|
| Status |
Public on Oct 05, 2023 |
| Title |
SET2 HMGA1 KD rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SET2 HMGA1 KD
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SET2
cell type: leukemic cells
disease state: MPN/AML
treatment: shHMGA1 lentivirus infected
|
| Treatment protocol |
Lentivirus is concentrated using Amicon Ultra-15 Centrifugal Filter Unit (sigma) at 4,000 × g for 0.5 hours, 4 °C. The virus pellet was resuspended in a fresh medium, and stored at −80°C until use. For lentivirus transduction, we used magnetic nanoparticles.
|
| Growth protocol |
DAMI cells (ATCC, CRL-9792) were cultured in RPMI 1640 medium (Corning) supplemented with 10% fetal bovine serum (Sigma) and SET-2 cells (DSMZ, CVCL_2187) were cultured in RPMI 1640 supplemented with 20% FBS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell pellets were stored in Trizol after which RNA was isolated (RNeasy mini kits; Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2Set2-kdA1-949
|
| Data processing |
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files, trimmed, and de-multiplexed using Illumina's bcl2fastq 2.17 software
Alignment was performed using Bowtie 2.2.1 with the default parameter to the GRCh37/hg19 genome assembly (NCBI) with TopHat using strand-specific parameters.
Feature and read summarization was performed using Feature Counts from the Subread package.
Log2 fold changes and false discovery rates (FDRs) were determined with DESeq2 in R with an adjusted P value of <0.05 considered significant
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Sep 03, 2021 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Linda M.S. Resar |
| Organization name |
Johns Hopkins University
|
| Department |
Department of Medicine / Division of Hematology
|
| Street address |
720 Rutland Avenue
|
| City |
BALTIMORE |
| State/province |
Maryland |
| ZIP/Postal code |
21210 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE183374 |
HMGA1 Chromatin Regulators Drive MPN Progression [RNA-Seq] |
| GSE189570 |
HMGA1 Chromatin Regulators Drive MPN Progression |
|
| Relations |
| BioSample |
SAMN21215474 |
| SRA |
SRX12008158 |
