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| Status |
Public on Sep 30, 2019 |
| Title |
Chick_HH18_hindlimb_rep3 |
| Sample type |
SRA |
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| Source name |
embryonic HH18 hindlimb somatopleure
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| Organism |
Gallus gallus |
| Characteristics |
developmental stage: HH18
tissue: hindlimb somatopleure
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was dissected from each embryo in cold PBS. Tissue was immediately transferred to 1x Trypsin in EDTA Solution (Sigma) for 10-15 minutes at room temperature. Following trypsinization, the tissue was transferred to a neutralizing culture media (DMEM (Gibco) with 10% FBS (Gibco) and 1% Pen Strep (Gibco)) and pipette-mixed until homogenized. Homogenate was filtered through 35µm nylon mesh filters and filtrate was taken immediately to cell counting.
50,000 live cells were utilized for ATAC-seq tagmentation as described in Buenrostro et al. (2015). Following tagmentation clean-up, 11 cycles of PCR were carried out and PCR products were cleaned using the Minelute PCR Purification Kit (QIAGEN).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
chromatin accessibility assay using Tn5 enzyme
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| Data processing |
Sequencing and basecalling was carried out on NextSeq_2_1_0.
Raw ATAC-seq reads were trimmed using NGmerge (https://github.com/jsh58/NGmerge) with adapter mode (-a) and a minumum overlap of 20 bases (-e 20).
Trimmed reads were aligned to droNov1 for emu and galGal4 for chicken using Bowtie2.2.4 with -X 2000.
Mitochondrial reads were removed with removeChrom (https://github.com/jsh58/harvard/blob/master/removeChrom.py) .
ATAC-seq peaks were called using MACS2 (v 2.1.0) first on individual libraries and then on pools for each species and tissue. Significant peaks were determined as described in the supplemental methods.
Homologous regions for emu peaks were identified using halLiftover (v2.1) as described in the supplementary methods.
Young_Grayson_2019_ATAC-seq_Matrix.txt was generated using bedtools annotate (v2.25.0). Columns are as follows: Chromosome, Start, Stop, and Size all pertain the the galGal4 genomic position of the peak; geneName is the closest annotated gene to the peak; the next 6 columns are the Chicken (C) and Emu (E) strict peak calls for flank (K), forelimb (FL), and hindlimb (HL), where the value is the proportion of the entire peak region that is overlapped by that dataset; the next 18 columns are the individual libraries for each species and tissue as described for the strict datasets; the next 15 columns are the porportion of the entire peak region that overlaps with previously-published ChIP-seq datasets for chicken (Seki et al. 2017); CNEE is the porportion of overlap of the entire peak region with Conserved Non-Exonic Elements described in Sackton et al. 2019.
Genome_build: droNov1, galGal4
Supplementary_files_format_and_content: strict_(species)_(tissue)_annotate.txt files represent peaks that were present across all three biological replicates for a given species and tissue,
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| Submission date |
Sep 03, 2019 |
| Last update date |
Oct 01, 2019 |
| Contact name |
John Young |
| E-mail(s) |
jyoung@genetics.med.harvard.edu
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Tabin
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19787 |
| Series (2) |
| GSE136775 |
Attenuated FGF signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae (ATAC-seq data) |
| GSE136776 |
Attenuated FGF signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae |
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| Relations |
| BioSample |
SAMN12684336 |
| SRA |
SRX6793638 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4057726_Chick_HH18_hindlimb_rep3.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSM4057726_Chick_HH18_hindlimb_rep3.bedGraph.gz |
130.9 Mb |
(ftp)(http) |
BEDGRAPH |
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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