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Sample Details

SRR6660158,SRR6660159,SRR6660161,...
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Technical details
Sample name Sample ID Paper identifier Protocol Library prep Control/Experimental Wildtype & Untreated QC score Replicate
SRR6660158 1527 Link2018analysis GRO-cap ligation experimental False 4 1
SRR6660159 1528 Link2018analysis GRO-cap ligation experimental False 4 2
SRR6660161 1530 Link2018analysis GRO-cap ligation control True 4 2
SRR6660301 1546 Link2018analysis GRO-cap ligation experimental False 3 2
SRR6660302 1547 Link2018analysis GRO-cap ligation control True 5 1
SRR6660303 1548 Link2018analysis GRO-cap ligation control True 2 2
SRR6660350 1554 Link2018analysis GRO-cap ligation experimental False 4 2
SRR6660351 1555 Link2018analysis GRO-cap ligation control True 4 1
SRR6660352 1556 Link2018analysis GRO-cap ligation control True 2 2
SRR6660400 1562 Link2018analysis GRO-cap ligation experimental False 4 2
SRR6660401 1563 Link2018analysis GRO-cap ligation control True 4 1
SRR6660402 1564 Link2018analysis GRO-cap ligation control True 4 2
SRR6936827 1569 Link2018analysis GRO-cap ligation experimental False 4 1
SRR6936828 1570 Link2018analysis GRO-cap ligation control True 4 1
SRR6660160 1529 Link2018analysis GRO-cap ligation control True 4 1
SRR6660300 1545 Link2018analysis GRO-cap ligation experimental False 5 1
SRR6660349 1553 Link2018analysis GRO-cap ligation experimental False 3 1
SRR6660399 1561 Link2018analysis GRO-cap ligation experimental False 5 1
SRR6660174 1531 Link2018analysis GRO-seq ligation experimental False 2 1
SRR6660175 1532 Link2018analysis GRO-seq ligation experimental False 4 2
SRR6660177 1534 Link2018analysis GRO-seq ligation control True 3 2
SRR6660226 1535 Link2018analysis GRO-seq ligation experimental False 2 1
SRR6660227 1536 Link2018analysis GRO-seq ligation experimental False 1 2
SRR6660229 1538 Link2018analysis GRO-seq ligation control True 1 2
SRR6660276 1539 Link2018analysis GRO-seq ligation experimental False 2 1
SRR6660277 1540 Link2018analysis GRO-seq ligation experimental False 3 2
SRR6660279 1542 Link2018analysis GRO-seq ligation control True 3 2
SRR6660292 1543 Link2018analysis GRO-seq ligation experimental False 2 1
SRR6660293 1544 Link2018analysis GRO-seq ligation control True 2 1
SRR6660317 1550 Link2018analysis GRO-seq ligation experimental False 4 2
SRR6660318 1551 Link2018analysis GRO-seq ligation control True 1 1
SRR6660319 1552 Link2018analysis GRO-seq ligation control True 4 2
SRR6660366 1558 Link2018analysis GRO-seq ligation experimental False 2 2
SRR6660367 1559 Link2018analysis GRO-seq ligation control True 2 1
SRR6660368 1560 Link2018analysis GRO-seq ligation control True 1 2
SRR6660417 1566 Link2018analysis GRO-seq ligation experimental False 1 2
SRR6660176 1533 Link2018analysis GRO-seq ligation control True 1 1
SRR6660228 1537 Link2018analysis GRO-seq ligation control True 1 1
SRR6660278 1541 Link2018analysis GRO-seq ligation control True 1 1
SRR6660316 1549 Link2018analysis GRO-seq ligation experimental False 2 1
SRR6660365 1557 Link2018analysis GRO-seq ligation experimental False 1 1
SRR6660416 1565 Link2018analysis GRO-seq ligation experimental False 3 1
SRR6660418 1567 Link2018analysis GRO-seq ligation control True 2 1
SRR6660419 1568 Link2018analysis GRO-seq ligation control True 5 2
Cellular details
Sample name Organism Sample type Cell type Clone/Individual Strain Genotype Construct
SRR6660158 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660159 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660161 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660301 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660302 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660303 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660350 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660351 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660352 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660400 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6660401 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6660402 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6936827 M. musculus primary cell bone marrow derived macrophage C57BL/6J
SRR6936828 M. musculus primary cell bone marrow derived macrophage C57BL/6J
SRR6660160 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660300 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660349 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660399 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6660174 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660175 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660177 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660226 M. musculus primary cell bone marrow derived macrophage C57BL/6J
SRR6660227 M. musculus primary cell bone marrow derived macrophage C57BL/6J
SRR6660229 M. musculus primary cell bone marrow derived macrophage C57BL/6J
SRR6660276 M. musculus primary cell bone marrow derived macrophage C57BL/6J mice(f) x PWK/PhJ(m)
SRR6660277 M. musculus primary cell bone marrow derived macrophage C57BL/6J mice(f) x PWK/PhJ(m)
SRR6660279 M. musculus primary cell bone marrow derived macrophage C57BL/6J mice(f) x PWK/PhJ(m)
SRR6660292 M. musculus primary cell bone marrow derived macrophage C57BL/6J mice(f) x SPRET/EiJ(m)
SRR6660293 M. musculus primary cell bone marrow derived macrophage C57BL/6J mice(f) x SPRET/EiJ(m)
SRR6660317 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660318 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660319 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660366 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660367 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660368 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660417 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6660176 M. musculus primary cell bone marrow derived macrophage BALB/cJ
SRR6660228 M. musculus primary cell bone marrow derived macrophage C57BL/6J
SRR6660278 M. musculus primary cell bone marrow derived macrophage C57BL/6J mice(f) x PWK/PhJ(m)
SRR6660316 M. musculus primary cell bone marrow derived macrophage NOD/ShiLtJ
SRR6660365 M. musculus primary cell bone marrow derived macrophage PWK/PhJ
SRR6660416 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6660418 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
SRR6660419 M. musculus primary cell bone marrow derived macrophage SPRET/EiJ
Conditions
Sample name Condition type Treatment Start time End time Duration
SRR6660158 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660159 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660161 no treatment None None None
SRR6660301 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660302 no treatment None None None
SRR6660303 no treatment None None None
SRR6660350 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660351 no treatment None None None
SRR6660352 no treatment None None None
SRR6660400 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660401 no treatment None None None
SRR6660402 no treatment None None None
SRR6936827 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6936828 no treatment None None None
SRR6660160 no treatment None None None
SRR6660300 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660349 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660399 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660174 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660175 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660177 no treatment None None None
SRR6660226 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660227 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660229 no treatment None None None
SRR6660276 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660277 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660279 no treatment None None None
SRR6660292 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660293 no treatment None None None
SRR6660317 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660318 no treatment None None None
SRR6660319 no treatment None None None
SRR6660366 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660367 no treatment None None None
SRR6660368 no treatment None None None
SRR6660417 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660176 no treatment None None None
SRR6660228 no treatment None None None
SRR6660278 no treatment None None None
SRR6660316 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660365 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660416 treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
SRR6660418 no treatment None None None
SRR6660419 no treatment None None None
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
SRR6660158 50 10,221,634 0.76796 0.6288 3.63348 0.1908 4 2
SRR6660159 20 14,779,578 0.91522 0.6237 2.45672 0.08595 4 1
SRR6660161 20 20,349,805 0.92972 0.5881 2.3357 0.08227 4 1
SRR6660301 76 41,757,751 0.7155 0.8095 2.52693 0.4904 3 2
SRR6660302 50 1,255,883 0.54321 0.7258 2.96774 0.14079 5 1
SRR6660303 76 39,016,644 0.59339 0.839 3.35195 0.53196 2 2
SRR6660350 20 7,359,996 0.8452 0.6326 2.71098 0.10717 4 1
SRR6660351 20 7,136,625 0.8315 0.6296 3.48299 0.11364 4 2
SRR6660352 76 34,184,374 0.64748 0.8035 4.73395 0.45112 2 2
SRR6660400 50 7,777,604 0.86567 0.5688 3.66879 0.07673 4 2
SRR6660401 20 11,229,961 0.882 0.6046 3.98618 0.09887 4 2
SRR6660402 50 9,237,762 0.89083 0.568 3.40526 0.07088 4 2
SRR6936827 20 21,912,445 0.90288 0.776 3.7963 0.15255 4 2
SRR6936828 20 25,869,242 0.86205 0.8735 4.33862 0.23927 4 2
SRR6660160 50 12,330,292 0.78919 0.5352 3.18947 0.18221 4 2
SRR6660300 50 7,238,337 0.88643 0.4538 2.32203 0.06497 5 1
SRR6660349 76 47,502,639 0.65775 0.7891 3.6307 0.49557 3 2
SRR6660399 77 4,736,852 0.88063 0.4836 3.6129 0.05905 5 2
SRR6660174 35 47,569,716 0.57062 0.7391 2.18985 0.57443 2 1
SRR6660175 20 51,873,257 0.85388 0.6761 1.73455 0.17824 4 1
SRR6660177 20 73,525,984 0.76977 0.6384 2.17354 0.27165 3 1
SRR6660226 35 49,240,473 0.63003 0.7834 2.04366 0.60804 2 1
SRR6660227 50 90,045,791 0.47667 0.8215 1.37535 0.75891 1 1
SRR6660229 50 46,584,346 0.31564 0.7995 1.50925 0.81334 1 1
SRR6660276 35 34,204,807 0.5313 0.683 2.06961 0.56025 2 1
SRR6660277 50 12,683,243 0.41497 0.7261 1.64898 0.57541 3 1
SRR6660279 50 11,689,299 0.36421 0.741 1.82781 0.62284 3 1
SRR6660292 35 58,739,930 0.53787 0.6507 2.33875 0.57728 2 1
SRR6660293 35 42,483,528 0.5023 0.676 2.48033 0.5659 2 1
SRR6660317 20 103,761,243 0.82581 0.7146 2.16838 0.24974 4 1
SRR6660318 35 51,681,507 0.4406 0.7225 2.2217 0.67015 1 1
SRR6660319 20 89,880,692 0.84431 0.6638 1.85639 0.24251 4 1
SRR6660366 50 107,496,056 0.50007 0.6985 1.6062 0.70469 2 1
SRR6660367 35 47,318,401 0.51589 0.6097 2.33684 0.56043 2 1
SRR6660368 50 34,774,757 0.35239 0.7391 1.52463 0.73385 1 1
SRR6660417 20 28,179,966 0.33713 0.6544 1.51282 0.69985 1 1
SRR6660176 1 58,392,013 0.44801 0.7801 1.58925 0.74019 1 1
SRR6660228 35 46,147,756 0.48762 0.7578 2.48445 0.63634 1 1
SRR6660278 35 30,011,599 0.43841 0.6728 2.31542 0.62474 1 1
SRR6660316 35 33,771,395 0.51084 0.6704 2.26739 0.55821 2 1
SRR6660365 35 50,611,929 0.48623 0.6626 2.33313 0.60311 1 1
SRR6660416 35 55,127,206 0.69235 0.5121 2.56867 0.37956 3 1
SRR6660418 35 45,364,550 0.52623 0.5848 3.19747 0.52547 2 2
SRR6660419 35 10,840 0.11041 0.5523 None 0.00942 5 0
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
SRR6660158 14787 4909 5976 2930 14537 6251 4716 2641
SRR6660159 4115 1440 1393 648 5578 2890 1304 844
SRR6660161 4405 1623 1359 770 6434 3388 1330 1057
SRR6660301 34844 8358 14727 10054 33872 8661 14483 9527
SRR6660302 6004 2158 2010 1441 5414 2771 1244 1039
SRR6660303 42422 11207 16682 12454 39264 9259 16594 11718
SRR6660350 None None None None 5643 2802 1534 991
SRR6660351 None None None None 7351 3928 1659 1244
SRR6660352 None None None None 40579 9465 17765 11808
SRR6660400 None None None None 5762 3181 1412 888
SRR6660401 None None None None 9767 4641 2758 1739
SRR6660402 None None None None 5062 2745 1346 701
SRR6936827 None None None None 15745 6305 5316 3200
SRR6936828 None None None None 27245 8216 10599 6860
SRR6660160 15482 4952 6030 3399 14973 6583 4464 2927
SRR6660300 1644 753 489 211 2592 1694 493 248
SRR6660349 None None None None 47633 9157 21822 14776
SRR6660399 None None None None 659 496 124 35
SRR6660174 26885 7846 10203 6722 22908 6159 9484 5779
SRR6660175 12266 4299 4519 1914 8848 3967 2621 1524
SRR6660177 22672 8076 7574 4954 19947 6913 6807 4833
SRR6660226 24389 6869 9661 5944 21211 5513 8908 5421
SRR6660227 31768 9110 11077 9571 34854 7165 15407 10426
SRR6660229 31914 9888 10749 8952 29803 7407 12323 8408
SRR6660276 21438 6429 7973 5277 16997 5170 6507 4129
SRR6660277 14947 4004 6224 3171 10376 3695 3593 2283
SRR6660279 17332 5064 6898 3479 11954 4481 3876 2558
SRR6660292 24182 6918 9026 6536 23196 5852 9817 6132
SRR6660293 25042 7470 8809 6926 24087 6678 9424 6442
SRR6660317 19704 6330 7183 4369 17609 5779 6256 4377
SRR6660318 31979 8828 10971 9839 28981 6852 11580 8781
SRR6660319 19326 6848 6654 3859 16525 6194 5213 3830
SRR6660366 None None None None 35036 7385 15288 10586
SRR6660367 None None None None 21850 6265 8288 5945
SRR6660368 None None None None 23689 6959 9261 6101
SRR6660417 None None None None 15807 4656 6352 3887
SRR6660176 33314 10474 11232 9259 31950 7685 13312 9163
SRR6660228 27100 9381 9082 6644 25206 6833 10042 6456
SRR6660278 22259 7404 7679 5442 19103 6199 7169 4458
SRR6660316 22888 6278 8456 6312 17678 5096 6757 4744
SRR6660365 None None None None 23212 5785 9344 6743
SRR6660416 None None None None 17333 5665 6424 4048
SRR6660418 None None None None 23998 6895 9433 6319
SRR6660419 None None None None 6 0 1 5
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