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Sample GSM5819418 Query DataSets for GSM5819418
Status Public on Apr 20, 2022
Title Peripheral T cells of patinet #14 before TTF treatment
Sample type SRA
 
Source name Peripheral T lymphocytes isolated from PBMC
Organism Homo sapiens
Characteristics sample id: 15_12-1
treatment: untreated
disease: Glioblastoma
Treatment protocol Blood was draw before and one month after TTField treatment started
Growth protocol Peripheral blood mononuclear cells (PBMCs) were obtained from blood by density gradient centrifugation (Ficoll-Hypaque) and cryopreserved at liquid nitrogen until processed.
Extracted molecule total RNA
Extraction protocol Frozen PBMC samples were quickly taken from liquid nitrogen and thaw at 37 degree. T lymphcytes were isolated using Pan T Cell Isolation Kit, human (Miltenyi Cat#130-096-535), and the total RNA was extracted using Qiagen RNA extraction kit.
RNA-seq library performed at ICBR Gene Expression & Genotyping (RRID:SCR_019145) using 25 ng of protein-free, DNase-treated total RNA (each sample processed individually) as input. Briefly, 25ng of total RNA was used for mRNA isolation using NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490 ). Then followed by RNA library construction with NEBNext Ultra II Directional Lib Prep (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, RNA is fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for desired time. This step is followed by first strand cDNA synthesis using reverse transcriptase and oligo dT primers. Synthesis of ds cDNA is performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation. Finally, library is enriched (each library has an unique barcode) by 12 cycles of amplification, and purified by Agencourt AMPure beads (Beckman Coulter, catalog # A63881).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Paired-end reads were trimmed with trimmomatic v/0.36.
Alignment and gene counts were generated against the GRCh38.p12 genome assembly using the annotation GeneCode release 28 by STAR v2.6.0b with default options and quantmode=GeneCounts. Gene expressions in transcripts per million (tpm) were calculated as described in Wagner et all, Theory Biosci. (2012) 131:281–285
the pair end reads from bulk non-targeted RNA-seq were supplied to MiXCR v.3.0.13, using the command analyze shotgun with the option of starting-material rna, only-productive.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in count or tpm unit and in Ensemble ID and Official gene name
Supplementary_files_format_and_content: Tab delimited format MixCR clonotype fraction file for each of (ALL, IGH, IGK, IGL, TRA, TRB, TRD, TRG) and each sample
 
Submission date Jan 14, 2022
Last update date Dec 04, 2022
Contact name SON B LE
E-mail(s) sble@usc.edu
Phone 3522843026
Organization name University of Southern California
Street address 1645 Amberwood Drive, Unit 11
City SOUTH PASADENA
State/province CA
ZIP/Postal code 91030
Country USA
 
Platform ID GPL24676
Series (1)
GSE193729 TTFields treatment effects on newly diagnosed Glioblastoma patients in peripheral T lymphocytes
Relations
BioSample SAMN25003000
SRA SRX13790817

Supplementary file Size Download File type/resource
GSM5819418_15_12-1_analysis.clonotypes.ALL.txt.gz 49.8 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.IGH.txt.gz 4.5 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.IGK.txt.gz 2.6 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.IGL.txt.gz 2.5 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.TRA.txt.gz 12.4 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.TRB.txt.gz 26.0 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.TRD.txt.gz 12.4 Kb (ftp)(http) TXT
GSM5819418_15_12-1_analysis.clonotypes.TRG.txt.gz 1.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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