HTR8/SVneo total RNA-seq data (Lee et al 2016)

We performed a knockdown experiment with human placenta cell line HTR8/SVneo and sent N=3 samples per group for total RNA-sequencing. This RNA-seq is a good resource for people interested not only in GATA3 (our gene of interest in this experiment), but also other genes. 

Use the control samples as a resource to see roughly how well other genes are expressed in HTR8/SVneo. Beware that there may be slight expression differences between different subcultures of HTR8/SVneo due to genetic drift and culture conditions.

Citation:

Bora Lee, Lindsay L Kroener, Ning Xu, Erica T Wang, Alexandra Banks, John Williams 3rd, Mark O Goodarzi, Yii-der I Chen, Jie Tang, Yizhou Wang, Vineela Gangalapudi, Margareta D Pisarska. "Function and Hormonal Regulation of GATA3 in Human First Trimester Placentation" Biol Reprod. 2016 Nov;95(5):113. doi: 10.1095/biolreprod.116.141861. Epub 2016 Oct 12.

 

Methods:

Total RNA was extracted from cells harvested 48 hours after transfection with an siRNA. RNA was  extracted with RNeasy Mini kit (QIAGEN). Libraries for sequencing were prepared with 1 ug RNA per sample with the Illumina TruSeq Stranded mRNA kit (Illumina). RNA-seq was performed with NextSeq500 (Illumina) with single end 75 bp fragments. Results have average 20 million reads per sample. Raw reads were mapped to human genome GENCODE version 23.

RNA-seq data for HTR8/SVneo cell line:

Our data is deposited at NCBI GEO accession number GSE85995.

• Controls = HTR8/SVneo treated with scrambled siRNA (doesn't target any particular gene)
• C1, C2, C3
• Experimental samples = HTR8/SVneo treated with siRNA to knockdown GATA3 (reduces GATA3 expression)
• G1, G2, G3

General notes about trophoblast cell lines:

• HTR8/SVneo comes from immortalized placenta cells from a pregnancy with a female fetus. They are used as a model for extravillous trophoblasts due to their cell migration phenotypes.
• JEG-3 and BeWo cell lines (not part of this study) come from a choriocarcinoma from a pregnancy with a male fetus. These two cell lines come from the same patient. The BeWo cell line is older and used as a model for cytotrophoblast fusion into syncytiotrophoblasts, and JEG-3 is a subculture of BeWo which is used as a model for extravillous trophoblasts.
• Swan-71 cells (not part of this study) are immortalized placenta cells from a pregnancy with a female fetus.