|
| Status |
Public on Jul 08, 2024 |
| Title |
DFLR LCL, bulk fraction, c3-2 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell line: LCL
cell type: EBV-transformed B cell
genotype: WT
fraction: Bulk
|
| Treatment protocol |
For BCR stimulation, LCLs were seeded at 300,000 cells/mL in culture media and treated with μg/mL AffiniPure F(ab)2 anti-human pan-Ig antibody (Jackson ImmunoResearch) for 72 hours
40,000 BCR-stimulated LCLs were sorted by FACS directly into TRIzol-LS (Thermo-Fisher) containing 1:125 dilution of 1 μL ERCC Spike-In RNA (Invitrogen)
|
| Growth protocol |
LCLs were maintained in RPMI 1640 supplemented with 10% FBS and 1% penicillin-streptomycin in a humidified atmosphere at 37°C with 5% CO2 at 37°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using the Direct-Zol RNA mini prep kit (Zymo Research) with the optional on-column DNase treatment.
PolyA-enriched strand-specific libraries were generated using the Illumina TruSeq Stranded mRNA kit, followed by 101 bp paired-end sequencing on the Illumina NovaSeq 6000 system. Library preparation and sequencing was performed by the Yale Center for Genome Analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
NASA GeneLab RNA-seq consensus pipeline (PMID: 33870146)
Sequence reads were mapped using STAR v2.7.6a following the parameters outlined in the NASA GeneLab RNA-seq consensus piepline
Read count and normalization was performed using RSEM v1.3.1 following the parameters outlined in the NASA GeneLab RNA-seq consensus pipeline
Assembly: GENCODE GRCh38 primary assembly (p14 genome and v45 annotation)
Assembly: ERCC genome and annotation (Thermo-Fisher
Assembly: DFLR M81 (derived from GenBank: KF373730)
Supplementary files format and content: RSEM output for gene-level expression of individual samples
Supplementary files format and content: RSEM output for isoform-level expression of individual samples
|
| |
|
| Submission date |
Jul 08, 2024 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Alejandro Casco |
| E-mail(s) |
casco@wisc.edu
|
| Phone |
2812530570
|
| Organization name |
University of Wisconsin-Madison
|
| Street address |
1111 Highland Ave
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE271717 |
Epstein-Barr virus induces host shutoff extensively via BGLF5-independent mechanisms [RNA-seq] |
|
| Relations |
| BioSample |
SAMN42370962 |
| SRA |
SRX25236719 |
