|
Status |
Public on Aug 17, 2022 |
Title |
Primary astrocyte, control_03 |
Sample type |
SRA |
|
|
Source name |
brain
|
Organism |
Rattus norvegicus |
Characteristics |
tissue: brain cell type: Primary astrocyte cells genotype: WT treatment: control 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 |
SAMN30308182 |
SRA |
SRX17062324 |