|
| Status |
Public on Nov 25, 2021 |
| Title |
Differentiated Rat trophoblast stem cell [Sample_D8-3] |
| Sample type |
SRA |
| |
|
| Source name |
Rat trophoblast stem cell
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: trophoblast stem cells
time point: differentiation day 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample_D8-3
|
| Data processing |
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Supplementary_files_format_and_content: Stem_vs_D8.xlsx: Excel file includes RPKM values.
|
| |
|
| Submission date |
Apr 08, 2021 |
| Last update date |
Nov 25, 2021 |
| Contact name |
Khursheed Iqbal |
| E-mail(s) |
kiqbal@kumc.edu
|
| Phone |
913 588 5690
|
| Organization name |
University of Kansas Medical Center
|
| Department |
Pathology
|
| Street address |
3901 Rainbow Blvd
|
| City |
Kansas City |
| State/province |
Kansas |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (2) |
| GSE171753 |
Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation [rat I] |
| GSE171755 |
Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation |
|
| Relations |
| BioSample |
SAMN18736607 |
| SRA |
SRX10596259 |
