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| Status |
Public on May 18, 2023 |
| Title |
WT-d12A |
| Sample type |
SRA |
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| Source name |
rat trophoblast stem cells
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| Organism |
Rattus norvegicus |
| Characteristics |
cell type: trophoblast cell
strain: Holtzman Sprague-Dawley
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| 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. Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (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 (null versus wild type).
RACE
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Rat TS cells were maintained in stem state medium (RPMI-1640 containing 20% FBS, 50 µm 2-mercaptoethanol, 1 mM sodium pyruvate, 100 µm penicilin and streptomycin, 25 ng/ml fibroblast growth factor 4, 1 µg/ml heparin and 70% embrynic fibroblast-conditioned medium. Differentiation was induced by the removal of FGF4, heparin and embrynic fibroblast-conditioned medium, and cells were cultured in RPMI medium containing 1% FBS for 12 days.
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| Data processing |
Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (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).
Assembly: rat reference genome (Rnor_6.0)
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| Submission date |
May 05, 2022 |
| Last update date |
May 18, 2023 |
| Contact name |
Khursheed Iqbal |
| E-mail(s) |
kiqbal@kumc.edu
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| Phone |
913 588 5690
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| Organization name |
University of Kansas Medical Center
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| Department |
Pathology
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| Street address |
3901 Rainbow Blvd
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| City |
Kansas City |
| State/province |
Kansas |
| ZIP/Postal code |
66160 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (2) |
| GSE202337 |
CITED2 is a conserved regulator of deep placentation (Rat I) |
| GSE202339 |
CITED2 is a conserved regulator of deep placentation |
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| Relations |
| BioSample |
SAMN28103384 |
| SRA |
SRX15168702 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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