GSM6600280: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse9_spleen; Mus... - SRA

SRX17704006: GSM6600280: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse9_spleen; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 22.1M spots, 2.2G bases, 743.7Mb downloads

External Id: GSM6600280_r1

Submitted by: Bioinformatics and Exploratory Data Analysis, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche

Study: HBcore-specific CXCR6+CD8 T cells during persistent HBV replication in mice lose their effector function and have high CREM activity

PRJNA884135 • SRP399537 • All experiments • All runs

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We investigated molecular profiles of CD8 T cells in persistent experimental Hepatitis B virus (HBV) infection. To this end, we established a preclinical in vivo model where HBV-replicating hepatocytes were cleared by virus-specific immunity after infection with 107 IU Ad-HBV, whereas persistent HBV replication developed after infection with 108 IU Ad-HBV, revealed by high serum HBeAg levels, high numbers of HBV genome copies and of HBcorepos hepatocytes in liver tissue. To overcome variable surface expression of the T cell receptor during chronic infection and unequivocally identify HBV-specific CD8 T cells, we adoptively transferred naïve CD45.1+HBcore-specific CD8 T cells from Cor93 transgenic mice (HBcoreCD8 T cells) the day before Ad-HBV infection. After clearance of HBV-replicating hepatocytes (d44 p.i.), liver CD45.1+HBcoreCD8 T cells expressed either CXCR6 or CX3CR1, and in the spleen only CX3CR1+ CD8 T cells were detected. Next, we evaluated the transcriptional profile of FACSorted HBcoreCD8 T cells after resolved compared to persistent infection employing SmartSeq2. The resulting dataset is reported here. Overall design: We compared expression profiles between subtypes of HBVcore-specific CD8 T cells in acute and chronic infection in either liver or spleen, and inferred gene regulatory networks underlying the observatios.

Sample: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse9_spleen

SAMN31012578 • SRS15234800 • All experiments • All runs

Organism: Mus musculus

Library:

Name: GSM6600280

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction 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.

Runs: 1 run, 22.1M spots, 2.2G bases, 743.7Mb

Run	# of Spots	# of Bases	Size	Published
SRR21706500	22,121,999	2.2G	743.7Mb	2024-05-08

ID:: 24606188

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