|
| Status |
Public on May 04, 2023 |
| Title |
ATAC-seq 48hours BM/Ikzf1/4 rep3 |
| 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+Ikzf1+Ikzf4
|
| Treatment protocol |
MEFs infected with doxycycline-inducible lentiviral vectors for Brn2, Myt1l, Ikzf1, and Ikzf4 were culture with doxycycline for 2 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
48 hours after doxycycline addition, 50000 MEF nuclei were isolated as previously reported (Buenrostro et al., 2015), with modifications described in (Mayran et al., 2018).
Isolated nuclei underwent transposase reaction: 2.5μl of 10x TD buffer, 10μl of water, and 12.5μl of enzyme (Illumina Nextera kit; FC-121–1031). DNA was purified with GeneRead Purification columns (Qiagen), enriched by PCR, and purified again with GeneRead Purification columns before being sequenced.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Bamcoverage .bigwig file/MACS2 peak calling .bed file
|
| 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 |
SAMN18474497 |
| SRA |
SRX10435067 |
