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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 31, 2021 |
| Title |
ATAC-seq wing bud HH20 replicate 2 |
| Sample type |
SRA |
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| Source name |
wing buds
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| Organism |
Gallus gallus |
| Characteristics |
strain: White Leghorn
tissue: wing buds
developmental stage: HH20
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Per biological replicate, a pair of forelimb bud of mouse at E9.75 and wing bud of chicken at HH20, HH22 and HH24 stages were microdissected in cold PBS. Cells were isolated from the tissue using a Dounce Tissue Grinder (VWR KT885300-002) pestl A for 20 strokes followed by B 20 strokes in 1ml cold PBS. Cells were counted using a Neubauer Counting chamber (VWR 631-0696)
75'000 cells were processed per sample for ATAC-Seq as described in Buenrostro et al., 2015.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
h20_ATAC_rep2
ATAC_WB_HH20_rep2
ATAC-seq of chicken wing buds at HH20 stage
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| Data processing |
Raw reads of 41 bp paired-end reads for developing mouse forelimb bud (E9.75, E10.5 and E11.5) and chicken wing bud (HH20, HH22 and HH24) stages were evaluated for quality using Trim galore v0.6.2 wrapper for Cutadapt (Martin, 2011) with --nextera --gzip --paired settings.
High-quality reads from mouse and chicken samples were aligned to the latest release of their respective reference genomes (mouse - GRCm38/mm10; chicken - Gallus_gallus-5.0/galGal5) using Bowtie2 v2.2.9 (Langmead B et al., 2012) following ENCODE settings.
CollectInsertSizeMetrics.jar and MarkDuplicates.jar utility from Picard v2.8.0 (BroadInstitute 2015) were used to generate fragment size statistics and eliminate PCR duplicates respectively. SAMtools commands utility (Li et al., 2009) was used for format conversion (view), indexing (index) and sorting (sort) of the alignment files.
bigWig profiles of normalized counts (reads per kilobase per million mapped reads) were generated using deeptools v3.0.0 (RamÃrez, Fidel, et al., 2016).
Genome_build: mm10, galGal5
Supplementary_files_format_and_content: bigWig
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| Submission date |
Jan 13, 2021 |
| Last update date |
Jul 31, 2021 |
| Contact name |
Shalu Jhanwar |
| E-mail(s) |
shalu.jhanwar@unibas.ch
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| Organization name |
University of Basel
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| Department |
Department of Biomedicine
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| Street address |
Mattenstrasse 28
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL19787 |
| Series (2) |
| GSE164736 |
Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [ATAC-seq] |
| GSE164738 |
Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development |
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| Relations |
| BioSample |
SAMN17306524 |
| SRA |
SRX9843123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5017898_h20_ATAC_rep2_dpProfiles.bw |
130.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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