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| Status |
Public on Oct 20, 2014 |
| Title |
H1B T48 eluate |
| Sample type |
SRA |
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| Source name |
Endoderm cells, RNA IP against m6A
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H1B
cell type: Endoderm
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells well harvested by direct addition of TRIzol reagent (Ambion Cat.#15596018) to the cell culture plate after removal of the media and extracted using Trizol reagent protocol. Subsequently, the total RNA was DNAse treated using DNAse I (Promega Cat.# M610A) for 20 minutes at 37ºC followed by acid phenol/chloroform extraction, chloroform extraction and overnight NaCl2 precipitation. The precipitated RNA was washed with 70ºC ethanol and re-suspended in ultra pure H2O. RNA concentration and purity were verified by nanodrop followed by BioAnalyzer for quality control. Double polyA+ RNA selection was performed using twice Invitrogen Dynabeads mRNA Purification Kit (Cat. #610.06) protocol. RNA concentration and purity were once again verified by nanodrop followed by BioAnalyzer for quality control.
For the input and post m6A-RNA IP fraction (i.e. m6A positive fraction), 100ng of RNA was used for library construction using TrueSeq Stranded mRNA Sample Preparation Guide, entering the protocol by adding the Fragment, Prime, Finish Mix, skipping the elution step and proceeding directly to synthesis of the First Strand cDNA. From that point on, the exact steps of the Illumina TruSeq Stranded mRNA sample Preparation Guide were followed to the end.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 3
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| Data processing |
50bp single-end RNA-Seq reads were mapped to hg19 genome using Tophat.
bam files were converted to bedgraphs using genomeCoverageBed, which were in turn converted to bigwigs using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs show number of reads uniquely mapped to the genome
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| Submission date |
Nov 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinkai Wang |
| Organization name |
University of California, Los Angeles
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| Street address |
650 Charles E. Young Drive South, CHS 33-228
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE52600 |
m6A RNA modification controls cell fate transition in mammalian embryonic stem cells |
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| Relations |
| BioSample |
SAMN02418730 |
| SRA |
SRX381117 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1272364_H1B_Eluate_T48_mainChr.bw |
37.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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