 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 26, 2024 |
| Title |
fetal pancreas,sample #3, ewe#336, 472-RNAi |
| Sample type |
SRA |
| |
|
| Source name |
fetal pancreas
|
| Organism |
Ovis aries |
| Characteristics |
tissue: fetal pancreas
genotype: SLC2A3-RNAi
developmental stage: 75 days gestational age
|
| Treatment protocol |
day 9 hatched blastocysts were infected with lentiviral constructs containing either non-targeting sequence (NTS) or SLC1A3-RNAi. Fetal pancreases were collected at mid-gestation (75 days) under general anesthesia before euthanasia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Mini Kit (Ref# 74104; QIAGEN)
Assessment of the RNA samples integrity and quality, library generation and RNA-Seq (2x150 cycles, 80 million paired-end reads/sample; NovSeq6000, Illumina, San Diego, CA, USA) was conducted by the Genomics Shared Resource Core Facility, Uni-versity of Colorado Anschutz Medical Campus (Aurora, CO)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3_472
|
| Data processing |
CLC Genomics Workbench v21
trimming of raw sequencing reads based on quality score (Q‐score > 30), read length (≥ 15 nucleotides), and removal of adapter sequences
Raw sequence reads were mapped to the reference ovine genome (Ovis aries, Oar.ra_1.0, Baylor College of Medicine)
Expression data was normalized using the trimmed mean of M-values (TMM) normali-zation method and presented as transcripts per kilobase per million mapped reads (TPM)
CLC Genomics Workbench Differential Expression tool and compared with DESeq2 package in R studio
Assembly: Ovis aries, Oar.ra_1.0, Baylor College of Medicine, NCBI RefSeq assembly GCF_002742125.1
Supplementary files format and content: xlsx file including TPM counts for each sample
|
| |
|
| Submission date |
Mar 19, 2024 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Victoria Kennedy |
| E-mail(s) |
Tori.Kennedy@colostate.edu
|
| Organization name |
Colorado State University
|
| Street address |
1683 Campus Delivery
|
| City |
Fort Collins |
| State/province |
Colorado |
| ZIP/Postal code |
80523-1683 |
| Country |
USA |
| |
|
| Platform ID |
GPL27721 |
| Series (1) |
| GSE261932 |
Fetal Hypoglycemia Induced by Placental SLC2A3 RNA Inter-ference Alters Fetal Pancreas Development and Transcriptome at Mid-Gestation |
|
| Relations |
| BioSample |
SAMN40546317 |
| SRA |
SRX23994409 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
