 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 01, 2020 |
| Title |
4-24-34a-3 [mRNA] |
| Sample type |
SRA |
| |
|
| Source name |
mRNA_424_34a
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: nCAR/miR-34a-5p
cell type: Embryonic kidney cells
passage: 6-8
genotype: 293/Dicer KO
|
| 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 using 1 ug of total RNA to isolate mRNAs using poly-T oligo-attached magnetic beads. Following mRNA fragmentation, cDNA was generated using random primers and an adapter was ligated at the 3' end of the fragment. Products were then purified, enriched by PCR amplification, and used to create DNB-based nanoarrays by RCR. Stepwise sequencing was performed using the combinatorial probe-anchor ligation (cPAL) approach and read on the BGISEQ-500 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequence reads were mapped to reference human genome assembly (Feb. 2009, GRCh37/hg19) with BWA.
Read counts derived from transfected recombinant RNAs were mapped to sequence reads from FASTQ-formatted data to the using a PERL script
Differentially expressed mRNAs between phenotypes were computed using EdgeR. Parameters: log2FC > 1.2 or log2FC < 0.8, P < 0.05, and log2CPM > 5.
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 |
Sep 29, 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) |
| GSE104442 |
Alteration of transcriptome by recombinant ncRNA agents |
| GSE104445 |
Alteration of miRNome and transcriptome by recombinant ncRNA agents |
|
| Relations |
| BioSample |
SAMN07722522 |
| SRA |
SRX3234434 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
