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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 10, 2020 |
| Title |
TP53KO w/o Wnt3a-0.2% Rspo rep2 |
| Sample type |
SRA |
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| Source name |
Colon
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon
source: Colon organoids
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| Treatment protocol |
Organoids were grown in full medium or medium without Wnt and 0.2% Rspo medium for 48h
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| Growth protocol |
Normal human colon organoids were cultured in advanced DMEM/F12 medium (Invitrogen), supplemented with B27 (Invitrogen), Nicotinamide (Sigma-Aldrich), N-acetylcysteine (Sigma-Aldrich), EGF (Peprotech), TGF-β type I receptor inhibitor A83-01 (Tocris), P38 inhibitor SB202190 (Sigma-Aldrich), Wnt3a-CM (50%), Noggin-CM (10%), Rspo1-CM (20%). Mutant TP53 organoids were cultured in the presence of 5 µM Nutlin-3 (Cayman Chemical).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids lines were lysed in RLT lysis buffer (Qiagen). RNA was obtained using the Qiagen QiaSymphony SP (Qiagen) according to the manufacturer’s protocol.
RNA-sequencing (RNA-seq) libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
JOR2520-11_AHT7TMBGX7
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| Data processing |
Single-end reads of 75 bp were aligned to GRCh37 with STAR [PMID: 23104886] with parameters outSJfilterIntronMaxVsReadN, chimJunctionOverhangMin and chimSegmentMin set to 10000000, 15 and 15, respectively.
Gene expression was quantified with edgeR with the human Ensembl transcript database version 74. Differential gene expression analysis was performed with DESeq2 [25516281], and its ‘rlogTransformation’ function was used for variance stabilization of gene expression data.
Genome_build: GRCh37
Supplementary_files_format_and_content: abundance measurements
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| Submission date |
Apr 03, 2019 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Madelon M Maurice |
| E-mail(s) |
[email protected]
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| Phone |
+3188757574
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| Organization name |
UMC Utrecht
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| Department |
Cell Biology
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| Lab |
H02.313
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| Street address |
Heidelberglaan 100
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584CX |
| Country |
Netherlands |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE129288 |
RNA sequencing of WT, TP53KO and onco-RNF43/TP53KO human colon organoid lines. |
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| Relations |
| BioSample |
SAMN11333270 |
| SRA |
SRX5630725 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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