|
Status |
Public on Aug 15, 2019 |
Title |
DKO-control_treament_replicate2 |
Sample type |
SRA |
|
|
Source name |
DKO-control_treament
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEK293T cell type: human embryonic kidney Cells genotype/variation: TUT4 and TUT7 Double Knockout
|
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 |
polyA 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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
DKO_control_replicate2
|
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)
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|
|
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 |
GPL11154 |
Series (1) |
GSE121327 |
3’ Uridylation Expands miRNA Target Repertoire |
|
Relations |
BioSample |
SAMN10246770 |
SRA |
SRX4892406 |