|
| Status |
Public on Apr 21, 2025 |
| Title |
WT d100 Sheep proximal lung rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
sheep proximal lung epithelial tissue
|
| Organism |
Ovis aries |
| Characteristics |
subject: healthy donor
age: Day 100
sample: SF152-2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
50-100mg of sample was excised from frozen tissue and mixed with 1mL TRIzol Reagent and ceramic beads over ice. Tissue was homogenized and incubated at RT to dissociate the nucleoprotein complex. Solution was then mixed with 200uL chloroform, centrifuged, and the aqueous phase removed. RNA was precipitated with 100% isopropanol, washed with 75% ethanol, and solubilized in water.
RNA concentration and purity were measured by nanodrop and 1ug was used for library preperation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA seq of d100 WT sheep lung rep2
RNA-seq
|
| Data processing |
Bulk RNA-seq mapped to the sheep (texel, Oar_v4.0) genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Assembly: Texel (ovis aries) sheep genome Oar_v4.0
Supplementary files format and content: Feature assignment of aligned reads to annotated sheep genes in TSV format.
|
| |
|
| Submission date |
May 02, 2022 |
| Last update date |
Apr 21, 2025 |
| Contact name |
Ann Harris |
| E-mail(s) |
axh575@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics and Genome Sciences
|
| Street address |
2109 Adelbert Rd Building
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL27721 |
| Series (1) |
| GSE202019 |
Transcriptomic analysis of lung development in the sheep |
|
| Relations |
| BioSample |
SAMN28032824 |
| SRA |
SRX15104721 |
