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| Status |
Public on Aug 25, 2016 |
| Title |
4C-seq-kit Promoter3 |
| Sample type |
SRA |
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| Source name |
expanded HSPCs sorted from mice
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| Organism |
Mus musculus |
| Characteristics |
cell type: hematopoietic stem and progenitor cells
protocol: expanded HSPCs, sorted
culture: 5 days in culture
primer set: Forward-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-BARCODE-CTCCCACCTTACTCCAGATC ; Reverse-CAAGCAGAAGACGGCATACGATGAACAGCAAAAGTGTTGAG
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS and crosslinked with 2% of formaledehyde for 10 minutes
Library was prepared according to previously published protocols (Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, Strino F, Parisi F, Kluger Y, Skok JA. 2012. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell 47: 873-885.)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
4C analysis from promoter view point
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| Data processing |
library strategy: 4C-Seq
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.17
Counts and wig files were normalized with DeSeq
Genome_build: mm9
Supplementary_files_format_and_content: Normalized wigs
Supplementary_files_format_and_content: csv files reporting normalized counts
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| Submission date |
Dec 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Beatriz Aranda-Orgilles |
| Organization name |
NYU School of Medicine
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| Street address |
522 First Avenue
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| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE76054 |
4C-seq analysis of the c-Kit locus |
| GSE76055 |
Regulation of enhancer dynamics by MED12 |
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| Relations |
| BioSample |
SAMN04338710 |
| SRA |
SRX1484943 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1973461_B2-Promoter_TCATGT_FINAL_norm.wig.gz |
14.0 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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