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GEO help: Mouse over screen elements for information. |
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Status |
Public on Aug 01, 2019 |
Title |
H3.1K36M rep2 |
Sample type |
SRA |
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Source name |
mES
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Organism |
Mus musculus |
Characteristics |
cell type: embryonic stem cell strain: J1
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Treatment protocol |
total RNA were extracted using Trizol reagent and used for mRNA capture.
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Growth protocol |
Mouse embryonic stem cells (mESCs, J1 strain) seeded on inactivated mouse embryonic fibroblast cells (MEF) feeder were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco#11995) supplemented with 10% fetal bovine serum (FBS, Gibco#16000-044), 1×non-essential amino acids (NEAA, Gibco#11140), 1×GlutaMAX-I (Gibco#35050-061), 7μM β-mercaptoethanol (Ameresco, Biotechnology grade, Cat#M8210), 10ng/ml mouse leukemia inhibitory factor (Millipore, Chemicon, Cat#LIF2050) and 1% antibiotic (Pen Strep, Gibco#15140-122). All mES cells were sub-passaged every 3-4 days by digesting the cell clone into single cell suspension using 0.25% Trypsin-EDTA (Gibco#25200072), and the resulted cells were divided on 3-5 fresh feeder-plates.
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimed for adaptor and low-quality sequence and then mapped to mm10 whole genome using tophat v2.0.13 with default parameters Differences in expression were determined using Cuffdiff v2.2.1 Genome_build: mm10 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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Submission date |
May 22, 2017 |
Last update date |
Aug 01, 2019 |
Contact name |
Jin Sun |
E-mail(s) |
sunjin@tongji.edu.cn
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Organization name |
Tongji University
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Department |
life science and technology
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Lab |
Jiang
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Street address |
siping1239
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City |
shanghai |
ZIP/Postal code |
200092 |
Country |
China |
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Platform ID |
GPL21273 |
Series (2) |
GSE99155 |
H3K36me3 protects the mouse epigenome from single nucleotide variations [mRNA-Seq] |
GSE99156 |
H3K36me3 protects the mouse epigenome from single nucleotide variations |
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Relations |
BioSample |
SAMN07151543 |
SRA |
SRX2840421 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2634297_H3K36M_rep2.txt.gz |
143.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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