|
| Status |
Public on Jan 21, 2020 |
| Title |
FBXL19fl_ES_RA72hrs_rep2_ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic stem cells, control, retinoic-acid treated (72hr RA), ATAC-seq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14 mouse embryonic stem cells
replicate: 2
treatment agent: retinoic acid (RA)
treatment time point: 72 hr
|
| Treatment protocol |
To induce RA-differentiation mouse ES cells were treated with 1uM retinoic acid (RA)
|
| Growth protocol |
Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al. 2013) as previously described (King and Klose 2017), using 5x10^5 nuclei.
ATAC-seq libraries were prepared by PCR amplification using custom-made Illumina barcodes (Buenrostro et al. 2013) and the NEBNext High-Fidelity 2X PCR Master Mix (NEB). Libraries were purified with two rounds of Agencourt AMPure XP bead cleanup (Agencourt, 1.5X bead:sample ratio), and were sequenced using the Illumina NextSeq 500 platform in biological quadruplicate using 75 bp paired-end reads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to mm10 genome using Bowtie 2 with the ‘-- no-mixed’ and ‘-- no-discordant’ options (Langmead and Salzberg 2012). Reads that were mapped more than once were discarded, PCR duplicates were removed using SAMTools (Li et al. 2009). Reads that mapped to a custom ‘blacklist’ of genomic regions with artificially high counts, including mitochondrial DNA sequences, were also discarded.
For data visualisation, mm10 reads were randomly subsampled by a factor that reflects the total number of reads in the same sample, as previously described (Bonhoure et al. 2014; Orlando et al. 2014; Hu et al. 2015).
For each condition, downsampled biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
ATAC-seq enrichments were quantified from BAM files using the summarizeOverlaps() function from GenomicFeatures. Log2 transformations were calculated following the addition of a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for raw and merged replicates of normalised ChIP-seq
|
| |
|
| Submission date |
Dec 12, 2019 |
| Last update date |
Jan 21, 2020 |
| Contact name |
Angelika Feldmann |
| E-mail(s) |
[email protected]
|
| Phone |
7983705260
|
| Organization name |
University of Oxford, Department of Biochemistry
|
| Street address |
South Parks Road
|
| City |
Oxford |
| State/province |
England |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE136424 |
CDK-Mediator and FBXL19 cooperate in the induction of developmental genes by promoting regulatory interactions |
| GSE141919 |
CDK-Mediator and FBXL19 cooperate in the induction of developmental genes by promoting regulatory interactions [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN13547509 |
| SRA |
SRX7354505 |
