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| Status |
Public on Aug 21, 2019 |
| Title |
Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: IBD diagnosis correlation with failure to achieve corticosteroid-free durable remission upon anti-TNF therapy
Results: Enrichment of the GIMATS module (unique cellular signature found in a small cohort of surgically resected iCD ileums by scRNAseq) was also present in early stages of disease, prior to any biological therapy
Conclusion: Confirmed the presence of the GIMATS module in bulk expression dataset and revealed that the presence of the module at diagnosis is associated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy in a pediatric inception cohort
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| Overall design |
Ileal gene expression profiles were analyzed for 199 treatment-naïve pediatric Crohn patients and non-IBD controls with 13 additional samples combined with samples from GSE101794
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| Contributor(s) |
Haberman-Ziv Y, Denson L, Karns R |
| Citation(s) |
31474370 |
| |
| Submission date |
Jul 25, 2019 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Yael Haberman |
| E-mail(s) |
yael.haberman@cchmc.org
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| Organization name |
CCHMC
|
| Street address |
3333 Burnet Av
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| City |
Cincinnati |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (199)
|
| GSM3975852 |
Ileal biopsy, J10201 |
| GSM3975854 |
Ileal biopsy, J10278 |
| GSM3975855 |
Ileal biopsy, J10362 |
| GSM3975857 |
Ileal biopsy, J10347 |
| GSM3975858 |
Ileal biopsy, J10033 |
| GSM3975860 |
Ileal biopsy, J10175 |
| GSM3975861 |
Ileal biopsy, J10174 |
| GSM3975863 |
Ileal biopsy, J10344 |
| GSM3975864 |
Ileal biopsy, J10291 |
| GSM3975866 |
Ileal biopsy, J10348 |
| GSM3975867 |
Ileal biopsy, J10231 |
| GSM3975868 |
Ileal biopsy, J10178 |
| GSM3975870 |
Ileal biopsy, J10095 |
| GSM3975871 |
Ileal biopsy, J10357 |
| GSM3975873 |
Ileal biopsy, J10197 |
| GSM3975874 |
Ileal biopsy, J10169 |
| GSM3975876 |
Ileal biopsy, J10079 |
| GSM3975877 |
Ileal biopsy, J10359 |
| GSM3975879 |
Ileal biopsy, J10370 |
| GSM3975880 |
Ileal biopsy, J10209 |
| GSM3975882 |
Ileal biopsy, J10315 |
| GSM3975883 |
Ileal biopsy, J10371 |
| GSM3975885 |
Ileal biopsy, J10286 |
| GSM3975886 |
Ileal biopsy, J10240 |
| GSM3975888 |
Ileal biopsy, J10386 |
| GSM3975889 |
Ileal biopsy, J10051 |
| GSM3975891 |
Ileal biopsy, J10014 |
| GSM3975892 |
Ileal biopsy, J10369 |
| GSM3975894 |
Ileal biopsy, J10380 |
| GSM3975895 |
Ileal biopsy, J10026 |
| GSM3975896 |
Ileal biopsy, J10055 |
| GSM3975898 |
Ileal biopsy, J10120 |
| GSM3975899 |
Ileal biopsy, J10288 |
| GSM3975901 |
Ileal biopsy, J10136 |
| GSM3975902 |
Ileal biopsy, J10057 |
| GSM3975904 |
Ileal biopsy, J10140 |
| GSM3975905 |
Ileal biopsy, J10255 |
| GSM3975907 |
Ileal biopsy, J10114 |
| GSM3975908 |
Ileal biopsy, J10329 |
| GSM3975910 |
Ileal biopsy, J10018 |
| GSM3975911 |
Ileal biopsy, J10163 |
| GSM3975913 |
Ileal biopsy, J10118 |
| GSM3975915 |
Ileal biopsy, J10127 |
| GSM3975916 |
Ileal biopsy, J10062 |
| GSM3975917 |
Ileal biopsy, J10129 |
| GSM3975919 |
Ileal biopsy, J10280 |
| GSM3975920 |
Ileal biopsy, J10170 |
| GSM3975922 |
Ileal biopsy, J10097 |
| GSM3975923 |
Ileal biopsy, J10070 |
| GSM3975925 |
Ileal biopsy, J10035 |
| GSM3975926 |
Ileal biopsy, J10396 |
| GSM3975928 |
Ileal biopsy, J10238 |
| GSM3975929 |
Ileal biopsy, J10403 |
| GSM3975931 |
Ileal biopsy, J10409 |
| GSM3975932 |
Ileal biopsy, J10393 |
| GSM3975934 |
Ileal biopsy, J10016 |
| GSM3975935 |
Ileal biopsy, J10053 |
| GSM3975937 |
Ileal biopsy, J10385 |
| GSM3975938 |
Ileal biopsy, J10098 |
| GSM3975939 |
Ileal biopsy, J10125 |
| GSM3975941 |
Ileal biopsy, J10072 |
| GSM3975942 |
Ileal biopsy, J10196 |
| GSM3975944 |
Ileal biopsy, J10253 |
| GSM3975945 |
Ileal biopsy, J10308 |
| GSM3975947 |
Ileal biopsy, J10404 |
| GSM3975948 |
Ileal biopsy, J10346 |
| GSM3975950 |
Ileal biopsy, J10252 |
| GSM3975951 |
Ileal biopsy, J10258 |
| GSM3975953 |
Ileal biopsy, J10275 |
| GSM3975954 |
Ileal biopsy, J10294 |
| GSM3975956 |
Ileal biopsy, J10183 |
| GSM3975957 |
Ileal biopsy, J10332 |
| GSM3975959 |
Ileal biopsy, J10269 |
| GSM3975960 |
Ileal biopsy, J10173 |
| GSM3975961 |
Ileal biopsy, J10092 |
| GSM3975963 |
Ileal biopsy, J10086 |
| GSM3975964 |
Ileal biopsy, J10135 |
| GSM3975966 |
Ileal biopsy, J10063 |
| GSM3975967 |
Ileal biopsy, J10065 |
| GSM3975969 |
Ileal biopsy, J10374 |
| GSM3975970 |
Ileal biopsy, J10153 |
| GSM3975972 |
Ileal biopsy, J10121 |
| GSM3975973 |
Ileal biopsy, J10283 |
| GSM3975974 |
Ileal biopsy, J10265 |
| GSM3975976 |
Ileal biopsy, J10119 |
| GSM3975977 |
Ileal biopsy, J10004 |
| GSM3975979 |
Ileal biopsy, J10143 |
| GSM3975980 |
Ileal biopsy, J10325 |
| GSM3975982 |
Ileal biopsy, J10377 |
| GSM3975983 |
Ileal biopsy, J10206 |
| GSM3975985 |
Ileal biopsy, J10273 |
| GSM3975986 |
Ileal biopsy, J10059 |
| GSM3975987 |
Ileal biopsy, J10402 |
| GSM3975989 |
Ileal biopsy, J10241 |
| GSM3975990 |
Ileal biopsy, J10090 |
| GSM3975992 |
Ileal biopsy, J10157 |
| GSM3975993 |
Ileal biopsy, J10186 |
| GSM3975995 |
Ileal biopsy, J10388 |
| GSM3975996 |
Ileal biopsy, J10106 |
| GSM3975998 |
Ileal biopsy, J10324 |
| GSM3975999 |
Ileal biopsy, J10061 |
| GSM3976001 |
Ileal biopsy, J10226 |
| GSM3976002 |
Ileal biopsy, J10367 |
| GSM3976004 |
Ileal biopsy, J10298 |
| GSM3976005 |
Ileal biopsy, J10384 |
| GSM3976007 |
Ileal biopsy, J10274 |
| GSM3976008 |
Ileal biopsy, J10264 |
| GSM3976009 |
Ileal biopsy, J10282 |
| GSM3976011 |
Ileal biopsy, J10250 |
| GSM3976012 |
Ileal biopsy, J10069 |
| GSM3976014 |
Ileal biopsy, J10335 |
| GSM3976015 |
Ileal biopsy, J10305 |
| GSM3976017 |
Ileal biopsy, J10214 |
| GSM3976018 |
Ileal biopsy, J10130 |
| GSM3976020 |
Ileal biopsy, J10117 |
| GSM3976021 |
Ileal biopsy, J10382 |
| GSM3976023 |
Ileal biopsy, J10233 |
| GSM3976024 |
Ileal biopsy, J10217 |
| GSM3976026 |
Ileal biopsy, J10303 |
| GSM3976027 |
Ileal biopsy, J10391 |
| GSM3976029 |
Ileal biopsy, J10405 |
| GSM3976030 |
Ileal biopsy, J10311 |
| GSM3976032 |
Ileal biopsy, J10236 |
| GSM3976033 |
Ileal biopsy, J10158 |
| GSM3976035 |
Ileal biopsy, J10394 |
| GSM3976036 |
Ileal biopsy, J10331 |
| GSM3976038 |
Ileal biopsy, J10299 |
| GSM3976039 |
Ileal biopsy, J10271 |
| GSM3976040 |
Ileal biopsy, J10133 |
| GSM3976042 |
Ileal biopsy, J10212 |
| GSM3976043 |
Ileal biopsy, J10019 |
| GSM3976045 |
Ileal biopsy, J10039 |
| GSM3976046 |
Ileal biopsy, J10224 |
| GSM3976047 |
Ileal biopsy, J10056 |
| GSM3976049 |
Ileal biopsy, J10172 |
| GSM3976050 |
Ileal biopsy, J10227 |
| GSM3976052 |
Ileal biopsy, J10334 |
| GSM3976053 |
Ileal biopsy, J10256 |
| GSM3976054 |
Ileal biopsy, J10300 |
| GSM3976056 |
Ileal biopsy, J10375 |
| GSM3976057 |
Ileal biopsy, J10390 |
| GSM3976059 |
Ileal biopsy, J10081 |
| GSM3976060 |
Ileal biopsy, J10047 |
| GSM3976062 |
Ileal biopsy, J10046 |
| GSM3976063 |
Ileal biopsy, J10378 |
| GSM3976065 |
Ileal biopsy, J10406 |
| GSM3976066 |
Ileal biopsy, J10131 |
| GSM3976068 |
Ileal biopsy, J10050 |
| GSM3976069 |
Ileal biopsy, J10161 |
| GSM3976071 |
Ileal biopsy, J10397 |
| GSM3976072 |
Ileal biopsy, J10109 |
| GSM3976073 |
Ileal biopsy, J10321 |
| GSM3976075 |
Ileal biopsy, J10107 |
| GSM3976076 |
Ileal biopsy, J10193 |
| GSM3976078 |
Ileal biopsy, J10276 |
| GSM3976079 |
Ileal biopsy, J10379 |
| GSM3976081 |
Ileal biopsy, J10319 |
| GSM3976082 |
Ileal biopsy, J10074 |
| GSM3976083 |
Ileal biopsy, J10132 |
| GSM3976085 |
Ileal biopsy, J10222 |
| GSM3976086 |
Ileal biopsy, J10071 |
| GSM3976088 |
Ileal biopsy, J10228 |
| GSM3976089 |
Ileal biopsy, J10399 |
| GSM3976091 |
Ileal biopsy, J10267 |
| GSM3976092 |
Ileal biopsy, J10296 |
| GSM3976094 |
Ileal biopsy, J10104 |
| GSM3976095 |
Ileal biopsy, J10257 |
| GSM3976096 |
Ileal biopsy, J10009 |
| GSM3976098 |
Ileal biopsy, J10302 |
| GSM3976099 |
Ileal biopsy, J10230 |
| GSM3976101 |
Ileal biopsy, J10333 |
| GSM3976102 |
Ileal biopsy, J10383 |
| GSM3976104 |
Ileal biopsy, J10025 |
| GSM3976106 |
Ileal biopsy, J10111 |
| GSM3976107 |
Ileal biopsy, J10395 |
| GSM3976109 |
Ileal biopsy, J10295 |
| GSM3976110 |
Ileal biopsy, J10330 |
| GSM3976111 |
Ileal biopsy, J10320 |
| GSM3976113 |
Ileal biopsy, J10401 |
| GSM3976114 |
Ileal biopsy, J10381 |
| GSM3976116 |
Ileal biopsy, J10215 |
| GSM3976117 |
Ileal biopsy, J10030 |
| GSM3976119 |
Ileal biopsy, J10328 |
| GSM3976120 |
Ileal biopsy, J10007 |
| GSM3976122 |
Ileal biopsy, J10100 |
| GSM3976123 |
Ileal biopsy, J10151 |
| GSM3976125 |
Ileal biopsy, J10155 |
| GSM3976126 |
Ileal biopsy, J10188 |
| GSM3976127 |
Ileal biopsy, J10194 |
| GSM3976129 |
Ileal biopsy, J10207 |
| GSM3976130 |
Ileal biopsy, J10216 |
| GSM3976132 |
Ileal biopsy, J10279 |
| GSM3976133 |
Ileal biopsy, J10293 |
| GSM3976135 |
Ileal biopsy, J10337 |
| GSM3976136 |
Ileal biopsy, J10340 |
| GSM3976138 |
Ileal biopsy, J10361 |
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| Relations |
| BioProject |
PRJNA556684 |
| SRA |
SRP216403 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE134881_RISKfpkmAll.csv.gz |
13.8 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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