|
| Status |
Public on Jul 09, 2020 |
| Title |
Rabbit 876 (18) dehydrated |
| Sample type |
SRA |
| |
|
| Source name |
larynx (vocal folds)
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
breed: New Zealand White
Sex: male
age: 6 months
tissue: larynx (vocal folds)
|
| Treatment protocol |
Rabbits (n=6) were systemically dehydrated with 5mg/Kg furosemide (IP injection) and euthanized when 5% dehydration was achieved (body weight loss). Four control (euhydrated) rabbits were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of vocal folds (control, n=4; dehydrated, n=6) was extracted with commercial kit RNeasy Fibrous Tissue Mini Kit (QIAGEN).
Library construction was done using NuGEN's Universal Plus mRNA Kit. Each library was performed with 200 ng of RNA. Unique barcodes were used for each library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned against Oryctolagus_cuniculus.OryCun2.0/ ENSEMBL 95 using STAR v. 2.5.4b with the following flags --runThreadN 8 --runMode alignReads --outSAMunmapped Within --outSAMattrIHstart 0 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif --twopassMode Basic
Gene expression was quantitated using HTSeq (v 0.7.0) with the following flags for all libraries: -m union -s yes -t gene -i gene_id
Genome_build: Oryctolagus_cuniculus.OryCun2.0/ ENSEMBL 95
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample
|
| |
|
| Submission date |
Jun 14, 2019 |
| Last update date |
Jul 09, 2020 |
| Contact name |
Jyothi Thimmapuram |
| E-mail(s) |
jthimmap@purdue.edu
|
| Phone |
765-496-6252
|
| Organization name |
Purdue University
|
| Department |
Bioinformatics Core
|
| Street address |
YONG 1022, 155 S. Grant Street
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL26786 |
| Series (1) |
| GSE132765 |
Unraveling the molecular pathobiology of vocal fold systemic dehydration using an in vivo rabbit model |
|
| Relations |
| BioSample |
SAMN12059999 |
| SRA |
SRX6073153 |
