Selected Cell
Cell:
Value:
Metadata Template
Metadata Example
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
| # This template/example is based on an Affymetrix ChIP-chip study where the results of the primary analysis are reported in BAR and BED files. | ||||||||||||||||||||
| # This template is suitable for other genomic comparison studies (e.g. aCGH, DNA metylation) in which test and control groups are analyzed together (using Tiling Array Software (TAS), for instance). | ||||||||||||||||||||
| # A complete submission will consist of: (1) a completed metadata worksheet, (2) the primary analysis results files (usually BAR/BED but can also be other file types), and (3) the original CEL files. | ||||||||||||||||||||
| # Click the Metadata Example tab below to view a completed worksheet | ||||||||||||||||||||
| # Field names (in blue on this page) should not be edited. Hover over cells containing field names to view field content guidelines or, | ||||||||||||||||||||
| # CLICK HERE for Field Content Guidelines Web page. | ||||||||||||||||||||
| SERIES | ||||||||||||||||||||
| # This section describes the overall experiment. | ||||||||||||||||||||
| title | ||||||||||||||||||||
| summary | ||||||||||||||||||||
| summary | ||||||||||||||||||||
| overall design | ||||||||||||||||||||
| contributor | ||||||||||||||||||||
| contributor (SEEKID) | ||||||||||||||||||||
| SEEK Project | Project | |||||||||||||||||||
| Experiment Class (assay Type) | transcripomics | |||||||||||||||||||
| Experiment Design type | ExperimentDesignType | |||||||||||||||||||
| Technology type | microarray | |||||||||||||||||||
| quality control type | QualityControlDescriptionType | |||||||||||||||||||
| SAMPLES | ||||||||||||||||||||
| # The Sample names in the first column are arbitrary | ||||||||||||||||||||
| # CLICK HERE to find the Affymetrix platform accession number (GPLxxxx). | ||||||||||||||||||||
| Sample name | title | results file | test: source name | test: CEL file | test: organism | characteristics:NCBI_ID | characteristics:Strain | characteristics:Genotype | characteristics:Phenotype | test: characteristics: tag | test: molecule | test: label | ctrl: source name | ctrl: CEL file | ctrl: organism | ctrl: characteristics: tag | ctrl: molecule | ctrl: label | description | platform |
| COMPARISON 1 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 2 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 3 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 4 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 5 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 6 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 7 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 8 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON 9 | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| COMPARISON X | organism | MaterialType | LabelCompound | organism | ||||||||||||||||
| PROTOCOLS | ||||||||||||||||||||
| # This section includes protocols and fields which are common to all Samples. | ||||||||||||||||||||
| # Protocols which are applicable to specific Samples (i.e. test or control) should be included in additional columns of the SAMPLES section instead. | ||||||||||||||||||||
| growth protocol | ||||||||||||||||||||
| treatment protocol | ||||||||||||||||||||
| extract protocol | ||||||||||||||||||||
| label protocol | ||||||||||||||||||||
| hyb protocol | ||||||||||||||||||||
| scan protocol | ||||||||||||||||||||
| data processing | ||||||||||||||||||||
| additional results files | ||||||||||||||||||||
| results file descriptions | ||||||||||||||||||||
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
AA
AB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
| SERIES | |||||||||||||||||||||||||||
| title | Genome-Wide Gli3 Binding Sites in the E11.5 Mouse Limb Bud | ||||||||||||||||||||||||||
| summary | Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clustering, highlighting the complexity of cis-regulatory interactions. Further, Gli3 binds inertly to previously identified neural-specific Gli enhancers, demonstrating the accessibility of their cis-regulatory elements. Intersection of DNA binding data with gene expression profiles predicted 205 putative limb target genes. | ||||||||||||||||||||||||||
| summary | The supplementary bed file contains all 5,274 high quality binding Gli3 binding sites reported in the paper. | ||||||||||||||||||||||||||
| overall design | RosaGli3T-FLAG limb buds ChIPed with FLAG (Gli3-repressor binding sites) vs. Input in E11.5 mouse limb buds. | ||||||||||||||||||||||||||
| contributor | Hongkai,,Ji | ||||||||||||||||||||||||||
| contributor | Steven,A,Vokes | ||||||||||||||||||||||||||
| SAMPLES | |||||||||||||||||||||||||||
| # The corresponding example matrix table is included in the next worksheet. | |||||||||||||||||||||||||||
| Sample name | title | results file | results file | test: source name | test: CEL file | test: CEL file | test: CEL file | test: organism | test: characteristics: age | test: characteristics: tissue | test: characteristics: tissue | test: characteristics: antibody | test: molecule | test: label | ctrl: source name | ctrl: CEL file | ctrl: CEL file | ctrl: CEL file | ctrl: organism | ctrl: characteristics: age | ctrl: characteristics: tissue | ctrl: characteristics: tissue | ctrl: characteristics: antibody | ctrl: molecule | ctrl: label | description | platform |
| Gli3Genome_mm8_1 | Gli3Genome_mm8_1 | Gli3Genome_mm8_1.fc.bar | Gli3Genome_mm8_1.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(A)_Gli3T_1_31.CEL | 060723_ChIP(A)_Gli3T_2_02.CEL | 060725_ChIP(A)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(A)_Gli3T_1_31.CEL | 060723_Input(A)_Gli3T_2_02.CEL | 060725_Input(A)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip A | GPL6444 |
| Gli3Genome_mm8_2 | Gli3Genome_mm8_2 | Gli3Genome_mm8_2.fc.bar | Gli3Genome_mm8_2.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(B)_Gli3T_1_31.CEL | 060723_ChIP(B)_Gli3T_2_02.CEL | 060725_ChIP(B)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(B)_Gli3T_1_31_Rescan.CEL | 060723_Input(B)_Gli3T_2_02.CEL | 060725_Input(B)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip B | GPL6445 |
| Gli3Genome_mm8_3 | Gli3Genome_mm8_3 | Gli3Genome_mm8_3.fc.bar | Gli3Genome_mm8_3.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(C)_Gli3T_1_31.CEL | 060723_ChIP(C)_Gli3T_2_02.CEL | 060725_ChIP(C)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(C)_Gli3T_1_31.CEL | 060723_Input(C)_Gli3T_2_02.CEL | 060815_Input(C)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip C | GPL6446 |
| Gli3Genome_mm8_4 | Gli3Genome_mm8_4 | Gli3Genome_mm8_4.fc.bar | Gli3Genome_mm8_4.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(D)_Gli3T_1_31.CEL | 060723_ChIP(D)_Gli3T_2_02.CEL | 060725_ChIP(D)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(D)_Gli3T_1_31.CEL | 060723_Input(D)_Gli3T_2_02.CEL | 060725_Input(D)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip D | GPL6447 |
| Gli3Genome_mm8_5 | Gli3Genome_mm8_5 | Gli3Genome_mm8_5.fc.bar | Gli3Genome_mm8_5.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(E)_Gli3T_1_31.CEL | 060724_ChIP(E)_Gli3T_2_02.CEL | 060726_ChIP(E)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(E)_Gli3T_1_31.CEL | 060724_Input(E)_Gli3T_2_02.CEL | 060726_Input(E)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip E | GPL6448 |
| Gli3Genome_mm8_6 | Gli3Genome_mm8_6 | Gli3Genome_mm8_6.fc.bar | Gli3Genome_mm8_6.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(F)_Gli3T_1_31.CEL | 060724_ChIP(F)_Gli3T_2_02.CEL | 060726_ChIP(F)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(F)_Gli3T_1_31.CEL | 060724_Input(F)_Gli3T_2_02.CEL | 060726_Input(F)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip F | GPL6449 |
| Gli3Genome_mm8_7 | Gli3Genome_mm8_7 | Gli3Genome_mm8_7.fc.bar | Gli3Genome_mm8_7.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_ChIP(G)_Gli3T_1_31.CEL | 060724_ChIP(G)_Gli3T_2_02.CEL | 060726_ChIP(G)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060706_Input(G)_Gli3T_1_31.CEL | 060724_Input(G)_Gli3T_2_02.CEL | 060815_Input(G)_Gli3T_2_03.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, chip G | GPL6450 |
| Gli1Promoter_mm8 | Gli1Promoter_mm8 | Gli1Limb_peak_1.fc.bar | Gli1Limb_peak_1.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli1-Flag limb buds | 060605_ChIP_Gli1_4_10.CEL | 060605_ChIP_Gli1_4_11.CEL | 060605_ChIP_Gli1_5_22.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli1-Flag limb buds | 060605_Input_Gli1_4_10.CEL | 060605_Input_Gli1_4_11.CEL | 060605_Input_Gli1_5_22.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI1 ChIP Biological Rep 1-3, promoter | GPL5811 |
| Gli3Promoter_mm8 | Gli3Promoter_mm8 | Gli3Limb_peak_1.fc.bar | Gli3Limb_peak_1.ma.bar | FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060504_ChIP_GliAct_EB.CEL | 516_ChIP_Gli3T_5_10.CEL | 060516_ChIP_Gli3T_5_8.CEL | Mus musculus | E11.5 | embryo | limb buds | FLAG M2 mouse monoclonal | genomic DNA | biotin | Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds | 060504_Input_EB.CEL | 060516_Input_Gli3T_5_11.CEL | 060516_Input_Gli3T_5_8.CEL | Mus musculus | E11.5 | embryo | limb buds | none | genomic DNA | biotin | GLI3 ChIP Biological Rep 1-3, promoter | GPL5811 |
| Ant_K4 | Ant_K4 | Ant_K4_1.fc.bar | Ant_K4_1.ma.bar | H3K4me3 ChIP DNA from E11.5 anterior limb buds | 060926_ChIP_Ant_K4.CEL | 061006_ChIP_Ant_K4.CEL | Mus musculus | E11.5 | embryo | limb buds (anterior 1/3d) | H3K4Me3 | genomic DNA | biotin | Input DNA from E11.5 anterior limb buds | 060926_ChIP_Ant_Input.CEL | 061006_ChIP_Ant_Input.CEL | Mus musculus | E11.5 | embryo | limb buds (anterior 1/3d) | none | genomic DNA | biotin | H3K4 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter | GPL5811 | ||
| Ant_K27 | Ant_K27 | Ant_K27_1.fc.bar | Ant_K27_1.ma.bar | H3K27me3 ChIP DNA from E11.5 anterior limb buds | 060926_ChIP_Ant_K27.CEL | 061006_ChIP_Ant_K27.CEL | Mus musculus | E11.5 | embryo | limb buds (anterior 1/3d) | H3K27Me3 | genomic DNA | biotin | Input DNA from E11.5 anterior limb buds | 060926_ChIP_Ant_Input.CEL | 061006_ChIP_Ant_Input.CEL | Mus musculus | E11.5 | embryo | limb buds (anterior 1/3d) | none | genomic DNA | biotin | H3K27 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter | GPL5811 | ||
| Ant_PanH3 | Ant_PanH3 | Ant_PanH3_1.fc.bar | Ant_PanH3_1.ma.bar | Pan Histone H3 ChIP DNA from E11.5 anterior limb buds | 060926_ChIP_Ant_PanH3.CEL | 061006_ChIP_Ant_PanH3.CEL | Mus musculus | E11.5 | embryo | limb buds (anterior 1/3d) | Histone H3 | genomic DNA | biotin | Input DNA from E11.5 anterior limb buds | 060926_ChIP_Ant_Input.CEL | 061006_ChIP_Ant_Input.CEL | Mus musculus | E11.5 | embryo | limb buds (anterior 1/3d) | none | genomic DNA | biotin | PanH3 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter | GPL5811 | ||
| Post_K4 | Post_K4 | Post_K4_1.fc.bar | Post_K4_1.ma.bar | H3K4me3 ChIP DNA from E11.5 posterior limb buds | 060926_ChIP_Post_K4.CEL | 061006_ChIP_Post_K4.CEL | Mus musculus | E11.5 | embryo | limb buds (posterior 2/3d) | H3K4Me3 | genomic DNA | biotin | Input DNA from E11.5 posterior limb buds | 060926_ChIP_Post_Input.CEL | 061006_ChIP_Post_Input.CEL | Mus musculus | E11.5 | embryo | limb buds (posterior 2/3d) | none | genomic DNA | biotin | H3K4 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter | GPL5811 | ||
| Post_K27 | Post_K27 | Post_K27_1.fc.bar | Post_K27_1.ma.bar | H3K27me3 ChIP DNA from E11.5 posterior limb buds | 060926_ChIP_Post_K27.CEL | 061006_ChIP_Post_K27.CEL | Mus musculus | E11.5 | embryo | limb buds (posterior 2/3d) | H3K27Me3 | genomic DNA | biotin | Input DNA from E11.5 posterior limb buds | 060926_ChIP_Post_Input.CEL | 061006_ChIP_Post_Input.CEL | Mus musculus | E11.5 | embryo | limb buds (posterior 2/3d) | none | genomic DNA | biotin | H3K27 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter | GPL5811 | ||
| Post_PanH3 | Post_PanH3 | Post_PanH3_1.fc.bar | Post_PanH3_1.ma.bar | Pan Histone H3 ChIP DNA from E11.5 posterior limb buds | 060926_ChIP_Post_PanH3.CEL | 061006_ChIP_Post_PanH3.CEL | Mus musculus | E11.5 | embryo | limb buds (posterior 2/3d) | Histone H3 | genomic DNA | biotin | Input DNA from E11.5 posterior limb buds | 060926_ChIP_Post_Input.CEL | 061006_ChIP_Post_Input.CEL | Mus musculus | E11.5 | embryo | limb buds (posterior 2/3d) | none | genomic DNA | biotin | PanH3 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter | GPL5811 | ||
| PROTOCOLS | |||||||||||||||||||||||||||
| growth protocol | |||||||||||||||||||||||||||
| treatment protocol | |||||||||||||||||||||||||||
| extract protocol | Rosa Gli3TFLAG c/c females mice were crossed with Prrx1Cre homozygous male drivers and litters were taken at E11.5. Embryos (generally 9) were dissected and forelimbs and hindlimbs were dissected into PBS, trypsinized in 300μl trypsin-EDTA for 5 minutes at 37º, inactivated by adding 700μl of DMEM with 10% calf serum, and cross-linked with 1% formaldehyde for 30 minutes. ChIP and LMPCR was performed according to our previous protocol (Vokes et al., 2007) with the following modifications. Chromatin was sonicated in 2ml of buffer 3 using 10x30 second pulses on a Branson 450 Sonifier (3 pulses on setting 4, then 7 on setting 5). For whole genome arrays, three ChIP reactions were set up in parallel with 500μl each (with 15μl of each biological sample reserved for an input control) – single promoter arrays used a single ChIP sample. At the final step, the samples were pooled and enrichment was validated using qPCR. For LMPCR, the pooled samples were divided into three and processed in parallel using 0.25mM dATP, dCTP, dGTP, 0.2mM dTTP and 0.05mM dUTP with 27 total cycles and then re-pooled after PCR cleanup. Each pooled set of reaction yielded >38μg of amplified sample. The linearity of amplification was confirmed by comparing qPCR values with the values from the unamplified samples. | ||||||||||||||||||||||||||
| label protocol | Samples (37.5-44μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments | ||||||||||||||||||||||||||
| hyb protocol | Approximately 8.25μg of DNA was hybridzed per array using the Affymetrix hybridization kit. For these 7 array sets, 4 arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays. | ||||||||||||||||||||||||||
| scan protocol | Arrays were scanned on an Affymetrix Scanner 3000 7G | ||||||||||||||||||||||||||
| data processing | Data was quantile normalized and analyzed with TileMap. Log2(IP/Input) fold changes (fc) and TileMap moving average (ma) statistics were reported in BAR files. | ||||||||||||||||||||||||||
| additional results files | GLI3SD6.bed | ||||||||||||||||||||||||||
| results file descriptions | fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe. File GLI3SD6.bed contains all 5,274 high quality binding Gli3 binding sites reported in the paper. | ||||||||||||||||||||||||||
