|
| Status |
Public on May 05, 2021 |
| Title |
ERCC synthetic RNA/Hela Total RNA 1 |
| Sample type |
SRA |
| |
|
| Source name |
Synthetic/Cell line
|
| Organisms |
Homo sapiens; synthetic construct |
| Characteristics |
tissue: Synthetic/Cell line
patient: Synthetic/Cell line
sample: Synthetic/Cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was obtained from ThermoFisher Scientific
LoopSeq sequencing libraries were prepared using LoopSeq Transcriptome Kit according to manufacturer’s protocol except when specified. 10 ng of total RNA from Hela Total RNA, 0.5ng of ERCC synthetic RNA, or a mixture of the two RNA sources were reverse transcribed and barcoded using LoopSeq Transcriptome Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: LoopSeq
Long reads were mapped to refseq RNA with human gene annotation or ERCC reference sequences by LoopSeq pipeline
Full-length sequences were extracted and compared with reference sequences to determine TSS and TTS using custom script
Full-length sequences were extracted, and the end sequences were compared to the reference mapping of the contig and with each other for chimera determination
Full-length sequences of contigs mapping to ERCC-0002 were extracted and aligned against the reference sequence to generate a variance table using Sequencher 5.4.6.
Genome_build: hg38
Supplementary_files_format_and_content: csv or xlsx files for analysis summary
|
| |
|
| Submission date |
Aug 08, 2020 |
| Last update date |
May 05, 2021 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
203 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL28989 |
| Series (2) |
| GSE155920 |
LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [Loop QC] |
| GSE155921 |
LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer |
|
| Relations |
| BioSample |
SAMN15767939 |
| SRA |
SRX8912273 |
