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Series GSE205753 Query DataSets for GSE205753
Status Public on Aug 01, 2022
Title RNA-seq of single cholangiocyte-derived organoids reveals high organoid-to-organoid variability
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Organoids have been established from the majority of tissue resident stem cells. In recent years, several reports hinted at intraculture organoid variability, but a systematic analysis of such a heterogeneity has not been performed before. Here, we used RNA-seq of individual organoids to address this question. Importantly, we find that batch-to-batch variation is very low, even when prepared by different researchers. On the other hand, there is organoid-to-organoid variability within a culture. Using differential gene expression, we did not identify specific pathways that drive this variability, pointing towards possible effects of the microenvironment within the culture condition.
Overall design Methods: Picking single organoids followed by bulk-RNA-seq with UMI libraries to assess heterogeneity. The impact of microenvironment (culturing method) on gene expression of organoid cultures by RNA-seq.The impact of passaging in gene expression.
Dataset 1: RNA-seq data of 35 cholangiocyte-derived organoids from liver tissue of four 3-months-old mice, only one liver for each set, Set 1: 8, Set 2: 10, Set 3: 5 , Set 4: 12 Dataset 2: RNA-seq data of three 3-months-old cholangiocyte-derived organoid from liver tissue cultures, generated by pooling digested material from different animals each (Pool A = 2 mice; Pool B = 4 mice; Pool C = 3 mice), cultured in either matrigel domes or shaking suspension (in total 6 samples). Dataset 3: RNAseq of 3 organoid sets (1, 3 and 4) in passage 4 and the same organoid sets in passage 11 (in total 6 samples- each sample consists of 2 technical replicates).
Contributor(s) Gehling K, Parekh S, Schneider F, Kirchner M, Kondylis V, Nikopoulou C, Tessarz P
Citation(s) 35914813
Submission date Jun 09, 2022
Last update date Aug 26, 2022
Contact name Peter Tessarz
Organization name Max Planck Institute
Street address Joseph-Stelzman-Str 9b
City Cologne
State/province Nordrhein-Westfalen
ZIP/Postal code 50931
Country Germany
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (60)
GSM6222702 Set1_10
GSM6222703 Set1_1
GSM6222704 Set1_2
BioProject PRJNA847447

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Supplementary file Size Download File type/resource
GSE205753_Organoids_dome_vs_suspension_countmatrix.txt.gz 208.6 Kb (ftp)(http) TXT
GSE205753_passageOrganoids_4vs11_countmatrix.txt.gz 302.3 Kb (ftp)(http) TXT
GSE205753_singleOrganoids_countmatrix.txt.gz 919.3 Kb (ftp)(http) TXT
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