|
Status |
Public on Jun 01, 2017 |
Title |
Lgr5-GFP-DTR ISC RNA-seq biological rep1 |
Sample type |
SRA |
|
|
Source name |
Lgr5-GFP-DTR+ mouse intestinal stem cells
|
Organism |
Mus musculus |
Characteristics |
strain: B6;129 mixed background cell type: Adult Epitheial cells; proximal 1/3 of intestine genotype: Lgr5EGFP-DTR
|
Treatment protocol |
No treatment
|
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 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP+ve intestinal stem cells were sorted by flow cytometry. 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 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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Lgr5-GFP-DTR ISC RNA-seq biological rep1 Lgr5_GFP-DTR_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
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|
|
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 |
SAMN05254219 |
SRA |
SRX1847672 |