|
| Status |
Public on Jun 30, 2022 |
| Title |
MT2_B2 |
| Sample type |
SRA |
| |
|
| Source name |
HBEC3kt MT2 cell isolate
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HBEC3kt
cell type: human bronchial epithelial cells (HBEC)
genotype/variation: U2AF1 S34F
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 1ug if RNA was reverse transcribed using Smart-Seq2 approach (polyA primed), and cDNA was sequencing using Oxford Nanopore minION using 1D sequencing approach.
RNA libraries were prepared for sequencing using standard Oxford Nanopore 1D suencing approaches (SQK-LSK108)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
RT using SmartSeq2
mut3_mt_b2
|
| Data processing |
Albabacore version 2.1.0 was used for basecalling with the options --flowcell FLO-MIN106 and --kit SQK-LSK108.
Sequenced reads were trimmed for adaptor sequence using Porechop.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurement; FLAIR GTF annotation file
|
| |
|
| Submission date |
Nov 20, 2019 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Angela N Brooks |
| E-mail(s) |
anbrooks@ucsc.edu
|
| Organization name |
University California Santa Cruz
|
| Department |
Biomolecular Engineering
|
| Street address |
1156 High Street
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE140734 |
Nanopore sequencing reveals isoform-specific alterations in human bronchial epithelial cells with U2AF1 S34F mutations |
|
| Relations |
| BioSample |
SAMN13337285 |
| SRA |
SRX7191852 |
