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Sample GSM8244991

Query DataSets for GSM8244991

Status

Public on May 01, 2024

Title

gut, D14FL3

Sample type

SRA

Source name

kaluga sturgeon

Organism

Huso dauricus

Characteristics

tissue: gut
treatment: stock enhancement for 14 d

Extracted molecule

total RNA

Extraction protocol

Commercial RNA sample extraction kit (DP419, TIANGEN, China) was selected to extract the total RNA in gut tissues. 90 mg fresh intestine tissue was ground by high-speed homogenizer (DHFSTPRP-32D, LAWSON, China) with 1 mL lysis buffer RZ to obtain homogenate and then trichloromethane was added. After staying at room temperature for 6 min, the mixture was centrifuged at 12000 rpm to obtain the aqueous phase that was mixed with absolute ethyl alcohol. RD solution was used to remove residual protein impurity in RNA samples and the purified total RNA was stored at RNase-free tubes after repeated centrifugation.
When RNA integrity number > 7.0 and A260/280 > 1.8, messenger RNA (mRNA) with poly A was caught using oligo(dT) dynabeads (25-61005, THERMO FISHER, USA) and then broken into fragment with the specific kit (E6150S, NEBNEST, USA). Double-strands complementary DNA was synthesized based on the reverse transcriptase and E. coli DNA polymerase I that was provided by LIANCHUAN BIO TECHNOLOGIES Co., LTD (Hangzhou, China). Paired-ends of the complementary DNA were added with a “A” base, which could combine with the adapter sequence. After the second strand was digested, the sequencing library (150 bp) was established by amplifying the target sequences.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Raw sequencing data format was shown as “.fastq” and the joint sequence (adapter) was removed from the original tags using CUTADAPT 1.9. Low quality and repetitive sequences were filtered to obtain clean data. De novo splicing in TRINITY tool (Version 2.4.0) was selected to assemble the clean reads and then the software was used to perform the transcript clustering based on shared sequences contents. The longest transcript in each cluster was regarded as one Unigene. All obtained Unigenes were annotated based on known databases. Quantitative assessment for fragments per kilobase of transcript per million mapped reads (FPKM) of each Unigene was executed with the SALMON package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: Unigene assembly result

Submission date

May 01, 2024

Last update date

May 01, 2024

Contact name

Yutao Li

E-mail(s)

liyutao@neau.edu.cn

Organization name

Northeast Normal University

Street address

Jingyue Street