|
| Status |
Public on Mar 01, 2020 |
| Title |
Donor A15133 Treatment Enrofloxacin Day 28 |
| Sample type |
SRA |
| |
|
| Source name |
Colon biopsy tissue
|
| Organism |
Macaca mulatta |
| Characteristics |
donor_id: A15133
treatment: Enrofloxacin
Sex: female
timepoint: 28 days
tissue: Colon biopsy tissue
|
| Treatment protocol |
no treament
|
| Growth protocol |
in vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from colon biopsies preserved in RNA-Later using RNeasy Micro from Qiagen.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rawCounts.csv
normalizedCounts.csv
S5
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to Mmul_8.0.1 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Homo sapiens Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+0.25) CPM
|
| |
|
| Submission date |
Jan 15, 2020 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Mark Cameron |
| E-mail(s) |
mjc230@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Population and Quantitative Health Sciences
|
| Lab |
Cameron
|
| Street address |
10900 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL19129 |
| Series (1) |
| GSE143729 |
Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques |
|
| Relations |
| BioSample |
SAMN13867420 |
| SRA |
SRX7569772 |
