|
| Status |
Public on Sep 01, 2019 |
| Title |
shTFEB NB4 ATRA 1 |
| Sample type |
SRA |
| |
|
| Source name |
NB4 leukemic cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: ATRA
cell line: NB4
knockdown: shTFEB
|
| Treatment protocol |
Standard lentiviral approaches were used to functionally deplete TFEB mRNA in the NB4 acute promyelocytic leukemia cell line. An scrambled sequence shRNA was used as a negative control. The parental wild type NB4 cell line was used as control. Biological replicates of wildtype NB4, scrambled shRNA control and TFEB knockdown NB4 cells were treated with either ethanol (control) or all-trans retinoic acid (1microM) for 72 hours and differentiation monitored. RNA was isolated and sequenced.
|
| Growth protocol |
NB4 cells were maintained in at 37C, 5%CO2 in RPMI supplemented with 10% heat inactivated fetal calf serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy columns coupled with on-column DNase digestion (Qiagen)
Illumina TruSeq RNA sample preparation protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Sample_shTFEB_RA_A
|
| Data processing |
standard Illumina HiSeq post-processing
alignment using TopHat
The aligned BAM files for biological replicates were uploaded to the galaxy server (usegalaxy.org) and expression levels calculated using the Galaxy implementation of Cufflinks and Cuffdiff.
Genome_build: HG19
Supplementary_files_format_and_content: fpkm
|
| |
|
| Submission date |
Dec 12, 2013 |
| Last update date |
Sep 01, 2019 |
| Contact name |
Nigel P Mongan |
| Organization name |
University of Nottingham
|
| Department |
Biodiscovery Institute
|
| Street address |
University Park
|
| City |
Nottingham |
| ZIP/Postal code |
NG7 2RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE53258 |
The role of TFEB in retinoid induced differentiation of NB4 APL leukemic cells (shTFEB) |
|
| Relations |
| BioSample |
SAMN02442664 |
| SRA |
SRX390782 |
