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Sample GSM5808473 Query DataSets for GSM5808473
Status Public on Jan 06, 2023
Title outputD
Sample type SRA
Source name Mouse embryonic stem cell
Organism Mus musculus
Characteristics cell line: E14 cell
Growth protocol Both mESCs and HEK293T were purchased from ATCC and cultured in accordance with ATCC's protocol.
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.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
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
Submission date Jan 11, 2022
Last update date Jan 06, 2023
Contact name JING LUO
Organization name Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences
Street address No 7,Pengfei Road,Dapeng District
City Shenzhen
ZIP/Postal code 518120
Country China
Platform ID GPL24247
Series (1)
GSE193494 MAE-seq refines regulatory elements across the genome
BioSample SAMN24849404
SRA SRX13732276

Supplementary file Size Download File type/resource
GSM5808473_outputD_effective_cv1nc_q0.01.txt.gz 3.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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