|
| Status |
Public on May 09, 2022 |
| Title |
B1_sgN_2_R2 |
| Sample type |
SRA |
| |
|
| Source name |
G401
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: SMARCB1 expressing loss of NSD1
|
| Treatment protocol |
G401 cells were engineered to express either GFP or SMARCB1 (B1) under doxycycline treatment and further transfected with either control (sgC) or NSD1 (sgN) targeting sgRNAs. Cells were then treated with 1ug/mL dox for 24h and collected for RNA extraction. For EZH2 inhibition studies, G401 cells stably expressing shCTRL or shNSD1 RNAs were treated for 72h with 1uM GSK126 and collected for RNA extraction.
|
| Growth protocol |
G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol and the DirectZol Mini Prep Plus kit (Zymo Research, R2070)
TruSeq Stranded mRNA Library Prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
X2030414_YDR942
SMARCB1 expressing loss of NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt
|
| Data processing |
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
Genome_build: GRCh37
Supplementary_files_format_and_content: quantified read counts are provided in the txt format for every sample for gencode v19
|
| |
|
| Submission date |
Jun 18, 2021 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Jacquelyn A Myers |
| E-mail(s) |
[email protected]
|
| Organization name |
St. Jude Children’s Research Hospital
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE178488 |
Inactivation of the histone H3 K36 methyltransferase NSD1 confers resistance to EZH2 inhibition [RNA-Seq] |
| GSE178490 |
Inactivation of the histone H3 K36 methyltransferase NSD1 confers resistance to EZH2 inhibition |
|
| Relations |
| BioSample |
SAMN19776516 |
| SRA |
SRX11181403 |
