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| Status |
Public on Jun 06, 2019 |
| Title |
ATAC-seq_Wt DP-R1hi rep1 |
| Sample type |
SRA |
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| Source name |
haemogenic endothelium
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| Organism |
Danio rerio |
| Characteristics |
age: 28-30 hpf
tissue: haemogenic endothelium
cell isolation: FACS isolated cells
cell population: double positive runx1-high mCherry+Citrinehigh
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| Growth protocol |
TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos, were raised to 28-30 hpf.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
whole embryos were prepaired for FACsorting. 2000-3000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation
Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. DNA was purified using the QIAquick PCR purification kit (Qiagen). Fragments were amplified for 16 cycles.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC-HE-70
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| Data processing |
Sequencing was performed on a NextSeq machine, using two 75bp paired-end chips loaded with the same Master-Library mix. Reads were combined to one raw data set. RAW data files represent the combined reads and combined lanes.
Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32).
Sequences were aligned to the Zebrafish Genome Zv10 with BWA (Version 0.7.12) with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
Peaks were identified using MAC2 software (Version 1.4.2), using the genomic DNA as input to define background. Differential peaks analysis was carried out using DiffBind (Bioconductor Package). tool).
Triplicates were analysed for consistency by PCA and correlation analysis and one outlying replicate has been removed for each, DP-R1hi and DP-R1lo. Using a GLM analysis with EdgeR methods a list of DE packs between DP-R1hi and DP-R1lo population has been identified, then annotated with Homer software (Version 3.0). Further, peaks were filtered for log2 Fold Change <-0.7 and >0.7. Selecting the specific peaks for DP-R1hi and DP-R1lo.
“De novo analysis” for transcription factor binding site has been carried out using the TSS, intergenic, and intron peaks list with “findMotifsGenome.pl” in Homer software package.
Genome_build: Zv10
Supplementary_files_format_and_content: bw files: bigwig files representing the Zv10 mapping data in bigwig format, for each tissue type and each replicates
Exp4-Wt-Flk1_S3_mergedLanes.sorted.bw Exp5-Wt-Flk1_S5_mergedLanes.sorted.bw Exp6-Wt-Flk1_S11_mergedLanes.sorted.bw Exp4-Wt-High_S6_mergedLanes.sorted.bw Exp5-Wt-High_S21_mergedLanes.sorted.bw Exp6-Wt-High_S23_mergedLanes.sorted.bw Exp4-Wt-Medium_S10_mergedLanes.sorted.bw Exp5-Wt-Medium_S13_mergedLanes.sorted.bw Exp6-Wt-Medium_S16_mergedLanes.sorted.bw Exp4-Wt-Low_S9_mergedLanes.sorted.bw Exp5-Wt-Low_S17_mergedLanes.sorted.bw Exp6-Wt-Low_S15_mergedLanes.sorted.bw Exp4-Wt-Negativ_S20_mergedLanes.sorted.bw Exp5-Wt-Negative_S2_mergedLanes.sorted.bw Exp6-Wt-Negative_S22_mergedLanes.sorted.bw gDNA-DA_S7_mergedLanes.sorted.bw
Supplementary_files_format_and_content: bed files: The tab delimited file contains the result of the differential peak analysis obtained with the diffBind package using the EdgeR package for the contrast. The sample used for the analysis are the Wt DP-R1hi vs Wt DP-R1Lo. The one with positive FoldChange represent the peaks close into the Wt DP-R1Lo population, and the one with negative FoldChange are the one with peaks close into the Wt DP-R1Hi population.
DE_peacks_CloseIntoLow_FC_annotation_gs.bed DE_peacks_CloseIntoHigh_FC_annotation_gs.bed
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| Submission date |
Jun 05, 2019 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Florian Bonkhofer |
| Organization name |
Oxford University
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| Street address |
John Radcliffe Hospital/Headley Way
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| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
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| Platform ID |
GPL20828 |
| Series (2) |
| GSE132258 |
ATACseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization |
| GSE132260 |
ATACseq and RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization |
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| Relations |
| BioSample |
SAMN11962945 |
| SRA |
SRX5978292 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3855033_Exp4-Wt-High_S6_mergedLanes.sorted.bw |
937.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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