|
| Status |
Public on Jul 17, 2018 |
| Title |
d3 Tg MEF +Mybl2 only rep1 80% chimeric |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Tg MEF +Mybl2 only 80% chimeric
cell type: Mouse embryonic fibroblasts
|
| Treatment protocol |
Trasgenic (Tg) MEFs carrying doxycycline-inducible Yamanaka factors were transduced with lentiviral particles encoding AmCyan or Mybl2-AmCyan and then reprogramming was induced by addition of doxycycline. Cells were collected after 3 days of reprogramming.
|
| Growth protocol |
DMEM with 1% Penicillin/Streptomycin, 2mM L-glutamine, 15% ESC qualified FBS, 1% non-essential amino acids, 0.1mM 2-mercaptoethanol, 0.01% LIF and 10μg/ml vitamin C. 200ng/ul Doxycycline was added to induce reprogramming.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were lysed in 10mM TrisHcl ph7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL. Nuclei were incubated with Tn5 transposase and 2% Digitonin. Then DNA was purified with Qiagen MiniElute kit.
10 μl of DNA was combined with 2.5 μl of indexing primers (Nextera Customized PCR Primer 1 and barcode Nextera PCR Primer 2), 25 μl of NEBNextHigh-Fidelity 2x PCR Master Mix (New England Biolabs). DNA was then amplified for 8 cycles to enrich the tagmented DNA fragments. A PCR clean-up was then performed using AMPure XP beads (Beckman Coulter), and the small fragments were then resuspended in 32.5 μl of resuspension buffer (provided in the Nextera kit). DNA was quantified using a Qubit fluorometer (Life Technologies), and library sizes were then determined using TapeStation (Agilent Technologies)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Day_4_80percent_1_2_mm10_bt2_auto_SPMR_treat_pileup.bdg.gz
|
| Data processing |
NextSeq Control Software v2.1.0.31 was used for basecalling
GenerateFASTQWorker v2.6.17.15 was used to generate fastq files
FASTQC v0.11.5 was used to trim low quality reads
bowtie2 v2.1.0 was used to align reads to genome using arguments: --very-sensitive-local
samtools v1.4 was used to convert alignes .sam to .bam
MACS v2.1.0 was used to call peaks using optional arguments: --keep-dup=auto -B --trackline -f BAMPE -g mm
bedtools
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph generated with MACS showing Tn5 accessible regions of the genome.
|
| |
|
| Submission date |
May 14, 2018 |
| Last update date |
Jul 17, 2018 |
| Contact name |
Carl Ward |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Birmingham
|
| Street address |
Edgbaston
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE107577 |
Fine-tuning Mybl2 levels are required for proper MET process during somatic reprogramming [ATAC-Seq] |
| GSE107579 |
Fine-tuning Mybl2 levels are required for proper MET process during somatic reprogramming |
|
| Relations |
| BioSample |
SAMN09208165 |
| SRA |
SRX4082624 |
