Background
Methods
Cell Culture and siRNA transfections
RNA assays
Quantitative reverse transcription-PCR
Branched DNA assay
Whole transcriptome analysis
Caspase 8 and Caspase 3/7 assays
Western blot analysis
Bioinformatic and statistical analysis
Gene expression microarray data
Gene expression microarray data analysis: Histone genes
Ref Seq | Gene Symbol | Chromosomal position | Agilent Probe | CASP8AP2/FLASH SILENCED SW480 cells | Published HeLa data | ||||
---|---|---|---|---|---|---|---|---|---|
Fold change (Log
2
) siCASP8AP2.3
|
q values
siCASP8AP2.3
|
Fold change (Log
2
) siCASP8AP2.6
|
q values
siCASP8AP2.6
|
Narita et al
|
Shepard et al PAS seq
#
| ||||
NM_012115 | CASP8AP2 | chr6:90640368-90640427 | A_23_P58898 |
-2.06
| 6.28E-15 |
-1.81
| 6.14E-13 | - | - |
NM_003548 | HIST2H4A/ HIST2H4B | chr1:146617469-146617528 | A_23_P436281 |
3.01
| 1.21E-20 |
2.61
| 4.73E-18 | chr1 - 148098952-1 | |
NM_003516 | HIST2H2AA3/ | chr1:146635701-146635760 | A_23_P309381 |
3.80
| 9.00E-09 |
4.24
| 4.19E-10 | Yes* | |
HIST2H2AA4 | |||||||||
NM_003516 | HIST2H2AA3/
1
| chr1:146636178-146636234 | A_23_P103981 |
3.83
| 3.55E-11 |
3.72
| 8.65E-11 | ||
HIST2H2AA4 | |||||||||
NM_003528 | HIST2H2BE | chr1:146669546-146669487 | A_24_P148321 |
3.78
| 5.33E-13 |
3.63
| 1.93E-12 | chr1-148122634-6, chr-148124269-1, chr1-148124357-1 | |
NM_003528 | HIST2H2BE | chr1:146670196-146670137 | A_23_P149545 |
2.24
| 8.74E-14 |
2.39
| 7.62E-15 | ||
NM_003528 | HIST2H2BE
2
| chr1:146671162-146671103 | A_24_P156911 |
3.52
| 6.07E-19 |
3.49
| 7.82E-19 | ||
NM_003517 | HIST2H2AC | chr1:146671911-146671970 | A_24_P8721 |
3.17
| 3.73E-16 |
2.97
| 3.91E-15 | chr1-148125568-4 | |
NM_003517 | HIST2H2AC | chr1:146671936-146671995 | A_23_P301247 |
-1.90
| 8.19E-10 |
-2.02
| 1.36E-10 | ||
NM_175065 | HIST2H2AB | chr1:146672317-146672258 | A_24_P68631 |
3.88
| 1.18E-17 |
3.77
| 3.43E-17 | ||
NM_033445 | HIST3H2A | chr1:224952044-224951985 | A_23_P149301 |
3.10
| 1.82E-16 |
3.17
| 7.19E-17 | ||
NM_175055 | HIST3H2BB | chr1:224952760-224952819 | A_23_P332992 |
3.50
| 2.92E-16 |
3.42
| 6.04E-16 | ||
NM_003537 | HIST1H3B | chr6:26139947-26139888 | A_24_P174924 |
1.57
| 9.00E-06 |
1.12
| 1.50E-03 | ||
NM_003537 | HIST1H3B | chr6:26139960-26139901 | A_23_P93258 |
3.48
| 1.00E-13 |
3.31
| 5.69E-13 | ||
NM_003513 | HIST1H2AB | chr6:26141499-26141440 | A_24_P223384 |
1.93
| 3.63E-10 |
1.95
| 2.41E-10 | ||
NM_021062 | HIST1H2BB | chr6:26151544-26151485 | A_23_P111054 |
3.14
| 2.36E-15 |
2.93
| 2.72E-14 | ||
NM_005319 | HIST1H1C | chr6:26164088-26164029 | A_23_P122443 |
3.33
| 1.27E-13 |
3.40
| 5.92E-14 | Yes | |
NM_003526 | HIST1H2BC | chr6:26232021-26231962 | A_23_P93180 |
3.36
| 5.81E-17 |
3.30
| 1.03E-16 | ||
NM_005321 | HIST1H1E | chr6:26264907-26264966 | A_23_P7976 |
3.35
| 1.45E-13 |
3.15
| 1.18E-12 | chr6-26265322-1 | |
NM_021063
3
| HIST1H2BD | chr6:26266453-26266512 | A_24_P146211 |
3.87
| 1.47E-19 |
3.77
| 4.38E-19 | Yes | ch6-26279217-1, ch6-26279551-20, chr6-26266834-7 |
NM_003523 | HIST1H2BE | chr6:26292319-26292378 | A_23_P30776 |
3.42
| 2.47E-16 |
3.44
| 1.72E-16 | Yes | |
NM_003530 | HIST1H3D | chr6:26305256-26305197 | A_23_P219045 |
3.82
| 1.30E-14 |
3.83
| 1.10E-14 | ||
NM_003530 | HIST1H3D | chr6:26305296-26305237 | A_24_P217834 |
2.99
| 3.58E-13 |
3.09
| 1.01E-13 | ||
NM_021065 | HIST1H2AD
4
| chr6:26307121-26307062 | A_23_P428184 |
4.23
| 6.78E-16 |
4.21
| 6.99E-16 | ||
NM_003522 | HIST1H2BF | chr6:26308082-26308141 | A_23_P42178 |
3.44
| 3.50E-16 |
3.41
| 4.47E-16 | Yes | |
NM_003518 | HIST1H2BG | chr6:26324755-26324696 | A_23_P167997 |
3.93
| 1.29E-20 |
3.78
| 6.51E-20 | chr6-26324393-2 | |
NM_021052 | HIST1H2AE | chr6:26325533-26325592 | A_23_P59045 |
4.32
| 9.87E-24 |
3.90
| 7.90E-22 | Yes | chr6-26325683-13 |
NM_005320 | HIST1H1D | chr6:26342737-26342678 | A_24_P260639 |
3.59
| 1.39E-13 |
3.22
| 5.45E-12 | ||
NM_003540 | HIST1H4F | chr6:26348797-26348856 | A_23_P359540 |
2.78
| 1.14E-16 |
2.44
| 1.42E-14 | ||
NM_021018 | HIST1H3F | chr6:26358626-26358567 | A_23_P30799 |
3.36
| 2.65E-14 |
3.15
| 2.41E-13 | chr6-26358379-1 | |
NM_003524 | HIST1H2BH | chr6:26360201-26360260 | A_23_P366216 |
3.19
| 4.08E-16 |
3.04
| 2.19E-15 | Yes | chr6-26360284-3 |
BC012185
5
| HIST1H3G | chr6:26377826-26377767 | A_32_P794894 |
3.07
| 7.43E-30 |
3.54
| 8.23E-33 | ||
NM_003534 | HIST1H3G | chr6:26379448-26379389 | A_23_P42198 |
1.15
| 1.39E-04 |
1.27
| 3.34E-05 | ||
NM_003525 | HIST1H2BI | chr6:26381354-26381413 | A_23_P111041 |
3.51
| 7.27E-15 |
3.69
| 1.12E-15 | Yes | chr6-26381629-2 |
NM_003543 | HIST1H4H | chr6:26393535-26393476 | A_23_P323685 |
4.03
| 1.13E-21 |
3.97
| 2.14E-21 | ||
NM_021058 | HIST1H2BJ | chr6:27208356-27208297 | A_24_P55148 |
3.81
| 3.69E-20 |
3.81
| 3.41E-20 | ||
NM_021064 | HIST1H2AG | chr6:27209136-27209195 | A_24_P303354 |
1.30
| 2.26E-10 |
1.08
| 3.92E-08 | chr6-27209294-1 ch6-27210796-2 chr6-272111049-7 | |
BC016677
6
| HIST1H2AG | chr6:27210269-27210328 | A_24_P414658 |
4.19
| 9.07E-25 |
4.05
| 4.31E-24 | ||
NM_003495 | HIST1H4I | chr6:27215204-27215263 | A_24_P20873 |
1.75
| 1.69E-06 |
2.63
| 4.38E-11 | ||
NM_080593 | HIST1H2BK | chr6:27221956-27221897 | A_23_P145238 |
2.96
| 4.33E-10 |
3.34
| 1.12E-11 | Yes | |
NM_080596 | HIST1H2AH | chr6:27223225-27223284 | A_23_P81859 |
1.67
| 1.41E-12 |
1.51
| 3.81E-11 | ||
NM_003519 | HIST1H2BL | chr6:27883324-27883265 | A_23_P8013 |
3.25
| 1.72E-14 |
3.10
| 8.91E-14 | chr6-27883235-1 | |
NM_003536 | HIST1H3H | chr6:27886003-27886062 | A_23_P333484 |
4.52
| 3.48E-25 |
4.05
| 4.51E-23 | Yes | |
NM_021066 | HIST1H2AJ/
7
HIST1H2AI | chr6:27890225-27890166 | A_23_P168014 |
2.30
| 6.42E-10 |
2.11
| 6.71E-09 | chr6-27890034-2 | |
NM_021066 | HIST1H2AJ/ HIST1H2AI | chr6:27890432-27890373 | A_24_P394510 |
2.44
| 5.52E-08 |
2.34
| 1.62E-07 | ||
NM_003521 | HIST1H2BM | chr6:27890982-27891041 | A_24_P3783 |
3.29
| 2.61E-14 |
3.39
| 8.13E-15 | ||
NM_003510 | HIST1H2AK | chr6:27913767-27913708 | A_24_P217848 |
1.56
| 1.98E-13 |
1.48
| 1.27E-12 | ||
NM_003520 | HIST1H2BN
8
| chr6:27914524-27914583 | A_23_P402081 |
3.46
| 6.89E-19 |
3.45
| 7.27E-19 | chr6-27927954-1 | |
NM_003511 | HIST1H2AL | chr6:27941481-27941540 | A_23_P363174 |
1.73
| 2.13E-11 |
1.97
| 2.31E-13 | chr6-27941554-1 | |
NM_005322 | HIST1H1B | chr6:27942667-27942608 | A_23_P250385 |
-1.35
| 8.17E-03 |
-1.61
| 2.22E-03 | ||
NM_003546 | HIST1H4L | chr6:27948987-27948928 | A_23_P70480 |
-1.46
| 3.81E-02 |
-1.59
| 3.28E-02 | ||
NM_003514 | HIST1H2AM | chr6:27968545-27968486 | A_32_P221799 |
4.10
| 3.17E-22 |
3.58
| 8.93E-20 | ||
NM_003514 | HIST1H2AM | chr6:27968615-27968556 | A_24_P86389 |
2.40
| 5.41E-15 |
2.35
| 1.10E-14 | ||
NM_003527 | HIST1H2BO | chr6:27969567-27969626 | A_23_P59069 |
3.25
| 1.97E-17 |
3.23
| 2.20E-17 | ||
9
BC020884 | HIST4H4 | chr12:14813388-14813329 | A_24_P261691 |
1.14
| 9.21E-09 |
1.68
| 5.34E-14 | ||
NM_002105 | H2AFX | chr11:118469860-118469801 | A_24_P38895 |
0.92
| 8.28E-06 |
0.82
| 6.13E-05 | ||
NM_177925 | H2AFJ | chr12:14818894-14818953 | A_24_P236003 |
1.08
| 1.95E-12 |
0.91
| 4.53E-10 | ||
NM_177925 | H2AFJ | chr12:14819082-14819141 | A_23_P204277 |
0.69
| 3.92E-06 |
0.80
| 1.51E-07 |