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| Status |
Public on May 17, 2013 |
| Title |
Jurkat Cells 245 |
| Sample type |
SRA |
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| Source name |
immortalized T-cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: TIB-152
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| Growth protocol |
The Jurkat cell line (TIB-152) was obtained from the American Type Culture Collection (ATCC, Manassas, VA). Jurkat cell culture was grown in 10% Fetal Bovine Serum and 90% RPMI-1640 buffer (ATCC, Manassas, VA) at 37°C. Cell concentration was measured using the TC10 Automated Cell Counter system (BioRad, Hercules, CA), which was validated via hemocytometer counting. Before harvesting, cells were grown to ~1.3x106 cells/mL and had 95%+ viability as measured with the trypan blue assay.
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| Extracted molecule |
total RNA |
| Extraction protocol |
~2e6 cells were pelleted, washed twice with cold PBS, and total RNA was extracted using the Trizol protocol.
RNA-Seq paired end libraries were prepared using the Illumina TruSeq RNA Sample Prep Rev. A (kit lot #6849988, Illumina, San Diego, CA).
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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 |
Basecalls performed using CASAVA version 1.8.
Annotated and unannotated junctions were detected using the Bowtie (v0.12.7) and Tophat (v1.4.0) splice-junction discovery programs (49, 50). All default Bowtie parameters were used. In Tophat, the mate inner distance was set to 150. Two rounds of Bowtie-Tophat processing were conducted with a supplied set of RefSeq gene model annotations in GTF format (7): the first round detected junctions only matching the gene annotation file (option --no-novel-junctions) and the second round detected all junctions, both aligning to the GTF file and novel (option -G).
RNA-Seq reads were processed by RSEM v1.1.20 (RNA-Seq by Expectation-Maximization) to estimate transcript abundances. All default parameters used for both Bowtie (v0.12.7) and RSEM.
Genome_build: hg19
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| Submission date |
Mar 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gloria Sheynkman |
| E-mail(s) |
gloria.kreitinger@gmail.com
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| Organization name |
UW-Madison
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| Department |
Chemistry
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| Lab |
Lloyd Smith
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| Street address |
1101 University Ave.
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE45428 |
Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides |
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| Relations |
| SRA |
SRX254397 |
| BioSample |
SAMN01985825 |
| 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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