|
| Status |
Public on Apr 01, 2021 |
| Title |
GRN R493X Macrophage rep2 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: GRN R493X HO
engineering target: Progranulin gene
cell type: iPSC Derived Macrophages
disease state: NCL Disease Model
|
| Treatment protocol |
End stage macrophages were harvested from the cell culture vessel and sample was centrifuged prior to addition of RLT lysis buffer
|
| Growth protocol |
iPSC were differentiated into Hematopoietic Progenitor Cells (HPC), expanded into Common Myeloid Progenitors (CMPs), and then further differentiatied into end stage Macrophages.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pelleted end stage macrophages were lysed using RLT Lysis buffer and stored at -800C. RNA extraction was preformed using Rneast Mini Kit according to the manufacturer's protocol. Post extraction the sample was incubated with Turbo DNase at 37°C for 30 minutes and subsequently re-purified using RNeasy clean-up protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GRN/Rep1
|
| Data processing |
Base calling was performed using RTA 3 on Illumina Novaseq 6000 platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using a splice-aware software Hisat2 v 2.1.0 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cuffdiff v2.2.1 program with default parameters which includes geometric library normalization method and pooled dispersion method
Cuffdiff output was reformatted to tab-delimited tabular file using in-house perl script
Genome_build: HG38
Supplementary_files_format_and_content: MO_Experiment_FCDI.txt.gz (tab-delimited text file includes FPKM values for each Sample)
|
| |
|
| Submission date |
Mar 31, 2021 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Deepika Rajesh |
| E-mail(s) |
deepika.rajesh@fujifilm.com
|
| Organization name |
Fujifilm Cellular Dynamics Inc.
|
| Department |
Life Sciences
|
| Lab |
R&D
|
| Street address |
525 Science Dr
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53711 |
| Country |
USA |
| |
|
| Platform ID |
GPL27644 |
| Series (1) |
| GSE171276 |
RNAseq Analysis Investigates Transcriptional Similarities and Differences Between Cryopreserved Parental and Engineered iPSC Derived Macrophages |
|
| Relations |
| BioSample |
SAMN18578279 |
