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Series GSE95071 Query DataSets for GSE95071
Status Public on Oct 25, 2017
Title Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB’s innate function as the repressor of DREAM target genes
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary The Retinoblastoma-like pocket proteins p130 and p107 act as gatekeepers of the cell cycle through their activity within the DREAM (Dp/Rb-like/E2F/MuvB) transcriptional repressor complex. The goal of this study was to address how the pocket protein contributes to DREAM complex assembly and function on chromatin by utilizing a protein null mutant of the only C. elegans pocket protein LIN-35. We performed ChIP-seq of C. elegans DRM subunits in wild-type and lin-35 null late embryos to assess the effect on their chromatin localization following loss of LIN-35.
 
Overall design Examination of 7 DRM complex subunits (DPL-1, EFL-1, LIN-35, LIN-9, LIN-37, LIN-52, and LIN-54) in lin-35(n745) (a protein null strain) and WT C. elegans late stage embryos to assess effects of loss of LIN-35 on DRM complex chromatin assembly.
Study includes reanalysis of GSM1195397 and GSM1195398 (GSE49204) with an additional replicate, generating the following processed data:
LIN-37.SDQ3166.N2.rep0.vsInputRep0.SES.bw
LIN-37.SDQ3166.N2.IDR.0.01.narrowPeak
 
Contributor(s) Goetsch PD, Garrigues JM, Strome S
Citation(s) 29091720
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM034059 Control of early germline development in C. elegans UNIVERSITY OF CALIFORNIA SANTA CRUZ Susan Strome
Submission date Feb 19, 2017
Last update date May 15, 2019
Contact name Paul Goetsch
Organization name UCSC
Department MCD Biology
Lab Strome lab
Street address 1156 High Street
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
 
Platforms (3)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
GPL22765 Illumina HiSeq 4000 (Caenorhabditis elegans)
Samples (46)
GSM2495690 DPL-1 ChIP-seq in wild-type late embryos, rep 1b
GSM2495691 DPL-1 ChIP-seq in wild-type late embryos, rep 2a
GSM2495692 DPL-1 ChIP-seq in wild-type late embryos, rep 3
Relations
Reanalysis of GSM1195397
Reanalysis of GSM1195398
BioProject PRJNA375929
SRA SRP100319

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
GSE95071_DPL-1.SDQ3599.N2.IDR.0.01.narrowPeak.gz 33.4 Kb (ftp)(http) NARROWPEAK
GSE95071_DPL-1.SDQ3599.N2.rep0.vsInputRep0.SES.bw 55.1 Mb (ftp)(http) BW
GSE95071_DPL-1.SDQ3599.lin-35.n745.IDR.0.01.narrowPeak.gz 19.5 Kb (ftp)(http) NARROWPEAK
GSE95071_DPL-1.SDQ3599.lin-35.n745.rep0.vsInputRep0.SES.bw 54.4 Mb (ftp)(http) BW
GSE95071_EFL-1.SDQ3590.N2.IDR.0.01.narrowPeak.gz 42.3 Kb (ftp)(http) NARROWPEAK
GSE95071_EFL-1.SDQ3590.N2.rep0.vsInputRep0.SES.bw 54.1 Mb (ftp)(http) BW
GSE95071_EFL-1.SDQ3590.lin-35.n745.IDR.0.01.narrowPeak.gz 15.5 Kb (ftp)(http) NARROWPEAK
GSE95071_EFL-1.SDQ3590.lin-35.n745.rep0.vsInputRep0.SES.bw 54.7 Mb (ftp)(http) BW
GSE95071_LIN-35.SDQ2003.N2.IDR.0.01.narrowPeak.gz 42.8 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-35.SDQ2003.N2.rep0.vsInputRep0.SES.bw 55.1 Mb (ftp)(http) BW
GSE95071_LIN-35.SDQ2003.lin-35.n745.rep0.vsInputRep0.SES.bw 54.7 Mb (ftp)(http) BW
GSE95071_LIN-37.SDQ3166.N2.IDR.0.01.narrowPeak.gz 40.2 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-37.SDQ3166.N2.rep0.vsInputRep0.SES.bw 54.8 Mb (ftp)(http) BW
GSE95071_LIN-37.SDQ3166.lin-35.n745.IDR.0.01.narrowPeak.gz 18.2 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-37.SDQ3166.lin-35.n745.rep0.vsInputRep0.SES.bw 53.9 Mb (ftp)(http) BW
GSE95071_LIN-52.BH00001.N2.IDR.0.01.narrowPeak.gz 44.3 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-52.BH00001.N2.rep0.vsInputRep0.SES.bw 54.7 Mb (ftp)(http) BW
GSE95071_LIN-52.BH00001.lin-35.n745.IDR.0.01.narrowPeak.gz 27.0 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-52.BH00001.lin-35.n745.rep0.vsInputRep0.SES.bw 54.6 Mb (ftp)(http) BW
GSE95071_LIN-54.BH00004.N2.IDR.0.01.narrowPeak.gz 43.0 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-54.BH00004.N2.rep0.vsInputRep0.SES.bw 55.2 Mb (ftp)(http) BW
GSE95071_LIN-54.BH00004.lin-35.n745.IDR.0.01.narrowPeak.gz 24.0 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-54.BH00004.lin-35.n745.rep0.vsInputRep0.SES.bw 55.1 Mb (ftp)(http) BW
GSE95071_LIN-9.BH00005.N2.IDR.0.01.narrowPeak.gz 38.8 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-9.BH00005.N2.rep0.vsInputRep0.SES.bw 54.6 Mb (ftp)(http) BW
GSE95071_LIN-9.BH00005.lin-35.n745.IDR.0.01.narrowPeak.gz 33.6 Kb (ftp)(http) NARROWPEAK
GSE95071_LIN-9.BH00005.lin-35.n745.rep0.vsInputRep0.SES.bw 54.1 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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