|
| Status |
Public on Mar 22, 2019 |
| Title |
Sample 4_ETS2_Input_F |
| Sample type |
SRA |
| |
|
| Source name |
ETS2_Input
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: embryo
injected with: tripple-FLAG tagged ETS2 mRNA
time point: mid-gastrulation (stage 11.5)
antibody: none
|
| Treatment protocol |
Embryos were injected with 750pg tripple-FLAG tagged ETS2 mRNA and collected mid-gastrulation (stage 11.5)
|
| Growth protocol |
Embryos were cultured in 1/3MR until stage 11.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated DNA and ETS2-tripple-FLAG bound DNA complexes were isolated with antibody.
Illumina TruSeq ChIP kit. Libraries were made by the UC Berkeley Functional Genomics Laboratory.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file:
RHRK_F_S56
ChIPETS_CF_M2_treat_pileup.bw
ChIPETS_CF_M2_peaks.bed
Ets_common_peaks.bed
|
| Data processing |
ChIP-seq reads were aligned to the Xenopus laevis genome version 9.1 assembly using bowtie 2.2.3.
Peaks were called using MACS2 using defalt settings
File with common peaks between replicate samples was created by R package ChipPeakAnno
bigwig files were created by first removing scaffolds from bedgraph files generated by MACS2, then with command, bedGraphToBigWig
Genome_build: http://www.xenbase.org/common/displayJBrowse.do?data=data/xl9_1
Supplementary_files_format_and_content:
ChIPETS_AD_M2_treat_pileup.bw: Peaks were called using MACS2 using default setings. ChIP sample is Sample 1 and Input Control is Sample 3. Bigwig was made by first removing scaffolds from bedgraph files generated by MACS2, then converted with nedGraphToBigWig command
ChIPETS_CF_M2_treat_pileup.bw: Peaks were called using MACS2 using default setings. ChIP sample is Sample 3 and Input Control is Sample 4. Bigwig was made by first removing scaffolds from bedgraph files generated by MACS2, then converted with nedGraphToBigWig command
ChIPETS_AD_M2_peaks.bed: Peaks were called using MACS2 using default setings. ChIP sample is Sample 1 and Input Control is Sample 3.
ChIPETS_CF_M2_peaks.bed: Peaks were called using MACS2 using default setings. ChIP sample is Sample 3 and Input Control is Sample 4.
Ets_common_peaks.bed: Common peaks were the intersect of peaks from Proccessed samples ChIPETS_AD_M2_peaks.bed and ChIPETS_CF_M2_peaks.bed using the ChIPpeakAnno R package.
|
| |
|
| Submission date |
Mar 23, 2018 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Richard Harland |
| Organization name |
University of California, Berkeley
|
| Street address |
Life Sciences Addition #3200
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL22393 |
| Series (1) |
| GSE112249 |
Genome-wide map of ETS2 binding in gastrula stage Xenopus.laevis embryos |
|
| Relations |
| BioSample |
SAMN08783512 |
| SRA |
SRX3836837 |
