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Sample GSM2723939 Query DataSets for GSM2723939
Status Public on Jan 31, 2018
Title BPS1
Sample type SRA
 
Source name B95-8 d472 LCL
Organism Homo sapiens
Characteristics size selection: 800- 2000 bp
cell type: Epstein-barr B95-9 infected Lymphoblastoid cell line (LCL)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent.
50 μg total RNA was mixed with 250 pmol of the W2 probe (5’-CTTCTTAGGAGCTGTCCGAG-3’). RNA and probe were heated to 95°C for 5 min and then allowed to slowly cool to room temperature. 20 μl MyOne Streptavidin C1 Dynabeads (ThermoFisher Scientific) beads washed and resuspend in 2x streptavidin binding buffer as described above. RNA annealed to probe and beads were mixed and rotated at room temperature for 30 min. Beads were washed with wash buffer as described in section 3.5.8. Isolated transcripts were released from the beads by resuspending the beads in 100 μl wash buffer, heating to 95°C for 5 min and immediately adding to a magnet and collecting the supernatant. Isolated transcripts were then reprecipitated and resuspended in 20 μl water. Transcripts were then subject to an Iso-seq cDNA library preparation using the SMARTer PCR cDNA synthesis kit (Clontech) and size selected for 800 - 2 kb and 2 kb+ sized transcripts. SMRTbell adapters were then added to the isolated libraries.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model PacBio RS II
 
Description primary B cell transformed with the B95-8 EBV strain to generate a lymphoblastoid cell line (LCL)
Data processing Library strategy: Iso-Seq
Full length non-chimeric (flnc) reads generated using RS_IsoSeq
flnc reads aligned to the human genome (hg19) using GMAP
flnc reads that failed to align to the human genome were aligned to the B95.8 EBV genome (V01555.2)
Genome_build: hg19; V01555.2
Supplementary_files_format_and_content: bed files; human and EBV GMAP alignments on sample records, Excel file with quantified alignments on series record.
 
Submission date Jul 31, 2017
Last update date May 15, 2019
Contact name Bryan Cullen
E-mail(s) bryan.cullen@duke.edu
Phone 9196845656
Organization name Duke University
Department MGM
Street address 213 Research Dr., 0045 CARL Bldg.
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL21311
Series (1)
GSE102102 PacBio sequencing of Cp/Wp-driven transcripts from B95-8 LCLs
Relations
BioSample SAMN07430082
SRA SRX3051416

Supplementary file Size Download File type/resource
GSM2723939_BPS1_EBVposthg19_FINAL.bed.gz 505 b (ftp)(http) BED
GSM2723939_BPS1_hg19.bed.gz 505.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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