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Sample GSM4048688 Query DataSets for GSM4048688
Status Public on Sep 17, 2019
Title ATAC-seq E09.5 replicate 1
Sample type SRA
 
Source name forelimb bud at E09.5
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: forelimb bud
age: E09.5
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).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
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
 
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
Phone 484679398
Organization name Center for Biosystems Dynamics Research
Lab Laboratory for Bioinformatics Research
Street address 312 Information Science Building, 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
 
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
Relations
BioSample SAMN12642419
SRA SRX6780610

Supplementary file Size Download File type/resource
GSM4048688_P313_01_320short.bw 128.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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