Supplementary Datafiles for ChIP-Seq samples in the compendium

ChIP-Seq Sample Information:
Peak-calling was performed for all ChIP-Seq assays for blood transcription factors in the compendium.  The relevant datafiles can be downloaded below.


Files for download (Hannah et al, 2011):


Combined Bed File:

The file below combines all binding profiles (peaks) from all ChIP-Seq assays in the compendium, and can be displayed on the UCSC geneome browser in 'pack' view in order to visualise combinatorial binding:

ChIP-Seq peaks (bed file) for ALL_PEAKS:
          download


Individual bed and bigwig files:

The files below can be used to display the individual ChIP-Seq binding profiles (peaks) in genome browsers:

CEBPa_GSM537984_Macrophage:
download peaks bed file
download bigwig file

CEBPb_GSM537985_Macrophage:
download peaks bed file
download bigwig file

CTCF_GSM535747_Pre-Adipocyte:
download peaks bed file
download bigwig file

CTCF_GSM546526_Pro-B-Cells:
download peaks bed file
download bigwig file

CTCF_GSM560352_ES-cells:
download peaks bed file
download bigwig file

E2A_GSM546517_Pre-Pro-B-Cells:
download peaks bed file
download bigwig file

E2A_GSM546523_Pro-B-Cells
download peaks bed file
download bigwig file

EBF_GSM499030_Pro-B-Cells
download peaks bed file
download bigwig file

ERG_MPP_HPC7
download peaks bed file
download bigwig file

Eto2_Erythroid_MEL:
download peaks bed file
download bigwig file

Eto2_induced_Erythroid_MEL
download peaks bed file
download bigwig file

Fli1_MPP_HPC7:
download peaks bed file
download bigwig file

Foxo1_GSM546525_Pro-B-Cells:
download peaks bed file
download bigwig file

Gata1_Erythroid_MEL:
download peaks bed file
download bigwig file

Gata1_GSM453997_Erythroid_G1ER:
download peaks bed file
download bigwig file

Gata1_induced_Erythroid_MEL:
download peaks bed file
download bigwig file

Gata2_HPC:
download peaks bed file
download bigwig file

Gata2_MPP_HPC7:
download peaks bed file
download bigwig file

Gfi1b_MPP_HPC7:
download peaks bed file
download bigwig file

Ldb1_Erythroid_MEL:
download peaks bed file
download bigwig file

Ldb1_HPC:
download peaks bed file
download bigwig file

Ldb1_induced_Erythroid_MEL:
download peaks bed file
download bigwig file

Lmo2_MPP_HPC7:
download peaks bed file
download bigwig file

Lyl1_MPP_HPC7:
download peaks bed file
download bigwig file

Meis1_MPP_HPC7:
download peaks bed file
download bigwig file

Mtgr1_Erythroid_MEL:
download peaks bed file
download bigwig file

Mtgr1_induced_Erythroid_MEL:
download peaks bed file
download bigwig file

Oct2_GSM537990_B-Cells:
download peaks bed file
download bigwig file

p300_GSM487448_Macrophage:
download peaks bed file
download bigwig file

P65_GSM611116_Activated_Macrophages:
download peaks bed file
download bigwig file

Pparg_GSM532739_Macrophage:
download peaks bed file
download bigwig file

Pu1_GSM537989_B-Cells:
download peaks bed file
download bigwig file

PU1_GSM487450_Macrophage:
download peaks bed file
download bigwig file

PU1_GSM487451_Activated_Macrophages:
download peaks bed file
download bigwig file

PU1_GSM537983_Macrophage:
download peaks bed file
download bigwig file

PU1_MPP_HPC7:
download peaks bed file
download bigwig file

RAG2_Thymocytes:
download peaks bed file
download bigwig file

Runx1_MPP_HPC7:
download peaks bed file
download bigwig file

Scl_Erythroid_MEL:
download peaks bed file
download bigwig file

Scl_HPC:
download peaks bed file
download bigwig file

Scl_induced_Erythroid_MEL:
download peaks bed file
download bigwig file

SCL_MPP_HPC7:
download peaks bed file
download bigwig file

SCL-RER_GSE18720_Erythroid_FL:
download peaks bed file
download bigwig file

SCL-WT_GSE18720_Erythroid_FL:
download peaks bed file
download bigwig file

Stat3_GSM540722_Th17-T-Cells:
download peaks bed file
download bigwig file

Stat4_GSM550303_Th1-T-Cells:
download peaks bed file
download bigwig file

Stat5a_GSE12346_2rounds_Th2-T-Cells:
download peaks bed file
download bigwig file

Stat5a_GSE12346_8hr_Th2-T-Cells:
download peaks bed file
download bigwig file

Stat5a_GSE12346_13hr_Th2-T-Cells:
download peaks bed file
download bigwig file

Stat5b_GSE12346_2rounds_Th2-T-Cells:
download peaks bed file
download bigwig file

Stat5b_GSE12346_8hr_Th2-T-Cells:
download peaks bed file
download bigwig file

Stat5b_GSE12346_13hr_Th2-T-Cells:
download peaks bed file
download bigwig file

Stat6_GSM550311_Th2-T-Cells:
download peaks bed file
download bigwig file


Matrix file:

The matrix file below can be used to extract binding patterns for combinations of transcription factors:

Matrix file:
     download


Contact details:  for any further information, please contact:


Rebecca Hannah

Lab. 6.15, Department of Haematology, 
Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY

Tel. 01223 336822

E-mail: rlh60@cam.ac.uk

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