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Sample GSM3916315 Query DataSets for GSM3916315
Status Public on Sep 14, 2021
Title Lgr5low-Itgb7 KO-2
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 low
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_low_Itgb7_KO_vs_WT_count.txt
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
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
BioSample SAMN12185300
SRA SRX6387553

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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