|
| Status |
Public on Sep 30, 2018 |
| Title |
JM3334_S12: TFEB/TFE3 RAW264.7 MEFs 8h Etoposide rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7 macrophage cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: RAW264.7 macrophage cell line
genotype: CRISPR TFEB/TFE3 DKO
|
| Treatment protocol |
Cells were untreated (control) or treated with 100 microMolar Etoposide for 8 hours
|
| Growth protocol |
Null and CRISPR TFEB/TFE3 DKO RAW264.7 were grown were grown in DMEM with high glucose, GlutaMAX, sodium pyruvate and supplemented with 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from samples with the PureLink RNA Mini Kit (Thermo Fisher 12183018A) or RNeasy Plus Mini Kit (QIAGEN 74134). Genomic DNA was removed from RNA preparations by DNAse digestion using QIAGEN RNAse-free DNAse Set (QIAGEN 79254)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
then mapped to mm10 whole genome using HISAT2 aligner
count tables were generated using featureCounts (http://bioinf.wehi.edu.au/featureCounts/)
|
| |
|
| Submission date |
Aug 14, 2018 |
| Last update date |
Sep 30, 2018 |
| Contact name |
Mehdi Pirooznia |
| E-mail(s) |
pirooznia@gmail.com
|
| Phone |
410-340-6052
|
| Organization name |
National Institutes of Health
|
| Street address |
12 SOUTH DR
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE118517 |
Transcriptome analysis of control and TFEB/TFE3 DKO RAW264.7 in response to DNA Damage |
| GSE118518 |
Transcriptome analysis of control and TFEB/TFE3 DKO MEFs and RAW264.7 in response to DNA Damage |
|
| Relations |
| BioSample |
SAMN09831284 |
| SRA |
SRX4551369 |
