GSE34448, CAGE data from several cell lines and locations

Description:

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.

Source

Files downloaded from the UCSC Genome Browser via URL: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage
Input file format: BAM

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly

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 -

Technical Notes:

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 center at position 0 as expected but at position -1. All the tags were then shifted accordingly to overcame this inconsistency.

References

  1. Djebali S, Davis CA, Merkel A, Dobin A et al.
    Landscape of transcription in human cells.
    Nature 2012 Sep 6;489(7414):101-8
    PMID: 22955620

  2. GEO series GSE34448 RNA Subcellular CAGE Localization from ENCODE/RIKEN.