 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 30, 2022 |
| Title |
WT saline control 5 [C5] |
| Sample type |
SRA |
| |
|
| Source name |
Infundibulum
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8-10 weeks
estrous stage: proestrus
treatment: saline as a control
tissue: Infundibulum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Infundibula were removed, immediately frozen in liquid nitrogen, and RNA was extracted using Trizol reagent with on-column purification using the Qiagen RNeasy kit. Illumina TruSeq Stranded mRNA Library prep kit was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Whole transcriptome sequencing was performed using the Illumina NovaSeq 6000 system. Samples were enriched for mRNA (stranded) and sequenced by 100 base pair (bp) paired end (PE) reads (PE100, 80 million reads per sample).
Reads were quality assessed using FastQC quality assessment software and trimmed using a quality threshold of 15 and Truseq adapter sequences (reads shorter than 20bp were discarded, Trimmomatic)
Reads were aligned to the mouse mm10 reference genome with a splice aware short read aligner (Hisat2, Samtools)
FeatureCounts was used to quantify raw counts and two group comparison, using DESeq2 to identify differentially expressed genes between control and PRL-treated animals
Assembly: mm10
Supplementary files format and content: scaled raw counts
|
| |
|
| Submission date |
Mar 23, 2022 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Ameae Walker |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California Riverside
|
| Department |
Biomedical Sciences
|
| Lab |
Walker Lab
|
| Street address |
900 University Ave.
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE199199 |
RNA sequencing of the Murine Oviduct Infundibulum |
|
| Relations |
| BioSample |
SAMN26886362 |
| SRA |
SRX14574480 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
