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Sample GSM1577791 Query DataSets for GSM1577791
Status Public on Jan 07, 2015
Title m6A-seq in Mettl3-KO ESCs, IP
Sample type SRA
 
Source name Embryonic Stem Cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Mettl3-KO
antibody: m6a
cell type: Embryonic Stem Cells
Growth protocol Maintenance of grounds state naïve murine pluripotent cells was conducted in FBS free N2B27-based media, and included 10μg recombinant human LIF and small-molecule inhibitors CHIR99021 (CH, 1-3 μM- Axon Medchem) and PD0325901 (PD, 1 μM - TOCRIS) termed 2i. For embryoied bodies formation 5x10^6 ESCs were disaggregated with trypsin and transfer to low non-adherent palte and culture in MEF medium (DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 15% FBS) for 8-21 days. MEF generation: E13.5 mouse embryo was decapitated and disaggregated with trypsin and culture in MEFs medium until MEFs population were expended.
Extracted molecule total RNA
Extraction protocol Cells were harvested and RNA was extracted using the 5 PRIME PerfectPure RNA Cell culture Kit (cat#2302340 ), according to manufacturer's manual
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description ES_m6A_KO_IP
negative control
Data processing library strategy: m6A-seq
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm10 reference genome (downloaded from ensemble) using TopHat version 2.0.10. Flags used: -M
We identified enriched intervals using MACS version 1.4.1, while using the input as control in order to define a background model.
Final peak list includes peaks that appaer in at least 2 out of 3 replicates (or 2 out of 2 in MEF), their MACS fold-change is >2, and FDR < 5%, and they fall in annotated gene whose expression level was equal or over the first quartile of the expression level of all genes.
Genome_build: mm10
Supplementary_files_format_and_content: final_peaks.xlsx: final list of peaks in ESC, EBs and MEFs, and their mapping to genes
 
Submission date Jan 07, 2015
Last update date May 15, 2019
Contact name Noa Novershtern
E-mail(s) noa.novershtern@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Molecular Genetics
Street address Weizmann Institute
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platform ID GPL17021
Series (2)
GSE61995 m6A mRNA Methylation Facilitates Resolution of Naïve Pluripotency Towards Differentiation (m6a-seq)
GSE61998 m6A mRNA Methylation Facilitates Resolution of Naïve Pluripotency Towards Differentiation
Relations
BioSample SAMN03276539
SRA SRX832076
Named Annotation GSM1577791_ESC_KO_peaks.bed.gz

Supplementary file Size Download File type/resource
GSM1577791_ESC_KO_peaks.bed.gz 17.6 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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