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| Status |
Public on Jan 11, 2023 |
| Title |
CUTRUN-TCFL5-pachyteneCell-rep2 |
| Sample type |
SRA |
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| Source name |
pachytene spermatocytes
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| Organism |
Mus musculus |
| Characteristics |
antibody: TCFL5
strain: C57BL/6J
Stage: adult
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
none provided by the submitter
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For small RNA-seq data, after removing 3′ adaptor sequence from the reads, we filtered reads whose PHRED score was <5. Those reads that passed the quality check were then mapped to mouse genome (mm10) using piPipes that uses bowtie 2.2.5 allowing one mismatch. For RNA-seq data, we first removed rRNA reads using bowtie 2.2.5 with default parameters and then the unaligned reads were further mapped to mouse genome (mm10) using STAR. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and Umitools. For ChIP-seq data, raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We then removed duplicate reads using SAMtools. Normalized genome coverage files in bigWig format were generated using homemade script. For CUT&RUN data, Raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We presented the data in bigWig file that was reported as unique mapping reads as read depth per million reads (rpm).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
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| Submission date |
Feb 03, 2021 |
| Last update date |
Jan 11, 2023 |
| Contact name |
Tianxiong Yu |
| Organization name |
Umass Med
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| Street address |
364 Plantation St
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE166104 |
The Testis-Specific Transcription Factor TCFL5 Responds to A-MYB to Elaborate Male Meiotic Program in Mammals |
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| Relations |
| BioSample |
SAMN17771016 |
| SRA |
SRX10013726 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5061805_4N-TCFL5-ID2_S13.rpm.uniq.bw |
288.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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