|
| Status |
Public on Sep 30, 2020 |
| Title |
Sample12809_Naive |
| Sample type |
SRA |
| |
|
| Source name |
Naïve B cells (CD21+CD27-)
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: adult living in Malaria-endemic Mali
subject id: Patient 2
age: 26 years
Sex: Male
tissue: Blood
cell type: Peripheral mononuclear blood cells (PBMCs)
cell subset: Naïve B cells (CD21+CD27-)
|
| Growth protocol |
Cell culture protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were further sorted into subsets by staining with fluorophore conjugated antibodies and FACS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with RLT buffer (Qiagen) and RNA was isolated using the Qiagen AllPrep 96 kit as per manufacturer's instructions except treatment with 27 units DNAse I to removegenomic DNA contamination. cDAN was synthesized using SMART-Seq v4 Ultra Low Input RNA kit
600 pg sheared cDNA was used as input into the low Inout Library Prep kit v2 (Clonetech/Takara Bio) and prepared following manufacturer's protocol Final NGS libraries were assessed on a BioAnalyzer 2100 using High Sensitivity Chips. The libraries were normalized to 0.5 nM, pooled equally and prepared for sequencing on the NextSeq (illumina, San Diego) following manufacturer's guidelines for two mid-output 2X76 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw NGS reads were trimmed to remove adapters and low-quality regions using Trimmomatic v0.33 and were aligned to the human hg38 reference genome and Gencode release 26 annotation using STAR v2.5.2b. Read and alignment quality were assessed using MultiQCv1.1 to aggregate QC metrics from Picard (http://broadinstitute.github.io/picard/), FastQC v0.11.5, FastQ screen v0.9.3 and RseQC v1.1.8. Gene-level expression was quantified using RSEM v1.3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: Text files generated using RSEM v1.3.0 containing raw counts and FPKM values.
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
Sep 30, 2020 |
| Contact name |
Arun Boddapati |
| E-mail(s) |
[email protected]
|
| Organization name |
Yerkes National Primate research center
|
| Department |
Genomics Core
|
| Street address |
954 Gatewood Road, NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE149727 |
Chronic Malaria drives functional heterogenity in B cell subpopulations and expansion of unswitched atypical memory B cells [Malaria bulkRNA-seq] |
| GSE149729 |
Chronic Malaria drives functional heterogenity in B cell subpopilations and expansion of unswitched atypical memory B cells |
|
| Relations |
| BioSample |
SAMN14791588 |
