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Sample GSM3431505 Query DataSets for GSM3431505
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.
 
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)
 
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

Supplementary file Size Download File type/resource
GSM3431505_DKO_control_replicate2_1.tab.gz 318.3 Kb (ftp)(http) TAB
GSM3431505_DKO_control_replicate2_2.tab.gz 318.4 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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