|
| Status |
Public on Jul 21, 2016 |
| Title |
S oligo 1 |
| Sample type |
SRA |
| |
|
| Source name |
GH4C1 cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: pituitary gland
cell line: GH4C1
cell type: somatolactotrope
|
| Growth protocol |
GH4C1 cell were grown in Ham-F12 medium supplemented with 15% horse serum and 2% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GH4C1 cell were fixed with 1% paraformaldehyde in PBS. Then nuclei were purified, lysed and sonicated. RNA pull-down was performed using two antisense DNA biotinylated oligonucleotide probes that target the lncRNA Neat1. Streptavidin-magnetic beads were added to hybridization reaction and complexes were captured by magnets. RNA was isolated using NucleoSpin®RNA XS (Macherey-Nagel).
Libraries were prepared according to instructions accompanying the Illumina TruSeq Stranded mRNA Sample Preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Paired-end reads (75bp) were aligned to the Rat reference genome (Rnor_6.0.80, Ensembl) using TopHat2 v2.209
Cuffflinks v2.2.1 was used to quantify mRNA level and fragment per kilobase per million of mapped reads (FPKM) were calculated
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
May 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Anne-Marie François-Bellan |
| E-mail(s) |
anne-marie.francois@univ-amu.fr
|
| Organization name |
CNRS-AMU
|
| Department |
Facute de Medecine
|
| Lab |
INP UMR 7051 CNRS-AMU
|
| Street address |
27 Bd Jean Moulin
|
| City |
Marseille |
| ZIP/Postal code |
13005 |
| Country |
France |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE81972 |
Determination of the RNA linked to the paraspeckle in the GH4C1 cell line |
|
| Relations |
| BioSample |
SAMN05180807 |
| SRA |
SRX1802705 |
