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| Status |
Public on Aug 03, 2022 |
| Title |
SOX9_ChIP3 |
| Sample type |
SRA |
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| Source name |
SOX9_ChIP3
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Mteci (EpCAM+CD45-MHCIIloItgb4+L1cam-)
age: 5-6 weeks
genotype: wildtype
chip antibody: anti-Sox9 (AB5535, Millipore)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. TEC were sorted and Six1 or Sox9 binding sites in the genome were determined by ChIPseq.
ChIPseq libraries were prepared for sequencing using a modified ChIPseq protocol (Blecher-Gonen et al., 2013, Bansal et al, 2017)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Paired-end ChIP-seq libraries were sequenced on Illumina NextSeq500. Reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 20 -m 25), and mapped to mm10 genome (Gencode) using bowtie2 (parameters: --local, -X 2000). Uniquely mapped reads were extracted using samtools (-F 4, -f 0x2, -q 39). Narrow peaks were called using MACS2 compared to background input samples (WCE, whole cell extract) (parameters: --bw 300 -B -f --SPMR -keep-dup auto -q 0.05 BAMPE --nomodel).
Assembly: mm10
Supplementary files format and content: Peaks detected by MACS2
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| Submission date |
May 24, 2022 |
| Last update date |
Aug 03, 2022 |
| Contact name |
Jakub Abramson |
| E-mail(s) |
jakub.abramson@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Department |
Department of Immunology
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| Street address |
234 Herzl st.
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE192875 |
Transcriptional regulation of the thymus master regulator Foxn1 |
| GSE204741 |
Transcriptional regulation of the thymus master regulator Foxn1 [ChIP-seq] |
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| Relations |
| BioSample |
SAMN28641151 |
| SRA |
SRX15441806 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6190449_Sox9_ChIP3_vs_Sox9_WCE3_peaks.narrowPeak.gz |
1.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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