|
| Status |
Public on Apr 19, 2020 |
| Title |
Gd6-siRNA-3 |
| Sample type |
SRA |
| |
|
| Source name |
primary human adipocytes culture_Gd6-siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary human adipocytes
genotype/variation: Gd6 LINC00473 siRNA knockdown
replicate: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using TriPure Trizol reagent. Trizol was added to the cells and incubated at room temperature for 5 minutes. Cells were collected into a GentleMACS M tube and dissociated using the GentleMACS Dissociator (Miltenyi Bio) Program RNA01.01. Tubes were centrifuged for 3 minutes at 800RPM and the mixture was transferred to a 2ml collection tube. Chloroform was added in a 1:5 ratio to the tripure/cell mix and tubes were inverted to mix, then incubated at room temperature for 3-5 minutes. Aqueous phase separation was performed, and the RNA-containing layer was mixed with an equal volume of 100% Isopropanol and incubated overnight at -20 degrees for precipitation. RNA was pelleted and washed with 80% ETOH and eluted in nuclease-free water.
cDNA library was prepared using TruSeq® Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions. For each clone, 1 ug of total RNA was used as input to synthesize cDNA which was subsequently amplified. All samples were processed concurrently during library preparation. Illumina sequencing indexes were added to the fragmented libraries and indexed libraries were amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Gd6-siRNA-3_S19
|
| Data processing |
The FASTQ files obtained were de-multiplexed using the bcl2fastq tool as a part the Illumina basepace workflow
RSEM was used to align the reads to the human genome assembly hg19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.
|
| |
|
| Submission date |
Apr 18, 2020 |
| Last update date |
Apr 20, 2020 |
| Contact name |
Silvia Corvera |
| E-mail(s) |
silvia.corvera@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Street address |
373 Plantation St
|
| City |
Worcester |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE148896 |
Transcriptomic changes in response to modulation of long-non-coding RNA, LINC00473 |
|
| Relations |
| BioSample |
SAMN14639016 |
| SRA |
SRX8136537 |
