|
| Status |
Public on Jun 01, 2022 |
| Title |
INS-1 line 16 (Control 3) |
| Sample type |
SRA |
| |
|
| Source name |
INS-1(832/13)::mCherry
|
| Organism |
Rattus norvegicus |
| Characteristics |
genotype: Control
|
| Treatment protocol |
none
|
| Growth protocol |
RPMI INS-1 media 7.5mM Glucose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol; Qiagen miRNeasy
Illumina Next-seq
rRNA depletion (Total RNA-Seq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
QC with FastQC v0.11.5 and adapter trimming with CutAdapt using wrapper in TrimGalor v0.4.5
Splice-aware genome alignement using STAR v2.7.0e
Gene-level feature counts with HTSeq v0.11.2 (with --mode union combined with --nonunique all or with --nonunique none ) or with RSEM v.1.3.1
Differential gene expression with DEseq2 v.3.9
Genome_build: Ensembl Rnor6.0 v98 + custom transgene and annotation tracks (see github.com/KoppesEA/INS-1_PWS_RNA-Seq for more information)
https://github.com/KoppesEA/INS-1_PWS_RNA-Seq/
Supplementary_files_format_and_content: .csv files for expression all rat genes in PWS vs Control samples; .txt files for custom annoation
Supplementary_files_format_and_content: .csv STAR/HTSeq/DESeq2 output
Supplementary_files_format_and_content: .csv STAR/HTSeq/DESeq2 output
Supplementary_files_format_and_content: .csv STAR/RSEM/DESeq2 output
Supplementary_files_format_and_content: .gtf of additional custom annotations
Supplementary_files_format_and_content: .fa sequence of mINS2-mCherryCP transgene
Supplementary_files_format_and_content: .fa sequence of hINS-NeoR transgene
|
| |
|
| Submission date |
Dec 07, 2021 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Erik Koppes |
| E-mail(s) |
koppesea@upmc.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
MWRI
|
| Street address |
204 Craft Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE190334 |
Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [RNA-seq] |
| GSE190337 |
Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones |
|
| Relations |
| BioSample |
SAMN23720057 |
| SRA |
SRX13339221 |
