|
Status |
Public on Jul 21, 2016 |
Title |
S oligo 2 |
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 |
SAMN05180808 |
SRA |
SRX1802706 |