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Sample GSM4263587 Query DataSets for GSM4263587
Status Public on May 06, 2022
Title MEF sh#Atoh8 rep2
Sample type SRA
 
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblasts
strain: C57BL/6
shRNA: sh#Atoh8
Growth protocol MEF were generated from E13.5 mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol.
Extracted molecule total RNA
Extraction protocol RNAs were extracted with Macherey-Nagel NucleoSpin RNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file: raw_count_MEF.txt
processed data file: normalized_count_MEF.txt
processed data file: model_fc_MEF.txt
Data processing Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DESeq2 package.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: raw_count_MEF.txt: Tab-delimited text file including raw counts for each sample.
Supplementary_files_format_and_content: normalized_count_MEF.txt: Tab-delimited text file including normalized counts for the each sample.
Supplementary_files_format_and_content: model_fc_MEF.txt: Tab-delimited text file including FC, p-value and adjusted p-value.
 
Submission date Jan 13, 2020
Last update date May 06, 2022
Contact name Fabrice Lavial
Organization name CRCL
Street address 28 rue Laennec
City Lyon
ZIP/Postal code 69008
Country France
 
Platform ID GPL17021
Series (2)
GSE137050 The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8
GSE143592 Identification of genes upregulated and downregulated in mouse embryonic fibroblasts (MEFs) upon Atoh8 depletion
Relations
BioSample SAMN13839693
SRA SRX7551132

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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