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Sample GSM2320001 Query DataSets for GSM2320001
Status Public on Apr 06, 2017
Title HL60-siCon Rep2 RNA-seq
Sample type SRA
 
Source name HL-60
Organism Homo sapiens
Characteristics induction: None
time: 24 hr
treatment: siRNA Control
Treatment protocol Differentiation of HL-60 cells into macrophage (Murao et al., 1983), monocytes (Mangelsdorf et al., 1984) and neutrophils (Breitman et al., 1980) was performed as previously described. Additionally, monocytes (120 hours post-differentiation) were stimulated with PMA to induce differentiation into monocyte-derived macrophages. Briefly, 1x10e6 undifferentiated HL-60 cells were washed in 1X PBS and transfected with the Lonza nucleofector cocktail, 1μg of GFP plasmid and either a human non-targeting siRNA (Dharmacon Inc, D-001206-13-05) or human PU.1 siRNA (Dharmacon Inc, E-010537-00-0005). HL-60 and differentiated myeloid cells were harvested 24 hours post-nucleofection. Cell viability was determined using trypan blue staining and counted using a hemocytometer prior to RNA isolation.
Growth protocol HL-60 cells (ATCC) were grown in Modified Dulbecco's Medium in a final concentration of 20% FBS with penicillin antibiotics (1%). Cells were routinely cultured at a density of 1x10^6 cells/ml.
Extracted molecule total RNA
Extraction protocol RNA quality was evaluated for all samples using an Agilent 2100 Bioanalyzer. Samples with a RIN > 9 were used to build RNA-seq libraries from 50,000 cells using the Smart-seq2 protocol (Picelli et al., 2013).
Reads were sequenced as 40 bp paired-end dual indexed reads using Illumina’s NextSeq 500
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to Gencode version 20 gene annotations using Cufflinks (Trapnell et al., 2010).
FPKM and counts were normalized for batch effects using Combat (Johnson et al., 2007).
Genome_build: hg38
Supplementary_files_format_and_content: FPKM
 
Submission date Sep 18, 2016
Last update date May 15, 2019
Contact name Ricardo Noel Ramirez
E-mail(s) ricardnr@uci.edu
Organization name University of California Irvine
Department Developmental and Cell Biology
Street address 2300 Biological Sciences III
City Irvine
State/province California
ZIP/Postal code 92697
Country USA
 
Platform ID GPL18573
Series (2)
GSE79046 Dynamic gene regulatory networks of human myeloid differentiation
GSE87055 Dynamic gene regulatory networks of human myeloid differentiation [RNA-seq_siRNA]
Relations
BioSample SAMN05786728
SRA SRX2174259

Supplementary file Size Download File type/resource
GSM2320001_HL60-siCon-Rep2.FPKM.txt.gz 80.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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