|
| Status |
Public on Jun 01, 2017 |
| Title |
Secretory Progenitors Rbpj RNA-seq biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse secretory progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129 mixed background
cell type: Adult Epitheial cells; proximal 1/3 of intestine
genotype: Rbpj F/F; Villin-CRE
|
| Treatment protocol |
Mice were injected with twice daily dose of 2mg Tamoxifen for 2 consecutive days, to activate tamoxifen-inducible Cre and recombine conditional alleles, and sacrificed on day 3.
|
| Growth 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. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 |
Secretory Progenitors Rbpj RNA-seq biological rep1
SP_Rbpj_Rep1
|
| Data processing |
Alignment: ATAC-seq and ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ATAC-seq peak calling: MACS, version 1.4
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types
|
| |
|
| Submission date |
Jun 15, 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) |
| GSE83394 |
Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells |
|
| Relations |
| BioSample |
SAMN05254225 |
| SRA |
SRX1847678 |
