|
| Status |
Public on Jan 16, 2024 |
| Title |
DN2 KO2 |
| Sample type |
SRA |
| |
|
| Source name |
Arpp21 KO_thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: thymocytes
developmental stage: DN2
genotype: Arpp21 KO
|
| Treatment protocol |
The populations of DN2 and DN3 developmental stages are sorted by flow cytometry.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the NucleoSpin RNA kit (Macherey-Nagel).
Library preparation was performed using SmartSeq V4 with Nextera. The libraries were sequenced with a length of 150 bp, paired-end on an Illumina HiSeq1500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Raw reads processed with kallisto (version 0.46, default paramters) for calculation of read counts and TPM per gene
Assembly: GRCm38, Ensembl annotation version 101
Supplementary files format and content: Tab delimited file with estimated_counts and tpm values
|
| |
|
| Submission date |
Mar 16, 2022 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Taku Kureha |
| E-mail(s) |
Taku.Kureha@med.uni-muenchen.de
|
| Phone |
+49-(0)89-2180-71211
|
| Organization name |
Ludwig-Maximilians-Universität
|
| Department |
Institute for Immunology
|
| Lab |
Molecular Immune Regulation
|
| Street address |
Grosshaderner Str. 9
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE198797 |
The RNA-binding protein Arpp21 interacts with and promotes Rag1 target mRNA expression to enable TCR rearrangement [RNA-seq] |
| GSE198798 |
The RNA-binding protein Arpp21 interacts with and promotes Rag1 target mRNA expression to enable TCR rearrangement |
|
| Relations |
| BioSample |
SAMN26727453 |
| SRA |
SRX14503872 |
