|
| Status |
Public on Jun 15, 2019 |
| Title |
ONT_K562_2 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Lymphoblastoid cell line
cell line: K562
|
| Growth protocol |
ENCODE protocols cell line specific
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNAeasy
Total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
S24_K562_ont_talon_abundance.tsv
|
| Data processing |
Fast5 basecalled with Albacore
Mapping was done using Minimap2 settings for direct-RNA seq
TranscriptClean was used for error correction using the default settings. The splice junction file was obtained using GENCODE v29 using one of the accesory scripts
TALON was used for annotation and quantification. The database was initialized with GENCODE v29
Genome_build: hg38
Supplementary_files_format_and_content: TSV table format;transcript counts
|
| |
|
| Submission date |
Jun 14, 2019 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Ali Mortazavi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California: Irvine
|
| Department |
Developmental and Cell Biology
|
| Lab |
Mortazavi Lab
|
| Street address |
2218 Biological Sciences III
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE132766 |
A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification |
|
| Relations |
| BioSample |
SAMN12060007 |
| SRA |
SRX6073163 |
