|
| Status |
Public on Feb 28, 2021 |
| Title |
NipblHET primary dissociated cortical neuron Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary dissociated cortical neuron
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Nipbl+/-
|
| Growth protocol |
Mouse cortices were dissected and dissociated from individual E17.5-E18.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 0.8 × 10^6 cells per well on 6-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and one third of the media in each well was replaced every 3 days. Cultures were treated with 5uM Cytosine β-D-arabinofuranoside (Ara-C, Sigma) from day 2-4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained in parallel from dissociated cortical neurons at DIV10 with QIAshredder and RNeasy mini kit (Qiagen).
RNA-seq libraries were prepared from 600 ng of total RNA (RNA integrity number (RIN) >8.0) with TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NipblHet_Rep2
|
| Data processing |
Illumina CASAVA 1.8.4 software used for basecalling.
The reads were aligned to mouse genome UCSC mm9 using Tophat2 with arguments “--library-type fr-firststrand”
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample
|
| |
|
| Submission date |
Nov 19, 2020 |
| Last update date |
Feb 28, 2021 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE150130 |
Partial rescue of neuronal genes deregulated in CdLS by cohesin |
| GSE161796 |
RNA-seq of primary dissociated cortical Nipbl+/- neurons |
|
| Relations |
| BioSample |
SAMN16834522 |
| SRA |
SRX9531463 |
