|
Status |
Public on Oct 05, 2023 |
Title |
DAMI TRC rep2 |
Sample type |
SRA |
|
|
Source name |
DAMI TRC
|
Organism |
Homo sapiens |
Characteristics |
cell line: DAMI cell type: leukemic cells disease state: MPN/AML treatment: Control 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 |
DAMI-kdTRC05-09-2018
|
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 |
SAMN21215466 |
SRA |
SRX12008149 |