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Status |
Public on Aug 04, 2023 |
Title |
rRNA Depleted total RNA from whole brain from untreated FXLE20 rats (replicate 1, sequencing batch 15) |
Sample type |
SRA |
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Source name |
whole brain
|
Organism |
Rattus norvegicus |
Characteristics |
strain: FXLE20/Stm batch: 15 treatment: none extraction protocol: RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA). tissue: whole brain
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Treatment protocol |
Tissue frozen in RNA later.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA). Libraries were constructed using the Illumina TruSeq Stranded total RNA Kit (Illumina, San Diego, CA, USA). rRNA depleted stranded total RNA
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
FXLE20_1_batch15 FXLE20_1_batch15 FXLE20_1_batch15 FXLE20_1_batch15
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Data processing |
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20 Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA genome Alignment Hisat2 (v2.1.0) Stringtie (v1.3.5) reconstruction Run Aptardi (v1.4) on each strain reconstructed GTF Merge aptardi output reconstruction Stringtie(v1.3.5) Run RSEM (v1.3.1) on reconstruction Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides Run RSEM(v1.3.1) on filtered reconstruction Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R) Remove technical artifacts including batch effects using Removal of Unwanted Variance (RUVg) with empirically-derived controls (RUVSeq package in R) Assembly: Rn7.2 Supplementary files format and content: TSV batch corrected/normalized expression values and GTF of the reconstructed transcriptome
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Submission date |
Aug 03, 2023 |
Last update date |
Aug 05, 2023 |
Contact name |
Laura Saba |
E-mail(s) |
Laura.Saba@cuanschutz.edu
|
Organization name |
University of Colorado Anschutz Medical Campus
|
Department |
Skaggs School of Pharmacy and Pharmaceutical Sciences
|
Street address |
12850 E. Montview Blvd
|
City |
Aurora |
State/province |
CO |
ZIP/Postal code |
80045 |
Country |
USA |
|
|
Platform ID |
GPL22396 |
Series (2) |
GSE199984 |
Whole brain RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org) |
GSE199987 |
RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org) |
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Relations |
BioSample |
SAMN36826336 |
SRA |
SRX21237909 |