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Sample GSM2483344 Query DataSets for GSM2483344
Status Public on Mar 01, 2017
Title Sample EBV3 capture replicate 2 with 50.0 ng cDNA input in experiment 2 by experimentalist 1
Sample type SRA
 
Source name EBV-transformed lymphocytes (LCLs)
Organism Homo sapiens
Characteristics cell type: LCL
amount cdna (ng) input used for smmip capture: 50
number of pcr cycles: 21
cdna sample id: EBV3-cDNA-2
Treatment protocol Except for the PBMC stimulation experiment, cells were not stimulated. In the PBMC experiment, cells were stimulated with heat-killed Candida Albicans.
Growth protocol Primary cells and cell lines were grown according to the description provided for each sample.
Extracted molecule total RNA
Extraction protocol The isolated total RNA was quantified using the Qubit RNA HS assay kit (Thermo Fisher Scientific, Waltham, MA, USA). cDNA synthesis of 2-5 µg of RNA was performed with iScript (BIO-RAD, Hercules, CA, USA) reverse trancriptase. After cDNA synthesis, the cDNA was purified using Qiaquick (Qiagen, Venlo, The Netherlands) purification columns, and cDNA quantity was measured using the Qubit ssDNA assay kit (Thermo Fisher Scientific).
Single-molecule inversion probes applied to cDNA. Main steps are 1) MIP phosphorylation 2) MIP capture 3) Exonuclease treatment; 4) PCR amplification
Targeted RNA-Seq using cDNA-smMIPs
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Human B-lymphoblast cells of two anonymized healthy individuals were immortalized by transformation with the Eppstein?Barr virus. Cells were cultured in RPMI1640 medium (Sigma, St Louis, MO) containing 10% (vol/vol) Fetal Bovine Serum (Sigma), 1% 10?U/ul penicillin and 10 ug/ul streptomycin (Sigma), at a density of 0.5x10^6 cells/ml. Fresh medium was supplied twice a week.
processed data file:
all_samples_molecule_counts.txt
cdna_mips_geuvadis.txt
Data processing Match each read pair to a designed smMIP probe (allowing two mismatches);
Remove likely extension-ligation dimers;
For all reads assigned to a given smMIP probe, identify the molecule counts from the unique molecular identifiers;
Determine the read-dependent threshold for UMIs due to sequencing errors;
Estimate normalized expression levels from error-corrected molecule counts integrating replicates using a dedicated Bayesian model.
Genome_build: Reads for the HEK/K562 allelic ratio experiment were mapped to hg19. For all other experiments, no read mapping was performed.
Supplementary_files_format_and_content:
Tab-delimited file with molecule counts for each smMIP and sample, corrected and uncorrected for sequencing errors in the molecular identifiers.
all_samples_molecule_counts.txt: txt file with molecule counts for all experiments
cdna_mips_ercc.txt: txt file with probe design for ERCC experiments
cdna_mips_geuvadis.txt: txt file with probe design for PBMC and EBV experiments
cdna_mips_ase-K562-HEK293.txt: txt file with probe design for allelic ratio experiments
 
Submission date Feb 10, 2017
Last update date May 15, 2019
Contact name Kees Albers
E-mail(s) kees.albers@radboudumc.nl
Organization name Radboud University Medical Center
Department Human Genetics
Street address Geert Grooteplein 10
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
 
Platform ID GPL18573
Series (1)
GSE94800 Quantification of differential gene expression by multiplexed targeted resequencing of cDNA
Relations
BioSample SAMN06322192
SRA SRX2553301

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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