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Sample GSM2611520 Query DataSets for GSM2611520
Status Public on Apr 24, 2018
Title H3.1K27M rep3
Sample type SRA
 
Source name fibroblast
Organism Homo sapiens
Characteristics cell type: fibroblast
genotype: lenti-virus mediated H3.1K27M overexpression
passages: 20
Treatment protocol Total RNA were extracted using Trizol reagent and used for mRNA capture.
Growth protocol HDFs were cultured in DMEM medium supplemented with 10% fetal bovine serum,100U/mL penicillin and 100μg/mL streptomycin at 37℃ in 5% CO2
Extracted molecule total RNA
Extraction protocol A total amount of 2μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manual instructions and index codes were added to attribute sequences to each sample. RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer instruction, and were sequenced on an Illumina HiSeq X-10).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat v2.0.13 with default parameters
Differences in expression were determined using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date May 10, 2017
Last update date May 15, 2019
Contact name Jin Sun
E-mail(s) sunjin@tongji.edu.cn
Organization name Tongji University
Department life science and technology
Lab Jiang
Street address siping1239
City shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL20795
Series (1)
GSE98768 Histone H3.1K27 methylation promotes NHEJ by antagonizing FANCD2 on Chromatin
Relations
BioSample SAMN06927200
SRA SRX2795425

Supplementary file Size Download File type/resource
GSM2611520_H3K27M_rep3.txt.gz 139.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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