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Sample GSM2024765 Query DataSets for GSM2024765
Status Public on Jun 12, 2017
Title 799: Macrophages_RPMI_None_4
Sample type SRA
Source name macrophage
Organism Homo sapiens
Characteristics sample id: 799
treatment: RPMI
time: 4
donor: F
Treatment protocol 24h co-incubation between TPC1 cell line and human primary macrophage
Growth protocol RPMI with gentamycin 5 mg/ml, pyruvate 100 mM, glutamax 200 mM and 10% Fetal Calf Serum
Extracted molecule polyA RNA
Extraction protocol RNeasy kits (Qiagen)
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against the hg19 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: hg19
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the hg19 reference genome
Submission date Dec 31, 2015
Last update date May 15, 2019
Contact name Joachim Schultze
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
Platform ID GPL18460
Series (1)
GSE76445 Trascriptome of thyroid cancer-induced macrophages
BioSample SAMN04378244
SRA SRX1509586

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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