The spatial transcriptomic landscape of the healing mouse intestine following damage
The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions,...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article (Journal) |
| Language: | English |
| Published: |
11 February 2022
|
| In: |
Nature Communications
Year: 2022, Volume: 13, Pages: 1-16 |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-022-28497-0 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41467-022-28497-0 Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41467-022-28497-0 
|
| Author Notes: | Sara M. Parigi, Ludvig Larsson, Srustidhar Das, Ricardo O. Ramirez Flores, Annika Frede, Kumar P. Tripathi, Oscar E. Diaz, Katja Selin, Rodrigo A. Morales, Xinxin Luo, Gustavo Monasterio, Camilla Engblom, Nicola Gagliani, Julio Saez-Rodriguez, Joakim Lundeberg & Eduardo J. Villablanca |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1801147221 | ||
| 003 | DE-627 | ||
| 005 | 20250107202124.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 220506s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1038/s41467-022-28497-0 |2 doi | |
| 035 | |a (DE-627)1801147221 | ||
| 035 | |a (DE-599)KXP1801147221 | ||
| 035 | |a (OCoLC)1341459710 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 33 |2 sdnb | ||
| 100 | 1 | |a Parigi, Sara M. |e VerfasserIn |0 (DE-588)1256966673 |0 (DE-627)1801146810 |4 aut | |
| 245 | 1 | 4 | |a The spatial transcriptomic landscape of the healing mouse intestine following damage |c Sara M. Parigi, Ludvig Larsson, Srustidhar Das, Ricardo O. Ramirez Flores, Annika Frede, Kumar P. Tripathi, Oscar E. Diaz, Katja Selin, Rodrigo A. Morales, Xinxin Luo, Gustavo Monasterio, Camilla Engblom, Nicola Gagliani, Julio Saez-Rodriguez, Joakim Lundeberg & Eduardo J. Villablanca |
| 264 | 1 | |c 11 February 2022 | |
| 300 | |a 16 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Gesehen am 06.05.2022 | ||
| 520 | |a The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses. | ||
| 650 | 4 | |a Data processing | |
| 650 | 4 | |a Gene expression analysis | |
| 650 | 4 | |a Inflammatory bowel disease | |
| 650 | 4 | |a Molecular medicine | |
| 700 | 1 | |a Larsson, Ludvig |e VerfasserIn |4 aut | |
| 700 | 1 | |a Das, Srustidhar |e VerfasserIn |4 aut | |
| 700 | 1 | |a Ramirez Flores, Ricardo O. |e VerfasserIn |0 (DE-588)1233991973 |0 (DE-627)1758398167 |4 aut | |
| 700 | 1 | |a Frede, Annika |e VerfasserIn |0 (DE-588)1285202457 |0 (DE-627)184106288X |4 aut | |
| 700 | 1 | |a Tripathi, Kumar P. |e VerfasserIn |4 aut | |
| 700 | 1 | |a Diaz, Oscar E. |e VerfasserIn |4 aut | |
| 700 | 1 | |a Selin, Katja |e VerfasserIn |4 aut | |
| 700 | 1 | |a Morales, Rodrigo A. |e VerfasserIn |4 aut | |
| 700 | 1 | |a Luo, Xinxin |e VerfasserIn |4 aut | |
| 700 | 1 | |a Monasterio, Gustavo |e VerfasserIn |4 aut | |
| 700 | 1 | |8 1\p |a Engblom, Camilla |e VerfasserIn |0 (DE-588)1333331339 |0 (DE-627)1891430203 |4 aut | |
| 700 | 1 | |8 2\p |a Gagliani, Nicola |e VerfasserIn |0 (DE-588)1249228743 |0 (DE-627)1785754408 |4 aut | |
| 700 | 1 | |a Sáez Rodríguez, Julio |d 1978- |e VerfasserIn |0 (DE-588)133764362 |0 (DE-627)555766632 |0 (DE-576)300083114 |4 aut | |
| 700 | 1 | |a Lundeberg, Joakim |e VerfasserIn |4 aut | |
| 700 | 1 | |a Villablanca, Eduardo J. |e VerfasserIn |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Nature Communications |d [London] : Springer Nature, 2010 |g 13(2022), Artikel-ID 828, Seite 1-16 |h Online-Ressource |w (DE-627)626457688 |w (DE-600)2553671-0 |w (DE-576)331555905 |x 2041-1723 |7 nnas |a The spatial transcriptomic landscape of the healing mouse intestine following damage |
| 773 | 1 | 8 | |g volume:13 |g year:2022 |g elocationid:828 |g pages:1-16 |g extent:16 |a The spatial transcriptomic landscape of the healing mouse intestine following damage |
| 856 | 4 | 0 | |u https://doi.org/10.1038/s41467-022-28497-0 |x Verlag |x Resolving-System |z lizenzpflichtig |3 Volltext |
| 856 | 4 | 0 | |u https://www.nature.com/articles/s41467-022-28497-0 |x Verlag |z lizenzpflichtig |3 Volltext |
| 883 | |8 1\p |a cgwrk |d 20241001 |q DE-101 |u https://d-nb.info/provenance/plan#cgwrk | ||
| 883 | |8 2\p |a cgwrk |d 20241001 |q DE-101 |u https://d-nb.info/provenance/plan#cgwrk | ||
| 951 | |a AR | ||
| 992 | |a 20220506 | ||
| 993 | |a Article | ||
| 994 | |a 2022 | ||
| 998 | |g 133764362 |a Sáez Rodríguez, Julio |m 133764362:Sáez Rodríguez, Julio |d 910000 |d 912900 |e 910000PS133764362 |e 912900PS133764362 |k 0/910000/ |k 1/910000/912900/ |p 14 | ||
| 998 | |g 1233991973 |a Ramirez Flores, Ricardo O. |m 1233991973:Ramirez Flores, Ricardo O. |d 140000 |e 140000PR1233991973 |k 0/140000/ |p 4 | ||
| 999 | |a KXP-PPN1801147221 |e 413000803X | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"recId":"1801147221","name":{"displayForm":["Sara M. Parigi, Ludvig Larsson, Srustidhar Das, Ricardo O. Ramirez Flores, Annika Frede, Kumar P. Tripathi, Oscar E. Diaz, Katja Selin, Rodrigo A. Morales, Xinxin Luo, Gustavo Monasterio, Camilla Engblom, Nicola Gagliani, Julio Saez-Rodriguez, Joakim Lundeberg & Eduardo J. Villablanca"]},"note":["Gesehen am 06.05.2022"],"origin":[{"dateIssuedDisp":"11 February 2022","dateIssuedKey":"2022"}],"language":["eng"],"person":[{"given":"Sara M.","family":"Parigi","role":"aut","display":"Parigi, Sara M."},{"role":"aut","display":"Larsson, Ludvig","given":"Ludvig","family":"Larsson"},{"family":"Das","given":"Srustidhar","display":"Das, Srustidhar","role":"aut"},{"given":"Ricardo O.","family":"Ramirez Flores","role":"aut","display":"Ramirez Flores, Ricardo O."},{"display":"Frede, Annika","role":"aut","family":"Frede","given":"Annika"},{"family":"Tripathi","given":"Kumar P.","display":"Tripathi, Kumar P.","role":"aut"},{"role":"aut","display":"Diaz, Oscar E.","given":"Oscar E.","family":"Diaz"},{"family":"Selin","given":"Katja","display":"Selin, Katja","role":"aut"},{"display":"Morales, Rodrigo A.","role":"aut","family":"Morales","given":"Rodrigo A."},{"role":"aut","display":"Luo, Xinxin","given":"Xinxin","family":"Luo"},{"display":"Monasterio, Gustavo","role":"aut","family":"Monasterio","given":"Gustavo"},{"display":"Engblom, Camilla","role":"aut","family":"Engblom","given":"Camilla"},{"given":"Nicola","family":"Gagliani","role":"aut","display":"Gagliani, Nicola"},{"role":"aut","display":"Sáez Rodríguez, Julio","given":"Julio","family":"Sáez Rodríguez"},{"display":"Lundeberg, Joakim","role":"aut","family":"Lundeberg","given":"Joakim"},{"given":"Eduardo J.","family":"Villablanca","role":"aut","display":"Villablanca, Eduardo J."}],"physDesc":[{"extent":"16 S."}],"id":{"eki":["1801147221"],"doi":["10.1038/s41467-022-28497-0"]},"type":{"bibl":"article-journal","media":"Online-Ressource"},"title":[{"title_sort":"spatial transcriptomic landscape of the healing mouse intestine following damage","title":"The spatial transcriptomic landscape of the healing mouse intestine following damage"}],"relHost":[{"title":[{"title_sort":"Nature Communications","title":"Nature Communications"}],"physDesc":[{"extent":"Online-Ressource"}],"language":["eng"],"disp":"The spatial transcriptomic landscape of the healing mouse intestine following damageNature Communications","note":["Gesehen am 13.06.24"],"pubHistory":["2010-"],"part":{"pages":"1-16","text":"13(2022), Artikel-ID 828, Seite 1-16","volume":"13","extent":"16","year":"2022"},"id":{"eki":["626457688"],"issn":["2041-1723"],"zdb":["2553671-0"]},"type":{"media":"Online-Ressource","bibl":"periodical"},"origin":[{"dateIssuedDisp":"[2010]-","publisher":"Springer Nature ; Nature Publishing Group UK","publisherPlace":"[London] ; [London]"}],"recId":"626457688"}]} | ||
| SRT | |a PARIGISARASPATIALTRA1120 | ||