Project description:Gene regulation is essential to placental function and fetal development. We built a genome-scale transcriptional regulatory network (TRN) of the human placenta using digital genomic footprinting and transcriptomic data. We integrated 475 transcriptomes and 12 DNase hypersensitivity datasets from placental samples to globally and quantitatively map transcription factor (TF)-target gene interactions. We performed siRNA knockdowns of 4 TFs and achieved concordance between the predicted gene targets in our TRN. This GEO dataset summarizes the results of the knockdowns for these 4 TFs: GCM1, CREB2L2, ESRRG, and GRHL2 compared to siRNA controls (SCR).
Project description:Gene regulation is essential to placental function and fetal development. We built a genome-scale transcriptional regulatory network (TRN) of the human placenta using digital genomic footprinting and transcriptomic data. We integrated 475 transcriptomes and 12 DNase hypersensitivity datasets from placental samples to globally and quantitatively map transcription factor (TF)-target gene interactions. We performed siRNA knockdowns of 4 TFs and achieved concordance between the predicted gene targets in our TRN.
Project description:AIM: To find molecular signatures associated to the siRNA-mediated knockdowns in order to be able to identify similarities among different knockdowns. DESCRIPTION: Each sample includes biological triplicates for 35 siRNA-mediated knockdowns targeting 30 chromatin-associated proteins during in early reprogramming to iPS at day 6. A daily timecourse from reprogramming cells, without treatment from MEFs until day 6 is also included in triplicate.
Project description:Knock down of fibroblast specific TF, FOXD1, HOXC4, LHX9, OSR1, PRRX1, TBX3, TWIST2 and NC(negative control siRNA) in fibroblast 24 Samples total.
Project description:To study the involvement of key Areg (CD142+ ASPC)-specifics factors in the inhibitory capacity of CD142+ ASPCs on adipogenesis, we performed transcriptomic profiling of CD142− ASPCs exposed to the secretome of CD142+ ASPCs carrying knockdowns of the indicated genes. CD142− ASPCs were co-cultured and co-differentiated (within the transwell set-up) with CD142+ ASPCs in which siRNA-based knockdowns of specific genes were performed. ASPCs were collected as Lin− (CD31− CD45− TER119−) CD29+ CD34+ SCA1+ cells of the mouse subcutaneous stromal vascular fraction using FACS.
Project description:We performed two independent siRNA mediated knockdowns of Srf (Srf si1 & Srf si2) and an unspecific siRNA (siNon) in mouse cardiomyocytes HL-1 cells. Small RNAs were sequenced by Illumina/Solexa next-generation (single-end) sequencing technology. The sequence reads were mapped to the mouse reference genome (NCBI v37, mm9) using MicroRazerS. MicroRazerS searches for the longest possible prefix-match of each read, i.e. the longest possible contiguous match starting at the first base. Hence, it is robust to possible adapter sequence at the 3' end of a read and requires no adapter trimming. Small RNA-seq profiles of two siRNA mediated knockdowns of Srf and an unspecific siRNA in mouse cardiomyocytes