SeqMonk Vistory

Project Summary

Basic Project Info

ParameterValue
Project Namepluripotency_exit_TET_Epi_ChIP.smk
Vistory Namepluripotency_exit_TET_Epi_CTCF_pmQC.smv
GenomeMus musculus GRCm38_v95
SeqMonk Version1.46.0

Data Sets

NameFile NameReadsImport Options
ATAC_TET_KO_Epi_1Reimported from ATAC_TET_KO_Day_2_15774704Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_KO_Epi_3Reimported from ATAC_TET_KO_Day_2_310914413Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_KO_ES_1Reimported from ATAC_TET_KO_Day_0_18566490Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_KO_ES_2Reimported from ATAC_TET_KO_Day_0_26288940Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_KO_ES_3Reimported from ATAC_TET_KO_Day_0_35255263Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_WT_Epi_1Reimported from ATAC_TET_WT_Day_2_19535108Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_WT_Epi_2Reimported from ATAC_TET_WT_Day_2_27231543Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_WT_Epi_3Reimported from ATAC_TET_WT_Day_2_310379258Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_WT_ES_1Reimported from ATAC_TET_WT_Day_0_120617976Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_WT_ES_2Reimported from ATAC_TET_WT_Day_0_29010381Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
ATAC_TET_WT_ES_3Reimported from ATAC_TET_WT_Day_0_310533040Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCF_TET_KO_Epi_1Reimported from CTCF_TET_KO_Epi_126298857Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCF_TET_KO_Epi_2Reimported from CTCF_TET_KO_Epi_221054019Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCF_TET_KO_Epi_3Reimported from CTCF_TET_KO_Epi_324296658Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_KO_ES_1Reimported from CTCT_TET_KO_ES_119737051Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_KO_ES_2Reimported from CTCT_TET_KO_ES_221194869Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_KO_ES_3Reimported from CTCT_TET_KO_ES_320997317Visible stores parser Remove DuplicatesNo Downsample to approx 21000000
CTCT_TET_WT_Epi_1Reimported from CTCT_TET_WT_Epi_124751665Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_WT_Epi_2Reimported from CTCT_TET_WT_Epi_220443178Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_WT_Epi_3Reimported from CTCT_TET_WT_Epi_313115524Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_WT_ES_1Reimported from CTCT_TET_WT_ES_119173141Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_WT_ES_2Reimported from CTCT_TET_WT_ES_220116937Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
CTCT_TET_WT_ES_3Reimported from CTCT_TET_WT_ES_315296315Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_KO_Epi_1Reimported from H3K27Ac_TET_KO_Epi_122666696Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_KO_Epi_2Reimported from H3K27Ac_TET_KO_Epi_240635475Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_KO_Epi_3Reimported from H3K27Ac_TET_KO_Epi_343087061Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_KO_ES_1Reimported from H3K27Ac_TET_KO_ES_128743297Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_KO_ES_2Reimported from H3K27Ac_TET_KO_ES_221784969Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_KO_ES_3Reimported from H3K27Ac_TET_KO_ES_334090958Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_WT_Epi_1Reimported from H3K27A_TET_WT_Epi_136294330Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_WT_Epi_2Reimported from H3K27A_TET_WT_Epi_231446082Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_WT_Epi_3Reimported from H3K27A_TET_WT_Epi_334414329Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_WT_ES_1Reimported from H3K27Ac_TET_WT_ES_150177766Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_WT_ES_2Reimported from H3K27Ac_TET_WT_ES_278223151Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27Ac_TET_WT_ES_3Reimported from H3K27Ac_TET_WT_ES_333871115Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_KO_Epi_1Reimported from H3K27me3_TET_KO_Epi_137961357Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_KO_Epi_2Reimported from H3K27me3_TET_KO_Epi_243815239Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_KO_Epi_3Reimported from H3K27me3_TET_KO_Epi_338717996Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_KO_ES_1Reimported from H3K27me3_TET_KO_ES_151173038Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_KO_ES_2Reimported from H3K27me3_TET_KO_ES_228379126Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_KO_ES_3Reimported from H3K27me3_TET_KO_ES_363561841Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_WT_Epi_1Reimported from H3K27me3_TET_WT_Epi_129975527Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_WT_Epi_2Reimported from H3K27me3_TET_WT_Epi_235926713Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_WT_Epi_3Reimported from H3K27me3_TET_WT_Epi_327796573Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_WT_ES_1Reimported from H3K27me3_TET_WT_ES_131439291Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_WT_ES_2Reimported from H3K27me3_TET_WT_ES_233164612Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K27me3_TET_WT_ES_3Reimported from H3K27me3_TET_WT_ES_336110016Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_KO_Epi_1Reimported from H3K4me1_TET_KO_Epi_121086050Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_KO_Epi_2Reimported from H3K4me1_TET_KO_Epi_228510322Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_KO_Epi_3Reimported from H3K4me1_TET_KO_Epi_328788967Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_KO_ES_1Reimported from H3K4me1_TET_KO_ES_120800571Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_KO_ES_2Reimported from H3K4me1_TET_KO_ES_227231978Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_KO_ES_3Reimported from H3K4me1_TET_KO_ES_343753860Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_WT_Epi_1Reimported from H3K4me1_TET_WT_Epi_122999037Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_WT_Epi_2Reimported from H3K4me1_TET_WT_Epi_222550544Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_WT_Epi_3Reimported from H3K4me1_TET_WT_Epi_320391338Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_WT_ES_1Reimported from H3K4me1_TET_WT_ES_124387779Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_WT_ES_2Reimported from H3K4me1_TET_WT_ES_218391201Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me1_TET_WT_ES_3Reimported from H3K4me1_TET_WT_ES_323999631Visible stores parser Remove DuplicatesNo Downsample to approx 24000000
H3K4me3_TET_KO_Epi_1Reimported from H3K4me3_TET_KO_Epi_167010101Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_KO_Epi_2Reimported from H3K4me3_TET_KO_Epi_255742974Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_KO_Epi_3Reimported from H3K4me3_TET_KO_Epi_349544081Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_KO_ES_1Reimported from H3K4me3_TET_KO_ES_125788388Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_KO_ES_2Reimported from H3K4me3_TET_KO_ES_249994576Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_KO_ES_3Reimported from H3K4me3_TET_KO_ES_342464146Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_WT_Epi_1Reimported from H3K4me3_TET_WT_Epi_145822179Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_WT_Epi_2Reimported from H3K4me3_TET_WT_Epi_236119660Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_WT_Epi_3Reimported from H3K4me3_TET_WT_Epi_330375817Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_WT_ES_1Reimported from H3K4me3_TET_WT_ES__142399100Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_WT_ES_2Reimported from H3K4me3_TET_WT_ES__262799915Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
H3K4me3_TET_WT_ES_3Reimported from H3K4me3_TET_WT_ES__349379963Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_KO_Epi_1Reimported from Input_TET_KO_Epi_128748312Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_KO_Epi_2Reimported from Input_TET_KO_Epi_230158764Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_KO_Epi_3Reimported from Input_TET_KO_Epi_327649281Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_KO_ES_1Reimported from Input_TET_KO_ES_121454456Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_KO_ES_2Reimported from Input_TET_KO_ES_225862197Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_KO_ES_3Reimported from Input_TET_KO_ES_323784386Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_WT_Epi_1Reimported from Input_TET_WT_Epi_135110585Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_WT_Epi_2Reimported from Input_TET_WT_Epi_229494785Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_WT_Epi_3Reimported from Input_TET_WT_Epi_328656960Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_WT_ES_1Reimported from Input_TET_WT_ES_135874422Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_WT_ES_2Reimported from Input_TET_WT_ES_232382683Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo
Input_TET_WT_ES_3Reimported from Input_TET_WT_ES_333738079Visible stores parser Filter by feature Excluding excluded regions Remove DuplicatesNo

Replicate Sets

ATAC_TET_KO_EpiATAC_TET_KO_ESATAC_TET_WT_EpiATAC_TET_WT_ESCTCF_TET_KO_EpiCTCT_TET_KO_ESCTCT_TET_WT_EpiCTCT_TET_WT_ESH3K27Ac_TET_KO_EpiH3K27Ac_TET_KO_ESH3K27Ac_TET_WT_EpiH3K27Ac_TET_WT_ESH3K27me3_TET_KO_EpiH3K27me3_TET_KO_ESH3K27me3_TET_WT_EpiH3K27me3_TET_WT_ESH3K4me1_TET_KO_EpiH3K4me1_TET_KO_ESH3K4me1_TET_WT_EpiH3K4me1_TET_WT_ESH3K4me3_TET_KO_EpiH3K4me3_TET_KO_ESH3K4me3_TET_WT_EpiH3K4me3_TET_WT_ESInput_TET_KO_EpiInput_TET_KO_ESInput_TET_WT_EpiInput_TET_WT_ES
ATAC_TET_KO_Epi_1ATAC_TET_KO_ES_1ATAC_TET_WT_Epi_1ATAC_TET_WT_ES_1CTCF_TET_KO_Epi_1CTCT_TET_KO_ES_1CTCT_TET_WT_Epi_1CTCT_TET_WT_ES_1H3K27Ac_TET_KO_Epi_1H3K27Ac_TET_KO_ES_1H3K27Ac_TET_WT_Epi_1H3K27Ac_TET_WT_ES_1H3K27me3_TET_KO_Epi_1H3K27me3_TET_KO_ES_1H3K27me3_TET_WT_Epi_1H3K27me3_TET_WT_ES_1H3K4me1_TET_KO_Epi_1H3K4me1_TET_KO_ES_1H3K4me1_TET_WT_Epi_1H3K4me1_TET_WT_ES_1H3K4me3_TET_KO_Epi_1H3K4me3_TET_KO_ES_1H3K4me3_TET_WT_Epi_1H3K4me3_TET_WT_ES_1Input_TET_KO_Epi_1Input_TET_KO_ES_1Input_TET_WT_Epi_1Input_TET_WT_ES_1
ATAC_TET_KO_Epi_3ATAC_TET_KO_ES_2ATAC_TET_WT_Epi_2ATAC_TET_WT_ES_2CTCF_TET_KO_Epi_2CTCT_TET_KO_ES_2CTCT_TET_WT_Epi_2CTCT_TET_WT_ES_2H3K27Ac_TET_KO_Epi_2H3K27Ac_TET_KO_ES_2H3K27Ac_TET_WT_Epi_2H3K27Ac_TET_WT_ES_2H3K27me3_TET_KO_Epi_2H3K27me3_TET_KO_ES_2H3K27me3_TET_WT_Epi_2H3K27me3_TET_WT_ES_2H3K4me1_TET_KO_Epi_2H3K4me1_TET_KO_ES_2H3K4me1_TET_WT_Epi_2H3K4me1_TET_WT_ES_2H3K4me3_TET_KO_Epi_2H3K4me3_TET_KO_ES_2H3K4me3_TET_WT_Epi_2H3K4me3_TET_WT_ES_2Input_TET_KO_Epi_2Input_TET_KO_ES_2Input_TET_WT_Epi_2Input_TET_WT_ES_2
ATAC_TET_KO_ES_3ATAC_TET_WT_Epi_3ATAC_TET_WT_ES_3CTCF_TET_KO_Epi_3CTCT_TET_KO_ES_3CTCT_TET_WT_Epi_3CTCT_TET_WT_ES_3H3K27Ac_TET_KO_Epi_3H3K27Ac_TET_KO_ES_3H3K27Ac_TET_WT_Epi_3H3K27Ac_TET_WT_ES_3H3K27me3_TET_KO_Epi_3H3K27me3_TET_KO_ES_3H3K27me3_TET_WT_Epi_3H3K27me3_TET_WT_ES_3H3K4me1_TET_KO_Epi_3H3K4me1_TET_KO_ES_3H3K4me1_TET_WT_Epi_3H3K4me1_TET_WT_ES_3H3K4me3_TET_KO_Epi_3H3K4me3_TET_KO_ES_3H3K4me3_TET_WT_Epi_3H3K4me3_TET_WT_ES_3Input_TET_KO_Epi_3Input_TET_KO_ES_3Input_TET_WT_Epi_3Input_TET_WT_ES_3

New Probe Set:2 kb tiles (1362779 probes)

Running windows of size 2000 with step size 2000

Probes Quantitated

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

KO_Epi_2, KO_ES_1 and WT_ES_3 less enriched than the others - cross checked in chromosome view.

Hm, some separation between WT and KO. That's a first as the other marks - if anything - separated by ES vs Epi

Genotype confirmed

Babraham Bioinformatics