|
| Status |
Public on May 04, 2023 |
| Title |
RNA-seq 48hours BM rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MEFs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblasts
mouse line: R26-M2rtTA
strain: C57BL/6
condition: Brn2+Myt1l
|
| Treatment protocol |
MEFs infected with doxycycline-inducible lentiviral vectors for Brn2 and Myt1l were culture with doxycycline for 2 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from MEF cultures was performed using the RNeasy Plus Micro Kit (Qiagen).
mRNA was isolated by Poly(A) mRNA magnetic isolation (NEBNext; E7490S), and cDNA libraries were generated with KAPA RNA HyperPrep kits (Roche; 08098197702).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Raw salmon counts/DESeq2
|
| Data processing |
Raw ATAC-seq fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using these parameters: --nomodel --shift -37 --extsize 73 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Bigwig tracks files for ATAC-seq conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
May 04, 2023 |
| Contact name |
Awais Javed |
| E-mail(s) |
awaisj14@gmail.com, awais.javed@ircm.qc.ca
|
| Phone |
5149875772
|
| Organization name |
IRCM
|
| Lab |
Michel Cayouette
|
| Street address |
110 Avenue des Pins
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H2W1R7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE169519 |
Direct neuronal reprogramming by temporal identity factors |
|
| Relations |
| BioSample |
SAMN18474495 |
| SRA |
SRX10435069 |
