|
| Status |
Public on May 20, 2016 |
| Title |
Wild-type Lgr5+ ISC RNA-seq biological rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Control mouse intestinal stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6;129 mixed
genotype/variation: Eed+/+; Lgr5-EGFP-IRES-CREERT2
cell type: Adult intestinal stem cell; proximal 1/3 of intestine
|
| Treatment protocol |
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry.
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Control_ISC_2
1304_Control_Lgr5_RNAseq
|
| Data processing |
Alignment: ChIP-seq:bowtie. RNA-seq: Tophat, version 2.0.6
ChIP-Seq - peak calling: SICER, version 1.1
RNA-Seq - normalized and differential expression: Cufflinks, version 2.0.1; default setting; Cuffdiff was used with default settings and FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq Tag Density bigwig file for visualizing aligned sequence tags
RNA-Seq: Differential expression table, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Control ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
RNA-Seq: Differential expression tables, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Eed-del Villus, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
|
| |
|
| Submission date |
Aug 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ramesh Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Shivdasani
|
| Street address |
450 Brookline Ave. Dana 720D
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE71713 |
Acquired tissue-specific promoter bivalency is a basis for PRC2 necessity in adult somatic cells |
|
| Relations |
| BioSample |
SAMN03956389 |
| SRA |
SRX1132743 |
