|
| Status |
Public on Dec 03, 2021 |
| Title |
TS188 TruSeq |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
disease: Tuberous sclerosis complex
library type: TruSeq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the peripheral blood mononuclear cells which were obtained from a patient with tuberous sclerosis complex was extracted with TRIzol reagent (Thermo Fisher Scientific) according to manufacturer instructions.
The libraries were constructed using the TruSeq stranded mRNA Library Prep Kit, SMART-Seq v4 ultra-low input RNA kit and TeloPrime Full-Lenth cDNA Amplification Kit V2 according to manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
The fastq fieles were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM) and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Dec 04, 2021 |
| Contact name |
Hiroki Ura |
| E-mail(s) |
h-ura@kanazawa-med.ac.jp
|
| Organization name |
Kanazawa Medical University Hospital
|
| Lab |
Center for Clinical Genomics
|
| Street address |
1-1 Daigaku
|
| City |
Uchinada |
| State/province |
Ishikawa |
| ZIP/Postal code |
920-0293 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE189019 |
Library comparison between TruSeq, SMARTer and TeloPrime |
|
| Relations |
| BioSample |
SAMN23242605 |
| SRA |
SRX13156529 |
