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Sample GSM3438040 Query DataSets for GSM3438040
Status Public on May 01, 2020
Title Tbx21_ko rep1
Sample type SRA
Source name NK cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: spleen
genotype: Tbx21 ko
Treatment protocol freshly isolated NK cells from chronically CR treated mice
Growth protocol freshly isolated NK cells
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).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description oligoT matrix facilitated
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
Submission date Oct 18, 2018
Last update date May 02, 2020
Contact name xiong wei
Organization name Tsinghua University
Street address qinghuayuan street
City Beijing
ZIP/Postal code 100084
Country China
Platform ID GPL21273
Series (1)
GSE121488 Caloric Restriction Triggers Anti-tumor Immunity via a Mechanism Involving NK Cells and Transcription Factor Eomesdermin
BioSample SAMN10258346
SRA SRX4904796

Supplementary file Size Download File type/resource 15.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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