SeqMonk Vistory

Project Summary

Basic Project Info

ParameterValue
Project Namepluripotency_exit_TET_Epi_ChIP.smk
Vistory Namepluripotency_exit_TET_Epi_K4me1_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

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

Like CTCF, here the separation is WT/KO rather than ES/Epi which is really interesting. Of course this is just on tiles.

Genotype confirmed.

Babraham Bioinformatics