csRNA-seq for Nematostella vectensis

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	MS_csRNAseq_r1.sga	whole organism\|csRNA-seq\|mixed stages\|rep1	csRNAseq	GSM4012742
2	MS_csRNAseq_r2.sga	whole organism\|csRNA-seq\|mixed stages\|rep2	csRNAseq	GSM4012743
3	MS_input_r2.sga	whole organism\|input\|mixed stages\|rep1	Input	GSM4012744
4	MS_input_r2.sga	whole organism\|input\|mised stages\|rep2	Input	GSM4012745
5	MS_csRNAseq_merged.sga	whole organism\|csRNA-seq\|mixed stages\|merged	csRNAseq	GSM4012742, GSM4012743
6	MS_input_merged.sga	whole organism\|input\|mixed stages\|merged	Input	GSM4012744, GSM4012745

Merged samples:

Merged samples contain replicates from the same type of experiments.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.10.8) and mapped to the genome using Bowtie2 v1.2.2. SAM output was then processed to SGA files with a custome Perl script.

References

Duttke SH, Chang MW, Heinz S, Benner C.
Identification and dynamic quantification of regulatory elements using total RNA.
Genome Res. 2019 Nov;29(11):1836-1846. doi: 10.1101/gr.253492.119. Epub 2019 Oct 24. PMID:31649059
GEO series GSE135498 Sequencing short capped RNAs captures acute transcription initiation and identifies promoter and distal regulatory elements across eukaryotes from total RNA

Last update: 28 Nov 2025

Page made by: Philipp Bucher

csRNA-seq for Nematostella vectensis.

Description

Source

Samples

Technical Notes

References