title: TTseq_TotalRNA_MDAMB231_Rep2

description:
MDAMB231_eRNAs.gtf
MDAMB231_enhancer.gtf
MDAMB231_eRNAs_conservative.gtf
MDAMB231_enhancer_conservative.gtf

tag: cell line

value: TT-seq

value: Total RNA


title: rep1 ribo-seq araP

status: Public on Jan 12 2021

type: SRA

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Rd

department: Genetics

country: USA

institute: Rutgers University

library_source: transcriptomic

data_processing:
Library strategy: Ribo-seq
adapter removal performed with cutadapt v2.8
demultiplexing using the fastX toolkit script fastx_barcode_splitter.pl
deduplication with the BBtools script dedupe.sh
removal of UMIs and barcodes with cutadapt v2.8
in silico rRNA depletion with hisat2 v2.1.0
transcript quantification with kallisto v0.46.2
alignment with hisat2 v2.1.0
Genome_build: Each cell lines individual genome was determined in Tenaillon et al 2016
Supplementary_files_format_and_content: A single csv file contains the counts and TPMs for each of the samples. These are not the original counts and TPMs. Counts were first rounded, and new TPMs were calculated from rounded counts. Analysis was based on rounded counts and the TPMs generated from them.

molecule: total RNA

organism: Escherichia coli

source_name: Long Term Evolution Experiment

growth_protocol: Bacteria were grown in the DM25 medium supplemented with 4g/L of glucose.

extract_protocol:
Cells were collected via vacuum filtration, flash frozen in liquid nitrogen, ground to a fine powder with frozen lysis buffer, then allowed to thaw to complete lysis. Lysis buffer contained 20 mM Tris pH 8, 10 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 1 mM chloramphenicol, 0.1% v/v sodium deoxycholate, 0.4% v/v Triton X-100, 100 U/mL DNase I, 1 uL/mL SUPERase-In (Thermo Fisher Scientific AM2694)
Each sample produced a matched set of RNA-seq and ribo-seq fragments which were size selected to a range of 18-50nt. These were ligated with a 5' linker (containing a 4nt UMI) and a 3' linker (containing a 5nt UMI and a 5nt sample barcode). rRNA depletion was completed with the Illumina Ribo-Zero rRNA Depletion Kit for bacteria.
RNA-seq and ribo-seq in E. coli cell lines from the Long Term Evolution Experiment

treatment_protocol: No treatments were applied to the samples.

tag: strain


title: #497 Rad

city: Singapore

first: Lucky

middle: Swarnalatha

last: Sasidharan

state: Singapore

address: 31 Biopolis Way

department: Institute of Bioengineering and Nanotechnology

country: Singapore

institute: A*STAR Research Entities

description: Stranded mRNA sequencing

data_processing:
Raw .fastq sequencing results are separated into human and mouse reads using Xenome with hg19 human genome and GRCm38 p6 mouse genome. Reads mapped exclusively to human are aligned to Gencode hg19 transcriptome using STAR and quantified by RSEM to obtain FPKM (Fragments Per Kilobase per Million mapped reads) and raw counts per gene for downstream analyses. Only the pr otein coding genes (n = 20330) were considered.
Gene ontology (GO) analysis was performed with Gene Set Enrichment Analysis (GSEA) when inferring from the whole protein-coding transcriptome, or with g:Profiler when inferring from a subset of labelled genes. We separately performed GO analysis using the GSEA Hallmark gene set, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, ontology of biological processes (GO:BP) and cellular components (GO:CC)
For GSEA, the input matrix was the read counts per gene calculated from RSEM, which was then normalized by size factor estimation from DESeq2 on a per-sample basis. Due to the limited number of available samples, false-discovery rate was controlled by permuting the gene sets instead of phenotypes. Ontologies with a family-wise error rate (FWER) < 0.05 were deemed significantly different between phenotypes.
Principal component analysis (PCA) was used in discerning the inter-sample differences. Principal components were calculated from the top 1000 most dispersed protein-coding genes, measured by the log mean-variance ratio (logVMR) of the log-FPKM expression values from RSEM. The ontology of genes contributing to the top principal components (PC) are further considered using g:Profiler. The analysis was separated by the positive and negative contributions to the PC, and ontology were deemed significantly different with adjusted p-value < 0.05.

Genome_build: hg19 human genome and GRCm38 p6 mouse genome
Supplementary_files_format_and_content: RSEM output

organism: Homo sapiens

source_name: Organoid

growth_protocol:
NPC patient participants and samples: Eighteen NPC tissue samples were obtained from patients who underwent biopsy or surgical resection at the National University Hospital Singapore between March 2015 and April 2019. Specimen collection and experimental use were approved by the Institutional Review Board of National Healthcare Group (DSRB Reference: 2015/00098-SRF0004). One part of the tissue collected from patients were immediately transferred to RPMI-1460 media with HEPES and L-Glutamine and 5X antibiotic/antimycotic and 5 µg/ml Metronidazole at 4°C. Other part was fixed in 10% neutral buffered formalin (10% NBF) for routine Hematoxylin and Eosin (H&E) staining and remaining tissues were snap frozen in liquid nitrogen for DNA and RNA extraction.
NPC PDX implantation: NPC patient sample was cut into 4-5 mm pieces and immersed in 1:1 Geltrex:HBSS (Gibco). For subcutaneous implantation, 2-3 mm nick was made on the skin of an anaesthetized NSG mice to insert the explanted tissue. For renal capsular implantation, an incision was made in the mouse kidney to insert the tumor tissue in the subcapsular space. All animal care and experimental procedures were approved by the Institutional Animal Care and Use Committee, A*Star Research Entities, Singapore.
Establishment of Organoid cultures:
A modified cancer tissue-originated spheroid (CTOS) method was adopted for establishment of NPC organoids from xenograft tumors (Fig. 1A). [16] Briefly, PDX tissues were manually minced into 1-2 mm3 pieces and subjected to enzymatic digestion using 0.28 U/mL Liberase DH (Roche) in RPMI-1460 containing 5% Penicillin-Streptomycin, 20 mM HEPES, 5 U/mL DNase1 and 30 µM Y-27632 (Stemcell Technologies) for 1.5 h at 37°C. The tissue digest was then resuspended in ice-cold HBSS with 5 U/mL DNase1 and 30 µM Y-27632. To remove large undigested pieces, the cell suspension was filtered through 100 µm cell strainer, followed by isolation of the 70-100 µm and 30-70 µm fractions using 70 µm and 30 µm MACS Smart Strainer (Miltenyi Biotech) respectively. Organoids were first counted and then gently mixed with Geltrex (Gibco) at 1.2% (w/v). 50 µl of the organoid suspension was seeded in 96 well ultra-low attachment plates (Corning). The gel matrix was then overlaid with 200 µl of complete PneumaCult™-ALI (P-ALI) media (Stemcell Technologies) supplemented with niche factors (NF): 4 µg/ml Heparin, 125 ng/ml Hydrocortisone, 50 ng/ml EGF , 50 ng/ml bFGF,  20 ng/ml FGF-10,  10 µM SB 202190, 500 nM A83-01, 10 µM Y-27632, and 2 mM Glutamax.
C666-1 cell monolayer and spheroids culture:
C666-1 cells (RRID:CVCL_7949) were authenticated using STR (Short tandem repeat) profiling and were free of mycoplasma contamination. The cells were cultured in RPMI‐1640 medium supplemented with 10% FBS at 37°C in a humidified incubator under 5% CO2. Confluent cells (70–80%) were sub-passaged by incubation with 0.05% trypsin for 5 min at 37°C and a splitting ratio of 1:3 was used. For monolayer cultures of C666-1 in 96 well high binding flat bottom plates, cells were seeded at a concentration of 5000 cells /well. For spheroid cultures, cells were seeded in 96 well flat bottomed ultra-low attachment plates at a concentration of 8000 cells/well.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Strand-specific RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, UK), as per manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq 6000 (Illumina, USA) to generate 150 bp paired-end reads. For patient samples, coding and long non-coding RNA was sequenced, whereas only the coding mRNA was sequenced for all other samples.

treatment_protocol: Normoxic Organoids were culture at 21% oxygen where as the hypoxic ones were cultured in 1% oxygen concentration. All irradiation was performed using Gammacell with 137Cs source (Nordion, Canada) at a dose rate of 1 Gy/min with ±15% error. The organoids were iraddiated on 3 consecutive days (day 5-day 7) at 5 Gy and harvested at day 12, followed by RNA extraction.

tag: sample type

value: Human cells in mouse xenograft model

tag: genotype

value: wild-type

tag: treatment

value: Normoxia+Radiation

tag: pdx success


title: #497

description: Stranded mRNA sequencing

value: Normoxia


title: BRAC861.2g_PLASMA [WT.PLASMA.3]

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) and STAR (2.5.2a) were used to align reads to the mouse Ensembl GRCm38 transcriptome.
Raw counts were normalised and differential expression analysis was performed with the DESeq2 package (version 1.18.1) within the R programming (version 3.4.3)
Genome_build: mouse Ensembl GRCm38
Supplementary_files_format_and_content: Transcripts per million (TPM) values. Rows represent Ensembl mouse genes and columns represent individual samples.

organism: Mus musculus

source_name: Plasma cells_wild type mouse

extract_protocol:
Spleen were disrupted using a 70uM mesh strainer. Samples were then washed with FACS buffer (2% FBS and 2 mM EDTA in PBS), incubated for 30 min on ice  with antibodies and  CD43 MicroBeads (Cat# 130-049-801, Miltenyi Biotec). Red blood cells were then  lysed for 5 min at room temperature with 5mL of Gey's buffer. After a wash , samples were passed through a 70 um filter LS columns (Miltenyi) for magnetic separation and B cell enrichment. After washing,  single-cell suspension was  sorted by flow cytometry. Samples were collected in eppendorffs containing RTL Buffer Plus (Qiagen) with 1% beta-mercaptoethanol. Samples were purified with AllPrep DNA/RNA Mini Kits (Cat# 80204, Qiagen) as per  manufacturer’s instructions.
Samples were prepared with Nugen cDNA kit and sequenced using Illumina HiSeq system

treatment_protocol: 8-12 week old female mice were intravenously immunised with 5x10^10 sheep red blood cells in 200uL of PBS and analysed 10 days after.

tag: age

value: 8-12 weeks

tag: Sex

value: female

tag: genotype/variation

value: wild type

value: 10 days after sheep red blood cells immunisation of mice

tag: tissue/cell type

value: Spleen Plasma cells

tag: cell population

value: B220lo CD138+ IgD- cells


title: TTseq_TotalRNA_BT20_Rep1

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

country: Germany

institute: Max-Planck-Institute for Multidisciplinary Scienes

description:
BT20_eRNAs.gtf
BT20_enhancer.gtf
BT20_eRNAs_conservative.gtf
BT20_enhancer_conservative.gtf

data_processing:
Paired-end 50 bp reads were first mapped to a single copy of the rDNA locus to remove rRNA related sequences. Reads that did not map to the rDNA were then aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0c (Dobin 2013) with the following specifications: outFilterMismatchNoverLmax 0.05, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (f99, f147, f83, f163) were selected. Fragment counts for different features were calculated with HTSeq (Anders 2015). Further data processing was carried out using the R/Bioconductor environment. To normalize TT-seq samples for sequencing depth and make them comparable between cell lines we used the median of ratios approach described in the DESeq2 R/Bioconductor package (Anders 2010). Transcription unit (TU) annotation and classification was done using the 4sU-labeled (L) samples as described (Michel, Demel 2017) with a few modifications. Briefly, strandspecific coverage was calculated from fragment midpoints in consecutive 200bp bins throughout the genome for all TTseq samples. Binning reduced the number of uncovered positions within expressed transcripts and increased the sensitivity for detection of lowly synthesized transcripts. The GenoSTAN R/Bioconductor package (Zacher 2017) was used to learn a twostate hidden Markov model with a PoissonLogNormal emission distribution in order to segment the genome into transcribed and untranscribed states, which resulted in 51,198  134,528 TUs per cell line. TUs that overlapped at least 25% of a proteincoding gene annotated in RefSeq (Release 109.20190607) or GENCODE (v31) and overlapped with an annotated exon of the corresponding gene were classified as mRNAs. Remaining TUs were annotated as non-coding (nc)RNAs. In order to overcome low expression or mappability issues, ncRNAs that were only 200 bp (1 bin) apart were merged. Subsequently, TU start and end sites were refined to nucleotide precision by finding borders of abrupt coverage increase or decrease between two consecutive segments in the two 200bp bins located around the initially assigned start and stop sites via fitting a piecewise constant curve to the coverage profiles (whole fragments) for all TTseq samples using the segmentation method from the R/Bioconductor package tilingArray (Huber 2006). In order to filter spurious predictions, TUs were further filtered with a minimal expression threshold of replicate-averaged normalized FPK >= 20 as described above (requiring at least 15 normalized FPK per replicate). ncRNAs overlapping with GENCODE (v31) annotated small non-coding RNA classes (snRNA, snoRNA, tRNA) were omitted from further analysis. The remaining ncRNAs were further classified according to their genomic location relative to protein-coding genes into four categories: upstream antisense RNA (uaRNA), convergent RNA (conRNA), antisense RNA (asRNA) and intergenic RNA. ncRNAs located on the opposite strand of an mRNA were classified as asRNA if the TSS was located > 1 kb downstream of the sense TSS, as uaRNA if the TSS was located < 1 kb upstream of the sense TSS, and as conRNA if the TSS was located < 1 kb downstream of the sense TSS. Each of the remaining ncRNAs was classified as intergenic.
eRNA annotation: Of the ncRNA classes defined above, we further classified intergenic and asRNAs as eRNAs, if their TSS +/- 500 bp overlapped with an enhancer state annotated by GenoSTAN (Zacher 2017) based on patterns of five histone modifications (H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3) in any of 127 cell types and tissues covering 111 datasets of the Roadmap Epigenomics project (Roadmap Epigenomics Consortium et al., 2015) as well as 16 datasets of the Encyclopedia of DNA Elements (ENCODE) Project (Dunham et al., 2012). Long antisense eRNAs that overlapped with the promoter region of the respective protein-coding gene (TSS +/- 1 kbp) were annotated to end 1 kbp downstream of the protein-coding TSS. Next, we introduced additional filtering criteria, as highly transcribed TUs can give rise to spurious downstream TUs, which do not represent independent TUs, but ongoing, gradually decreasing transcription by Pol II downstream of the main TU. To avoid misclassification of such downstream TUs as putative eRNAs, we did the following:
First, we restricted our set of intergenic eRNAs to only those originating from regions with TT-seq detected transcription on both strands, with an allowed gap of up to 750 bp between divergently transcribed eRNA pairs. To this end, a non-coding TU had to be annotated on the opposite strand, but it was not required to lie above the expression threshold. Second, we also restricted our set of antisense eRNAs. To this end, non-coding TUs downstream of mRNA/uaRNA TUs were sequentially merged with the upstream mRNA/uaRNA if the gap between TUs was less than 5 kbp. Subsequently, non-coding TUs, which had been classified as antisense eRNAs and were constituents of such merged regions were excluded from further analyses, unless their TT-seq signal (normalized FPK) was at least 2-fold higher than TT-seq signal over the end (last 1 kbp) of the upstream mRNA/uaRNA.
Enhancer annotation: To define intergenic enhancer regions, we selected the region between the TSSs of each pair of intergenic bidirectional eRNAs and extended it by 500 bp in both directions. To define intragenic enhancer regions, we selected the region covering 750 bp upstream to 500 bp downstream of the TSS of antisense eRNAs. Since we allowed a gap of maximum 750 bp between bidirectional intergenic eRNAs, we selected 750 bp also as putative enhancer region upstream of antisense eRNAs. Based on this definition all intragenic enhancer regions were 1250 bp long whereas the length of intergenic enhancer regions was dependent on the gap or overlap between bidirectional eRNAs. Strongly transcribed intergenic enhancer regions gave rise to uninterrupted bidirectional TT-seq signal over long genomic stretches, which could not be resolved at the resolution of individual enhancers, and did therefore result in the definition of some enhancer regions covering several kbp.
Dealing with annotated lncRNAs: The FANTOM consortium has shown that the majority of intergenic lncRNAs originate from enhancer regions, and thus we only excluded eRNAs/enhancers if they overlapped a functional lncRNA originating from an intergenic promoter DHS (24 lncRNAs, e.g. Malat1; taken from Supplementary Table 5 in (Hon 2017) selecting CAT_geneCategory = p_lncRNA_intergenic).
The resulting annotations of eRNAs and enhancer regions reported in Lidschreiber et al. are provided as eRNAs/enhancer .gtf files. In addition, conservative subsets of the eRNAs/enhancer regions reported in Lidschreiber et al. are provided. The conservative annotations contain only intragenic enhancer regions defined by eRNAs >= 300 nt and with normalized FPK >= 30; intergenic enhancer regions / eRNAs are the same as in Lidschreiber et al.
processed data files format and content: eRNA and transcribed enhancer annotations are provided for each of the cell lines as .gtf files. Strand-specific bigWig files contain size factor normalized fragment coverages for each TT-seq labeled RNA sample.

source_name: human cancer cell line

growth_protocol: Cells were cultured in cell culture media supplemented with 1% penicillin/streptomycin (GE Healthcare) and 10% fetal bovine serum (Sigma) at 37°C in a humidified 5% CO2 incubator. BT-20 (ATCC HTB-19), DU 145 (ATCC® HTB-81) and SK-UT-1 (ATCC HTB114) cells were cultured in MEM (Gibco) supplemented with 0.1 mM NEAA (Gibco) and 1 mM sodium pyruvat (Gibco). 769-P (ATCC CRL-1933) and 786-O (ATCC CRL-1932) cells were cultured in RPMI-1640 (Gibco A1049101). MDA-MB-231 (ATCC HTB-26) and LoVo (ATCC CCL-229) cells were cultured in DMEM-GlutaMAX (Gibco 21885-25). U-118 MG (ATCC HTB-15) and GP5d (Sigma) cells were cultured in DMEM (Gibco). GP5d cells were cultivated in cell culture flasks coated with poly-L-lysine (Sigma). M059J (ATCC CRL-2366) cells were cultivated in DMEM/F-12 (Gibco), HCT 116 (ATCC CCL-247) cells in McCoy's 5a Medium Modified (Gibco) and PC-3 (ATCC CRL-1435) cells in F-12K (ATCC 30-2004).

extract_protocol:
Total RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was extracted according to Gressel at al., protocols.io, 2019.
Sequencing libraries were prepared with the Ovation Universal RNA-Seq System (NuGEN) following the manufacturer's’ instructions

treatment_protocol: 48 hours before experiment cells were seeded in 15 cm dishes to obtain 70 % confluent cells at time of 4sU labeling. Cells were labeled with 500 µM 4-thiouridine (4sU) (Sigma-Aldrich) for 5 min at 37 °C under 5% CO2. Cells were harvested using TRIzol (Life Technologies).

tag: cell type

value: cancer

tag: 4su labelling

value: 5min 4sU

tag: method

tag: labeled molecule


title: BRAC861.2f_PLASMA [WT.PLASMA.2]


title: rep1 ribo-seq araM


title: TTseq_TotalRNA_U118MG_Rep2

description:
U118MG_eRNAs.gtf
U118MG_enhancer.gtf
U118MG_eRNAs_conservative.gtf
U118MG_enhancer_conservative.gtf


title: TTseq_TotalRNA_MDAMB231_Rep1


title: 296T P12 #497

description: Stranded mRNA sequencing

source_name: PDX tumor used to make organoid #497

value: 296 PDX Passage 12


title: #477 Hyp Rad

description: Stranded mRNA sequencing

value: Hypoxia+Radiation


title: BRAC861.2e_PLASMA [WT.PLASMA.1]


title: RA4

city: Kansas City

first: Venkatesh

last: Sampath

state: MO

address: 2401 Gillham Road

department: Neonatology

institute: Children's Mercy Hospital

description: Room-air mouse 4

data_processing:
Cell Ranger 3.0.2 was used to generate FASTQs, followed by Cell Ranger count to generate read matrices
Data were processed using the 10X refdata-cellranger-mm10-2.1.0 reference
Genome_build: mm10
Supplementary_files_format_and_content: MarketMatrix (mtx) file with read counts per gene, and associated genes and barcodes TSV

source_name: whole lung

extract_protocol:
For each sample, 1 well of a Chromium Chip B (10x Genomics Cat No. 1000153) was loaded with 16,000 freshly dissociated cells.
scRNAseq was performed using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (10x Genomics Cat No. 1000075) according to the manufacturer's protocol.

treatment_protocol: C57Bl6 pups were exposed to RA from day of life 1-14.

tag: tissue

value: whole lung


title: TTseq_TotalRNA_M059J_Rep1

description:
M059J_eRNAs.gtf
M059J_enhancer.gtf
M059J_eRNAs_conservative.gtf
M059J_enhancer_conservative.gtf

value: TT-seq


title: TTseq_TotalRNA_U118MG_Rep1

value: Total RNA


title: #477 Rad

description: Stranded mRNA sequencing

value: Human cells in mouse xenograft model


title: RA3

description: Room-air mouse 3


title: #477 Hyp Con

description: Stranded mRNA sequencing

value: wild-type

value: Hypoxia


title: TTseq_TotalRNA_M059J_Rep2


title: BRAC1235.6h_MEMO [WT.BCELLS.3]

source_name: Memory B cells_wild type mouse

value: Spleen Memory B cells

value: B220+ CD138Neg IgDneg CD38+ CD273+ cells


title: TTseq_LabeledRNA_K562_Rep2

description:
K562_eRNAs.gtf
K562_enhancer.gtf
K562_eRNAs_conservative.gtf
K562_enhancer_conservative.gtf

value: 4sU-labeled RNA


title: TTseq_LabeledRNA_K562_Rep1


title: 296T P12 #477

description: Stranded mRNA sequencing

source_name: PDX tumor used to make organoid #477


title: HCC827 and Sequin Mix B replicate 2

city: PARKVILLE

first: Xueyi

last: Dong

state: VIC

address: 1G ROYAL PARADE

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Base calling and quality scoring: Read-Time Analysis on board software v2.4.6
FASTQ file generation and de-multiplexing: bcl2fastq conversion software v2.15.0.4
Sequenced reads were mapped to the RNA Sequin decoy chromosome using the align function in the Rsubread package (version 1.16.1, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using using the RNA sequin annotation 2.4 GTF file.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.22.0, Smyth, 2005).
Genome_build: RNA sequin decoy chromosome 2.4
Supplementary_files_format_and_content: tab-delimited text files with columns representing Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.
Gene sequences rnasequin_sequences_2.4.fa and the decoy genome rnasequin_decoychr_2.4.fa. To be noticed that these files above are not produced by us. They are provided by Hardwick et al. (Nature methods, 2016, PMID: 27502218)

source_name: Human lung cancer cell line HCC827 and RNA Sequins Mix B

extract_protocol:
1ml TRIzol reagent was added to T150 flask and transferred to tubes. 0.2 mL of chloroform were added and aqueous phase containing the RNA were transferred to new tube after centrifugation. The RNA was then precipitated by isopropanol and washed by 75% ethanol. After washing the RNA was solubilized on 30ul RNase-free water and frozen at -80 degree immediately.
Methods - Library prep: the sequin+total RNA mixtures were subjected to polyA selection (NEBNext PolyA E7490) and library prep (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina) following manufacturer's instructions; we performed 9 PCR cycles

tag: replicate

tag: sequencing protocol

value: paired-end


title: RA2

description: Room-air mouse 2

tag: strain


title: Endogenous and in vitro cardiomyocyte maturation reference

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

data_processing:
I7 tag + Cell Barcode+UMI
cDNA Read
Mapping of the data was done with kallisto|bustools (0.46.2), using an index generated from the CellRanger mouse reference concatenated with the ERCC spike-in sequences.
Genome_build: GRCm38_r92
Supplementary_files_format_and_content: We provide the following processed files. Those with the prefix “gene_mult” are the direct outputs of kallisto|bustools. However, due to some errors in sample preparation, there were accidental barcode collisions, leading to the need to remove some cells. We provide a metadata table (phenotype_good) that contains all of the acceptable barcodes as well as all of the appropriate metadata for each cell. Lastly, we also include a processed counts table (processed_counts). The difference between this and the kb output matrix is that the table is in matrix (as opposed to MM) format, has gene symbols for gene names, and is filtered to only include the acceptable barcodes (e.g. those in phenotype_good).

source_name: Cardiomyocytes

growth_protocol: To generate mice for our reference dataset, we crossed aMHC-cre (Jackson Laboratory, Stock No. 011038) with mTmG (Jackson Laboratory, Stock No. 007676) mice. Both mice have C57BL/6J congenic background.  To generate mESCs for in vitro studies, mice of the above strain were crossed and observed for the presence of a vaginal plug (considered embryonic day 0.5). On embryonic day 3.5, blastocysts were flushed, isolated, and maintained in pre-gelatinized 96 well plates with 2i media. Four genotype-verified mESC lines were expanded and tested for differentiation capability to the cardiomyocyte lineage.  All animals were maintained compliant to protocols by the Johns Hopkins Animal Care and Use Committee.

extract_protocol:
For isolation of endogenous CMs from e14-p4 timepoints, we used the neonatal cardiomyocyte isolation kit from Miltenyi Biotec in conjunction with the gentleMACS Dissociator. For later timepoints, Langendorff perfusion was performed based on established literature protocols using collagenase and protease. We used a horizontal (i.e. non-hanging) Langendorff apparatus with a chamber filled with perfusion buffer. To perform isolation, we first performed isofluorane anaesthesia on non-heparinized mice. Mice were observed until clearly anaesthetized and unresponsive to toe pinch, and subsequently euthanized by cervical dislocation. The heart was then rapidly excised from the chest and cannulated to the Langendorff apparatus. We flowed digestion buffer for 9 minutes at 1.5 mL/min. Subsequently, the ventricle was excised and minced. We filtered isolated cells through a 100 µM screen to eliminate large tissue chunks, spun down at 800 RPM for 1 minute (Eppendorf centrifuge 5702), and resuspended cells in 10 mL Tyrode’s buffer. All cells were isolated using LP-FACS, as outlined in Kannan et al. (Circ Res 2019).    PSC-CMs were dissociated from culture flasks with TrypLE (5-10 minutes, depending on the timepoint). Cells were strained to remove clumps and clusters and subsequently sorted into prepared collection plates on either a MoFlo Legacy or MoFlo XDP.
We performed sequencing using the mcSCRB-seq protocol. The protocol has been described at protocols.io at dx.doi.org/10.17504/protocols.io.p9kdr4w. We sequenced the final, pooled library on a NovaSeqS4 as 150-base pair paired-end reads. We subsequently demultiplexed into two files such that the read 1 file contains the 8 base pair i7 tag, 6 base pair cell barcode, and 8 base pair UMI, while read 2 contains the 150 base pair cDNA read. We have provided these final demultiplexed reads to GEO. However, if the original paired-end reads from the sequencer are desired, we are happy to provide on request.

treatment_protocol: Our PSC-CM differentiation protocol was adapted from multiple previously published protocols. The day prior to initiation of differentiation protocol (D-1), cells were changed to expansion media with 1000 U Lif/mL with no CHIR99021 or PD0325901. On Day 0 of differentiation, cells were dissociated with TrypLE (Thermo Fisher) and suspended in a serum-free differentiation media (SFD). SFD was composed of ¾ volume IMDM to ¼ volume Ham’s F12 media, with 0.5% v/v N2 supplement (Gibco), 1% v/v B27 without retinoic acid (Gibco), 0.5% v/v BSA (Invitrogen) in PBS, 0.75% v/v glutamine (Gibco), 0.75% v/v penicillin-streptomysin (Gibco), 50 ug/mL ascorbic acid (Sigma), and 0.039 ul/mL 1-thiogylcerol. For the first four days of differentiation, differentiating cells were maintained as embryoid bodies. On Day 2, media was replaced with fresh SFD plus 3uM CHIR99021 (Selleckchem) and 2.5 ng/mL BMP4 (R&D Systems). On Day 4, cells were dissociated with TrypLE and replated as a confluent monolayer on gelatin-coated flasks. At this time, cells were cultured with SFD with 0.1% v/v XAV939. On Day 6, the media was changed to SFD. From Day 10 to Day 13, lactate selection was performed by culturing the cells in DMEM without glucose plus lactate. Subsequently, the cells were cultured in SFD, with media changes every two days.

tag: strain/background

value: aMHC-cre x mTmG

value: Cardiomyocyte


title: BRAC861.2g_MEMO [WT.BCELLS.2]

value: 8-12 weeks

value: female

value: wild type

value: 10 days after sheep red blood cells immunisation of mice


title: BRAC861.2e_MEMO [WT.BCELLS.1]


title: TTseq_LabeledRNA_Jurkat_Rep2

description:
Jurkat_eRNAs.gtf
Jurkat_enhancer.gtf
Jurkat_eRNAs_conservative.gtf
Jurkat_enhancer_conservative.gtf

tag: cell line

value: Jurkat

value: cancer

value: 5min 4sU


title: RNA_Mapk8-KO_S1

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description: RNA-seq in mouse keratinocytes from mapk8-KO sample

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome mm10 by using STAR_2.5.3 software with default parameters
Reads from the alignment were sorted and indexed according to chromosomes
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1
Raw read counts were normalized and a differential expression analysis was performed with DESeq2 by applying an adjusted p-value <0.05 and an absolute log2-ratio larger than 1
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing differential expression analysis results and comma-separated file containing normalized read counts for each sample and gene

source_name: Whole skin

extract_protocol:
Keratinocytes RNA was extracted with the RNeasy Minikit (Qiagen)
Libraries were prepared using Ovation® SoLo RNA-Seq system (NuGEN Technologies)

treatment_protocol: Mice were topically treated with a cream containing 5% imiquimod (Aldara cream®, 3M pharmaceuticals) over 8 consecutive days  Carrier-free rmIL17A (R&D Systems, #7956ML025/CF) 500 ng/ear/day were injected for 8 days  Carrier-free rmIL23 (Biolegend, #589006) 1µg/ear/day or carrier-free rmAREG (Peprotech, #31536) 1µg/ear/day were injected for 4 days  When indicated, SP600125 30 mg/kg/d (VWR), AG1478 15mg/kg/d (VWR) or DMSO was injected intraperitoneally to mice, once per day for 9 days

value: keratinocytes

tag: genotype


title: RNA_Mapk8-KO_S3


title: HCC827 and Sequin Mix B replicate 1


title: RNA_Mapk8-KO_S2


title: TLR250-P8

description: Stranded mRNA sequencing

source_name: PDX tumor

tag: sample type

value: Human cells in mouse xenograft model

tag: treatment

value: 296 PDX Passage 8

tag: pdx success


title: H1975 and Sequin Mix A replicate 2

source_name: Human lung cancer cell line NCI-H1975 and RNA sequins Mix A


title: TTseq_LabeledRNA_Jurkat_Rep1

value: TT-seq


title: RNA_WT_S2

description: RNA-seq in mouse keratinocytes from Wild Type sample

value: Wild Type


title: TLR250-P6

description: Stranded mRNA sequencing

value: wild-type

value: 296 PDX Passage 6


title: RNA_WT_S3


title: H1975 and Sequin Mix A replicate 1

value: paired-end


title: Quiescent HASMCs rep3

city: shi jia zhuang

first: shaoguang

last: sun

state: Hebei

address: zhong shan dong lu 361

department: biochemistry and molecular biology

country: China

institute: Hebei medical university

description:
tRNA-derived small RNAs (tsRNAs)
s_6

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer. After Illumina quality control, the sequencing reads were 5ʹ, 3ʹ-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001
The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: xlsx file with abundance

source_name: aortic artery

extract_protocol:
RNAsimple Total RNA Kit was used to extract total RNA from proliferative and quiescent HASMCs.
In order to eliminate the interference of RNA modification on the construction of small RNA-seq library, the total RNA samples were first pretreated as follows: 3ʹ-aminoacyl (charged) was deacylated to 3ʹ-OH for 3ʹ adaptor ligation, 3ʹ-cP (2ʹ, 3ʹ-cyclic phosphate) was removed to 3ʹ-OH for 3ʹ adaptor ligation, 5ʹ-OH (hydroxyl group) was phosphorylated to 5ʹ-P for 5ʹ-adaptor ligation, m1A and m3C were demethylated for effective reverse transcription. Subsequently, the commercial kit for tRF & tiRNA sequencing library preparation was used to construct the tsRNA-seq libraries. The kit includes 3ʹ-adapter and 5ʹ-adapter ligation adaptor ligation, cDNA synthesis and library PCR amplification. PCR amplified fragments with a size of 135~160 bp (corresponding to the size range of 15~40 nt small RNA) were selected as tsRNA-seq libraries. Finally, the prepared tsRNA-seq libraries were quantified using Agilent BioAnalyzer 2100, and then sequenced using Illumina NextSeq 500.

treatment_protocol: HASMCs were cultured using Smooth Muscle Cell Medium containing 1% 100 × Smooth Muscle Cell Growth Supplement and 1% 100 × Penicillin/Streptomycin Solution for 24 hours

value: human aortic vascular smooth muscle cell

value: quiescent type


title: TLR250-P1

description: Stranded mRNA sequencing

value: 296 PDX Passage 1


title: Quiescent HASMCs rep2

description:
tRNA-derived small RNAs (tsRNAs)
s_5


title: TTseq_LabeledRNA_SKUT1_Rep2

description:
SKUT1_eRNAs.gtf
SKUT1_enhancer.gtf
SKUT1_eRNAs_conservative.gtf
SKUT1_enhancer_conservative.gtf

value: 4sU-labeled RNA


title: TTseq_LabeledRNA_SKUT1_Rep1


title: ATAC_Mapk8-KO_S1

description: ATAC-seq in mouse keratinocytes from mapk8-KO sample

library_source: genomic

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome mm10 by using STAR_2.5.3 software with default parameters
Reads from the alignment were sorted and indexed according to chromosomes
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping in chrM were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

molecule: genomic DNA

extract_protocol:
Keratinocytes RNA was extracted with the RNeasy Minikit (Qiagen)
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.


title: RNA_WT_S1


title: TLR250-P2

description: Stranded mRNA sequencing

value: 296 PDX Passage 2


title: ATAC_Mapk8-KO_S2


title: TLR250-P4

description: Stranded mRNA sequencing

value: 296 PDX Passage 4


title: Quiescent HASMCs rep1

description:
tRNA-derived small RNAs (tsRNAs)
s_4


title: ATAC_WT_S2

description: ATAC-seq in mouse keratinocytes from Wild Type sample


title: TTseq_LabeledRNA_DU145_Rep2

description:
DU145_eRNAs.gtf
DU145_enhancer.gtf
DU145_eRNAs_conservative.gtf
DU145_enhancer_conservative.gtf


title: TTseq_LabeledRNA_PC3_Rep1

description:
PC3_eRNAs.gtf
PC3_enhancer.gtf
PC3_eRNAs_conservative.gtf
PC3_enhancer_conservative.gtf


title: Proliferative HASMCs rep3

description:
tRNA-derived small RNAs (tsRNAs)
s_3

treatment_protocol: HASMCs were cultured using Smooth Muscle Cell Medium containing 2% fetal bovine serum, 1% 100 × Smooth Muscle Cell Growth Supplement and 1% 100 × Penicillin/Streptomycin Solution

value: proliferative type


title: TLR296-P12

description: Stranded mRNA sequencing

value: 296 PDX Passage 12


title: ATAC_WT_S1


title: TTseq_LabeledRNA_PC3_Rep2

value: cancer

value: 5min 4sU


title: Proliferative HASMCs rep2

description:
tRNA-derived small RNAs (tsRNAs)
s_2


title: TTseq_LabeledRNA_DU145_Rep1


title: TLR296-P8

description: Stranded mRNA sequencing

value: Human cells in mouse xenograft model


title: TLR296-P6

description: Stranded mRNA sequencing


title: Proliferative HASMCs rep1

description:
tRNA-derived small RNAs (tsRNAs)
s_1


title: TLR296-P14

description: Stranded mRNA sequencing

value: 296 PDX Passage 14


title: CD8 T cells normal rabbit serrum CUT&RUN

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
Library strategy: CUT&RUN
reads were trimed from their adapter using cutadupt and aligned to mm10 genome with bowtie.
Only non mitochondrial, reads with unique alignment were selected for further analysis.
For the Cut&Run sample, we selected read pairs with inter distance < 120 bp
peak calling was performed witn MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig - alignment profile, txt - macs2 peak calling

source_name: Adult  spleen

extract_protocol:
CD8 T cells were isolated from mouse spleeen using anti-mouse CD8a magnetic beads (BD 55151).  50M were isolated for Chip and kept frozen (from 5 mice) and 150,000 were isolated from one mouse and freshly used for CUT&RUN.  For ChIP: cells were thawed, lyzed and sonicated followed by ChIP with rabbit anti -Runx3 serum (1:200) and capturing of DNA-Ab complexes using protein-A sepharose magnetic beads. For CUT&RUN, cells were immobilised on ConA magnetic beads, permeabilized and incubated with rabbit anti-Runx3 serum (1:200) and procedure followed according to (Skene P J  2017 eLife e21856).
Following deproteinization, DNA fragments were used for library construction through the protocol NEBNEXT Ultra II DNA library prep (E7645) with 12 cycles of PCR amplification. Samples were sequenced on Illumina Next-seq 500 machine.

value: spleen

value: CD8 T cells

value: wild type

tag: antibody


title: TTseq_LabeledRNA_786O_Rep2

description:
786O_eRNAs.gtf
786O_enhancer.gtf
786O_eRNAs_conservative.gtf
786O_enhancer_conservative.gtf

value: TT-seq


title: CD8 T cells WCE

data_processing:
reads were trimed from their adapter using cutadupt and aligned to mm10 genome with bowtie.
Only non mitochondrial, reads with unique alignment were selected for further analysis.
For the Cut&Run sample, we selected read pairs with inter distance < 120 bp
peak calling was performed witn MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig - alignment profile, txt - macs2 peak calling

tag: fraction

value: whole cell extract


title: LNCaP cell line - 24h PDA-66 rep3

city: Hannover

first: Jan Torben

last: Schille

address: Buenteweg 9

department: Small Animal Clinic

institute: University of Veterinary Medicine Hannover

data_processing:
For the human PC-3 and LNCaP cells, mapping and read counting were conducted using the RNA Express (version: 1.0.0) workflow within the Illumina basespace environment. In brief, after mapping to the human HG19 reference genome using the STAR (2.3.1s) aligner read counts for 23710 annotated RefSeq genes were generated.   For CT1258, sequences were aligned to the canine genome (Broad CanFam3.1/canFam3, Sep. 2011) using the Burrows-Wheeler Aligner (BWA). For each of the 24,581 annotated protein-coding canine genes (EMBL gene ID nomenclature), the aligned reads were counted using the R package GAGE.
Differential gene expression analyses for canine and human samples were conducted using the BioconductorR package edgeR 3.14.0. The average total read counts mapped within annotated genes were 12.2M (STD: 0.7M), 15.8M (STD: 1.1M), 13.5M (STD: 0.9M) for CT1258, PC-3 and LNCaP samples, respectively. Each PDA-66 treatment group (12 h or 24 h) was compared to the respective control cells treated with DMSO.
After multidimensional scaling and plotting of the data, one PC-3 DMSO treated control sample (PD1) was identified as outlier and was excluded from further analyses so that the PC-3-24 h-DMSO control group consisted of only two independent samples.
Genes with a false discovery rate adjusted p-value (FDR) of less than 0.001 were considered to have significantly different expressions compared to the control samples. These genes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for functional enrichment analyses using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Functional Annotation Tool.
Genome_build: HG19 and CanFam3.1
Supplementary_files_format_and_content: edgeR gene counts for the three cell lines
Gene tables with fold changes and FDRs for every treatment vs control

source_name: Prostate carcinoma cells

growth_protocol: PC-3 cells were cultivated in DMEM/Ham´s F-12 medium (Biochrom GmbH, Berlin, Germany). LNCaP cells were grown in RPMI 1640 medium (Biochrom GmbH). CT1258 cells were cultivated in medium 199 (Live Technologies GmbH, Darmstadt, Germany). All media were supplemented with 10% heat-inactivated fetal bovine serum (FBS Superior, Biochrom GmbH) and 2% penicillin/streptomycin (Biochrom GmbH). All cells were cultivated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen GmbH, Hilden, Germany) in accordance with the manufacturer’s protocol. RNA integrity numbers (RIN) were determined using a Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA).
Sequencing libraries were prepared using 1 μg total RNA with RIN > 7. PolyA RNA was enriched and ligated to sequencing adapters using the NEBNext Ultra RNA preparation kit (New England Biolabs Inc., Ipswich, MA, USA) in accordance with the manufacturer’s protocols.

treatment_protocol: Cells were treated with 15 µM PDA-66 for 12 h or 24 h with 3 replicates per cell line and incubation period. Control cells were treated with 0.15% (v/v) DMSO as PDA-66 is dissolved in DMSO.

value: LNCaP

value: prostate adenocarcinoma cell line derived from lymph node metastasis

value: treated with 15 µM PDA-66 for 24 h


title: TTseq_LabeledRNA_786O_Rep1

value: 4sU-labeled RNA


title: TLR296-P4

description: Stranded mRNA sequencing

value: wild-type


title: TTseq_LabeledRNA_769P_Rep2

description:
769P_eRNAs.gtf
769P_enhancer.gtf
769P_eRNAs_conservative.gtf
769P_enhancer_conservative.gtf


title: TTseq_LabeledRNA_LoVo_Rep2

description:
LoVo_eRNAs.gtf
LoVo_enhancer.gtf
LoVo_eRNAs_conservative.gtf
LoVo_enhancer_conservative.gtf

value: LoVo


title: LNCaP cell line - 12h PDA-66 rep3

value: treated with 15 µM PDA-66 for 12 h


title: CD8 T cells CUT&RUN


title: LNCaP cell line - 24h PDA-66 rep1


title: CD8 T cells ChIP

value: IP


title: TTseq_LabeledRNA_769P_Rep1

value: cancer


title: TLR296-P10

description: Stranded mRNA sequencing

value: 296 PDX Passage 10


title: TLR296-P2

description: Stranded mRNA sequencing

value: Human cells in mouse xenograft model

value: 296 PDX Passage 2


title: TLR296-P0

description: Stranded mRNA sequencing

value: 296 PDX Passage 0


title: mRNA-seq_WT_rep2_2020

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

description:
processed data file:
GSE142519_RNASEQ_TPM_2020.xlsx

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk), and they were mapped to mouse genome mm9 using HISAT2, and assembled by HOMER to get Transcripts per million (TPM) for each gene.
Differentially expressed genes were generated by limma  with fold change >2 and p <0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file for RNA-seq TPM and differentially expressed genes for sample_1 to sample_6.

molecule: polyA RNA

source_name: mouse embryonic stem cells

growth_protocol: mESCs (E14Tg2A line) were kindly provided by Dr. Fei Lan. mESCs were maintained in 90% Dulbecco’s Modified Eagle Medium (DMEM) (Life technologies, Carlsbad), 10% fetal bovine serum (FBS) (Life technologies, Carlsbad, CA), 1% non-essential amino acid (NEAA), 1% penicillin and streptomycin (100× stock) (Gibco-Thermo Fisher, Waltham, MA), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), and 200 Units/mL murine leukemia inhibitory factor (LIF) (ESGRO; Merck-Millipore, Germany). mESC expansion was performed in gelatin-coated flasks (BBI Life Sciences, China).

extract_protocol: Non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module (Excell Bio, Shanghai, China), and sequencing libraries were prepared with the TrueLib mRNA Library Prep Kit for Illumina (ExCell Bio, Shanghai, China).

value: mouse embryonic stem cells (mESCs)

tag: genotype/variation


title: C666-1 Monolayer 3

description: Stranded mRNA sequencing

source_name: Cell Line

value: Human NPC cell line

value: Adherent monolayer culture


title: mRNA-seq_WT_rep3_2020

tag: cell type

value: wild type


title: mRNA-seq_WT_rep1_2020


title: TTseq_LabeledRNA_LoVo_Rep1

tag: 4su labelling

value: 5min 4sU

value: TT-seq


title: TTseq_LabeledRNA_HCT116_Rep2

description:
HCT116_eRNAs.gtf
HCT116_enhancer.gtf
HCT116_eRNAs_conservative.gtf
HCT116_enhancer_conservative.gtf

value: HCT 116

tag: method


title: LNCaP cell line - 24h PDA-66 rep2

value: LNCaP

value: prostate adenocarcinoma cell line derived from lymph node metastasis

value: treated with 15 µM PDA-66 for 24 h


title: LNCaP cell line - 12h PDA-66 rep2

value: treated with 15 µM PDA-66 for 12 h


title: LNCaP cell line - 12h PDA-66 rep1


title: mRNA-seq_Bach1-KO_rep3_2020

source_name: Bach1 knock out mouse embryonic stem cells

value: Bach1 -/-


title: C666-1 Monolayer 2

description: Stranded mRNA sequencing

value: wild-type


title: TTseq_LabeledRNA_HCT116_Rep1

value: cancer

tag: labeled molecule

value: 4sU-labeled RNA


title: C666-1 Monolayer 1

description: Stranded mRNA sequencing


title: LNCaP cell line - control rep1

value: treated with 0.15% (v/v) DMSO for 24 h


title: LNCaP cell line - control rep2


title: TTseq_LabeledRNA_GP5d_Rep2

description:
GP5d_eRNAs.gtf
GP5d_enhancer.gtf
GP5d_eRNAs_conservative.gtf
GP5d_enhancer_conservative.gtf


title: C666-1 Spheroid 2

description: Stranded mRNA sequencing

value: In media suspension


title: TTseq_LabeledRNA_GP5d_Rep1


title: C666-1 Spheroid 1

description: Stranded mRNA sequencing


title: TLR250

description: Long non-coding RNA sequencing

source_name: NPC patient tumor biopsy

value: NPC patient tumor biopsy

value: FFPE

value: Successful


title: input_DoxBach1_mESC_2

description: S597_fudan-A_10-input-Dox--1104_AH5JJWDSXX_S128_L004

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to mouse genome mm9 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS1.4  and MACS2 .
RNA-seq data were mapped to mouse genome mm9 using STAR  (020201) and assembled by StringTie  (1.3.4d) with parameter -eB (did not consider novel isoforms) to get RPKM.
The RPKM value of genes was converted to Transcripts per million (TPM)  to eliminate the statistical biases inherent in the RPKM measure.
Differentially expressed genes were generated by limma  with fold change >1.5 and p <0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files for ChIP-seq peaks in sample_1 to sample_13. Tab-delimited text files for RNA-seq RPKM and TPM for sample_18 to sample_24. Excel file for differentially expressed genes for sample_18 to sample_24.

source_name: mESCs

extract_protocol:
Chromatin immunoprecipitation (ChIP) sequencing: Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.125 M glycine for 10 minutes; then, the cell pellets were resuspended in high salt Lysis buffer (50 mM HEPES/KOH, PH 7.5, 500 mM NaCl, 1% Trixon-X 100, 0.05% SDS, 10 mM EDTA, and proteinase inhibitors), and sonicated with a Bioruptor (Diagenode) for 20 minutes in 30-second intervals to shear the chromatin into 200- to 400-bp lengths.  Chromatin was immunoprecipitated with the indicated antibodies and Dynabeads protein A and protein G (Thermo Fisher, Waltham, MA). For, Bach1-Flag ChIP, DoxBach1 mESCs were treated with 0.5 μg/μL doxycycline (Selleck chemicals, Houston, TX) for 6 hours. Then cells were cross-linked, quenched, and washed as described above. Cell nucleus were extracted before sonication. And the sonicated chromatin was incubated with anti-Flag affinity M2 agarose gel (Sigma-Aldrich, St. Louis, MO) overnight at 4℃. RNA-seq: Non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module (Excell Bio, Shanghai, China), and sequencing libraries were prepared with the TrueLib mRNA Library Prep Kit for Illumina (ExCell Bio, Shanghai, China).
ChIP DNA libraries and input DNA samples were prepared as directed by protocol of KAPA Hyper Prep Kit for Illumina (Kapa Biosystems, Wilmington, MA).

treatment_protocol: Bach1-Flag expression was induced by treating DoxBach1 mESCs with 0.5 μg/μL doxycycline (Selleck chemicals, Houston, TX) for 6 hours.

value: mouse embryonic stem cells (mESCs)

value: wild type


title: TTseq_LabeledRNA_MDAMB231_Rep2

description:
MDAMB231_eRNAs.gtf
MDAMB231_enhancer.gtf
MDAMB231_eRNAs_conservative.gtf
MDAMB231_enhancer_conservative.gtf

source_name: human cancer cell line

value: 5min 4sU

value: TT-seq


title: TLR512

description: Long non-coding RNA sequencing

value: Fresh frozen

value: Not successful


title: PC-3 cell line - 24h PDA-66 rep3

value: prostate adenocarcinoma cell line derived from bone marrow metastasis

value: treated with 15 µM PDA-66 for 24 h


title: TTseq_LabeledRNA_MDAMB231_Rep1


title: #477

description: Stranded mRNA sequencing

source_name: Organoid

value: Human cells in mouse xenograft model

value: Normoxia


title: PC-3 cell line - 24h PDA-66 rep1


title: input_DoxBach1_mESC_1

description: S596_fudan-A_09-input-Dox-1104_AH5JJWDSXX_S127_L004


title: LNCaP cell line - control rep3

value: LNCaP

value: prostate adenocarcinoma cell line derived from lymph node metastasis


title: PC-3 cell line - 24h PDA-66 rep2


title: C666-1 Spheroid 3

description: Stranded mRNA sequencing

value: Human NPC cell line

value: wild-type


title: mRNA-seq_Bach1-KO_rep2_2020

value: Bach1 -/-


title: TLR15

description: Long non-coding RNA sequencing

value: NPC patient tumor biopsy


title: TTseq_LabeledRNA_BT20_Rep2

description:
BT20_eRNAs.gtf
BT20_enhancer.gtf
BT20_eRNAs_conservative.gtf
BT20_enhancer_conservative.gtf

value: cancer

value: 4sU-labeled RNA


title: Flag-Bach1_ChIP_in_DoxBach1_mESC

description: S594_fudan-A_07-Flag-B1-Dox6h-1104_AH5JJWDSXX_S125_L004

source_name: Dox induced Flag-Bach1 overexpressed mESCs

value: mouse embryonic stem cells (mESCs)

tag: chip antibody

value: ANTI-FLAG M2 Affinity Gel (Sigma-Aldrich, Cat# A2220)


title: PC-3 cell line - 12h PDA-66 rep3

value: treated with 15 µM PDA-66 for 12 h


title: TTseq_LabeledRNA_BT20_Rep1

value: 5min 4sU

value: TT-seq


title: H3K4me1_ChIP_in_Bach1-KO

description: S593_fudan-A_06-K4me1-BKO-1104_AH5JJWDSXX_S124_L004

source_name: Bach1 knock out mESCs

value: H3K4me1 (Active Motif, Cat# 39635)


title: mRNA-seq_Bach1-KO_rep1_2020


title: TTseq_LabeledRNA_U118MG_Rep2

description:
U118MG_eRNAs.gtf
U118MG_enhancer.gtf
U118MG_eRNAs_conservative.gtf
U118MG_enhancer_conservative.gtf


title: TLR427

description: Long non-coding RNA sequencing

value: Fresh frozen

value: Not successful


title: H3K4me1_ChIP_in_WT

description: S592_fudan-A_05-K4me1-mESC-1104_AH5JJWDSXX_S123_L004

value: wild type


title: PC-3 cell line - 12h PDA-66 rep2

value: prostate adenocarcinoma cell line derived from bone marrow metastasis


title: TLR361

description: Long non-coding RNA sequencing


title: Nanog_ChIP_in_Bach1-KO_2_rep1

description:
S252_fudan-A_02-Nanog-BKO-1104-buce_AHLLV2DSXX_S252_L002
processed data file:
02_Nanog_BKO_1104_S497+591_bamPE_peaks-black.narrowPeak

value: Nanog (Cell Signaling Technology, Cat# 8822)


title: TLR228

description: Long non-coding RNA sequencing


title: PC-3 cell line - 12h PDA-66 rep1


title: Nanog_ChIP_in_Bach1-KO_1_rep1

description:
S591_fudan-A_02-Nanog-BKO-1104_AH5JJWDSXX_S122_L004
processed data file:
02_Nanog_BKO_1104_S497+591_bamPE_peaks-black.narrowPeak


title: PC-3 cell line - control rep3

value: treated with 0.15% (v/v) DMSO for 24 h


title: TTseq_LabeledRNA_U118MG_Rep1


title: TTseq_LabeledRNA_M059J_Rep2

description:
M059J_eRNAs.gtf
M059J_enhancer.gtf
M059J_eRNAs_conservative.gtf
M059J_enhancer_conservative.gtf


title: PC-3 cell line - control rep2


title: TTseq_LabeledRNA_M059J_Rep1


title: Nanog_ChIP_in_WT_2_rep1

description:
S590_fudan-A_01-Nanog-mESC-1104_AH5JJWDSXX_S121_L004
processed data file:
01_Nanog_mESC_1104_S590+211_bamPE_peaks-black.narrowPeak


title: Nanog_ChIP_in_WT_1_rep1

description:
S211_fudan-A_01-Nanog-mESC-1104_BHFCWJDSXX_S13_L003
processed data file:
01_Nanog_mESC_1104_S590+211_bamPE_peaks-black.narrowPeak


title: WT mouse

city: Daegu

first: Jae-Yeol

last: Joo

address: 61, cheomdan-ro, Dong-gu,

country: South Korea

institute: Korea Brain Research Institute

data_processing:
Base-calling was performed by the BGISEQ-500 software version 0.3.8.1111
The quality of the RNA-seq libraries was first evaluated using the FastQC v0.11.5 software.
(1) trimming and cleaning reads that aligned to primers and/or adaptors, (2) reads with over 50% of low-quality bases (quality value ≤5) in one read, and (3) reads with over 10% unknown bases (N bases)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks 2.2.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Cortex

extract_protocol:
Total RNA was extracted from mouse cortex using TRIzol method. cDNA synthesis using High-Capacity reverse transcription kit (Applied Biosystems) according to the manufacturer protocols
TruSeq Stranded Total RNA Library Prep kit (Illumina,Inc)

tag: tissue

value: Cortex

tag: age

value: 6 month


title: Coronary artery disease [HC155]

status: Public on Jan 11 2021

type: genomic

city: Mumbai

first: TESTER

middle: F

last: ASHAVAID

state: Maharashtra

address: Lalita Girdhar bldg,3rd floor,Biochemistry Dept.,, V.S.Marg, Mahim

department: Lab Medicine

country: India

institute: P.D. HINDUJA HOSPITAL & MRC

description: Genomic DNA extracted from whole blood was genotyped using Illumina Cardiometabo Beadchip Infinium II assay (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation in Illumina Hybridization Oven, single-base extension and allele specific extension was performed.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a  Illumina BeadArray Reader.

data_processing:
Genomic DNA extracted from whole blood was genotyped using Infinium II assay on Illumina Human CardioMetabo-Beadchip.
Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (Illumina).

label: Cy3, Cy5

source_name: Coronary artery disease

label_protocol: A minimum of 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh whole blood sample was performed using modified Miller et al Salting out method.

tag: gender

value: male

tag: group

value: control


title: Coronary artery disease [HC152]

value: female


title: Coronary artery disease [HC153]


title: Coronary artery disease [HC151]


title: Coronary artery disease [HC150]


title: Coronary artery disease [HC148]


title: Coronary artery disease [HC149]


title: Coronary artery disease [HC146]


title: Coronary artery disease [HC142]


title: 5xFAD mouse

tag: strain


title: HUVEC3+DMSO static

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from static Human umbilical vein endothelial cells (HUVECs) from donor 4 exposed in DMSO

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: HUVECs, donor 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were freshly isolated from individual umbilical cords and grown on collagen I-bonded BioFlex® plates (Flexcell International) in culture medium (M199).

extract_protocol: RNA was isolated and processed for DNA microarray analysis according to manufacturers’ instructions

treatment_protocol: HUVECs were cultured under static conditions in culture medium (M199) supplemented with DMSO (solvent control) for 6 hours.

tag: donor id

tag: exposed to

value: DMSO


title: Coronary artery disease [HC140]


title: Coronary artery disease [HC144]


title: PC-3 cell line - control rep1

tag: cell line

tag: treatment


title: HUVEC2+DMSO static

description: Gene expression data from static Human umbilical vein endothelial cells (HUVECs) from donor 3 exposed in DMSO

source_name: HUVECs, donor 2


title: Coronary artery disease [HC154]


title: HUVEC1+DMSO static

description: Gene expression data from static Human umbilical vein endothelial cells (HUVECs) from donor 1 exposed in DMSO

source_name: HUVECs, donor 1


title: Coronary artery disease [HC137]


title: Coronary artery disease [HC139]


title: Coronary artery disease [HC138]


title: Coronary artery disease [HC135]


title: Coronary artery disease [HC136]


title: Coronary artery disease [HC134]


title: Coronary artery disease [HC133]


title: Coronary artery disease [HC131]


title: Coronary artery disease [HC132]


title: Coronary artery disease [HC128]


title: Coronary artery disease [HC127]


title: Coronary artery disease [HC126]


title: Coronary artery disease [HC125]


title: Coronary artery disease [HC145]


title: Coronary artery disease [HC141]


title: Coronary artery disease [HC143]


title: Coronary artery disease [HC122]


title: Coronary artery disease [HC121]


title: Coronary artery disease [HC119]


title: Coronary artery disease [HC120]


title: Coronary artery disease [HC123]


title: Coronary artery disease [HC117]


title: Coronary artery disease [HC118]


title: Coronary artery disease [HC112]


title: Coronary artery disease [HC113]


title: Coronary artery disease [HC111]


title: Coronary artery disease [HC115]


title: Coronary artery disease [HC114]


title: Coronary artery disease [HC116]


title: Coronary artery disease [HC129]


title: Coronary artery disease [HC130]


title: Coronary artery disease [HC147]


title: Coronary artery disease [HC110]


title: Coronary artery disease [HC108]


title: Coronary artery disease [HC109]


title: Coronary artery disease [HC105]


title: Coronary artery disease [HC124]


title: Coronary artery disease [HC107]


title: Coronary artery disease [HC104]


title: Coronary artery disease [HC99]


title: Coronary artery disease [HC101]


title: Coronary artery disease [HC103]


title: Coronary artery disease [HC102]


title: Coronary artery disease [HC98]


title: Coronary artery disease [HC106]


title: Coronary artery disease [HC87]


title: Coronary artery disease [HC91]


title: Coronary artery disease [HC100]


title: Coronary artery disease [HC84]


title: Coronary artery disease [HC82]


title: Coronary artery disease [HC83]


title: Coronary artery disease [HC79]


title: Coronary artery disease [HC78]


title: Coronary artery disease [HC76]


title: Coronary artery disease [HC97]


title: Coronary artery disease [HC75]


title: Coronary artery disease [HC74]


title: Coronary artery disease [HC96]


title: G16-H02

city: Vladivostok

first: Valeriia

last: Gulaia

address: 10 Ajax Bay

department: School of Biomedicine

country: Russia

institute: Far Eastern Federal University

data_processing:
quality control with FastQC (version 0.11.9)
trimming Nextera sequencing adapters with Trim Galore (parameter “--nextera”)
mapping to GRCh38.p12 human reference genome using STAR-2.6.0c
exclusion of cells expressing 0 genes
normal cells exclusion on the basis of particular cell markers: all hematopoietic cell - CD45 (PTPRC); naïve CD4+ T cells – IL7R, CCR7;  memory CD4+ cells – S100A4; monocytes – CD14, LYZ, FCGR3A, MS4A7; B-cells – MS4A1 (CD20); CD8+ T cells – CD8A; NK-cells – GNLY (NKG5), NKG7; dendritic cells – FCER1A, GST3; platelet – PPBP; stromal cells – CD34; endothelial cells – PECAM1 (CD31)
analysis of copy number variations (CNVs) using CaSpER
cell cycle classification performed by Cyclone
population analysis performed by SingleCellExperiment, Seurat, and Scanpy
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: loom data file containing population analysis from Seurat

source_name: SOX2+ glioma nucleus

extract_protocol:
Frozen tumor tissue of approximate size 0.2-0.5 cm3 was placed in cold tissue lysis buffer (5M NaCl, 1M MgCl2, 1M Tris buffer (pH 8.0), 10% NP40 (Sigma, USA), 1uM DTT (Invitrogen), 1x Complete protease inhibitor (Roche), 0.4 U/ul RNAseIn (Takara Bio, Japan), 0.2 U/ul SuperaseIn  (ThermoFisher Scientific) and incubated on ice for 15 min with gentle swirling every 2-3 minutes. Then the tissue was triturated, filtered through 40um cell strainer and centrifuged at 1000g for 5 min at 4°C. The sedimented nuclei were resuspended in cold staining buffer (RNAse-free PBS pH 7.4, 1% BSA, RNAseIn, 1M MgCl2, 1mM DTT) and stained with anti-Sox2 antibody (Invitrogen) or respective IgG isotype control (BD), Alexa Fluor 488 Goat anti-Rabbit IgG antibody (Invitrogen) was used as secondary. Nuclei were visualized with 7-AAD (Sigma) staining. Thereafter, Sox2 positive nuclei were sorted a FACS Aria I or III at 4°C in skirted 96-well PCR plates containing 2 ul cell lysis buffer (2U/ul RNAseIn in 0,2% (vol/vol) Triton X-100 (Sigma)). After sorting plates were immediately sealed and placed on dry ice.
The library preparation was done using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer instructions, the Illumina Nextera Adapters (sequences provided on http://ngs.biodiv.tw/NGSCore/wp-content/uploads/Documents/illumina-adapter-sequences-1000000002694-08.pdf) were synthetized and HPLC purified in Biomers (http://www.biomers.net/).
single cell RNA-seq

value: patient derived glioma tissue

tag: sample name

tag: genotype

value: wt


title: Coronary artery disease [HC69]


title: Coronary artery disease [HC95]


title: Coronary artery disease [HC68 ]


title: Coronary artery disease [HC66 ]


title: Coronary artery disease [HC94]


title: Coronary artery disease [HC80]


title: Coronary artery disease [HC92]


title: Coronary artery disease [HC58 ]


title: Coronary artery disease [HC86]


title: Coronary artery disease [HC90]


title: Coronary artery disease [HC89]


title: Coronary artery disease [HC88]


title: Coronary artery disease [HC59 ]


title: Coronary artery disease [HC85]


title: Coronary artery disease [HC50 ]


title: Coronary artery disease [HC63 ]


title: Coronary artery disease [HC77]


title: Coronary artery disease [HC81]


title: Coronary artery disease [HC73]


title: Coronary artery disease [HC48 ]


title: Coronary artery disease [HC70 ]


title: Coronary artery disease [HC93]


title: Coronary artery disease [HC46 ]


title: Coronary artery disease [HC45 ]


title: Coronary artery disease [HC44 ]


title: Coronary artery disease [HC62 ]


title: Coronary artery disease [HC61 ]


title: Coronary artery disease [HC41 ]


title: Coronary artery disease [HC60 ]


title: Coronary artery disease [HC56 ]


title: Coronary artery disease [HC40 ]


title: Coronary artery disease [HC57 ]


title: Coronary artery disease [HC37 ]


title: Coronary artery disease [HC39 ]


title: Coronary artery disease [HC51 ]


title: Coronary artery disease [HC53 ]


title: Coronary artery disease [HC52 ]


title: Coronary artery disease [HC49 ]


title: Coronary artery disease [HC54 ]


title: Coronary artery disease [HC36 ]


title: Coronary artery disease [HC35 ]


title: Coronary artery disease [HC34 ]


title: Coronary artery disease [HC47 ]


title: Coronary artery disease [HC32 ]


title: Coronary artery disease [HC33 ]


title: Coronary artery disease [HC55 ]


title: Coronary artery disease [HC42 ]


title: Coronary artery disease [HC43 ]


title: Coronary artery disease [HC27 ]


title: Coronary artery disease [HC25 ]


title: Coronary artery disease [HC24 ]


title: Coronary artery disease [HC29 ]


title: Coronary artery disease [HC31 ]


title: Coronary artery disease [HC38 ]


title: Coronary artery disease [HC30]


title: Coronary artery disease [HC21 ]


title: Coronary artery disease [HC28 ]


title: Coronary artery disease [HC26 ]


title: Coronary artery disease [HC18]


title: Coronary artery disease [HC17]


title: Coronary artery disease [HC22 ]


title: Coronary artery disease [HC19]


title: Coronary artery disease [HC15]


title: Coronary artery disease [HC20]


title: Coronary artery disease [HC13]


title: Coronary artery disease [HC14]


title: Coronary artery disease [HC16]


title: Coronary artery disease [HC12]


title: Coronary artery disease [HC11]


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS58

city: Newark

first: Behnam

last: Abasht

state: DE

address: 531 S. College Ave.

institute: University of Delaware

hyb_protocol: Please see “CodeSet Hybridization Setup”  document

scan_protocol: Please see “nCounter® Analysis System User Manual”

data_processing: For normalization of gene expression, negative control probes were used for detection of “background counts” in each hybridization reaction, and the medians of background counts were applied to background subtraction (NanoString User Manual, 2012). Next, 12 designated housekeeping genes were used for normalization of gene expression (nSolver software package; version 2.5). To prevent saturation issues that may occur due to 2 of the genes (GAPDH and MYH1E) that are highly expressed in muscle tissue, these 2 genes have been attenuated to 10% raw count levels for the samples that were proceed on 7/18/2014 (see the “Expression Assay Data” column). So, the normalized count levels for these two genes for these samples were divided by “0.1” to make them comparable with the values of prior processed samples on 12/05/2013 and 12/06/2013. Note that no attenuation was performed on GAPDH and MYH1E or any other genes for samples processed on 12/05/2013 or 12/06/2013.

label: fluorescent tag barcodes

organism: Gallus gallus

source_name: Pectoralis major muscle from Purebred Line C

growth_protocol: Animal experiments for crossbred (BCD) and purebred chickens (line B and line C) are described in studies by Zhou et al. (Zhou, N., Lee, W.R. and Abasht, B., 2015. Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency. BMC genomics, 16(1), p.195.) and Mutryn et al. (Mutryn, M.F., Brannick, E.M., Fu, W., Lee, W.R. and Abasht, B., 2015. Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing. BMC genomics, 16(1), p.399.), respectively.

extract_protocol: Total RNA was extracted from the tissue samples using the mirVanaTM miRNA Isolation Kit according to the manufacturer’s protocol (Life Technologies®).

treatment_protocol: Samples were smashed into pieces in frozen state by hammering. Pulverized tissues were stored at -80°C until RNA extraction.

value: Pectoralis major muscle

value: 47 days posthatch

tag: Sex

value: Male

tag: wb status

value: WB-Unaffected

tag: chicken type

value: Purebred Line C

tag: hatch

tag: bird plant wt (kg)

tag: breast muscle wt (kg)

tag: skinless legs wt (kg)

tag: p. major phu

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: l*

tag: a

tag: b


title: Pectoralis major muscle_Purebred Line C_WB-Affected-Severe MUS61

label_protocol: Please see “CodeSet Hybridization Setup”  document

tag: tissue

tag: age

value: WB-Affected-Severe


title: Pectoralis major muscle_Purebred Line C_WB-Affected-Severe MUS60


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS48159

source_name: Pectoralis major muscle from Crossbred BCD

value: WB-Affected-Partial

value: Crossbred BCD

tag: live wt (kg) day 29

tag: live wt (kg) day 46

tag: feed consumption (kg) day 29-46

tag: abdominal fat wt (g)


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS57

tag: Sex

tag: wb status

tag: chicken type


title: Coronary artery disease [HC8]

tag: gender

tag: group


title: Coronary artery disease [HC23 ]


title: Coronary artery disease [HC10]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47896

tag: hatch

tag: bird plant wt (kg)

tag: breast muscle wt (kg)

tag: p. major phu


title: Coronary artery disease [HC9]


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS54

tag: skinless legs wt (kg)

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: l*

tag: a


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47893

tag: tissue

tag: age

tag: live wt (kg) day 29

tag: live wt (kg) day 46


title: Coronary artery disease [HC6]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Severe MUS47860

tag: Sex

tag: wb status

tag: feed consumption (kg) day 29-46

tag: abdominal fat wt (g)


title: Coronary artery disease [HC4]

tag: gender

tag: group


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47870

tag: chicken type

tag: hatch

tag: bird plant wt (kg)

tag: breast muscle wt (kg)


title: Coronary artery disease [HC3]


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS56

tag: skinless legs wt (kg)

tag: p. major phu

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: b


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47489

tag: tissue

tag: age

tag: live wt (kg) day 29


title: Coronary artery disease [HC5]


title: Coronary artery disease [HC1]


title: Pectoralis major muscle_Purebred Line C_WB-Affected-Severe MUS59

tag: Sex

tag: wb status

tag: l*

tag: a


title: Coronary artery disease [HP154]

tag: gender

tag: group

value: case


title: Coronary artery disease [HC2]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47828

tag: chicken type

tag: hatch

tag: live wt (kg) day 46

tag: feed consumption (kg) day 29-46

tag: abdominal fat wt (g)


title: Coronary artery disease [HP151]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47415

tag: bird plant wt (kg)

tag: breast muscle wt (kg)

tag: p. major phu


title: Coronary artery disease [HC7]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47445

tag: tissue


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47326

tag: age


title: Coronary artery disease [HP150]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47832

tag: live wt (kg) day 29


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47350

tag: Sex


title: Coronary artery disease [HP148]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47313

tag: wb status


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47352


title: Coronary artery disease [HP153]


title: Coronary artery disease [HP147]


title: Coronary artery disease [HP152]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS43815


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47319


title: Coronary artery disease [HP149]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS47321


title: Coronary artery disease [HP146]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS42756


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS42748


title: Coronary artery disease [HP143]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47825


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS42725


title: Coronary artery disease [HP142]


title: Coronary artery disease [HP144]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS40197


title: Coronary artery disease [HP145]


title: Coronary artery disease [HP141]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS40107


title: Coronary artery disease [HP140]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39798


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39754


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39729


title: Coronary artery disease [HP138]


title: Coronary artery disease [HP137]


title: Coronary artery disease [HP139]


title: Coronary artery disease [HP135]


title: Coronary artery disease [HP136]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS39670


title: Coronary artery disease [HP134]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39687


title: Coronary artery disease [HP133]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS39705


title: Coronary artery disease [HP132]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS39400


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS39345


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS38953


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS39336


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Severe MUS38842


title: Coronary artery disease [HP131]


title: Coronary artery disease [HP129]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS13963


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS38831


title: Coronary artery disease [HP130]


title: Coronary artery disease [HP126]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS38803


title: Coronary artery disease [HP128]


title: Coronary artery disease [HP125]


title: Pectoralis major muscle_Purebred Line B_WB-Affected-Severe MUS218440

source_name: Pectoralis major muscle from Purebred Line B

value: 48 days posthatch

value: Purebred Line B

tag: skinless legs wt (kg)

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: l*

tag: b


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS13815

tag: chicken type

tag: hatch


title: Coronary artery disease [HP124]

tag: gender

value: male

tag: group


title: Pectoralis major muscle_Purebred Line B_WB-Affected-Severe MUS218630

tag: bird plant wt (kg)

tag: a


title: Coronary artery disease [HP123]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39601

tag: live wt (kg) day 46

tag: feed consumption (kg) day 29-46

tag: breast muscle wt (kg)

tag: abdominal fat wt (g)

tag: p. major phu


title: Coronary artery disease [HP122]


title: Pectoralis major muscle_Purebred Line B_WB-Affected-Severe MUS218373

tag: tissue

tag: age

tag: Sex

tag: wb status


title: Coronary artery disease [HP120]


title: Coronary artery disease [HP121]


title: Pectoralis major muscle_Purebred Line B_WB-Unaffected MUS218862

tag: skinless legs wt (kg)

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: l*


title: Coronary artery disease [HP119]

tag: gender


title: Pectoralis major muscle_Purebred Line B_WB-Unaffected MUS219660

tag: chicken type

tag: hatch

tag: b


title: Pectoralis major muscle_Purebred Line B_WB-Unaffected MUS219746

tag: a


title: Pectoralis major muscle_Purebred Line B_WB-Affected-Severe MUS218884

tag: bird plant wt (kg)


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS13808

tag: live wt (kg) day 29

tag: live wt (kg) day 46

tag: feed consumption (kg) day 29-46

tag: breast muscle wt (kg)


title: Pectoralis major muscle_Purebred Line B_WB-Unaffected MUS219825

tag: tissue

tag: age

tag: p. major phu


title: Coronary artery disease [HP115]

tag: group


title: Coronary artery disease [HP117]


title: Coronary artery disease [HP116]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Severe MUS42717

tag: Sex

tag: wb status

tag: abdominal fat wt (g)


title: Coronary artery disease [HP113]

tag: gender


title: Coronary artery disease [HP127]


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Severe MUS42736

tag: chicken type


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS43812

tag: hatch


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Severe MUS43103


title: Coronary artery disease [HP112]


title: Coronary artery disease [HP111]


title: Coronary artery disease [HP110]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS43826


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Severe MUS43838


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47379


title: Coronary artery disease [HP109]


title: Coronary artery disease [HP118]


title: Pectoralis major muscle_Purebred Line C_WB-Affected-Severe MUS66

tag: skinless legs wt (kg)

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: l*

tag: b


title: Coronary artery disease [HP108]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47754

tag: live wt (kg) day 29

tag: live wt (kg) day 46

tag: feed consumption (kg) day 29-46

tag: bird plant wt (kg)


title: Coronary artery disease [HP107]


title: Pectoralis major muscle_Purebred Line C_WB-Affected-Severe MUS63

tag: tissue

tag: age

tag: breast muscle wt (kg)

tag: p. major phu

tag: a


title: Coronary artery disease [HP106]

tag: gender

tag: group


title: Coronary artery disease [HP105]


title: Coronary artery disease [HP114]


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS55

tag: Sex

tag: wb status

tag: chicken type

tag: hatch


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS53

tag: skinless legs wt (kg)

tag: p. major top thickness (mm)

tag: p. major middle thickness (mm)

tag: l*


title: Coronary artery disease [HP103]


title: Coronary artery disease [HP104]


title: Pectoralis major muscle_Purebred Line C_WB-Affected-Severe MUS62

tag: b


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS51

tag: bird plant wt (kg)


title: Coronary artery disease [HP101]


title: Coronary artery disease [HP102]


title: Pectoralis major muscle_Purebred Line C_WB-Unaffected MUS52

tag: tissue


title: Coronary artery disease [HP100]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39348

tag: age

tag: live wt (kg) day 29

tag: live wt (kg) day 46

tag: feed consumption (kg) day 29-46

tag: abdominal fat wt (g)


title: Coronary artery disease [HP99]

tag: gender

tag: group


title: Coronary artery disease [HP98]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS38847

tag: Sex

tag: wb status

tag: breast muscle wt (kg)

tag: p. major phu


title: Coronary artery disease [HP96]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS22370

tag: chicken type

tag: hatch


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS40128


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS48797


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS48883


title: Coronary artery disease [HP95]


title: Coronary artery disease [HP94]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39629


title: Coronary artery disease [HP93]


title: Coronary artery disease [HP91]


title: Coronary artery disease [HP92]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS22237


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS47424


title: Pectoralis major muscle_Crossbred BCD_WB-Affected-Partial MUS14000


title: Coronary artery disease [HP90]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS39663


title: Coronary artery disease [HP89]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS48713


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS48704


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS40679


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS40012


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS22360


title: Pekin duck, Replicate 3

city: New Haven

first: Viktor

last: Feketa

state: CT

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University

description:
Pekin duck
RNASeq_Nikolaev_et_al_2020_Duck_Bill_Skin.xlsx

data_processing:
Primary analysis performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.36 (Bolger et al., 2014) with default parameters.
Filtered high-quality reads from all samples were aligned to duck reference genome using STAR aligner v2.5.4b with default parameters (Dobin et al., 2013).
Aligned reads were counted by featureCounts program within the Subread package v1.6.2 with default parameters (Liao et al., 2014).
Raw read counts were processed and converted to ‘‘mRNA fragments per kilobase of exon per million mapped fragments’’ (FPKM) values by EdgeR v3.22.3 (Robinson et al., 2010).
Genome_build: Anas platyrhynchos [assembly BGI_duck_1.0], ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.fna.gz ; annotation: NCBI Release 102, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.gff.gz ; files accessed on 8/5/2018. The gene annotation was filtered to include only protein-coding genes.
Supplementary_files_format_and_content: Processed data file contains raw read counts and FPKM values for 3 replicates/sample for protein-coding genes in the annotation.

organism: Anas platyrhynchos

source_name: Bill Skin

growth_protocol: Eggs of bird species were incubated at 37°C and 55%-75% humidity. Embryos were extracted for dissection when they had broken through the inner shell membrane (24-48 hrs before hatching).

extract_protocol:
Bill skin was dissected from duck embryos, flash-frozen and stored at -80°C until RNA isolation. Total RNA was isolated from the stored bill skin tissue using the TRIzol reagent (ThermoFisher, Waltham, MA) according to manufacturer’s instructions. RNA quality and integrity were confirmed by running on Agilent Bioanalyzer.
mRNA was purified from ~200 ng total RNA with oligo-dT beads. Strand-specific sequencing libraries were prepared using the KAPA mRNA Hyper Prep kit (Roche Sequencing, Pleasanton, CA).

value: Bill skin

tag: developmental stage

value: Embryonic Day 24-26


title: Coronary artery disease [HP85]

value: female


title: Coronary artery disease [HP87]


title: Coronary artery disease [HP88]


title: Pekin duck, Replicate 1


title: Coronary artery disease [HP86]


title: Coronary artery disease [HP83]


title: Coronary artery disease [HP82]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS13917


title: Coronary artery disease [HP78]


title: Coronary artery disease [HP81]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS40707


title: Seeds sample Rc rep 1 RUN 2

city: Błonie

first: Maja

last: Boczkowska

address: Instytut Hodowli i Aklimatyzacji Roślin - PIB Radzików, 1

country: Poland

data_processing:
The raw data was filtered: adapters, low-quality sequences (Q<30), and sequences shorter than 17 bp and longer than 25 bp were removed. The UEA Small RNA Work-bench: Adapter Removal and Filter software was used to remove the adaptor sequences, sequences containing ambiguous nucleotides, and t/r RNA contamination. High-quality reads were forwarded for further analysis. Using the Sequence Alignment UEA Small RNA Workbench, the miRNA sequences were mapped to the Hordeum vulgare reference genome (Hv_IBSC_PGSB_v2) obtained from Ensembl Plants database release 40 accessed 16.03.2020. UEA Small RNA Workbench miRProf was used to find known miRNAs deposited in the miRBase version 22.1 database and their isoforms with no mismatch allowed. Identification of novel miRNAs was performed in the miRCat UEA Small RNA Workbench with plant parameters.
Genome_build: Hordeum vulgare reference genome (Hv_IBSC_PGSB_v2)
Supplementary_files_format_and_content: Matrix table with DE by DESeq2, file format xlsx

organism: Hordeum vulgare

source_name: Seeds sample Rc

extract_protocol:
The embryo and the scutellum from dry seeds were dissected and were crushed into fine powder in a mortar under liquid nitrogen. miRNA was isolated using a Micro RNA kit (A&A Biotechnology). The miRNA was quantitatively evaluated using Nanodrop 1000 spectrofotometer (Thermo Fisher Scientific) and agarose electrophoresis. To confirm the results and evaluate miRNA integrity 2100 Bioanalyzer with Small RNA Kit (Agilent) was used.
NebNext Multiplex Small RNA Library Prep Set for Illumina (New England, BioLabs)

treatment_protocol: Barley seeds of cv. ’Damazy’ harvested in 1972, were dried to 2,96% water content. Seeds which showed viability above 95% were placed in two air-filled glass flasks and hermetically sealed. All flasks were stored under the same conditions, i.e. in a basement with limited light, at an ambient temperature (10-25° C) and a relative humidity in the room of about 80-90%. Germination tests were carried out again in 2015 and it turned out that seeds viability differed between flasks. A sample of the high viable seeds was taken and the seeds were then stored further. The high viable sample was regenerated in the field (in 2017/2018) according to the gene bank standards and provided the reference material after drying them to a low water content (approx. 7%).

tag: cultivar

value: Damazy

tag: treatment

value: Rc - after seed regeneration; non-stored control

value: dry embryo + scutellum

tag: molecule subtype

value: small RNA

tag: ngs run


title: Coronary artery disease [HP79]


title: Seeds sample Rc rep 3

institute: Instytut Hodowli i Aklimatyzacji Roślin - PIB

tag: tissue

value: RUN 1


title: Coronary artery disease [HP80]


title: Seeds sample Rc rep 1 RUN 1


title: Coronary artery disease [HP77]


title: Seeds sample Lv rep 3

source_name: Seeds sample Lv

value: Lv - seeds after long-term storage 1972-2018 (germination 2%)


title: Coronary artery disease [HP76]


title: Seeds sample Rc rep 2


title: Seeds sample Lv rep 2


title: Coronary artery disease [HP70 ]


title: Coronary artery disease [HP71 ]


title: Coronary artery disease [HP66 ]


title: Coronary artery disease [HP75]


title: Coronary artery disease [HP84]


title: Coronary artery disease [HP64 ]


title: Pekin duck, Replicate 2


title: Seeds sample Hv rep 2

source_name: Seeds sample Hv

value: Hv - seeds after long-term storage 1972-2018 (germination 86,7%)


title: Seeds sample Lv rep 1


title: Coronary artery disease [HP74]


title: Coronary artery disease [HP67 ]


title: Seeds sample Hv rep 1


title: Coronary artery disease [HP65 ]


title: Coronary artery disease [HP97]


title: Coronary artery disease [HP60 ]


title: Seeds sample Hv rep 3


title: Coronary artery disease [HP57 ]


title: Coronary artery disease [HP58 ]


title: Coronary artery disease [HP59 ]


title: Coronary artery disease [HP56]


title: Coronary artery disease [HP54 ]


title: Coronary artery disease [HP55 ]


title: Coronary artery disease [HP62 ]


title: Coronary artery disease [HP63 ]


title: Coronary artery disease [HP53 ]


title: Pectoralis major muscle_Crossbred BCD_WB-Unaffected MUS40752

value: Pectoralis major muscle

tag: age

value: 47 days posthatch

value: Male

value: WB-Unaffected

tag: live wt (kg) day 29

tag: live wt (kg) day 46

tag: bird plant wt (kg)


title: Coronary artery disease [HP61 ]

tag: gender

tag: group

value: case


title: Coronary artery disease [HP49 ]


title: Coronary artery disease [HP52 ]


title: COM_P6_100310_020616

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: Gene expression data from adults

hyb_protocol: Standard GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: HTA 2.0 chips were scanned at the Cologne Center for Genomics, Cologne, Germany.

data_processing: Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 3.5.0; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/). Pre-processing and quality control was performed by using the Oligo package. The core array data were background corrected by Robust Multi-array Average (RMA) and quantiles-normalized.

source_name: blood

label_protocol: 100ng total RNA was labeled using standard GeneChip buffers and reagents (Affymetrix)

growth_protocol: Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.

extract_protocol: Total RNA was isolated in accordance with the PAXgene blood miRNA isolation (QIAGEN) procedure using the QIAcube instrument.

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (approx. 2 hours) while mixing by inversion.

value: blood


title: COM_P6_100314_080616

description: Gene expression data from adults

value: male

value: endotoxemia


title: Coronary artery disease [HP48]


title: COM_P6_100312_030616

description: Gene expression data from adults


title: COM_P6_100232_080616

description: Gene expression data from adults


title: COM_P6_100266_070616

description: Gene expression data from adults


title: COM_P6_100234_030616

description: Gene expression data from adults


title: COM_P6_10026B_080616

description: Gene expression data from adults


title: COM_P6_1003124_020616

description: Gene expression data from adults


title: Coronary artery disease [HP51 ]


title: COM_P6_100174_020616

description: Gene expression data from adults


title: Coronary artery disease [HP46 ]


title: COM_P6_1002324_030616

description: Gene expression data from adults


title: COM_P6_10017B_070616

description: Gene expression data from adults


title: COM_P6_100122_070616

description: Gene expression data from adults


title: COM_P6_1001224_080616

description: Gene expression data from adults


title: Coronary artery disease [HP47 ]


title: COM_P6_1001724_020616

description: Gene expression data from adults


title: COM_P6_100172_080616

description: Gene expression data from adults


title: COM_P6_100262_080616

description: Gene expression data from adults


title: COM_P6_10012B_030616

description: Gene expression data from adults


title: COM_P6_100236_070616

description: Gene expression data from adults


title: Coronary artery disease [HP45 ]


title: Coronary artery disease [HP43 ]


title: COM_P6_100230_020616

description: Gene expression data from adults


title: Coronary artery disease [HP44 ]


title: Coronary artery disease [HP50 ]


title: Coronary artery disease [HP40 ]


title: COM_P6_10011B_020616

description: Gene expression data from adults


title: COM_P6_100120_030616

description: Gene expression data from adults


title: Coronary artery disease [HP39 ]


title: Coronary artery disease [HP42 ]


title: Coronary artery disease [HP38 ]


title: Coronary artery disease [HP36 ]


title: COM_P6_10007B_080616

description: Gene expression data from adults


title: COM_P6_100076_080616

description: Gene expression data from adults


title: COM_P6_1000724_030616

description: Gene expression data from adults


title: Coronary artery disease [HP41 ]


title: COM_P6_100070_070616

description: Gene expression data from adults


title: COM_P6_10002B_020616

description: Gene expression data from adults


title: Coronary artery disease [HP34 ]


title: Coronary artery disease [HP35 ]


title: COM_P6_100026_020616

description: Gene expression data from adults


title: COM_P6_100072_030616

description: Gene expression data from adults


title: Coronary artery disease [HP33 ]


title: Coronary artery disease [HP31 ]


title: Coronary artery disease [HP32 ]


title: Coronary artery disease [HP30 ]


title: Coronary artery disease [HP29 ]


title: Coronary artery disease [HP37 ]


title: COM_P4_100170_200416

description: Gene expression data from adults


title: Coronary artery disease [HP25 ]


title: Coronary artery disease [HP26 ]


title: Coronary artery disease [HP27 ]


title: Coronary artery disease [HP24 ]


title: Coronary artery disease [HP23 ]


title: COM_P4_1001124_070416

description: Gene expression data from adults


title: Coronary artery disease [HP28 ]


title: COM_P4_100114_050416

description: Gene expression data from adults


title: COM_P4_100020_050416

description: Gene expression data from adults


title: Coronary artery disease [HP22 ]


title: COM_P4_100024_050416

description: Gene expression data from adults


title: 6489

description: Gene expression data from adults

tag: disease state

value: sepsis


title: Coronary artery disease [HP20 ]


title: Coronary artery disease [HP21 ]

value: female


title: 6448

description: Gene expression data from adults


title: 6414

description: Gene expression data from adults


title: 6303

description: Gene expression data from adults


title: 6429

description: Gene expression data from adults

value: noninfectious


title: COM_P4_100126_200416

description: Gene expression data from adults


title: 6268

description: Gene expression data from adults


title: Coronary artery disease [HP17]


title: COM_P4_1001224_200416

description: Gene expression data from adults


title: COM_P4_100110_070416

description: Gene expression data from adults


title: Coronary artery disease [HP16]


title: Coronary artery disease [HP15]


title: Coronary artery disease [HP13]


title: 6069

description: Gene expression data from adults


title: 6200

description: Gene expression data from adults


title: 6430

description: Gene expression data from adults


title: 6331

description: Gene expression data from adults


title: 6366

description: Gene expression data from adults


title: Coronary artery disease [HP14]


title: Coronary artery disease [HP12]


title: Coronary artery disease [HP18]


title: Coronary artery disease [HP10]


title: 6048

description: Gene expression data from adults


title: 6194

description: Gene expression data from adults


title: 5945

description: Gene expression data from adults


title: 6018

description: Gene expression data from adults


title: Coronary artery disease [HP8]


title: Coronary artery disease [HP9]


title: 5894

description: Gene expression data from adults


title: Coronary artery disease [HP7]


title: Coronary artery disease [HP5]


title: Coronary artery disease [HP6]


title: Coronary artery disease [HP3]


title: Coronary artery disease [HP1]


title: Coronary artery disease [HP4]


title: Coronary artery disease [HP2]