|
| Status |
Public on Feb 05, 2024 |
| Title |
GFP_LOW, replicate 1, 48hr, bulkRNA |
| Sample type |
SRA |
| |
|
| Source name |
Raji
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Raji
genotype: Smarca4+/+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturers protocol.
mRNA-seq library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR), following the manufacturer’s protocol. Library size distribution and concentration were evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read alignment using STAR-aligner. Count matrices were created using featureCounts of subread package.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated matrix file
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Michael Green |
| E-mail(s) |
mgreen5@mdanderson.org
|
| Phone |
713-745-4244
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Department of Lymphoma/Myeloma
|
| Street address |
7455 Fannin Street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE254899 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions [rajiAUD_rna] |
| GSE254908 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions |
|
| Relations |
| BioSample |
SAMN39746888 |
| SRA |
SRX23507506 |
