|
| Status |
Public on Oct 27, 2017 |
| Title |
F1040_Lv_H4K16ac |
| Sample type |
SRA |
| |
|
| Source name |
Liver, Female, H4K16ac ChIP
|
| Organism |
Anolis carolinensis |
| Characteristics |
Sex: Female
tissue: Liver
developmental stage: Adult
marker: H4K16ac
chip antibody: H4K16ac (EMD Millipore, cat#: 07-329, lot# 2716753)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA was purified using QIAquick PCR Purification columns (Qiagen) according to manufacturer’s instructions.
5 ng of input and ChIPed DNA were used to prepare sequencing libraries using NEBNext Ultra II Library Prep kit as described by the manufacturer (New England Biolab, E7645S).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.
ChIP-Seq reads were aligned to the AnoCar2.0 genome assembly using BWA v0.7.15 with default parameters.
PCR duplicates and reads mapping to multiple genome positions were filtered out from the alignments.
In order to allow comparisons between different samples and across genomic features, the data were: i) normalized by library size; ii) all samples were input normalized by dividing the read counts of ChIPed samples by the read counts in the corresponding input over a window size of 50bp; these analyses were performed using the deepTools (v2.4.0).
Genome_build: AnoCar2.0
Supplementary_files_format_and_content: BigWig files were produced using deepTools v2.4.0.
|
| |
|
| Submission date |
May 05, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Diego Cortez |
| E-mail(s) |
diegoclaudio.cortezquezada@unil.ch
|
| Organization name |
Univerity of Lausanne - CIG
|
| Street address |
Rue de Lausanne
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23433 |
| Series (1) |
| GSE97367 |
BioProject PRJNA381064: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage (Gene expression profiling in several tetrapod species, bulk tissue RNA-seq) |
|
| Relations |
| BioSample |
SAMN06899465 |
