harvested, crosslinked with 1% formaldehyde for 12 min at room temperature, and quenched with 0.125 M Glycine for 10 mins at room temperature. Following 1 PBS wash, 10 x106 cells were lysed in 1 ml Cell Lysis Buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, protease inhibitor) for 10 min on ice. Nuclei were collected by centrifugation at 4,200 rpm for 30 sec, lysed in 500 µl Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, protease inhibitor) for 15 min on ice, and sonicated using the Bioruptor (Diagenode) for 15 min at 4ºC with the following settings: medium intensity, On/Off 30s, for 15 cycles. The sonicated chromatin was centrifuged at 13,000 rpm for 15 min at 4ºC. 50 µl of the supernatant was stored at 4ºC as Input chromatin DNA. Remaining supernatant was diluted in 3.5 ml IP Dilution Buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.01% SDS), incubated with p63 antibody for 2 hrs at 4ºC, and then combined with 30 µl of magnetic beads to rotate overnight at 4ºC. The following day, beads were washed once with IP Wash Buffer I (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash Buffer II (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and twice with TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA). Immunoprecipitated chromatin (ChIP DNA) was eluted in 200 µl Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubation at 65ºC for 15 min. Input DNA was  then reverse-crosslinked along with ChIP DNA using 12 µl of 5 M NaCl and 1 µg/ml RNase A in 65ºC waterbath overnight, followed by treatment with 4 µg/ml Proteinase K at 42ºC for 2 hrs and purification was conducted using MinElute PCR purification kit (QIAGEN). Next-gen sequencing was used to identify enriched chromatin in the IP samples. Data was processed in Galaxy where FastQC was first used to confirm the quality of the samples. Bowtie mapper was then used to map reads to the reference genome and peak calling was performed through MACS14. Data was visualized in the UCSC genome browser. Finally, MEME-ChIP analysis was applied via the MEME suite to confirm enrichment of the p63 binding motif [35]. The experiment was run in duplicate and common targets were evaluated for further study. For p63 IP 2, trimmomatic was used to improve the quality of reads before proceeding with bowtie mapper.
Libraries were constructed following the Illumina TruSeq ChIP Protocol

value: IP

tag: antibody

value: Anti-p63 (D9L7L) from CST


title: HSC-5 Control-1


title: 1231A3, NCC expansion PN0, rep1

value: Passage Number 0 (PN0)


title: 1231A3, NCC day10, CD271 high, rep3

value: NCC differentiation

value: day10 CD271 high


title: 1231A3, NCC expansion PN0, rep2


title: 1231A3, NCC expansion PN0, rep3


title: prostaspheres, Pb, A27 (AA25)

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file reporting raw counts with genes in rows and samples in columns

source_name: RWPE-1 prostaspheres, 1 μM Pb, 7 days

growth_protocol: human prostaspheres derived from an immortalized human prostate epithelial cell line RWPE-1 cells were treated with metals and cultured on ultra-low attachment matrices

extract_protocol:
Total RNA were extracted from the treated human prostaspheres using mirVana miRNA Isolation Kit according to the manufacturer's recommended protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: immortalized human prostate epithelial cells RWPE-1

value: prostate epithelial stem progentior cells enriched as prostaspheres

value: prostate

value: treated with 1 μM Pb (#4)


title: HSC-5 Input 2

value: Input


title: prostaspheres, Cu, A27 (AA24)

source_name: RWPE-1 prostaspheres, 10 μM Cu, 7 days

value: treated with 10 μM Cu (#4)


title: 1231A3, NCC day10, CD271 high, rep2

value: NCCs from iPSCs

value: WT


title: HSC-5 p63 IP 1


title: Young_control

description: Single-cell profiling of young control mouse skin

value: Dorsal skin

value: 2.5 months-old

value: Yap1 fl/fl; Wwtr1 fl/fl

value: Tamoxifen-treated


title: prostaspheres, Cr, A27 (AA23)

source_name: RWPE-1 prostaspheres, 1 μM Cr, 7 days

value: treated with 1 μM Cr (#4)


title: prostaspheres, Ti, A27 (AA22)

source_name: RWPE-1 prostaspheres, 10 μM Ti, 7 days

value: treated with 10 μM Ti (#4)


title: prostaspheres, Cd, A27 (AA21)

source_name: RWPE-1 prostaspheres, 5 μM Cd, 7 days

value: treated with 5 μM Cd (#4)


title: HSC-5 Input 1


title: prostaspheres, iAs, A27 (AA20)

source_name: RWPE-1 prostaspheres, 5 μM iAs, 7 days

value: treated with 5 μM iAs (#4)


title: prostaspheres, Cu, A27 (AA17)

value: treated with 10 μM Cu (#3)


title: RC-4B/C, control (R24_S33)

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

data_processing:
FASTQ Generation | Version: 1.0.0  on Illumina BaseSpaceFS version: 2.0.1018 system
Sequenced reads were trimmed for adaptor and low-quality sequence with trim_galore version 0.4.1 and cutadapt version 1.14
The trimmed sequence sets were aligned to the rat genome with TopHat v2.1.0 (bowtie2-align-s version 2.3.4.3), using default parameters
Performed union-CDS based count with R Rsubread package version 1.34.7 , and count processing and rpkm calculation with R edgeR package version 3.26.8
Assembly: Rattus_norvegicus.Rnor_6.0.dna_sm.toplevel.fa
Supplementary files format and content: csv file includes union-CDS based RPKM values and annotation information for each Sample

organism: Rattus

extract_protocol:
Total RNA was extracted with Qiagen MiRNeasy Mini kit (217004, Qiagen, Hilden, Germany)
NGS library preparation was done using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with Purification Beads (NEB #E7760S/L)
PolyA NGS library preparation

value: pituitary cell

value: DMSO


title: prostaspheres, control, A27 (AA19)

source_name: RWPE-1 prostaspheres, no treatment control, 7 days

value: immortalized human prostate epithelial cells RWPE-1

value: prostate epithelial stem progentior cells enriched as prostaspheres

value: prostate

value: control, no metal treatment (#4)


title: MTR4KD-sonic-1

city: Kyoto

first: Seiji

last: Masuda

state: Kyoto

address: Kitashirakawa Oiwakecho, Sakyo-ku

institute: Division of Integrated Life Sciences, Graduate School of Biostudies

data_processing:
Illumina RTA software used for basecalling.
Illumina bcl2fastq 2.17 used for demutiplexing.
Sequences were trimmed using TrimGalore v0.6.5 to remove low-quality base calls from the 3’end of the reads, to detect and remove i7 index (AGATCGGAAGAGC) and to discard trimmed reads shorter than 20 bases.
R1 reads were mapped to the ERCC sequence combined GRCh37.75 as single–end reads, using STAR aligner v2.5.3a with options of --outFilterType BySJout --outFilterMultimapNmax 1, to generate bam files.
Mapped reads were counted by HTseq htseq-count v0.9.5 with options of -m intersection-nonempty -s yes -f bam –r pos, using the genome annotation for GRCh37.75 from ENSEMBL combined with the ERCC spike-in annotation from Thermo Fisher Scientific.
Read counts from each replicate were separately subjected to the differential expression analyses using DESeq2 v1.24.0.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptoolsv3.4.3 bamCoverage with options --binSize=1 --samFlagExclude 16 to geneate fw_coverage.bw and --binSize=1 --samFlagInclude 16 to generate rv_coverage.bw.
Supplementary_files_format_and_content: csv files were output files fromDESeq2 analysis following htseq-count using Homo_sapiens.GRCh37.75 gtf and PROMPTs gtf provided in Wu,G et al., Cell Reports 2020.

source_name: sonic-method, HeLa, MTR4 KD, rep1

extract_protocol:
Harvested cells were lysed in NP-40 containig buffer and nuclei were collected by centrifugation. Total nuclear RNAs were prepared with Sepasol-RNA I Super G (Nacalai Tesque) either by hp-method or by sonic-method.
RNA libraries were prepared with QuantSeq 3'mRNA-Seq Library Prep Kit (FWD)(LEXOGEN) according to the manufacture’s instructions for sequencing using standard Illumina protocols.

value: HeLa

tag: knockdown

tag: preparation method

value: sonic

value: nuclear RNA


title: RRP6MPP6KD-sonic-2

source_name: sonic-method, HeLa, RRP6/MPP6 KD, rep2


title: prostaspheres, Ti, A27 (AA16)

value: treated with 10 μM Ti (#3)


title: MTR4KD-sonic-2

source_name: sonic-method, HeLa, MTR4 KD, rep2


title: RRP6DIS3KD-sonic-2

source_name: sonic-method, HeLa, RRP6/DIS3 KD, rep2


title: RRP6MPP6KD-sonic-1

source_name: sonic-method, HeLa, RRP6/MPP6 KD, rep1


title: RC-4B/C, control (R22_S31)


title: 1231A3, NCC day10, CD271 high, rep1

value: NCCs from iPSCs

value: WT

value: NCC differentiation

value: day10 CD271 high


title: RRP6DIS3KD-sonic-1

source_name: sonic-method, HeLa, RRP6/DIS3 KD, rep1


title: MPP6KD-sonic-2

source_name: sonic-method, HeLa, MPP6 KD, rep2


title: prostaspheres, control, A27 (AA14)

value: control, no metal treatment (#3)


title: prostaspheres, Pb, A27 (AA13)

value: treated with 1 μM Pb (#2)


title: RC-4B/C, ASA treated (R20_S29)

value: ASA


title: EMseq_ABKn8

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

data_processing:
illumina and hairpin adapter sequence was trimmed using custom script TrimRead.py
Read Deconvolution using custom scripts
XM tag was added for methylation extraction using custom script AddXMtag.py
Assembly: gencode GRCh38.p5 Release 24
Supplementary files format and content: WGS Methyl-SNP-seq identified SNP of NA12878 (common SNP between Deconvoluted Read and Read2, ~/NA12878_AccurateSeq/variant_bowtie2/rtg_common_R1_R2/Methyl-SNP-seq_NA12878.vcf)
Supplementary files format and content: WGS Methyl-SNP-seq methylation file of NA12878 generated by bismark_methylation_extractor (~/NA12878_AccurateSeq/methylation_bowtie2/NoCX/AccMerge_Deconvolution_Calibration_R1.sort.bismark.cov)

organism: Clostridium acetobutylicum

source_name: EM-seq on C. acetobutylicum

growth_protocol: strandard growth protocol for GM12878 cell line

extract_protocol:
genomic DNA isolated from the GM12878 cell line by Coriell Institute
Methyl-SNP-seq

tag: strain


title: prostaspheres, Cd, A27 (AA15)

value: treated with 5 μM Cd (#3)


title: RC-4B/C, control (R23_S32)

value: pituitary cell

value: DMSO


title: DIS3KD-sonic-2

source_name: sonic-method, HeLa, DIS3 KD, rep2

tag: molecule subtype


title: RC-4B/C, ASA treated (R19_S28)


title: prostaspheres, iAs, A27 (AA10)

value: immortalized human prostate epithelial cells RWPE-1

value: prostate epithelial stem progentior cells enriched as prostaspheres

value: treated with 5 μM iAs (#2)


title: RC-4B/C, ASA treated (R21_S30)


title: prostaspheres, Cr, A27 (AA9)

value: prostate

value: treated with 1 μM Cr (#2)


title: prostaspheres, Ti, A27 (AA8)

value: treated with 10 μM Ti (#2)


title: Methyl-SNP-seq_Ecoli

organism: Escherichia coli

source_name: Methyl-SNP-seq on E.coli


title: Methyl-SNP-seq_NA12878_TargetEnrich_Rep1

source_name: Methyl-SNP-seq on NA12878, exome target enrichment, 400bp sonication


title: Liver KI rep3

city: Nanjing

first: Chen

last: Shuai

address: Xuefu Road 12

institute: Nanjing University

data_processing:
The illumina high-throughput sequencing results initially existed as original image data files and were converted into original sequencing sequence (raw read) by BCL2FastQ2
The raw read were filtrated through removing adaptor, low-quality and N ratio greater than 5% sequence.
The filtrated read was mapped to mouse reference transcripts (GENCODE Release version M21) using softwave Salmon (version0.14.0)
Gene expression value was quantitatively estimated through Fragments per Kilobase per Million Mapped Fragments (FPKM)
Gene differential expression between the three groups was analyzed by DESeq2 (version1.30.0).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
RNA was harvested using Takara Trizol reagent and standard RNA lsolation protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 60% fat diet for 3 months

value: liver

value: trim24 C52/55A KI

value: High fat diet

value: 5 months


title: DIS3KD-sonic-1

source_name: sonic-method, HeLa, DIS3 KD, rep1

value: HeLa

value: sonic

value: nuclear RNA


title: Methyl-SNP-seq_NA12878_Rep2_lane2

source_name: Methyl-SNP-seq on NA12878, WGS, Replicate 2, lane2


title: MPP6KD-sonic-1

source_name: sonic-method, HeLa, MPP6 KD, rep1


title: RRP6KD-sonic-2

source_name: sonic-method, HeLa, RRP6 KD, rep2


title: prostaspheres, control, A27 (AA7)

source_name: RWPE-1 prostaspheres, no treatment control, 7 days

value: control, no metal treatment (#2)


title: Methyl-SNP-seq_NA12878_TargetEnrich_Rep2

source_name: Methyl-SNP-seq on NA12878, exome target enrichment, 500bp sonication


title: prostaspheres, Cr, A27 (AA5)

source_name: RWPE-1 prostaspheres, 1 μM Cr, 7 days

value: treated with 1 μM Cr (#1)


title: Methyl-SNP-seq_NA12878_Rep1_lane2

source_name: Methyl-SNP-seq on NA12878, WGS, Replicate 1, lane2


title: prostaspheres, Cu, A27 (AA6)

source_name: RWPE-1 prostaspheres, 10 μM Cu, 7 days

value: treated with 10 μM Cu (#1)


title: ControlKD-sonic-2

source_name: sonic-method, HeLa, Control KD, rep2

value: Control


title: Liver WT rep1

value: wild type


title: Liver KI rep1


title: prostaspheres, Ti, A27 (AA4)

source_name: RWPE-1 prostaspheres, 10 μM Ti, 7 days

value: immortalized human prostate epithelial cells RWPE-1

value: prostate epithelial stem progentior cells enriched as prostaspheres

value: treated with 10 μM Ti (#1)


title: Liver WT rep3


title: Methyl-SNP-seq_NA12878_Rep2_lane1

source_name: Methyl-SNP-seq on NA12878, WGS, Replicate 2, lane1


title: RRP6DIS3KD-hotphenol-2

source_name: hp-method, HeLa, RRP6/DIS3 KD, rep2

value: hp


title: Methyl-SNP-seq_NA12878_Rep1_lane1

source_name: Methyl-SNP-seq on NA12878, WGS, Replicate 1, lane1


title: MI heart + weekly prednisone3

first: Mattia

last: Quattrocelli

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were trimmed using Trimmomatic and aligned to mm10 using HiSat2
Isoform counts were obtained through Kallisto as CPM
Genome_build: mm10
Supplementary_files_format_and_content: Table reporting CPM values for each RNA isoform for each sample

source_name: myocardium

extract_protocol:
Total RNA was isolated through Trizol and purified through Qiagen Rneasy columns
True-Seq stranded mRNA library (Illumina)

treatment_protocol: Prednisone (Sigma #P6254) was injected  as once-weekly IP solution of 1mg/kg in 100ul PBS from a 5mg/kg stock solution in DMSO in male C57BL/6 WT mice of approximately 10 weeks of age at ZT0 (lights-on), starting from 2-weeks  after sham or MI surgery. 24 hours after last injection myocardial tissue was obtained from each mouse and RNA isolated and purified.

tag: drug treatment

value: 6-week-long weekly prednisone

tag: model specs

value: ~16wo C57BL/6 WT male mouse


title: RRP6KD-sonic-1

source_name: sonic-method, HeLa, RRP6 KD, rep1

tag: cell line


title: RRP6DIS3KD-hotphenol-1

source_name: hp-method, HeLa, RRP6/DIS3 KD, rep1


title: prostaspheres, Cd, A27 (AA3)

source_name: RWPE-1 prostaspheres, 5 μM Cd, 7 days

tag: cell type

value: prostate

value: treated with 5 μM Cd (#1)


title: Liver WT rep2

source_name: Liver

value: liver

value: High fat diet

tag: age

value: 5 months


title: ControlKD-sonic-1

source_name: sonic-method, HeLa, Control KD, rep1

value: HeLa

value: sonic

value: nuclear RNA


title: MI heart + weekly prednisone1


title: the hypopharynx tissue of patient 5

city: Jinan

first: Rui

last: Guan

state: Shandong

address: West Wenhua Road

institute: Shandong University

library_source: transcriptomic single cell

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read 2 by featureCounts software.
Supplementary files format and content: matrix files

source_name: hypopharynx

extract_protocol:
Hypopharynx tissues were removed and stored in the GEXSCOPE® Tissue Preservation Solution, and scRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit. Individual libraries were diluted to 4nM and pooled for sequencing.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

value: hypopharynx

value: untreated


title: prostaspheres, iAs, A27 (AA2)

source_name: RWPE-1 prostaspheres, 5 μM iAs, 7 days

value: treated with 5 μM iAs (#1)


title: the hypopharynx tissue of patient 1


title: Liver KI rep2

value: trim24 C52/55A KI


title: cytoplasm_CHERP_1

description:
cytoplasm_EGFP_vs_CHERP_GeneMat.de
cytoplasm_EGFP_vs_CHERP_A3SS.MATS.ReadsOnTargetAndJunctionCounts
cytoplasm_EGFP_vs_CHERP_A5SS.MATS.ReadsOnTargetAndJunctionCounts
cytoplasm_EGFP_vs_CHERP_MXE.MATS.ReadsOnTargetAndJunctionCounts
cytoplasm_EGFP_vs_CHERP_RI.MATS.ReadsOnTargetAndJunctionCounts
cytoplasm_EGFP_vs_CHERP_SE.MATS.ReadsOnTargetAndJunctionCounts

data_processing:
Reads were aligned to hg19 genome using STAR (version2.5.2b)
mRNA expression analysis was performed using RSEM (version1.2.25)
Alternative mRNA splicing analysis was performed using rMATS (version3.2.5)
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generate using rMATS (version3.2.5)

molecule: cytoplasmic RNA

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle medium (FUJIFILM Wako Pure Chemical, Osaka, Japan) containing 10% fatal bovine serum (Thermo Fisher Scientific KK., Waltham, MA, USA).

extract_protocol:
U2OS cells transfected with EGFP or CHERP#2 siRNA were scraped, washed with PBS and treated with cell lysis buffer [20 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM MgCl2, 1% NP-40] on ice for 5 min. Then, the cytoplasmic fraction was isolated by taking the supernatant after brief spin. Whole or cytoplasmic RNA was isolated by Sepasol RNA I super G (Nacalai tesque, Kyoto, Japan) according to the manufacturer’s instructions.
RNA-seq library was prepared using Truseq Stranded mRNA Library Prep Kit (Illumina, CA, USA) and sequenced on an NextSeq High Output (Illumina, CA, USA) following the manufacturer's protocol.

treatment_protocol: U2OS cells (20% confluency) were transfected with EGFP or CHERP#2 siRNA (Integrated DNA Technologies, Coralville, IA, USA). Those siRNAs were transfected at a concentration of 20nM for 48h, respectively.

tag: transfection

value: CHERP siRNA#2


title: MI heart + vehicle3

value: 6-week-long weekly vehicle


title: the hypopharynx tissue of patient 3


title: prostaspheres, control, A27 (AA1)

source_name: RWPE-1 prostaspheres, no treatment control, 7 days

value: immortalized human prostate epithelial cells RWPE-1

value: prostate epithelial stem progentior cells enriched as prostaspheres

value: control, no metal treatment (#1)


title: RC: U87 cells, CCA-1.1, 72 h

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

data_processing:
The qualities of cleaned reads were assessed using FastQC version 0.11.9 (https://github.com/s-andrews/FastQC)
the reports were compiled using MultiQC version 1.1 (https://multiqc.info).
The transcript were quantified using the pseudo-alignment method employing kallsito version 0.461
Supplementary files format and content: tab-delimited text files

source_name: Brain

growth_protocol: U87 cells were culture using RPMI supplemented with 10% of FBS in 5% CO2 incubator

extract_protocol:
RNA was harvested using Bioline - Isolate II RNA Mini Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CCA-1.1 or DMSO

value: Brain

value: Glioblastoma

value: WT


title: the hypopharynx tissue of patient 4


title: MI heart + vehicle2

value: ~16wo C57BL/6 WT male mouse


title: ControlKD-hotphenol-1

source_name: hp-method, HeLa, Control KD, rep1

value: Control

value: hp


title: cytoplasm_EGFP_1

value: EGFP siRNA


title: ControlKD-hotphenol-2

source_name: hp-method, HeLa, Control KD, rep2

value: HeLa

value: nuclear RNA


title: MI heart + weekly prednisone2

value: 6-week-long weekly prednisone


title: MI heart + vehicle1


title: RK: U87 cells, DMSO, 72 h

value: DMSO


title: sham heart + weekly prednisone2


title: the hypopharynx tissue of patient 2

value: hypopharynx

value: untreated


title: Mature antheridia wild type (biol rep 3)

city: Freiburg

first: Volker

middle: Michael

last: Lüth

address: Schänzlestr. 1

institute: University of Freiburg

description:
WM3
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
WM_WF_Galaxy971_DESeq2_result_file.tabular
PM_WM_Galaxy961_DESeq2_result_file.tabular

data_processing:
Galaxy base
Trimming was done with Trim Galore (V 0.6.6) in combination with Cutadapt (V.2.10) (adapter stringency = 1 bp; minimum required sequence length for retaining a read pair = 20 bp; 3' clipping = 1 bp
Mapping with HISAT2 (Galaxy Version 2.1.0)
Counts with feature counts (Galaxy Version 2.0.1) (excluding chimeric fragments and only allowing fragments with both reads aligned, GFF feature type filter = CDS, GFF gene identifier = gene_id)
Expression analysis using DESeq2 (Galaxy Version 2.11.40.6+galaxy1)
Assembly: P.patens_218_v3.3
Supplementary files format and content: tabular files
The names of the columns 1-7 for all the tabular files are:
1) gene identifiers
2) mean normalised counts
3) log2 fold change
4) standard error
5) Wald statistic
6) p value
7) adjusted p value (Benjamini-Hochberg)

organism: Physcomitrium patens

source_name: antheridia

extract_protocol:
Samples were collected using thin forcettes and stored directly in TRIzol ® (Fisher Scientific GmbH, Schwerte, Germany) on wet ice. Tissues were homogenized with a small pistill and mixed with chloroform. The aqueous phase was further processed according to Direct-zol RNA Microprep Kit (Zymp Research Europe GmbH, Freiburg, Germany). Extracted RNA was treated with Ribolock RNase Inhibitor (Fisher Scientific GmbH, Schwerte, Germany).
cDNA library was created at Genomics Unit, Instituto Gulbenkian de Ciencia, Portugal according to (Picelli et al 2014:Full-length RNA-seq from single cells using Smart-seq2. Nature Protocols 9: 171–181.)

value: antheridia

value: Gransden

value: gametangia

value: wild type


title: Mature archegonia wild type (biol rep 1)

description:
WF1
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
WM_WF_Galaxy971_DESeq2_result_file.tabular
PF_WF_Galaxy963_DESeq2_result_file.tabular

source_name: archegonia

value: archegonia


title: UCCLBBS449 MRS broth vs MRS broth 30 ppm iso-a-acids Dye swap

city: Cork

first: Marine

last: Feyereisen

state: Cork

address: Western raod

country: Ireland

institute: Univeristy College Cork

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).  Data processing  DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 2-FL or 3-FL/sorbitol or lactose, or  2-FL or lactose/ribose ratios from a single array experiment.

organism: Levilactobacillus brevis

source_name: Lactobacillus brevis UCCLBBS449

label_protocol: Labelling was performed as described previously  (Ainsworth, S.; Zomer, A.; Mahony, J.; van Sinderen, D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied environmental microbiology 2013, 79, 4786-4798, doi:10.1128/aem.01197-13).

growth_protocol: Lb. brevis strains were grown in MRS broth supplemented or not with 5 % EtOH, 30 ppm iso-a-acids or adjusted to pH4. Cultures were grown at 30 degrees

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (Ainsworth, S.; Zomer, A.; Mahony, J.; van Sinderen, D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied environmental microbiology 2013, 79, 4786-4798, doi:10.1128/aem.01197-13).

value: UCCLBBS124 grown in MRSbroth

value: UCCLBBS449 grown with 30 ppm iso-a-acids


title: cytoplasm_EGFP_2


title: whole_EGFP_1

description:
whole_EGFP_vs_CHERP_A3SS.MATS.ReadsOnTargetAndJunctionCounts
whole_EGFP_vs_CHERP_A5SS.MATS.ReadsOnTargetAndJunctionCounts
whole_EGFP_vs_CHERP_MXE.MATS.ReadsOnTargetAndJunctionCounts
whole_EGFP_vs_CHERP_RI.MATS.ReadsOnTargetAndJunctionCounts
whole_EGFP_vs_CHERP_SE.MATS.ReadsOnTargetAndJunctionCounts


title: Mature archegonia wild type (biol rep 3)

description:
WF3
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
WM_WF_Galaxy971_DESeq2_result_file.tabular
PF_WF_Galaxy963_DESeq2_result_file.tabular


title: sham heart + vehicle2

value: 6-week-long weekly vehicle

value: ~16wo C57BL/6 WT male mouse


title: UCCLBBS449 MRS broth vs MRS broth 30 ppm iso-a-acids


title: Mature archegonia wild type (biol rep 2)

description:
WF2
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
WM_WF_Galaxy971_DESeq2_result_file.tabular
PF_WF_Galaxy963_DESeq2_result_file.tabular


title: UCCLBBS449 MRS broth vs MRS broth pH4 Dye swap

value: UCCLBBS449 grown at pH4


title: UCCLBBS449 MRS broth vs MRS broth 5% EtOH Dye swap

value: UCCLBBS449 grown with 5% EtOH


title: cytoplasm_CHERP_2

value: CHERP siRNA#2


title: whole_CHERP_2


title: whole_CHERP_1


title: sham heart + weekly prednisone3


title: Day 3 post-MI

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

data_processing:
The sequenced data were processed into expression matrices with the Cell Ranger Single Cell software suite v3.0.1 by 10x Genomics.
Raw base-call files from HiSeq2500 sequencer were demultiplexed into library-specific FASTQ files using Cell Ranger mkfastq option.
Sequencing reads were mapped to the mm10 version 3.0.0 reference
Cell barcodes and unique molecular identifiers underwent filtering and correction. Reads associated with the retained barcodes were quantified using Cell Ranger count option and used to build a transcript count table.
Genome_build: mm10
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: CD45+ cells from heart

extract_protocol:
We sorted total viable CD45+ leukocytes from the mouse heart. Five samples were analyzed: control, after 1, 3, 5, and 7 days of myocardial infarction.
The single-cell library preparation relied on a commercially available droplet method, the 10x Genomic Chromium System (10x Genomic Inc., San Francisco, CA), with 10x Genomics Single Cell 3’ v3 Reagent kit according to the manufacturer’s protocol. In brief, dissociated cells were counted by hemocytometer (ThermoFisher) and 16,000 cells per sample were added to each channel. The cells were then partitioned into gel beads in emulsion (GEMs) in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred. cDNA was synthesized and amplified for 14 cycles. cDNA clean-up was performed using a SPRIselect Reagent Kit (Beckman Coulter, Brea, CA). 50 ng of the amplified cDNA were used for each sample to construct indexed sequencing libraries.

value: Heart

value: sorted CD45+ leukocytes

tag: disease state

value: Myocardial Infarction

value: Day 3 post-MI


title: Mature archegonia pinC#29 (biol rep 1)

description:
PF1
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
PM_PF_Galaxy969_DESeq2_result_file.tabular
PF_WF_Galaxy963_DESeq2_result_file.tabular

tag: tissue

value: PpPINC mutant


title: whole_EGFP_2

value: EGFP siRNA


title: Mature antheridia wild type (biol rep 2)

description:
WM2
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
WM_WF_Galaxy971_DESeq2_result_file.tabular
PM_WM_Galaxy961_DESeq2_result_file.tabular

value: antheridia

value: Gransden

tag: genotype


title: Mature antheridia pinC#29 (biol rep 3)

description:
PM3
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
PM_PF_Galaxy969_DESeq2_result_file.tabular
PM_WM_Galaxy961_DESeq2_result_file.tabular

value: gametangia


title: Day 7 post-MI VISIUM

data_processing:
The sequenced data were processed into expression matrices with the Space Ranger software v1.0.0 (10X Genomic)
Raw base-call files from NovaSeq 6000 sequencer were demultiplexed into library-specific FASTQ files using Space Ranger mkfastq option.
Sequencing reads were mapped to the mm10 version 3.0.0 reference
Cell barcodes and unique molecular identifiers underwent filtering and correction. Reads associated with the retained barcodes were quantified using Space Ranger count option and used to build a transcript count table.
Genome_build: mm10
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Space Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: mouse heart

extract_protocol:
Frozen samples from day 1, 3, 5, and 7 post-MI were embedded in OCT (TissueTek), and cryosectioned into 10 μm slices at -10℃. Sections were placed on chilled Visium Spatial Gene Expression slide (10X Genomics).
cDNA libraries were generated using Visium Spatial Gene Expression slide & Reagent Kit according to the manufacture’s instruction (10X Genomics).

tag: cell marker


title: sham heart + weekly prednisone1

source_name: myocardium

value: 6-week-long weekly prednisone


title: Mature antheridia wild type (biol rep 1)

description:
WM1
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
WM_WF_Galaxy971_DESeq2_result_file.tabular
PM_WM_Galaxy961_DESeq2_result_file.tabular

value: wild type


title: Day 3 post-MI VISIUM


title: sham heart + vehicle3


title: Mature archegonia pinC#29 (biol rep 3)

description:
PF3
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
PM_PF_Galaxy969_DESeq2_result_file.tabular
PF_WF_Galaxy963_DESeq2_result_file.tabular

value: archegonia


title: Mature antheridia pinC#29 (biol rep 1)

description:
PM1
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
PM_PF_Galaxy969_DESeq2_result_file.tabular
PM_WM_Galaxy961_DESeq2_result_file.tabular


title: BM sample pre/post allo-SCT

city: Fukuoka

first: Teppei

last: Sakoda

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

institute: Kyushu University

description:
This file were multiplexed using BD Single-cell Multiplexing Kit Sample Tag - Human
Sample name | Title | Sample Tag
Sample7 | UPN57: diagnosis| BD Single-cell Multiplexing Kit Sample Tag 7
Sample8 | UPN57: hCR at day 28 post SCT | BD Single-cell Multiplexing Kit Sample Tag 8
Sample9 | UPN57: Relapse at day 84 post-SCT | BD Single-cell Multiplexing Kit Sample Tag 9
Sample10 | UPN36: diagnosis| BD Single-cell Multiplexing Kit Sample Tag 10
Sample11 | UPN36: hCR at day17 post SCT| BD Single-cell Multiplexing Kit Sample Tag 11
Sample12 | UPN36: Relapse at day 224 post SCT| BD Single-cell Multiplexing Kit Sample Tag 12

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422.
FASTQ files obtained from sequencing were provided to the BD Targeted Multplex Rhapsody Analysis Pypeline Version 1.8 (BD Biosciences) with the default settings.
Molecule count data were adjusted using the distribution-based error correction (DBEC) algorithm.
Assembly: Hg19
Supplementary files format and content: Matrix table with counted mols per cells for every gene and every sample

source_name: BM aspiration from UPN57 and UPN36

extract_protocol:
We prepared BM samples at three time points from identical patients: non-hCR before SCT, CR at engraftment after allo-SCT, and non-hCR at relapse. We purified CD34+ cells from each sample using an indirect CD34 MicroBead Kit (Miltenyi Biotec). Cells (4,000) from each sample were used for single-cell isolation using BD Rhapsody Single-Cell Analysis System (BD Biosciences). Before single-cell isolation, all cells were labeled using a BD Single-Cell Multiplexing Kit and BD AbSeq antibody against TIM-3; six samples derived from two patients were loaded onto a single cartridge
cDNA library preparation was performed according to the manufacturer’s instructions. For cDNA amplification, we used costumed 435 primer pairs (46 genes associated with stem cell signature on BD Onco-BC Panel Hs, which contains 389 genes). An aliquot of the PCR products was used for assessing concentration and for the quality check of size and integrity using a Qubit (High Sensitivity dsDNA kit, Thermo Fisher Scientific) and the Agilent 4200 TapeStation system (High Sensitivity D1000 screen tape, Agilent), respectively.

value: BM aspiration from UPN57 and UPN36

value: CD34-purified bone marrow cells

tag: indice

value: illumina index 1 (i7) sequence:Library reverse primer 2(CGAGGCTG)


title: Day 7 post-MI

tag: time

value: Day 7 post-MI


title: UCCLBBS449 MRS broth vs MRS broth 5% EtOH

tag: treatment

value: UCCLBBS124 grown in MRSbroth

value: UCCLBBS449 grown with 5% EtOH


title: UCCLBBS124 MRS broth vs MRS broth pH4

source_name: Lactobacillus brevis UCCLBBS124

value: UCCLBBS124 grown at pH4


title: Day 1 post-MI VISIUM

value: Heart

value: Myocardial Infarction


title: Day 5 post-MI

value: sorted CD45+ leukocytes

value: Day 5 post-MI


title: Mature archegonia pinC#29 (biol rep 2)

description:
PF2
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
PM_PF_Galaxy969_DESeq2_result_file.tabular
PF_WF_Galaxy963_DESeq2_result_file.tabular

value: PpPINC mutant


title: sham heart + vehicle1

value: 6-week-long weekly vehicle

value: ~16wo C57BL/6 WT male mouse


title: Day 5 post-MI VISIUM


title: UCCLBBS124 MRS broth vs MRS broth 30 ppm iso-a-acids Dye swap

value: UCCLBBS124 grown with 30 ppm iso-a-acids


title: Steady-state

value: Normal

value: Steady-state


title: Mature antheridia pinC#29 (biol rep 2)

description:
PM2
Gametangia_RNA_Count_Matrix_feature_counts_FilteredafterCDScountfeature.txt
Male_Female_Galaxy967_DESeq2_result_file.tabular
Pko_WT_Galaxy965_DESeq2_result_file.tabular
PM_PF_Galaxy969_DESeq2_result_file.tabular
PM_WM_Galaxy961_DESeq2_result_file.tabular

value: antheridia

value: Gransden

value: gametangia


title: UCCLBBS449 MRS broth vs MRS broth pH4

value: UCCLBBS449 grown at pH4


title: Day 1 post-MI

value: Day 1 post-MI


title: Methyl-SNP-seq_MockMicrobiome

organism:
Escherichia coli
Clostridium acetobutylicum

source_name: Methyl-SNP-seq on mock microbiome including E.coli and C. acetobutylicum

value: MG1655 and ABKn8


title: CSS_3_TI

status: Public on Jun 18 2022

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Sequencing data were processed with illumina2bam-tools v. 1.12
BAM files were converted to fastq format using SamToFastq.jar (picard-tools v1.100) with the INCLUDE_NON_PF_READS parameter set to FALSE (implemented in RefFreeDMA)
All reads were trimmed for adapter sequences and low-quality sequences using trimgalore v0.3.3 with the following command: trim_galore -q 20 --phred33 -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" --stringency 1 -e 0.1 --length 16 --output_dir $output_dir $input_fastq.
Reference-free processing (creation of the deduced genomes and processing) was performed using the RefFreeDMA software/pipeline (http://RefFreeDMA.computational-epigenetics.org)
Bisulfite alignment of the RRBS reads to the deduced genomes and to the reference genomes was performed using BSMAP v2.74 with the following command line: bsmap -a $input_fastq -d $ref_genome_fasta -o $output_bam -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -S 1 -f 5 –u (implemented in RefFreeDMA).
DNA methylation calling was performed using the biseqMethCalling.py software (Bock, 2010)(implemented in RefFreeDMA).
Genome_build: processed files list contains consensus genomes for each of 580 species
Supplementary_files_format_and_content: Tab-delimited text files include CpG methylation calls for each sample. The columns in the file correspond to thr chromosome, start and end of a CpG region, rationof methylated/non metylated, mean methylation in ‰ and the strand.

organism: Boltenia echinata

source_name: Tissue

extract_protocol:
Reduced representation bisulfite sequencing (RRBS) was performed as described in Klughammer et al., Cell Reports 2015, using 100 ng of genomic DNA for most samples, while occasionally going down to 1 ng for samples with low DNA amounts (Supplementary Table 1). To assess the bisulfite conversion efficiency independent of CpG context, methylated and unmethylated spike-in controls were added at a concentration of 0.1%. For most samples, DNA was digested using the restriction enzymes MspI and TaqI in combination (as opposed to only MspI in the original protocol) in order to increase genome-wide coverage. For certain older samples, only MspI was used
Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. Fi-nally, the libraries were size selected by performing a 0.75× cleanup with AMPure XP beads (Beckman Coulter, A63881) retaining fragments of about 100 bp to 1000 bp length. The amount of effective li-brary was determined by qPCR, and samples were multiplexed in pools of 10 with similar qPCR Ct values. The pools were then subjected to bisulfite conversion, followed by library enrichment with PCR. Enrichment cycles were determined using qPCR and ranged from 6 to 18 (median: 11). After con-firming adequate fragment size distributions on Bioanalyzer High Sensitivity DNA chips (Agilent),

value: Tissue

tag: Sex

tag: individual

tag: sample type

value: converted


title: WPF_2_S

organism: Scophthalmus aquosus

source_name: Spleen

value: Spleen


title: UCCLBBS124 MRS broth vs MRS broth pH4 Dye swap

value: UCCLBBS124 grown in MRSbroth

value: UCCLBBS124 grown at pH4


title: WPF_2_L_uc

source_name: Liver

value: Liver

value: unconverted


title: UCCLBBS124 MRS broth vs MRS broth 30 ppm iso-a-acids


title: WPF_2_G

source_name: Gills

value: Gills


title: UCCLBBS124 MRS broth vs MRS broth 5% EtOH Dye swap

value: UCCLBBS124 grown with 5% EtOH


title: CSS_2_W_uc


title: CSS_2_W


title: CSS_1_W


title: WPF_1_K

source_name: Kidney

value: Kidney


title: WPF_2_L


title: RD_2_H

organism: Rangifer tarandus

source_name: Heart

value: Heart

value: f

value: adult


title: RD_2_L


title: WPF_2_K


title: WPF_2_H


title: WPF_1_S


title: RD_2_H_uc


title: UCCLBBS124 MRS broth vs MRS broth 5% EtOH


title: RD_1_L


title: RD_1_H


title: WPF_1_H


title: WPF_1_G


title: WPF_1_L


title: NSS_2_G

organism: Illex illecebrosus


title: NSS_1_G


title: NSS_1_MA

source_name: Mantle

value: Mantle


title: NSS_1_F

source_name: Fin

value: Fin


title: WPF_1_M

source_name: Muscle

value: Muscle


title: LIS_2_H

organism: Doryteuthis pealeii


title: WPF_2_M


title: LIS_1_H


title: NSS_2_H


title: LIS_2_F


title: NSS_2_MA


title: NSS_1_F_uc


title: WIS_2_S

organism: Leucoraja ocellata


title: LIS_1_F_uc


title: WIS_2_H


title: NSS_1_H


title: WIS_2_F


title: LIS_1_F


title: WIS_1_F


title: WIS_2_M


title: WIS_1_L


title: WIS_2_L_uc


title: WIS_2_SK

source_name: Skin

value: Skin


title: WIS_2_G


title: WIS_1_SK


title: WIS_1_H


title: WIS_1_S


title: WIS_1_G


title: WIS_1_M


title: RXS_3_G

organism: Glyptocephalus zachirus


title: RXS_2_G_uc


title: RXS_1_G


title: RXS_2_G


title: SST_1_G_uc

organism: Sebastolobus alascanus

value: m


title: WEP_1_G

organism: Gadus chalcogrammus

value: converted


title: SST_1_G


title: WEP_2_G


title: SPS_2_G

organism: Triglops scepticus


title: WEP_3_G


title: SST_2_G


title: WEP_1_G_uc


title: CCL_1_L

organism: Shinisaurus crocodilurus


title: SST_3_G


title: SPS_1_G


title: CCL_1_H_uc


title: CSD_3_AT

organism: Echinarachnius parma


title: CSD_3_E

source_name: Esophagus

value: Esophagus


title: CSD_2_E


title: CSD_2_AT_uc


title: WIS_2_L


title: DHF_1_F_uc

organism: Bodianus diana

value: juvenile


title: DHF_1_F


title: GCF_1_O_uc

organism: Rhabdamia gracilis

source_name: Operculum

value: Operculum


title: DHF_1_O


title: GCF_1_M


title: DHF_1_M


title: GCF_1_F


title: CSD_1_AT


title: FOF_2_S

organism: Hippoglossina oblonga

value: Spleen


title: CSD_1_E


title: CCL_1_H


title: GCF_1_O


title: Mouse Placenta, 50 ppm Cadmium Exposed, e18.5, Rep3

city: Raleigh

first: Michael

last: Cowley

state: NC

address: Campus Box 7633

institute: North Carolina State University

data_processing:
Illumina adapter reads were trimmed using Trim Galore! and a custom script was used to trim additional bases added during library creation to facilitate sequencing. Reads were mapped to the genome using Bismark and Bowtie 2 allowing for no mismatches. Following alignment, PCR duplicates were removed using a custom script. Each unique read had a randomized 6-mer barcode and if more than one read had the same start and end coordinates and the same barcode, all but one of the reads were discarded. Methylation at CpG sites were extracted using Bismark and CpG sites covered by at least 10 reads were analyzed using the methylKit R package. Differentially methylated bases and regions were identified using a Fisher’s exact test for pairwise comparisons and a Chi-squared test for analyses with more than two groups.
Assembly: mm10
Supplementary files format and content: *.bedgraph
Supplementary files format and content: CpG_report.txt.gz

organism: Mus musculus

source_name: Placenta

extract_protocol:
Tissues were homogenized and DNA was isolated with an AllPrep DNA/RNA/miRNA kit (Qiagen).
Ovation RRBS Methyl-Seq System

value: Placenta

tag: developmental stage

value: C57Bl/6J x CAST/EiJ hybrid

value: 50 ppm cadmium chloride

tag: molecule subtype

value: Bisulfite-treated gDNA


title: FOF_2_K

value: Kidney


title: TIB_1_F_uc

organism: Ecsenius

value: unconverted


title: RET_1_M

organism: Paracanthurus hepatus


title: TIB_1_F


title: RET_1_O


title: FOF_1_S


title: FOF_1_K


title: Mouse Placenta, Control, e18.5, Rep4

value: 0 ppm cadmium chloride


title: FOF_2_M


title: TIB_1_M


title: SPS_1_G_uc

value: Gills

value: adult


title: FOF_2_G


title: RET_1_F_uc

value: Fin


title: FOF_1_H

value: Heart


title: FOF_1_G


title: FOF_1_H_uc


title: Mouse Placenta, 50 ppm Cadmium Exposed, e18.5, Rep1


title: FOF_2_H


title: FOF_1_M

value: Muscle


title: CSD_2_AT

value: converted


title: Mouse Placenta, Control, e18.5, Rep3


title: WEF_2_L

organism: Cynoscion regalis

value: Liver


title: RET_1_F


title: Mouse Placenta, 50 ppm Cadmium Exposed, e18.5, Rep4


title: Mouse Placenta, 50 ppm Cadmium Exposed, e18.5, Rep2


title: ATK_2_M

organism: Nothobranchius furzeri


title: WEF_2_M


title: WEF_2_K


title: WEF_2_SB

source_name: Swimbladder

value: Swimbladder


title: JL_1_GO

organism: Lethenteron camtschaticum

source_name: Gonad

value: Gonad

value: m


title: Mouse Placenta, Control, e18.5, Rep2

value: Placenta


title: ATK_1_M_uc


title: WEF_1_M


title: Seedlings, bbx4-1 rep2

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

data_processing:
After trimming adapter sequences and filtering low-quality reads with Q < 20 from the 5' and 3' ends of the remaining reads, the clean reads were mapped onto the TAIR10 reference genome  using hisat2 (version 2.1.0). Differential expression between accessions was assessed statistically using the R/Bioconductor package edgeR (v.3.0.8). Genes with P value < 0.05 and foldchange >1.5, as determined using edgeR, were identified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis Col and bbx4-1 mutant seeling were grown in constant red light  in a growth chamber at 22ºC for 4 days.

extract_protocol:
Total RNA was extracted from approximately 80~100 mg powder of each sample using the RNeasy plant mini kit (Qiagen, www.qiagen.com) according to the manufacturer’s protocol.
The complementary DNA (cDNA) libraries were prepared according to Zhang et al. (2016) by performing a series of procedures, including poly(A) enrichment, RNA fragmentation, cDNA synthesis, linker ligation, size selection and PCR amplification.

tag: ecotype

value: Col

value: seedlings


title: WEF_1_L_uc


title: WEF_2_G


title: ATK_1_M


title: JL_1_GO_uc


title: WEF_1_L


title: WEF_1_K


title: Seedlings, bbx4-1 rep1


title: WEF_1_H


title: WEF_1_SB


title: WEF_2_S

value: Spleen


title: ESH_1_GO_uc

organism: Callorhinchus milii


title: SJD_2_M

organism: Zenopsis conchifer


title: WEF_1_G


title: Seedlings, wild-type rep3

description: WT.FPKM.txt

value: WT


title: ESH_1_GO


title: Mouse Placenta, Control, e18.5, Rep1

value: C57Bl/6J x CAST/EiJ hybrid

value: Bisulfite-treated gDNA


title: SJD_2_L


title: Seedlings, wild-type rep2

description: WT.FPKM.txt


title: Seedlings, bbx4-1 rep3


title: WEF_2_H


title: SJD_2_K

value: Kidney


title: Seedlings, wild-type rep1

description: WT.FPKM.txt


title: SJD_2_H


title: SJD_2_G_uc

value: Gills

value: unconverted


title: SAF_1_M_uc

organism: Histrio histrio


title: SJD_2_SB


title: SAF_1_M


title: SJD_1_L


title: CSH_1_G_uc

organism: Semicossyphus pulcher

value: adult


title: SJD_1_M

value: Muscle


title: CSH_1_G

value: converted


title: CP_279380

first: Wei

last: Sun

state: Jiangsu

address: Nanjing, Jiangsu, China

institute: Jiangsu People's Hospital

data_processing:
Star Matching Transcripts
StringTie splice transcripts and merge transcripts
Htseq quantitative
Assembly: Human hg38：  BSgenome.Hsapiens.UCSC.hg38  EnsDb.Hsapiens.v86
Supplementary files format and content: counts

organism: Homo sapiens

source_name: Cervical

extract_protocol:
After the samples are qualified, the total RNA library preparation and library inspection are carried out according to the following experimental steps: (1) rRNA removal: Ribo-zero kit was used to remove rRNA, followed by high temperature and metal ions. (2) Synthesis and purification of cDNA: using RNA as a template, a six-base random primer is used to synthesize a strand of cDNA,Then add buffer, dNTPs, and enzyme to synthesize double-stranded cDNA, and then use VAHTSTM DNA Clean Beads Purification of double-stranded cDNA; (3) Fragment screening: the purified double-stranded cDNA is first subjected to end repair, A-tail, and sequencing ligation  head, followed by fragment screening with VAHTSTM DNA Clean Beads; (4) PCR enrichment: UDG enzyme degrades the second strand of cDNA containing U, and performs PCR enrichment, Finally, use VAHTSTM DNA Clean eads to purify the PCR product; (5) Library inspection: use Qubit to accurately quantify the library concentration, and Agilent 2100 Bioanalyzer to determine Library fragment size distribution to assess suitability for onboarding.
Ribo-zero kit for rRNA removal;One-stranded cDNA was synthesized using RNA as a template and six-base random primers; The second-stranded cDNA was synthesised by adding buffer, dNTPs and enzymes, followed by purification of the double-stranded cDNA using VAHTSTM DNA Clean Beads. purification of double-stranded cDNA;Accurate quantification of library concentrations with Qubit, determination of library fragment size distribution with Agilent 2100 Bioanalyzer

value: Cervical

tag: tissue type

value: paracancerous tissue

value: circRNA


title: SJD_2_G


title: CA_279380

value: primary cervical cancer


title: SJD_1_SB

value: Swimbladder


title: SJD_1_S


title: SJD_1_H

value: Heart


title: CA_1103118


title: SJD_1_G


title: BSP_1_G_uc

organism: Embiotoca jacksoni


title: CA_277242


title: BSP_1_G