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| Status |
Public on Dec 01, 2023 |
| Title |
MECLP1 |
| Sample type |
SRA |
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| Source name |
mammary gland
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| Organism |
Capra hircus |
| Characteristics |
tissue: mammary gland
cell type: mammary epithelial cell
treatment: lactation period
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cell preparation was begin with harvesting and counting intact and homogenous cell, which followed by centrifuging those 50,000 cells for about 5min at 500g, 4°C. Washing those cells once with 50μl of cold PBS buffer and centrifuging them again under the same condition after removing and discarding supernatant. Removing and discarding supernatant again, and pipetted up and down to resuspend the cell pellet in 50μl of cold lysis buffer gently, which also obey centrifuge but for 10 min this time.
After discarding the supernatant, the resuspension of the nuclei pellet we obtained should be carried out immediately in the prepared transposition reaction mix which contained Nextera Tn5 Transposase from Nextera kit. Incubated the transposition reaction at 37°C for 30 min. A Qiagen MinElute PCR Purification Kit is used to transposition, purify instantly, following by which the 10μl elution buffer (Buffer EB from the MinElute kit consisting of 10 mM Tris·Cl, pH 8) was applied to elute transposed DNA. Finally the PCR amplification was performed to amplify transposed DNA fragments, combine the following in a 0.2 ml PCR tube with enough thermal cycle. Prior to amplification, adapters have to be completed with a 72°C extension step, as well as the qPCR and library quality control using gel electrophoresis is provided. Libraries were pooled at equimolar ratios with barcodes and sequenced on the BGISEQ-500 platform.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters: filter -l 5 -q 0.5 -n 0.1 -Q 2 -5 1 -c 50. Cleaned reads were mapped to the reference genome using Bowtie2 (version: 2.2.5).
MACS2 was used (version: 2.1.2) to call peaks (open chromatin regions), in which '--bw 200 -s 50 -p 1e-5 -m 10 30 --broad -B --trackline' was used. With which the IDR (v2.0.4) was applied to measure the reproducibility of findings identified from replicate sample.
The different enrichment peaks from different sample was plotted by MAnorm (v1.1), the significant regions were picked up if |M|≥ 1 and p-value ≤10-5.
To identify the position of nucleosomes, broad peaks called by MACS2 were analyzed using NucleoATAC (v0.3.4)
Assembly: Capra hircus (assembly ARS1.2)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: bigWig, xls
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| Submission date |
Feb 20, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Zhenliang Zhu |
| E-mail(s) |
zhuzhenliang@nwafu.edu.cn
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| Phone |
+86 18829351022
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| Organization name |
Northwest A&F University
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| Street address |
3 Taicheng Road
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| City |
Yangling |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL33145 |
| Series (1) |
| GSE225654 |
Integrating into dairy goats chromatin accessible sites during lactation promotes transgene expression efficiency |
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| Relations |
| BioSample |
SAMN33385971 |
| SRA |
SRX19447586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7053856_MECLP1_treat_pileup.bw |
126.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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