|
| Status |
Public on Apr 22, 2019 |
| Title |
THESCs-NTsi-1 |
| Sample type |
SRA |
| |
|
| Source name |
T HESCs (ATCC CRL-4003)
|
| Organism |
Homo sapiens |
| Characteristics |
sirna: nontargeting siRNA
experiment number: experiment 1
|
| Treatment protocol |
nontargeting vs. EGR1 siRNA transfection for 48 hours; cells were collected following 48h siRNA transfection
|
| Growth protocol |
Plated 1x10^5 cells per well in 6-well format. 48 hours allowed for growth before siRNA transfection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plus kit (Qiagen Inc., Germantown, MD)
Libraries for mRNA sequencing were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) from 250 ng of RNA. Quality analysis of libraries was performed using Agilent 4200 TapeStation with D1000 ScreenTape assays (Agilent Technologies). Libraries were pooled and then quantified by two methods: 1) on a 2100 Bioanalyzer with DNA chips using High Sensitivity DNA Kit (Agilent Technologies); and 2) with KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
THESC control siRNA exp.1
|
| Data processing |
The pair-ended reads were mapped to the human genome using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference. STAR generated read count for each gene.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt file; 10 columns: 6 columns with counts (JY12130.Control.siRNA_1; JY12131.EGR1.siRNA_1; JY12132.Control.siRNA_2; JY12136.EGR1.siRNA_2; JY12134.Control.siRNA_3; JY12135.EGR1.siRNA_3) and 4 columns with gene descriptors (EntrezGene; symbol; Description; Description2)
|
| |
|
| Submission date |
Dec 06, 2018 |
| Last update date |
Mar 12, 2023 |
| Contact name |
Maria Szwarc |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor College of MEdicine
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| ZIP/Postal code |
77025 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE123472 |
EGR1-controlled transcriptome of T HESCs |
|
| Relations |
| BioSample |
SAMN10531275 |
| SRA |
SRX5104230 |
