|
| Status |
Public on Feb 19, 2021 |
| Title |
mutant NCC [82742] |
| Sample type |
SRA |
| |
|
| Source name |
iPS derived neural crest cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neural crest cells derived from monoallelic CHD6 mutant iPS cells
age: p 2
genotype: monoallelic CHD6 mutant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from different genotypes/differentiations were harvested in Trizol (Life Technologies) and total RNA was isolated and DNase-treated using the Direct-zol RNA miniprep kit as per manufacturer’s instructions (Zymo Research). In the case of cardiomyocytes, cells at D10-D11 of differentiation were used, while in the case of NCCs, cells were obtained by collecting migratory cells from dissected and re-plated rosettes.
polyA-enriched RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
polyA-enriched total RNA-Seq
K002000198_82742
|
| Data processing |
Sequenced reads were mapped with STAR v2.2.2a with parameters --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were mapped to exons were counted by htseq-count using the following parameters: minimum alignment 30
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts (output of htseq-count), bigWig files (strand-specific), raw fastq files.
|
| |
|
| Submission date |
Sep 04, 2019 |
| Last update date |
Feb 19, 2021 |
| Contact name |
Yulia Kargapolova |
| Organization name |
Cologne University
|
| Department |
CMMC
|
| Lab |
AG Papantonis
|
| Street address |
Robert-Koch-Straße 21
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE135832 |
Impaired CHD6 function links misregulation of autophagy and DNA damage response to premature ageing [RNA-Seq] |
| GSE161120 |
Impaired CHD6 function links misregulation of autophagy and DNA damage response to premature ageing |
|
| Relations |
| BioSample |
SAMN12690322 |
| SRA |
SRX6799413 |
