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Sample GSM4263591 Query DataSets for GSM4263591
Status Public on May 06, 2022
Title TC sh#Atoh8 rep1
Sample type SRA
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblasts
strain: C57BL/6
shRNA: sh#Atoh8
treatment: Malignant transformation induction
Growth protocol TCs were cultivated in DMEM medium supplemented with 5% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS)
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_TC.txt
processed data file: normalized_count_TC.txt
processed data file: model_fc_TC.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_TC.txt: Tab-delimited text file including raw counts for each sample.
Supplementary_files_format_and_content: normalized_count_TC.txt: Tab-delimited text file including normalized counts for the each sample.
Supplementary_files_format_and_content: model_fc_TC.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
GSE143593 Identification of genes upregulated and downregulated in transformed cells (TCs) derived upon Atoh8 depletion
BioSample SAMN13839716
SRA SRX7551173

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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