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| Status |
Public on Sep 17, 2019 |
| Title |
ATAC-seq E11.5 replicate 3 |
| Sample type |
SRA |
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| Source name |
forelimb bud at E11.5
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: forelimb bud
age: E11.5
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For sampling, mouse forelimb buds of each stage were dissected and treated with collagenase for 10 min at RT. Then, cells were dissociated into single-cell suspensions by pipetting and 40 μm mesh filter (Funakoshi, Cat. No. HT-AMS-14002), and frozen in CryoStor® media (Stemcell technologies Cat. No. ST07930) with Mr. Frosty™ (Thermo Scientific, Cat. No. 5100-0001) at −80°C for overnight
Stored cells were melted in 38 °C water bus, and spun down at 500 g for 5min at 4 °C, which was followed by a wash using 50 μl of cold PBS once and centrifugation at 500g for 5 min. Ten thousands of cells per sample were collected without distinguishing dead cells, and lysed using 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1 % IGEPAL CA-630). Immediately after lysis, cells were spun at 1000 g for 10 min at 4 °C, and the supernatant was discarded. For transposition reaction, cells were re-suspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water), and incubated for 30 min at 37 °C. For control, 50 ng control genome DNA was also transposed. The reaction mix was purified using DNA Clean & Concentrator-5 (zymo, Cat. No. D4004) by adding 350 μl of DNA binding buffer, and eluted in 10 μl. After 5 cycle pre PCR amplification, the optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be 4 cycles. The PCR products were purified using 1.8x volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Basecalling with Illumina RTA 1.18.64
Short reads were aligned to mouse mm10 genome using bwa with mem option.
Peaks were called using MACS2 version 2.1.1 (options: --nomodel --shift -100 --extsize 200 -f BAMPE -g mm -B -q 0.01).
Coverage files were generated using bamCoverage command in deepTools (options: --normalizeUsing BPM --effectiveGenomeSize 2652783500 -e).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
Aug 27, 2019 |
| Last update date |
Sep 18, 2019 |
| Contact name |
Koh Onimaru |
| E-mail(s) |
koh.onimaru@gmail.com, koh.onimaru@riken.jp
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| Phone |
484679398
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| Organization name |
Center for Biosystems Dynamics Research
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| Lab |
Laboratory for Bioinformatics Research
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| Street address |
312 Information Science Building, 2-1 Hirosawa
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| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE136415 |
A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq] |
| GSE136445 |
A comparison of evolutionary changes and constraints on gene regulation between fin and limb development |
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| Relations |
| BioSample |
SAMN12642411 |
| SRA |
SRX6780618 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4048696_P313_09_320short.bw |
137.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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