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| Status |
Public on Jun 15, 2022 |
| Title |
Naive-input-1 (18734X8) |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6
cell type: Mouse naive CD4 T cells
infection: Not Infected
timepoint: naïve
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sorted cells were fixed with 16% formaldehyde to a final concentration of 1% and crosslinking was stoped by the addition of glycine. Cells were sonicated in RIPA buffer then incubated with Foxo1 antibody (Cell signaling, C29H4) at 4C overnight .After washing, DNA was eluted with IP elution buffer (1%SDS/0.1M NaHCO3).Samples were purified with QiaQuick spin columns (Qiagen).
ChIP-Seq with NEBNext Ultra II DNA Library Prep Kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
18734X8
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| Data processing |
Between 58 and 112 million paired-end Illumina sequencing reads were aligned to the mouse Mm10 reference genome using Novocraft novoalign v4.02.02, allowing for one random alignment of multi-mapping reads, and providing the adapter sequences for automatic trimming concordant with alignment
ChIP was analyzed using the MultiRepMacsChIPSeq pipeline v15.2, using options “--pe --optdist 10000 --dupfrac 0.05 --mapq 10 --cutoff 2 --peaksize 300 --peakgap 100 --species mouse --chrskip ‘chrM|PhiX’ --blacklist mm10.blacklist.bed”.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file of Foxo1 peaks in activated (CD44high) CD4+ T cells
Supplementary_files_format_and_content: BigWig file of Foxo1 peaks in naïve CD4+ T cells
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| Submission date |
Sep 02, 2021 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Jeffrey Scott Hale |
| E-mail(s) |
scott.hale@path.utah.edu
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| Phone |
801-587-1885
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| Organization name |
University of Utah
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| Department |
Pathology
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| Lab |
Hale Lab
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| Street address |
15 North Medical Drive
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| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE183315 |
Tet2-mediated epigenetic programing of T follicular helper cell differentiation (ChIP-Seq) |
| GSE183317 |
Tet2-mediated epigenetic programing of T follicular helper cell differentiation |
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| Relations |
| BioSample |
SAMN21209240 |
| SRA |
SRX12002281 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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