SeqMonk Vistory

DataSet Added

H3K4me1_DNMT_KO_ES_1_reimport Reimported from H3K4me1_DNMT_KO_ES_1 Visible stores parser Remove DuplicatesNo Downsample to approx 26000000

Replicate Set Changed

H3K4me1_DNMT_KO_ES H3K4me1_DNMT_KO_ES_2 H3K4me1_DNMT_KO_ES_3

Data Set Removed

H3K4me1_DNMT_KO_ES_1

Data Set Renamed

H3K4me1_DNMT_KO_ES_1_reimport changed to H3K4me1_DNMT_KO_ES_1

Replicate Set Changed

H3K4me1_DNMT_KO_ES H3K4me1_DNMT_KO_ES_1 H3K4me1_DNMT_KO_ES_2 H3K4me1_DNMT_KO_ES_3

Probes Quantitated

Read Count Quantitation using All Reads correcting for total count per million reads log transformed

Project Summary

Basic Project Info

ParameterValue
Project Namepluripotency_exit_DNMT_Epi_ChIP.smk
Vistory Namepluripotency_exit_DNMT_Epi_K4me1_pmQC.smv
GenomeMus musculus GRCm38_v95
SeqMonk Version1.46.0

Data Sets

NameFile NameReadsImport Options
ATAC_DNMT_KO_Epi_1Reimported from ATAC_DNMT_KO_Epi_17113690Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_Epi_2Reimported from ATAC_DNMT_KO_Epi_25547643Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_Epi_3Reimported from ATAC_DNMT_KO_Epi_35522265Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_ES_1Reimported from ATAC_DNMT_KO_ES_16125661Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_ES_2Reimported from ATAC_DNMT_KO_ES_25027523Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_ES_3Reimported from ATAC_DNMT_KO_ES_35026670Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_Epi_1Reimported from ATAC_DNMT_WT_Epi_15413360Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_Epi_2Reimported from ATAC_DNMT_WT_Epi_24775153Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_Epi_3Reimported from ATAC_DNMT_WT_Epi_34936556Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_ES_1Reimported from ATAC_DNMT_WT_ES_15973065Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_ES_2Reimported from ATAC_DNMT_WT_ES_25012136Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_ES_3Reimported from ATAC_DNMT_WT_ES_37445720Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_Epi_1Reimported from CTCF_DNMT_KO_Epi_123334028Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_Epi_2Reimported from CTCF_DNMT_KO_Epi_229180491Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_Epi_3Reimported from CTCF_DNMT_KO_Epi_325907443Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_ES_1Reimported from CTCF_DNMT_KO_ES_118454754Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_ES_2Reimported from CTCF_DNMT_KO_ES_221974831Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_ES_3Reimported from CTCF_DNMT_KO_ES_322701344Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_Epi_1Reimported from CTCF_DNMT_WT_Epi_126298680Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_Epi_2Reimported from CTCF_DNMT_WT_Epi_220824648Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_Epi_3Reimported from CTCF_DNMT_WT_Epi_322115922Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_ES_1Reimported from CTCF_DNMT_WT_ES_118591373Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_ES_2Reimported from CTCF_DNMT_WT_ES_223250934Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_ES_3Reimported from CTCF_DNMT_WT_ES_319583044Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_Epi_1Reimported from H3K27Ac_DNMT_KO_Epi_135150191Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_Epi_2Reimported from H3K27Ac_DNMT_KO_Epi_215686066Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_Epi_3Reimported from H3K27Ac_DNMT_KO_Epi_332506101Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_ES_1Reimported from H3K27Ac_DNMT_KO_ES_125969291Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_ES_2Reimported from H3K27Ac_DNMT_KO_ES_229683025Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_ES_3Reimported from H3K27Ac_DNMT_KO_ES_326980378Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_Epi_1Reimported from H3K27Ac_DNMT_WT_Epi_128768816Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_Epi_2Reimported from H3K27Ac_DNMT_WT_Epi_224498898Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_Epi_3Reimported from H3K27Ac_DNMT_WT_Epi_319975962Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_ES_1Reimported from H3K27Ac_DNMT_WT_ES_119220000Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_ES_2Reimported from H3K27Ac_DNMT_WT_ES_225182652Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_ES_3Reimported from H3K27Ac_DNMT_WT_ES_325003296Visible stores parser Remove DuplicatesNo Downsample to approx 25000000
H3K27me3_DNMT_KO_Epi_1Reimported from H3K27me3_DNMT_KO_Epi_117404172Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_Epi_2Reimported from H3K27me3_DNMT_KO_Epi_218889750Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_Epi_3Reimported from H3K27me3_DNMT_KO_Epi_318764791Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_ES_1Reimported from H3K27me3_DNMT_KO_ES_113753176Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_ES_2Reimported from H3K27me3_DNMT_KO_ES_217595389Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_ES_3Reimported from H3K27me3_DNMT_KO_ES_317142083Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_Epi_1Reimported from H3K27me3_DNMT_WT_Epi_117748539Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_Epi_2Reimported from H3K27me3_DNMT_WT_Epi_219673457Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_Epi_3Reimported from H3K27me3_DNMT_WT_Epi_315929372Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_ES_1Reimported from H3K27me3_DNMT_WT_ES_119719565Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_ES_2Reimported from H3K27me3_DNMT_WT_ES_218655219Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_ES_3Reimported from H3K27me3_DNMT_WT_ES_314377071Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_Epi_1Reimported from H3K4me1_DNMT_KO_Epi_127153874Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_Epi_2Reimported from H3K4me1_DNMT_KO_Epi_226355411Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_Epi_3Reimported from H3K4me1_DNMT_KO_Epi_323473276Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_ES_1Reimported from H3K4me1_DNMT_KO_ES_126000699Visible stores parser Remove DuplicatesNo Downsample to approx 26000000
H3K4me1_DNMT_KO_ES_2Reimported from H3K4me1_DNMT_KO_ES_226186351Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_ES_3Reimported from H3K4me1_DNMT_KO_ES_326314723Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_Epi_1Reimported from H3K4me1_DNMT_WT_Epi_124073496Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_Epi_2Reimported from H3K4me1_DNMT_WT_Epi_227935129Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_Epi_3Reimported from H3K4me1_DNMT_WT_Epi_328759185Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_ES_1Reimported from H3K4me1_DNMT_WT_ES_123759911Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_ES_2Reimported from H3K4me1_DNMT_WT_ES_228868709Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_ES_3Reimported from H3K4me1_DNMT_WT_ES_326527195Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_Epi_1Reimported from H3K4me3_DNMT_KO_Epi_120378459Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_Epi_2Reimported from H3K4me3_DNMT_KO_Epi_234087532Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_Epi_3Reimported from H3K4me3_DNMT_KO_Epi_329542675Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_ES_1Reimported from H3K4me3_DNMT_KO_ES_132057373Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_ES_2Reimported from H3K4me3_DNMT_KO_ES_228351839Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_ES_3Reimported from H3K4me3_DNMT_KO_ES_325539542Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_Epi_1Reimported from H3K4me3_DNMT_WT_Epi_127309497Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_Epi_2Reimported from H3K4me3_DNMT_WT_Epi_227178120Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_Epi_3Reimported from H3K4me3_DNMT_WT_Epi_3286654573Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_ES_1Reimported from H3K4me3_DNMT_WT_ES_138055549Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_ES_2Reimported from H3K4me3_DNMT_WT_ES_232201989Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_ES_3Reimported from H3K4me3_DNMT_WT_ES_336742727Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_Epi_1Reimported from Input_DNMT_KO_Epi_119707695Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_Epi_2Reimported from Input_DNMT_KO_Epi_220493345Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_Epi_3Reimported from Input_DNMT_KO_Epi_324969245Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_ES_1Reimported from Input_DNMT_KO_ES_128680534Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_ES_2Reimported from Input_DNMT_KO_ES_221088413Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_ES_3Reimported from Input_DNMT_KO_ES_312203802Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_Epi_1Reimported from Input_DNMT_WT_Epi_128080334Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_Epi_2Reimported from Input_DNMT_WT_Epi_222301904Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_Epi_3Reimported from Input_DNMT_WT_Epi_320285377Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_ES_1Reimported from Input_DNMT_WT_ES_128413707Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_ES_2Reimported from Input_DNMT_WT_ES_222900860Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_ES_3Reimported from Input_DNMT_WT_ES_320708029Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo

Replicate Sets

ATAC_DNMT_KO_EpiATAC_DNMT_KO_ESCTCF_DNMT_KO_EpiCTCF_DNMT_KO_ESCTCF_DNMT_WT_EpiCTCF_DNMT_WT_ESH3K27Ac_DNMT_KO_EpiH3K27Ac_DNMT_KO_ESH3K27Ac_DNMT_WT_EpiH3K27Ac_DNMT_WT_ESH3K27me3_DNMT_KO_EpiH3K27me3_DNMT_KO_ESH3K27me3_DNMT_WT_EpiH3K27me3_DNMT_WT_ESH3K4me1_DNMT_KO_EpiH3K4me1_DNMT_KO_ESH3K4me1_DNMT_WT_EpiH3K4me1_DNMT_WT_ESH3K4me3_DNMT_KO_EpiH3K4me3_DNMT_KO_ESH3K4me3_DNMT_WT_EpiH3K4me3_DNMT_WT_ESInput_DNMT_KO_EpiInput_DNMT_KO_ESInput_DNMT_WT_EpiInput_DNMT_WT_ES
ATAC_DNMT_KO_Epi_1ATAC_DNMT_KO_ES_1CTCF_DNMT_KO_Epi_1CTCF_DNMT_KO_ES_1CTCF_DNMT_WT_Epi_1CTCF_DNMT_WT_ES_1H3K27Ac_DNMT_KO_Epi_1H3K27Ac_DNMT_KO_ES_1H3K27Ac_DNMT_WT_Epi_1H3K27Ac_DNMT_WT_ES_1H3K27me3_DNMT_KO_Epi_1H3K27me3_DNMT_KO_ES_1H3K27me3_DNMT_WT_Epi_1H3K27me3_DNMT_WT_ES_1H3K4me1_DNMT_KO_Epi_1H3K4me1_DNMT_KO_ES_1H3K4me1_DNMT_WT_Epi_1H3K4me1_DNMT_WT_ES_1H3K4me3_DNMT_KO_Epi_1H3K4me3_DNMT_KO_ES_1H3K4me3_DNMT_WT_Epi_1H3K4me3_DNMT_WT_ES_1Input_DNMT_KO_Epi_1Input_DNMT_KO_ES_1Input_DNMT_WT_Epi_1Input_DNMT_WT_ES_1
ATAC_DNMT_KO_Epi_2ATAC_DNMT_KO_ES_2CTCF_DNMT_KO_Epi_2CTCF_DNMT_KO_ES_2CTCF_DNMT_WT_Epi_2CTCF_DNMT_WT_ES_2H3K27Ac_DNMT_KO_Epi_2H3K27Ac_DNMT_KO_ES_2H3K27Ac_DNMT_WT_Epi_2H3K27Ac_DNMT_WT_ES_2H3K27me3_DNMT_KO_Epi_2H3K27me3_DNMT_KO_ES_2H3K27me3_DNMT_WT_Epi_2H3K27me3_DNMT_WT_ES_2H3K4me1_DNMT_KO_Epi_2H3K4me1_DNMT_KO_ES_2H3K4me1_DNMT_WT_Epi_2H3K4me1_DNMT_WT_ES_2H3K4me3_DNMT_KO_Epi_2H3K4me3_DNMT_KO_ES_2H3K4me3_DNMT_WT_Epi_2H3K4me3_DNMT_WT_ES_2Input_DNMT_KO_Epi_2Input_DNMT_KO_ES_2Input_DNMT_WT_Epi_2Input_DNMT_WT_ES_2
ATAC_DNMT_KO_Epi_3ATAC_DNMT_KO_ES_3CTCF_DNMT_KO_Epi_3CTCF_DNMT_KO_ES_3CTCF_DNMT_WT_Epi_3CTCF_DNMT_WT_ES_3H3K27Ac_DNMT_KO_Epi_3H3K27Ac_DNMT_KO_ES_3H3K27Ac_DNMT_WT_Epi_3H3K27Ac_DNMT_WT_ES_3H3K27me3_DNMT_KO_Epi_3H3K27me3_DNMT_KO_ES_3H3K27me3_DNMT_WT_Epi_3H3K27me3_DNMT_WT_ES_3H3K4me1_DNMT_KO_Epi_3H3K4me1_DNMT_KO_ES_3H3K4me1_DNMT_WT_Epi_3H3K4me1_DNMT_WT_ES_3H3K4me3_DNMT_KO_Epi_3H3K4me3_DNMT_KO_ES_3H3K4me3_DNMT_WT_Epi_3H3K4me3_DNMT_WT_ES_3Input_DNMT_KO_Epi_3Input_DNMT_KO_ES_3Input_DNMT_WT_Epi_3Input_DNMT_WT_ES_3

Quantitation

NameParentProbesDescriptionComments
2 kb tiles1362779Running windows of size 2000 with step size 2000. Quantitated with Read Count Quantitation using All Reads correcting for total count per million reads log transformed

Different enrichments, not consistent between replicates ....

You can already spot the problematic ones from a screenshot ...

Unfortunately, KO_Epi_1 really has an enrichment problem and I think we should kick it out. 3 isn't great either, but I don't want to go down to 1 replicate only.

Replicate Set Changed

H3K4me1_DNMT_KO_Epi H3K4me1_DNMT_KO_Epi_2 H3K4me1_DNMT_KO_Epi_3

overall these could be a bit more consistently enrichted. But then again it's K4me1 and for that it's looking pretty ok

Babraham Bioinformatics