|
| Status |
Public on Oct 23, 2018 |
| Title |
FD41486 P35 SRC-2/NCOA2 siRNA day 0 EPC |
| Sample type |
SRA |
| |
|
| Source name |
endometrial stromal cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endometrial stromal cells
sirna: SRC-2/NCOA2 siRNA
genotype: SRC-2/NCOA2 knockdown
agent: untreated
time: day 0 EPC
individual: volunteer P35
|
| Treatment protocol |
nontargeting vs. SRC-2/NCOA2 siRNA transfection for 48 hours; followed by EPC (estradiol, medroxprogesterone acetate, cAMP) treatment for 0 or 3 days
|
| Growth protocol |
Plated 8x10^4 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)
250ng of total RNA as input, the TruSeqTM RNA library preparation kit v2 (Illumina®, Inc., San Diego, CA) was used for mRNA isolation, fragmentation, and subsequent first and second strand DNA synthesis. The kit also was used for follow up end-repair along with base- and adaptor- ligation before products were purified and then enriched by PCR (15 cycles) to create the cDNA libraries. The resulting libraries were quantitated using the NanoDropTM spectrometer and fragment size assessed using a DNA 1000 chip on the Agilent 2100 Bioanalyzer. A qPCR assay was performed on the libraries to determine the concentration of adapter-ligated fragments using the Applied Biosystems ViiATM 7 Real-Time PCR System (Thermo Fisher Scientific®) with a KAPA library Quant kit (Kapabiosystems, Inc., Wilmington, MA). Relevant samples were pooled in equimolar amounts and re-quantitated by qPCR. Library pools (27pM) were loaded into a high output flow cell for clonal cluster generation by bridge amplification using the cBot 2 system (Illumina®, Inc.). Indexed paired-end sequencing (2x100bp read lengths) was performed using the ultrahigh-throughput HiSeq 2500 sequencing system (Illumina®, Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SRC-2/NCOA2 siRNA day 0 EPC
FD41486
|
| Data processing |
Raw reads in fastq file format were mapped to human genome hg19 (Human assembly: GRCh37/hg19; http://genome.ucsc.edu) through use of the ultrafast universal RNA-seq aligner: Spliced Transcripts Alignment to a Reference (STAR) software
To reduce possible PCR bias, read duplicates were removed with Picard Tools (http://broadinstitute.github.io/picard/).
The number of reads aligned to known genes was determined by the Python-based software package HTSeq
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt; 13 columns; headers: "GeneSymbol" and raw count data for each of the 12 samples: "FD41481" "FD41482" "FD41483" "FD41484" "FD41485" "FD41486" "FD41694" "FD41488" "FD41489" "FD41490" "FD41491" "FD41494"
|
| |
|
| Submission date |
Oct 22, 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 |
GPL16791 |
| Series (1) |
| GSE121584 |
Steroid Receptor Coactivator-2 Regulated Transcriptome in Human Endometrial Stromal Cells |
|
| Relations |
| BioSample |
SAMN10266940 |
| SRA |
SRX4911607 |
