|
| Status |
Public on Aug 15, 2019 |
| Title |
HEK293T-endogenous-miRNAs rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T-endogenous-miRNAs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: human embryonic kidney Cells
genotype/variation: WT
|
| Treatment protocol |
HEK293T and DKO cells were transfected with Lipofectamine 3000 (Life Technologies) according to the manufacturer's’ instructions
|
| Growth protocol |
HEK293T cells were maintained in DMEM (high glucose) (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1X MEM Non-Essential Amino Acids (Gibco), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco). HEK293T-TUT4/TUT7 DKO cells were generated by using CRISPR/Cas9.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted by using Trizol.
Sequencing libraries were constructed by either Illumina® TruSeq® RNA sample preparation kit or NEBNext® Multiplex Small RNA Library Prep Set according to the manufacturer's’ protocol with minor modifications.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
293T-endo-1
|
| Data processing |
3ʹ adaptor sequences were removed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 18 nt were discarded
For miRNA isoform analyses based on small-RNA-seq, QuagmiR (on Seven Bridges Cancer Genomics Cloud) was used with default or custermized motif files
For gene expression analyses based on RNA-seq, Raw reads were aligned to the human genome (GRCh37.75) using STAR 2.5.1.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: 1) isomiR profile (tsv files) (small-RNA-seq) 2) gene expression counts (tab files) (RNA-seq)
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Shuo Gu |
| E-mail(s) |
shuo.gu@nih.gov
|
| Phone |
3018465447
|
| Organization name |
National Cancer Institute
|
| Lab |
RNA Biology Lab
|
| Street address |
1050 Boyles Str. Building 560 Room 11-6B
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE121327 |
3’ Uridylation Expands miRNA Target Repertoire |
|
| Relations |
| BioSample |
SAMN10246788 |
| SRA |
SRX4892388 |
