This experiment contains CAGE data (Cap Analysis of Gene Expression) from 15 cell lines and 3 sub-cellular compartments (nucleus, cytoplasm and cell) for poly-A(+) and poly-A(-) long-RNA. It provides a genome wide catalog of transcription start sites.
Additional information on the cell lines can be found on the ENCODE Common Cell Types page at UCSC.
Transcription Profiling data:
| Filename | Description | Feature | GEO-ID | |
| 1 | A549_cell_longPolyA_rep1.sga | A549 cell longPolyA rep1 | CAGE | - |
| 2 | A549_cell_longPolyA_rep2.sga | A549 cell longPolyA rep2 | CAGE | - |
| 3 | A549_cytosol_longPolyA_rep3.sga | A549 cytosol longPolyA rep3 | CAGE | - |
| 4 | A549_cytosol_longPolyA_rep4.sga | A549 cytosol longPolyA rep4 | CAGE | - |
| 5 | A549_nucleus_longPolyA_rep3.sga | A549 nucleus longPolyA rep3 | CAGE | - |
| 6 | A549_nucleus_longPolyA_rep4.sga | A549 nucleus longPolyA rep4 | CAGE | - |
| 7 | AG04450_cell_longPolyA_rep1.sga | AG04450 cell longPolyA rep1 | CAGE | - |
| 8 | AG04450_cell_longPolyA_rep2.sga | AG04450 cell longPolyA rep2 | CAGE | - |
| 9 | BJ_cell_longPolyA_rep1.sga | BJ cell longPolyA rep1 | CAGE | - |
| 10 | BJ_cell_longPolyA_rep2.sga | BJ cell longPolyA rep2 | CAGE | - |
| 11 | CD20+_cell_longPolyA_rep1.sga | CD20+ cell longPolyA rep1 | CAGE | - |
| 12 | CD20+_cell_longPolyA_rep2.sga | CD20+ cell longPolyA rep2 | CAGE | - |
| 13 | CD34+_Mobilized_cell_longPolyA_rep1.sga | CD34+ Mobilized cell longPolyA rep1 | CAGE | - |
| 14 | GM12878_cell_longPolyA_rep1.sga | GM12878 cell longPolyA rep1 | CAGE | - |
| 15 | GM12878_cell_longPolyA_rep2.sga | GM12878 cell longPolyA rep2 | CAGE | - |
| 16 | GM12878_cytosol_longNonPolyA.sga | GM12878 cytosol longNonPolyA | CAGE | - |
| 17 | GM12878_cytosol_longNonPolyA_rep0.sga | GM12878 cytosol longNonPolyA rep0 | CAGE | - |
| 18 | GM12878_cytosol_longPolyA_rep1.sga | GM12878 cytosol longPolyA rep1 | CAGE | - |
| 19 | GM12878_cytosol_longPolyA_rep2.sga | GM12878 cytosol longPolyA rep2 | CAGE | - |
| 20 | GM12878_nucleolus_total.sga | GM12878 nucleolus total | CAGE | - |
| 21 | GM12878_nucleus_longNonPolyA.sga | GM12878 nucleus longNonPolyA | CAGE | - |
| 22 | GM12878_nucleus_longNonPolyA_rep1.sga | GM12878 nucleus longNonPolyA rep1 | CAGE | - |
| 23 | GM12878_nucleus_longPolyA_rep1.sga | GM12878 nucleus longPolyA rep1 | CAGE | - |
| 24 | GM12878_nucleus_longPolyA_rep2.sga | GM12878 nucleus longPolyA rep2 | CAGE | - |
| 25 | H1-hESC_cell_longNonPolyA.sga | H1-hESC cell longNonPolyA | CAGE | - |
| 26 | H1-hESC_cell_longNonPolyA_rep0.sga | H1-hESC cell longNonPolyA rep0 | CAGE | - |
| 27 | H1-hESC_cell_longPolyA_rep1.sga | H1-hESC cell longPolyA rep1 | CAGE | - |
| 28 | H1-hESC_cell_longPolyA_rep2.sga | H1-hESC cell longPolyA rep2 | CAGE | - |
| 29 | H1-hESC_cytosol_longPolyA_rep2.sga | H1-hESC cytosol longPolyA rep2 | CAGE | - |
| 30 | H1-hESC_nucleus_longPolyA_rep2.sga | H1-hESC nucleus longPolyA rep2 | CAGE | - |
| 31 | HAoAF_cell_longPolyA_rep1.sga | HAoAF cell longPolyA rep1 | CAGE | - |
| 32 | HAoAF_cell_longPolyA_rep2.sga | HAoAF cell longPolyA rep2 | CAGE | - |
| 33 | HAoEC_cell_longPolyA_rep1.sga | HAoEC cell longPolyA rep1 | CAGE | - |
| 34 | HAoEC_cell_longPolyA_rep2.sga | HAoEC cell longPolyA rep2 | CAGE | - |
| 35 | HCH_cell_longPolyA_rep1.sga | HCH cell longPolyA rep1 | CAGE | - |
| 36 | HCH_cell_longPolyA_rep2.sga | HCH cell longPolyA rep2 | CAGE | - |
| 37 | HFDPC_cell_longPolyA_rep1.sga | HFDPC cell longPolyA rep1 | CAGE | - |
| 38 | HFDPC_cell_longPolyA_rep2.sga | HFDPC cell longPolyA rep2 | CAGE | - |
| 39 | HMEpC_cell_longPolyA_rep1.sga | HMEpC cell longPolyA rep1 | CAGE | - |
| 40 | HOB_cell_longPolyA_rep1.sga | HOB cell longPolyA rep1 | CAGE | - |
| 41 | HOB_cell_longPolyA_rep2.sga | HOB cell longPolyA rep2 | CAGE | - |
| 42 | HPC-PL_cell_longPolyA_rep1.sga | HPC-PL cell longPolyA rep1 | CAGE | - |
| 43 | HPC-PL_cell_longPolyA_rep2.sga | HPC-PL cell longPolyA rep2 | CAGE | - |
| 44 | HPIEpC_cell_longPolyA_rep1.sga | HPIEpC cell longPolyA rep1 | CAGE | - |
| 45 | HPIEpC_cell_longPolyA_rep2.sga | HPIEpC cell longPolyA rep2 | CAGE | - |
| 46 | HSaVEC_cell_longPolyA_rep1.sga | HSaVEC cell longPolyA rep1 | CAGE | - |
| 47 | HSaVEC_cell_longPolyA_rep2.sga | HSaVEC cell longPolyA rep2 | CAGE | - |
| 48 | HUVEC_cell_longPolyA_rep1.sga | HUVEC cell longPolyA rep1 | CAGE | - |
| 49 | HUVEC_cell_longPolyA_rep2.sga | HUVEC cell longPolyA rep2 | CAGE | - |
| 50 | HUVEC_cytosol_longNonPolyA.sga | HUVEC cytosol longNonPolyA | CAGE | - |
| 51 | HUVEC_cytosol_longNonPolyA_rep0.sga | HUVEC cytosol longNonPolyA rep0 | CAGE | - |
| 52 | HUVEC_cytosol_longPolyA_rep3.sga | HUVEC cytosol longPolyA rep3 | CAGE | - |
| 53 | HUVEC_cytosol_longPolyA_rep4.sga | HUVEC cytosol longPolyA rep4 | CAGE | - |
| 54 | HUVEC_nucleus_longNonPolyA_rep1.sga | HUVEC nucleus longNonPolyA rep1 | CAGE | - |
| 55 | HUVEC_nucleus_longPolyA_rep3.sga | HUVEC nucleus longPolyA rep3 | CAGE | - |
| 56 | HUVEC_nucleus_longPolyA_rep4.sga | HUVEC nucleus longPolyA rep4 | CAGE | - |
| 57 | HVMF_cell_longPolyA_rep1.sga | HVMF cell longPolyA rep1 | CAGE | - |
| 58 | HVMF_cell_longPolyA_rep2.sga | HVMF cell longPolyA rep2 | CAGE | - |
| 59 | HWP_cell_longPolyA_rep1.sga | HWP cell longPolyA rep1 | CAGE | - |
| 60 | HWP_cell_longPolyA_rep2.sga | HWP cell longPolyA rep2 | CAGE | - |
| 61 | HeLa-S3_cell_longPolyA_rep1.sga | HeLa-S3 cell longPolyA rep1 | CAGE | - |
| 62 | HeLa-S3_cell_longPolyA_rep2.sga | HeLa-S3 cell longPolyA rep2 | CAGE | - |
| 63 | HeLa-S3_cytosol_longNonPolyA.sga | HeLa-S3 cytosol longNonPolyA | CAGE | - |
| 64 | HeLa-S3_cytosol_longNonPolyA_rep0.sga | HeLa-S3 cytosol longNonPolyA rep0 | CAGE | - |
| 65 | HeLa-S3_cytosol_longPolyA_rep1.sga | HeLa-S3 cytosol longPolyA rep1 | CAGE | - |
| 66 | HeLa-S3_cytosol_longPolyA_rep2.sga | HeLa-S3 cytosol longPolyA rep2 | CAGE | - |
| 67 | HeLa-S3_nucleolus_total.sga | HeLa-S3 nucleolus total | CAGE | - |
| 68 | HeLa-S3_nucleus_longNonPolyA_rep1.sga | HeLa-S3 nucleus longNonPolyA rep1 | CAGE | - |
| 69 | HeLa-S3_nucleus_longPolyA_rep1.sga | HeLa-S3 nucleus longPolyA rep1 | CAGE | - |
| 70 | HeLa-S3_nucleus_longPolyA_rep2.sga | HeLa-S3 nucleus longPolyA rep2 | CAGE | - |
| 71 | HepG2_cell_longPolyA_rep1.sga | HepG2 cell longPolyA rep1 | CAGE | - |
| 72 | HepG2_cell_longPolyA_rep2.sga | HepG2 cell longPolyA rep2 | CAGE | - |
| 73 | HepG2_cytosol_longNonPolyA.sga | HepG2 cytosol longNonPolyA | CAGE | - |
| 74 | HepG2_cytosol_longNonPolyA_rep0.sga | HepG2 cytosol longNonPolyA rep0 | CAGE | - |
| 75 | HepG2_cytosol_longPolyA_rep1.sga | HepG2 cytosol longPolyA rep1 | CAGE | - |
| 76 | HepG2_cytosol_longPolyA_rep2.sga | HepG2 cytosol longPolyA rep2 | CAGE | - |
| 77 | HepG2_nucleolus_total.sga | HepG2 nucleolus total | CAGE | - |
| 78 | HepG2_nucleus_longNonPolyA.sga | HepG2 nucleus longNonPolyA | CAGE | - |
| 79 | HepG2_nucleus_longNonPolyA_rep0.sga | HepG2 nucleus longNonPolyA rep0 | CAGE | - |
| 80 | HepG2_nucleus_longPolyA_rep1.sga | HepG2 nucleus longPolyA rep1 | CAGE | - |
| 81 | HepG2_nucleus_longPolyA_rep2.sga | HepG2 nucleus longPolyA rep2 | CAGE | - |
| 82 | IMR90_cell_longPolyA_rep1.sga | IMR90 cell longPolyA rep1 | CAGE | - |
| 83 | IMR90_cell_longPolyA_rep2.sga | IMR90 cell longPolyA rep2 | CAGE | - |
| 84 | IMR90_cytosol_longPolyA_rep1.sga | IMR90 cytosol longPolyA rep1 | CAGE | - |
| 85 | IMR90_cytosol_longPolyA_rep2.sga | IMR90 cytosol longPolyA rep2 | CAGE | - |
| 86 | IMR90_nucleus_longPolyA_rep1.sga | IMR90 nucleus longPolyA rep1 | CAGE | - |
| 87 | IMR90_nucleus_longPolyA_rep2.sga | IMR90 nucleus longPolyA rep2 | CAGE | - |
| 88 | K562_cell_longPolyA_rep1.sga | K562 cell longPolyA rep1 | CAGE | - |
| 89 | K562_cell_longPolyA_rep2.sga | K562 cell longPolyA rep2 | CAGE | - |
| 90 | K562_chromatin_total.sga | K562 chromatin total | CAGE | - |
| 91 | K562_cytosol_longNonPolyA.sga | K562 cytosol longNonPolyA | CAGE | - |
| 92 | K562_cytosol_longNonPolyA_rep0.sga | K562 cytosol longNonPolyA rep0 | CAGE | - |
| 93 | K562_cytosol_longPolyA.sga | K562 cytosol longPolyA | CAGE | - |
| 94 | K562_cytosol_longPolyA_rep1.sga | K562 cytosol longPolyA rep1 | CAGE | - |
| 95 | K562_cytosol_longPolyA_rep2.sga | K562 cytosol longPolyA rep2 | CAGE | - |
| 96 | K562_nucleolus_total.sga | K562 nucleolus total | CAGE | - |
| 97 | K562_nucleoplasm_total.sga | K562 nucleoplasm total | CAGE | - |
| 98 | K562_nucleus_longNonPolyA.sga | K562 nucleus longNonPolyA | CAGE | - |
| 99 | K562_nucleus_longNonPolyA_rep0.sga | K562 nucleus longNonPolyA rep0 | CAGE | - |
| 100 | K562_nucleus_longPolyA_rep1.sga | K562 nucleus longPolyA rep1 | CAGE | - |
| 101 | K562_nucleus_longPolyA_rep2.sga | K562 nucleus longPolyA rep2 | CAGE | - |
| 102 | K562_polysome_longNonPolyA.sga | K562 polysome longNonPolyA | CAGE | - |
| 103 | K562_polysome_longNonPolyA_rep0.sga | K562 polysome longNonPolyA rep0 | CAGE | - |
| 104 | MCF-7_cell_longPolyA_rep1.sga | MCF-7 cell longPolyA rep1 | CAGE | - |
| 105 | MCF-7_cell_longPolyA_rep2.sga | MCF-7 cell longPolyA rep2 | CAGE | - |
| 106 | MCF-7_cytosol_longPolyA_rep3.sga | MCF-7 cytosol longPolyA rep3 | CAGE | - |
| 107 | MCF-7_cytosol_longPolyA_rep4.sga | MCF-7 cytosol longPolyA rep4 | CAGE | - |
| 108 | MCF-7_nucleus_longPolyA_rep3.sga | MCF-7 nucleus longPolyA rep3 | CAGE | - |
| 109 | MCF-7_nucleus_longPolyA_rep4.sga | MCF-7 nucleus longPolyA rep4 | CAGE | - |
| 110 | Monocytes-CD14+_cell_longPolyA_rep1.sga | Monocytes-CD14+ cell longPolyA rep1 | CAGE | - |
| 111 | Monocytes-CD14+_cell_longPolyA_rep2.sga | Monocytes-CD14+ cell longPolyA rep2 | CAGE | - |
| 112 | NHDF_cell_longPolyA_rep1.sga | NHDF cell longPolyA rep1 | CAGE | - |
| 113 | NHDF_cell_longPolyA_rep2.sga | NHDF cell longPolyA rep2 | CAGE | - |
| 114 | NHEK_cell_longPolyA_rep1.sga | NHEK cell longPolyA rep1 | CAGE | - |
| 115 | NHEK_cell_longPolyA_rep2.sga | NHEK cell longPolyA rep2 | CAGE | - |
| 116 | NHEK_cytosol_longNonPolyA.sga | NHEK cytosol longNonPolyA | CAGE | - |
| 117 | NHEK_cytosol_longNonPolyA_rep0.sga | NHEK cytosol longNonPolyA rep0 | CAGE | - |
| 118 | NHEK_cytosol_longPolyA_rep3.sga | NHEK cytosol longPolyA rep3 | CAGE | - |
| 119 | NHEK_cytosol_longPolyA_rep4.sga | NHEK cytosol longPolyA rep4 | CAGE | - |
| 120 | NHEK_nucleus_longNonPolyA.sga | NHEK nucleus longNonPolyA | CAGE | - |
| 121 | NHEK_nucleus_longNonPolyA_rep0.sga | NHEK nucleus longNonPolyA rep0 | CAGE | - |
| 122 | NHEK_nucleus_longPolyA_rep3.sga | NHEK nucleus longPolyA rep3 | CAGE | - |
| 123 | NHEK_nucleus_longPolyA_rep4.sga | NHEK nucleus longPolyA rep4 | CAGE | - |
| 124 | NHEM.f_M2_cell_longPolyA_rep1.sga | NHEM.f M2 cell longPolyA rep1 | CAGE | - |
| 125 | NHEM.f_M2_cell_longPolyA_rep2.sga | NHEM.f M2 cell longPolyA rep2 | CAGE | - |
| 126 | NHEM_M2_cell_longPolyA_rep1.sga | NHEM M2 cell longPolyA rep1 | CAGE | - |
| 127 | NHEM_M2_cell_longPolyA_rep2.sga | NHEM M2 cell longPolyA rep2 | CAGE | - |
| 128 | SK-N-SH_RA_cell_longPolyA_rep1.sga | SK-N-SH RA cell longPolyA rep1 | CAGE | - |
| 129 | SK-N-SH_RA_cell_longPolyA_rep2.sga | SK-N-SH RA cell longPolyA rep2 | CAGE | - |
| 130 | SK-N-SH_cell_longPolyA_rep3.sga | SK-N-SH cell longPolyA rep3 | CAGE | - |
| 131 | SK-N-SH_cell_longPolyA_rep4.sga | SK-N-SH cell longPolyA rep4 | CAGE | - |
| 132 | SK-N-SH_cytosol_longPolyA_rep3.sga | SK-N-SH cytosol longPolyA rep3 | CAGE | - |
| 133 | SK-N-SH_cytosol_longPolyA_rep4.sga | SK-N-SH cytosol longPolyA rep4 | CAGE | - |
| 134 | SK-N-SH_nucleus_longPolyA_rep3.sga | SK-N-SH nucleus longPolyA rep3 | CAGE | - |
| 135 | SK-N-SH_nucleus_longPolyA_rep4.sga | SK-N-SH nucleus longPolyA rep4 | CAGE | - |
| 136 | SkMC_cell_longPolyA_rep1.sga | SkMC cell longPolyA rep1 | CAGE | - |
| 137 | SkMC_cell_longPolyA_rep2.sga | SkMC cell longPolyA rep2 | CAGE | - |
| 138 | hMSC-AT_cell_longPolyA_rep1.sga | hMSC-AT cell longPolyA rep1 | CAGE | - |
| 139 | hMSC-AT_cell_longPolyA_rep2.sga | hMSC-AT cell longPolyA rep2 | CAGE | - |
| 140 | hMSC-BM_cell_longPolyA_rep1.sga | hMSC-BM cell longPolyA rep1 | CAGE | - |
| 141 | hMSC-BM_cell_longPolyA_rep2.sga | hMSC-BM cell longPolyA rep2 | CAGE | - |
| 142 | hMSC-UC_cell_longPolyA_rep1.sga | hMSC-UC cell longPolyA rep1 | CAGE | - |
| 143 | hMSC-UC_cell_longPolyA_rep2.sga | hMSC-UC cell longPolyA rep2 | CAGE | - |
| 144 | prostate_cell_longNonPolyA.sga | prostate cell longNonPolyA | CAGE | - |
| 145 | prostate_cell_longNonPolyA_rep0.sga | prostate cell longNonPolyA rep0 | CAGE | - |
| 146 | all_cell_longPolyA.sga | All samples cell longPolyA | CAGE | - |
| 147 | all_cytosol_longPolyA.sga | All samples cytosol longPolyA | CAGE | - |
| 148 | all_nucleus_longPolyA.sga | All samples nucleus longPolyA | CAGE | - |
| 149 | all_cell_longNonPolyA.sga | All samples cell longNonPolyA | CAGE | - |
| 150 | all_cytosol_longNonPolyA.sga | All samples cytosol longNonPolyA | CAGE | - |
| 151 | all_nucleus_longNonPolyA.sga | All samples nucleus longNonPolyA | CAGE | - |
| 152 | all_samples.sga | All samples | CAGE | - |
BAM files were downloaded from UCSC
and converted in sga format using bamToBed
(SamTools) and bed2sga
(ChIP-Seq v. 1.5.2).
Samples marked as "All samples" are generated concatenating all
samples that belong to the same category (for example "All samples
cytosol longPolyA" is the result of concatenating all samples from
cytosol and longPlyA).
After a close inspection of the peak generated by these files, it appared clear that they were shifted of 1 nucleotide. In fact, Init element was not centered at position 0 as expected but at position -1. All the tags were then shifted accordingly to overcome this inconsistency.