|
| Status |
Public on Dec 26, 2018 |
| Title |
Conditioned_1 |
| Sample type |
SRA |
| |
|
| Source name |
Conditioned_Small intestinal (Jejunum) tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
mouse status: HA107-conditioned mouse
tissue: Small intestinal (Jejunum) tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small intestinal (Jejunum) tissues were removed, placed in Trizol solution, and flash frozon in liquid nitrogen. RNA was harvested using Trizol reagent and subsequent Rnsasy MinElute kit (Qiagen). Ribosomal DNA was removed with Ribominus Transcriptome Isolation Kit (Invitrogen). RNA libraries were prepared with TruSeq RNA sample preparation v2 kit (TruSeq Stranded mRNA Sample Preparation, Illumina).
RNA libraries were prepared for Illumina HiSeq 2500 sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling software for Illumina HiSeq 2500
Sequence quality control with fastqc 0.11.2
Adaptor trimming with trimmomatic 0.33
Sequence alignment with tophat 2.0.13
Sequence counting with HTSeq 0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPG (read counts per gene) values for each Sample;
Supplementary_files_format_and_content: Row counts with HTSeq
Supplementary_files_format_and_content: Normalized counts with DEseq2
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J. Macpherson |
| E-mail(s) |
andrew.macpherson@dbmr.unibe.ch
|
| Organization name |
University of Bern
|
| Department |
Department for BioMedical Research
|
| Lab |
Gastroenterogy
|
| Street address |
Murtenstrasse 35
|
| City |
Bern |
| State/province |
Bern |
| ZIP/Postal code |
3008 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE102543 |
Next generation sequencing facilitates quantitative transcriptomic comparison between HA107 conditioned and unconditioned germ-free small intestinal tissue. |
|
| Relations |
| BioSample |
SAMN07499050 |
| SRA |
SRX3088445 |
