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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 03, 2023 |
| Title |
Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler |
| Organisms |
Mus musculus; unidentified plasmid |
| Experiment type |
Other
|
| Summary |
SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.
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| Overall design |
Investigating an ATP-Dependent Chromatin Remodeler ATPase via single-molecule chromatin profiling with m6A methyltransferase footprinting and SMRT long-read sequencing. 128 in vitro chromatin samples were analyzed (two replicates per condition), including the following controls: unremodeled methylated arrays and methylated/unmethylated unassembled template DNA. 35 in vivo samples were analyzed, including SAMOSA SNF2h KO/WT re-expression/E14 mESC SAMOSA samples (three biological replicates and technical replicates) and unmethylated/methylated mESC controls.
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| Contributor(s) |
Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V |
| Citation(s) |
37696956 |
| |
| Submission date |
Mar 06, 2022 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Megan Ostrowski |
| E-mail(s) |
megan.ostrowski@gladstone.ucsf.edu
|
| Organization name |
Gladstone Institutes
|
| Lab |
Ramani
|
| Street address |
1700 Owens
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (2) |
|
| Samples (235)
|
| GSM5935101 |
S2, array 5:1 +M -ATP, ST |
| GSM5935102 |
S1, array, 20:1 +M -ATP, ST |
| GSM5935103 |
S1, array, 15:1 +M -ATP, ST |
| GSM5935104 |
S1, array, 10:1 +M -ATP, ST |
| GSM5935105 |
S1, array, 5:1 +M -ATP, ST |
| GSM5935106 |
S2, array, 20:1 +ATP, ST, rep1 |
| GSM5935107 |
S2, array, 15:1 +ATP, ST, rep1 |
| GSM5935108 |
S2, array, 10:1 +ATP, ST, rep1 |
| GSM5935109 |
S2, array, 5:1 +ATP, ST, rep1 |
| GSM5935110 |
S1, array, 20:1 +ADP, ST, rep1 |
| GSM5935111 |
S1, array, 15:1 +ADP, ST, rep1 |
| GSM5935112 |
S1, array, 10:1 +ADP, ST, rep1 |
| GSM5935113 |
S1, array, 5:1 +ADP, ST, rep1 |
| GSM5935114 |
S1, DNA, +m |
| GSM5935115 |
S1, DNA, -m |
| GSM5935116 |
S2, DNA, +m |
| GSM5935117 |
S2, DNA, -m |
| GSM5935118 |
S1, array, 20:1, unrem, +M, rep1 |
| GSM5935119 |
S1, array 15:1, unrem, +M, rep1 |
| GSM5935120 |
S1, array 10:1, unrem, +M, rep1 |
| GSM5935121 |
S1, array 5:1, unrem, +M, rep1 |
| GSM5935122 |
S2, array, 20:1, unrem, +M, rep1 |
| GSM5935123 |
S2, array, 15:1, unrem, +M, rep1 |
| GSM5935124 |
S2, array, 10:1, unrem, +M, rep1 |
| GSM5935125 |
S2, array, 5:1, unrem, +M, rep1 |
| GSM5935126 |
S1, array 20:1, +ATP, ST, rep1 |
| GSM5935127 |
S1, array 15:1 +ATP, ST, rep1 |
| GSM5935128 |
S1, array 10:1 +ATP, ST, rep1 |
| GSM5935129 |
S1, array 5:1 +ATP, ST, rep1 |
| GSM5935130 |
S2, array 20:1 +ADP, ST, rep1 |
| GSM5935131 |
S2, array 15:1 +ADP, ST, rep1 |
| GSM5935132 |
S2, array 10:1 +ADP, ST, rep1 |
| GSM5935133 |
S2, array 5:1 +ADP, ST, rep1 |
| GSM5935134 |
S2, array, 20:1, +ATP, ST, rep2 |
| GSM5935135 |
S2, array, 15:1, +ATP, ST, rep2 |
| GSM5935136 |
S2, array, 10:1, +ATP, ST, rep2 |
| GSM5935137 |
S2, array, 5:1, +ATP, ST, rep2 |
| GSM5935138 |
S1, array, 20:1, +ATP, ST, rep2 |
| GSM5935139 |
S1, array, 15:1, +ATP, ST, rep2 |
| GSM5935140 |
S1, array, 10:1, +ATP, ST, rep2 |
| GSM5935141 |
S1, array, 5:1, +ATP, ST, rep2 |
| GSM5935142 |
S2, array, 20:1, +ADP, ST, rep2 |
| GSM5935143 |
S2, array, 15:1, +ADP, ST, rep2 |
| GSM5935144 |
S2, array, 10:1, +ADP, ST, rep2 |
| GSM5935145 |
S2, array, 5:1, +ADP, ST, rep2 |
| GSM5935146 |
S1, array, 20:1, +ADP, ST, rep2 |
| GSM5935147 |
S1, array, 15:1, +ADP, ST, rep2 |
| GSM5935148 |
S1, array, 10:1, +ADP, ST, rep2 |
| GSM5935149 |
S1, array, 5:1, +ADP, ST, rep2 |
| GSM5935150 |
S2, array, 20:1, +ATP, MT, rep1 |
| GSM5935151 |
S2, array, 15:1, +ATP, MT, rep1 |
| GSM5935152 |
S2, array, 10:1, +ATP, MT, rep1 |
| GSM5935153 |
S2, array, 5:1, +ATP, MT, rep1 |
| GSM5935154 |
S1, array, 20:1, +ATP, MT, rep1 |
| GSM5935155 |
S1, array, 15:1, +ATP, MT, rep1 |
| GSM5935156 |
S1, array, 10:1, +ATP, MT, rep1 |
| GSM5935157 |
S1, array, 5:1, +ATP, MT, rep1 |
| GSM5935158 |
S2, array, 20:1, +ADP, MT, rep1 |
| GSM5935159 |
S2, array, 15:1, +ADP, MT, rep1 |
| GSM5935160 |
S2, array, 10:1, +ADP, MT, rep1 |
| GSM5935161 |
S2, array, 5:1, +ADP, MT, rep1 |
| GSM5935162 |
S1, array, 20:1, +ADP, MT, rep1 |
| GSM5935163 |
S1, array, 15:1, +ADP, MT, rep1 |
| GSM5935164 |
S1, array, 10:1, +ADP, MT, rep1 |
| GSM5935165 |
S1, array, 5:1, +ADP, MT, rep1 |
| GSM5935166 |
S2, array, 20:1, +ATP, MT, rep2 |
| GSM5935167 |
S2, array, 15:1, +ATP, MT, rep2 |
| GSM5935168 |
S2, array, 10:1, +ATP, MT, rep2 |
| GSM5935169 |
S2, array, 5:1, +ATP, MT, rep2 |
| GSM5935170 |
S1, array, 20:1, +ATP, MT, rep2 |
| GSM5935171 |
S1, array, 15:1, +ATP, MT, rep2 |
| GSM5935172 |
S1, array, 10:1, +ATP, MT, rep2 |
| GSM5935173 |
S1, array, 5:1, +ATP, MT, rep2 |
| GSM5935174 |
S2, array, 20:1, +ADP, MT, rep2 |
| GSM5935175 |
S2, array, 15:1, +ADP, MT, rep2 |
| GSM5935176 |
S2, array, 10:1, +ADP, MT, rep2 |
| GSM5935177 |
S2, array, 5:1, +ADP, MT, rep2 |
| GSM5935178 |
S1, array, 20:1, +ADP, MT, rep2 |
| GSM5935179 |
S1, array, 15:1, +ADP, MT, rep2 |
| GSM5935180 |
S1, array, 10:1, +ADP, MT, rep2 |
| GSM5935181 |
S1, array, 5:1, +ADP, MT, rep2 |
| GSM5935182 |
S1, array, 20:1, unrem, +M, rep2 |
| GSM5935183 |
S1, array 15:1, unrem, +M, rep2 |
| GSM5935184 |
S1, array 10:1, unrem, +M, rep2 |
| GSM5935185 |
S1, array 5:1, unrem, +M, rep2 |
| GSM5935186 |
S2, array, 20:1, unrem, +M, rep2 |
| GSM5935187 |
S2, array, 15:1, unrem, +M, rep2 |
| GSM5935188 |
S2, array, 10:1, unrem, +M, rep2 |
| GSM5935189 |
S2, array, 5:1, unrem, +M, rep2 |
| GSM5935190 |
SNF2hKO, mESC, +m, biorep1, techrep1 |
| GSM5935191 |
SNF2hKO, mESC, +m, biorep2, techrep1 |
| GSM5935192 |
SNF2hKO, mESC, -m, biorep1 |
| GSM5935193 |
SNF2hKO, mESC, -m, biorep2 |
| GSM5935194 |
SNF2hWTAB, mESC, +m, biorep1, techrep1 |
| GSM5935195 |
SNF2hWTAB, mESC, +m, biorep2, techrep1 |
| GSM5935196 |
SNF2hWTAB, mESC, -m, biorep1 |
| GSM5935197 |
SNF2hWTAB, mESC, -m, biorep2 |
| GSM5935198 |
E14, mESC, -m, biorep1 |
| GSM5935199 |
E14, mESC, -m, biorep2 |
| GSM5935200 |
E14, mESC, +m, biorep1, techrep1 |
| GSM5935201 |
E14, mESC, +m2, biorep2, techrep1 |
| GSM5935202 |
E14, mESC, gDNA, +m |
| GSM5935203 |
E14, mESC, +m, biorep3, techrep1 |
| GSM5935204 |
Snf2hWTAB, mESC, +m, biorep3, techrep1 |
| GSM5935205 |
SNF2hKO, mESC, +m, biorep3, techrep1 |
| GSM5935206 |
SNF2h, ATPasemutAB, -m, biorep1 |
| GSM5935207 |
SNF2h, ATPasemutAB, -m, biorep2 |
| GSM5935208 |
E14, mESC, +m, biorep1, techrep2 |
| GSM5935209 |
E14, mESC, +m2, biorep2, techrep2 |
| GSM5935210 |
E14, mESC, +m, biorep3, techrep2 |
| GSM5935211 |
SNF2hKO, mESC, +m, biorep3, techrep2 |
| GSM5935212 |
Snf2hWTAB, mESC, +m, biorep3, techrep2 |
| GSM5935213 |
E14, mESC, +m, biorep3, techrep3 |
| GSM5935214 |
SNF2hKO, mESC, +m, biorep3, techrep3 |
| GSM5935215 |
Snf2hWTAB, mESC, +m, biorep3, techrep3 |
| GSM5935216 |
SNF2hKO, mESC, +m, biorep1, techrep2 |
| GSM5935217 |
SNF2hKO, mESC, +m, biorep2, techrep2 |
| GSM5935218 |
SNF2hWTAB, mESC, +m, biorep1, techrep2 |
| GSM5935219 |
SNF2hWTAB, mESC, +m, biorep2, techrep2 |
| GSM5935220 |
E14, mESC, +m, biorep1, techrep3 |
| GSM5935221 |
SNF2hKO, mESC, +m, biorep2, techrep3 |
| GSM5935222 |
SNF2hKO, mESC, +m, biorep1, techrep3 |
| GSM5935223 |
SNF2hKO, mESC, +m, biorep1, techrep4 |
| GSM5935224 |
SNF2hWTAB, mESC, +m, biorep1, techrep3 |
| GSM6829690 |
CTCF_10:1_2uM_ACF_15min_biolrep1_techrep1 |
| GSM6829691 |
CTCF_10:1_2uM_ACF_15min_biolrep2_techrep1 |
| GSM6829692 |
CTCF_10:1_2uM_ACF_75min_biolrep1_techrep1 |
| GSM6829693 |
CTCF_10:1_2uM_ACF_75min_biolrep2_techrep1 |
| GSM6829694 |
CTCF_10:1_320nM_ACF_15min_biolrep1_techrep1 |
| GSM6829695 |
CTCF_10:1_320nM_ACF_15min_biolrep2_techrep1 |
| GSM6829696 |
CTCF_10:1_320nM_ACF_75min_biolrep1_techrep1 |
| GSM6829697 |
CTCF_10:1_320nM_ACF_75min_biolrep2_techrep1 |
| GSM6829698 |
CTCF_10:1_320nM_SNF2h_15min_biolrep1_techrep1 |
| GSM6829699 |
CTCF_10:1_320nM_SNF2h_15min_biolrep2_techrep1 |
| GSM6829700 |
CTCF_10:1_320nM_SNF2h_75min_biolrep1_techrep1 |
| GSM6829701 |
CTCF_10:1_320nM_SNF2h_75min_biolrep2_techrep1 |
| GSM6829702 |
CTCF_10:1_9uM_SNF2h_15min_techrep1 |
| GSM6829703 |
CTCF_10:1_9uM_SNF2h_75min_biolrep1_techrep1 |
| GSM6829704 |
CTCF_10:1_9uM_SNF2h_75min_biolrep2_techrep1 |
| GSM6829705 |
CTCF_15:1_2uM_ACF_15min_biolrep1_techrep1 |
| GSM6829706 |
CTCF_15:1_2uM_ACF_15min_biolrep2_techrep1 |
| GSM6829707 |
CTCF_15:1_2uM_ACF_75min_biolrep1_techrep1 |
| GSM6829708 |
CTCF_15:1_2uM_ACF_75min_biolrep2_techrep1 |
| GSM6829709 |
CTCF_15:1_320nM_ACF_15min_biolrep1_techrep1 |
| GSM6829710 |
CTCF_15:1_320nM_ACF_15min_biolrep2_techrep1 |
| GSM6829711 |
CTCF_15:1_320nM_ACF_75min_biolrep1_techrep1 |
| GSM6829712 |
CTCF_15:1_320nM_ACF_75min_biolrep2_techrep1 |
| GSM6829713 |
CTCF_15:1_320nM_SNF2h_15min_biolrep1_techrep1 |
| GSM6829714 |
CTCF_15:1_320nM_SNF2h_15min_biolrep2_techrep1 |
| GSM6829715 |
CTCF_15:1_320nM_SNF2h_75min_biolrep1_techrep1 |
| GSM6829716 |
CTCF_15:1_320nM_SNF2h_75min_biolrep2_techrep1 |
| GSM6829717 |
CTCF_15:1_9uM_SNF2h_15min_techrep1 |
| GSM6829718 |
CTCF_15:1_9uM_SNF2h_75min_biolrep1_techrep1 |
| GSM6829719 |
CTCF_15:1_9uM_SNF2h_75min_biolrep2_techrep1 |
| GSM6829720 |
CTCF_DNA_2uM_ACF_15min_techrep1 |
| GSM6829721 |
CTCF_DNA_2uM_ACF_75min_techrep1 |
| GSM6829722 |
CTCF_DNA_9uM_SNF2h_15min_techrep1 |
| GSM6829723 |
CTCF_DNA_9uM_SNF2h_75min_techrep1 |
| GSM6829724 |
Methylated_array_10:1_techrep1 |
| GSM6829725 |
Methylated_array_15:1_techrep1 |
| GSM6829726 |
CTCF_10:1_2uM_ACF_15min_biolrep1_techrep2 |
| GSM6829727 |
CTCF_10:1_2uM_ACF_15min_biolrep2_techrep2 |
| GSM6829728 |
CTCF_10:1_2uM_ACF_75min_biolrep1_techrep2 |
| GSM6829729 |
CTCF_10:1_2uM_ACF_75min_biolrep2_techrep2 |
| GSM6829730 |
CTCF_10:1_320nM_ACF_15min_biolrep1_techrep2 |
| GSM6829731 |
CTCF_10:1_320nM_ACF_15min_biolrep2_techrep2 |
| GSM6829732 |
CTCF_10:1_320nM_ACF_75min_biolrep1_techrep2 |
| GSM6829733 |
CTCF_10:1_320nM_ACF_75min_biolrep2_techrep2 |
| GSM6829734 |
CTCF_10:1_320nM_SNF2h_15min_biolrep1_techrep2 |
| GSM6829735 |
CTCF_10:1_320nM_SNF2h_15min_biolrep2_techrep2 |
| GSM6829736 |
CTCF_10:1_320nM_SNF2h_75min_biolrep1_techrep2 |
| GSM6829737 |
CTCF_10:1_320nM_SNF2h_75min_biolrep2_techrep2 |
| GSM6829738 |
CTCF_10:1_9uM_SNF2h_15min_techrep2 |
| GSM6829739 |
CTCF_10:1_9uM_SNF2h_75min_biolrep1_techrep2 |
| GSM6829740 |
CTCF_10:1_9uM_SNF2h_75min_biolrep2_techrep2 |
| GSM6829741 |
CTCF_15:1_2uM_ACF_15min_biolrep1_techrep2 |
| GSM6829742 |
CTCF_15:1_2uM_ACF_15min_biolrep2_techrep2 |
| GSM6829743 |
CTCF_15:1_2uM_ACF_75min_biolrep1_techrep2 |
| GSM6829744 |
CTCF_15:1_2uM_ACF_75min_biolrep2_techrep2 |
| GSM6829745 |
CTCF_15:1_320nM_ACF_15min_biolrep1_techrep2 |
| GSM6829746 |
CTCF_15:1_320nM_ACF_15min_biolrep2_techrep2 |
| GSM6829747 |
CTCF_15:1_320nM_ACF_75min_biolrep1_techrep2 |
| GSM6829748 |
CTCF_15:1_320nM_ACF_75min_biolrep2_techrep2 |
| GSM6829749 |
CTCF_15:1_320nM_SNF2h_15min_biolrep1_techrep2 |
| GSM6829750 |
CTCF_15:1_320nM_SNF2h_15min_biolrep2_techrep2 |
| GSM6829751 |
CTCF_15:1_320nM_SNF2h_75min_biolrep1_techrep2 |
| GSM6829752 |
CTCF_15:1_320nM_SNF2h_75min_biolrep2_techrep2 |
| GSM6829753 |
CTCF_15:1_9uM_SNF2h_15min_techrep2 |
| GSM6829754 |
CTCF_15:1_9uM_SNF2h_75min_biolrep1_techrep2 |
| GSM6829755 |
CTCF_15:1_9uM_SNF2h_75min_biolrep2_techrep2 |
| GSM6829756 |
CTCF_DNA_2uM_ACF_15min_techrep2 |
| GSM6829757 |
CTCF_DNA_2uM_ACF_75min_techrep2 |
| GSM6829758 |
CTCF_DNA_9uM_SNF2h_15min_techrep2 |
| GSM6829759 |
CTCF_DNA_9uM_SNF2h_75min_techrep2 |
| GSM6829760 |
Methylated_array_10:1_techrep2 |
| GSM6829761 |
Methylated_array_15:1_techrep2 |
| GSM6829762 |
CTCF_10:1_2uM_ACF_15min_biolrep1_techrep3 |
| GSM6829763 |
CTCF_10:1_2uM_ACF_15min_biolrep2_techrep3 |
| GSM6829764 |
CTCF_10:1_2uM_ACF_75min_biolrep1_techrep3 |
| GSM6829765 |
CTCF_10:1_2uM_ACF_75min_biolrep2_techrep3 |
| GSM6829766 |
CTCF_10:1_320nM_ACF_15min_biolrep1_techrep3 |
| GSM6829767 |
CTCF_10:1_320nM_ACF_15min_biolrep2_techrep3 |
| GSM6829768 |
CTCF_10:1_320nM_ACF_75min_biolrep1_techrep3 |
| GSM6829769 |
CTCF_10:1_320nM_ACF_75min_biolrep2_techrep3 |
| GSM6829770 |
CTCF_10:1_320nM_SNF2h_15min_biolrep1_techrep3 |
| GSM6829771 |
CTCF_10:1_320nM_SNF2h_15min_biolrep2_techrep3 |
| GSM6829772 |
CTCF_10:1_320nM_SNF2h_75min_biolrep1_techrep3 |
| GSM6829773 |
CTCF_10:1_320nM_SNF2h_75min_biolrep2_techrep3 |
| GSM6829774 |
CTCF_10:1_9uM_SNF2h_15min_techrep3 |
| GSM6829775 |
CTCF_10:1_9uM_SNF2h_75min_biolrep1_techrep3 |
| GSM6829776 |
CTCF_10:1_9uM_SNF2h_75min_biolrep2_techrep3 |
| GSM6829777 |
CTCF_15:1_2uM_ACF_15min_biolrep1_techrep3 |
| GSM6829778 |
CTCF_15:1_2uM_ACF_15min_biolrep2_techrep3 |
| GSM6829779 |
CTCF_15:1_2uM_ACF_75min_biolrep1_techrep3 |
| GSM6829780 |
CTCF_15:1_2uM_ACF_75min_biolrep2_techrep3 |
| GSM6829781 |
CTCF_15:1_320nM_ACF_15min_biolrep1_techrep3 |
| GSM6829782 |
CTCF_15:1_320nM_ACF_15min_biolrep2_techrep3 |
| GSM6829783 |
CTCF_15:1_320nM_ACF_75min_biolrep1_techrep3 |
| GSM6829784 |
CTCF_15:1_320nM_ACF_75min_biolrep2_techrep3 |
| GSM6829785 |
CTCF_15:1_320nM_SNF2h_15min_biolrep1_techrep3 |
| GSM6829786 |
CTCF_15:1_320nM_SNF2h_15min_biolrep2_techrep3 |
| GSM6829787 |
CTCF_15:1_320nM_SNF2h_75min_biolrep1_techrep3 |
| GSM6829788 |
CTCF_15:1_320nM_SNF2h_75min_biolrep2_techrep3 |
| GSM6829789 |
CTCF_15:1_9uM_SNF2h_15min_techrep3 |
| GSM6829790 |
CTCF_15:1_9uM_SNF2h_75min_biolrep1_techrep3 |
| GSM6829791 |
CTCF_15:1_9uM_SNF2h_75min_biolrep2_techrep3 |
| GSM6829792 |
CTCF_DNA_2uM_ACF_15min_techrep3 |
| GSM6829793 |
CTCF_DNA_2uM_ACF_75min_techrep3 |
| GSM6829794 |
CTCF_DNA_9uM_SNF2h_15min_techrep3 |
| GSM6829795 |
CTCF_DNA_9uM_SNF2h_75min_techrep3 |
| GSM6829796 |
Methylated_array_10:1_techrep3 |
| GSM6829797 |
Methylated_array_15:1_techrep3 |
|
| Relations |
| BioProject |
PRJNA813226 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197979_RAW.tar |
279.5 Gb |
(http)(custom) |
TAR (of PICKLE) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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