|
| Status |
Public on Jun 22, 2022 |
| Title |
NG06917 |
| Sample type |
SRA |
| |
|
| Source name |
Skin Fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
tissue: Skin Fibroblast
age: 3 yr
cell line: NG06917
genotype: HGPS (2036C>T, GLY608GLY)
biomaterial provider: https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AG06917&Product=CC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ten micrograms of purified RNA from several progeria cell lines were acquired from the Coriell Institute (Camden, NJ).
RNA-seq library construction and analysis was carried out by Genewiz using Illumina PolyA selection (South Plainfield, NJ).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The fastq reads were first processed for adapter and quality trimming using the BBDuk. Following that, the reads were aligned to the reference genome hg19 using STAR aligner. Finally, the mapped reads were sorted based on genomic coordinates and feature count was performed with HTSeq-Counts.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw gene count values for each sample.
|
| |
|
| Submission date |
Jun 22, 2022 |
| Last update date |
Jun 22, 2022 |
| Contact name |
Rachel Patton McCord |
| E-mail(s) |
rmccord@utk.edu
|
| Organization name |
University of Tennessee Knoxville
|
| Department |
Department of Biochemistry & Cellular and Molecular Biology
|
| Lab |
Rachel Patton McCord Lab
|
| Street address |
1311 Cumberland Avenue
|
| City |
Knoxville |
| State/province |
Tennessee |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE206684 |
Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. [RNA-Seq] |
| GSE206707 |
Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. |
|
| Relations |
| BioSample |
SAMN29250268 |
| SRA |
SRX15828470 |
