GSE34448, CAGE data from several cell lines and locations.

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.

• Raw data was downloaded from: UCSC
• Input file format: BAM
• Download date: 26-9-2015

From H. sapiens (Feb 2009 GRCh37/hg19).

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	-

Merged samples:

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).

BAM file were converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).
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.

• Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR
  Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. 22955620
• GEO series GSE34448: RNA Subcellular CAGE Localization from ENCODE/RIKEN