Project description:Transcriptome changes in seeds derived from crosses of osd1 (omission of second division 1) maternal plants pollinated with wild-type pollen in comparison to wild-type plants pollinated with wild-type pollen at 6DAP. Seeds of about 20 siliques were manually isolated and used to extract RNA. Plants were grown under long day conditions at 18 C.
Project description:GATA4 is the second most expressed GATA factor in the pancreas. GATA4 mRNA is enriched in classical, compared to basal-like pancreatic adenocarcinomas. We utilized CUT&RUN to profile genomic loci bound by GATA4 in PaTu8988S pancreatic adenocarcinoma cells.
Project description:High-throughput sequencing of cellular tRNAs is severely hindered by the presence of base modifications. These modifications impair the reverse transcription (RT) enzyme and prevent a large fraction of transcripts to be converted into cDNA in conventional sequence library preparation. Recent attempts to circumvent this issue made use of enzymatic treatments to remove methyl groups (Cozen et al. 2015; Zeng et al. 2015). This approach is, however, not fully satisfactory because it can clear the way to the RT enzyme for only a fraction of all tRNAs. Another approach takes advantage of the interference of modifications with RT enzymes to detect and identify them in fragmented RNA transcripts (Hauenschild et al. 2015; Helm and Motorin 2017; Schwartz and Motorin 2017). In line with this second approach, we present results of an alternate method that is simpler and fully adapted to the direct characterization and quantification of mature tRNA transcripts. An analysis of the obtained read coverages enables to generate highly reproductible patterns of termination signals that can be used to assess the modification state of all tRNAs.
Project description:RNA-seq of mouse heart tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:RNA-seq of human pancreas tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:RNA-seq of mouse brain tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:RNA-seq of human spleen tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:RNA-seq of mouse kidney tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:RNA-seq of mouse adipose tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
