title: MDMs_RNAseq_UT-rep6

city: Oxford

first: Ping

last: Zhang

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics

institute: University of Oxford

description: MDMs_UT_rep123456_RPKM.bw; MDMs_UT_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_UT_rep123456_RPKM_FR.bedgraph.gz

data_processing:
RNA Sequencing reads were trimmed using Trim Galore (version 0.6.2), and mapped to human genome assembly hg38 using the HISAT2 (version 2.1.0).  The aligned Binary-sequence Alignment Format (BAM) files were used to determine the transcript counts through featureCounts (version 1.6.2) and GENCODE annotations (release 31). For gene differential expression analysis, the raw read counts were used as input into the R package DESeq2 (version 1.28.1) for pair-wise comparisons. For differential exon usage analysis, a featureCounts readable GTF file for exonic regions was generated through (https://github.com/vivekbhr/Subread_to_DEXSeq). The number of reads overlapping with each exonic region was counted by featureCounts with parameters -p -f -O -s 2 -t exonic_part. The exonic regions with read counts ≥ 10 in at least 30% of samples were used as input into the R package DEXSeq (version 1.32.0). The strandedness of the RNA-seq reads was extracted using Samtools, and the normalized bidirectional bedgrapgh files were generated using Bedtools and Bedops. The RPKM (Reads Per Kilobase per Million mapped reads) normalized bigwig files were generated using the bamCoverage function of deepTools (version 3.3.1).
Differential analyses for chromatin accessibility (ATAC) and histone modifications (H3K27ac and H3K4me3) were processed via an in-house pipeline. Briefly, sequencing reads were aligned to human genome assembly hg38 using bowtie2. The resulting BAM files were filtered to remove non-uniquely mapped reads, non-properly paired reads, reads mapped to mitochondrial chromosome, duplicate reads and reads with a mapping quality score less than 30 using Picard (version 2.0.1) and Samtools (version 1.9). Peaks were called using MACS2 (version 2.1.0) with the appropriate input dataset (paired non-ChIP data were used as controls for histone modifications). ATAC peaks were called using parameters --nomodel --shift -100 --extsize 200, and H3K27ac and H3K4me3 peaks were called using --bw 200. Peaks that overlay the ENCODE Blacklist and with p value > 1e-08 were filtered out. Peaks called in at least 30% of samples were defined as recurrent, and merged as a list of coordinates to count the number of overlapping reads in each condition using htseq-count (version 0.6.1). Finally, the reads were normalized using DESeq2 and then pair-wise comparisons were performed to determine the differential (fold change >2, FDR < 0.05) ATACs and histone modifications per condition. Potential batch effect or technical variable was examined by principal component analysis and was included as a covariate in DESeq2 design formula. The normalized bigwig files showing the average sequencing depth across samples with same treatment were generated using wiggletools and wigToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig; bedgraph

source_name: MDMs

growth_protocol: Peripheral blood samples were obtained from healthy volunteers and PBMC isolated by Ficoll-Paque centrifugation. Monocytes (CD14+), T-cells (CD4+ and CD8+) and B-cells (CD19+) were separated from peripheral blood mononuclear cells (PBMCs) by positive selection with magnetic MicroBeads (Miltenyi Biotec). The isolated CD14 monocytes were differentiated into macrophages (MDMs) by culturing cells for 6 days in RPMI-1640 (Sigma) supplemented with 20% FBS (Sigma), L-glutamine (Sigma), sodium pyruvate (Sigma), non-essential amino acids (Sigma) and 20 ng/mL M-CSF (Gibco). Induced pluripotent stem cell (iPSC) line (SFC840-03-03) was reprogramed from dermal fibroblasts from a healthy donor recruited by the Oxford Parkinson’s Disease Centre, and cultured with feeder-free TeSR-E8 media (STEMCELL) on tissue culture plates coated with Matrigel (Corning). iPSCs were then transferred into AggreWell plate (STEMCELL) with E8 media (Gbico) supplemented with 50ng/mL BMP4 (ThermoFisher), 50 ng/mL VEGF (ThermoFisher) and 20 ng/mL SCF (Miltenyi) for four days to generate Embryoid Bodies (EBs) which were then used for generation of macrophage precursor in XVIVO-15 media (Lonza) supplemented with 25 ng/mL IL-3 (Gibco), GlutaMax, 2-mercaptoethanol and 100 ng/mL M-CSF.

extract_protocol: RNA-seq library was prepared using a standardised rRNA depletion and dUTP protocol (NEB) followed by sequencing on either a HiSeq4000 or NextSeq500 platform.(Illumina) at the Oxford Genomics Centre (Wellcome Centre for Human Genetics, Oxford, UK). Omni-ATAC-seq and ChIP for histone modifications were amplified for optimized cycles and were subjected to sequencing using a HiSeq4000 platform (Illumina).

treatment_protocol: Cells were treated with 20 ng/ml LPS for 6 hours (HD) or 2 ng/ml LPS for 16 hours and subsequent 20 ng/ml LPS challenge for 6 hours (LDHD).

value: monocyte-derived macrophage


title: MDMs_RNAseq_HD-rep6

status: Public on Jun 01 2022

type: SRA

country: United Kingdom

description: MDMs_HD_rep123456_RPKM.bw; MDMs_HD_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_HD_rep123456_RPKM_FR.bedgraph.gz

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: MDMs_RNAseq_LDHD-rep5

description: MDMs_LDHD_rep123456_RPKM.bw; MDMs_LDHD_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_LDHD_rep123456_RPKM_FR.bedgraph.gz


title: MDMs_RNAseq_HD-rep5


title: MDMs_RNAseq_UT-rep5


title: iPSMs_RNAseq_LDHD-rep3

molecule: polyA RNA

source_name: iPSMs

value: induced pluripotent stem cell-derived macrophages


title: iPSMs_RNAseq_HD-rep3


title: iPSMs_RNAseq_UT-rep3


title: iPSMs_RNAseq_LDHD-rep2


title: iPSMs_RNAseq_HD-rep2


title: iPSMs_RNAseq_LDHD-rep1


title: MDMs_RNAseq_LDHD-rep6


title: H3K4me3_rep2_UT

library_source: genomic

molecule: genomic DNA

tag: chip abs

value: H3K4me3 (Diagenode Cat# pAb-003-050, RRID:AB_2616052)


title: H3K4me3_rep3_UT


title: H3K4me3_rep2_HD


title: H3K4me3_rep2_LDHD


title: H3K4me3_rep3_LDHD


title: H3K4me3_rep1_UT


title: H3K4me3_rep1_LDHD


title: ChIPm_input_rep3_UT


title: H3K27ac_rep3_UT


title: iPSMs_RNAseq_HD-rep4


title: iPSMs_RNAseq_UT-rep4


title: ChIPm_input_rep3_HD


title: iPSMs_RNAseq_LDHD-rep4


title: H3K27ac_rep3_HD


title: H3K27ac_rep2_HD


title: ChIPm_input_rep3_LDHD


title: H3K27ac_rep3_LDHD


title: ChIPm_input_rep2_UT


title: ChIPm_input_rep2_HD


title: iPSMs_RNAseq_UT-rep2


title: H3K27ac_rep2_UT


title: ChIPm_input_rep2_LDHD


title: iPSMs_RNAseq_HD-rep1


title: H3K4me3_rep3_HD


title: H3K27ac_rep2_LDHD


title: iPSMs_RNAseq_UT-rep1


title: H3K27ac_rep1_UT


title: ChIPm_input_rep1_UT


title: H3K27ac_rep1_HD


title: ChIPm_input_rep1_HD


title: H3K4me3_rep1_HD


title: ChIPm_input_rep1_LDHD


title: CD8-ATAC_rep2

value: CD8 T cells


title: CD19-ATAC_rep2

value: CD19 B cells


title: H3K27ac_rep1_LDHD


title: CD4-ATAC_rep2

value: CD4 T cells


title: CD8-ATAC_rep1


title: CD4-ATAC_rep1


title: CD19-ATAC_rep1


title: CD14-ATAC_rep1

value: CD14 monocytes


title: CD8-ATAC_rep3


title: CD4-ATAC_rep3


title: CD14-ATAC_rep3


title: iPSMs-UT-ATAC_rep2


title: iPSMs-UT-ATAC_rep3


title: CD19-ATAC_rep3


title: iPSMs-UT-ATAC_rep4


title: iPSMs-UT-ATAC_rep1


title: iPSMs-LDHD-ATAC_rep4


title: iPSMs-LDHD-ATAC_rep2


title: iPSMs-HD-ATAC_rep4


title: iPSMs-HD-ATAC_rep3


title: iPSMs-HD-ATAC_rep2


title: iPSMs-LDHD-ATAC_rep1


title: CD14-ATAC_rep2


title: MDMs_HD_ATAC_rep6


title: MDMs_HD_ATAC_rep5


title: MDMs_UT_ATAC_rep6


title: MDMs_LDHD_ATAC_rep6


title: MDMs_LDHD_ATAC_rep5


title: MDMs_UT_ATAC_rep5


title: MDMs_HD_ATAC_rep4


title: MDMs_UT_ATAC_rep3


title: MDMs_LDHD_ATAC_rep4


title: MDMs_HD_ATAC_rep3


title: MDMs_LDHD_ATAC_rep3


title: MDMs_LDHD_ATAC_rep2


title: MDMs_UT_ATAC_rep1


title: MDMs_UT_ATAC_rep2


title: iPSMs-LDHD-ATAC_rep3


title: MDMs_HD_ATAC_rep2


title: iPSMs-HD-ATAC_rep1


title: IgG control

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

data_processing:
For ChIP-seq, the single-end reads were mapped on the human genome build hg19 using bowtie version 2.1.6 (Langmead et al., 2009), using the pre-set sensitive parameter.
MACS version 2.0.10 (model-based analysis of ChIPseq) peak finding algorithm was used to identify regions of ChIP-seq enrichment over the background (Feng et al., 2012), using broad peaks parameters.
Unique mapped read values were normalized to library size. Peaks were annotated as per human genome EnsDb.Hspaiens.v75 - hg19
For long-read RNAseq, raw fast5 files were basecalled using Guppy v.4.2.2 using fast basecalling settings, and samples were demultiplexed according to barcodes with the guppy_barcoder.
The resulting FASTQ reads were aligned to the hg19 human reference with Minimap2 version 2.17-r941
Raw read counts were obtained with the featureCounts tool from the Subread package v 2.0.0, using the exon counting mode (Li, 2018; Liao et al., 2014) and normalized as Counts per Million (CPM).
Genome_build: hg19
Supplementary_files_format_and_content: MBTD1_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MBTD1 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: WTZMYND11_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the full length (WT) ZMYND11 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: trZMYND_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the truncated ZMYND11 [aa1-409] 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: Fusion_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the ZMYND11-MBTD1 fusion 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: JC_MD_exp.genes.cpm.txt is a tab separated text file containing read counts for genes normalized to CPM for all long-read RNA-seq samples.
Supplementary_files_format_and_content: JC_MD_exp.transcripts.cpm.txt is a tab separated text file containing read counts for transcripts normalized to CPM for all long-read RNA-seq samples.

source_name: K562 from ATCC

growth_protocol: RPMI, 10% NBCS, 1ug/ml Puromycin

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq4000 SR50 following the manufacturer's protocols.

tag: cell line

value: lymphoblast from chronic myelogenous leukemia (CML)

tag: growth conditions

value: normal growth conditions

tag: chip antibody

value: IgG, Rabbit polyclonal, Millipore, Cat# PP64, RRID:AB_97852

tag: expressing


title: full length (WT) ZMYND11 3xFlag-2xstrep

value: FLAG M2 , Mouse monoclonal, Sigma-Aldrich ,Cat# F1804, RRID:AB_262046

tag: treatment

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease, puromycin selection

value: full length (WT) ZMYND11 3xFlag-2xstrep


title: ZMYND11-MBTD1 fusion 3xFlag-2xstrep

value: FLAG M2 , Mouse monoclonal, Sigma-Aldrich ,Cat# F1804, RRID:AB_262048

value: ZMYND11-MBTD1 fusion 3xFlag-2xstrep


title: MBTD1 3xFlag-2xstrep

value: FLAG M2 , Mouse monoclonal, Sigma-Aldrich ,Cat# F1804, RRID:AB_262045

value: MBTD1 3xFlag-2xstrep


title: truncated ZMYND11 [aa1-409] 3xFlag-2xstrep

value: FLAG M2 , Mouse monoclonal, Sigma-Aldrich ,Cat# F1804, RRID:AB_262047


title: MDMs_HD_ATAC_rep1

value: monocyte-derived macrophage


title: ST20

city: Sunnyvale

first: Xin

last: Zhou

state: CA - California

address: 3165 Porter Drive

department: Department of Genetics

country: USA

institute: Stanford University

description: Pair end single cell RNA sequencing

data_processing:
bcl2fastq2/2.20.0 is used to process raw bcl file
CellRanger 2.2 is used to process fastq file generated from bcl2fastq2/2.20.0
CellRanger 2.2 is used for quality controls and aglinement
CellRanger 2.2 is used for aggregate of seven samples into one matrix
Genome_build: Homo sapiens (human) genome assembly GRCh37 (hg19) is used as reference genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (Unique Molecular Identifier)

source_name: Conventional dendritic cells

extract_protocol:
Freshly isolated DCs are immediately processed for extraction. An aliquot of each cell suspension was stained with trypan blue.  Concentration and viability were determined using the BioRad TC20 automated cell counter.
Final library concentration was determined using the Qubit High Sensitivity dsDNA Assay .  Libraries were normalized to a common concentration prior to being pooled and sequenced on the Illumina HiSeq-4000.
Single cell libraries were prepared using the 10X Genomics Chromium V2’ Gene Expression Solution

value: Human Conventional dendritic cells

tag: disease state

value: PAH patient subject 2

tag: targeted cell recovery


title: ST11-1

description: Pair end single cell RNA sequencing

value: Control subject 3


title: GSC1517_Alvocidib_rep1_RNA-seq

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

country: China

institute: Fudan University

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport function to obtain gene expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: RNA count and abundance (Transcripts Per Million, TPM) matrix at the gene level.

source_name: patient-derived cells

extract_protocol:
Total RNA was extracted using the Zymo Direct-zol RNA MiniPrep Kit (catalog R2052) and TRI reagent (catalog R2050) according to the manufacturer’s instructions
Total RNA was used for library construction using Illumina TruSeq Stranded Total RNA Library Prep Kit. The library was sequenced as paired-end 150bp read.

tag: tissue

value: glioblastoma stem cells

value: Alvocidib


title: GSC1517_Control_rep3_RNA-seq

value: DMSO


title: ST21

description: Pair end single cell RNA sequencing

value: PAH patient subject 3


title: ST15-1

description: Pair end single cell RNA sequencing

value: Control subject 4


title: ST19

description: Pair end single cell RNA sequencing

value: PAH patient subject 1


title: MDMs_UT_ATAC_rep4


title: GSC1517_Control_rep2_RNA-seq


title: MDMs_LDHD_ATAC_rep1


title: GSC1517_Alvocidib_rep2_RNA-seq


title: GSC1517_Alvocidib_rep3_RNA-seq


title: GSC1517_Control_rep1_RNA-seq


title: ST06

description: Pair end single cell RNA sequencing

value: Control subject 2


title: GSC3028_shYY1_RNA-seq


title: GSC23_YY1_rep1_ChIP-seq

data_processing:
Raw FASTQ files were trimmed using TrimGalore and aligned to the hg19 human genome using Bowtie2.
SamTools was used to sort and index the BAM files.
The bigwig files were generated using the DeepTools “bamCoverage”
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
ChIP was performed using Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (MilliporeSigma, 17-10085) according to the manufacturer’s instructions
Library was constructed using NEB NEBNext® Ultra™ DNA Library Prep Kit for Illumina for sequencing

tag: antibody

value: YY1 antibody (Active Motif, cat # 61779)


title: GSC1517_shYY1_RNA-seq


title: GSC1517_shCONT_RNA-seq

value: shCONT


title: GSC23_shCONT_RNA-seq


title: GSC23_Input_ChIP-seq

value: Input


title: GSC23_YY1_rep2_ChIP-seq


title: ST05-1

description: Pair end single cell RNA sequencing

value: Control subject 1


title: WL17 (D7R2)

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

institute: Northwestern University

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 17

data_processing:
We trimmed and filterd the reads using cutadapt and Trimgalore_v0.4.0with default parameters.
Quality was further checked using fastqc.
We used STAR (version 2.5.2b) to map the filtered reads to genome build GRCh38. We used default parameters and --quantMode GeneCounts
Counts files obtained from STAR were used to provide raw counts to DESSeq2. Differential genes and normalizec counts were obtained using DESeq2.
The cutoff for the differential gene list was set as q-val less than 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Files containing raw and normalized count using DESeq2

source_name: day 7 of directed differentiation to nephron progenitor cells

growth_protocol: H9 cells underwent directed differentiation to nephron progenitor cells over 10 days according to the protocol published by Morizane and Bonventre, 2017.

extract_protocol:
RNAeasy MiniKit (Qiagen) and DNA-free™ DNA Removal Kit (Life Technologies, AM1906)
RNA-Seq libraries were generated using Illumina stranded mRNA kits (Illumina). Library QC (quality and quantity) was performed using an Agilent 2100 Bioanalyzer (Agilent).
Sequencing was performed on an Illumina HiSeq4000 (single end 50bp) (Illumina).

treatment_protocol: Cells were collecte at each of the specified time points and RNA was extracted.

value: H9 human embryonic stem cells

tag: time


title: WL7 (D9R1 wo Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 9_1

source_name: day 9 of directed differentiation to nephron progenitor cells grown in the absence of glutamine

treatment_protocol: Cell were grown either in the presence of absence of glutamine from D0 through D9 of the differentiation protocol. Cells were collected at the end of D9 and RNA was extracted.

value: nephron progenitor cells

value: glutamine deprivation


title: WL18 (D7R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 18


title: WL8 (D9R2 wo Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 9_2


title: WL20 (D9R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 20

source_name: day 9 of directed differentiation to nephron progenitor cells


title: WL4 (D9R1+Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 0_1

source_name: day 9 of directed differentiation to nephron progenitor cells grown in the presence of glutamine

value: complete media


title: WL16 (D7R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 16


title: WL15 (D6R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 15

source_name: day 6 of directed differentiation to nephron progenitor cells


title: WL11 (D4R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 11

source_name: day 4 of directed differentiation to nephron progenitor cells


title: WL13 (D6R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 13


title: GSC23_shYY1_RNA-seq


title: GSC3028_shCONT_RNA-seq


title: WL14 (D6R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 14


title: WL9 (D3R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 09

source_name: day 3 of directed differentiation to nephron progenitor cells


title: WL8 (D3R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 08


title: WL6 (D9R3+Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 0_3


title: WL5 (D9R2+Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 0_2


title: WL21 (D9R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 21


title: WL1 (D0R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 01

source_name: day 0 of directed differentiation to nephron progenitor cells


title: WL4 (D1R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 04

source_name: day 1 of directed differentiation to nephron progenitor cells


title: WL3 (D0R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 03


title: WL2 (D0R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 02


title: WL12 (D4R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 12


title: WL9 (D9R3 wo Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 9_3


title: WL5 (D1R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 05


title: WL7 (D3R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 07


title: WL10 (D4R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 10


title: WL19 (D9R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 19


title: WL6 (D1R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 06


title: MSC-Exo-1

city: beijing

first: yuyan

last: xiong

address: No.167 North Lishi Road, Xicheng District

institute: fuwai hospital

data_processing:
The software Cutadapt(Version 2.7) was used to process the sequencing connectors, and the low quality and less than 16bp reads.
Software Perl5 (Version 26) was used to remove reads with UMIs less than 12bp and reads without UMI, and identify UMIs
Software Bowtie (Version 1.2.2) was used for comparison to miRBase piRNAbank database Rfam database
Supplementary_files_format_and_content: Table with raw gene counts and CPM for every gene and every sample

organism: Rattus norvegicus

source_name: exosomes derived from normal MSCs

extract_protocol:
Exosome RNA was extracted by The QIAseq miRNA Library Kit.
Small RNA libraries obtained from different samples were then performed on an Illumina Nova seq platform (Illumina, San Diego, CA, USA).

treatment_protocol: For TXL pretreatment, MSCs were pretreated by 400 μg/mL of TXL for 24 hours.

value: mesenchymal stem cells

tag: strain

value: Sprague-Dawley rat


title: MSCTXL-Exo-1

source_name: exosomes derived from TXL pretreated MSCs


title: MSCTXL-Exo-2


title: TCE_NAC_Female_Rat17_AS

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

data_processing:
Reads were aligned to the rat genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to Rnor_6.0 genes using featureCounts.
Genes with mean read counts-per-million less than six across all samples were filtered out and excluded from the analysis to reduce dispersion due to low expression levels.
Data were normalized using the median of ratios method .
RUV(Remove Unwanted Variation) normalization factors were generated for each sample using the RUVSeq package RUVr function
Differential gene expression testing was performed using the DESeq2 package (version 1.28.1) for R statistical computing. Negative binomial general linear modeling was used for differential gene expression testing.
Genome_build: rn6

source_name: placental tissue

extract_protocol:
RNA was extracted from placental tissue using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommended protocol with a modification. A FastPrep-24 tissue lyser (MP Biomedicals; Solon, OH, USA) was utilized prior to the gDNA elimination step to achieve maximum quality tissue homogenization. DNA was extracted from placental using the NucleoSpin Tissue kit (Machery-Nagel; Düren, Germany) according to the manufacture’s recommended protocol. RNA and DNA concentrations were determined using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific; Waltham, MA, USA). Isolated nucleic acids were subsequently stored at -80°C until further processing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Timed-pregnant Wistar rats were exposed to 480 mg TCE mg/kg/day, 200 mg/kg/day NAC or co-exposure with both chemicals via ingestion (treated mini vanilla wafer) on gestation days 6-16 (tissue collection day).

tag: strain:

value: placenta

tag: dam

value: dam 17

tag: Sex

value: female

value: 480 ml/kg trichloroethylene + N-acetylcysteine

tag: treatment duration

value: gestation days 6-16


title: MSCTXL-Exo-3

tag: cell type


title: MSC-Exo-3


title: TCE_NAC_Female_Rat33_AS

value: dam 33


title: OND-S_530 VS DND-S_475

type: RNA

city: Malaga

first: Eduardo

last: García-Fuentes

state: Malaga

address: Plaza del Hospital Civil s/n

country: Spain

institute: Instituto de Investigación Biomédica de Málaga (IBIMA)/Hospital Regional Universitario, Málaga, Spain.

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: duodenum

tag: gender

tag: type of patient

value: patient with morbid obesity and low insulin resistance

value: non-obese patient with low insulin resistance


title: OD-S_486 VS OND-S_429

value: patient with morbid obesity and high insulin resistance


title: TCE_NAC_Female_Rat30_AS

value: dam 30


title: TCE_NAC_Female_Rat19_AS

value: dam 19


title: DND-S_475 VS DD-S_420

value: non-obese patient with high insulin resistance


title: OD-S_584 VS DD-S_381


title: OND-S_459 VS OD-S_523


title: OND-S_383 VS OD-S_405


title: TCE_NAC_Female_Rat10_AS

value: dam 10


title: OND-S_567 VS DND-S_461


title: OD-S_399 VS OND-S_397


title: DD-S_395 VS OD-S_579


title: TCE_NAC_Female_Rat5_AS

value: dam 5


title: DD-S_469 VS DND-S_483


title: TCE_NAC_Male_Rat5_AS

value: male


title: NAC_Female_Rat27_AS

value: dam 27

value: 200 mg/kg/day N-acetylcysteine


title: TCE_NAC_Male_Rat33_AS

value: placenta


title: TCE_NAC_Male_Rat30_AS


title: TCE_NAC_Male_Rat19_AS


title: MSC-Exo-2

value: mesenchymal stem cells

value: Sprague-Dawley rat


title: NAC_Female_Rat15_AS

value: dam 15

value: female

value: gestation days 6-16


title: DND-S_380 VS OND-S_544

value: duodenum

value: patient with morbid obesity and low insulin resistance


title: OD-S_576 VS DD-S_424

value: patient with morbid obesity and high insulin resistance


title: DND-S_484 VS DD-S_477

value: non-obese patient with low insulin resistance


title: DD-S_389 VS OD-S_527


title: NAC_Male_Rat37_AS

value: dam 37


title: NAC_Male_Rat23_AS

value: dam 23


title: NAC_Female_Rat23_AS


title: TCE_Female_Rat36_AS

value: dam 36

value: 480 mg/kg/day trichloroethylene


title: TCE_Female_Rat9_AS

value: dam 9


title: TCE_Female_Rat16_AS

value: dam 16


title: TCE_Female_Rat1_AS

value: dam 1


title: TCE_NAC_Male_Rat17_AS

value: placenta

value: dam 17

value: male

value: 480 ml/kg trichloroethylene + N-acetylcysteine


title: TCE_NAC_Male_Rat10_AS

value: dam 10


title: NAC_Female_Rat37_AS

value: female

value: 200 mg/kg/day N-acetylcysteine

value: gestation days 6-16


title: TCE_Male_Rat1_AS


title: TCE_Male_Rat26_AS

value: dam 26


title: NAC_Female_Rat7_AS

value: dam 7


title: Control_Female_Rat3_AS

value: dam 3

value: vehicle control (corn oil)


title: Control_Female_Rat22_AS

value: dam 22


title: NAC_Male_Rat27_AS

value: dam 27


title: NAC_Male_Rat15_AS

value: dam 15


title: Control_Male_Rat35_AS

value: dam 35


title: Control_Male_Rat22_AS


title: NAC_Male_Rat7_AS


title: NAC_Male_Rat2_AS

value: dam 2


title: TCE_Female_Rat26_AS

value: placenta

value: 480 mg/kg/day trichloroethylene


title: NAC_Female_Rat2_AS


title: Control_Male_Rat11_AS

value: dam 11

value: male


title: Control_Male_Rat3_AS


title: TCE_Female_Rat24_AS

value: dam 24


title: TCE_Male_Rat36_AS

value: dam 36


title: TCE_Male_Rat24_AS


title: TCE_Male_Rat16_AS

value: dam 16


title: TCE_Male_Rat9_AS

value: dam 9

value: gestation days 6-16


title: Control_Female_Rat29_AS

value: dam 29

value: female


title: Control_Male_Rat18_AS

value: dam 18

value: vehicle control (corn oil)


title: Control_Female_Rat18_AS


title: Control_Female_Rat11_AS


title: Control_Male_Rat29_AS


title: BC39-CTC_EMT

city: Bratislava

first: Lubos

last: Klucar

address: Dubravska cesta 21

country: Slovakia

institute: Institute of Molecular Biology SAS

description: RNA-seq BioSample: SAMN20520700

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/g cRNA) was fragmented at 60°C for 30 minutes in a reaction volume 25l containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25l of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarray slides were scanned at resolution 2 µm using the SureScan Microarray Scanner and Agilent Microarray Scan Control software. Dye channel was set to Green and Green PMT was set to 100%

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.2(Agilent) using default parameters (protocol GE1-1200_Jun14 and Grid: 072363_D_F_20200924) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary breast tumour

label_protocol: cRNA was prepared and labeled from 50ng RNA using the One-Color Low Input Quick Amp Gene Expression Labeling Kit-Cy3 (Agilent) according to the manufacturer's instructions, followed by GeneJET RNA Purification Kit (ThermoScientific ). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. according manufacturer protocol Low Input Quick Amp Gene Expression Labeling Kit-Cy3

extract_protocol: Tissue samples were homogenized in liquid nitrogen and immediately mixed with 700 ul of DNA/RNA Shield (Zymo Research, Irvine, CA, USA). Total RNA was extracted using Quick DNA/RNA Miniprep Plus kit (Zymo Research). RNA concentration was measured by RNA BR  Assay Kit (Invitrogen, Life Technologies, Eugene Oregon, USA) on Qubit fluorometer  (Invitrogen, Life Technologies, Carlsbad, CA, USA). Samples that didn’t have sufficient  RNA concentration for downstream analyses were concentrated using RNA Clean & Concentrator - 5 kit (Zymo Research).

value: primary breast tumour

tag: ctc marker positivity

value: CTC EMT


title: BC31-K

description: RNA-seq BioSample: SAMN20520694

source_name: normal breast tissue

value: normal breast tissue

value: normal tissue


title: Exp35-HB-22F4

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: HB IFN-a-DHFR - rep. 3

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated count file

organism: Mus musculus

source_name: Healthy Brain

extract_protocol:
Total RNA from healthy brain was extracted by using the Promega-Maxwell 16 LEV Simply RNA Tissue kit, following the manufacturers' indications. Total RNA from sorted GBM cells was extracted by using Rneasy Micro Kit (Qiagen), following the manufacturers' indications.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification ,  and  Illumina  Nextera  XT  library  was  used  for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments.

value: Healthy Brain (HB)

value: IFN-a-DHFR


title: Exp35-HB-22F1

description: HB IFN-a-DHFR - rep. 1


title: Control_Female_Rat35_AS

value: placenta

value: dam 35


title: BC43-K

description: RNA-seq BioSample: SAMN20520703


title: BC42-CTC_EMT

description: RNA-seq BioSample: SAMN20520702


title: UT skin Fb, replicate 1, scRNAseq

first: Xiaojie

last: Cai

address: 650 Xinsongjiang Road, Fangsong Street, Songjiang District

department: Precision Research Center for Refractory Diseases

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were processed using Cell Ranger software provided by 10x Genomics.
Assembly: mm10
Supplementary files format and content: tsv files with barcodes and genes
Supplementary files format and content: mtx files with gene counts for every gene and every cell with a unique barcode

source_name: Dermis

extract_protocol:
Fresh skin was placed in saline at 4 °C until further processing. The epidermis was separated from the dermis by Dispase II (Roche, cat: 04942078001) digestion overnight at 4 °C. Single-cell suspensions were generated by enzyme digestion and subjected to fluorescence-activated cell sorting (FACS) to exclude doublets, debris, and DAPI+ dead cells, and dermal CD45-tdTomato+ live cells were sorted from untreated or 7-day-IMQ-induced PdgfraDreER-tdTomato mouse skin for scRNA-seq.
Libraries were generated using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.

tag: genotype

value: PdgfraDreER-tdTomato

value: Dermis

tag: age

value: 8 week

value: UT


title: BC7-CTC_EMT

description: RNA-seq BioSample: SAMN20520685


title: BC37-CTCneg

description: RNA-seq BioSample: SAMN20520698

value: CTC negative


title: BC41-CTC_EMT_EP

description: RNA-seq BioSample: SAMN20520701

value: CTC EMT, epithelial


title: BC34-K

description: RNA-seq BioSample: SAMN20520696

value: female


title: BC28-CTCneg

description: RNA-seq BioSample: SAMN20520691


title: BC29-CTCneg

description: RNA-seq BioSample: SAMN20520692


title: BC20-CTCneg

description: RNA-seq BioSample: SAMN20520690


title: BC36-CTCneg

description: RNA-seq BioSample: SAMN20520697


title: BC38-K

description: RNA-seq BioSample: SAMN20520699


title: BC33-K

description: RNA-seq BioSample: SAMN20520695


title: BC30-CTCneg

description: RNA-seq BioSample: SAMN20520693


title: IMQ skin Fb, replicate 1, scRNAseq

description: 10x Genomics

tag: treatment

value: IMQ


title: Exp35-HB-22F3

description: HB IFN-a-DHFR - rep. 2


title: BC8-CTCneg

description: RNA-seq BioSample: SAMN20520686


title: BC6-CTC_EMT

description: RNA-seq BioSample: SAMN20520684


title: Exp35-GFP-22F3

description: GBM cells IFN-a-DHFR - rep. 2

source_name: GBM

value: Glioblastoma (GB)


title: BC10-CTCneg

description: RNA-seq BioSample: SAMN20520688

value: primary breast tumour


title: Exp35-HB-22B3

description: HB rIFN-a - rep. 2

value: rIFN-a


title: Exp35-GFP-22B1

description: GBM cells rIFN-a - rep. 1


title: Exp35-GFP-22A3

description: GBM cells control - rep. 2

value: Control

value: control


title: Exp35-HB-22A3

description: HB Control - rep. 2

value: Healthy Brain (HB)


title: Exp35-HB-22D1

description: HB Control - rep. 3


title: Exp35-HB-22B4

description: HB rIFN-a - rep. 3


title: Exp35-HB-22B1

description: HB rIFN-a - rep. 1


title: Exp35-GFP-22A2

description: GBM cells control - rep. 1


title: Exp35-HB-22A2

description: HB Control - rep. 1


title: Exp35-GFP-22F4

description: GBM cells IFN-a-DHFR - rep. 3

value: IFN-a-DHFR


title: Exp35-GFP-22B4

description: GBM cells rIFN-a - rep. 3


title: C.31_S27

city: Columbus

first: Phillip

middle: G.

last: Popovich

state: OH

address: 460 W 12th Ave

department: Department of Neuroscience

institute: The Ohio State University

description:
extract protocol 1, library construction protocol 1, library strategy 1
processed data file: Complete_geneList.xlsx

data_processing:
RNA-seq:
Reads were aligned to the mouse GRCm38 reference genome using STAR (v.2.4.0).
Read counts for RefSeq genes (mm10) were generated by HTSeq v.0.6.1.
Low-count genes were filtered and fragments per kilobase per million mapped reads (FPKM) values were generated
scRNA-seq:
Fastq sequence files were de-multiplexed, aligned, and annotated using the mouse ENSMBL database and Cell Ranger software.
Gene expression was counted using unique molecular identifier barcodes  and gene-cell matrices were constructed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts, normalized gene counts, and FPKM values for every gene and every sample
Supplementary_files_format_and_content: Barcode, Matrix and Features files for Seurat Object generation

source_name: Bulk Spinal Cord RNAseq

growth_protocol: 8-10 week old female mice were purchased from Jackson labs and housed under conventional conditions, 12 hr light cycle and free access to food and water. All procedures were performed in accordance with The Ohio State University Institutional Animal Care and Use Committee.

extract_protocol:
protocol 1: Mice were euthanized with 1.5x the surgical dose of ketamine and xylazine then perfused transcardially with DEPC buffer until the liver and blood were cleared. A 1 cm piece of spinal cord (centered on the T9 laminectomy site) was quickly dissected and homogenized in 1 ml of TRIzol reagent (ThermoFisher). RNA was extracted according to the manufacturers instructions. Briefly, the tissue lysate was centrifuged at 4°C for 5 mins at 12 000 g. The supernatant was incubated for 5 mins to dissociate nucleoproteins. Samples were incubated with 0.2 ml of chloroform for 2.5 mins then shaken vigorously for 15 sec.  Samples were centrifuged at 4°C for 15 mins at 12 000 g. The aqueous phase was collected and mixed with 0.5 ml of isopropanol with 2 ul of glycogen then stored at -20°C. Samples were centrifuged (4°C, 5 mins, 12 000 g) and the pellet resuspended in 75% ethanol. The sample was vortexed, centrifuged (4°C, 5 mins, 7 5 00 g), the supernatant removed and pellet dried for 5-10 mins. The pellet was resuspended in 20 μl RNAse free water and warmed to 55°C. RNA yield was determined using Nanodrop. RNA was purified using the QIAGEN RNeasy spin column steps according to manufacturers instructions. RNA quality and final yield was then measured using a RNA 6000 NanoAssay by Chip. Samples with RIN > 7 were included for analysis (average RIN = 8.6). Samples were stored at -80°C until sequencing.
protocol 2: Mice were euthanized with 1.5x the surgical dose of ketamine and xylazine. A 1 cm piece of unperfused, fresh spinal cords (centered on the T9 laminectomy site) was quickly dissected. Tissue was dissociated to a single cell suspension using a gentleMACS dissociator (Miltenyi) and mouse adult brain dissociation kit (Miltenyi, 130-107-677). Dissociated cells were passed through a sterile 70 μm filter to remove large particulate debris. Myelin debris was removed using myelin removal beads (Miltenyi, 130-096-733). Dead cells were removed using Viahance dead cell removal (BioPAL, #CP-50VQ02). Cells were diluted to 1000 cells/μl.
protocol 1: RNA-seq was carried out by the UCLA Technology Center for Genomics and Bioinformatics. The library was prepared using Nugen Ovation RNA Ultra Low Input (500 pg) + Kapa Hyper. The quantity and quality of cDNA were assessed using an Agilent 2100 Expert High Sensitivity DNA Assay. cDNA samples were sequenced at UCLA Technology Center for Genomics and Bioinformatics. Reads were aligned to the mouse GRCm38 reference genome using STAR (v.2.4.0). Read counts for RefSeq genes (mm10) were generated by HTSeq v.0.6.1. Low-count genes were filtered and fragments per kilobase per million mapped reads (FPKM) values were generated.
protocol 2: The single cell suspension and Chromium Single Cell 3’ V3 reagents (10X Genomics) were loaded into chips to collect individual cells encapsulated by gel beads in emulsion (GEMs) using the 10X Chromium Controller. cDNA and library amplification for an optimal signal was 13-16 cycles. Sequencing was conducted on HiSeq4000 (Novogene).

treatment_protocol: Mice are fed diet laced with PLX5622 (1200 ppm) (Plexxikon Inc.) or Vehicle chow for 2 weeks before undergoing a T9 contusion SCI or sham (laminectomy) surgery. Mice remain on diet until the end point at 7 or 28 days post-surgery.

value: Homogenized mouse spinal cord

value: Spinal cord cells

tag: mouse strain

tag: disease state

value: Sham


title: Exp35-GFP-22B3

description: GBM cells rIFN-a - rep. 2

tag: tissue


title: Exp35-GFP-22F1

description: GBM cells IFN-a-DHFR - rep. 1


title: C.5_S26


title: Exp35-GFP-22D1

description: GBM cells control - rep. 3


title: D.32_S29

value: 76 kdyne T9 contusion SCI


title: A.3_S1

value: Vehicle


title: D.6_S7

value: 77 kdyne T9 contusion SCI


title: B.2_S24

value: 75 kdyne T9 contusion SCI


title: C.7_S5


title: A.27_S3


title: E12-5_WT_embryo2_Ftpos_ATAC

city: San Francisco

first: James

middle: D

last: Price

address: 1550 4th Street

department: Psychiatry

institute: UC San Francisco

description: WTvsD12_FTpos_GenrichPeaks_AUC500.narrowPeak

data_processing:
Alignment of reads to mm10 genome performed using bwa (alignment via Burrows-Wheeler transformation) v 0.7.17-r1188
Fastq files were converted to bam format using view function of samtools v1.10
Duplicate reads were removed using the rmdup function of samtools v1.10
ATAC samples were subsampled to 6MM reads using samtools v1.10
ChIP narrowPeak files were called using macs2 (v2.2.7.1) using the following parameters: --nomodel -p 1e-5
ATAC peaks were called using Genrich with the following parameters: -p 0.01 -a 500
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deeptools
Supplementary_files_format_and_content: ChIP narrowPeak files generated using macs2 using Input samples as control, ATAC narrowPeak files are comparative peak calls using Genrich

source_name: Basal Ganglia

extract_protocol:
ChIP: Cells were treated with 5mM DSG followed by 1% PFA prior to generating nuclear extracts. Extracts were sonicated for 10 minutes prior to adding listed antibody to pull down bound DNA
Libraries were constructed using Nugen Ovation Ultralow DR Multiplex System and size selected in the range of 180-400bp

tag: genotype/variation

value: WT


title: E12-5_WT_embryo1_Ftpos_ATAC


title: D.30_S8


title: C.29_S6


title: B.4_S4


title: A.25_S2


title: BC9-CTCneg

description: RNA-seq BioSample: SAMN20520687

value: female

value: CTC negative


title: E12-5_Dlx1/2KO_embryo3_Ftpos_ATAC

description: D12vsWT_FTpos_GenrichPeaks_AUC500.narrowPeak


title: BC14-CTC_EMT_EP

description: RNA-seq BioSample: SAMN20520689

value: CTC EMT, epithelial


title: A.1_S23


title: E12-5_Dlx1/2KO_embryo2_FTneg_ATAC

description: D12vsWT_FTneg_GenrichPeaks_AUC500.narrowPeak


title: E13-5_BasalGanglia_Input2

tag: chip antibody


title: E12-5_WT_embryo3_Ftpos_ATAC

tag: strain


title: E12-5_Dlx1/2KO_embryo1_FTneg_ATAC


title: E13-5_BasalGanglia_Input3


title: E12-5_WT_embryo3_FTneg_ATAC

description: WTvsD12_FTneg_GenrichPeaks_AUC500.narrowPeak


title: E13-5_BasalGanglia_RBBP7_ChIP

description: paired with Input3

value: Life Technologies, MA5-25735


title: E13-5_BasalGanglia_Input1


title: E12-5_WT_embryo1_FTneg_ATAC


title: E13-5_BasalGanglia_RBBP4_ChIP

description: paired with Input3

value: GeneTex, GTX70232


title: B.26_S25


title: BC5-CTC_EP

description: RNA-seq BioSample: SAMN20520683

value: primary breast tumour

value: CTC epithelial


title: E12-5_Dlx1/2KO_embryo2_Ftpos_ATAC


title: E13-5_BasalGanglia_MBD3_ChIP

description: paired with Input2

value: Bethyl, A302-528A


title: E13-5_BasalGanglia_HDAC2_ChIP

description: paired with Input1

value: Bethyl, A300-705A


title: E12-5_WT_embryo2_FTneg_ATAC


title: BC4-CTC_EMT

description: RNA-seq BioSample: SAMN20520682

value: CTC EMT


title: E12-5_Dlx1/2KO_embryo1_Ftpos_ATAC


title: CD4+ T cells - 4E_heavy_rep3 [4E-3-ReSubmission_S30]

city: New York

first: Robert

last: Schneider

address: 450 E29th Str

institute: NYUSOM

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie used to align the reads to the reference, and the aligned reads were counted per gene.
DGE and translational efficiency were calculated using RIVET (Ernlund etal, BMC Gen, 2018)
Genome_build: mm9
Supplementary_files_format_and_content: NormalisedCounts

source_name: CD4+ T cells

extract_protocol:
Sucrose gradients were run; RNA was extracted from isolated CD4+ T cells and CD4+ TFH cells for total mRNA using Trizol, and from heavy and lightribosome sucrose gradient fractions from translatomic analysis.  RNAs were subjected to Zymo clean and concentrated.
Illumina automated stranded RNA-seq library prep, polyA selection

treatment_protocol: Mice were immunized with AOV alum then treated for 7 days with daily PO treatment of vehicle alone orwith eIF4E inhibitor 4EGI-1 at 25 mg/kg. CD4+ T cells and TFH cells were FACS isolated gating on CD4+CD45+ or CD4+PD1_CXCR5+, respectively.

value: CD4+ T cells

tag: molecule subtype

value: heavy polysome fraction polyA RNA


title: E13-5_BasalGanglia_HDAC1_ChIP

description: paired with Input1

value: Bethyl, A300-713A


title: E12-5_Dlx1/2KO_embryo3_FTneg_ATAC


title: CD4+ T cells - 4E_input_rep2 [4E-2total_S35]


title: CD4+ T cells - 4E_heavy_rep2 [4E-2_S29]


title: CD4+ T cells - 4E_input_rep3 [4E-3total_S36]


title: E13-5_BasalGanglia_CHD4_ChIP

description: paired with Input2

value: Abcam, ab72418


title: CD4+ T cells - OA_heavy_rep3 [OA3_S27]


title: CD4+ T cells - OA_heavy_rep2 [OA2_S26]


title: CD4+ T cells - OA_heavy_rep1 [OA1_S25]


title: CD4+ T cells - OA_input_rep1 [OA1-total_S31]


title: CD4+ T cells - OA_input_rep3 [OA3-total_S33]


title: CD4+ T cells - OA_input_rep2 [OA2-total_S32]


title: CD4+ T cells - 4E_input_rep1 [4E1total_S34]


title: S120: Nuc_PolyA_ZT20_S2_CryKO

city: Lausanne

first: Felix

last: Naef

state: Vaud

address: AAB 040 Station 15

department: Institute of Bioengineering

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

data_processing:
Quantification of pre-mRNA and mRNA expression levels was performed using Kallisto version 0.46.0 (Braye et al. 2016). A combined index was built using reference fasta files from Ensembl for mus musculus (GRCm38) and rattus norvegicus (RGSC 6.0). In particular, pre-mRNA (introns and exons) and mRNA (exons) reference sequences were used as an input and named accordingly
Pseudoalignement parameters (Kallisto, version 0.46.0): --single --rf-stranded -l 100 -s 30 -s 30
Genome_build: chimeric genome of mm10 Rn6
Supplementary_files_format_and_content: comma-separated file containing estimated counts by Kallisto's algorithm for each RNA transcripts and pre-RNA transcripts of the mouse genome for each sample

source_name: Nuclear PolyA CryKO

extract_protocol:
Pieces of the big lobe of the mouse liver were dissected. RNA from unfractionnated liver: pieces of liver were snap-frozen in liquid nitrogen and extracted on spin-columns from miRNEasy kit  following manufacturer's instruction (QIAGEN, Germany). Nuclear and cytoplasmic RNA were extracted following the protocole of nascent-seq described in Menet et al. 2012. Briefly, liver pieces were homogenised in a 2.2M sucrose buffer, layered on top of 2.05M sucrose cushion and ultra-centrifuged. Cytoplasmic RNA in sucrose was precipitated in ethanol 70% overnight at -80° and extracted on spin-columns from the miRNEAsy kit (Qiagen). Nuclear RNA in the pellet was resuspended in a guanidium thiocyanate-containing extraction buffer and collected on spin-column from the miRNEasy kit (Qiagen). Additional DNAse treatment (Qiagen, Germany) was performed to remove genomic DNA. In the nuclear and cytoplasmic RNA, spike-in RNA extracted from rat liver (male Wistar) were added. Rat RNA was extracted from a mass of liver corresponding to 5% of the biopsie of the mouse liver.
Polyadenylated (PolyA) nuclear and cytoplasmic RNA libraries were prepared with the TruSeq stranded mRNA LT kit (Illumina, San Diego, USA), starting from 650 ng of RNA, according to the manufacturer's protocol. Total RNA libraries (nuclear, cytoplasmic and unfractionnated) were prepared with the Kapa RNA hyperPrep with Riboerase prep combined with KAPA Unique Dual-Indexed Adapter Kit (Illumina, San Diego, USA), starting from 650 ng RNA. Libraries were sequenced on a Hiseq4000. We used a SBS 50 cycles and SR cluster kit, performing a single read sequencing of 65 nucleotides. We sequenced on average 70M reads for Nuclear PolyA and Nuclear Total samples,  25M reads for Cytoplasmic PolyA and Cytoplasmic Total samples, and 50M reads for the Unfractionated samples.

value: Liver

tag: fraction

value: Nuclear

tag: rna population

value: Nuclear PolyA RNA


title: S113: Nuc_PolyA_ZT08_S1_CryKO


title: S115: Nuc_PolyA_ZT12_S1_CryKO


title: S118: Nuc_PolyA_ZT16_S2_CryKO


title: S114: Nuc_PolyA_ZT08_S2_CryKO


title: S112: Nuc_PolyA_ZT04_S2_CryKO


title: S119: Nuc_PolyA_ZT20_S1_CryKO


title: CD4+ T cells - 4E_heavy_rep1 [4E-1_S28]


title: S109: Nuc_PolyA_ZT00_S1_CryKO


title: S110: Nuc_PolyA_ZT00_S2_CryKO


title: S111: Nuc_PolyA_ZT04_S1_CryKO


title: S107: Cyt_PolyA_ZT20_S1_CryKO

source_name: Cytoplasmic PolyA CryKO

value: Cytoplasmic

value: Cytoplasmic PolyA RNA


title: S106: Cyt_PolyA_ZT16_S2_CryKO


title: S103: Cyt_PolyA_ZT12_S1_CryKO


title: S108: Cyt_PolyA_ZT20_S2_CryKO


title: S117: Nuc_PolyA_ZT16_S1_CryKO


title: S104: Cyt_PolyA_ZT12_S2_CryKO


title: S102: Cyt_PolyA_ZT08_S2_CryKO


title: S100: Cyt_PolyA_ZT04_S2_CryKO


title: S116: Nuc_PolyA_ZT12_S2_CryKO


title: S101: Cyt_PolyA_ZT08_S1_CryKO


title: S96: Unf_Total_ZT20_S2_CryKO

source_name: Unfractionnated Total CryKO

value: Unfractionnated

value: Unfractionnated Total RNA


title: S98: Cyt_PolyA_ZT00_S2_CryKO


title: S99: Cyt_PolyA_ZT04_S1_CryKO


title: S97: Cyt_PolyA_ZT00_S1_CryKO


title: AMA40 Mueller Hinton 50% Urine replicate 2

city: Fullerton

first: M. S.

last: Ramirez

address: 800 N. State College Blvd

institute: California State University Fullerton

data_processing:
Low-quality reads were removed using Trimmomatic v0.32
Reads were aligned witth Burrows Wheeler Alignment software (BWA) v0.7.17
Bigwig files were generated with custom bash scripts and BEDtools
Read counts per gene were determined using featureCounts
RNA-seq differential expression analysis was performed using DESeq
Supplementary files format and content: .txt files containing the output of featureCounts for each sample

organism: Acinetobacter baumannii

growth_protocol: Overnight cultures of A. baumannii strains were diluted 1:10 in fresh iron depleted cation adjusted Mueller Hinton or cation adjusted Mueller Hinton and incubated with agitation for 18 h at 37ºC.

extract_protocol:
RNA was extracted using Direct-zol RNA Kit (Zymo Research, Irvine, CA, USA)
Illumina RNA-seq

treatment_protocol: When indicated, Mueller Hinton was supplemented with 50 % of human urine

value: Mueller Hinton 50% Urine


title: AMA40 Mueller Hinton replicate 2

value: Mueller Hinton


title: AMA40 Mueller Hinton replicate 1


title: AAV control 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from whole liver tissue of animals transfected with AAV control vector.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray mogene20stmmentrezgcdf R package (version 24.0.0).

label: biotin

source_name: whole liver tissue

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: 10-week-old C57BL/6J mice were fed a high-fat high-fructose diet containing 40 Kcal% fat (palm oil), 20 Kcal% fructose, and 2% cholesterol (Opensource diet D09100310, Research Diets) for 32 weeks.

extract_protocol: Tissue samples were powdered in liquid nitrogen, and RNA was isolated using TRIzol reagent (Invitrogen) following the manufacturer’s protocol.

treatment_protocol: AAV-Cont or AAV-Glrx (1 × 1E12 vg) was administrated by intraperitoneal injection after 20 weeks of NASH diet, and maintained for another 12 weeks.

tag: diet

value: High-fat high-fructose

tag: disease

value: Non-alcoholic steatohepatitis

tag: transfection

value: AAV control


title: S93: Unf_Total_ZT16_S1_CryKO


title: AAV-Glrx 1

description: Gene expression data from whole liver tissue of animals transfected with AAV-Glrx vector.

value: AAV-Glrx


title: AB5075 Mueller Hinton 50% Urine replicate 3


title: AMA40 Mueller Hinton replicate 3


title: S105: Cyt_PolyA_ZT16_S1_CryKO


title: AB5075 Mueller Hinton replicate 2


title: S95: Unf_Total_ZT20_S1_CryKO


title: AAV-Glrx 2


title: S94: Unf_Total_ZT16_S2_CryKO


title: AMA40 Mueller Hinton 50% Urine replicate 3


title: AB5075 Mueller Hinton 50% Urine replicate 1


title: AAV-Glrx 3


title: S91: Unf_Total_ZT12_S1_CryKO


title: S90: Unf_Total_ZT08_S2_CryKO


title: AB5075 Mueller Hinton 50% Urine replicate 2


title: AMA40 Mueller Hinton 50% Urine replicate 1


title: S92: Unf_Total_ZT12_S2_CryKO


title: AAV control 1


title: AB5075 Mueller Hinton replicate 1


title: AB5075 Mueller Hinton replicate 3


title: CuFluc_2

city: OEIRAS

first: Catarina

last: Pimentel

state: LISBOA

address: Av. da República

department: MOSTMICRO

country: Portugal

institute: ITQB-NOVA

data_processing:
The quality of the RNA-Seq raw data was analysed using the FastQC tool. Reads were mapped against Candida glabrata genome (GCA_000002545.2 downloaded from NCBI genome database) using Bowtie2.The mapping files were sorted by genomic position using Samtools and the quantification of the transcripts expression was done using the FeatureCounts software. The differential expression analysis was done with the R package edgeR
Genome_build: GCA_000002545.2
Supplementary_files_format_and_content: Tab delimited .txt file generated using edgeR and containing the Log2FC, Log2CPM, pvalue and FDR for each Candida glabrata gene, identified with the correspondent geneID. FC - fold change; CPM - counts per million

organism: Nakaseomyces glabratus

source_name: Exponential culture cells

growth_protocol: Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600 0.15 and grown to exponential phase (OD600 0.8) at 37 ºC with shaking at 180 rpm in synthetic complete (SC) medium pH 5.5 ( SC: MP CSM 0.77 g/L; yeast nitrogen Base w/o amino acids and ammonium sulphate 1.7 g/L; ammonium sulphate 5.4 g/L; glucose 2%). After reaching an OD600 of 0.8 cells were left untreated or treated with 1.25 mM CuSO4, 32 µg/mL fluconazole or both compounds for one hour.

extract_protocol:
RNA was isolated following cell lysis (lysis buffer: 0.1 M LiCl; 0.01M Na2EDTA; 0.01M Tris-HCl pH 7.4; 0.2% SDS, dissolved in bi-distillated sterile water) using the glass bead method and phenol:chloroform extraction. Samples were then vortexed 10 minutes at 4ºC and centrifugation at 14000 rpm to separate the organic from the aqueous fraction. The aqueous fraction was transferred to a microcentrifuge tube, ethanol 100% was added and RNA was precipitated overnight at -20ºC. RNA was collected by centrifugation at 14000 rpm for 15 minutes and the pellet was resuspended in RNAse free water and incubated 15 minutes at 65ºC to help the solubilisation of the pellet. RNA samples were treated with DNAse (TURBO DNAse Ambion) according to manufacturer’s instructions, at 37ºC for 40 minutes. RNA samples were then purified using RNeasy Mini Kit (QIAGEN).The integrity of RNA samples was evaluated by agarose gel electrophoresis.
RNA libraries were prepared for sequencing by the Genomics Facility of the Gulbenkian Institute of Science, Oeiras, Portugal, using the SMART-SEQ2 protocol

treatment_protocol: Cells were harvested by centrifugation at 3600 g for 5 min

value: treated with 1.25 mM CuSO4 and 32 ug/mL fluconazole for 1 hour


title: S89: Unf_Total_ZT08_S1_CryKO


title: Fluc_3

value: treated with 32 ug/mL fluconazole for 1 hour


title: CuFluc_1


title: S88: Unf_Total_ZT04_S2_CryKO


title: Fluc_2


title: Fluc_1


title: AAV control 2


title: CuFluc_3


title: Cu_1

value: treated with 1.25 mM CuSO4 for 1 hour


title: Cu_3


title: Untreated_3

description:
controlvscu_edgeR.txt
controlvsfluc_edgeR.txt
controlvscufluc_edgeR.txt

value: untreated


title: S85: Unf_Total_ZT00_S1_CryKO

value: Liver


title: S86: Unf_Total_ZT00_S2_CryKO


title: S87: Unf_Total_ZT04_S1_CryKO


title: S84: Nuc_Total_ZT20_S2_CryKO

source_name: Nuclear Total CryKO

value: Nuclear

value: Nuclear Total RNA


title: S83: Nuc_Total_ZT20_S1_CryKO


title: Untreated_1


title: S82: Nuc_Total_ZT16_S2_CryKO


title: S80: Nuc_Total_ZT12_S2_CryKO


title: T98_A_V_24H_rep3

city: Shenzhen

first: Ping

last: Li

address: Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastp (version 0.12.4) software was use to do reads filtering, including adapter removing, low quality base removing (lower than 20),et. al.
HISAT2 (version 2.1.0)software were used to do alignmnet with reference genome with bwa algorithm
Reads count mapping to each chromosome were calculated using HTSeq (0.10.0) software and FPKM was used to measure gene expression
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include expression values for genes

growth_protocol: T98 were cultured in DMEM and 10% FBS 1XP.S.

extract_protocol:
Total RNA was extracted using Trizol reagent (invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quntity and purity were analyzed by Life Invitrogen Qubit® 3.0 and NanoDrop™.
RNA libraries were prepared for sequencing using standard illunima protocols

treatment_protocol: Pretreated with the CDK4&6 inhibitor Abemaciclib, then infected with the VSV-M51 for 24 hours.

tag: agent

value: Abemaciclib and VSV-M51

tag: cell type

value: human glioma cells


title: T98_A_V_24H_rep1


title: S81: Nuc_Total_ZT16_S1_CryKO

tag: genotype


title: T98_A_V_24H_rep2


title: T98_VSV51_24H_rep2


title: T98_DMSO_24H_rep3

value: DMSO


title: Cu_2


title: Untreated_2


title: T98_DMSO_24H_rep1


title: Control 1

city: Nanning

first: Jiajia

last: Liao

address: Shuangyong road

institute: Guangxi Medical University

description: circRNA expression in plasma

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software limma package

source_name: plasma

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

tag: gender

value: male

tag: age


title: P39-AZA-R (transcriptome)

city: Pokfulam

first: Rita

middle: Lok Hay

last: Yim

address: Room 311, 3rd Floor, Professorial Block, Queen Mary Hospital,

department: Department of Medicine

country: Hong Kong

institute: Hong Kong University

description: P39-AZA-R (transcriptome)

data_processing:
SOAPnuke
HISAT2
StringTie & Cuffcompare
Bowtie2
RSEM
Genome_build: hg19
Supplementary_files_format_and_content: differential expression table

source_name: Bone Marrow Cell Line

growth_protocol: RPMI-1640 GlutaMAX supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Qiagen RNAeasy mini kit
High quality RNA were enriched for mRNA by Oligo(dT) followed by preparation into whole transcriptomic library. Paired-end sequencing was performed on BGISEQ-500 sequencer to acquire at least 5 million reads of 100bp in length per read.
Cleaned reads pre-processed by SOAPnuke toolkit were mapped to reference genome hg19 and spliced-aligned reads mapped by HISAT2 was subjected to StringTie and Cuffcompare to reconstruct transcripts for novel transcript predictions. The combined transcriptomic assembly was used as reference for reads re-alignment by Bowtie2 followed by gene expression level calculation with RSEM.

treatment_protocol: Parental P39 sensitive to HMA were treated with 1µM of AZA or DEC for 48 hours, namely P39-AZA-S, P39-DEC-S. To establish derivative cell lines resistant to AZA or DEC, both cell lines were continuously exposed to AZA or DEC starting at a concentration of 5nM. P39 resistant to at least 10µM of AZA or DEC was established as P39-AZA-R and P39-DEC-R

tag: cell line

tag: treatment

value: AZA, continuously exposed

tag: phenotype

value: HMA resistant


title: S75: Nuc_Total_ZT04_S1_CryKO

tag: tissue


title: S79: Nuc_Total_ZT12_S1_CryKO


title: T98_DMSO_24H_rep2


title: Control 3

description: circRNA expression in plasma

value: female


title: Control 2

description: circRNA expression in plasma


title: P39-DEC-R (transcriptome)

description: P39-DEC-R (transcriptome)

value: DEC, continuously exposed


title: S76: Nuc_Total_ZT04_S2_CryKO


title: P39-AZA-S (transcriptome)

description: P39-AZA-S (transcriptome)

value: AZA, 48 hours

value: HMA sensitive


title: S77: Nuc_Total_ZT08_S1_CryKO


title: S74: Nuc_Total_ZT00_S2_CryKO


title: T98_VSV51_24H_rep3


title: PD 2

description: circRNA expression in plasma


title: T98_VSV51_24H_rep1


title: PD 1

description: circRNA expression in plasma


title: S78: Nuc_Total_ZT08_S2_CryKO


title: ASW_C07_2016-07-29

first: Cynthia

middle: A.

last: Bradham

address: 24 Cummington Mall

department: Biology

description:
cell collection protocol: t 18 hours post-fertilization, embryos were collected and disaggregated into single cells. Embryos were exposed to pronase, washed in calcium-free sea water, incubated in hyaline extraction medium (0.3 M glycine, 0.3 M NaCl, 10 mM KCl, 10 mM MgS04, 10 mM Tris, 2 mM EGTA), washed in calcium free-sea water, then triturated with a pipette to separate cells.
FACS protocol: PMC-specific antibody 6a9 (1:5) and anti-mouse alexa Fluor 488 (Invitrogen, 1:500) in BSA-ASW block was added to the cell suspension for 5 min, then washed out. SYTOX dead stain (1:1000) was added. Cells were gated to exclude doublets and dead cells and sorted into RNA lysis buffer.

data_processing:
Read concatentation: Reads sequenced across multiple lanes were concatenated together for single cells using the “cat” command in a linux terminal
Quality control: Reads and bases in reads were filtered and quality controlled using fastp (version 0.20.0) with specified parameters “-y -Y 30” and default parameters otherwise
GFF conversion: The GFF annotation file was converted to a GTF file using gffread with default parameters
Genome Alignment: Reads were aligned for to the most recent L. variegatus genome using STAR (version 2.7.1a). The index was built with specified parameter “--sjdbOverhang 151” and default otherwise. Alignment was run using default parameters.
Alignment Quantification: Read quantification was performed using featureCounts (v1.6.4) with the fragment specification option “-p” enabled, and default parameters otherwise
Count Normalization: Prior to normalization, cells with fewer that 50,000 feature counts, and genes with total counts less than 0.5 cpm were filtered out. Counts were normalized per batch for downstream analysis using the “computeSumFactors” function in the scran library (version 1.12.1) in R (version 3.6.2). Normalized counts were subsequently batch corrected using the function “multiBatchNorm” function in the scran library.
Genome_build: L. variegatus genome (Li et al., 2020)
Supplementary_files_format_and_content: Comma-separated text files containing raw and normalized count matrices for all cells used in the analysis, their associated metadata, and genome annotation information.

organism: Lytechinus variegatus

source_name: Primary Mesenchyme Cells

growth_protocol: Sea urchin gametes were collected from wild-caught Lytechinus variegatus. Eggs were fertilized in artificial sea water at room temperature and embryos were cultured in artificial sea water at 23°C.

extract_protocol:
Individual PMCs were sorted directly into RNA lysis buffer supplemented with 1% β-mercaptoethanol.
Transcripts were purified, reverse-transcribed, and amplified according to the SMART-Seq2 protocol (Tombetta et al., Curr Protoc Mol Biol, 2014). Libraries were prepared using the Nextera XT kit (Illumina) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 using 100bp paired end reads.

treatment_protocol: MK-886 in DMSO was added to embryo cultures at 12 hours post-fertilization to a final concentration 1.5µM.  Chlorate in ASW was added to embryo cultures at 12 hpf to a total concentration of 30 mM. Volume-matched DMSO was added to DMSO control samples.

value: primary mesenchyme

tag: developmental stage

value: 18 hours post-fertilization


title: ASW_G02_2016-07-29


title: Chlorate_A11_2016-07-29

value: Chlorate (30mM final)


title: Chlorate_C10_2016-07-29


title: P39-DEC-S (transcriptome)

description: P39-DEC-S (transcriptome)

value: DEC, 48 hours


title: S72: Cyt_Total_ZT20_S2_CryKO

source_name: Cytoplasmic Total CryKO

value: Liver

value: Cytoplasmic

value: Cytoplasmic Total RNA


title: Chlorate_C01_2016-07-29


title: Chlorate_C08_2016-07-29


title: Chlorate_C05_2016-07-29


title: S71: Cyt_Total_ZT20_S1_CryKO


title: Chlorate_A10_2016-07-29


title: ASW_G07_2016-07-29


title: S70: Cyt_Total_ZT16_S2_CryKO


title: S68: Cyt_Total_ZT12_S2_CryKO


title: PD 3

description: circRNA expression in plasma


title: Chlorate_A06_2016-07-29


title: ASW_G03_2016-07-29


title: ASW_G06_2016-07-29


title: ASW_G08_2016-07-29


title: Chlorate_A03_2016-07-29


title: Chlorate_A07_2016-07-29


title: S69: Cyt_Total_ZT16_S1_CryKO


title: ASW_C08_2016-07-29


title: S73: Nuc_Total_ZT00_S1_CryKO

value: Nuclear

value: Nuclear Total RNA


title: ASW_C10_2016-07-29


title: S66: Cyt_Total_ZT08_S2_CryKO


title: ASW_G01_2016-07-29


title: S67: Cyt_Total_ZT12_S1_CryKO


title: Chlorate_C12_2016-07-29


title: S65: Cyt_Total_ZT08_S1_CryKO


title: S64: Cyt_Total_ZT04_S2_CryKO


title: ASW_C12_2016-07-29


title: ASW_G12_2016-07-29


title: ASW_C05_2016-07-29


title: Chlorate_A12_2016-07-29


title: ASW_C09_2016-07-29


title: ASW_A10_2016-07-29


title: ASW_E10_2016-07-29


title: Chlorate_C03_2016-07-29


title: S60: Nuc_PolyA_ZT20_S2_WT

source_name: Nuclear PolyA WT

value: Nuclear PolyA RNA


title: S59: Nuc_PolyA_ZT20_S1_WT


title: ASW_A08_2016-07-29


title: S61: Cyt_Total_ZT00_S1_CryKO


title: S62: Cyt_Total_ZT00_S2_CryKO


title: ASW_A03_2016-07-29


title: S58: Nuc_PolyA_ZT16_S2_WT


title: ASW_A07_2016-07-29


title: S57: Nuc_PolyA_ZT16_S1_WT


title: ASW_E05_2016-07-29


title: ASW_G09_2016-07-29


title: ASW_A09_2016-07-29


title: S56: Nuc_PolyA_ZT12_S2_WT


title: S55: Nuc_PolyA_ZT12_S1_WT


title: Chlorate_C09_2016-07-29


title: Chlorate_C07_2016-07-29


title: ASW_E11_2016-07-29


title: S63: Cyt_Total_ZT04_S1_CryKO


title: ASW_A02_2016-07-29


title: Chlorate_C06_2016-07-29


title: ASW_E12_2016-07-29


title: S54: Nuc_PolyA_ZT08_S2_WT


title: S53: Nuc_PolyA_ZT08_S1_WT


title: S52: Nuc_PolyA_ZT04_S2_WT


title: ASW_A11_2016-07-29


title: Chlorate_C11_2016-07-29


title: ASW_E07_2016-07-29


title: ASW_A05_2016-07-29


title: ASW_G04_2016-07-29


title: ASW_E02_2016-07-29


title: Chlorate_C02_2016-07-29


title: ASW_C02_2016-07-29


title: S51: Nuc_PolyA_ZT04_S1_WT


title: S49: Nuc_PolyA_ZT00_S1_WT


title: S50: Nuc_PolyA_ZT00_S2_WT


title: ASW_E06_2016-07-29


title: ASW_E04_2016-07-29


title: ASW_E09_2016-07-29


title: S48: Cyt_PolyA_ZT20_S2_WT

source_name: Cytoplasmic PolyA WT

value: Cytoplasmic PolyA RNA


title: S47: Cyt_PolyA_ZT20_S1_WT


title: ASW_G10_2016-07-29


title: S46: Cyt_PolyA_ZT16_S2_WT


title: Chlorate_A01_2016-07-29


title: ASW_A12_2016-07-29


title: ASW_A04_2016-07-29


title: ASW_A06_2016-07-29


title: ASW_A01_2016-07-29


title: ASW_G11_2016-07-29


title: ASW_C04_2016-07-29


title: ASW_C01_2016-07-29


title: ASW_E08_2016-07-29


title: ASW_G05_2016-07-29


title: S43: Cyt_PolyA_ZT12_S1_WT


title: ASW_C06_2016-07-29


title: S41: Cyt_PolyA_ZT08_S1_WT


title: Chlorate_A02_2016-07-29


title: S45: Cyt_PolyA_ZT16_S1_WT


title: S42: Cyt_PolyA_ZT08_S2_WT


title: Chlorate_A09_2016-07-29


title: Chlorate_C04_2016-07-29


title: ASW_E01_2016-07-29


title: ASW_E03_2016-07-29


title: S40: Cyt_PolyA_ZT04_S2_WT


title: ASW_C03_2016-07-29


title: S39: Cyt_PolyA_ZT04_S1_WT


title: ASW_C11_2016-07-29


title: Chlorate_A04_2016-07-29


title: S44: Cyt_PolyA_ZT12_S2_WT


title: S38: Cyt_PolyA_ZT00_S2_WT


title: Chlorate-PMCs-2-F09_2018-7-11

description:
NOTE: This cell filtered out of analysis for quality reasons
cell collection protocol: t 18 hours post-fertilization, embryos were collected and disaggregated into single cells. Embryos were exposed to pronase, washed in calcium-free sea water, incubated in hyaline extraction medium (0.3 M glycine, 0.3 M NaCl, 10 mM KCl, 10 mM MgS04, 10 mM Tris, 2 mM EGTA), washed in calcium free-sea water, then triturated with a pipette to separate cells.
FACS protocol: PMC-specific antibody 6a9 (1:5) and anti-mouse alexa Fluor 488 (Invitrogen, 1:500) in BSA-ASW block was added to the cell suspension for 5 min, then washed out. SYTOX dead stain (1:1000) was added. Cells were gated to exclude doublets and dead cells and sorted into RNA lysis buffer.


title: Chlorate-PMCs-2-H11_2018-7-11


title: MK886-PMCs-2-F06_2018-7-11

value: MK-886 (1.5uM final)


title: Chlorate-PMCs-1-F09_2018-7-11


title: S37: Cyt_PolyA_ZT00_S1_WT


title: ASW-PMCs-2-A07_2018-7-11


title: S36: Unf_Total_ZT20_S2_WT

source_name: Unfractionnated Total WT

value: Unfractionnated

value: Unfractionnated Total RNA


title: DMSO-PMCs-1-G04_2018-7-11

value: DMSO


title: MK886-PMCs-3-D09_2018-7-11


title: DMSO-PMCs-1-E09_2018-7-11


title: S35: Unf_Total_ZT20_S1_WT


title: DMSO-PMCs-1-F11_2018-7-11


title: S34: Unf_Total_ZT16_S2_WT


title: MK886-PMCs-2-H11_2018-7-11


title: Chlorate_A05_2016-07-29


title: Chlorate-PMCs-1-C05_2018-7-11


title: S33: Unf_Total_ZT16_S1_WT


title: DMSO-PMCs-1-H06_2018-7-11


title: DMSO-PMCs-1-B03_2018-7-11


title: ASW-PMCs-2-C12_2018-7-11


title: S31: Unf_Total_ZT12_S1_WT


title: ASW-PMCs-2-B02_2018-7-11


title: DMSO-PMCs-1-E05_2018-7-11


title: S30: Unf_Total_ZT08_S2_WT


title: S32: Unf_Total_ZT12_S2_WT


title: Chlorate-PMCs-1-D09_2018-7-11


title: S29: Unf_Total_ZT08_S1_WT


title: Chlorate-PMCs-2-D05_2018-7-11


title: MK886-PMCs-2-H09_2018-7-11


title: MK886-PMCs-2-F12_2018-7-11


title: Chlorate-PMCs-1-E11_2018-7-11


title: S28: Unf_Total_ZT04_S2_WT


title: S27: Unf_Total_ZT04_S1_WT


title: MK886-PMCs-2-B10_2018-7-11


title: Chlorate-PMCs-1-H10_2018-7-11


title: S26: Unf_Total_ZT00_S2_WT


title: Chlorate-PMCs-2-B10_2018-7-11


title: ASW-PMCs-2-E05_2018-7-11


title: S25: Unf_Total_ZT00_S1_WT


title: Chlorate-PMCs-1-E03_2018-7-11


title: MK886-PMCs-3-C07_2018-7-11


title: DMSO-PMCs-1-H08_2018-7-11


title: DMSO-PMCs-1-E12_2018-7-11


title: S23: Nuc_Total_ZT20_S1_WT

source_name: Nuclear Total WT


title: ASW-PMCs-2-E03_2018-7-11


title: Chlorate-PMCs-2-C06_2018-7-11


title: S24: Nuc_Total_ZT20_S2_WT


title: DMSO-PMCs-1-F07_2018-7-11


title: MK886-PMCs-2-A06_2018-7-11


title: ASW-PMCs-2-D07_2018-7-11


title: Chlorate-PMCs-1-H03_2018-7-11


title: S22: Nuc_Total_ZT16_S2_WT


title: S21: Nuc_Total_ZT16_S1_WT


title: S20: Nuc_Total_ZT12_S2_WT


title: Chlorate-PMCs-1-G08_2018-7-11


title: MK886-PMCs-2-E12_2018-7-11


title: DMSO-PMCs-1-G03_2018-7-11


title: S19: Nuc_Total_ZT12_S1_WT


title: MK886-PMCs-2-A10_2018-7-11


title: DMSO-PMCs-1-E11_2018-7-11


title: MK886-PMCs-3-G10_2018-7-11


title: MK886-PMCs-2-D09_2018-7-11


title: Chlorate-PMCs-2-C05_2018-7-11


title: S18: Nuc_Total_ZT08_S2_WT


title: S17: Nuc_Total_ZT08_S1_WT


title: Chlorate-PMCs-1-A09_2018-7-11


title: Chlorate-PMCs-1-F12_2018-7-11


title: Chlorate-PMCs-2-D06_2018-7-11


title: MK886-PMCs-3-A04_2018-7-11


title: S13: Nuc_Total_ZT00_S1_WT


title: S16: Nuc_Total_ZT04_S2_WT


title: Chlorate-PMCs-2-H03_2018-7-11


title: Chlorate-PMCs-1-B11_2018-7-11


title: DMSO-PMCs-1-F04_2018-7-11


title: MK886-PMCs-2-C01_2018-7-11


title: MK886-PMCs-3-E01_2018-7-11


title: ASW-PMCs-2-D11_2018-7-11


title: MK886-PMCs-2-D06_2018-7-11


title: Chlorate-PMCs-1-D12_2018-7-11


title: S09: Cyt_Total_ZT16_S1_WT

source_name: Cytoplasmic Total WT


title: Chlorate-PMCs-1-B08_2018-7-11


title: Chlorate-PMCs-1-E12_2018-7-11


title: DMSO-PMCs-1-A03_2018-7-11


title: S07: Cyt_Total_ZT12_S1_WT


title: Chlorate-PMCs-1-D02_2018-7-11


title: S14: Nuc_Total_ZT00_S2_WT


title: S15: Nuc_Total_ZT04_S1_WT


title: MK886-PMCs-3-F06_2018-7-11


title: S10: Cyt_Total_ZT16_S2_WT


title: MK886-PMCs-2-A07_2018-7-11


title: Chlorate-PMCs-1-G11_2018-7-11


title: Chlorate-PMCs-2-H05_2018-7-11


title: S04: Cyt_Total_ZT04_S2_WT


title: S11: Cyt_Total_ZT20_S1_WT


title: MK886-PMCs-2-H08_2018-7-11


title: ASW-PMCs-2-G11_2018-7-11


title: MK886-PMCs-3-C06_2018-7-11


title: S03: Cyt_Total_ZT04_S1_WT


title: S08: Cyt_Total_ZT12_S2_WT


title: MK886-PMCs-3-B12_2018-7-11


title: S12: Cyt_Total_ZT20_S2_WT


title: ASW-PMCs-2-A03_2018-7-11


title: S01: Cyt_Total_ZT00_S1_WT


title: MK886-PMCs-2-B05_2018-7-11


title: Chlorate-PMCs-1-B01_2018-7-11


title: MK886-PMCs-3-G11_2018-7-11


title: S05: Cyt_Total_ZT08_S1_WT


title: S02: Cyt_Total_ZT00_S2_WT


title: MK886-PMCs-3-F10_2018-7-11


title: Chlorate-PMCs-1-C10_2018-7-11


title: Chlorate-PMCs-1-D05_2018-7-11


title: Exosomes, Normal-3

city: GuangZhou

first: zhiping

last: wan

data_processing:
software: fastqc, BWA, miRDeep2
Clean reads were used to calculate length distribution and common/specific sequences.
The clean reads were compared with the mature miRNA in miRase database (version 21) to calculate the expression level.
Classify and annotate clean reads, annotate all miRNA fragments.
Assembly: hg38
Supplementary files format and content: txt file including miRNA expression levels for each sample

source_name: peripheral blood

extract_protocol:
After exosomes were isolated from peripheral blood, exosomal RNA was extracted. 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RiboBio mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: peripheral blood

tag: Sex

value: male

tag: sample type

value: Exosomes

tag: disease state

value: control


title: Chlorate-PMCs-2-A03_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization

value: Chlorate (30mM final)


title: MK886-PMCs-3-B03_2018-7-11


title: MK886-PMCs-2-A12_2018-7-11


title: ASW-PMCs-2-E04_2018-7-11


title: Exosomes, NASH-2

value: NASH


title: ASW-PMCs-2-C08_2018-7-11


title: MK886-PMCs-2-B09_2018-7-11


title: Exosomes, Normal-2

value: female


title: Chlorate-PMCs-1-B05_2018-7-11


title: Chlorate-PMCs-2-A06_2018-7-11


title: S06: Cyt_Total_ZT08_S2_WT

value: Liver

tag: fraction

value: Cytoplasmic

tag: rna population

value: Cytoplasmic Total RNA


title: Chlorate-PMCs-1-A12_2018-7-11


title: MK886-PMCs-2-B04_2018-7-11


title: Exosomes, NASH-3


title: MK886-PMCs-3-G09_2018-7-11


title: Exosomes, NASH-1


title: Exosomes, Normal-1


title: DMSO-PMCs-1-E03_2018-7-11


title: DMSO-PMCs-1-A08_2018-7-11


title: Chlorate-PMCs-2-F05_2018-7-11


title: Chlorate-PMCs-2-A11_2018-7-11


title: DMSO-PMCs-1-E02_2018-7-11


title: ASW-PMCs-2-F05_2018-7-11


title: MK886-PMCs-3-F11_2018-7-11


title: HYC50

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: GRCh38
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: foreskin tissue

growth_protocol: Indiana University (IU) Health Hospitals Riley Hospital for Children and Franciscan Health, Indianapolis, Indiana, USA provided samples for the current study. Informed consent and HIPAA authorization were obtained the legal guardians of from all minor age participants prior to the clinical sample collection. The study protocol was approved by the Indiana University Institutional Review Board (IRB) #1503167555. All research was performed in accordance with relevant guidelines and regulations. Following IRB approval foreskin samples were prospectively collected from 51 non-Hispanic white males less than 20 months of age who were undergoing a surgical repair for hypospadias (cases) or simple circumcision (controls).

extract_protocol:
Frozen human foreskin tissue samples were stored at -80 ºC and thawed for analysis. Genomic DNA from foreskin tissue samples was prepared as follows: The foreskin tissue was suspended in 750 μl of cell lysis solution and 3.5 µl of Proteinase K (20 mg/ml). This suspension was incubated at 55 ºC for 3 hours, then vortexed and centrifuged briefly. The lysis solution was then transferred to a new 1.5 µl microcentrifuge tube. The microcentrifuge tube with the foreskin tissue was centrifuged again to retain any remaining solution which was combined with the transferred lysis solution. The foreskin tissue had 300 µl of protein precipitation solution (Promega, A795A, Madison, WI) added to the lysis solution. The sample was incubated on ice for 15 minutes, then centrifuged at 4 ºC for 30 minutes. The supernatant was transferred to a fresh 2 ml microcentrifuge tube and 1,000 µl ice cold isopropanol was added along with 2 µl glycoblue. This suspension was mixed thoroughly and incubated at -20 ºC overnight. The suspension was then centrifuged at 4ºC for 20 minutes, the supernatant was discarded, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1X Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10 mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 ºC, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 ºC. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 ml 1X PBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1X IP buffer (50 mM sodium phosphate ph 7.0, 700 mM NaCl, 0.25% Triton X-100) as the initial volume of beads. 50μl of beads were added to the 500 μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 ºC. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1X IP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 ºC, then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000 x g for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000 x g for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500 μl ethanol were added and mixed well, then precipitated in -20 ºC freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000 x g for 20 min at 4 ºC and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 ºC freezer for 15 min then centrifuged again at 14,000 x g for 5 min at 4 ºC and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at room temperature until it looked dry (about 5 min) then resuspended in 20 μl H2O or TE buffer. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer. NGS was performed at WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 10-32 million reads per sample, and 10-11 sample libraries each were run in one lane.

treatment_protocol: Of the 51 participants, 36 (70.6%) were cases and 15 (29.4%) were controls. Controls were mean age matched to cases with no statistical difference. The mean±SD age for cases was 11±3.8 months and for controls 13±5.8 months was not significant (p<0.068). Hypospadias cases were categorized by levels of severity by the Urologist in accordance with the medical and surgical procedure codes: n=17 (47.2%) mild, n=13 (36.1%) moderate, n=6 (16.7%) severe. Foreskin tissues were after collection stored at -20 ºC until shipment and then stored at -80 ºC

value: foreskin


title: HYC49


title: MK886-PMCs-2-H05_2018-7-11

value: MK-886 (1.5uM final)


title: HYC51


title: MK886-PMCs-2-A08_2018-7-11


title: HYC47


title: Chlorate-PMCs-2-H04_2018-7-11


title: ASW-PMCs-2-C10_2018-7-11


title: Chlorate-PMCs-2-C10_2018-7-11


title: MK886-PMCs-3-A05_2018-7-11


title: MK886-PMCs-3-F07_2018-7-11


title: MK886-PMCs-2-D04_2018-7-11


title: HYC48


title: HYC45


title: ASW-PMCs-2-G02_2018-7-11


title: MK886-PMCs-3-C09_2018-7-11


title: HYC46


title: MK886-PMCs-3-H03_2018-7-11


title: MK886-PMCs-2-C08_2018-7-11


title: HYC44


title: HYC43


title: DMSO-PMCs-1-G11_2018-7-11


title: HYC42


title: HYC41


title: ASW-PMCs-2-D04_2018-7-11


title: ASW-PMCs-2-D12_2018-7-11


title: MK886-PMCs-2-F10_2018-7-11


title: MK886-PMCs-2-E11_2018-7-11


title: HYC40


title: Chlorate-PMCs-2-E03_2018-7-11


title: Chlorate-PMCs-2-G02_2018-7-11


title: ASW-PMCs-2-B11_2018-7-11


title: Chlorate-PMCs-2-H01_2018-7-11


title: HYC39


title: Chlorate-PMCs-2-D09_2018-7-11


title: Chlorate-PMCs-2-B11_2018-7-11


title: HYS36

value: moderate


title: Chlorate-PMCs-1-E02_2018-7-11


title: Chlorate-PMCs-1-A06_2018-7-11


title: ASW-PMCs-2-E01_2018-7-11


title: MK886-PMCs-2-F01_2018-7-11


title: Chlorate-PMCs-2-G03_2018-7-11


title: HYC37


title: HYC38


title: Chlorate-PMCs-2-E07_2018-7-11


title: Chlorate-PMCs-2-D11_2018-7-11


title: Chlorate-PMCs-2-H09_2018-7-11


title: HYS35

value: severe


title: MK886-PMCs-2-A09_2018-7-11


title: MK886-PMCs-2-D08_2018-7-11


title: Chlorate-PMCs-2-E05_2018-7-11


title: Chlorate-PMCs-2-E04_2018-7-11


title: HYS33


title: HYS34


title: MK886-PMCs-2-B01_2018-7-11


title: MK886-PMCs-2-F03_2018-7-11


title: MK886-PMCs-3-B06_2018-7-11


title: Chlorate-PMCs-1-F08_2018-7-11


title: Chlorate-PMCs-2-D07_2018-7-11


title: MK886-PMCs-2-E06_2018-7-11


title: HYS29


title: HYS30


title: HYS31


title: ASW-PMCs-2-G03_2018-7-11


title: MK886-PMCs-2-B07_2018-7-11


title: HYS32


title: HYS28


title: ASW-PMCs-2-F01_2018-7-11


title: HYS27


title: MK886-PMCs-3-H05_2018-7-11


title: Chlorate-PMCs-2-A07_2018-7-11


title: HYS26


title: Chlorate-PMCs-1-G02_2018-7-11


title: Chlorate-PMCs-2-G01_2018-7-11


title: HYS25


title: DMSO-PMCs-1-G01_2018-7-11

value: DMSO


title: Chlorate-PMCs-2-A04_2018-7-11


title: MK886-PMCs-3-F09_2018-7-11


title: Chlorate-PMCs-1-F10_2018-7-11


title: HYS22


title: HYS24


title: Chlorate-PMCs-2-G09_2018-7-11


title: HYS21


title: HYS23


title: Chlorate-PMCs-1-F06_2018-7-11


title: ASW-PMCs-2-H02_2018-7-11


title: Chlorate-PMCs-2-G04_2018-7-11


title: ASW-PMCs-2-H10_2018-7-11


title: HYS20


title: HYS19


title: Chlorate-PMCs-1-B03_2018-7-11


title: ASW-PMCs-2-B03_2018-7-11


title: DMSO-PMCs-1-H12_2018-7-11


title: ASW-PMCs-2-D06_2018-7-11


title: ASW-PMCs-2-D09_2018-7-11


title: MK886-PMCs-3-B07_2018-7-11


title: Chlorate-PMCs-1-C08_2018-7-11


title: ASW-PMCs-2-E02_2018-7-11


title: DMSO-PMCs-1-B12_2018-7-11


title: ASW-PMCs-2-B01_2018-7-11


title: HYM16

value: mild


title: Chlorate-PMCs-1-H05_2018-7-11


title: Chlorate-PMCs-2-H12_2018-7-11


title: MK886-PMCs-3-E12_2018-7-11


title: ASW-PMCs-2-G06_2018-7-11


title: MK886-PMCs-3-D08_2018-7-11


title: Chlorate-PMCs-2-G10_2018-7-11


title: HYM15


title: HYM14


title: ASW-PMCs-2-A12_2018-7-11


title: HYM12


title: MK886-PMCs-3-A07_2018-7-11


title: Chlorate-PMCs-1-B04_2018-7-11


title: HYM13


title: Chlorate-PMCs-1-H02_2018-7-11


title: HYS18


title: HYM17


title: MK886-PMCs-3-E08_2018-7-11


title: MK886-PMCs-3-H11_2018-7-11


title: Chlorate-PMCs-1-A08_2018-7-11


title: HYM10


title: HYM11


title: DMSO-PMCs-1-H04_2018-7-11


title: HYM9


title: ASW-PMCs-2-G05_2018-7-11


title: HYM7


title: HYM6


title: MK886-PMCs-3-F12_2018-7-11


title: Chlorate-PMCs-1-D03_2018-7-11


title: MK886-PMCs-2-G09_2018-7-11


title: DMSO-PMCs-1-D01_2018-7-11


title: Chlorate-PMCs-1-H11_2018-7-11


title: ASW-PMCs-2-C04_2018-7-11


title: MK886-PMCs-2-G03_2018-7-11


title: Chlorate-PMCs-1-G01_2018-7-11


title: HYM4


title: HYM8


title: DMSO-PMCs-1-G06_2018-7-11


title: MK886-PMCs-2-B02_2018-7-11


title: MK886-PMCs-2-G01_2018-7-11


title: HYM5


title: DMSO-PMCs-1-F12_2018-7-11


title: MK886-PMCs-3-G05_2018-7-11


title: Chlorate-PMCs-2-H02_2018-7-11


title: MK886-PMCs-2-A02_2018-7-11


title: HYM2


title: HYM1


title: DMSO-PMCs-1-E08_2018-7-11


title: Chlorate-PMCs-2-C08_2018-7-11


title: VIC95

city: Chaoyang District

first: Tiejun

last: Liu

state: Beijing

address: Panjiayuan

institute: Chinese Academy of Medical Science

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 hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed Mean of M-values (TMM) were calculated using edgeR in Rstudio.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Trimmed Mean of M-values (TMM) for each Sample …

source_name: platelet

extract_protocol:
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

treatment_protocol: Total RNA was extracted from isolated platelets frozen in 5 ml PBS using Trizol Reagent and Qiagen RNeasy minElute spin column as described in the manufacturer's instructions. The integrity of the total RNA was determined using an Agilent 2100 Bioanalyzer and RNA was quantified using a Thermo Scientific NanoDrop.

value: Healthy Control

value: platelet


title: DMSO-PMCs-1-H01_2018-7-11


title: DMSO-PMCs-1-E10_2018-7-11


title: VIC91


title: Chlorate-PMCs-1-E06_2018-7-11


title: HYM3


title: VIC89


title: MK886-PMCs-3-D10_2018-7-11


title: VIC88


title: MK886-PMCs-2-F05_2018-7-11


title: MK886-PMCs-3-B11_2018-7-11


title: MK886-PMCs-3-E11_2018-7-11


title: MK886-PMCs-2-H07_2018-7-11


title: ASW-PMCs-2-A08_2018-7-11


title: MK886-PMCs-2-E02_2018-7-11


title: ASW-PMCs-2-F02_2018-7-11


title: MK886-PMCs-3-B05_2018-7-11


title: Chlorate-PMCs-2-B06_2018-7-11


title: VIC93


title: VIC84


title: MK886-PMCs-2-F08_2018-7-11


title: VIC85


title: VIC86


title: Chlorate-PMCs-1-A11_2018-7-11


title: VIC87


title: DMSO-PMCs-1-E04_2018-7-11


title: DMSO-PMCs-1-D07_2018-7-11


title: VIC80


title: VIC82


title: Chlorate-PMCs-1-E08_2018-7-11


title: ASW-PMCs-2-F12_2018-7-11


title: VIC79


title: Chlorate-PMCs-2-D04_2018-7-11


title: ASW-PMCs-2-E10_2018-7-11


title: MK886-PMCs-2-B12_2018-7-11


title: MK886-PMCs-2-G08_2018-7-11


title: Chlorate-PMCs-2-A05_2018-7-11


title: MK886-PMCs-2-C07_2018-7-11


title: VIC74


title: VIC77


title: VIC72


title: MK886-PMCs-3-F04_2018-7-11


title: ASW-PMCs-2-E11_2018-7-11


title: DMSO-PMCs-1-F06_2018-7-11


title: DMSO-PMCs-1-E01_2018-7-11


title: MK886-PMCs-2-D07_2018-7-11


title: VIC78


title: VE9

value: ESCC


title: MK886-PMCs-3-H12_2018-7-11

value: primary mesenchyme


title: Chlorate-PMCs-1-A07_2018-7-11

value: 18 hours post-fertilization


title: VIC73


title: ASW-PMCs-2-A04_2018-7-11


title: Chlorate-PMCs-2-H07_2018-7-11

value: Chlorate (30mM final)


title: Chlorate-PMCs-1-E10_2018-7-11


title: MK886-PMCs-3-G01_2018-7-11


title: VE8


title: DMSO-PMCs-1-A02_2018-7-11


title: VE71


title: MK886-PMCs-3-E10_2018-7-11


title: VE7


title: ASW-PMCs-2-A09_2018-7-11


title: Chlorate-PMCs-1-F11_2018-7-11


title: Chlorate-PMCs-1-E07_2018-7-11


title: Chlorate-PMCs-1-G09_2018-7-11


title: VE66


title: VE68


title: DMSO-PMCs-1-A10_2018-7-11


title: Chlorate-PMCs-1-C02_2018-7-11


title: Chlorate-PMCs-2-G05_2018-7-11


title: ASW-PMCs-2-H11_2018-7-11


title: VE65


title: DMSO-PMCs-1-F02_2018-7-11


title: MK886-PMCs-2-G07_2018-7-11


title: DMSO-PMCs-1-H11_2018-7-11


title: ASW-PMCs-2-D08_2018-7-11


title: ASW-PMCs-2-G09_2018-7-11


title: MK886-PMCs-2-F07_2018-7-11


title: ASW-PMCs-2-B04_2018-7-11


title: MK886-PMCs-2-D05_2018-7-11


title: MK886-PMCs-3-D03_2018-7-11


title: MK886-PMCs-2-E07_2018-7-11


title: MK886-PMCs-3-H06_2018-7-11


title: Chlorate-PMCs-2-B04_2018-7-11


title: MK886-PMCs-3-B04_2018-7-11


title: ASW-PMCs-2-F07_2018-7-11


title: MK886-PMCs-2-B03_2018-7-11


title: MK886-PMCs-3-A08_2018-7-11


title: Chlorate-PMCs-1-H01_2018-7-11


title: Chlorate-PMCs-1-F04_2018-7-11


title: ASW-PMCs-2-H06_2018-7-11


title: Chlorate-PMCs-2-D03_2018-7-11


title: ASW-PMCs-2-G04_2018-7-11


title: MK886-PMCs-2-G02_2018-7-11


title: Chlorate-PMCs-2-D02_2018-7-11


title: Chlorate-PMCs-1-D06_2018-7-11


title: ASW-PMCs-2-D03_2018-7-11


title: ASW-PMCs-2-G07_2018-7-11


title: ASW-PMCs-2-F03_2018-7-11


title: VE45


title: Chlorate-PMCs-2-C03_2018-7-11


title: Chlorate-PMCs-1-G12_2018-7-11


title: VE48


title: VE56


title: VE64


title: VE46


title: VE58


title: VE54


title: VE6


title: VE47


title: VE44


title: VE5


title: VE53


title: VE51


title: VE63


title: VE59


title: VE61


title: VE42


title: MK886-PMCs-3-G04_2018-7-11


title: MK886-PMCs-3-E05_2018-7-11


title: ASW-PMCs-2-C06_2018-7-11


title: MK886-PMCs-2-G06_2018-7-11


title: VE41


title: ASW-PMCs-2-F09_2018-7-11


title: Chlorate-PMCs-1-F05_2018-7-11


title: MK886-PMCs-2-H02_2018-7-11


title: Chlorate-PMCs-1-C01_2018-7-11


title: MK886-PMCs-3-H07_2018-7-11


title: Chlorate-PMCs-1-H09_2018-7-11


title: MK886-PMCs-3-A09_2018-7-11


title: VE4


title: VE36


title: VE32


title: VE33


title: MK886-PMCs-3-E09_2018-7-11


title: MK886-PMCs-2-A01_2018-7-11


title: VE34


title: VE39


title: MK886-PMCs-3-D06_2018-7-11


title: VE31


title: MK886-PMCs-3-G07_2018-7-11


title: Chlorate-PMCs-1-B02_2018-7-11


title: DMSO-PMCs-1-F05_2018-7-11


title: Chlorate-PMCs-1-A01_2018-7-11


title: ASW-PMCs-2-H03_2018-7-11


title: DMSO-PMCs-1-F09_2018-7-11


title: Chlorate-PMCs-2-F04_2018-7-11


title: DMSO-PMCs-1-F03_2018-7-11


title: Chlorate-PMCs-2-F06_2018-7-11


title: VE30


title: VE28


title: MK886-PMCs-3-E03_2018-7-11


title: DMSO-PMCs-1-C12_2018-7-11


title: Chlorate-PMCs-1-C03_2018-7-11


title: VE26


title: Chlorate-PMCs-1-B12_2018-7-11


title: MK886-PMCs-3-E04_2018-7-11


title: MK886-PMCs-3-G02_2018-7-11


title: VE25


title: VE24


title: DMSO-PMCs-1-D12_2018-7-11


title: Chlorate-PMCs-2-F01_2018-7-11


title: MK886-PMCs-3-E06_2018-7-11


title: DMSO-PMCs-1-A12_2018-7-11


title: ASW-PMCs-2-E12_2018-7-11


title: MK886-PMCs-3-H02_2018-7-11


title: VE21


title: Chlorate-PMCs-1-H12_2018-7-11


title: VE23


title: MK886-PMCs-2-E10_2018-7-11


title: VE18


title: VE22


title: ASW-PMCs-2-B08_2018-7-11


title: VE17


title: MK886-PMCs-3-C10_2018-7-11


title: ASW-PMCs-2-C11_2018-7-11


title: VE14


title: DMSO-PMCs-1-G10_2018-7-11


title: MK886-PMCs-2-G05_2018-7-11


title: MK886-PMCs-2-G10_2018-7-11


title: VE13


title: Chlorate-PMCs-1-H08_2018-7-11


title: Chlorate-PMCs-2-C09_2018-7-11


title: VE11


title: VE12


title: ASW-PMCs-2-A11_2018-7-11


title: Chlorate-PMCs-1-F01_2018-7-11


title: DMSO-PMCs-1-B09_2018-7-11


title: MK886-PMCs-3-A01_2018-7-11


title: MK886-PMCs-3-C12_2018-7-11


title: Chlorate-PMCs-2-H06_2018-7-11


title: VE10