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Series GSE164775 Query DataSets for GSE164775
Status Public on Aug 31, 2021
Title Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary In this study we use targeted DamID to assay RNA polymerase occupancy across the genome specifically within the seam cells and hypodermis of C. elegans to identify genes expressed in these cell-types.
 
Overall design Identification of sets of expressed genes within the seam cells and the hypodermis of C. elegans by cell-type-specific expression of a DAM:RPB-6 fusion using the seam cell promoter srf-3i1 and the hypodermal promoter dpy-7syn1. DAM:RPB-6 occupancy across the genome is assayed in the form of GATC 6mA methylation in comparison to that of an equivalent control DAM:NLS-GFP fusion and genes with significant levels of occupancy are identified. Two biological replicates were aquired for every fusion and cell-type at each of the L2 and L4 developmental stages.
 
Contributor(s) Katsanos D, Barkoulas M
Citation(s) 34397094
Submission date Jan 13, 2021
Last update date Aug 31, 2021
Contact name Dimitris Katsanos
Organization name Imperial College London
Department Life Sciences
Lab Michalis Barkoulas
Street address Sir Alexander Fleming building, Imperial College Road
City London
ZIP/Postal code SW7 2AZ
Country United Kingdom
 
Platforms (1)
GPL22765 Illumina HiSeq 4000 (Caenorhabditis elegans)
Samples (16)
GSM5018551 srf-3i1-NLS-GFP_L2_rep1
GSM5018552 srf-3i1-rpb-6_L2_rep1
GSM5018553 dpy-7syn1-NLS-GFP_L2_rep1
Relations
BioProject PRJNA691926
SRA SRP301617

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

Supplementary file Size Download File type/resource
GSE164775_RAW.tar 48.6 Mb (http)(custom) TAR (of GFF)
GSE164775_dpy-7syn1-dam-rpb-6_L2_F-allreps_pairwise_averageoflogs.gff.gz 2.8 Mb (ftp)(http) GFF
GSE164775_dpy-7syn1-dam-rpb-6_L4_F-allreps_pairwise_averagoflogs.gff.gz 3.0 Mb (ftp)(http) GFF
GSE164775_dpy-7syn1_L2-FDR0.05_protein-coding_genes.txt.gz 60.4 Kb (ftp)(http) TXT
GSE164775_dpy-7syn1_L4-FDR0.05_protein-coding_genes.txt.gz 60.0 Kb (ftp)(http) TXT
GSE164775_srf-3i1-dam-rpb-6_L2-F-allreps_pairwise_averageoflogs.gff.gz 2.9 Mb (ftp)(http) GFF
GSE164775_srf-3i1-dam-rpb-6_L4_F-allreps_pairwise_averageoflogs.gff.gz 2.8 Mb (ftp)(http) GFF
GSE164775_srf-3i1_L2-FDR0.05_protein-coding_genes.txt.gz 50.3 Kb (ftp)(http) TXT
GSE164775_srf-3i1_L4-FDR0.05_protein-coding_genes.txt.gz 54.8 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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