|
| Status |
Public on Feb 27, 2018 |
| Title |
TMX2 (PR50) - 3 |
| Sample type |
SRA |
| |
|
| Source name |
primary cortical neuron cultures
|
| Organism |
Mus musculus |
| Characteristics |
treatment: TMX2 sgRNAs (+PR50 lenti)
experiment grouping: Experiment 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
SafePR50_vs_TMX2PR50-ExpDiff (neurons).csv
|
| Data processing |
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: hg38 for human samples, mm10 for mouse samples
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)
|
| |
|
| Submission date |
Jan 14, 2018 |
| Last update date |
Feb 27, 2018 |
| Contact name |
Nicholas J Kramer |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE109177 |
CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9orf72 dipeptide repeat protein toxicity |
|
| Relations |
| BioSample |
SAMN08362867 |
| SRA |
SRX3584673 |
