|
| Status |
Public on Oct 22, 2020 |
| Title |
WT Control 3 |
| Sample type |
SRA |
| |
|
| Source name |
Coriell #GM00969
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary fibroblasts
genotype: euploid
|
| Biomaterial provider |
Coriell; https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM00969
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Cells were grown for 48 hours and 2 x 10^5 cells were harvested between 50 to 70% confluency. Cells were maintained in Minimum Essential Media (MEM with NEAA; Gibco 10370088) supplemented with 15 % FBS and 2 mM L-glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNAeasy Kit from Qiagen (cat # 74104) was used to purify the RNA and a nanoDrop was used to measure concentration. Samples were shipped for on dried ice for transcriptome sequencing to BGI
BGI protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Paired-end reads were aligned to human primary genome hg38, with star_2.5.3a 1, annotated with GENECODE GRCh38.p12 annotation release 292.
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2 3
Expression normalization was performed using the TPM (Transcripts Per Kilobase Million) method.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx, normalized expression values
|
| |
|
| Submission date |
Jul 14, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Eduardo M Torres |
| E-mail(s) |
Eduardo.Torres@umassmed.edu
|
| Phone |
5088564353
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Department of Molecular, Cell and Cancer Biology
|
| Lab |
Torres
|
| Street address |
364 Plantation Street, LRB-523
|
| City |
worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE154418 |
Consequences of aneuploidy in human fibroblasts with trisomy 21 |
|
| Relations |
| BioSample |
SAMN15529946 |
| SRA |
SRX8727296 |
