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| Status |
Public on Jan 20, 2017 |
| Title |
hsHelaPacbioPost |
| Sample type |
SRA |
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| Source name |
Hela
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Hela
developmental stage: adult
rna source: Gingeras lab, CSHL (ENCODE cell cultures)
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| Extracted molecule |
total RNA |
| Extraction protocol |
See Samples – RNA source
Ribo-depleted, oligodT-primed cDNA, barcoded, captured separately in human and mouse
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
PacBio RS II |
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| Description |
“*Post*” and “*Pre*” contain post- and pre-capture data, respectively
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| 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
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| Submission date |
Jan 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Julien Lagarde |
| E-mail(s) |
julienlag@gmail.com
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| Organization name |
CRG
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| Department |
Bioinformatics and Genomics
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| Lab |
Computational Biology of RNA Processing
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| Street address |
Dr. Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platform ID |
GPL21311 |
| Series (1) |
| GSE93848 |
High-throughput manual-quality annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS) |
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| Relations |
| BioSample |
SAMN06242218 |
| SRA |
SRX2505545 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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