|
| Status |
Public on Jun 01, 2017 |
| Title |
CD274+69+ DT-Treated RNA-seq biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CD 274,69 labeled mouse intestinal cells after DT treatment
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6;129 mixed background
genotype/variation: wild type
tissue/cell type: Adult Epitheial cells; proximal 1/3 of intestine
|
| Treatment protocol |
Mice were injected with diphtheria toxin (50 µg/kg mouse weight) four times on alternate days, and sacrificed 1 day after the last injection.
|
| 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. Crypts were disaggregated with 0.5U/ml Dispase in DMEM for 30 minutes at 37°C. Cell were stained with antibodies against CD69 (BV421 conjugate, BD Biosciences 562920 ) and CD274 (APC conjugate, BD Biosciences 564715) at 4°C for 30 minutes. CD 69+ 274+ cells were sorted by flow cytometry and immediately used for chromatin transposition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) 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 |
processed data file: Read_Counts_All_Cells.txt
|
| 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; read density
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types
|
| |
|
| Submission date |
Feb 15, 2017 |
| 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 |
SAMN06335541 |
| SRA |
SRX2564007 |
