|
| Status |
Public on Jun 29, 2018 |
| Title |
1_eos_Sto_1mth |
| Sample type |
SRA |
| |
|
| Source name |
1_eos_Sto_1mth
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Stomach
treatment: H. pylori-infected
|
| Growth protocol |
Eosinphils were sorted by flow-cytometry from the mouse gastric lamina propria.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, Thermofisher Scientific).
Library Prep was done using the NuGEN Ovation SoLo RNA-seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned with STAR STAR-2.5.1b with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the R method Rsubread::featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: text files holding gread counts per gene
|
| |
|
| Submission date |
Oct 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hubert Rehrauer |
| E-mail(s) |
Hubert.Rehrauer@fgcz.ethz.ch
|
| Organization name |
ETH Zurich / University of Zurich
|
| Department |
FGCZ
|
| Street address |
Winterthurerstr. 190
|
| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE105143 |
H.pylori infections induces a transcriptional signature in gastric eosinophils, as determined by RNA sequencing |
|
| Relations |
| BioSample |
SAMN07811023 |
| SRA |
SRX3298801 |
