|
| Status |
Public on Aug 17, 2022 |
| Title |
Primary astrocyte, Aβ40_03 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
cell type: Primary astrocyte cells
genotype: WT
treatment: Aβ40
time: 24hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E.Z.N.A.® Total RNA Kit II - https://www.omegabiotek.com/product/e-z-n-a-total-rna-kit-ii/
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol by Omega Bioservice Company.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basespace RNA-Seq Alignment APP - Read mapping using the STAR aligner; Quantification of reference genes and transcripts using salmon; Rattus norvegicus UCSC rn5 (RefSeq gene annotation) - SNVs and INDELs called by Strelka Variant caller - Gene fusions detected by Manta https://support.illumina.com/help/BS_App_RNASeq_Alignment_v2_OLH_1000000006112/Content/Source/Informatics/Apps/WkflDescr_swBS_appRNASeq.htm
Read mapping using the STAR aligner; Quantification of reference genes and transcripts using salmon; Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
SNVs and INDELs called by Strelka Variant caller
Gene fusions detected by Manta
Basespace DESeq2 APP - produces gene counts, gene FPKMs
Assembly: Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
Supplementary files format and content: tab-delimited text files include gene FPKMs values for each Sample
|
| |
|
| Submission date |
Aug 14, 2022 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Willam Van Nostrand |
| E-mail(s) |
wvannostrand@uri.edu
|
| Organization name |
University of Rhode Island
|
| Department |
College of Pharmacy
|
| Lab |
360
|
| Street address |
7 Greenhouse Rd
|
| City |
Kingston |
| State/province |
Rhode Island |
| ZIP/Postal code |
02881 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE211198 |
RNAseq analysis of primary astrocyte and microglia under Aβ40WT and Aβ42WT fibrils treatment |
|
| Relations |
| BioSample |
SAMN30308176 |
| SRA |
SRX17062330 |
