Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: RNA-seq of coding RNA from antibody variable regions isolated from cells of a single or nine (pooled) NP-CGG immunised mouse/mice to study reproducibility and robustness of the sequencing protocol in studying antibody repertoires      
availability:
available
aggregation:
instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
05-02-2014
ID:
E-MTAB-1896
description:
Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology by providing quantitative molecular information on polyclonal humoral immune responses. Reproducible and robust information on antibody repertoires is valuable for basic and applied immunology studies, thus it is essential to establish the reliability of antibody NGS data. Therefore, two conditions of immunological relevance were assessed for NGS reproducibility. First, we pooled spleen plasmablasts and plasma cells (CDR138-enriched) and bone marrow plasma cells (CD45R-depleted and CD138-enriched 4) of 1 mouse (1M) immunized with NP-CGG (chicken gamma globulin (CGG) conjugated to 4-hydroxy-3-nitrophenylacetyl) and sacrificed 14 days post-immunization (dpi). The thus created cell pool contained approximately 3 x 106 viable ASCs. Second, in order to model extreme antibody diversity, we repeated the same cell isolation procedure from 9 immunized mice (9M) resulting in an ASC pool of approximately 2.5 x 10^7 viable cells. From isolated cells, we recovered total RNA and used RT-PCR to amplify expressed rearranged IgG variable heavy VDJ genes; PCR was performed using a well-characterized and utilized primer set based on variable framework 1 region forward primers and one IgG constant region 1 reverse primer (covering all IgG isotypes) 43. Similarly to previously published methods (Vollmers et al., 2013, PNAS), Illumina adaptors were added during the PCR step by using a direct addition approach where adaptors are added at the 5’ end of the gene-specific portion of the primer set, thus circumventing the need for ligation of adaptors following PCR. For each of the two conditions (1M/9M), triplicates were prepared, where a triplicate signifies three separately indexed samples prepared from the same starting cDNA pool; thus variable region PCR was independently performed in each of the triplicates. All six samples (triplicates of 1M and 9M) were sequenced using the Illumina MiSeq platform with 250bp paired-end reads.
keywords:
RNA-seq of coding RNA
format:
HTML
storedIn:
Array Express
qualifier:
not compressed
accessType:
landing page
authorization:
none
authentication:
none
primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1896
format:
JSON
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-MTAB-1896.json
format:
XML
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-MTAB-1896.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/