NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE135498 Query DataSets for GSE135498
Status Public on Sep 16, 2019
Title Sequencing short capped RNAs captures acute transcription initiation and identifies promoter and distal regulatory elements across eukaryotes from total RNA
Organisms Oryza sativa; Neurospora crassa; Homo sapiens; Mus musculus; Nematostella vectensis; Capsaspora owczarzaki
Experiment type Other
Summary The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSS) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pre-miRNAs, antisense transcripts and promoter upstream transcripts in multicellular animals, plants and fungi spanning 1.6 million years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSS of stable transcripts, while H3K27ac marked nucleosomes downstream of all active TSS, suggesting an ancient role for post-translational histone modifications in transcription. Our findings demonstrate that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single nucleotide resolution in eukaryotes.
 
Overall design Sequencing of short capped RNAs to identify transcription initiation sites
Web link http://homer.ucsd.edu/homer/
 
Contributor(s) Benner C, Heinz S, Chang MW, Duttke SH
Citation(s) 31649059
Submission date Aug 07, 2019
Last update date Nov 25, 2019
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platforms (10)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (40)
GSM4012721 K562 csRNA-seq r1
GSM4012722 K562 csRNA-seq r2
GSM4012723 K562 csRNAinput r1
Relations
BioProject PRJNA559095
SRA SRP217687

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135498_BMDM-csRNA-KLA1h-combo.ucscneg.ucsc.bigWig 12.3 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csRNA-KLA1h-combo.ucscpos.ucsc.bigWig 11.1 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csRNA-notx-combo.ucscneg.ucsc.bigWig 12.7 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csRNA-notx-combo.ucscpos.ucsc.bigWig 14.7 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csinput-KLA1h-combo.ucscneg.ucsc.bigWig 5.0 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csinput-KLA1h-combo.ucscpos.ucsc.bigWig 4.3 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csinput-notx-combo.ucscneg.ucsc.bigWig 4.7 Mb (ftp)(http) BIGWIG
GSE135498_BMDM-csinput-notx-combo.ucscpos.ucsc.bigWig 4.2 Mb (ftp)(http) BIGWIG
GSE135498_H9-csRNA-combo.ucscneg.ucsc.bigWig 8.9 Mb (ftp)(http) BIGWIG
GSE135498_H9-csRNA-combo.ucscpos.ucsc.bigWig 6.6 Mb (ftp)(http) BIGWIG
GSE135498_H9-csinput-combo.ucscneg.ucsc.bigWig 5.2 Mb (ftp)(http) BIGWIG
GSE135498_H9-csinput-combo.ucscpos.ucsc.bigWig 5.0 Mb (ftp)(http) BIGWIG
GSE135498_Hct116-csRNA-combo.ucscneg.ucsc.bigWig 13.1 Mb (ftp)(http) BIGWIG
GSE135498_Hct116-csRNA-combo.ucscpos.ucsc.bigWig 12.1 Mb (ftp)(http) BIGWIG
GSE135498_Hct116-csinput-combo.ucscneg.ucsc.bigWig 3.3 Mb (ftp)(http) BIGWIG
GSE135498_Hct116-csinput-combo.ucscpos.ucsc.bigWig 3.6 Mb (ftp)(http) BIGWIG
GSE135498_K562-csRNA-combo.ucscneg.ucsc.bigWig 12.1 Mb (ftp)(http) BIGWIG
GSE135498_K562-csRNA-combo.ucscpos.ucsc.bigWig 11.8 Mb (ftp)(http) BIGWIG
GSE135498_K562-csinput-combo.ucscneg.ucsc.bigWig 5.3 Mb (ftp)(http) BIGWIG
GSE135498_K562-csinput-combo.ucscpos.ucsc.bigWig 4.5 Mb (ftp)(http) BIGWIG
GSE135498_capsaspora.csRNA.neg.bw 903.3 Kb (ftp)(http) BW
GSE135498_capsaspora.csRNA.pos.bw 599.1 Kb (ftp)(http) BW
GSE135498_capsaspora.csinput.neg.bw 1010.6 Kb (ftp)(http) BW
GSE135498_capsaspora.csinput.pos.bw 925.8 Kb (ftp)(http) BW
GSE135498_nematostella.csRNA.neg.bw 2.0 Mb (ftp)(http) BW
GSE135498_nematostella.csRNA.pos.bw 1.7 Mb (ftp)(http) BW
GSE135498_nematostella.csinput.neg.bw 1.2 Mb (ftp)(http) BW
GSE135498_nematostella.csinput.pos.bw 1.0 Mb (ftp)(http) BW
GSE135498_neurospora.csRNA.neg.bw 5.2 Mb (ftp)(http) BW
GSE135498_neurospora.csRNA.pos.bw 4.8 Mb (ftp)(http) BW
GSE135498_neurospora.csinput.neg.bw 904.0 Kb (ftp)(http) BW
GSE135498_neurospora.csinput.pos.bw 1.1 Mb (ftp)(http) BW
GSE135498_rice.csRNA.neg.bw 9.9 Mb (ftp)(http) BW
GSE135498_rice.csRNA.pos.bw 9.3 Mb (ftp)(http) BW
GSE135498_rice.csinput.neg.bw 15.0 Mb (ftp)(http) BW
GSE135498_rice.csinput.pos.bw 12.6 Mb (ftp)(http) BW
GSE135498_tss.csRNA.BMDM-KLA1h.txt.gz 4.1 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.BMDM-notx.txt.gz 4.9 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.H9.txt.gz 5.5 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.HCT116.txt.gz 5.2 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.K562.txt.gz 4.7 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.capsaspora.txt.gz 529.8 Kb (ftp)(http) TXT
GSE135498_tss.csRNA.nematostella.txt.gz 1.3 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.neurospora.txt.gz 1.3 Mb (ftp)(http) TXT
GSE135498_tss.csRNA.rice.txt.gz 2.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap