|
| Status |
Public on May 01, 2023 |
| Title |
circMLLe9-10_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T cells
genotype/variation: circular RNA overexpression (circMLLe9-10)
|
| Treatment protocol |
Briefly, circMLLexon9-10 overexpression constructs (in pcDNA3.1 vector backbone) or the empty pcDNA3.1 vector were transfected into HEK 293T cells using lipofectamine 2000, with 1 x 107 cells fixed at 24 hrs post-transfection. Overexpression was confirmed by RT-PCR.
|
| Growth protocol |
Cell lines were grown in DMEM with 10% FBS at 37oC, with 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using phenol chloroform as per van de Werken et al (2012) Methods Enzymology 513: 89-112. The MLL genomic region targeted as the bait was hg38 chr11:118,484,077-118,484,578, exploiting primary and secondary restriction enzyme NlaII and BglII, respectively.
As per van de Werken et al (2012) Methods Enzymology 513: 89-112
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CCG_B4
|
| Data processing |
Library strategy: 4C-Seq
High-throughput sequencing was performed using Illumina NextSeq (SE100).
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.13, setting minimum-length option to 15, error-rate 0.2 and overlap 5.
The resulting FASTQ files were mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm (version 2.7.0e)
The resulting STAR produced alignment BAM file for each sample used for counting the reads mapped to genes using featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample
|
| |
|
| Submission date |
Aug 15, 2019 |
| Last update date |
May 01, 2023 |
| Contact name |
Simon Conn |
| E-mail(s) |
simon.conn@flinders.edu.au
|
| Organization name |
Flinders University
|
| Department |
College of Medicine and Public Health
|
| Lab |
Circular RNAs in Cancer Laboratory
|
| Street address |
Sturt Road, Bedford Park
|
| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE135872 |
4C analysis with circular RNA overexpression |
|
| Relations |
| BioSample |
SAMN12583366 |
| SRA |
SRX6720387 |
