|
| Status |
Public on Oct 01, 2019 |
| Title |
siH19 rep1 (USMC) |
| Sample type |
SRA |
| |
|
| Source name |
UtSMC (Lonza, Cat: CC-2562)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Uterine Smooth Muscle Cell (USMC)
sirna: siH19
genotype: H19 knockdown
|
| Treatment protocol |
Cells were transfected with either control siRNA or H19 siRNA. 48h later, cells were harvested for RNA extraction.
|
| Growth protocol |
USMC cells purchased from Lonza were maintained in smooth muscle cell basal medium supplemented with growth supplements including hEGF, Insulin, hFGF-B, FBS and GA-1000. The smooth muscle cell basal medium and the growth supplements were included in the Clonetics™ SmGM™-2 BulletKit™ (CC-3182) from Lonza.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using PureLink RNA Mini Kit.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fragments were adenylated and then ligated to indexing adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
USMC_counts_data.txt
USMC_siCon_vs_siH19_sig_diff_pooled.txt
|
| Data processing |
RTA 2.4.11 software was used for basecalling
Alignments were made using Tophat v2.1.1, read counts for each gene were estimated using featureCounts v1.5.0
Differential expression of genes between siCon and siH19 samples was determined using DESeq2 v1.14.1 (within R v3.3.3)
Genes that have significant differentiatial expression between siCon and siH19 triplicates (q Value <0.1) were presented in the processed data file
Genome_build: hg38
Supplementary_files_format_and_content: [USMC_counts_data.txt] Tab-delimited text file includes counts.
[USMC_siCon_vs_siH19_sig_diff_pooled.txt] Tab-delimited text file includes log2 fold change of relative gene expression levels between siCon and siH19 conditions.
|
| |
|
| Submission date |
Feb 13, 2018 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Ying Jiang |
| E-mail(s) |
ying.jiang@yale.edu
|
| Organization name |
Department of Obstetrics, Gynecology & Reproductive Sciences
|
| Street address |
310 Cedar Street
|
| City |
New Haven |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE110557 |
RNA-seq analysis reveals profound changes in transcript profiles between siCon- and siH19-transfected uterine smooth muscle cells (USMC) |
|
| Relations |
| BioSample |
SAMN08527132 |
| SRA |
SRX3691808 |
