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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 16, 2023 |
| Title |
Regulatory Enhancer Profiling of Mesenchymal-type Gastric Cancer Reveals Subtype-Specific Epigenomic Landscapes and Targetable Vulnerabilities |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Recent studies have highlighted mesenchymal-subtype GC (Mes-GC) as a clinically aggressive subtype with few treatment options. Genome-wide chromatin profiles of primary GCs and GC cell lines were generated to identify Mes-GC-specific enhancer landscapes. Computational analysis uncovered TEAD1 as a master regulator of Mes-GC enhancers. TEAD1 ChIP-seq and RNA-seq/H3K27ac ChIP-seq following TEAD1 knockdown was performed as validation experiments.
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| Overall design |
Genome-wide chromatin profiles of 49 primary GCs and GC cell lines were analyzed. TEAD1 ChIP-seq in 3 GC cell lines and RNA-seq/H3K27ac ChIP-seq following TEAD1 knockdown in 2 GC cell lines were also performed.
Raw files for primary tissue RNA-seq were not submitted due to patient privacy concerns.
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| Contributor(s) |
Ho S, Tan P |
| Citation(s) |
35817555 |
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| Submission date |
Oct 25, 2021 |
| Last update date |
Aug 17, 2023 |
| Contact name |
Shamaine Ho |
| E-mail(s) |
e0223167@u.nus.edu
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| Organization name |
Genome Institute of Singapore
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| Street address |
60 Biopolis Street
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| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
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| Samples (163)
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| GSM5655085 |
HGC27 H3K27ac |
| GSM5655086 |
Hs746T H3K27ac |
| GSM5655087 |
IM95 H3K27ac |
| GSM5655088 |
KATOIII H3K27ac |
| GSM5655089 |
LMSU H3K27ac |
| GSM5655090 |
MKN1 H3K27ac |
| GSM5655091 |
MKN7 H3K27ac |
| GSM5655092 |
NCC19 H3K27ac |
| GSM5655093 |
NCC59 H3K27ac |
| GSM5655094 |
OCUM1 H3K27ac |
| GSM5655095 |
RERFGC1B H3K27ac |
| GSM5655096 |
SNU16 H3K27ac |
| GSM5655097 |
SNU1750 H3K27ac |
| GSM5655098 |
SNU1967 H3K27ac |
| GSM5655099 |
SNU484 H3K27ac |
| GSM5655100 |
SNU719 H3K27ac |
| GSM5655101 |
TMK1 H3K27ac |
| GSM5655102 |
YCC10 H3K27ac |
| GSM5655103 |
YCC11 H3K27ac |
| GSM5655104 |
YCC20 H3K27ac |
| GSM5655105 |
YCC21 H3K27ac |
| GSM5655106 |
YCC22 H3K27ac |
| GSM5655107 |
YCC3 H3K27ac |
| GSM5655108 |
AGS Input |
| GSM5655109 |
CLS145 Input |
| GSM5655110 |
FU97 Input |
| GSM5655111 |
HGC27 Input |
| GSM5655112 |
Hs746T Input |
| GSM5655113 |
IM95 Input |
| GSM5655114 |
KATOIII Input |
| GSM5655115 |
LMSU Input |
| GSM5655116 |
MKN1 Input |
| GSM5655117 |
MKN7 Input |
| GSM5655118 |
NCC19 Input |
| GSM5655119 |
NCC59 Input |
| GSM5655120 |
OCUM1 Input |
| GSM5655121 |
RERFGC1B Input |
| GSM5655122 |
SNU16 Input |
| GSM5655123 |
SNU1750 Input |
| GSM5655124 |
SNU1967 Input |
| GSM5655125 |
SNU484 Input |
| GSM5655126 |
SNU719 Input |
| GSM5655127 |
TMK1 Input |
| GSM5655128 |
YCC10 Input |
| GSM5655129 |
YCC11 Input |
| GSM5655130 |
YCC20 Input |
| GSM5655131 |
YCC21 Input |
| GSM5655132 |
YCC22 Input |
| GSM5655133 |
YCC3 Input |
| GSM5655134 |
FU97 H3K4me1 |
| GSM5655135 |
KATOIII H3K4me1 |
| GSM5655136 |
NCC59 H3K4me1 |
| GSM5655137 |
OCUM1 H3K4me1 |
| GSM5655138 |
RERFGC1B H3K4me1 |
| GSM5655139 |
SNU16 H3K4me1 |
| GSM5655140 |
Hs746T H3K4me1 |
| GSM5655141 |
IM95 H3K4me1 |
| GSM5655142 |
SNU1750 H3K4me1 |
| GSM5655143 |
SNU1967 H3K4me1 |
| GSM5655144 |
YCC10 H3K4me1 |
| GSM5655145 |
YCC21 H3K4me1 |
| GSM5655146 |
YCC3 H3K4me1 |
| GSM5655147 |
LMSU TEAD1 ChIP |
| GSM5655148 |
LMSU Input (for TEAD1 ChIP) |
| GSM5655149 |
SNU1750 TEAD1 ChIP |
| GSM5655150 |
SNU1750 Input (for TEAD1 ChIP) |
| GSM5655151 |
YCC11 TEAD1 ChIP |
| GSM5655152 |
YCC11 Input (for TEAD1 ChIP) |
| GSM5655153 |
LMSU shLuc #1 H3K27ac |
| GSM5655154 |
LMSU shLuc #2 H3K27ac |
| GSM5655155 |
LMSU shLuc #3 H3K27ac |
| GSM5655156 |
LMSU shTEAD1 #1 H3K27ac |
| GSM5655157 |
LMSU shTEAD1 #2 H3K27ac |
| GSM5655158 |
LMSU shTEAD1 #3 H3K27ac |
| GSM5655159 |
LMSU shLuc #1 Input |
| GSM5655160 |
LMSU shLuc #2 Input |
| GSM5655161 |
LMSU shLuc #3 Input |
| GSM5655162 |
LMSU shTEAD1 #1 Input |
| GSM5655163 |
LMSU shTEAD1 #2 Input |
| GSM5655164 |
LMSU shTEAD1 #3 Input |
| GSM5655165 |
LMSU shLuc #1 RNA-seq |
| GSM5655166 |
LMSU shLuc #2 RNA-seq |
| GSM5655167 |
LMSU shLuc #3 RNA-seq |
| GSM5655168 |
LMSU shTEAD1 #1 RNA-seq |
| GSM5655169 |
LMSU shTEAD1 #2 RNA-seq |
| GSM5655170 |
LMSU shTEAD1 #3 RNA-seq |
| GSM5655171 |
SNU1750 shLuc #1 H3K27ac |
| GSM5655172 |
SNU1750 shLuc #2 H3K27ac |
| GSM5655173 |
SNU1750 shLuc #3 H3K27ac |
| GSM5655174 |
SNU1750 shTEAD1 #1 H3K27ac |
| GSM5655175 |
SNU1750 shTEAD1 #2 H3K27ac |
| GSM5655176 |
SNU1750 shTEAD1 #3 H3K27ac |
| GSM5655177 |
SNU1750 shLuc #1 Input |
| GSM5655178 |
SNU1750 shLuc #2 Input |
| GSM5655179 |
SNU1750 shLuc #3 Input |
| GSM5655180 |
SNU1750 shTEAD1 #1 Input |
| GSM5655181 |
SNU1750 shTEAD1 #2 Input |
| GSM5655182 |
SNU1750 shTEAD1 #3 Input |
| GSM5655183 |
SNU1750 shLuc #1 RNA-seq |
| GSM5655184 |
SNU1750 shLuc #2 RNA-seq |
| GSM5655185 |
SNU1750 shLuc #3 RNA-seq |
| GSM5655186 |
SNU1750 shTEAD1 #1 RNA-seq |
| GSM5655187 |
SNU1750 shTEAD1 #2 RNA-seq |
| GSM5655188 |
SNU1750 shTEAD1 #3 RNA-seq |
| GSM5655189 |
P001 H3K27ac |
| GSM5655190 |
P002 H3K27ac |
| GSM5655191 |
P003 H3K27ac |
| GSM5655192 |
P004 H3K27ac |
| GSM5655193 |
P005 H3K27ac |
| GSM5655194 |
P006 H3K27ac |
| GSM5655195 |
P007 H3K27ac |
| GSM5655196 |
P008 H3K27ac |
| GSM5655197 |
P009 H3K27ac |
| GSM5655198 |
P001 Input |
| GSM5655199 |
P002 Input |
| GSM5655200 |
P003 Input |
| GSM5655201 |
P004 Input |
| GSM5655202 |
P005 Input |
| GSM5655203 |
P006 Input |
| GSM5655204 |
P007 Input |
| GSM5655205 |
P008 Input |
| GSM5655206 |
P009 Input |
| GSM5655207 |
P001 RNA-seq |
| GSM5655208 |
P002 RNA-seq |
| GSM5655209 |
P003 RNA-seq |
| GSM5655210 |
P004 RNA-seq |
| GSM5655211 |
P005 RNA-seq |
| GSM5655212 |
P006 RNA-seq |
| GSM5655213 |
P007 RNA-seq |
| GSM5655214 |
P008 RNA-seq |
| GSM5655215 |
P009 RNA-seq |
| GSM6160199 |
AGS, H3K4me1 |
| GSM6160200 |
HGC27, H3K4me1 |
| GSM6160201 |
LMSU, H3K4me1 |
| GSM6160202 |
NCC19, H3K4me1 |
| GSM6160203 |
NUGC4, H3K4me1 |
| GSM6160204 |
SNU484, H3K4me1 |
| GSM6160205 |
SNU719, H3K4me1 |
| GSM6160206 |
YCC11, H3K4me1 |
| GSM6160207 |
NUGC4, Input |
| GSM6160208 |
SNU1750 Homo clone #1, H3K27ac |
| GSM6160209 |
SNU1750 Homo clone #2, H3K27ac |
| GSM6160210 |
SNU1750 Homo clone #3, H3K27ac |
| GSM6160211 |
SNU1750 Homo clone #4, H3K27ac |
| GSM6160212 |
SNU1750 Homo clone #5, H3K27ac |
| GSM6160213 |
SNU1750 WT clone #1, H3K27ac |
| GSM6160214 |
SNU1750 WT clone #2, H3K27ac |
| GSM6160215 |
SNU1750 WT clone #3, H3K27ac |
| GSM6160216 |
SNU1750 WT clone #4, H3K27ac |
| GSM6160217 |
SNU1750 WT clone #5, H3K27ac |
| GSM6160218 |
SNU1750 Homo clone #1, Input |
| GSM6160219 |
SNU1750 Homo clone #2, Input |
| GSM6160220 |
SNU1750 Homo clone #3, Input |
| GSM6160221 |
SNU1750 Homo clone #4, Input |
| GSM6160222 |
SNU1750 Homo clone #5, Input |
| GSM6160223 |
SNU1750 WT clone #1, Input |
| GSM6160224 |
SNU1750 WT clone #2, Input |
| GSM6160225 |
SNU1750 WT clone #3, Input |
| GSM6160226 |
SNU1750 WT clone #4, Input |
| GSM6160227 |
SNU1750 WT clone #5, Input |
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| Relations |
| BioProject |
PRJNA774273 |
| SRA |
SRP343001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186521_RAW.tar |
8.4 Gb |
(http)(custom) |
TAR (of BW, RESULTS, TXT, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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