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| Status |
Public on Mar 03, 2020 |
| Title |
RNA-Seq for a differential gene expression bewteen KLHL14 wild-type(+/+) and KLHL14 knockout(-/-) TMD8 ABC-DLBCL cell line upon treatment with a BTK inhibitor, ibrutinib |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goal of this study is to examine gene expression changes in TMD8 KLHL14(+/+) or TMD8 KLHL14(-/-) cells during ibrutinib treatment. The samples have 35 to 63 million pass filter reads with more than 92% of bases above the quality score of Q30.The average mapping rate of all samples is 95%. Unique alignment is above 86%. There are 3.65 to 6.25% unmapped reads.The mapping statistics are calculated using Picard software. The samples have between 0.86-1.29% ribosomal bases. Percent coding bases are between 58-62%. Percent UTR bases are 27-31%, and mRNA bases are between 87-90% for all the samples. We show that TMD8 KLHL14(-/-) cells have less down-regulation of NF-kB signatures and IL10/JAK1/STAT3 signatures upon ibrutinib treatment when compared to TMD8 KLHL14(+/+) cells.
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| Overall design |
mRNA profilies of TMD8 KLHL14(+/+) and KLHL14(-/-) cells treated with either DMSO or Ibrutinib (2nM) for 24h were generated by paired-end sequencing on HiSeq4000
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| Contributor(s) |
Choi J, Staudt L |
| Citation(s) |
32127472 |
| |
| Submission date |
Nov 27, 2019 |
| Last update date |
Jun 02, 2020 |
| Contact name |
David Huang |
| Organization name |
National Cancer Institute
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892-0001 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA592209 |
| SRA |
SRP233585 |
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