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Sample GSM2463825 Query DataSets for GSM2463825
Status Public on Jan 20, 2017
Title hsTestesPacbioPost
Sample type SRA
 
Source name Testes
Organism Homo sapiens
Characteristics tissue: Testes
developmental stage: adult
rna source: Ambion AM6000
Extracted molecule total RNA
Extraction protocol See Samples – RNA source
Ribo-depleted, oligodT-primed cDNA, barcoded, captured separately in human and mouse
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model PacBio RS II
 
Description “*Post*” and “*Pre*” contain post- and pre-capture data, respectively
Data processing Read mapping software: STAR v.2.4.0.1
Read merging: compmerge v.1.3
Genome_build: hg38, mm10
Supplementary_files_format_and_content: “Compmerge” BED files contain merged transcript models generated using compmerge on the BAM files produced by STAR, with PacBio reads as input. Four flavors are provided per sample: “*.all.bed”: all merged transcript models from confidently mapped reads, “*.cage+polyASupported.bed”: subset of “*all.bed” containing full-length (i.e., with CAGE support at their 5’ end and polyA support at their 3’ end) merged transcript models, “*.cageSupported.bed”: subset of “*all.bed” containing merged transcript models with 5’ end CAGE support, “*.polyASupported.bed”: subset of “*all.bed” containing merged transcript models with 3’ end polyA support
 
Submission date Jan 19, 2017
Last update date May 15, 2019
Contact name Julien Lagarde
E-mail(s) julienlag@gmail.com
Organization name CRG
Department Bioinformatics and Genomics
Lab Computational Biology of RNA Processing
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL21311
Series (1)
GSE93848 High-throughput manual-quality annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)
Relations
BioSample SAMN06242209
SRA SRX2505554

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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