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Sample GSM7100057

Query DataSets for GSM7100057

Status

Public on Jun 30, 2023

Title

CON 1

Sample type

SRA

Source name

colon

Organism

Mus musculus

Characteristics

tissue: colon
treatment: Control (water)

Treatment protocol

We divided the mice into a control, dextran sodium sulfate (DSS), and DSS combined with the EA (DSS + EA) groups.
In the DSS and DDS + EA groups, mice were given 2.5% DSS (MP Biomedicals, California, USA) in drinking water for 7 days whereas the control group received distilled water.
After 5 days of UC modeling, mice in the DSS + EA group were treated with EA once a day for 5 days. A custom-made mouse frame was used to hold the animals and both of the Zusanli acupoint points (ST36, located ~3 mm below the capitulum fibulae) were targeted by EA for 30 minutes (2 Hz, 0.2 mA).

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the tissue using TRIzol reagent (Takara, Kyoto, Japan) according to the manufacturer’s instructions. RNA purity was tested using the Nano Photometer spectrophotometer (IMPLEN, Westlake Village, USA).
cDNA libraries were constructed from 1 μg of total RNA by using a cDNA-PCR Sequencing Kit (SQKPCS109) according to the protocol. Briefly, the reverse transcriptase was used to enrich full-length cDNAs and added defined PCR adapters to both ends of the first-strand of cDNA and following cDNA PCR for 14 circles with LongAmp Tag DNA polymerase (New England Biolabs, Ipswich, MA, USA) (8 min for elongation time). The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA). Agencourt XP beads (Beckman Coulter, Brea,USA) were used for DNA purification. The final cDNA libraries were subjected to FLOMIN109 flow cells and analyzed on a PromethION platform at Biomarker Technology Company (Beijing, China).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

MinION

Description

CON 1_Count

Data processing

Oxford Nanopore Technologies Long Read Processing
As a first step, the original reads were filtered to select those with a minimum mean quality score of 7 and a minimum length of 500 bases.
Then, we mapped ribosomal RNA to the rRNA database and discarded it. After looking for primers on both ends of each read, FLNC (full-length, non-chimeric) transcripts were identified and mapped to the reference genome by MIMimap2.
Consensus subtypes were obtained by polishing within each cluster by Pinfish. By using GFFCompare, transcripts were validated against reference transcript annotations.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene COUNTS values for each Sample

Submission date

Mar 15, 2023

Last update date

Jun 30, 2023

Contact name

Zhang RuiBin

E-mail(s)

[email protected]

Organization name

chengdu university of traditional chinese medicine

Street address

No. 37, Shi Er Qiao Road, JinNiu District