|
| Status |
Public on Sep 14, 2021 |
| Title |
Lgr5low-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 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
Itgb7-3-GFPlow
|
| 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 |
SAMN12185299 |
| SRA |
SRX6387554 |
