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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2019 |
| Title |
Empty vector3 control organoids cultured 5 months and further grown in full medium for 3 weeks |
| Sample type |
SRA |
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| Source name |
organoid culture
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Control
gender: Male
tissue: Proximal colon-derived cultured organoid
culture time: 5 months
culture medium: Full for 3 weeks
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| Growth protocol |
Male mice from each genotype around the age of 40 days were euthanized by Carbon Dioxide. The first 2.5cm of proximal colon is collected from the mice. The colon crypts were isolated and the culture was established as described previously. Organoids were plated within Matrigel (Corning #356231). Culture media was made of 50% of Wnt3a conditioned media, 20% of R-Spondin conditioned media, 20% of Advanced DMEM/F12 (ThermoFisher #12634010) with B27® (ThermoFisher #17504044), 10% of Noggin conditioned media and EGF. The conditioned media for Wnt3a, R-Spondin and Noggin were made as described previously. A total of 0.5 million cells were injected subcutaneously in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) (JAX™) with Matrigel. Injection sites were examined every week for tumor growth.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from cells and xenograft tissues was extract using Allprep kit mini or micro (Qiagen).
Fragmented genomic DNA was used for Illumina TruSeq library construction. Paired-end sequencing, resulting in 100 or 150 bases from each end of the DNA fragments for the exome or targeted sequencing libraries, respectively, was performed using Illumina HiSeq 2000/2500 instrumentation.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
BRAF3_EV
Exome analysis
processed data file: Exon_seq_results.xlsx
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| Data processing |
Library strategy: Exome-seq
Potential somatic single nucleotide variants (SNVs) and small insertion/deletions in BrafCA-IND & BrafEV-12m/14m samples were identified using Varscan (v2.3.9) (Koboldt et al., 2012), and the matched BrafEV samples were used as normal control. From the result, somatic mutations were identified based on the following major criteria: (1) high mapping quality bases (read mapping quality ≥30); (2) mutations should not be significantly enriched within 5 bp of the 5′ or 3′ ends of the read; (3) there should be a significant allele frequency change (somatic_p_value <0.05); (4) the variant reads in BrafEV samples should be less than 2, and the variant reads in BrafCA-IND and BrafEV-12m/14m samples should be larger than 5. ANNOVAR was used to annotate confident variant results (Yang and Wang, 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Exon_seq_results.xlsx: Potential somatic single nucleotide variants (SNVs) and small insertion/deletions in Braf_Base and BrafEV-12m/14m samples were identified using Varscan (v2.3.9), and the matched BrafEV samples were used as normal control. As shown in Exon_seq_results.xlsx, the identified somatic single nucleotide variants (SNVs) and small insertion/deletions in BRAF1_Base/BRAF2_Base/BRAF3_Base/BRAF1_EV_12m/BRAF3_EV_14m were listed. We only presented the Missense mutations, Nonsense mutations, and Frameshift mutations. The p-value were calculated by Varscan to represent the significance of allele frequency change. Also, when the mutations hit the frequent mutated genes in COSMIC cancer database, we also annotated them.
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| Submission date |
Oct 23, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
hari easwaran |
| Organization name |
Johns Hopkins University
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| Department |
Oncology
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| Lab |
Steve Baylin
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| Street address |
1650 Orleans Street, CRB1, Room 530
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| City |
BALTIMORE |
| State/province |
MD |
| ZIP/Postal code |
21209 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE114801 |
Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation |
| GSE121672 |
Transcriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [Exome-seq] |
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| Relations |
| BioSample |
SAMN10280842 |
| SRA |
SRX4923773 |
| 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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