|
| Status |
Public on Dec 16, 2021 |
| Title |
ILEUM HC288 |
| Sample type |
SRA |
| |
|
| Source name |
ileum
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8-12 weeks old
genotype: CD19-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ileal tissues (~30mg) was collected from mice and immediately preserved in RNAlater and RNA was extracted using RNEasy Extraction Kit (Qiagen)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
20180717-pool-19
|
| Data processing |
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the GRCm38.88 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes gencode.vM15.annotation.gtf were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample
|
| |
|
| Submission date |
Oct 22, 2021 |
| Last update date |
Dec 16, 2021 |
| Contact name |
HAO JI |
| E-mail(s) |
ji5@email.sc.edu
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE186435 |
RNAseq analysis of ileal transcriptomes to understand the effect of humoral immunodeficiency on small intestinal mucosal homeostasis |
|
| Relations |
| BioSample |
SAMN22512933 |
| SRA |
SRX12742628 |
