|
| Status |
Public on Jul 03, 2019 |
| Title |
ToxKO_Day8_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ToxKO_Day8
|
| Organism |
Mus musculus |
| Characteristics |
cell type: T-cells
genotype: Tox KO
developmental stage: P14
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Agencourt RNAdvance Cell v2 kit (A47942, Beckman Coulter). RNA integrity number (RIN) and yield were assessed using RNA 6000 Pico Kit (5067-1513, Agilent).
cDNA synthesis and PCR amplification using 1 ng of total RNA from each sample was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634891, Takara/Clontech). After cDNA synthesis, each sample was subjected to 12 cycles of PCR amplification. The generated amplicons were assessed and their concentration was determined with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). 150 pg of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). After PCR amplification of the fragmented libraries, the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 µl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010, Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
name in processed data file:
L26-Seq29-FA-13-KO-I
|
| Data processing |
Sequencing quality was assessed with fastqc
Filtering was performed by trimmomatic v0.36
Mapping was performed by STAR v2.5.3a with genome Mus_musculus.GRCm38
Counting by htseq v0.9.1 with annotation Mus_musculus.GRCm38.91
multiqc v1.2 was applied for supervising results from STAR and fastqc
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include raw and normalized readcount values for each Sample
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Jul 09, 2019 |
| Contact name |
Dietmar Zehn |
| E-mail(s) |
[email protected]
|
| Phone |
+49 8161 71 3508
|
| Organization name |
Technical University of Munich
|
| Department |
Division of Animal Physiology and Immunology
|
| Street address |
Weihenstephaner Berg 3
|
| City |
Freising |
| ZIP/Postal code |
85354 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE131643 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection |
| GSE132030 |
Tox reinforces the phenotype and longevity of dysfunctional T cell populations during chronic viral infection [KO vs WT Day 8] |
|
| Relations |
| BioSample |
SAMN11909884 |
| SRA |
SRX5938640 |
