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Sample GSM8383386 Query DataSets for GSM8383386
Status Public on Jul 08, 2024
Title DFLR LCL, bulk fraction, c4-1
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 SAMN42370954
SRA SRX25236727

Supplementary file Size Download File type/resource
GSM8383386_WT_17.genes.results.gz 1.8 Mb (ftp)(http) RESULTS
GSM8383386_WT_17.isoforms.results.gz 3.8 Mb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA

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