|
| Status |
Public on Jun 07, 2019 |
| Title |
ESC_ATRXKO_H33 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57Bl/6/129sV
genotype/variation: ATRX KO
cell type: Embryonic stem cells
chip type: crosslink
chip antibody: H3.3 (09-838, Millipore)
|
| Growth protocol |
ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with MNase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cells were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina TruSeq protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al., 2009).
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
May 16, 2018 |
| Last update date |
Jun 07, 2019 |
| Contact name |
Laura Banaszynski |
| E-mail(s) |
Laura.banaszynski@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Green Center for Reproductive Biology Sciences
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE114548 |
H3.3 phosphorylation promotes enhancer acetylation and lineage specification [ChIP-seq] |
| GSE114551 |
H3.3 phosphorylation promotes enhancer acetylation and lineage specification |
|
| Relations |
| BioSample |
SAMN09214629 |
| SRA |
SRX4090660 |
