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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 15, 2019 |
| Title |
P1+3MI_rep2 |
| Sample type |
SRA |
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| Source name |
Mouse ventricle below left anterior descending artery ligation plane
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| Organism |
Mus musculus |
| Characteristics |
strain: ICR/CD1
surgery performed at developmental age: Postnatal day 1
sample collected at post-surgical day: day 3
surgery type: MI
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each heart was dissected in ice-cold PBS and a transverse cut on ligation plane was made, separating it into above ligation plane (ALP) part and below ligation plane (BLP) part. BLP parts were flash-frozen with liquid nitrogen and stored in -80°C for RNA-Seq. The collected tissue samples were ground to powder in liquid nitrogen, resuspended in 1 mL Trizol per 50 mg of tissue, and homogenized using 20G1/2 needles. After chloroform extraction, the aqueous phase was mixed with an equal volume of 75% ethanol and further purified using RNeasy Mini Kit (QIAGEN, 74104) according to manufacturer’s protocol.
Stranded mRNA-Seq libraries were generated using KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCm38 (mm10) reference genome using HiSTAT2 (Version 2.0.4) with default settings and --rna-strandness F.
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (Version 3.20.5) using the GLM approach. For each comparison, genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to select differentially expressed genes between sample group comparisons. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw count values, CPM values or RPKM values for each sample
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| Submission date |
Dec 14, 2018 |
| Last update date |
Jul 15, 2019 |
| Contact name |
Zhaoning Wang |
| E-mail(s) |
zhw063@health.ucsd.edu
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| Organization name |
UC San Diego
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| Department |
Cellular and Molecular Medicine
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| Lab |
Bing Ren Lab
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE123863 |
Transcriptome profiling of neonatal heart regeneration |
| GSE123868 |
Mechanistic basis of neonatal heart regeneration revealed by transcriptome and histone modification profiling |
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| Relations |
| BioSample |
SAMN10593857 |
| SRA |
SRX5131334 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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