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| Status |
Public on Dec 31, 2021 |
| Title |
L. ag. + L. av. feeding, rep1 |
| Sample type |
SRA |
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| Source name |
intestinal crypt
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| Organism |
Gallus gallus |
| Characteristics |
variety: HY-LINE VARIETY BROWN
laying period: peak egg production
tissue: intestinal crypt
feeding: L. ag. + L. av. feeding
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| Treatment protocol |
Hens were randomly divided into four groups. One control group (fed the base diet) and three lactobacillus supplement groups, which include (1) L. sa. + L. ag., (2) L. sa. + L. av. and (3) L. ag. + L. av. groups, which were fed with a base diet containing corresponding lactobacillus (10e8 CFUs/hen/day) respectively, and fed for 30 consecutive days.
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| Growth protocol |
HyLine laying hens (Gallus) at the period of laying peak were raised in a commercial chicken farm. The ambient temperature is 21℃. The relative humidity is 60%. Give the laying hens clean food, water and 12 hours of light every day.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of chicken’s intestinal crypt was performed base on the protocol previously published (Li et al., 2018). Briefly, clean duodenum tissues were cut into 2 to 4 mm3 pieces and shaken gently in 2 mM cold EDTA (ethylenediaminetetraacetic acid, pH 7.4) on an orbital shaker (30 min thrice, 4°C). The supernatant was collected and passed through a 70 μm strainer and centrifuged at 25 × g for 2 min. The purified crypt was further used for mRNA transcription assay. Crypt RNA was extracted using TRIzol reagent (Invitrogen) and RNeasy®.
RNA-seq libraries were generated using the TruSeq® RNA-Seq Sample Preparation kit according to the manufacturer's protocol (Illumina Inc., San Diego, CA, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Lagav_1
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| Data processing |
Basecalls performed using CASAVA version 1.8
Clean data (clean read) is obtained by removing reads containing adapters, reads containing ploy-N, and low-quality reads from the raw data
Use HISAT2 software to quickly and accurately compare Clean Reads with the reference genome to obtain the position information of the Reads on the reference genome
The reads numbers mapped to each gene were count by featureCounts v1.5.0-p3. Then calculate the FPKM of each gene based on the length of the gene, and map the read count to that gene.
Genome_build: Gallus_gallus
Supplementary_files_format_and_content: TXT file includes FPKM of all genes for each sample
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| Submission date |
Jun 06, 2021 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Jian Li |
| E-mail(s) |
lijiannp@zju.edu.cn
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| Organization name |
Zhejiang University
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| Street address |
866 Yuhangtang Rd
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL26853 |
| Series (1) |
| GSE176247 |
Paneth cell plays critical role during the regulation of Lactobacillus salivarius and Lactobacillus agilis on the activity of intestinal stem cell in hens |
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| Relations |
| BioSample |
SAMN19588542 |
| SRA |
SRX11079130 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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