|
| Status |
Public on Feb 14, 2018 |
| Title |
WT rep3 |
| Sample type |
SRA |
| |
|
| Source name |
dorsal root ganglia
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: dorsal root ganglia
age: post natal day 30
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dorsal root ganglia were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 250g 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 HiSeq 2500 |
| |
|
| Data processing |
bcl2fastq Conversion Software v1.8.4 from illumina was used to generate fastq files
reads were mapped to the Rat Rnor_5.0 genome with STAR_2.3.1z --genomeDir Rnor_5.0 --readFilesIn R1.fastq R2.fastq --runThreadN 16 --readFilesCommand zcat --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
differential gene expression was deterimined using cufflinks -p 16 -b genome.fa -u -G annotation.gtf cuffdiff --max-bundle-frags 100000000 --max-mle-iterations 15000 -v --emit-count-tables -u -b genome.fa -p 16
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id
|
| |
|
| Submission date |
Oct 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aritra Bhattacherjee |
| Organization name |
University of Kansas Medical Center
|
| Department |
Molecular and Integrative Physiology
|
| Street address |
3901 Rainbow Blvd
|
| City |
Kansas |
| State/province |
Kansas |
| ZIP/Postal code |
66103 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE87855 |
Neuronal cytoskeletal gene dysregulation drives mechanical hypersensitivity in Rett Syndrome |
|
| Relations |
| BioSample |
SAMN05897804 |
| SRA |
SRX2239184 |
