|
Status |
Public on Dec 21, 2020 |
Title |
Larynx, LH29 |
Sample type |
SRA |
|
|
Source name |
Larynx (vocal folds)
|
Organism |
Oryctolagus cuniculus |
Characteristics |
breed: New Zealand White Sex: Male age: 7 months treatment: low relative humidity tissue: Larynx (vocal folds)
|
Treatment protocol |
Rabbits (n=6) were exposed to a low relative humidity environment for 8 hours. Control rabbits (n=6) were held in a moderate realtive humidity environment.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA of vocal folds (low humidity n=6, moderate humidity 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 file includes count values for each Sample
|
|
|
Submission date |
Apr 13, 2020 |
Last update date |
Dec 21, 2020 |
Contact name |
Shaojun Xie |
E-mail(s) |
xie186@purdue.edu
|
Phone |
7657140672
|
Organization name |
Purdue University
|
Street address |
3135 Decatur Street
|
City |
WEST LAFAYETTE |
State/province |
Indiana |
ZIP/Postal code |
47906 |
Country |
USA |
|
|
Platform ID |
GPL26786 |
Series (1) |
GSE148588 |
RNA-Seq of vocal folds of rabbits exposed to a low relative humidity environment |
|
Relations |
BioSample |
SAMN14592581 |
SRA |
SRX8111220 |