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Fresh vs. frozen cell preparations of colorectal cancer single-cell RNA sequencing

Type: RNASeq
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001005191	To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods.	Illumina HiSeq 2500	10

Publications	Citations
Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. Uhlitz F, Bischoff P, Peidli S, Sieber A, Trinks A, Lüthen M, Obermayer B, Blanc E, Ruchiy Y, Sell T, Mamlouk S, Arsie R, Wei TT, Klotz-Noack K, Schwarz RF, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N, Morkel M. EMBO Mol Med 13: 2021 e14123	39
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Joanito I, Wirapati P, Zhao N, Nawaz Z, Yeo G, Lee F, Eng CLP, Macalinao DC, Kahraman M, Srinivasan H, Lakshmanan V, Verbandt S, Tsantoulis P, Gunn N, Venkatesh PN, Poh ZW, Nahar R, Oh HLJ, Loo JM, Chia S, Cheow LF, Cheruba E, Wong MT, Kua L, Chua C, Nguyen A, Golovan J, Gan A, Lim WJ, Guo YA, Yap CK, Tay B, Hong Y, Chong DQ, Chok AY, Park WY, Han S, Chang MH, Seow-En I, Fu C, Mathew R, Toh EL, Hong LZ, Skanderup AJ, DasGupta R, Ong CJ, Lim KH, Tan EKW, Koo SL, Leow WQ, Tejpar S, Prabhakar S, Tan IB. Nat Genet 54: 2022 963-975	103
The role of tetraspanins pan-cancer. Huang R, Sun H, Lin R, Zhang J, Yin H, Xian S, Li M, Wang S, Li Z, Qiao Y, Jiang M, Yan P, Meng T, Huang Z. iScience 25: 2022 104777	16
A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Zhou RW, Xu J, Martin TC, Zachem AL, He J, Ozturk S, Demircioglu D, Bansal A, Trotta AP, Giotti B, Gryder B, Shen Y, Wu X, Carcamo S, Bosch K, Hopkins B, Tsankov A, Steinhagen R, Jones DR, Asara J, Chipuk JE, Brody R, Itzkowitz S, Chio IIC, Hasson D, Bernstein E, Parsons RE. Nat Commun 13: 2022 6041	14