 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 07, 2023 |
| Title |
in vivo, HT_splenic CD8 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
sample type: in vivo
tissue: spleen
cell line: primary
cell type: CD8+ T
genotype: WT
treatment: heart transplantation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
IN VIVO All_samples_rpkm.txt
WTHT_S_CD8
|
| Data processing |
Illumina NovaSeq 6000 or DNBSEQ-T7 were used for basecalling. Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequencing data contains a number of connectors, low-quality Reads, fastp (v0.21.0) software was used to filter the sequencing data to get high quality sequence for further analysis .
Trimmed sequence reads were mapped to GRCh38 and GRCm38 using HISAT2 v2.1.0. (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
StringTie(v2.1.5) statistics were used to compare the Read Count values on each gene as the original expression of the gene, and FPKM were used to standardize the expression.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: RPKMs
|
| |
|
| Submission date |
Oct 27, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Xiaosheng Tan |
| E-mail(s) |
txs900416@hust.edu.cn
|
| Phone |
13871387473
|
| Organization name |
Huazhong university of science and technology
|
| Street address |
#1095, Jiefang Avenu
|
| City |
Wuhan |
| ZIP/Postal code |
430030 |
| Country |
China |
| |
|
| Platform ID |
GPL28330 |
| Series (1) |
| GSE216671 |
RNA-seq of T cell with/without lycorine treatment in vitro and RNA-seq of T cell in spleen and allograft |
|
| Relations |
| BioSample |
SAMN31476471 |
| SRA |
SRX18043643 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
