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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 20, 2017 |
| Title |
LV69 |
| Sample type |
SRA |
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| Source name |
Lymphoma cells from CD1dTet- tumor in payer's patch of 26 week old mouse
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| Organism |
Mus musculus |
| Characteristics |
strain: L-DKO
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| Treatment protocol |
None
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| Growth protocol |
None
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lysed tumor tissue using an RNAqueous Kit (Life Technology) according to manufacturer’s protocol
mRNA library was prepared using a TruSeq RNA Stranded mRNA kit (Illumina) according to manufacturer's protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw reads in fastq format 2 were masked for Illumina adapter sequences, barcodes, and Phred-scaled base qualities of 10 and less using GATK
Reads were aligned to mouse genome using default settings in Tophat for paired end sequences, which were output as BAM files and merged using Picard (http://picard.sourceforge.net/)
Fragments per kilobase of transcript per million reads (FPKM) values and differential expression analysis were done using TopHat and Cufflinks from Biospace
Broad filtering criteria were used to remove genes with below baseline levels of expression using cutsom R scripts
Z scores were calculated using Microsoft excel
Genome_build: mm9
Supplementary_files_format_and_content: excel file with FPKM values and z scores for each sample
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| Submission date |
Jun 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuan Zhuang |
| E-mail(s) |
yuan.zhuang@duke.edu
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| Phone |
919-613-7824
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| Organization name |
Duke University
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| Department |
Immunology
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| Lab |
Zhuang lab
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| Street address |
207 Research Drive
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27705 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE83760 |
Gene expression in neonatal NKT cells and lymphoma samples from mice with high E protein levels [RNA-Seq] |
| GSE83761 |
Gene expression in neonatal NKT cells and lymphoma samples from mice with high E protein levels |
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| Relations |
| BioSample |
SAMN05294390 |
| SRA |
SRX1879651 |
| 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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