|
| Status |
Public on Oct 29, 2018 |
| Title |
WT_rep3 [37EF] |
| Sample type |
SRA |
| |
|
| Source name |
wild type marmoset fibroblasts
|
| Organism |
Callithrix jacchus |
| Characteristics |
age: newborn
genotype/variation: wild type
tissue: skin
|
| Treatment protocol |
Immortalized cells were generated by transfection of piggyBac transposon carrying hTERT and puromycin resistance expression cassettes (pTT-PB-hTERT-Puro) and piggyBac transposase (pcA3-PBase-Tomato). The cells expressing hTERT were selected with puromycin.
|
| Growth protocol |
All cells were grown on 10 cm tissue culture plates were coated with 0.1% gelatine. Medium used was DMEM high glucose supplemented with 10% FBS, GlutaMax, 1xNEAA, and Penicillin/Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with TRIzol reagent. The RNA quality was assessed by measuring the RIN (RNA Integrity Number) using Agilent 2100 Bioanalyzer.
Library construction was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122–2002) starting from 500 ng of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
r1056s37EF_cj_rna_sr_DPZ_D_3_CTTGTA_L005
|
| Data processing |
Demultiplexing was performed using Illumina CASAVA-1.8.2
Quality check was performed using FastQC
Sequence Alignment was performed using star-2.3
Read counting was performed using featurecount
Differential gene expression analysis was performed using DESeq2_1.8.2
Genome_build: C_jacchus3.2.1
Supplementary_files_format_and_content: normalized counts and differential gene expression as indicated in the file names
|
| |
|
| Submission date |
May 28, 2018 |
| Last update date |
Oct 29, 2018 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21580 |
| Series (1) |
| GSE114965 |
Comparison of the transcriptomes of hTERT-immortalized and wild type marmoset fibroblasts by next-generation RNA sequencing. |
|
| Relations |
| BioSample |
SAMN09272509 |
| SRA |
SRX4132482 |
