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| Status |
Public on Feb 03, 2015 |
| Title |
B6-2 |
| Sample type |
SRA |
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| Source name |
Eye
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| Organism |
Mus musculus |
| Characteristics |
tissue: eye
strain: C57BL/6
genotype: Wild Type
age: Post natal day 21
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| Extracted molecule |
total RNA |
| Extraction protocol |
Eyes were removed and fixed in RNALater solution and RNA was isolated using the Qiagen Rneasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat (v2.0.12)
Transcripts were assembled and analyzed sequentially by Cufflinks (v2.2.1), Cuffdiff (v2.2.1) and CummeRbund (v2.6.1)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: n/a
Supplementary_files_format_and_content: RPKM
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| Submission date |
Dec 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Michael Kevany |
| E-mail(s) |
bmk47@case.edu
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| Phone |
2163683063
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| Organization name |
Case Western Reserve University
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| Department |
Pharmacology
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| Lab |
W317
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| Street address |
10900 Euclid Ave.
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE63810 |
Next Generation Sequencing Comparison of C57BL/6J and BC027072 -/- Eye Transcriptomes |
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| Relations |
| BioSample |
SAMN03251866 |
| SRA |
SRX794141 |
| 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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