|
| Status |
Public on Jun 10, 2016 |
| Title |
Sample_194 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8+ T cells
subpopulation: CD62L-CX3CR1+
|
| Growth protocol |
Cells were isolated from peripheral blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kit v2 was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences.
Paired-end fastq-files of two separate runs for each sample were aligned separately using TopHat v2.0.1.1.
BAM files from both alignments were merged using samtools to obtain a single BAM alignment file for each sample.
mRNA quantification was performed according to RefSeq Transcripts - 2014-07-30 using Partek® Genomics Suite® (PGS) software v6.6©.
Raw read counts were normalized by DESeq2 method.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes DESeq2 normalized expression values for each sample.
|
| |
|
| Submission date |
Nov 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15433 |
| Series (2) |
| GSE63144 |
CX3CR1/Fractalkine receptor expression separates memory CD8+ T cells with distinct functional profiles (RNA-seq) |
| GSE63147 |
CX3CR1/Fractalkine receptor expression separates memory CD8+ T cells with distinct functional profiles |
|
| Relations |
| BioSample |
SAMN03174525 |
| SRA |
SRX756972 |
