|
| Status |
Public on Jul 16, 2019 |
| Title |
ZEN_low_j rep4 |
| Sample type |
SRA |
| |
|
| Source name |
ZEN_low_jejunum
|
| Organism |
Sus scrofa |
| Characteristics |
age: post weaned day 28
treatment: 0.17 mg/kg ZEN (ZEN medium) for 28 days
tissue: jejunum
molecule subtype: small RNA
|
| Treatment protocol |
Small pieces of the uterus and the mid-jejunum were dissected, placed into 1 mL of RNAlater (Ambion Inc.), stored overnight at 4 °C, and transferred to -80 °C until transcriptomics analysis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 30 mg of tissue were disrupted via a bead-beating step, and the total RNA, including RNA from approximately 18 nucleotides upwards, was extracted and purified with the miRNeasy Mini Kit (Qiagen).
1 µg of total RNA was used for construction of small RNA sequencing libraries with the NEBNext Multiplex Small RNA Library preparation set for Illumina (New England Biolabs Inc.). Adapter ligated total RNA was reverse transcribed into cDNA, which served as template for PCR amplification (15 cycles) using Illumina´s SR Primer and Index Primers 1-18. Barcoded DNA libraries were purified using the QIAQuick PCR purification protocol (Qiagen) and quantified by DNA 1000 high sensitivity chip (Agilent Technologies). Purified samples were pooled at equimolar (50 nM) concentration. Size selection was performed using gel purification to select for insert sizes between 18 and 50 nucleotides.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
50j; 5307-032
processed data file: data_ref_5307_Pool2_Jejunum.xlsx
|
| Data processing |
Raw data were de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina)
Total reads were adapter trimmed using Cutadapt and quality filtered (Q-Score > 30) using the FastQC tool v0.10.1
Trimmed and quality filtered reads were aligned to reference microRNA sequences in miRBase release 21 (www.mirbase.org) using bowtie2 v2.2.6. Subsequently, reads were mapped against the Sus scrofa genome assembly Sscrofa10.2 as well as Ensembl small non-coding RNA reference databases
Reads were normalized to the total read count per library to generate tags per million (TPM) values
EdgeR was used for differential expression analysis based on TPM values. The p-values obtained were adjusted for multiple testing using Benjamini-Hochberg false discovery rate (FDR).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: abundance measurements & expression analysis
|
| |
|
| Submission date |
Feb 25, 2019 |
| Last update date |
Jul 16, 2019 |
| Contact name |
Bertrand Grenier |
| E-mail(s) |
[email protected]
|
| Organization name |
BIOMIN
|
| Department |
Research Center
|
| Street address |
Technopark 1
|
| City |
Tulln |
| ZIP/Postal code |
3430 |
| Country |
Austria |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE126989 |
Small RNA sequencing reveals new mode of action and potential biomarkers for the mycotoxin Zearalenone |
|
| Relations |
| BioSample |
SAMN10995987 |
| SRA |
SRX5417084 |
