|
| Status |
Public on Jan 17, 2020 |
| Title |
Eed_KO_Day12_Adult_ISC_scRNA |
| Sample type |
SRA |
| |
|
| Source name |
mouse intestinal villus cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129 mixed background
cell type: Adult Epithelial cells; proximal 1/3 of intestine
genotype: Eed F/F; Lgr5EGFP-IRES-CreERT
|
| Treatment protocol |
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days and every alternate day after that to activate tamoxifen-inducible Cre and recombine conditional alleles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C followed by digestion in TrypLE solution at 37°C for 30 min to generate single-cell suspensions and FACS to isolate GFP+ ISCs. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
About 104 cells were loaded onto Chromium Chip B using the 3’ GEM Library & Gel Bead Kit v3, followed by reverse transcription, cDNA amplification, and library preparation according to the 10X Genomics recommendations. Libraries were sequenced on a HiSeq4000 instrument.
About 104 cells were loaded onto Chromium Chip B using the 3’ GEM Library & Gel Bead Kit v3, followed by reverse transcription, cDNA amplification, and library preparation according to the 10X Genomics recommendations. Libraries were sequenced on a HiSeq4000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-seq:bowtie2 version 2.3.4.3. For 150bp paired-end data, reads from the 'Read1' file were trimmed to 75bp and used for further analysis, RNA-seq: STAR aligner version 2.5.3a
ChIP-seq peak calling: SICER v0.0.1
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
scRNA-Seq – reads were processed using Cell Ranger v3.0.2
Genome_build: mm9
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
Supplementary_files_format_and_content: scRNA-Seq: raw gene-cell count matrix files
|
| |
|
| Submission date |
Nov 27, 2019 |
| Last update date |
Jan 17, 2020 |
| 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) |
| GSE128671 |
Replicational dilution of H3K27me3 in mammalian cells and the role of poised promoters |
|
| Relations |
| BioSample |
SAMN13413294 |
| SRA |
SRX7229007 |
