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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 08, 2020 |
| Title |
MyH3+/+ replicate 5 Quad |
| Sample type |
SRA |
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| Source name |
Quadriceps muscle
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Skeletal Muscle
age: Postnatal day 0
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Muscles were isolated from P0 stage neonates, flash frozen in liquid nitrogen, and RNA was harvested using the Qiagen RNEasy Lipid Tissue Mini kit.
Library preparation was performed using the Illumina TruSeq Stranded mRNA sample preparation kit with oligo dT selection
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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 |
Reads were aligned to mm10 + splice junctions using pysano (Alignments/Raw)
Spliced alignments were converted back to space, poor quality and repetitive alignments were dropped using USeq's SamTranscriptomeParser (Alignments/Processed)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Normalized coverage tracks (coverage per million mapped reads) were created using Sam2USeq and USeq2UCSCExe (CoverageTracks).
Differential expression was determined using USeq's DefinedRegionDifferentialSeq (Analysis/Tables).
Counts were extracted and used in a paired-sample differential expression analysis.
RNASeq metrics were generated using Picard's CollectRnaSeqMetrics.
Samples were clustered using custom R scripts (Analysis/Plots).
Signficiant genes were run in IPA to generate pathway analyses.
Genome_build: mm10
Supplementary_files_format_and_content: excel files with counts, 0-5 represents replicate 1-6, respectively
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| Submission date |
Jun 21, 2017 |
| Last update date |
Mar 08, 2020 |
| Contact name |
Sam J Mathew |
| E-mail(s) |
sjmathew@rcb.res.in
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| Phone |
911292848822
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| Organization name |
Regional Centre for Biotechnology
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| Department |
Developmental Genetics
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| Street address |
NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway,
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| City |
Faridabad |
| State/province |
Haryana |
| ZIP/Postal code |
121001 |
| Country |
India |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE100331 |
Myosin Heavy Chain-embryonic is a crucial regulator of skeletal muscle development and differentiation. |
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| Relations |
| BioSample |
SAMN07269145 |
| SRA |
SRX2947010 |
| 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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