NBDC Research ID: hum0469.v1
SUMMARY
Aims: In utero CMV infection is the most frequent perinatal viral infection causing neurological sequelae in infants. When a pregnant woman is first infected with CMV, approximately 40% of cases cross the placenta, resulting in congenital CMV infection. In this study, we focused on the maternal immune response to CMV infection and analyzed the clonality of B cell receptors (BCR) and T cell receptors (TCR) that react to CMV-derived antigen peptides to elucidate their functions and characteristics, and to investigate the usefulness of current screening methods for mother-to-child CMV infection. The aim is to examine the usefulness of current screening methods for mother-to-child transmission of CMV, and to develop vaccines and treatments.
Methods: PBMCs were used for single-cell RNA sequence analysis.
Participants/Materials: Pregnant women undergoing early pregnancy screening (around 12 weeks' gestation) at the University of Tokyo Hospital
4 specimens around 12 weeks, 7 specimens around 20 weeks, 1 specimen at 28 weeks, 3 specimens around 36 weeks
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000728 | NGS (scRNA-seq) | Controlled-access (Type I) | 2024/08/14 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
Pregnant women undergoing early pregnancy screening (ICD10: O35.3): 10 cases 15 samples a pair at 12 weeks and 20 weeks: 1 case a pair at 12 weeks and 36 weeks: 1 case a pair at 20 weeks and 36 weeks: 2 cases a pair at 20 weeks and 28 weeks: 1 case 2 specimens around 12 weeks 3 specimens around 20 weeks |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD8+ T cells |
| Cell Lines | - |
| Library Construction (kit name) |
Chromium Next GEM Chip G Single Cell Kit Chromium Next GEM Single Cell 5ʹ Library and Gel Bead Kit v2 Chromium Single Cell V(D)J |
| Fragmentation Methods | according to manufacturers' instructions |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 28×90 bp |
| Software |
- Cell Ranger v6.1.2 (10x Genomics) with the “multi” option - Python package Scanpy v1.9.3 (scRNA-seq analysis)、Scirpy v0.13.0 (TCR genotyping) |
| Reference Genome Sequence | GRCh38 |
| QC |
the following criteria were excluded: - Number of expressed genes: < 1000 or > 4000 - Total count of gene expression: < 2000 or > 10,000 - Mitochondrial gene expression percentage: > 10% - TCR fragment genes |
| Gene Number | 36,601 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000861 |
| Total Data Volume | 71.5 GB (fastq, csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Mari Ichinose
Affiliation: Obstetrics and Gynecology, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Kanzawa Medical Research Foundation | Elucidation of immunokinetics and development of diagnostic modality for congenital cytomegalovirus infection by antigen-specific T cell profiling at single cell level | - |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Development, validation, and application of machine learning system for TCR epitope prediction | 20K06610 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multifaceted profiling of virus-specific CD8 T cells reveals distinct immune signatures against cytomegalovirus infection states during pregnancy | JGAD000861 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
