|
| Status |
Public on May 20, 2016 |
| Title |
Wild-type Lgr5+ ISC H3K27me3 ChIP-Seq rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Lgr5+ve ISC H3K27me3 ChIP-Seq
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6;129 mixed
genotype/variation: Eed+/+; Lgr5-EGFP-IRES-CREERT2
injected with: none
tissue/cell type source: Crypts; proximal 1/3 of small intestine
cell type: Control mouse villus cells
chip antibody: H3K27me3 antibody (07-449, Millipore)
|
| Treatment protocol |
Not injected with tamoxifen.
|
| Extracted molecule |
genomic DNA |
| 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. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Lgr5_H3K27me3_ChIP-seq_rep2
|
| Data processing |
Alignment: ChIP-seq:bowtie2. 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: bigwig file for visualizing aligned sequence tags (Tag Density bigwig format)
Supplementary_files_format_and_content: 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.
Supplementary_files_format_and_content: 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 |
Feb 18, 2016 |
| 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 |
| SRA |
SRX1590936 |
| BioSample |
SAMN04502901 |
