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GSE148039

GSE GEO
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Ythdf m6A readers compensate each other in a context dependent manner

Organism: Mus musculus
Platform: GPL13112
Samples: 93
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Apr 03 2020
Last Updated: Sep 22 2020
Status: Public on Jun 04 2020
Contact: Noa,,Novershtern (Weizmann Institute of Science)

Relations

SuperSeries of: GSE147849 SuperSeries of: GSE148038 SuperSeries of: GSE148536 SuperSeries of: GSE151788 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622932

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (7 steps)

View Data Processing
Processing steps for GSE148039
  1. We used Illumina CASAVA 1.8.2 software to generate fastq files.
  2. Reads were trimmed using cutadapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -q 20 -m 25).
  3. Reads were mapped to genome mm10 using STAR (Dobin et al.
  4. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
  5. Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes.
  6. Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al.
  7. 2014) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE.

Supplementary Files (1)

GSE148039_RAW.tar Download
GEO Samples (93)
GSM4447050 GSM4447051 GSM4447052 GSM4447053 GSM4447054 GSM4447055 GSM4447056 GSM4447057 GSM4447058 GSM4447059 GSM4447060 GSM4447061 GSM4447062 GSM4447063 GSM4447064 GSM4447065 GSM4447066 GSM4447067 GSM4447068 GSM4447069 GSM4447070 GSM4447071 GSM4447072 GSM4447073 GSM4447074 GSM4447075 GSM4447076 GSM4452888 GSM4452889 GSM4452890 GSM4452891 GSM4452892 GSM4452893 GSM4452894 GSM4452895 GSM4452896 GSM4452897 GSM4452898 GSM4452899 GSM4452900 GSM4452901 GSM4452902 GSM4452903 GSM4452904 GSM4452905 GSM4452906 GSM4452907 GSM4452908 GSM4452909 GSM4452910 GSM4452911 GSM4452912 GSM4452913 GSM4452914 GSM4452915 GSM4452916 GSM4452917 GSM4452918 GSM4452919 GSM4452920 GSM4452921 GSM4452922 GSM4452923 GSM4452924 GSM4452925 GSM4452926 GSM4452927 GSM4452928 GSM4452929 GSM4452930 GSM4452931 GSM4452932 GSM4452933 GSM4452934 GSM4452935 GSM4452936 GSM4452937 GSM4473269 GSM4473270 GSM4473271 GSM4473272 GSM4473273 GSM4473274 GSM4473275 GSM4473276 GSM4473277 GSM4473278 GSM4473279 GSM4473280 GSM4590952 GSM4590953 GSM4590954 GSM4590955

Dataset Citations (1)

Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
PMID 32943573 · 2020 · Genes & development
Lior Lasman, Vladislav Krupalnik, Sergey Viukov, Nofar Mor, Alejandro Aguilera-Castrejon, Dan Schneir, Jonathan Bayerl, Orel Mizrahi, Shani Peles, Shadi Tawil, Shashank Sathe, Aharon Nachshon, Tom Shani, Mirie Zerbib, Itay Kilimnik, Stefan Aigner, Archana Shankar, Jasmine R Mueller, Schraga Schwartz, Noam Stern-Ginossar, Gene W Yeo, Shay Geula, Noa Novershtern, Jacob H Hanna

Linked Publications (1)

Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
Genes & development · 2020