|
| Status |
Public on May 08, 2024 |
| Title |
AdHBV_persistent_CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse11_liver |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cells.nuclei.targeted: 100
cell type: CXCR6pos_CX3CR1pos_CD45_1pos_CD8
simpletreatment: AdHBV_persistent
treatment: persistent AdHBV infection
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
100 cells were directly sorted into 96 well plates prepared with 1X Reaction Buffer consisting of lysis buffer and RNase Inhibitor for low input RNA sequencing (Takara Bio USA). Plates were spun down and immediately stored on dry ice or at -80°C until further processing.
Sample plates containing lysed cells were subjected to cDNA library preparation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, USA) followed by sequencing library preparation using the Nextera XT DNA Library Preparation Kit (Illumina) as per manufacturer’s instructions with minor modifications. Briefly, full-length cDNA was generated by reverse-transcription, template-switching reaction and PCR pre-amplification of polyadenylated mRNA as previously described (Picelli et al. 2013). cDNA libraries were quantified using the Qubit dsDNA High Sensitivity Kit and quality was assessed on a Bioanalyzer using DNA High Sensitivity chips (Agilent Technologies). Double-stranded cDNA was subjected to fragmentation and PCR-based addition of Illumina barcoded sequencing adapters at both fragment ends. Sequencing library quantity and quality was assessed as described above.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse11_liver
AdHBV_persistent__liver__CXCR6pos_CX3CR1pos_CD45_1pos_CD8
|
| Data processing |
We mapped reads to mouse referenge genome mm10 provided by NCBI with bksnake, a Roche-internal analysis pipeline.
Differential gene expresison analysis was performed with edgeR.
Assembly: mm10
Supplementary files format and content: 20220925-RocheTUM-HBVTcells-counts.gct: gene count table, in GCT format
Supplementary files format and content: 20220925-RocheTUM-HBVTcells-sampleAnnotation.tsv: sample annotation, in TSV format
Supplementary files format and content: 20220925-RocheTUM-HBVTcells-featureAnnotation.tsv: feature annotation, in TSV format
|
| |
|
| Submission date |
Sep 25, 2022 |
| Last update date |
May 08, 2024 |
| Contact name |
Jitao David Zhang |
| E-mail(s) |
jitao_david.zhang@roche.com
|
| Phone |
+41616886251
|
| Organization name |
F. Hoffmann-La Roche
|
| Department |
Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel
|
| Lab |
Pharmaceutical Sciences
|
| Street address |
Grenzacherstrasse 124
|
| City |
Basel |
| ZIP/Postal code |
4070 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE214151 |
HBcore-specific CXCR6+CD8 T cells during persistent HBV replication in mice lose their effector function and have high CREM activity |
|
| Relations |
| BioSample |
SAMN31012567 |
| SRA |
SRX17704017 |
