 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2024 |
| Title |
Pancreatic islet, SPF, P20, Female, biol rep 6 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic Islet
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreatic Islet
microbiota: SPF
developmental stage: P20
Sex: F
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purification from acinar tissue was achieved by several rounds of hand picking and islets were immersed in TRIzol before RNA extraction with Direct-zol RNA miniprept kit (Zymo Research).
Total RNA was first hybridized with the NEBNext rRNA Depletion kit v2 (NEB, cat# E7400) to diminish rRNA from the samples. Stranded RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat# E7760L).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were adapter trimmed and quality filtered with trim galore (0.6.6) using minimum quality of 20 and minimum length of 20 after trimming.
Adapter/quality-trimmed reads were processed with Salmon (1.3.0) using the quant command against the mm10 reference transcriptome with fragment GC bias correction enabled.
Assembly: mm10
Supplementary files format and content: Directory of Salmon quant output files including quant.sf reporting transcript counts and auxilliary files.
|
| |
|
| Submission date |
Sep 24, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
W. Zac Stephens |
| Organization name |
University of Utah
|
| Department |
Pathology
|
| Lab |
Round Lab
|
| Street address |
15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84121-3808 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE243754 |
Neonatal microbes shape islet-immune interactions that determine life-long host metabolic capacity [scRNA-seq and bulk RNA-seq]. |
|
| Relations |
| BioSample |
SAMN37525685 |
| SRA |
SRX21870249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7798205_19831X7_salm_quant.sf.tar.gz |
1.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
