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| Status |
Public on Sep 17, 2019 |
| Title |
Uninjured cardiomyocytes rep2 |
| Sample type |
SRA |
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| Source name |
Cardiac ventricle tissue
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| Organism |
Danio rerio |
| Characteristics |
tissue: Cardiac ventricle apex
strain: Gata4:GFP
batch: uninjured
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ventricle apexes were removed and cleared of injury tissue, then dissociated using the Miltenyi neonate heart dissociation kit, pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS-sorted directly into RLT lysis buffer (RNeasy micro-prep RNA extraction kit, Qiagen). RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical). cDNA samples were generated using the Ovation low input v2 kit (Nugen) according to the manufacturer’s. The resulting 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 2X40 nt using the Illumina HiSeq 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Data Processing
Reads from three replicates of uninjured (“uninjured”) and 5 days
post injury (“5 dpa”) heart samples were aligned against the GRCz10 genome assembly
of the Zebrafish, ENSEMBL 89 annotation using STAR v. 2.5.3a in paired-end mode
with parameters --runThreadN 16 --runMode alignReads --outFilterType BySJout --
outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --
outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --
alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode
TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed
using RSEM v. 1.3.0 using following flags --paired-end --calc-ci --alignments
-p 8 --forward-prob 0. Posterior mean estimates of counts, RPKM and TPM were
retrieved for each gene in each sample.
Differential expression analysis between uninjured and 5 dpa samples was performed
using DESeq2 in the R statistical environment (v. 3.3.3) on protein-coding genes
(according to ENSEMBL’s biotype assignments).
Supplementary_files_format_and_content csv files are a DEseq2 estimations of changes in read density of protein coding genes (according to ENSEMBL release 89’s biotype assignments) between experimental groups.
Supplementary_files_format_and_content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data (.tdf) files (Thorvaldsdottir et al. 2013).
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| Submission date |
Mar 22, 2017 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Raz Ben-Yair |
| E-mail(s) |
razbe@weizmann.ac.il
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| Phone |
6177553081
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| Organization name |
MGH
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| Department |
CVRC
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| Lab |
Caroline Burns
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| Street address |
13th st.
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| City |
Charlestown, MA |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
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| Platform ID |
GPL14875 |
| Series (2) |
| GSE96929 |
H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA-seq] |
| GSE96930 |
H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration |
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| Relations |
| BioSample |
SAMN06628149 |
| SRA |
SRX2661987 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2546209_Gata4u2.tdf.gz |
74.4 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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