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| Status |
Public on Apr 20, 2022 |
| Title |
Peripheral T cells of patinet #14 after TTF treatment |
| Sample type |
SRA |
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| Source name |
Peripheral T lymphocytes isolated from PBMC
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| Organism |
Homo sapiens |
| Characteristics |
sample id: 16_12-2
treatment: TTFields
disease: Glioblastoma
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| Treatment protocol |
Blood was draw before and one month after TTField treatment started
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| Growth protocol |
Peripheral blood mononuclear cells (PBMCs) were obtained from blood by density gradient centrifugation (Ficoll-Hypaque) and cryopreserved at liquid nitrogen until processed.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jan 14, 2022 |
| Last update date |
Dec 04, 2022 |
| Contact name |
SON B LE |
| E-mail(s) |
sble@usc.edu
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| Phone |
3522843026
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| Organization name |
University of Southern California
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| Street address |
1645 Amberwood Drive, Unit 11
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| City |
SOUTH PASADENA |
| State/province |
CA |
| ZIP/Postal code |
91030 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE193729 |
TTFields treatment effects on newly diagnosed Glioblastoma patients in peripheral T lymphocytes |
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| Relations |
| BioSample |
SAMN25002999 |
| SRA |
SRX13790818 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5819419_16_12-2_analysis.clonotypes.ALL.txt.gz |
111.0 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.IGH.txt.gz |
2.8 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.IGK.txt.gz |
1.3 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.IGL.txt.gz |
2.1 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.TRA.txt.gz |
31.4 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.TRB.txt.gz |
65.4 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.TRD.txt.gz |
31.4 Kb |
(ftp)(http) |
TXT |
| GSM5819419_16_12-2_analysis.clonotypes.TRG.txt.gz |
2.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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