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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 03, 2018 |
| Title |
transgenic spleen |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Oncorhynchus mykiss |
| Characteristics |
genotype: transgenic bearing cecropin P1 transgene
age: 1 year
tissue: spleen
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| Treatment protocol |
OSU protocol # 4282
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| Growth protocol |
OSU protocol # 4282
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were collected and flash frozen in dry ice. Total RNA was extracted by TRIzol reagen (Invitrogen, Carlsbad, CA) with standard protocols from manufacturer. Genomic DNA was removed by treating samples with RNase free DNase-I (M610A, Promega, Madison, WI).
RNA library was prepared by Beijing Genomic Institute (BGI) using non-transgenic samples with standard Illumina protocols as a commercial service.
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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 |
Non-transgenic samples were sequenced by Illumina HiSeqTM 2000
The reads of adaptor, reads of >5% unknown nucleotides and reads with low quality bases were removed to gain clean reads.
De novo assembly was done by Trinity software to construct the unigenes as reference database.
Transgenic samples were sequenced by Illumina HiSeqTM 2000, and clean reads were collected by the same procedure. Then, clean reads were mapped to reference database by SOAPaligner/SOAP2 software.
Reads per kilobase of transcript per million mapped reads (RPKM) was calculated by BGI in tissue specific manner. The ratio among transgenic and non-transgenic was then determined, and log2 ratio of RPKM was used to represent the differential expression level.
Genome_build: non-transgenic unigenes reference database
Supplementary_files_format_and_content: rpkm.xlsx containing RPKM values for each sample
Supplementary_files_format_and_content: annotated non-transgenic unigenes.xlsx: unigene list with FPKM & annotation
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| Submission date |
Mar 02, 2018 |
| Last update date |
Mar 03, 2018 |
| Contact name |
Yueh-chiang Han |
| E-mail(s) |
[email protected]
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| Organization name |
University of Connecticut
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| Department |
Molecular and cell biology
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| Lab |
Chen
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| Street address |
92 N. Eagleville Rd., Unit 3125, TLS 415
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| City |
Storrs |
| State/province |
CT |
| ZIP/Postal code |
06269-3125 |
| Country |
USA |
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| Platform ID |
GPL19277 |
| Series (1) |
| GSE111373 |
Next generation sequencing establishes the differentially expression profiles of transgenic rainbow trout bearing cecropin P1 transgene |
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| Relations |
| BioSample |
SAMN08631133 |
| SRA |
SRX3758248 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3029707_Transgenic-spleen.Gene.rpkm.xlsx |
12.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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