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| Status |
Public on Aug 04, 2015 |
| Title |
Human thymocytes-R2 G6 |
| Sample type |
SRA |
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| Source name |
thymocytes
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| Organism |
Homo sapiens |
| Characteristics |
cell type: thymocytes
genotype: n/a
strain: n/a
chip antibody: RAG2
age: 4 months
Sex: female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were crosslinked with 1% HCHO, quenched with 0.125 M glycine, washed and resuspended in RIPA buffer (10 mM Tris pH 7.4, 1 mM EDTA, 1% tritonX-100, 0.1% sodium deoxycholate, 0.1% SDS) containing 0.8 M NaCl and sonicated using a water bath sonicator (Diagenode) to obtain DNA of ≈ 300–500 bp.
libraries were prepared and sequenced following standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
control: input
G6
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| Data processing |
mouse and human ChIP-seq reads were aligned to the GRCm38p2/mm10 and GRCh37/hg19 genome assemblies, respectively.
Alignment done using bowtie version 0.12.7, with the parameters: --best --all --strata -n 2 -m1 -l 36
peaks were called using MACS version 1.4.2 with default parameters
Genome_build: GRCm38p2/mm10 for mouse and GRCh37/hg19 for human
Supplementary_files_format_and_content: wig files were generated using MACS with parameter --space 100, and then normalized to RPM. Scores in the wig files represent the averaged RPM over overlapping 100bp window
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| Submission date |
Jun 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yaakov Maman |
| Organization name |
Bar-Ilan University
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| Department |
Azrieli Faculty of Medicine
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| Lab |
Genome Instability & Cancer
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| Street address |
Henrietta Szold 8
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| City |
Safed |
| ZIP/Postal code |
1311502 |
| Country |
Israel |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE69475 |
RAG Represents a Widespread Threat to the Lymphocyte Genome - (ChIP-seq) |
| GSE69478 |
RAG Represents a Widespread Threat to the Lymphocyte Genome |
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| Relations |
| BioSample |
SAMN03757512 |
| SRA |
SRX1046558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1701807_G6.wig.gz |
18.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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