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Sample GSM4474574 Query DataSets for GSM4474574
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
Organization name Purdue University
Street address 155 South Grant 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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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