Submission S00004 (Davide Bagnara)
Submission Details
| Submission ID | S00004 |
| Submission Date | 2018-11-16 00:00:00 |
| Submission Status | complete |
| Submitter | Davide Bagnara |
| Submitter Address | davide.bagnara@edu.unige.it |
| Species | Homo sapiens |
| Ethnicity | UN |
Inferred Sequences
The inferred novel alleles from each genotype that are submitted for review. This table lists all inferences put forward by the submitter. Where IARC has affirmed a sequence based on an inference, the corresponding sequence record will be listed in the Published column. Inferences for which no published sequence is shown have not been affirmed.
Genotypes
Each genotype that has been inferred, along with the descriptive name of the inference tool and settings that were used.
| Genotype Name | Subject ID | Locus | Sequence Type | Genotype Filename | Tool/Setting Name | |
|---|---|---|---|---|---|---|
| B12 | B12 | IGH | V | ISS_IARC001_gen.csv | IgDiscover |
Acknowledgements
Individuals who should be acknowledged as contributing to the inferences listed in this submission.
| Name | Institution | ORCID ID |
|---|---|---|
| Martin Corcoran | Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institute, Stockholm Sweden. |
Repertoire Details
Details of the repertoire from which the inferences are based. This corresponds, for example, to an NIH Project or an ENA study.
| Repository | NCBI SRA |
| Accession Number | PRJNA381394 |
| Project/Study Title | Ig-seq_method |
| Dataset URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA381394 |
| MiAIRR Compliant? | No |
| MiAIRR URL | |
| Sequencing Platform | Miseq |
| Read Length | R1=325 R2=285 |
| Primers Overlapping? | No |
Repertoire Publications
Publications associated with this study.
| PubMed ID | Title | Authors |
|---|---|---|
| 28959265 | Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution. | Vergani S, Korsunsky I, Mazzarello AN, Ferrer G, Chiorazzi N, Bagnara D |
Sequences of the PCR primers used in the study.
RV CH region
reverse primers on the CH region (IgM, IgG, IgA) used for PCR amplification
| Primer Name | Primer Sequence |
|---|---|
| HCA-n2m | GGGAAGACCTTGGGGCTGGT |
| HCM-n2m | AAAGGGTTGGGGCGGATGC |
| HCG-n2m | GGAAGACCGATGGGCCCTT |
FW Leader Primers
| Primer Name | Primer Sequence |
|---|---|
| L3_VH1* | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCAACTACAGGTGCCCACTCC |
| L3_VH1-46 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNTAGCTCCAGGTGCTCACTCC |
| L3_VH1-69 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNNCAGCYACAGGTGTCCASTCC |
| L3_VH1-2 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCMACAGGWGCCCACTCC |
| L3_VH1-45 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNAGCCACAGATGCCTACTCC |
| L3_VH1-24 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNCTACAGGCACCCACGCC |
| L3_VH2 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNCCKTCCTGGGTCTTRTCC |
| L3_VH2-70*09 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCCTTCATGGGTCTTGTCT |
| L3_VH3* | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNTTWAAAGGTGTCCAGTGTGARG |
| L3_VH3-30/33/11 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNWTAARAGGTGTCCAGTGTCAGG |
| L3_VH4 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCCAGATGGGTCCTGYCC |
| L3_VH5-51 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNTTCTCCAAGGAGTCTGTKCC |
| L3_VH6-1 | GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCCATGGGGTGTCCTGTCA |
Inference Tools and Settings
Details of the inference tools and settings used to infer novel alleles. Each combination of tool and setting is listed here, and provided with a descriptive name.
| Tool/Settings Name | Tool Name | Tool Version | |
|---|---|---|---|
| IgDiscover | IgDiscover | 0.8.0+188.g8b9dbd8 |
Notes
No notes provided