|
| Status |
Public on Mar 28, 2024 |
| Title |
human primary T cell lymphoma MR01 |
| Sample type |
SRA |
| |
|
| Source name |
human primary T cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Anaplastic Large cell lymphoma (ALCL)
|
| Growth protocol |
No cultered cells were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared according to Illumina's TruSeq RNAseq protocol (Illumina, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total RNA
|
| Data processing |
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long paired-end reads were mapped to the reference human genome sequence, hg19, using Tophat2 aligner (Daehwan et al, Genome Biology 2013,14:R36) with the default parameters. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515) in the Tophat2 package.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values
|
| |
|
| Submission date |
Jun 18, 2018 |
| Last update date |
Mar 28, 2024 |
| Contact name |
Huimin Geng |
| E-mail(s) |
huimin.geng@ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Department of Laboratory Medicine
|
| Street address |
513 Parnassus Ave., MSB S-1480
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE115917 |
RNAseq of human primary T cell lymphoma |
|
| Relations |
| BioSample |
SAMN09435701 |
| SRA |
SRX4225813 |
