Supporting data for "SCIGA: A software for large-scale, single-cell immunoglobulin repertories analysis"

Dataset type: Software, Bioinformatics
Data released on May 15, 2021

Ye H; Cheng L; Ju B; Xu G; Liu Y; Zhang S; Wang L; Zhang Z (2021): Supporting data for "SCIGA: A software for large-scale, single-cell immunoglobulin repertories analysis" GigaScience Database. http://dx.doi.org/10.5524/100893

DOI10.5524/100893

10X single-cell V(D)J sequencing enables the determining of B cell immunoglobulin repertoires with paired heavy- and light- chain. Precisely and quickly analyzing 10X single-cell immunoglobulin repertoires remains a challenge, due to the high diversity of immunoglobulin repertoires and the lack of specialized software that can analyze such diverse data. In this study, the SCIGA, a specialized software for 10X single-cell immunoglobulin repertoires analysis, was developed. SCIGA is an easy-to-use pipeline that performs reads trimming, immunoglobulin sequence assembling and annotating, heavy- and light- chain pairing, statistical analysis, visualization and integrating multiple samples, all by using one line command. SCIGA was then used to profile the single-cell immunoglobulin repertoires of nine coronavirus disease 2019 (COVID-19) patients. From these repertoires, four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. The single-cell V(D)J sequencing data used in our study is a part of another project.
All raw data has been reported to the Ministry of Science and Technology of People's Republic of China, the record-filing number is 2021BAT3238.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 34585238)

Github links:

https://github.com/sciensic/SCIGA

Accessions (data generated as part of this study):

BioProject: PRJNA682839





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
B19606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012605
Common name:human
...
+
B29606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012606
Common name:human
...
+
B39606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012607
Common name:human
...
+
B49606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012608
Common name:human
...
+
B59606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012609
Common name:human
...
+
B69606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012610
Common name:human
...
+
B79606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012611
Common name:human
...
+
B89606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012612
Common name:human
...
+
B99606HumanhumanHomo sapiens Description:RNA extracted and amplified for V(D)J ...
Alternative accession-BioSample:SAMN17012613
Common name:human
...
+
Displaying 1-9 of 9 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataCSV189.31 KB2021-04-30
Tabular dataCSV595.83 KB2021-04-30
Tabular dataCSV729.44 KB2021-04-30
Tabular dataCSV656.27 KB2021-04-30
Tabular dataCSV423.55 KB2021-04-30
Tabular dataCSV1.14 MB2021-04-30
Tabular dataCSV398.58 KB2021-04-30
Tabular dataCSV1.82 MB2021-04-30
Tabular dataCSV532.75 KB2021-04-30
Tabular dataTSV0.17 KB2021-04-30
Displaying 1-10 of 22 File(s).
Funding body Awardee Award ID Comments
National Science Fund for Distinguished Young Scholars Z Zhang 82025022
National Key Plan for Scientific Research and Development of China Z Zhang 2020YFC0848800
National Key Plan for Scientific Research and Development of China Z Zhang 2020YFC0844200
National Science and Technology Major Project of the Infectious Diseases Z Zhang & S Zhang 2018ZX10301404
Science and Technology Innovation Committee of Shenzhen Municipality Z Zhang 202002073000002
Science and Technology Innovation Committee of Shenzhen Municipality Z Zhang 2020A1111350032
Sanming Project for Medicine of Shenzhen L Wang SZSM201612053
National Natural Science Foundation of China B Ju 82002140
Natural Science Foundation of Guangdong Province of China B Ju 2019A1515011197
Science and Technology Innovation Committee of Shenzhen Municipality B Ju JCYJ20190809115617365
Date Action
June 15, 2021 Dataset publish
June 28, 2021 Manuscript Link added : 10.1093/gigascience/giab050
July 20, 2021 Dataset publish
September 15, 2021 Description updated from : 10X single-cell V(D)J sequencing enables the determining of B cell immunoglobulin repertoires with paired heavy- and light- chain. Precisely and quickly analyzing 10X single-cell immunoglobulin repertoires remains a challenge, due to the high diversity of immunoglobulin repertoires and the lack of specialized software that can analyze such diverse data. In this study, the SCIGA, a specialized software for 10X single-cell immunoglobulin repertoires analysis, was developed. SCIGA is an easy-to-use pipeline that performs reads trimming, immunoglobulin sequence assembling and annotating, heavy- and light- chain pairing, statistical analysis, visualization and integrating multiple samples, all by using one line command. SCIGA was then used to profile the single-cell immunoglobulin repertoires of nine coronavirus disease 2019 (COVID-19) patients. From these repertoires, four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. The single-cell V(D)J sequencing data used in our study is a part of another project. The data release has been approved by the Ministry of Science and Technology of the People's Republic of China under the ID number BF2021020504297.
November 29, 2021 Manuscript Link updated : 10.1093/gigascience/giab050