|
| Status |
Public on May 10, 2022 |
| Title |
Germinal Center B cell Donor 180 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Germinal Center B cell Donor 180
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Sorted Germinal Center B Cells from Tonsil
markers: CD19+CD21+CD38+IgD-CD27-
|
| Biomaterial provider |
Children’s Hospital of Philadelphia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tonsillar mononuclear cells were isolated from tissues by mechanical disruption (tonsils were minced and pressed through a 70-micron cell screen) followed by Ficoll-Paque centrifugation
RNA was isolated from ~1 million of each cell type using Trizol Re- agent (Invitrogen), purified using the Directzol RNA Miniprep Kit (Zymo Research), and depleted of contaminating genomic DNA using DNAse I. Purified RNA was checked for quality on a Bioanlayzer 2100 using the Nano RNA Chip and samples with RIN>7 were used for RNA-seq library preparation. RNA samples were depleted of rRNA using QIAseq Fastselect RNA removal kit (Qiagen).
RNA samples were depleted of rRNA using the QIAseq FastSelect RNA Removal Kit then processed into libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Quality and quantity of the libraries was measured using the Bioanalyzer 2100 DNA chip and Qubit Fluorometer. Libraries were pooled and sequenced on the NovaSeq 6000 platform using paired-end 51bp reads at the Center for Spatial and Functional Genomics at CHOP.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Bases were called using Illumina bcl2fastq2 conversion v2.29
TPM values of bulk RNA-seq data were calculated using the pseudo-aligner Kallisto quant 0.46.2 with fastq files with the default parameters except with --rf-stranded set
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes TPM for each sample
|
| |
|
| Submission date |
May 18, 2021 |
| Last update date |
May 10, 2022 |
| Contact name |
Matthew C Pahl |
| E-mail(s) |
pahlm@email.chop.edu
|
| Phone |
5704282303
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Center for Spatial and Functional Genomics
|
| Lab |
Struan Grant and Andrew Wells
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE174657 |
Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types [RNA-seq] |
| GSE174658 |
Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types |
|
| Relations |
| BioSample |
SAMN19245027 |
| SRA |
SRX10928330 |
