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Sample GSM5556467 Query DataSets for GSM5556467
Status Public on Oct 05, 2023
Title DAMI HMGA1 KD rep3
Sample type SRA
Source name DAMI HMGA1 KD
Organism Homo sapiens
Characteristics cell line: DAMI
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 DAMI-kdA1-94905-09-2018
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
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
BioSample SAMN21215470
SRA SRX12008153

Supplementary file Size Download File type/resource
GSM5556467_DAMI-kdA1-94905-09-2018.counts.txt.gz 4.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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