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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 13, 2022 |
| Title |
Zfp1 |
| Sample type |
SRA |
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| Source name |
Zfp335 cKO DP 1
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6
genotype/variation: Zfp335 cKO
cell type: DP Thymocyte
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| Growth protocol |
Mice were maintained under specific pathogen-free conditions
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| Extracted molecule |
total RNA |
| Extraction protocol |
DP thymocytes were isolated by FACS sorting. Cells were lysed in trizol and total RNA isolated using the Zymo Direct-zol RNA Microprep kit.
Adopted from Turchaninova et al., Nat Prot, 2016 & Mamedov et al., Front Immunol, 2013
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Raw reads were demultiplexed, UMI size distributions were determined and cutoff value for minimum UMI collisions (threshold=4) were determined using migec.
Reads were aligned to the mouse TCRa locus and clonotypes assembled and exported using mixcr.
Unweighted V and J-segment usage was determined using VDJtools command CalcSegmentUsage with the argument -u.
Assembly: mm10
Supplementary files format and content: Processed files are .txt files of assembled clonotypes for each sample. Which can be read into VDJtools for analysis.
Library strategy: TCRa-seq
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| Submission date |
Jun 01, 2022 |
| Last update date |
Sep 13, 2022 |
| Contact name |
Jeremy Ratiu |
| E-mail(s) |
[email protected]
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| Phone |
5868505692
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| Organization name |
Duke University
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| Department |
Immunology
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| Lab |
Zhuang/ Shinohara
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| Street address |
328 Jones Bldg, Box 3010
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| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE205323 |
Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-B-selection pre-T cells [TCRa-seq] |
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| Relations |
| BioSample |
SAMN28815144 |
| SRA |
SRX15562312 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6210406_Zfp335cKO1.ct4.txt.gz |
251.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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