|
| Status |
Public on Sep 23, 2013 |
| Title |
579_E11+E12_H3K27me3_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
E13 fetal brain_H3K27me3_ChIP-seq
|
| Organism |
Monodelphis domestica |
| Characteristics |
strain: LL1 mother (A0579) x LL2 father (A0573)
gender: female
developmental stage: embryonic day 13
tissue: fetal brain
chip antibody: H3K27me3
chip antibody vendor: Upstate-Millipore
chip antibody cat. #: 07-449
chip antibody lot #: JBC1873477
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted, digested with micrococcal nuclease, pooled (sisters only), and quantified using Qubit. Chromatin was equally divided and ChIP was performed using the indicated antibodies. Samples were purified using the Minelute PCR Purification Kit by Qiagen. Enrichment was checked by qPCR.
ChIP-seq libraries were constructed using a modified version of the Illumina TruSeq RNA Sample Prep protocol. All libraries were constructed at Global Biologics, Columbia, MO.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
pooled tissue from two sister fetuses
processed data file: Female_Fetal_Brain_H3K27me3_MACS_Peaks.bed
|
| Data processing |
Illumina CASAVA 1.7 software was used for basecalling.
Adapter sequences were removed from the raw reads by custom scripts.
The short reads were aligned to the opossum reference genome (monDom5) using Bowtie v. 1.1.2
Significant Peaks were called using MACS v. 1.0.1
Genome_build: UCSC monDom5 (http://www.ncbi.nlm.nih.gov/assembly/237648/)
Supplementary_files_format_and_content: BED files containing peaks, peak coordinates, and -10*log10(pvalue) of each peak
|
| |
|
| Submission date |
Mar 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kory Douglas |
| E-mail(s) |
[email protected]
|
| Organization name |
Texas A&M University
|
| Street address |
4458 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL15381 |
| Series (1) |
| GSE45186 |
Chromosome-wide profiling of X-inactivation status and epigenetic regulation in fetal brain |
|
| Relations |
| SRA |
SRX250052 |
| BioSample |
SAMN01978885 |
