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| Status |
Public on Mar 01, 2023 |
| Title |
donor 3 2016 D28 FcRL5+ H1+ MBC |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
donor: 3
tissue: blood
cell type: H1 Tetramer+ FcRL5+ IgD- B Cell
treatment: influenza vaccine
vaccine year: 2016
days post vaccine: 28
number of_cells: 3975
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| Treatment protocol |
n/a
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNA-micro kit was used to extract RNA from all samples.
Amplification of BCR using primers specific for VH1-7 and constant region as per PMID 26006614.
Amplification using Illumina MiSeq v3 600 cycle reagents and tags.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
17
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz
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| Data processing |
Join forward and reverse reads with FastqJoin: Aronesty E (2011) eaUtils: Command line tools for processing biological sequencing data. https://expressionanalysis.github.io/ea-utils/
Apply quality filtering to joined reads: sequences with <= 200bp were omitted, as were those with low quality bases, >0bp with scores < 10, >=5bp with scores < 20 or >=15bp with quality scores < 30.
Determine isotypes of each sequence by searching against list of IgA, IgG and IgM sequences.
Submitting sequences to IMGT/High V-QUEST for V(D)J gene annotation and mutation statistics (Alamyar et al., 2012; PMID 22665256).
Clustering annotated sequences into lineages - sequences with same V annotation, J annotation, CDR3 length and >= 85% CDR3 nucleotide sequence similarity (see Tipton et al., 2015; PMID 26006014).
Write IMGT output tables with isotypes and lineage assignments into SQLite databases for in-house developed downstream analysis tools.
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs (table does not include day 120 IgD- memory).
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs (table does not include day 120 IgD- memory).
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs (table does not include day 120 IgD- memory).
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_1_HD52_day_120_1FG.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs; this table only includes early HA-specific memory and day 120 IgD- memory.
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_2_HD54_day_120_1FG.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs; this table only includes early HA-specific memory and day 120 IgD- memory.
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_3_HD46_day_120_1FG.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs; this table only includes early HA-specific memory and day 120 IgD- memory.
Library strategy: Rep-Seq
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| Submission date |
Jan 09, 2023 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Alexander Rosenberg |
| E-mail(s) |
afr@uab.edu
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| Organization name |
University of Alabama at Birmingham
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| Street address |
1720 2nd Avenue South, Suite 276/11
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL15520 |
| Series (2) |
| GSE222474 |
Influenza-specific effector memory B cells predict long-lived antibody responses to vaccination in humans [Rep-Seq] |
| GSE222476 |
Influenza-specific effector memory B cells predict long-lived antibody responses to vaccination in humans |
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| Relations |
| BioSample |
SAMN32644344 |
| SRA |
SRX18980792 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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