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| Status |
Public on Nov 16, 2020 |
| Title |
LacZ-3 |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Mus musculus |
| Characteristics |
strain: ICR
tissue: Testis
age: post natal day 35
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Germ cell isolated from the testis of wild-type mouse were cross-linked, lysed and sonicated, and then incubated with probesets of Gm4665. Following hybridization of biotinylated probesets to Gm4665 transcript, Gm4665-bound chromatin was retrieved. The purified DNA fragments were sequenced using high throughput next generation sequencing (Illumina HiseqXten-PE150)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
gene_matrix.txt
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| Data processing |
Library strategy: ChIRP-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
For each sample, reads from even and odd lanes were aligned separately, and per-base coverage was normalized as if there were 10 M mappable reads. For each base pair of the genome, true coverage of this base in this sample was defined as the minimum coverage of the even lane and odd lane.
Genome-wide signal consists of a combine lane, based on which, a SAM file was generated for peak calling.
Peaks of each sample were called using MACS against its corresponding input with p-value cutoff 1 × 10−5
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include enrichment for each Sample
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| Submission date |
Feb 12, 2020 |
| Last update date |
Nov 16, 2020 |
| Contact name |
Xu jia yue |
| E-mail(s) |
xujiayue78@126.com
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| Organization name |
Peking Union Medical College
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| Street address |
NO.3 Dongdan street, Beijing
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| City |
Beijing |
| ZIP/Postal code |
100010 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE145189 |
Next Generation Sequencing Facilitates Quantitative Analysis of chromatin interaction of lncRNA Gm4665 with regulatory region of target genes in male germ cells. |
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| Relations |
| BioSample |
SAMN14088575 |
| SRA |
SRX7713714 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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