|
| Status |
Public on May 07, 2015 |
| Title |
Calibrating ChIP-seq with nucleosomal internal standards to measure histone modification density genome-wide |
| Organisms |
Drosophila melanogaster; Homo sapiens; Mus musculus; synthetic construct |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Despite serving as a central experimental technique in epigenetics research, chromatin immunoprecipitation (ChIP) suffers from several serious drawbacks: it is a relative measurement untethered to any external scale that obviates fair comparison amongst experiments; it employs antibody reagents that have differing affinity and specificity for target epitopes, which are in turn variable in abundance; and it is frequently not reproducible. To address these problems, we developed internal standard calibrated ChIP (ICeChIP), a method of spiking a native chromatin sample with nucleosomes reconstituted from recombinant and semisynthetic histones on barcoded DNA prior to immunoprecipitation. ICeChIP measures local histone modification densities on a biologically meaningful scale, enabling unbiased trans-experimental comparisons and revealing a correlation between the apparent symmetry of H3K4me3 in promoter nucleosomes and gene expression. Direct in situ assessment of immunoprecipitation accommodates for a number of experimental pitfalls, and provides a critical examination of untested assumptions inherent in conventional ChIP.
|
| |
|
| Overall design |
Examination of spiked-in semi-synthetic nucleosomes in ICeChIP-seq experiments performed for HEK293, mESC E14 and DM S2 cell line
|
| |
|
| Contributor(s) |
Grzybowski AT, Chen Z, Ruthenburg AJ |
| Citation(s) |
26004229, 26212453 |
| Submission date |
Aug 13, 2014 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Alexander Ruthenburg |
| Organization name |
The University of Chicago
|
| Department |
Molecular Genetics and Cell Biology
|
| Lab |
Ruthenburg Laboratory of Chromatin Biochemistry & Structure
|
| Street address |
920 E 58th St
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (4)
|
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
| GPL19604 |
Illumina HiSeq 2500 (synthetic construct) |
|
| Samples (27)
|
|
| Relations |
| BioProject |
PRJNA258581 |
| SRA |
SRP045657 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60378_AR3_IP_mQ13_Genome_Coverage_.bigwig |
198.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3_IP_mQ13_e150_Genome_Coverage_.bigwig |
244.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_INPUT_mQ13_Genome_Coverage_.bigwig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_INPUT_mQ13_e150_Genome_Coverage_.bigwig |
1.4 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_IP_INPUT_mQ13_c0_HMD.bigwig |
1.4 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_IP_INPUT_mQ13_c0_e150_HMD.bigwig |
1.7 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_IP_INPUT_mQ13_c0_e150_max95_CI_HMD.bigwig |
1.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_IP_INPUT_mQ13_c0_e150_min95_CI_HMD.bigwig |
1.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_IP_INPUT_mQ13_c0_max95_CI_HMD.bigwig |
1.5 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR3andAR4_IP_INPUT_mQ13_c0_min95_CI_HMD.bigwig |
1.5 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR5_INPUT_mQ0_e150_Genome_Coverage_.bigwig |
1.0 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR5_IP_INPUT_L0_mQ0_c0_e150_HMD.bigwig |
1.5 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR5_IP_mQ0_e150_Genome_Coverage_.bigwig |
335.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR6_H3vsH4_HMD.bigwig |
1.7 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_INPUT-7c_mQ20_L0-220_S1_Genome_Coverage_.bigwig |
2.2 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_INPUT-7c_mQ20_L0_S1_Genome_Coverage_.bigwig |
2.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0-220_c0_S1_HMD.bigwig |
3.0 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0-220_c0_S2_HMD.bigwig |
2.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0-220_maxCI95_HMD_S1.bigwig |
3.2 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0-220_maxCI95_HMD_S2.bigwig |
2.9 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0-220_minCI95_HMD_S1.bigwig |
1.2 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0-220_minCI95_HMD_S2.bigwig |
1004.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_HMD.bigwig |
3.1 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_maxCI95_HMD.bigwig |
3.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_minCI95_HMD.bigwig |
3.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_mQ20_L0-220_S1_Genome_Coverage_.bigwig |
628.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR7_IP-7c_mQ20_L0_S1_Genome_Coverage_.bigwig |
592.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P0_mQ20_L190_HMD.bigwig |
210.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P0_mQ20_L190_HMD_maxCI95.bigwig |
217.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P0_mQ20_L190_HMD_minCI95.bigwig |
219.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P1000_mQ20_L190_HMD.bigwig |
202.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P1000_mQ20_L190_HMD_maxCI95.bigwig |
209.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P1000_mQ20_L190_HMD_minCI95.bigwig |
211.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P500_mQ20_L190_HMD.bigwig |
195.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P500_mQ20_L190_HMD_maxCI95.bigwig |
203.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_P500_mQ20_L190_HMD_minCI95.bigwig |
204.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_PAvg_mQ20_L190_HMD.bigwig |
433.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig |
425.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig |
435.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_P0_mQ20_L190_Genome_Coverage.bigwig |
70.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_P1000_mQ20_L190_Genome_Coverage.bigwig |
68.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_P500_mQ20_L190_Genome_Coverage.bigwig |
62.3 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_CHIP_Padded_mQ20_L190_Genome_Coverage.bigwig |
122.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_Input_P0_mQ20_L190_Genome_Coverage.bigwig |
127.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_Input_P1000_mQ20_L190_Genome_Coverage.bigwig |
123.3 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_Input_P500_mQ20_L190_Genome_Coverage.bigwig |
122.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_Input_Padded_mQ20_L190_Genome_Coverage.bigwig |
152.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P0_mQ20_L190_HMD.bigwig |
207.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P0_mQ20_L190_HMD_maxCI95.bigwig |
216.3 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P0_mQ20_L190_HMD_minCI95.bigwig |
218.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P1000_mQ20_L190_HMD.bigwig |
206.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P1000_mQ20_L190_HMD_maxCI95.bigwig |
214.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P1000_mQ20_L190_HMD_minCI95.bigwig |
216.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P500_mQ20_L190_HMD.bigwig |
196.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P500_mQ20_L190_HMD_maxCI95.bigwig |
204.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_P500_mQ20_L190_HMD_minCI95.bigwig |
205.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_PAvg_mQ20_L190_HMD.bigwig |
434.6 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig |
426.8 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig |
436.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_P0_mQ20_L190_Genome_Coverage.bigwig |
69.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_P1000_mQ20_L190_Genome_Coverage.bigwig |
72.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_P500_mQ20_L190_Genome_Coverage.bigwig |
63.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR8_qCHIP_Padded_mQ20_L190_Genome_Coverage.bigwig |
123.6 Mb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-1_IP_Input_mQ20_L200_c0_HMD.bigwig |
4.5 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-1_IP_Input_mQ20_L200_c0_HMD_K4_K9_K27_Corrected_.bigwig |
2.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-1_IP_Input_mQ20_L200_c0_maxCI95.bigwig |
4.6 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-1_IP_Input_mQ20_L200_c0_minCI95.bigwig |
4.6 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-1_IP_mQ20_L200_c0_Genome_Coverage.bigwig |
1.0 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-3_IP_Input_mQ20_L200_C0_HMD_K4_K9_K27_Corrected_.bigwig |
4.1 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-3_IP_Input_mQ20_L200_c0_HMD.bigwig |
4.6 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-3_IP_Input_mQ20_L200_c0_maxCI95.bigwig |
4.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-3_IP_Input_mQ20_L200_c0_minCI95.bigwig |
4.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-3_IP_mQ20_L200_c0_Genome_Coverage.bigwig |
1.2 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-4_IP_Input_mQ20_L200_c0_HMD.bigwig |
4.7 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-4_IP_Input_mQ20_L200_c0_HMD_K4_K9_K27_Corrected_.bigwig |
4.4 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-4_IP_Input_mQ20_L200_c0_maxCI95.bigwig |
4.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-4_IP_Input_mQ20_L200_c0_minCI95.bigwig |
4.9 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-4_IP_mQ20_L200_c0_Genome_Coverage.bigwig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-6_IP_Input_mQ20_L200_c0_HMD.bigwig |
4.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-6_IP_Input_mQ20_L200_c0_HMD_K4_K9_K27_K36_K79_Corrected_.bigwig |
7.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-6_IP_Input_mQ20_L200_c0_maxCI95.bigwig |
4.9 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-6_IP_Input_mQ20_L200_c0_minCI95.bigwig |
5.0 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-6_IP_mQ20_L200_c0_Genome_Coverage.bigwig |
1.4 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-8_IP_Input_mQ20_L200_c0_HMD.bigwig |
4.7 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-8_IP_Input_mQ20_L200_c0_HMD_K4_K9_K27_K36_K79_Corrected_.bigwig |
7.5 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-8_IP_Input_mQ20_L200_c0_maxCI95.bigwig |
4.8 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-8_IP_Input_mQ20_L200_c0_minCI95.bigwig |
4.9 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-8_IP_mQ20_L200_c0_Genome_Coverage.bigwig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSE60378_AR9-9_Input_mQ20_L200_c0_Genome_Coverage.bigwig |
3.0 Gb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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