|
| Status |
Public on Sep 01, 2020 |
| Title |
293T-MSA-2 |
| 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-2
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) |
[email protected]
|
| 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 |
SAMN07585222 |
| SRA |
SRX3151271 |
