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| Status |
Public on Aug 01, 2018 |
| Title |
bulk ChIP seq (SOX30_cKO) |
| Sample type |
SRA |
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| Source name |
Germ cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Testis
cell type: germ cells
cell type: Sox30 knock out
developmental stage: round spermatids
chip antibody: Sox30 (Abclonal, A11715)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNA-seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L).
For ChIP-seq data, we constructed the sequencing libraries using Next Gen DNA Library Kit and Next Gen Indexing Kit(ACTIVE MOTIF #53216&53264).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Description |
A16_combined
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| Data processing |
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome mm10) using TopHat (v 2.0.12) -pass mapping steps.
For ChIP-seq data, trimmed clean reads were aligned to mouse reference genome mm10) using bowtie2 (v 2.2.3) -pass mapping steps.
Genome_build: mm10
Supplementary_files_format_and_content: UMIcount.txt files include the UMI count values of RefSeq genes
Supplementary_files_format_and_content: INCLUSION_LEVELS_FULL.tab files include RNA-seq alternative splicing result, in which '_R1' column represents estimated percent of sequence inclusion (PSI/PSU/PIR, PSI: percent spliced in (for EX), PSU: percent splice site usage (for ALTD and ALTA), PIR: percent intron retention (for INT)) and '_R1-Q' column represents quality scores and number of corrected inclusion and exclusion reads
Supplementary_files_format_and_content: bedgraph files include of signal density of ChIP-seq
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| Submission date |
Dec 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuxuan Zheng |
| Organization name |
Fudan University
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| Street address |
825 Zhangheng Rd.
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| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE107644 |
Single-cell RNA-seq Uncovers Dynamic Processes and Critical Regulators in Mouse Spermatogenesis |
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| Relations |
| BioSample |
SAMN08127274 |
| SRA |
SRX3440417 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2874159_SOX30_cKO.bedgraph.gz |
124.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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