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| Status |
Public on Jan 06, 2023 |
| Title |
output2 |
| Sample type |
SRA |
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| Source name |
Human kidney epithelial cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
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| Growth protocol |
Both mESCs and HEK293T were purchased from ATCC and cultured in accordance with ATCC's protocol.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were transfected with lipo3000, and the cells were collected for flow screening after 48 hours.
DNA was extracted from the collected fluorescent cells. Components were added according to the TruePrep DNA Library Prep kit (Vazyme; Cat.TD202) and followed by one-step PCR (72℃ for 3min, 98℃ for 30s; followed by 5-15 cycles of 98℃ for 15s, 60℃ for 30s, 72℃ for 3min; 72℃ for 5mins). The product was recovered by 2% agarose gel electrophoresis for 35 min (120v, 130mA) and sent for high-throughput sequencing. Sequence after one-step PCR amplification is 5’-AATGATACGGCGACCACCGAGATCTACACIIIIIIIITCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-NNNNNN-CTGTCTCTTATACACATCTCCGAGCCCACGAGACIIIIIIIIATCTCGTATGCCGTCTTCTGCTTG-3’, IIIIIIII: Index 2 (i5), IIIIIIII: Index 1 (i7), -NNNNNN-: random sequence.
MAE-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
the MEA-seq sequences were aligned to mm9/hg19 by using bwa -aln (version 0.7.5a-r405) with default parameters
The uniq mapped fragment counts were normalized
The poisson test was used to calculate the significant difference between input and output data, then, the Benjaminiand Hochberg test was used to select the loci with q value which were lower than 0.01 as effective signals
Genome_build: mm9,hg19
Supplementary_files_format_and_content: MAE-seq enhancers text file
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| Submission date |
Jan 11, 2022 |
| Last update date |
Jan 06, 2023 |
| Contact name |
JING LUO |
| E-mail(s) |
luoj17@lzu.edu.cn, luojing9520@163.com
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| Organization name |
Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences
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| Street address |
No 7,Pengfei Road,Dapeng District
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| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE193494 |
MAE-seq refines regulatory elements across the genome |
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| Relations |
| BioSample |
SAMN24849402 |
| SRA |
SRX13732279 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5808475_output2_effective_cv1nc_q0.01.txt.gz |
528.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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