|
| Status |
Public on Jul 27, 2020 |
| Title |
WT BOB UD UT 72h Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
BOBSC hiSPCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC
passage: 15
genotype: Wild-type
|
| Treatment protocol |
MMS treated cells were treated with 5ppm MMS at 24 hours.
|
| Growth protocol |
Essential 8 Flex Medium or Endoderm differentiation medium was used for Undifferentiated (UD) samples and Endoderm differentiated (ENDO) samples respectively. Cells were treated to differentiate as described in Yiangou et al Stem Cell Reports 2019.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Rneasy Qiagen Extraction Mini Kit
NEBnext Ultra II
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
WT_p53_BOB_TC_wMMS_gene_exp.diff
|
| Data processing |
Adaptors were removed and reads quality trimmed using TrimGalore v0.4.4 (https://github.com/FelixKrueger/TrimGalore) with default settings
Read were aligned to the Human genome version GRCh38.87 using TopHat v2.1.0 (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36)
Reads were quantified per genomic region and differential expression was calculated using Cufflinks v2.2.1 (https://www.nature.com/articles/nbt.2450)
Genome_build: human GRCh38.87
Supplementary_files_format_and_content: Cufflinks tab-delimited expression values
|
| |
|
| Submission date |
Mar 02, 2020 |
| Last update date |
Jul 27, 2020 |
| Contact name |
Alastair Crisp |
| Organization name |
MRC Laboratory of Molecular Biology
|
| Street address |
Francis Crick Avenue
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE146225 |
Wild-type and TP53 genetic knockout BOBSC hiPS cells were maintained in the undifferentiated state or differentiated to definitive endoderm over 72 hours, with or without 5 ppm MMS treatment at 24 hours. |
|
| Relations |
| BioSample |
SAMN14258806 |
| SRA |
SRX7827544 |
