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Sample GSM3916310 Query DataSets for GSM3916310
Status Public on Sep 14, 2021
Title Lgr5high-Itgb7 KO -3
Sample type SRA
 
Source name small intestine
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: small intestine
age: 8-week
genotype: Itgb7-/- Lgr5-GFP
cell type: epithelial cell
cell population: Lgr5-GFP high
Extracted molecule total RNA
Extraction protocol The small intestine was dissected, flushed with cold PBS, opened longitudinally and cut into small fragments roughly 2-4 mm in length. Intestine fragments were washed twice with cold PBS and then incubated with 20 mM EDTA-PBS on ice for 30 min. The tissue was then shaken vigorously, and the supernatant was collected as fraction1 in a new conical tube. The tissue was incubated in fresh EDTA-PBS and a new fraction was collected every 30 min. Fractions were collected until the supernatant consisted almost entirely of crypts. The final fraction was filtered through a 70-μm cell strainer (enriched for crypts), washed twice in PBS, centrifuged at 300 g for 3 min, and dissociated with TrypLE Express (Invitrogen) at 37 ºC for 5 min. The single-cell suspension was then passed through a 40-μm cell strainer. Cells were stained with antibodies and gated on 7AAD- CD45- CD31- TER119- EpCAM+, GFP high (stem cells) and GFP low (TA cells), and sorted by a BD AriaIII cell sorter. Sorted samples were processed by extracting RNA with RNeasy Micro Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
Itgb7-3-GFPhi
Data processing Basecalls performed using Real Time Analysis 3.4.4
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
For mapping analysis using tophat2 software,tophat2 -a 8 -m 0 -i 50 -I 500000 -N 2 --read-gap-length 2 --read-edit-dist 2 -g --library-type fr-unstranded -p 8 -G -r 50 --microexon-search;For FPKM valuse analysis using RSEM software,RSEM --paired-end --bowtie2 -p 8 --bowtie2-path.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
 
Submission date Jul 02, 2019
Last update date Sep 14, 2021
Contact name Chen Shiyang
E-mail(s) chenshiyang2014@sibcb.ac.cn
Organization name Shanghai Institute of Biochemistry and Cell Biology (CAS)
Lab Jianfeng Chen's Lab
Street address Room 413, New biochemistry building, YueYang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL24247
Series (1)
GSE133691 Gene expression profiles of Lgr5-GFP high and Lgr5-GFP low cells in small intestines of Itgb7+/+ Lgr5-GFP mice and Itgb7-/- Lgr5-GFP mice
Relations
BioSample SAMN12185305
SRA SRX6387548

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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