NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2768988 Query DataSets for GSM2768988
Status Public on Sep 01, 2020
Title 293T-MSA-3
Sample type SRA
 
Source name Embryonic kidney cells
Organism Homo sapiens
Characteristics cell type: Embryonic kidney cells
passage: 6-8
genotype: Dicer WT
treatment: control tRNA
Treatment protocol cells were treated with 20nM of control tRNA, nCAR/miR-34a-5p, or nCAR/miR-34a-3p and harvested 48h post-transfection
Growth protocol 293T and Dicer-KO 293T cells were maintained in DMEM media supplemented with 10% FBS and 10ug/ml gentamycin, routinely passaged, and plated onto 6-well plates for treatment
Extracted molecule total RNA
Extraction protocol RNA was harvested using TRIzol-chloroform.
Sequencing libraries were constructed by BGI following the BGI-500 kit, using 1 ug of total RNA subjected to isolation of small RNAs less than 30 nt by gel separation (15% Urea-PAGE). Small RNA fragments were ligated to adenylated 3’ adapters annealed to unique barcodes, followed by the ligation of 5’ adapters and reverse transcription (RT). Samples were pooled to make a single strand DNA circle (ssDNA circle) to yield the final small RNA library, after a second size selection by gel separation. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end reads of 50bp were read on the BGISEQ-500 platform.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model BGISEQ-500
 
Description 293T-MSA-3
match_MSA_107nt_matrix_ReadCount
Data processing Read counts of known miRNAs were analyzed using the miRDeep module
Read counts derived from transfected recombinant RNAs were mapped to sequence reads from FASTQ-formatted data to the using a PERL script
Differentially expressed miRNAs between phenotypes were computed using EdgeR. Parameters: P < 0.05 and log2CPM > 6.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts (CPM), fold change (FC), p-value, and FDR values generated by EdgeR.
 
Submission date Aug 31, 2017
Last update date Sep 01, 2020
Contact name Pui Yan Ho
E-mail(s) puiho@ucdavis.edu
Organization name UC Davis
Street address 2700 Stockton Blvd., Rm2120B
City Sacramento
State/province CA
ZIP/Postal code 95817
Country USA
 
Platform ID GPL23227
Series (2)
GSE103349 Alteration of miRNome by recombinant ncRNA agents
GSE104445 Alteration of miRNome and transcriptome by recombinant ncRNA agents
Relations
BioSample SAMN07585221
SRA SRX3151272

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap