|
| Status |
Public on Mar 01, 2023 |
| Title |
P54d7_FcrL5neg_TETpos_IgDneg_MBC_1 |
| Sample type |
SRA |
| |
|
| Source name |
FCRL5 negative HA+IgD neg B cell
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: 54
Sex: Male
sorting markers: IgDneg CD38 lo/med CD19+ CD3 neg CD4 neg
h1 tetramer: positive
tissue: PBMC
days post influenza pr8 infection: 7
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were FACS sorted from PBMCs according to the indicated sort markers into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
geneRpkm.detected.csv
|
| Data processing |
Raw sequencing reads were mapped to the hg38 using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to fragments per kilobase per million (FPKM). Genes were filtered for detection based on being expressed at greater than or equal to 10 reads per million in all samples for at least one group.
Genome_build: hg38
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.
|
| |
|
| Submission date |
Dec 29, 2020 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Chris Scharer |
| E-mail(s) |
cdschar@emory.edu
|
| Organization name |
Emory University
|
| Department |
Microbiology and Immunology
|
| Lab |
Chris Scharer
|
| Street address |
1510 Clifton Rd, Suite 3086A
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE163989 |
Transcriptome differences in FCRL5 positive and negative Influenza-specific memory B cells |
| GSE222476 |
Influenza-specific effector memory B cells predict long-lived antibody responses to vaccination in humans |
|
| Relations |
| BioSample |
SAMN17178104 |
| SRA |
SRX9751577 |
