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Sample GSM4200738 Query DataSets for GSM4200738
Status Public on Dec 02, 2021
Title Control 2
Sample type SRA
 
Source name Peripheral blood mononuclear cells_control
Organism Homo sapiens
Characteristics cell type: Immune cells
tissue: Peripheral blood
patient diagnosis: SLE
Treatment protocol Human PBMCs derived from an SLE patient were cultured with Medium (Control) or Medium supplemented with human hemoglobin (Test) for 24 hours.
Extracted molecule total RNA
Extraction protocol PBMCs were isolated from human blood using Ficoll (Amersham) gradient separation at 20°C, 400g for 40 min
The sequencing library was prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Raw reads are filtered based on length (read length should be greater than 50) and quality using Trimmomatic-0.39
Filtered reads are aligned using STAR-Aligner v 2.5.4b
HTSeq v0.11.2 is used to get read count of genes
Insert size and SD are calculated from BAM files using RSeQC v3.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab deliminated files include gene name and their raw counts in each sample
 
Submission date Dec 02, 2019
Last update date Dec 02, 2021
Contact name Rahul Pal
E-mail(s) rahul@nii.ac.in
Phone 91-11-26703787
Organization name National Institute of Immunology
Street address Aruna Asaf Ali Marg
City New Delhi
State/province Delhi
ZIP/Postal code 110067
Country India
 
Platform ID GPL24676
Series (1)
GSE141318 Hemoglobin induced changes in the transcriptome of lupus patients.
Relations
BioSample SAMN13450656
SRA SRX7256199

Supplementary file Size Download File type/resource
GSM4200738_Control2.tab.gz 193.3 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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