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Sample GSM5170102

Query DataSets for GSM5170102

Status

Public on Mar 12, 2024

Title

ileal crypt cells, CPT1

Sample type

SRA

Source name

ileal crypt cells

Organism

Mus musculus

Characteristics

strain: C57BL/6
cell type: ileal crypt cells
treatment: CPT-11

Treatment protocol

Mice were treated with CPT-11 (20 mg/kg) for 7 days.

Extracted molecule

total RNA

Extraction protocol

mice ileum was dissected, flushed, opened and incubated in cold PBS containing 20 mM EDTA for 90 min followed by shaking. Incubation (30 min for each time) and shaking were repeated for two more times, and the supernatant was filtered through a 70-μm strainer and centrifuged at 350 g, 4℃ for 5 min to collect crypts. Isolated crypts were then incubated in 0.05% trypsin at 37℃ for 10 min to obtain single cells.
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

Data processing

Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 whole genome using bowtie2 v2.4.1
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Mar 12, 2021

Last update date

Mar 12, 2024

Contact name

Min Huang

Organization name

Shanghai Institute of Materia Medica

Street address

555, Zuchongzhi Road

City

Shanghai