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Status |
Public on May 01, 2020 |
Title |
Ctrl_ko rep2 |
Sample type |
SRA |
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Source name |
NK cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: spleen genotype: Eomes ko
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Treatment protocol |
freshly isolated NK cells from chronically CR treated mice
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Growth protocol |
freshly isolated NK cells
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Extracted molecule |
total RNA |
Extraction protocol |
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit RNA-seq: total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L). For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629). For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA. Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method. ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Eomes ChIP-seq, the RIPA buffer was diluted 1 to 10. The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq X-ten(Illumina).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Description |
oligoT matrix facilitated
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Data processing |
FASTX-Toolkit for assessing sequencing quality Alignment: Bowtie 2 version 2.2.1 for chip-seq and TopHat v2.0.11 for RNA-seq cufflinks v2.2.0 for RNA-seq assembling and differential analysis peaks were called using MACS1.4 Genome_build: mm9 Supplementary_files_format_and_content: bigwig files for RNA-seq and CHIP-Seq
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Submission date |
Oct 18, 2018 |
Last update date |
May 02, 2020 |
Contact name |
xiong wei |
E-mail(s) |
xwillwei@sina.com
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Organization name |
Tsinghua University
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Street address |
qinghuayuan street
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City |
Beijing |
ZIP/Postal code |
100084 |
Country |
China |
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Platform ID |
GPL21273 |
Series (1) |
GSE121488 |
Caloric Restriction Triggers Anti-tumor Immunity via a Mechanism Involving NK Cells and Transcription Factor Eomesdermin |
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Relations |
BioSample |
SAMN10258330 |
SRA |
SRX4904806 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3438050_Ctrl_ko_rep2.bw |
17.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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