|
| Status |
Public on Sep 05, 2020 |
| Title |
HGPS167 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Hutchinson-Gilford progeria syndrome (HGPS) skin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: patient derived skin fibroblast
passage: 10
|
| Growth protocol |
Primary fibroblast cell lines were cultured in DMEM High glucose with glutamax supplemented with 15% FBS and 1% Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA libraries were prepared from total RNA, extracted with Trizol.
We constructed libraries by using Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero GOLD. cDNA fragments of ~300 bp were purified from each library and were sequenced for 125bp, using an Illumina HiSeq 2500 instrument according to manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Transcript level quantification was done with Kallisto (version 0.43.0) to estimate transcript level read counts and TPM (Transcripts Per Million) values. The GENCODE v27 annotation was used to build the transcriptome index. Kallisto was run with the --bias option to perform sequence based bias correction on each sample.
Genome_build: GENCODE v27
Supplementary_files_format_and_content: tsv: length, effective length, estimated read count and TPM for transcripts from the GENCODE v27 annotation.
|
| |
|
| Submission date |
Aug 16, 2018 |
| Last update date |
Sep 05, 2020 |
| Contact name |
Chiara Lanzuolo |
| E-mail(s) |
[email protected]
|
| Phone |
0200660358
|
| Organization name |
CNR and Istituto Nazionale Genetica Molecolare
|
| Lab |
Lanzuolo Lab
|
| Street address |
Via Francesco Sforza 35
|
| City |
Milan |
| State/province |
--- |
| ZIP/Postal code |
20122 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE118633 |
SAMMY-seq, H3K9me3 and H3K27me3 ChIP-seq and RNA-seq of control and progeria fibroblasts |
|
| Relations |
| BioSample |
SAMN09727152 |
| SRA |
SRX4475542 |
