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Sample Details

SRR930669,SRR930670,SRR930671,...
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Technical details
Sample name Sample ID Paper identifier Protocol Library prep Control/Experimental Wildtype & Untreated QC score Replicate
SRR930669 1137 Kaikkonen2013remodeling GRO-seq circularization control False 3 1
SRR930670 1138 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 1
SRR930671 1139 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 2
SRR930672 1140 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 2
SRR930673 1141 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 2
SRR930674 1142 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 2
SRR930675 1143 Kaikkonen2013remodeling GRO-seq circularization control False 4 1
SRR930676 1144 Kaikkonen2013remodeling GRO-seq circularization control False 1 2
SRR930679 1145 Kaikkonen2013remodeling GRO-seq circularization experimental False 4 3
SRR930680 1146 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 4
SRR930681 1147 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 3
SRR930684 1148 Kaikkonen2013remodeling GRO-seq circularization control True 1 1
SRR930685 1149 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 1
SRR930686 1150 Kaikkonen2013remodeling GRO-seq circularization experimental False 1 1
SRR930687 1151 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 1
SRR930688 1152 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 1
SRR930689 1153 Kaikkonen2013remodeling GRO-seq circularization experimental False 1 1
SRR930690 1154 Kaikkonen2013remodeling GRO-seq circularization experimental False 4 2
SRR930717 1155 Kaikkonen2013remodeling GRO-seq circularization control False 1 1
SRR930718 1156 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 1
SRR930719 1157 Kaikkonen2013remodeling GRO-seq circularization experimental False 1 1
SRR930720 1158 Kaikkonen2013remodeling GRO-seq circularization experimental False 1 1
SRZ930649 1159 Kaikkonen2013remodeling GRO-seq circularization control False 1 1
SRZ930653 1160 Kaikkonen2013remodeling GRO-seq circularization control False 4 1
SRZ930655 1161 Kaikkonen2013remodeling GRO-seq circularization control False 3 1
SRZ930657 1162 Kaikkonen2013remodeling GRO-seq circularization control False 4 1
SRZ930659 1163 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 1
SRZ930663 1164 Kaikkonen2013remodeling GRO-seq circularization experimental False 4 1
SRZ930665 1165 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 1
SRZ930667 1166 Kaikkonen2013remodeling GRO-seq circularization experimental False 4 1
SRZ930677 1167 Kaikkonen2013remodeling GRO-seq circularization control False 3 3
SRZ930682 1168 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 5
SRZ930691 1169 Kaikkonen2013remodeling GRO-seq circularization control True 3 2
SRZ930695 1170 Kaikkonen2013remodeling GRO-seq circularization experimental False 2 2
SRZ930701 1171 Kaikkonen2013remodeling GRO-seq circularization experimental False 4 1
SRZ930707 1172 Kaikkonen2013remodeling GRO-seq circularization experimental False 4 1
SRZ930712 1173 Kaikkonen2013remodeling GRO-seq circularization experimental False 3 1
Cellular details
Sample name Organism Sample type Cell type Clone/Individual Strain Genotype Construct
SRR930669 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930670 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930671 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930672 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930673 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930674 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930675 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930676 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930679 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930680 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930681 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930684 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930685 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930686 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930687 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930688 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930689 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930690 M. musculus primary cell peritoneal macrophage C57BL/6
SRR930717 M. musculus cell line hematopoietic progenitor cell PU.1 -/-
SRR930718 M. musculus cell line hematopoietic progenitor cell PU.1 -/-
SRR930719 M. musculus cell line hematopoietic progenitor cell PU.1 -/-; tamoxifen-inducible PU.1 exogenous (stable)
SRR930720 M. musculus cell line hematopoietic progenitor cell PU.1 -/-; tamoxifen-inducible PU.1 exogenous (stable)
SRZ930649 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930653 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930655 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930657 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930659 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930663 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930665 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930667 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930677 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930682 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930691 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930695 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930701 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930707 M. musculus primary cell peritoneal macrophage C57BL/6
SRZ930712 M. musculus primary cell peritoneal macrophage C57BL/6
Conditions
Sample name Condition type Treatment Start time End time Duration
SRR930669 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRR930670 treatment Kdo2-Lipid A (100 ng/mL) -10 min 0 min 10 min
treatment serum starvation (0.5% FBS) -850 min 0 min 850 min
SRR930671 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930672 treatment Kdo2-Lipid A (100 ng/mL) -6 hr 0 hr 6 hr
treatment serum starvation (0.5% FBS) -20 hr 0 hr 20 hr
SRR930673 treatment Kdo2-Lipid A (100 ng/mL) -12 hr 0 hr 12 hr
treatment serum starvation (0.5% FBS) -26 hr 0 hr 26 hr
SRR930674 treatment Kdo2-Lipid A (100 ng/mL) -24 hr 0 hr 1 day
treatment serum starvation (0.5% FBS) -38 hr 0 hr 38 hr
SRR930675 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRR930676 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRR930679 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930680 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930681 treatment Kdo2-Lipid A (100 ng/mL) -6 hr 0 hr 6 hr
treatment serum starvation (0.5% FBS) -20 hr 0 hr 20 hr
SRR930684 vehicle DMSO -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930685 treatment flavopiridol (1 microM) -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930686 treatment IBET151 (1 microM) -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930687 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
vehicle DMSO -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930688 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment flavopiridol (1 microM) -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930689 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment IBET151 (1 microM) -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930690 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment flavopiridol (1 microM) -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRR930717 no treatment None None None
SRR930718 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
SRR930719 treatment hydroxytamoxifen (100 nM) -24 hr 0 hr 1 day
SRR930720 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment hydroxytamoxifen (100 nM) -24 hr 0 hr 1 day
SRZ930649 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRZ930653 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRZ930655 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRZ930657 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRZ930659 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRZ930663 treatment Kdo2-Lipid A (100 ng/mL) -6 hr 0 hr 6 hr
treatment serum starvation (0.5% FBS) -20 hr 0 hr 20 hr
SRZ930665 treatment Kdo2-Lipid A (100 ng/mL) -12 hr 0 hr 12 hr
treatment serum starvation (0.5% FBS) -26 hr 0 hr 26 hr
SRZ930667 treatment Kdo2-Lipid A (100 ng/mL) -24 hr 0 hr 1 day
treatment serum starvation (0.5% FBS) -38 hr 0 hr 38 hr
SRZ930677 treatment serum starvation (0.5% FBS) -14 hr 0 hr 14 hr
SRZ930682 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRZ930691 vehicle DMSO -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRZ930695 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
vehicle DMSO -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRZ930701 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment actinomycin D (5 microg/mL) -2 hr 0 hr 2 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
SRZ930707 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
treatment triptolide (1 microM) -2 hr 0 hr 2 hr
SRZ930712 treatment Kdo2-Lipid A (100 ng/mL) -1 hr 0 hr 1 hr
treatment alpha-amanitin (10 microg/mL) -5 hr 0 hr 5 hr
treatment serum starvation (0.5% FBS) -15 hr 0 hr 15 hr
Sample metrics
Sample name Raw read length Trim read depth Duplication proportion Proportion reads mapped Exon/intron ratio Unique read proportion Sample QC score Sample NRO score
SRR930669 53 14,652,975 0.41466 0.8653 2.89841 0.61214 3 1
SRR930670 53 14,784,417 0.4799 0.8617 3.46129 0.54398 3 2
SRR930671 53 12,141,823 0.38925 0.8695 3.08007 0.62163 3 2
SRR930672 53 16,530,347 0.46798 0.8714 3.62973 0.56838 2 2
SRR930673 53 14,782,247 0.42695 0.8584 3.43322 0.59234 3 2
SRR930674 53 14,278,287 0.45014 0.8448 3.28957 0.5638 3 2
SRR930675 34 8,362,505 0.44435 0.759 2.73077 0.48814 4 1
SRR930676 53 27,038,801 0.39913 0.8488 2.77742 0.7207 1 1
SRR930679 34 8,226,437 0.57469 0.7057 2.82534 0.33866 4 1
SRR930680 53 25,115,966 0.55564 0.8689 2.53439 0.606 2 1
SRR930681 53 23,274,349 0.64894 0.8745 2.94449 0.52792 2 1
SRR930684 49 28,932,394 0.40179 0.8094 2.58689 0.72596 1 1
SRR930685 49 23,211,380 0.67215 0.7759 5.28696 0.39826 3 3
SRR930686 49 27,757,426 0.49563 0.7943 3.0303 0.6115 1 2
SRR930687 49 18,845,726 0.34191 0.8174 2.25117 0.71865 2 1
SRR930688 49 15,928,654 0.61055 0.765 4.29399 0.42324 2 2
SRR930689 49 22,443,927 0.40913 0.8013 2.92542 0.66597 1 1
SRR930690 53 17,134,258 0.89711 0.7361 4.56522 0.15251 4 2
SRR930717 53 22,006,644 0.48145 0.7847 5.03026 0.55869 1 3
SRR930718 53 18,644,269 0.34852 0.8236 4.44818 0.68178 2 2
SRR930719 53 23,304,185 0.36633 0.8479 4.18363 0.6785 1 2
SRR930720 53 21,924,705 0.42174 0.8274 4.83737 0.62937 1 2
SRZ930649 34 34,639,029 0.47222 0.735 2.41795 0.60527 1 1
SRZ930653 34 6,528,653 0.28742 0.7693 2.88031 0.67407 4 1
SRZ930655 34 12,497,027 0.39004 0.7013 2.62269 0.60328 3 1
SRZ930657 34 6,103,414 0.35741 0.7581 3.62679 0.60087 4 2
SRZ930659 34 35,871,470 0.60138 0.7323 2.30218 0.51317 2 1
SRZ930663 34 6,350,381 0.27607 0.7635 3.16733 0.66651 4 2
SRZ930665 34 12,762,409 0.51555 0.6959 2.89931 0.47796 3 1
SRZ930667 34 6,087,558 0.32471 0.7587 3.76303 0.63428 4 2
SRZ930677 48 44,423,326 0.77125 0.8749 3.44941 0.53473 3 2
SRZ930682 48 43,052,425 0.76129 0.8596 3.11931 0.49242 3 2
SRZ930691 51 14,431,972 0.69886 0.7728 2.66111 0.3216 3 1
SRZ930695 51 22,088,798 0.63512 0.7515 2.4797 0.41471 2 1
SRZ930701 51 21,591,056 0.83501 0.7317 3.58041 0.18549 4 2
SRZ930707 51 17,980,970 0.8936 0.6794 2.65455 0.12205 4 3
SRZ930712 51 15,050,316 0.76527 0.7045 2.44619 0.23624 3 2
Bidirectionals
Sample name Tfit total bidirs Tfit promoter bidirs Tfit intronic bidirs Tfit intergenic bidirs dREG total bidirs dREG promoter bidirs dREG intronic bidirs dREG intergenic bidirs
SRR930669 18549 7851 5793 3123 12926 5438 3744 2379
SRR930670 9815 3363 3391 1703 7443 2727 2476 1562
SRR930671 13991 5877 4723 1939 10336 4443 3107 1576
SRR930672 13913 5559 4588 2151 10507 4230 3209 1944
SRR930673 16278 7211 5007 2526 12110 5278 3464 2078
SRR930674 18330 7952 5618 3012 12883 5793 3454 2260
SRR930675 12971 5401 4031 1989 9074 4665 2244 1346
SRR930676 23345 8866 7263 5316 19541 5902 6968 4883
SRR930679 9860 3935 3407 1483 6892 3407 1946 899
SRR930680 17760 6563 6300 3369 14432 4965 5201 2880
SRR930681 16753 6488 5482 3229 13778 5287 4556 2737
SRR930684 27783 8975 9428 7395 24154 6911 9221 6311
SRR930685 23184 7088 10182 3995 24466 6926 10801 5012
SRR930686 20794 7019 7430 4538 19267 6213 7071 4481
SRR930687 22321 7140 8272 5239 17281 5732 6611 3731
SRR930688 20437 5142 9021 4407 18963 5193 8032 4513
SRR930689 25465 7553 10154 5861 21394 5995 8824 5019
SRR930690 6142 1824 2519 874 5089 1952 1934 918
SRR930717 16506 6664 5656 2470 15500 6088 4993 2829
SRR930718 15867 6369 5599 2490 15167 5817 5157 2770
SRR930719 19751 6576 7064 4693 19732 6352 7329 4671
SRR930720 17082 5245 6180 3997 16068 5288 5966 3711
SRZ930649 22177 9222 6942 4048 18399 6250 6391 3975
SRZ930653 10976 4776 3594 1461 6595 3404 1615 900
SRZ930655 15231 5877 4958 2606 10137 4670 2658 1853
SRZ930657 12948 5692 4072 1948 8912 4776 2072 1262
SRZ930659 18448 7072 6375 3200 14825 5128 5407 2803
SRZ930663 10413 4473 3395 1540 7048 3631 1798 955
SRZ930665 12237 4806 3925 2056 8358 4070 2220 1366
SRZ930667 12392 5394 3790 2030 9177 4847 2183 1414
SRZ930677 23943 9728 7445 4807 19116 6822 6305 4324
SRZ930682 18886 7604 6263 3383 16011 5908 5490 3115
SRZ930691 6457 2819 1987 758 6045 3376 1352 680
SRZ930695 11645 5155 3759 1400 9888 4741 2721 1306
SRZ930701 6793 2782 2347 155 4035 1910 1084 401
SRZ930707 996 140 360 129 820 146 303 253
SRZ930712 2659 539 1021 175 1495 362 498 435
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