|
| Status |
Public on Jul 09, 2021 |
| Title |
miRNA IGROV1-LIN28A positive-wildtype-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
IGROV1 ovarian cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
disease: ovarian cancer
genotype: LIN28A+; TUT4+; TUT7+
type: parental
passage number: P7
|
| Treatment protocol |
TUT4 (exon12) and TUT7 (exon 14) were targeted using CRISPR
|
| Growth protocol |
DU145 was routinely cultured in EMEM complete media (EMEM,10%FBS,1X NEAA, 1X antibiotics (Penicillin-streptomycin) and 1X sodium pyruvate) and IGROV1 was routinely cultured in RPMI complete media (RPMI-1640 ,10%FBS,1X NEAA and 1X antibiotics)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIsure (BIO-38033) followed by phenol-chloroform RNA extraction.
mRNA libraries were prepared after poly(A) selection using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads kit (NEB E7765S) and miRNA libraries were prepared from total RNA using NextFlex Small RNA-seq v3 kit (BIOO Scientific).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
i2
|
| Data processing |
Trim low quality reads and apapters: Trimmomatic V0.39 - ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
Remove ribosomal RNA: SortmeRNA
map to the reference genome: HISAT2 V2.1.0.
Count reads on features: htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-count files, mirDeep2 matrix and chimera output
|
| |
|
| Submission date |
Jul 08, 2021 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Jonathan Lewis Price |
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Inst.
|
| Lab |
Miska Lab
|
| Street address |
The Gurdon Inst. Tennis Court Road
|
| City |
cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE179741 |
RNA sequencing of wildtype and catalytic knockouts of TUT4/7 |
|
| Relations |
| BioSample |
SAMN20121792 |
| SRA |
SRX11380451 |
