|
| Status |
Public on Mar 03, 2020 |
| Title |
nf1-1 |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC-derived NPCs_nf1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived neural progenitor cells
passage: 10-15
genotype/variation: NF1 mutation (1185+1G>A)
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Cells were grown in NPC maturation media (50% DMEM/F12, 50% Neurobasal medium supplemented with N2, B27, 2mM GlutaMax, 10ng/mL hLIF, 3µM CHIR99021 and 2µM SB431541)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN Rneasy mini kit
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
nf1-2.CGGAGCGATA-CTTAACAAGG.CGGAGCGATA-CTTAACAAGG_S57
|
| Data processing |
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
The raw gene count matrix was imported into Partek Flow software, version 8.0. Normalization size factors were calculated for all gene counts by CPM to adjust for differences in sequencing depth. Ribosomal genes and genes not expressed in the smallest group size minus samples greater than one count-per-million were excluded from further analysis.
Gene-specific analysis was then performed using the lognormal with shrinkage model (limma-trend method) to analyze for differential expression between the three groups of samples
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing normalized gene counts for each sample and also output from GSA differential analysis
|
| |
|
| Submission date |
Jan 31, 2020 |
| Last update date |
Mar 03, 2020 |
| Contact name |
David Gutmann |
| Organization name |
Washington University in St Louis
|
| Department |
Neurology
|
| Lab |
NF Center
|
| Street address |
660 S Euclid Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE144601 |
Human iPSC-derived neurons and cerebral organoids establish differential effects of germline NF1 gene mutations |
|
| Relations |
| BioSample |
SAMN13956041 |
| SRA |
SRX7655666 |
