title: Dhf-255

city: Ananindeua

first: Layanna

middle: Freitas de

last: Oliveira

state: Pará

address: BR 316 Km 7

department: Arbovirology Section

country: Brazil

institute: Evandro Chagas Institute

data_processing:
Illumina Off-Line Basecaller (OLB v1.8.0) software used for basecalling.
Pre-processing: Sequences were trimmed for 3’ adapters and only N sequences removal (running with FastXToll Kit); Redundant sequences were collapsed and reads shorter than 17 nt were eliminated (mapper.pl available in miRDeep2 software).
Mapping: Reads counts generation, annotated mature miRNAs at miRBase v.21 and predict novel miRNAs (miRDeep2, Bowtie v.1)
Differencial Expression: Using edgeR-Biocondictor to normalized counts per million (CPM) expression. Exact Fisher and GLM (General Linear Model) statistical tests were applied with FDR (False Discovery Rate Benjamini-Hochberg) used to adjust the p value. miRNAs with less than five aligned reads aligned were excluded from this process.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separeted file include CPM values for each sample and estatistical results (fold change, p-value and FDR).

source_name: Liver

extract_protocol:
The small RNAs, including microRNAs, were extracted from 5μm sections of FFPE liver tissue, using the High Pure miRNA Isolation Kit (Roche 454 Life Sciences, Branford, CT, USA), with 16 hours overnight incubation with proteinase K.
Libraries were constructed using TruSeq Small RNA Library Prep (Illumina Inc., San Diego, CA, USA) with reverse transcription by PCR reaction to cDNA synthesis and library fragments selected in PAGE 6%.

tag: Cause of death

value: dengue hemorrhagic fever

value: liver

tag: age

tag: Sex

value: M


title: Control-14

status: Public on Jul 31 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: acute myocardial infarction

tag: tissue

value: F


title: Dhf-347


title: Control-13


title: 6_somites_Mutant_rep1

city: Charlestown

first: Caroline

last: Burns

state: MA

address: CVRC, 4th floor, 4138E 149 13th Street

department: Cardiovascular Research Center

country: USA

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
Reads were aligned against the Zebrafish danRer7/ZV9 genome using tophat v. 2.0.8 (tophat -p 8 --no-novel-juncs --segment-length 20 --solexa1.3-quals --read-realign-edit-dist 0 --library-type fr-unstranded -G Danio_rerio.Zv9.70.chr.gtf danRer7).
Gene expression was estimated using cufflinks v. 2.1.1 (cufflinks -p 8  -u -b danRer7.fa --compatible-hits-norm  --library-type fr-unstranded -G Danio_rerio.Zv9.70.chr.gtf)
The resulting output files were merged and compared using cuffmerge (cuffmerge -p 8  -s danRer7.fa -g Danio_rerio.Zv9.70.chr.gtf) and differential expression was performed using cuffdiff v. 2.0.2   (cuffdiff  -p 8 -u --geometric-norm    -b danRer7.fa --compatible-hits-norm merged.gtf ).
Genome_build: Zv9 70
Supplementary_files_format_and_content: Tab-delimited text files with cufflinks RPKM output, 95% Confidence intervals, Pass/Fail flags for each gene and sample

molecule: polyA RNA

organism: Danio rerio

extract_protocol:
The tip of the tail and a little bit of the yolk close to the tail was dissected using iridectomy scissors at 6 ss to be utilized for genotyping and the rest of the embryo was placed in Trizol Reagent (Life Technologies, Carlsbad, CA). Total RNA was extracted from 6 ss (12 hpf) tbx1 null and wild type embryos using SV Total RNA Isolation System (Promega, Madison, WI).
RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical). The mRNA was purified by polyA-tail enrichment, fragmented, and reverse transcribed into cDNA (Illumina TruSeq). cDNA samples were then end-repaired and adaptor-ligated using the SPRI-works Fragment Library System I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for paired-end sequencing using the Illumina HiSeq 2000.
polyA-based mRNA capture using SPRI beads

tag: genotype/variation

value: vgo; tbx1 mutant

tag: developmental stage

value: 6 somites

value: total embryo


title: 6_somites_Mutant_rep2


title: 6_somites_Ctrl_rep2

value: WT


title: Dhf-253


title: Dhf-198


title: ChIP-seq pie1-5 input DNA replicate 1

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

library_source: genomic

data_processing:
Strand-specific sequencing was performed using the Illumina HiSeq platform according to the manufacturer's instructions.
Short reads were trimmed of adapter sequences and low-quality bases using Trimmomatic.
Reads were mapped to the TAIR10 genome using NCBI Magic-BLAST (RNA-seq) or Bowtie2 in very-sensitive-end-to-end mode (ChIP-seq).
Differential expression of RNAs was determined using edgeR and the Araport11 gene annotations. Regions of enrichment and differential enrichment of epigenetic marks was determined using SICER and SICER-df. Differentially enriched genes were identified by cross-referencing regions of enrichment from SICER-df with the Araport11 gene annotations using the closestBed function of BEDtools.
ChIP-seq alignments were converted to normalized bigwig files using the bamCoverage utility of deepTools2 with the RPKM normalization method.
Genome_build: TAIR10
Supplementary_files_format_and_content: The untrimmed counts matrix and final output from the edgeR analysis are provided as tab-delimited text and contain the gene expression data and differential expression scores. The raw SICER-df outputs are provided as tab-delimited text and were analyzed relative to WT and relative to H3 and contain the p-value calculations for regions of differential enrichment. Bigwig tracks of the ChIP-seq data were generated using deepTools2 with RPKM normalization.
H3 files used in this study were for normalization of the other samples (i.e. no processed files for individual H3 samples)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 3-week-old shoots

growth_protocol: Seeds were sown in soil pots, stratified for 3d at 4°C, and grown under 16h light for three weeks prior to sample collection.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Plant Mini Kit and DNAse-treated with a Zymo RNA Clean and Concentrator kit. Chromatin extraction and IP was performed as described in doi: 10.1074/jbc.M802129200.
cDNA libraries were prepared using the Rubicon Genomics ThruPLEX DNA-seq kit. ChIP DNA libraries were prepared using the NEB Ultra II DNA Library prep kit. Libraries were prepared according to manufacturer's instructions.

value: 3-week-old shoots

tag: genotype

tag: chip antibody

value: No IP (input)


title: Control-94


title: Dhf-277


title: Dhf-236


title: Dhf-299


title: ID8_1

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Library strategy: DREAM
Illumina fastq files were aligned to the Mus musculus genome (mm9) using Bowtie2. Uniquely mapped reads were sorted into bam files using samtools.
We used a python script to map aligned sequencing reads to target CCCGGG sites in the Rattus norvegicus genome (rn4) and enumerate signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG for each target site.
We used an R script to calculate methylation levels at each SmaI/XmaI site based on the following formula: let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text file with numbers of reads and percent methylation at individual CCCGGG sites

organism: Mus musculus

source_name: ID8 ovarian cancer cell line

growth_protocol: ID8 cell line was cultured in RPMI medium with 10% fetal bovine serum and gentamicin sulfate (5mg/mL).

extract_protocol:
Gentra Puregene
Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of ID8 mouse ovarian cancer cell line. Briefly, genomic DNA spiked with methylation standards was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion. 3’ recesses were filled in and Illumina adaptors were ligated to the ends of restriction fragments. Barcoded library pools were sequenced using Illumina HiSeq2500 instrument.

treatment_protocol: Baseline, no treatment

tag: strain

value: ovarian cancer cell line

tag: cell type

value: mouse ovarian surface epithelial cells

tag: gender

value: female


title: ID8_3


title: Dhf-173


title: Dhf-140


title: Dhf-884


title: iMLL-ENL B220Low_3

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description:
4_counts_ME-LOW_ME-HIGH.csv
4_cpms_ME-HIGH_ME-LOW.csv

data_processing:
The first base of each read was trimmed using the preprocessReads function of the R/Bioconductor package QuasR (version 1.12.0)
Reads were mapped using the QuasR::qAlign function
The QuasR::qCount function was used for calculation of gene levels
Counts Per Million mapped reads (CPM) values were calculated using the 'cpm' function of the R/Bioconductor package edgeR
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: 2 csv files per comparison (wtLSK vs iMLL-ENL and iMLL-ENL B220High vs iMLL-ENL B220Low) are provided: a GeneCount table containing raw counts per gene, and a CPM table containing CPM values for each gene.

source_name: Total bone marrow leukemic cells

growth_protocol: wtLSK were isolated by FACS following Lin- depletion and using the surface markers, c-kit, Sca-1 (control mice). iMLL-ENL leukemic samples were isolated from total BM cells. iMLL-ENL leukemic cells expressing HIGH or LOW B220 levels were isolated independently by FACS.

extract_protocol:
Total RNA was isolated from sorted cells using the Pico Pure RNA Isolation Kit.
The RNA sequencing library was prepared using the NuGen Ovation RNA-Seq kit (unstranded)

treatment_protocol: For each genotype (control and iMLL-ENL Doxycycline-inducible KI), we isolated cells from three animals. iMLL-ENL mice were treated with Doxycycline until they developed acute leukemia.

value: Bone marrow

value: MLL-ENL inducible KI


title: iMLL-ENL B220High_1


title: iMLL-ENL B220Low_1


title: 6_somites_Ctrl_rep1


title: Control-63


title: iMLL-ENL B220High_3


title: iMLL-ENL_3

description:
4_counts_WT-LSK_ME-M.csv
4_cpms_ME-M_WT-LSK.csv


title: iMLL-ENL B220High_2


title: Control-81


title: ID8_2


title: wtLSK_3

source_name: wt Hematopoietic stem cells

value: wild type/control


title: iMLL-ENL_1


title: iMLL-ENL_2


title: iMLL-ENL B220Low_2


title: Grape_Seed_Seededless_rep3 [677-06]

city: Logroño

first: NURIA

last: MAURI

state: La Rioja

address: Carretera de Burgos, km 6 "Finca La Grajera"

department: Genomics

country: Spain

institute: Instituto de Ciencias de la Vid y del Vino

description:
Sample 6
Vitis vinifera Red Globe × Crimson Seedless F1 sdi- hybrid seeds collected 4 weeks after anthesis

data_processing:
Library sequencing was performed on an Illumina HiSeq 2000 using v4 chemistry (flow cells and sequencing reagents). Paired-end strand-specific reads of 125 nt were produced.
Gapped alignment of reads to the PN40024 12X.0 grapevine reference genome assembly (http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/) was carried out using TopHat2 v.2.0.13. TopHat2 was run under default parameters with the exception of gap length ≤8, mismatch ≤8 and edit distance ≤8, that were allowed in 125 nt reads. These values were adjusted to compensate the relatively high genetic distance between the table grape genotypes studied here and the reference genome of the wine grape-related PN40024 reference genome.
As post-filtering, only uniquely mapped single copy reads with quality ≥20, aligned in the same chromosome and paired in the expected orientation were kept for further analysis.
The htseq-count tool (v.0.5.4p5) from HTSeq was used to estimate unambiguous read count per 12X V1 annotated transcript.
Normalization of counts following the trimmed mean of M-values (TMM) method was performed in edgeR v.2.2.6
Seed trace versus seed differential expression analysis (adjusted Benjamini-Hochberg P ≤0.05 and ≥2-fold change) was performed in edgeR v.2.2.6
Reads per kb of exon per million fragments mapped (RPKM) was calculated using edgeR and low expressed transcripts were filtered out if average RPKM was <1 in both seed traces and seeds.
tab-delimited text files include RPKM values for each Sample. RPKM were estimated in edgeR v.2.2.6 for the gene features annotated in the grapevine reference genome 12X V1 gene annotations (http://genomes.cribi.unipd.it/)
Genome_build: grapevine reference genome 12X V1 gene annotations (http://genomes.cribi.unipd.it/)
Supplementary_files_format_and_content: RPKM

organism: Vitis vinifera

growth_protocol: A Red Globe×Crimson Seedless F1 table grape cross populations was generated from controlled crosses carried out in 2003. Progeny plants were grown in the same experimental field belonging to Sociedad Murciana de Investigación y Tecnología de Uva de Mesa (ITUM) located in Blanca, Murcia, Spain. Plants were grafted onto 1103 Paulsen rootstock conducted under parral trellis, ferti-irrigated and cultivated under the same management practices.

extract_protocol:
Berries were allowed to briefly thaw in the laboratory, opened by cutting with a scalpel and then, seed content was rapidly recovered with tweezers and refrozen in N2. Seed content from 12-50 fruits collected from ≥2 different clusters was used for each RNA extraction. Total RNA was extracted from frozen seed-related tissues of Red Globe × Crimson Seedless F1 hybrids using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) with the manufacturer’s protocol. An in column DNase digestion step with the RNase-Free DNase Set (QIAGEN) was added.
The six corresponding cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep kit starting from 1 µg of total RNA. The adapter-ligated library was amplified  with 15 PCR cycles, followed by purification with Ampure beads. Finally, the libraries were run on a Bioanalyzer DNA1000 chip and quantified using a real-time PCR kit (Kapa Biosciences). A mean fragment size of 302-bp was obtained.

treatment_protocol: Three sdi+ seedless (669-60, 670-17, 675-17) and three sdi- seeded (665-17, 671-19, 677-06) Red Globe × Crimson Seedless F1 hybrids were compared by RNA-seq. RNA was obtained form seed trace or seeds extracted from pea size (10-12 mm) developmental stage

tag: population

value: Red Globe X Crimson Seedless F1 hybrid

value: sdi-

tag: phenotype

value: seeded

value: seed


title: wtLSK_2


title: Grape_Seed_Seededless_rep2 [671-19]

description:
Sample 5
Vitis vinifera Red Globe × Crimson Seedless F1 sdi- hybrid seeds collected 4 weeks after anthesis


title: Nerve Macrophage, Day 8, Rep 2

city: Montreal

first: Jo Anne

last: Stratton

state: Quebec

address: 3801 University Road

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

data_processing:
After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Alignment was performed using bwa 0.7.12 in “mem” alignment mode against mm10 reference genome with default parameters.
R programming language for GenomicAlignments, Pheatmap, and DESeq2 packages. Expression was summarized at the gene level using the “union” mode of summarize overlaps. A false discovery rate corrected p-value of 0.05 for the Wald test was used for linear model of factors.
Genome_build: mm10
Supplementary_files_format_and_content: Text file including FPKM values for each sample

source_name: Sciatic nerve-derived at Day 8 post-nerve injury

extract_protocol:
All cells were sorted directly into lysis buffer (Ambion), then triturated and vortexed before storage at -80 °C. For RNA extractions, all samples were processed together following manufacturers recommendations (AM1561, Ambion). Total RNA extracts were quantitated using a Qubit Fluorimeter and the Qubit HS assay kit (Invitrogen). All samples were subjected to reverse transcription and Multiple Displacement Amplification (MDA) with REPLI-g SensiPhi DNA Polymerase and oligo-dT primers as per the Qiagen REPLI-g Single Cell RNA Library preparation kit (150073) and the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cx3cr1-GFP+/- :Ccr2-RFP+/-

value: Nerve

tag: genotype, cell type

value: CCR2+ Cx3cr1+ Macrophages at Day 8 post-nerve injury

value: 3 months

value: Female


title: Grape_Seed_trace_Stenospermocarpic_seedless_rep2 [670-17]

description:
Sample 2
Vitis vinifera Red Globe × Crimson Seedless F1 sdi+ hybrid stenospermocarpic seed traces collected 4 weeks after anthesis

value: sdi+

value: seedless

value: seed trace


title: Nerve Macrophage, Day 8, Rep 1


title: Grape_Seed_trace_Stenospermocarpic_seedless_rep1 [669-60]

description:
Sample 1
Vitis vinifera Red Globe × Crimson Seedless F1 sdi+ hybrid stenospermocarpic seed traces collected 4 weeks after anthesis


title: Nerve Macrophage, Day 3, Rep 2

source_name: Sciatic nerve-derived at Day 3 post-nerve injury

value: CCR2+ Cx3cr1+ Macrophages at Day 3 post-nerve injury


title: Nerve Macrophage, Day 3, Rep 1


title: WT bulk rep2

city: San Diego

first: Sole

last: Gatto

state: CA

address: 12636 High Bluff Drive, Suite 400

institute: Monoceros Biosystems

description: Barcode: TACATCGG

data_processing:
We used the FASTQC package (v0.11.3) to assess the quality of sequenced libraries. All passed quality control.
Because we were using the Ovation SoLo RNA-Seq System by NuGEN, we adhered to the manual suggestions and trimmed 5 bases from the 5’ of the sequences.
Reads were mapped to the reference genome using TopHat2 v.2.1.1. We used the following non-default TopHat2 parameters: -p 48 -g 1 --library-type fr-firststrand. The number of mapped reads ranged between 23 and 44*106 and the percentage of mapping was between 79 and 92%.
The quality control of the reads distribution along transcripts was performed using infer_experiment.py from RSeQC package v2.6.3. All samples had a uniform distribution of reads along transcripts.
The sequenced read counts per annotated gene (version 85 of GRCm38) were derived with the use of htseq-count script distributed with HTSeq v0.5.4p5
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: HT-seq generated tab-delimited text files include raw count values for each sample.

source_name: muscle Fibro-Adipogenic Progenitors

extract_protocol:
SubFAPs and FAPs were isolated from hind limb muscles of mice. The number of cells ranged between 7700 and 230000. RNA from FAPs was extracted using miRNeasy Micro kit (Qiagen) following the manufacturer’s protocol. RNA was shipped to the sequencing facility as dry pellet in RNAstable® (Biomatrica). For each experimental condition two independent experiments were carried out for the isolation of RNA. All biological duplicates are from different mice, sorted at different times.
The libraries for sequencing were prepared using Ovation SoLo RNA-Seq System by NuGEN.

value: hind limb muscle

tag: cell type-subpopulation

value: muscle Fibro-Adipogenic Progenitors

value: 70 days

tag: injury

value: unperturbed

value: wild type

tag: code


title: WT bulk rep1

description: Barcode: GTACACCT


title: Monocyte, Rep 2

source_name: Blood-derived monocyte

value: Blood

value: CCR2+ Cx3cr1+ Monocytes


title: WT Tie2+ rep2

description: Barcode: AACTTGCC

value: muscle Fibro-Adipogenic Progenitors Tie2+


title: MDX Tie2+ rep2

description: Barcode: CTTCCTTC

value: chronic injury

value: Dmd/mdx


title: Monocyte, Rep 1

value: Cx3cr1-GFP+/- :Ccr2-RFP+/-


title: WT Tie2+ rep1

description: Barcode: AATCCAGC

value: 59 days


title: MDX DN rep2

description: Barcode: ACTCCTAC

value: muscle Fibro-Adipogenic Progenitors DN


title: MDX Vcam1+ rep2

description: Barcode: ACCATCCT

value: muscle Fibro-Adipogenic Progenitors Vcam1+


title: MDX bulk rep1

description: Barcode: ACGAGAAC

value: 84 days


title: MDX Vcam1+ rep1

description: Barcode: ACAACAGC

value: 64 days


title: WT-inj d1 bulk rep1

description: Barcode: AACTTGCC

value: acute injury


title: MDX bulk rep2

description: Barcode: ATCGTCTC

value: hind limb muscle


title: MDX Tie2+ rep1

description: Barcode: GTCGAGAA


title: WT-inj d1 bulk rep2

description: Barcode: GTACACCT

value: muscle Fibro-Adipogenic Progenitors


title: WT-inj d1 Vcam1+ rep2

description: Barcode: CGTCCATT

value: 70 days


title: MDX DN rep1

description: Barcode: AACTCGGA


title: WT DN rep1

description: Barcode: ATGACAGG

value: unperturbed


title: WT-inj d1 Tie2+ rep2

description: Barcode: GTCGAGAA

value: wild type


title: WT-inj d1 DN rep2

description: Barcode: AACTCGGA


title: WT-inj d3 bulk rep1

description: Barcode: CGACCTAA


title: WT-inj d3 bulk rep2

description: Barcode: CCAACACT


title: WT-inj d1 Tie2+ rep1

description: Barcode: AATCCAGC


title: WT-inj d1 DN rep1

description: Barcode: CGCTACAT


title: WT-inj d3 Tie2+ rep2

description: Barcode: TCTTCGAC


title: WT-inj d3 Vcam1+ rep2

description: Barcode: GACTACGA


title: Grape_Seed_trace_Stenospermocarpic_seedless_rep3 [675-17]

description:
Sample 3
Vitis vinifera Red Globe × Crimson Seedless F1 sdi+ hybrid stenospermocarpic seed traces collected 4 weeks after anthesis

value: Red Globe X Crimson Seedless F1 hybrid

value: sdi+

value: seedless

value: seed trace


title: WT DN rep2

description: Barcode: CGTCCATT


title: WT-inj d3 DN rep2

description: Barcode: CTCCTAGT


title: WT-inj d3 Vcam1+ rep1

description: Barcode: CGTCTAAC


title: WT-inj d3 Tie2+ rep1

description: Barcode: AATCCAGC

value: muscle Fibro-Adipogenic Progenitors Tie2+


title: WT-inj d1 Vcam1+ rep1

description: Barcode: CGTCTAAC


title: rox1 CoCl2 rep2

city: Zürich

first: Markus

middle: S

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

institute: ETH Zürich

description: rox1 deletion + CoCl2 sample 2

data_processing:
Raw Illumina reads were generated in-house (single-end reads), or provided by BGI (paired-end reads).
Fastq files were aligned to the N. castellii genome using TopHat2, using strand-specific option for dUTP, single-end/paired-end mode and default arguments.
BAM files were processed with HTSeq version 0.6.0 to count mapped reads per transcript. Default options were used with mode set to intersection-nonempty.
Genome_build: http://www.ncbi.nlm.nih.gov/assembly/GCF_000237345.1; http://ygob.ucd.ie/
Supplementary_files_format_and_content: Comma separated text files include raw counts per transcript values for each Sample.

organism: Naumovozyma castellii

source_name: rox1 deletion + CoCl2

growth_protocol: Cells were grown overnight in 5 ml YPD at 30°C, 200 rpm, and 21% oxygen, sub-cultured to an A600 of 0.2 in 50 ml YPD medium, grown until A600 reached 1, and then grown for an additional 2 hours in the presence of 0.6 mM CoCl2.

extract_protocol:
Strand-specific RNA-seq libraries were generated in-house by incorporation of dUTP as described in Ding C et al. (2011), PLoS One 6(12):e28151
Strand-specific 42 bp single-end RNA-seq
RNA was extracted by using a RiboPure Yeast Kit (Ambion) or Isolate II RNA Mini Kit (Bioline).

tag: strain background

tag: growth phase

value: growth to A600=1 + 2 hrs in presence of CoCl2


title: rox1/rox2 CoCl2 rep2

description: rox1/rox2 double deletion + CoCl2 sample 2

source_name: rox1/rox2 double deletion + CoCl2


title: rox2 CoCl2 rep2

description: rox2 deletion + CoCl2 sample 2

source_name: rox2 deletion + CoCl2


title: rox2 CoCl2 rep1

description: rox2 deletion + CoCl2 sample 1


title: rox1 CoCl2 rep1

description: rox1 deletion + CoCl2 sample 1


title: rox1/rox2 rep2

description: rox1/rox2 double deletion sample 2

source_name: rox1/rox2 double deletion

growth_protocol: Cells were grown overnight in 5 ml YPD at 30°C, 200 rpm, and 21% oxygen, sub-cultured to an A600 of 0.2 in 50 ml YPD medium, grown until A600 reached 1, and then grown for an additional 2 hours.

value: growth to A600=1 + 2 hrs in absence of CoCl2


title: rox1/rox2 CoCl2 rep1

description: rox1/rox2 double deletion + CoCl2 sample 1


title: WT CoCl2 rep1

description: Wild type + CoCl2 sample 1

source_name: Wild type + CoCl2


title: rox2 rep3

description: rox2 deletion sample 3

source_name: rox2 deletion


title: rox1/rox2 rep1

description: rox1/rox2 double deletion sample 1


title: WT CoCl2 rep2

description: Wild type + CoCl2 sample 2


title: E2O

city: Changsha

first: Minghua

last: Hou

state: Hunan

address: 138 Tong-Zi Po Street, Yue-lu District

department: Department of Otolaryngology-Head Neck Surgery

country: China

institute: Third Xiangya Hospital, Central South University

data_processing:
1)Quality control: Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. 2)Reads mapping to the reference sequence: The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference. 3)Known miRNA alignment: Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively. 4)miRNA editing analysis: Position 2~8 of a mature miRNA were called seed region which were highly conserved. The target of a miRNA might be different with the changing of nucleotides in this region. In our analysis pipeline, miRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch. 5)Target gene prediction: Predicting the target gene of miRNA was performed by psRobot_tar in psRobot (Wu et al, 2012) for plants or miRanda (Enright et al, 2003) for animals. 6)Quantification of miRNA: miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000. 7)Differential expression of miRNA: Differential expression analysis of two samples was performed using the DEGseq (2010) R package. P-value was adjusted using qvalue (Storey et al, 2003). qvalue1 was set as the threshold for significantly differential expression by default.
Illumina Casava1.7 software used for basecalling.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements (readcount, TPM)

source_name: nasal mucosa tissue

extract_protocol:
Nasal mucosa were removed, flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent.RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA,USA).RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H– ). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.

value: BALB/c

tag: age

value: eight week old

tag: group

value: Non-allergic mice

tag: treatment

value: pre-treated with IB before intranasal normal saline challenge for 2 weeks

value: nasal mucosa


title: D2O

value: pre-treated with normal saline before intranasal normal saline challenge for 2 weeks

tag: tissue


title: D1B

value: OVA-induced AR mice

value: pre-treated with IB before intranasal OVA challenge for 2 weeks


title: rox2 rep2

description: rox2 deletion sample 2

tag: genotype/variation


title: E1B

value: pre-treated with IB before intranasal OVA challenge for 4 weeks


title: CM0

value: pre-treated with normal saline before intranasal OVA challenge for 2 weeks


title: rox1 rep2

description: rox1 deletion sample 2

source_name: rox1 deletion


title: rox1 rep1

description: rox1 deletion sample 1


title: WT rep3

description: Wild type sample 3

source_name: Wild type

value: wild type


title: rox2 rep1

description: rox2 deletion sample 1


title: WT rep2

description: Wild type sample 2


title: WT hypoxia rep3

description: Wild type hypoxia sample 3

source_name: Wild type hypoxia

growth_protocol: Cells were grown overnight in 5 ml YPD at 30°C, 200 rpm, and 21% O2, sub-cultured to an A600 of 0.2 in 50 ml YPD medium, and grown for six hours at 30°C at 1% oxygen.

extract_protocol:
Strand-specific RNA-seq libraries were prepared by BGI (www.genomics.cn, Hong-Kong) for sequencing using standard Illumina protocols.
Strand-specific 90 bp paired-end RNA-seq
RNA was extracted by using a RiboPure Yeast Kit (Ambion) or Isolate II RNA Mini Kit (Bioline).

value: 6h at 1% oxygen


title: WT hypoxia rep2

description: Wild type hypoxia sample 2


title: WT hypoxia rep1

description: Wild type hypoxia sample 1


title: WT-inj d3 DN rep1

description: Barcode: CGCTACAT

value: hind limb muscle

value: muscle Fibro-Adipogenic Progenitors DN

value: 64 days

value: acute injury

tag: genotype


title: WT normoxia rep3

description: Wild type normoxia sample 3

source_name: Wild type normoxia

growth_protocol: Cells were grown overnight in 5 ml YPD at 30°C, 200 rpm, and 21% O2, sub-cultured to an A600 of 0.2 in 50 ml YPD medium, and grown for six hours at 30°C at 21% oxygen.

value: 6h at 21% oxygen


title: WT normoxia rep2

description: Wild type normoxia sample 2


title: WT normoxia rep1

description: Wild type normoxia sample 1


title: 17-43_36.5_B

city: Beaufort

first: Dana

last: Hunt

state: NC

address: 135 Duke Marine Lab Road

institute: Duke University Marine Lab

data_processing:
During the preprocessing of the Illumina reads, data cleaning required a minimum quality cutoff of Q30 on the leading and trailing bases, and a 4 nt window with a Q25 running quality threshold (Bolger et al. 2014). Any resulting reads shorter than 40 bases were discarded.
After screening for PhiX and rRNA contamination using Bowtie2 (Ben Langmead and Salzberg 2012), we used Rockhopper v2 (McClure et al. 2013) with the following parameters: allowed mismatch= 0.025, minimum seed length=0.33, minimum expression of UTRs and ncRNAs=1, to identify predicted transcripts not previously annotated as genes; this step should improve the identification of non-coding regions including tRNAs and small RNAs.
The cleaned Illumina reads were then aligned against the sequenced draft genomes (Bowtie2 indexed) using Bowtie2, allowing one base pair mismatch.
We then used Bowtie2 to map the processed reads onto the annotated draft genome, including the hypothetical transcripts identified by Rockhopper.
Read counts for each gene and hypothetical transcript were determined using HTSeq (Anders et al. 2014). Differentially expressed genes were identified using DEseq2
Genome_build: The draft genome assemblies were deposited in the NCBI whole genome shotgun archive under project ID PRJNA292554, However, the WGS submission has not been released yet.
Supplementary_files_format_and_content: tab-delimited text files include raw transcript counts for each sample

organism: Vibrio sp. PID17_43

source_name: Vibrio sp. PID17_43 _36.5ºC

growth_protocol: Triplicate biological replicates were cultured in glucose minimal media supplemented with 10 mM ammonium, F/2 trace metals and F/2 vitamins. Cultures were incubated at the designated temperature with constant agitation until entering mid-exponential phase. These cultures were then diluted 1:100 in fresh media and incubated at the designated temperature with constant shaking at 120 rpm.

extract_protocol:
Cells were harvesting at OD600=0.26-0.29 during early exponential phase. 10mL of cell culture were concentrated on a 0.2 μm polyethersulfone membrane filter (Pall Supor-200) at low vacuum pressure. Filters were then fixed with RNA Protect Bacteria Reagent mixture (Qiagen) for 5 min and then immediately flash-frozen in liquid nitrogen. Filters were stored <2 weeks at -80°C until RNA extraction. Total RNA was extracted from the filter using an RNeasy Mini kit (QIAGEN) according to the standard QIAGEN RNeasy protocol with on-column RNase-free DNase treatment. RNA samples were further DNase treated using the Turbo DNA-free DNase Kit (Ambion) according to the manufacturer's 'rigorous' protocol. The DNase-treated RNA was then checked for DNA contamination by PCR with hsp60 gene as previously described (Hunt et al. 2008b). The RNA integrity was monitored by analysis with a Bioanalyzer (Agilent Technologies). Only samples with an RNA integrity number ≥9.7 were used in further experiments. Ribosomal RNAs (rRNAs) were selectively removed using a previously-developed subtractive hybridization protocol (Stewart et al. 2010) with modifications. In short, gDNA from each strain was used to generate biotin- labeled antisense RNA (aRNA) probes specific to the 16S and 23S rRNA of each strain. Probes were added to 1 μg total RNA in an estimated 2:1 molar ratio, and two independent hybridization reactions were performed on each sample. Probe-bound RNAs and excess probe were removed with three rounds of streptavidin-coated magnetic beads (100 μl each; New England Biolabs). mRNA-enriched samples were subsequently tested for residual rRNA and/or probe contamination using the RNA 6000 Pico Kit (Agilent). Samples with >5% rRNA contamination were not used for downstream processes. mRNA samples were quantified using Qubit’s 2.0 fluorometer with Qubit’s RNA High Sensitivity Assay Kit. A minimum of 10ng of enriched mRNA from each sample was sent Duke Center for Genomic and Computational Biology for library preparation and sequencing.
TruSeq RNA libraries were sequenced using a HiSeq2000 (Illumina) with read lengths of 50nt.

treatment_protocol: Three temperature (Vibrio sp. PID17_43: 12.5°C, 32°C, 36.5°C; Vibrio sp. PID23_8: 12°C, 28°C, 36.5°C)

tag: source

value: coastal seawater

tag: incubation temperature


title: 23-8_36.5_A

organism: Vibrio sp. PID23_8

source_name: Vibrio sp. PID23_8_36.5ºC


title: 23-8_36.5_C


title: 23-8_28_B

source_name: Vibrio sp. PID23_8_28ºC


title: 23-8_12_A

source_name: Vibrio sp. PID23_8_12ºC


title: 23-8_12_B


title: 17-43_36.5_C


title: 23-8_36.5_B


title: WT rep1

description: Wild type sample 1

value: growth to A600=1 + 2 hrs in absence of CoCl2


title: 23-8_28_A


title: 23-8_12_C


title: 17-43_32_B

source_name: Vibrio sp. PID17_43 _32ºC


title: 17-43_32_C


title: 17-43_12.5_C

source_name: Vibrio sp. PID17_43_12.5ºC


title: 17-43_36.5_A


title: 17-43_32_A


title: 17-43_12.5_B


title: untreated control 1

description: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP reporter expression

data_processing:
Fastq files were trimmed to remove Illumina adapters and aligned to the bisulfite-converted Homo sapiens genome (hg19) using Bismark v0.18.1  and Bowtie2.
Methylation values were extracted using Bismark v0.18.1.
We used methylKit v1.3.3 to analyze differential methylation.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with numbers of reads and percent methylation at individual CpG sites

source_name: SW48-derived YB5 colon cancer cell line

growth_protocol: YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

extract_protocol:
Puregene Gentra
Triplicate samples of YB5 cells treated with 10 µM HH1 and DMSO controls were analyzed for DNA methylation changes by reduced representation bisulfite sequencing (RRBS) (Gu et al. Nature Protocols 2011, doi:10.1038/nprot.2010.190). We followed the NEB protocol for methylated adaptors. Briefly, 1 microgram of genomic DNA was spiked 100 picograms of lambda phage DNA as the unmethylated standard and digested with MspI. Ends of restriction fragments were filled in, 3’-dA tailed and methylated adaptors (NEB E7535) were ligated to the ends of restriction fragments. Bisulfite treatment using the Epitect kit (Qiagen) followed. Bisulfite-converted libraries were amplified using EpiMark Taq DNA polymerase (NEB) and primers with barcode indices. The libraries were pooled and sequenced at Fox Chase Cancer Center Genomics Facility on Illumina HiSeq2500 instrument using single end reads of 50 bases. We used Bismark v0.18.1 to align the sequences to hg19 human genome assembly. We used methylKit v1.3.3 to analyze differential methylation.

treatment_protocol: Cells were treated with either DMSO or 10uM HH1 with a single dose for four days (one-dose and let the drug in the media for two days. Drug-free media were changed on day three before performing RRBS on day four).

tag: cell line

value: SW48-derived YB5 colon cancer cell line

tag: cell type

value: Dukes' type C, grade IV, colorectal adenocarcinoma

tag: gender

value: female


title: 17-43_12.5_A


title: untreated control 2


title: HH1_10uM_4day_3


title: HH1_10uM_4day_1


title: HH1_10uM_4day_2


title: DMSO_4day_3


title: DMSO_4day_2


title: 23-8_28_C


title: DMSO_4day_1


title: SALK43_10mM_rep4_str13 (run2)

status: Public on Jul 30 2018

city: Davis

first: Siobhan

last: Brady

address: 451 Health Sciences Drive, 4303 GBSF

department: GBSF

institute: UC Davis

data_processing:
Before and after read processing, libraries were analyzed with FastQC.
Barcodes were trimmed using fastx_trimmer (-f 9 -v -Q 33) and further quality trimmed/adapter removal was done with reaper (-geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late)
Trimmed reads were mapped to the reference genome of Arabidopsis thaliana (TAIR 10) using bowtie (-a --best --strata -n 1 -m 1 -p 4 --sam --tryhard) with subsequent conversion to BAM format using samtools.
HTSeq-count was used to obtain raw counts
Differential expression was assessed with limma-voom using the voomWithQualityWeights() function.
Genome_build: TAIR v10
Supplementary_files_format_and_content: tab delimited files with raw counts for each sample.

source_name: root

growth_protocol: 200-300 seeds per plate were sown on petri plates with media containing 1mM KNO3 or 10mM and nylon mesh and stratified for two nights at 4 degrees. Two plates of seedlings per genotype were grown and combined for each biological replicate.

extract_protocol:
Extraction and RNA-seq libraries were prepared following the BRAD-Seq DGE protocol (Townsley, 2015)
Extraction and RNA-seq libraries were prepared following the BRAD-Seq DGE protocol (Townsley, 2015)

treatment_protocol: Media components: 1 or 10mM KNO3, 4mM MgSO4, 2mM KH2PO4, 1mM CaCl2, 10mM KCl, 36mg/L FeEDTA, 0.146g/L MES (2-MorpholinoEthaneSulfonic acid), 1.43mg/L H2BO3, 0.905mg/L MnCl2·4H2O, 0.055mg/L ZnCL2, 0.025mg/L CuCl2·2H2O, 0.0125 Na2MoO4·2H2O, 1% Sucrose, 0.75% Phytagel, pH 5.7.

tag: line

tag: replicate

tag: run

value: roots


title: SALK12_10mM_rep4_str12 (run2)


title: GABI36_10mM_rep4_str13 (run2)


title: GABI32_10mM_rep4_str13 (run2)


title: SALK30_10mM_rep4_str13 (run2)


title: SALK35_10mM_rep4_str13 (run2)


title: SAIL39_10mM_rep4_str13 (run2)


title: GABI45_10mM_rep4_str13 (run2)


title: SALK41_10mM_rep4_str13 (run2)


title: SALK26_10mM_rep4_str12 (run2)


title: SALK3_10mM_rep4_str12 (run2)


title: SAIL39_10mM_rep3_str11 (run2)


title: GABI45_10mM_rep3_str12 (run2)


title: SALK22_10mM_rep4_str12 (run2)


title: GABI36_10mM_rep3_str11 (run2)


title: GABI32_10mM_rep3_str11 (run2)


title: SALK41_10mM_rep3_str12 (run2)


title: SALK35_10mM_rep3_str11 (run2)


title: SALK26_10mM_rep3_str11 (run2)


title: SALK22_10mM_rep3_str11 (run2)


title: SALK12_10mM_rep3_str11 (run2)


title: SALK3_10mM_rep3_str10 (run2)


title: SALK30_10mM_rep3_str11 (run2)


title: GABI45_1mM_rep4_str10 (run2)


title: Col0_10mM_rep3_str10 (run2)

value: Col


title: SALK43_1mM_rep4_str10 (run2)


title: wtLSK_1

source_name: wt Hematopoietic stem cells

tag: strain

value: Bone marrow

value: wild type/control


title: Col0_10mM_rep4_str12 (run2)


title: SALK43_10mM_rep3_str12 (run2)


title: SALK35_1mM_rep4_str10 (run2)


title: SAIL39_1mM_rep4_str10 (run2)


title: SALK26_1mM_rep4_str9 (run2)


title: GABI36_1mM_rep4_str10 (run2)


title: SALK3_1mM_rep4_str9 (run2)


title: SALK30_1mM_rep4_str9 (run2)


title: SALK22_1mM_rep4_str9 (run2)


title: SALK12_1mM_rep4_str9 (run2)


title: GABI32_1mM_rep4_str9 (run2)


title: SALK43_1mM_rep3_str8 (run2)


title: GABI36_1mM_rep3_str8 (run2)


title: SALK35_1mM_rep3_str8 (run2)


title: GABI45_1mM_rep3_str9 (run2)


title: SALK41_1mM_rep3_str8 (run2)


title: GABI32_1mM_rep3_str8 (run2)


title: SALK30_1mM_rep3_str8 (run2)


title: SALK22_1mM_rep3_str7 (run2)


title: SALK26_1mM_rep3_str8 (run2)


title: SALK12_1mM_rep3_str7 (run2)


title: Col0_1mM_rep3_str7 (run2)


title: SALK3_1mM_rep3_str7 (run2)


title: GABI45_10mM_rep2_str7 (run2)


title: SALK41_10mM_rep2_str7 (run2)


title: SALK41_1mM_rep4_str10 (run2)


title: SALK43_10mM_rep2_str7 (run2)


title: SALK35_10mM_rep2_str6 (run2)


title: GABI32_10mM_rep2_str6 (run2)


title: SAIL39_10mM_rep2_str7 (run2)


title: GABI36_10mM_rep2_str6 (run2)


title: SAIL39_1mM_rep3_str8 (run2)


title: SALK3_10mM_rep2_str6 (run2)


title: SALK26_10mM_rep2_str6 (run2)


title: Col0_10mM_rep2_str5 (run2)


title: SALK22_10mM_rep2_str6 (run2)


title: SALK41_10mM_rep1_str5 (run2)


title: SALK43_10mM_rep1_str5 (run2)


title: GABI45_10mM_rep1_str5 (run2)


title: SALK12_10mM_rep2_str6 (run2)


title: GABI32_10mM_rep1_str5 (run2)


title: SALK35_10mM_rep1_str5 (run2)


title: Grape_Seed_Seededless_rep1 [665-17]

description:
Sample 4
Vitis vinifera Red Globe × Crimson Seedless F1 sdi- hybrid seeds collected 4 weeks after anthesis

tag: population

value: Red Globe X Crimson Seedless F1 hybrid

value: sdi-

tag: phenotype

value: seeded

value: seed


title: SALK30_10mM_rep1_str4 (run2)


title: SALK26_10mM_rep1_str4 (run2)


title: SALK3_10mM_rep1_str4 (run2)


title: SALK12_10mM_rep1_str4 (run2)


title: SALK30_10mM_rep2_str6 (run2)


title: GABI45_1mM_rep2_str4 (run2)


title: SAIL39_1mM_rep2_str3 (run2)


title: SALK41_1mM_rep2_str3 (run2)


title: SAIL39_10mM_rep1_str5 (run2)


title: GABI36_10mM_rep1_str5 (run2)


title: SALK35_1mM_rep2_str3 (run2)


title: GABI32_1mM_rep2_str3 (run2)


title: SALK22_1mM_rep2_str3 (run2)


title: SALK30_1mM_rep2_str3 (run2)


title: Col0_1mM_rep2_str2 (run2)


title: SALK26_1mM_rep2_str3 (run2)


title: SALK12_1mM_rep2_str2 (run2)


title: SALK3_1mM_rep2_str2 (run2)


title: Col0_1mM_rep4_str9 (run2)


title: SAIL39_1mM_rep1_str2 (run2)


title: SALK35_1mM_rep1_str1 (run2)


title: SALK43_1mM_rep1_str2 (run2)


title: GABI36_1mM_rep1_str2 (run2)


title: Col0_10mM_rep1_str4 (run2)


title: SALK30_1mM_rep1_str1 (run2)


title: GABI32_1mM_rep1_str1 (run2)


title: SALK22_10mM_rep1_str4 (run2)


title: SALK43_1mM_rep2_str4 (run2)


title: SALK26_1mM_rep1_str1 (run2)


title: SALK22_1mM_rep1_str1 (run2)


title: GABI36_1mM_rep2_str3 (run2)


title: GABI45_10mM_rep4_str13 (run1)


title: Col0_1mM_rep1_str1 (run2)


title: SALK43_10mM_rep4_str13 (run1)


title: SALK12_1mM_rep1_str1 (run2)


title: SALK41_1mM_rep1_str2 (run2)


title: GABI45_1mM_rep1_str2 (run2)


title: SALK41_10mM_rep4_str13 (run1)


title: SALK3_1mM_rep1_str1 (run2)


title: GABI36_10mM_rep4_str13 (run1)


title: SALK35_10mM_rep4_str13 (run1)


title: SAIL39_10mM_rep4_str13 (run1)


title: GABI32_10mM_rep4_str13 (run1)


title: GABI45_10mM_rep3_str12 (run1)


title: SALK3_10mM_rep4_str12 (run1)


title: SALK26_10mM_rep4_str12 (run1)


title: Col0_10mM_rep4_str12 (run1)


title: SALK41_10mM_rep3_str12 (run1)


title: SALK22_10mM_rep4_str12 (run1)


title: SALK12_10mM_rep4_str12 (run1)


title: SALK43_10mM_rep3_str12 (run1)


title: SAIL39_10mM_rep3_str11 (run1)


title: SALK22_10mM_rep3_str11 (run1)


title: GABI36_10mM_rep3_str11 (run1)


title: SALK35_10mM_rep3_str11 (run1)


title: GABI32_10mM_rep3_str11 (run1)


title: SALK30_10mM_rep3_str11 (run1)


title: SALK26_10mM_rep3_str11 (run1)


title: SALK12_10mM_rep3_str11 (run1)


title: SALK43_1mM_rep4_str10 (run1)


title: SALK3_10mM_rep3_str10 (run1)


title: GABI36_1mM_rep4_str10 (run1)


title: SAIL39_1mM_rep4_str10 (run1)


title: GABI45_1mM_rep4_str10 (run1)


title: SALK35_1mM_rep4_str10 (run1)


title: SALK41_1mM_rep4_str10 (run1)


title: GABI32_1mM_rep4_str9 (run1)


title: SALK30_1mM_rep4_str9 (run1)


title: SALK26_1mM_rep4_str9 (run1)


title: SALK12_1mM_rep4_str9 (run1)


title: SALK3_1mM_rep4_str9 (run1)


title: Col0_1mM_rep4_str9 (run1)


title: GABI45_1mM_rep3_str9 (run1)


title: SALK43_1mM_rep3_str8 (run1)


title: SALK22_1mM_rep4_str9 (run1)


title: SALK26_1mM_rep3_str8 (run1)


title: GABI36_1mM_rep3_str8 (run1)


title: SALK41_1mM_rep3_str8 (run1)


title: Col0_10mM_rep3_str10 (run1)


title: GABI32_1mM_rep3_str8 (run1)


title: SAIL39_1mM_rep3_str8 (run1)


title: SALK22_1mM_rep3_str7 (run1)


title: SALK3_1mM_rep3_str7 (run1)


title: SALK35_1mM_rep3_str8 (run1)


title: SALK43_10mM_rep2_str7 (run1)


title: SALK41_10mM_rep2_str7 (run1)


title: GABI45_10mM_rep2_str7 (run1)


title: Col0_1mM_rep3_str7 (run1)


title: SALK30_10mM_rep4_str13 (run1)


title: SAIL39_10mM_rep2_str7 (run1)


title: GABI36_10mM_rep2_str6 (run1)


title: GABI32_10mM_rep2_str6 (run1)


title: SALK35_10mM_rep2_str6 (run1)


title: SALK30_10mM_rep2_str6 (run1)


title: SALK12_10mM_rep2_str6 (run1)


title: SALK22_10mM_rep2_str6 (run1)


title: SALK26_10mM_rep2_str6 (run1)


title: SALK30_1mM_rep3_str8 (run1)


title: GABI45_10mM_rep1_str5 (run1)


title: SALK43_10mM_rep1_str5 (run1)


title: SALK3_10mM_rep2_str6 (run1)


title: SALK41_10mM_rep1_str5 (run1)


title: SAIL39_10mM_rep1_str5 (run1)


title: GABI32_10mM_rep1_str5 (run1)


title: SALK30_10mM_rep1_str4 (run1)


title: GABI36_10mM_rep1_str5 (run1)


title: SALK35_10mM_rep1_str5 (run1)


title: SALK12_1mM_rep3_str7 (run1)


title: SALK22_10mM_rep1_str4 (run1)


title: Col0_10mM_rep1_str4 (run1)


title: SALK3_10mM_rep1_str4 (run1)


title: SALK26_10mM_rep1_str4 (run1)


title: SALK43_1mM_rep2_str4 (run1)


title: GABI36_1mM_rep2_str3 (run1)


title: SAIL39_1mM_rep2_str3 (run1)


title: GABI45_1mM_rep2_str4 (run1)


title: GABI32_1mM_rep2_str3 (run1)


title: SALK30_1mM_rep2_str3 (run1)


title: SALK41_1mM_rep2_str3 (run1)


title: SALK26_1mM_rep2_str3 (run1)


title: SALK12_1mM_rep2_str2 (run1)


title: SALK22_1mM_rep2_str3 (run1)


title: Col0_1mM_rep2_str2 (run1)


title: GABI45_1mM_rep1_str2 (run1)


title: Col0_10mM_rep2_str5 (run1)


title: SALK35_1mM_rep2_str3 (run1)


title: SALK12_10mM_rep1_str4 (run1)


title: SALK35_1mM_rep1_str1 (run1)


title: GABI32_1mM_rep1_str1 (run1)


title: SALK3_1mM_rep1_str1 (run1)


title: SALK30_1mM_rep1_str1 (run1)


title: GABI36_1mM_rep1_str2 (run1)


title: SALK26_1mM_rep1_str1 (run1)


title: SALK12_1mM_rep1_str1 (run1)


title: H3K27ac ChIP-seq TAC operation (Week 8)

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Reads were mapped to the mouse genome (mm9) using Bowtie (version 1.1.1) with the parameters ‘-S -m 1 -l 36 -n 2 mm9’.
RPKM was calculated with reads mapped to the nuclear genome using DEGseq (version 1.8.0).
ChIP-seq peaks were identified with the MACS program version 1.3.7.1 with a P value < 1e-5. The other parameters were as follows: --tsize ‘36’, --gsize ‘1865500000’, --mfold ‘10’, --nomodel, --nolambda, --wig.
Sequence reads aligning to the region were extended by 300 bp and the density of reads in each region was normalized to the total number of million mapped reads for producing the normalized read density in units of reads per million mapped reads (RPM).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized ChIP-seq counts (bigWig file) and ChIP-seq peak calls (BED file) were generated using the MACS program.

source_name: Cardiomyocytes

growth_protocol: C57BL/6 mice were purchased from CLEA JAPAN. All mice were maintained in specific pathogen-free conditions in the animal facilities of the University of Tokyo. All animal experiments were approved by Ethics Committee for Animal Experiments of the University of Tokyo and strictly adhered to the animal experiment guidelines. Male mice at 8 weeks of age were used for all experiments.

extract_protocol:
Cardiomyocytes (1,000,000 cells) were isolated from two mice at 1 and 8 weeks after the TAC operation with Langendorff perfusion, were crosslinked with 1% formaldehyde at room temperature for 10 min and were quenched with 0.125 M glycine. After sonication, soluble chromatin was added with 4 μl recombinant histone 2B (New England Biolabs) and 0.5 μl of mouse RNA (Qiagen) and was incubated with the antibody-bead complex (5 μg of anti-H3K27ac antibody (Abcam, ab4729) and 20 μl of Dynabeads Protein G (Thermo Fisher Scientific, 10003D)) at 4 °C overnight. Immunoprecipitates were washed, reverse-crosslinked and incubated with proteinase K and RNase A. DNA was purified using a MinElute PCR Purification Kit (QIAGEN).
Sequencing libraries were prepared using the TruSeq Kit (Illumina) for high-throughput sequencing on an Illumina HiSeq 2500 according to the manufacturer’s protocol.

treatment_protocol: Mice (8 weeks old) underwent transverse aortic constriction (TAC) to induce heart failure. The transverse aorta was constricted with a 7-0 silk suture paralleled with a 27-gauge blunt needle, which was removed after constriction. Transthoracic echocardiography was performed on conscious mice with a Vevo 2100 imaging system (VisualSonics). M-mode echocardiographic images were obtained from a longitudinal view to measure left ventricular size and function and were used to assess whether the heart was appropriately exposed to pressure overload.

tag: operation

value: TAC operation (Week 8)

tag: histone modification


title: SALK3_1mM_rep2_str2 (run1)


title: SALK43_1mM_rep1_str2 (run1)


title: H3K27ac ChIP-seq TAC operation (Week 1)

extract_protocol:
Cardiomyocytes (1,000,000 cells) were isolated from two mice 1 week after the TAC operation with Langendorff perfusion, were crosslinked with 1% formaldehyde at room temperature for 10 min and were quenched with 0.125 M glycine. After sonication, soluble chromatin was added with 4 μl recombinant histone 2B (New England Biolabs) and 0.5 μl of mouse RNA (Qiagen) and was incubated with the antibody-bead complex (5 μg of anti-H3K27ac antibody (Abcam, ab4729) and 20 μl of Dynabeads Protein G (Thermo Fisher Scientific, 10003D)) at 4 °C overnight. Immunoprecipitates were washed, reverse-crosslinked and incubated with proteinase K and RNase A. DNA was purified using a MinElute PCR Purification Kit (QIAGEN).
Sequencing libraries were prepared using the TruSeq Kit (Illumina) for high-throughput sequencing on an Illumina HiSeq 2500 according to the manufacturer’s protocol.

value: TAC operation (Week 1)


title: WT_TAC_W2_44

description: single-cardiomyocyte RNA-seq of p53CKO mice.txt

data_processing:
Reads were mapped to the mouse genome (mm9) using Bowtie (version 1.1.1) with the parameters ‘-S -m 1 -l 36 -n 2 mm9’.
RPKM was calculated with reads mapped to the nuclear genome using DEGseq (version 1.8.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample

growth_protocol: C57BL/6 mice were purchased from CLEA JAPAN and α-MHC-Cretg mice were from Jackson Laboratory. Trp53flox/flox mice were obtained from Dr. Anton Berns (The Netherlands Cancer Institute, Amsterdam, Netherlands). All mice were maintained in specific pathogen-free conditions in the animal facilities of the University of Tokyo and Osaka University. All animal experiments were approved by Ethics Committee for Animal Experiments of the University of Tokyo and Osaka University and strictly adhered to the animal experiment guidelines. Conditional deletion of Trp53 in cardiomyocytes was achieved by crossing Trp53flox/flox homozygous mice with α-MHC-Cretg hemizygous mice. Trp53flox/flox; α-MHC-Cretg (Trp53α-MHC-Cre) mice were used as p53 cardiomyocyte-specific knockout (p53CKO) mice. Male mice at 8 weeks of age were used for all experiments. All mice were on a C58BL/6 background.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricular free wall 2 weeks after the sham operation and 3 days and 1, 2, 4 and 8 weeks after the TAC operation. Echocardiography was used to evaluate left ventricular function and assess whether the heart was appropriately exposed to pressure overload. Rod-shaped live cardiomyocytes (viability of cardiomyocytes was over 80% for all time points) were immediately collected from two mice at each time point with a 0.2–2-µl pipette (sample volume, 0.5 µl) and incubated in lysis buffer.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol and the efficiency of reverse transcription was assessed by examining the Ct (Cycle threshold) values from real-time quantitative RT-PCR of control genes (Tnnt2, Cox6a2) using a CFX96 real-time PCR detection system (Bio-Rad) and by examining the distribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for real-time quantitative RT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC; Cox6a2 mRNA forward, CGTAGCCCTC TGCTCCCTTA; Cox6a2 mRNA reverse, GGATGCGGAG GTGGTGATAC. A Ct value of 25 was set as threshold. The remaining libraries were sequenced using a Hiseq 2500 system (Illumina).

treatment_protocol: Mice (8 weeks old) underwent transverse aortic constriction (TAC) to induce heart failure or a sham operation. The transverse aorta was constricted with a 7-0 silk suture paralleled with a 27-gauge blunt needle, which was removed after constriction. Sham-operated mice, which were used as controls, were consisted of mice that had undergone a similar surgical procedure without aortic constriction 2 weeks previously. Transthoracic echocardiography was performed on conscious mice with a Vevo 2100 imaging system (VisualSonics). M-mode echocardiographic images were obtained from a longitudinal view to measure left ventricular size and function.

value: WT (TAC Week 2)

tag: single cell or bulk

value: single cell


title: WT_TAC_W2_43


title: WT_TAC_W2_45


title: WT_TAC_W2_47


title: WT_TAC_W2_41


title: WT_TAC_W2_42


title: WT_TAC_W2_46


title: WT_TAC_W2_48


title: SAIL39_1mM_rep1_str2 (run1)

tag: tissue


title: SALK22_1mM_rep1_str1 (run1)


title: SALK41_1mM_rep1_str2 (run1)


title: WT_TAC_W2_40


title: WT_TAC_W2_39


title: WT_TAC_W2_38


title: WT_TAC_W2_32


title: WT_TAC_W2_30


title: WT_TAC_W2_37


title: WT_TAC_W2_36


title: WT_TAC_W2_35


title: WT_TAC_W2_29


title: WT_TAC_W2_31


title: WT_TAC_W2_34


title: WT_TAC_W2_33


title: WT_TAC_W2_28


title: WT_TAC_W2_27


title: WT_TAC_W2_26


title: WT_TAC_W2_25


title: WT_TAC_W2_19


title: WT_TAC_W2_22


title: WT_TAC_W2_20


title: WT_TAC_W2_21


title: WT_TAC_W2_13


title: WT_TAC_W2_24


title: WT_TAC_W2_14


title: WT_TAC_W2_16


title: WT_TAC_W2_11


title: WT_TAC_W2_17


title: WT_TAC_W2_15


title: WT_TAC_W2_9


title: WT_TAC_W2_12


title: WT_TAC_W2_10


title: WT_TAC_W2_8


title: WT_TAC_W2_7


title: WT_TAC_W2_6


title: Col0_1mM_rep1_str1 (run1)


title: WT_TAC_W2_4


title: WT_TAC_W2_5


title: WT_TAC_W2_23


title: WT_TAC_W2_3


title: WT_TAC_W2_1


title: p53CKO_TAC_W2_48

value: p53CKO (TAC Week 2)


title: WT_TAC_W2_18


title: WT_TAC_W2_2


title: p53CKO_TAC_W2_47


title: p53CKO_TAC_W2_46


title: p53CKO_TAC_W2_44


title: p53CKO_TAC_W2_43


title: p53CKO_TAC_W2_40


title: p53CKO_TAC_W2_42


title: p53CKO_TAC_W2_41


title: p53CKO_TAC_W2_45


title: p53CKO_TAC_W2_39


title: p53CKO_TAC_W2_37


title: p53CKO_TAC_W2_35


title: p53CKO_TAC_W2_36


title: p53CKO_TAC_W2_32


title: p53CKO_TAC_W2_34


title: p53CKO_TAC_W2_31


title: p53CKO_TAC_W2_33


title: p53CKO_TAC_W2_38


title: p53CKO_TAC_W2_27


title: p53CKO_TAC_W2_28


title: p53CKO_TAC_W2_26


title: p53CKO_TAC_W2_25


title: p53CKO_TAC_W2_23


title: p53CKO_TAC_W2_22


title: p53CKO_TAC_W2_24


title: p53CKO_TAC_W2_21


title: p53CKO_TAC_W2_19


title: p53CKO_TAC_W2_20


title: p53CKO_TAC_W2_17


title: p53CKO_TAC_W2_18


title: p53CKO_TAC_W2_16


title: p53CKO_TAC_W2_15


title: p53CKO_TAC_W2_11


title: p53CKO_TAC_W2_12


title: p53CKO_TAC_W2_14


title: p53CKO_TAC_W2_10


title: p53CKO_TAC_W2_30


title: p53CKO_TAC_W2_13


title: p53CKO_TAC_W2_8


title: p53CKO_TAC_W2_7


title: p53CKO_TAC_W2_5


title: p53CKO_TAC_W2_3


title: p53CKO_TAC_W2_6


title: p53CKO_TAC_W2_29


title: p53CKO_TAC_W2_2


title: Morphology_TAC_W1_41

description: Integrative data of single-cell RNA-seq and morphology.txt

value: TAC Week 1 for integration with single-cell morphology


title: Morphology_TAC_W1_40


title: Morphology_TAC_W1_39


title: Morphology_TAC_W1_35


title: p53CKO_TAC_W2_9


title: Morphology_TAC_W1_37


title: p53CKO_TAC_W2_1


title: Morphology_TAC_W1_33


title: Morphology_TAC_W1_34


title: Morphology_TAC_W1_31


title: Morphology_TAC_W1_36


title: Morphology_TAC_W1_30


title: Morphology_TAC_W1_38


title: Morphology_TAC_W1_32


title: p53CKO_TAC_W2_4


title: Morphology_TAC_W1_28


title: Morphology_TAC_W1_29


title: Morphology_TAC_W1_26


title: Morphology_TAC_W1_24


title: Morphology_TAC_W1_27


title: Morphology_TAC_W1_21


title: Morphology_TAC_W1_22


title: Morphology_TAC_W1_23


title: Morphology_TAC_W1_19


title: Morphology_TAC_W1_18


title: Morphology_TAC_W1_14


title: Morphology_TAC_W1_17


title: Morphology_TAC_W1_16


title: Morphology_TAC_W1_13


title: Morphology_TAC_W1_25


title: Morphology_TAC_W1_12


title: Morphology_TAC_W1_15


title: Morphology_TAC_W1_10


title: Morphology_TAC_W1_9


title: Morphology_TAC_W1_7


title: Morphology_TAC_W1_11


title: Morphology_TAC_W1_6


title: Morphology_TAC_W1_2


title: Morphology_TAC_W1_8


title: Morphology_TAC_W1_1


title: Morphology_TAC_W1_5


title: Morphology_TAC_W1_4


title: TAC_W8_2_42

description: single-cardiomyocyte RNA-seq.txt

value: TAC Week 8


title: TAC_W8_2_Bulk

description: single-cardiomyocyte RNA-seq.txt

value: bulk sample (about 100 cells)


title: Morphology_TAC_W1_20


title: Morphology_TAC_W1_3


title: TAC_W8_2_43

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_41

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_38

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_40

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_39

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_43

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_41

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_40

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_42

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_39

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_38

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_2_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_44

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_37

description: single-cardiomyocyte RNA-seq.txt

value: TAC Week 4


title: TAC_W4_2_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W8_1_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_2_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_48

description: single-cardiomyocyte RNA-seq.txt

value: TAC Week 2


title: TAC_W4_1_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_45

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_44

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_40

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_43

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_38

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W4_1_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_47

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_46

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_39

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_48

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_43

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_40

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_41

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_46

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_38

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_47

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_39

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_2_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_Bulk

description: single-cardiomyocyte RNA-seq.txt

value: TAC Week 1


title: TAC_W1_2_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W2_1_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_46

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_42

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_43

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_44

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_41

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_40

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_39

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_45

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_38

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_2_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_31

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_30

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_6

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_2_3

description: single-cardiomyocyte RNA-seq.txt

value: TAC Day 3


title: TAC_W1_1_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_2_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_W1_1_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_66

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_2_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_64

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_65

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_62

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_2_1

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_63

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_60

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_56

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_58

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_54

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_53

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_57

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_59

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_52

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_50

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_51

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_49

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_48

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_47

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_46

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_45

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_44

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_61

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_42

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_40

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_41

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_39

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_38

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_55

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_32

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_33

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_29

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_22

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_23

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_24

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_43

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_19

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_17

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_37

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_11

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_16

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_13

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_14

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_10

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_12

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_28

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_20

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_18

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_9

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_27

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_4

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_25

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_34

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_7

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_21

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_15

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_2

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_3

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_8

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_1

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_Bulk

description: single-cardiomyocyte RNA-seq.txt

value: Sham


title: Sham_2_44

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_42

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_41

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_38

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_39

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_40

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_36

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_5

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_6

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_33

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_32

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_35

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_30

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_31

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_28

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_27

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_34

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_29

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_26

description: single-cardiomyocyte RNA-seq.txt


title: TAC_D3_1_31

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_30

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_22

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_25

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_24

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_43

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_23

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_20

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_19

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_21

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_18

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_17

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_14

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_16

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_15

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_10

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_11

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_9

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_7

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_3

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_4

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_5

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_6

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_2

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_37

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_1

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_Bulk

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_42

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_43

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_40

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_44

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_41

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_37

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_38

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_39

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_33

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_34

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_12

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_35

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_31

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_32

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_13

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_30

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_29

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_28

description: single-cardiomyocyte RNA-seq.txt


title: Sham_2_8

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_27

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_26

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_23

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_24

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_22

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_21

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_25

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_36

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_20

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_16

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_10

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_14

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_19

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_18

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_13

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_15

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_11

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_8

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_6

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_7

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_3

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_1

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_4

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_5

description: single-cardiomyocyte RNA-seq.txt


title: Sham_1_2

description: single-cardiomyocyte RNA-seq.txt


title: sw-cbf123 2-week-cold rep2

city: Beltsville

first: Sunchung

last: Park

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

description: Plants grown at 22⁰C on soil under a photoperiod of 12 h for 23 days, sampled at ZT4

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64  software used for basecalling.
Reads were mapped to the Arabidopsis reference genome (TAIR10) using Tophat version 2.1.0 in default mode with minimum and maxmum intron lengths being set to 10 and 15,000 bp, respectively. The transcript abundance (FPKM) was estimated using Cufflinks (version 2.1.1). Cuffdiff was run using default parameters with inputs of the TAIR10 genome and transcript annotations.
Genome_build: TAIR v10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

source_name: aerial part

growth_protocol: Plants were grown on soil at 22⁰C under a 12 h photoperiod with 100-120 μmol m-2 s-1 light intensity

extract_protocol:
RNA was extracted using the RNeasy plant mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Cold treatment was for 24 hour or 2 weeks at 4⁰C under a 12 h photoperiod of ~35 µmol m-2 sec-1
Cold treated and control samples (all samples) were collected at ZT4

value: entire aerial part

tag: age

value: 23 days after germination

value: Swedish ecotype


title: sw-cbf123 2-week-cold rep1

tag: genotype


title: Sham_1_17

description: single-cardiomyocyte RNA-seq.txt


title: sw-cbf123 24hr-cold rep1


title: Sham_1_12

description: single-cardiomyocyte RNA-seq.txt


title: sw-cbf123 warm rep1


title: Sham_1_9

description: single-cardiomyocyte RNA-seq.txt


title: sw-cbf2 2-week-cold rep2


title: sw-cbf2 24hr-cold rep1


title: sw-cbf23 24hr-cold rep1


title: sw-cbf23 warm rep1


title: sw-cbf23 2-week-cold rep2


title: sw-cbf23 24hr-cold rep2


title: SW 24hr-cold rep2


title: sw-cbf2 warm rep2


title: sw-cbf23 warm rep2


title: sw-cbf2 2-week-cold rep1


title: SW warm rep2


title: it8 2-week-cold rep2

value: Italian ecotype


title: sw-cbf2 warm rep1


title: SW 2-week-cold rep1


title: sw-cbf123 warm rep2


title: SW 2-week-cold rep2


title: sw-cbf23 2-week-cold rep1


title: sw-cbf123 24hr-cold rep2


title: SW 24hr-cold rep1


title: it8 2-week-cold rep1


title: SW warm rep1


title: it8 24hr-cold rep1


title: it8 warm rep2


title: it8 warm rep1


title: it33 2-week-cold rep2


title: sw-cbf2 24hr-cold rep2


title: it33 24hr-cold rep2


title: IT 2-week-cold rep2


title: it33 warm rep2


title: it33 24hr-cold rep1


title: it33 2-week-cold rep1


title: IT 2-week-cold rep1


title: IT 24hr-cold rep2


title: IT warm rep2


title: 35s warm rep2


title: 35s warm rep1


title: NRO-seq in A673 cell line infected with shEWSFLI1

city: Boston

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

description:
nascent RNA
A673.shEWSFLI1.NRO

data_processing:
Library strategy: NRO-seq
Reads were aligned to GRCh37(hg19) using bwa mem. PCR duplicates were removed using Picard(http://broadinstitute.github.io/picard). Genome-wide smoothed signals were generated by counting reads in 150-bp sliding windows with 20 bp overlap using bedtools coverage. All signals were normalized for sequencing depth and scaled to 10 million reads.
Genome_build: hg19

source_name: cell line

extract_protocol:
Freshly extracted nuclei were incubated 30 minutes at 30°C in presence of BrUTP (Roche). Nuclear RNA was extracted using the NucleoSpin miRNA kit (Clontech) and nascent RNA was immunoprecipitated with an anti-BrdU monoclonal antibody (Santa Cruz). Following washes, purified RNA was isolated using the NucleoZOL extraction kit (Clontech).
Nascent RNA samples were treated with RiboGone oligonucleotides to remove ribosomal RNA (Clontech). Illumina compatible sequencing libraries were constructed using SMARTer Stranded Total RNA sample Prep Kit (Clontech) according to the manufacturer’s instructions

tag: infection

value: infected with shEWSFLI1


title: NRO-seq in SKNMC cell line infected with shEWSFLI1

description:
nascent RNA
SKNMC.shEWSFLI1.NRO

value: SKNMC


title: NRO-seq in A673 cell line infected with control

description:
nascent RNA
A673.shGFP.NRO

value: infected with control


title: NRO-seq in SKNMC cell line infected with control

description:
nascent RNA
SKNMC.shGFP.NRO


title: NRO-seq in A673 cell line

description:
nascent RNA
A673.NRO

value: uninfected