|
| Status |
Public on Aug 01, 2022 |
| Title |
PARN mutant patient1 iPSCs_CRISPR-Cas9 mediated PAPD5 knockout |
| Sample type |
SRA |
| |
|
| Source name |
PARN mutant patient1 iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblast derived iPSCs
treatment: CRISPR-Cas9 mediated PAPD5 knockout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Ambion) according to manufacturer’s protocol.
RNA-Seq library prepared using Illumina TruSeq stranded total RNA with RiboZero Gold or RiboZero Plus, per the manufacturer instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
5075_mix-O68C4-C11_S4_L007
|
| Data processing |
basecalling and demultiplex with Illumina bcl2fastq
Reads mapping to genome using HISAT2
Produces normalized read count FPKM and differential expression analysis using Cuffdiff (of the Cufflink package v2.1.1)
Normalized read count is then further analyzed and visualized with Qlucore Omics Explorer (v3.7)
Genome_build: hg38
|
| |
|
| Submission date |
Dec 04, 2021 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Suneet Agarwal |
| Organization name |
Boston Children's Hospital
|
| Department |
Hematology/Oncology
|
| Street address |
Karp 07214, 1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE190173 |
Domain-specific mutations in dyskerin disrupt 3´end processing of snoRNAs |
|
| Relations |
| BioSample |
SAMN23637020 |
| SRA |
SRX13314017 |
