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Sample GSM1019088 Query DataSets for GSM1019088
Status Public on Apr 18, 2013
Title Tdg -/- polyA RNA-Seq replicate 1
Sample type SRA
 
Source name Tdg -/- polyA RNA-Seq
Organism Mus musculus
Characteristics strain: C57BL/6-ICR
cell: ES cells
Treatment protocol NA
Extracted molecule polyA RNA
Extraction protocol 25 ng of 5fC-enriched DNA, 5hmC-enriched DNA, or non-enriched sonicated input genomic DNA was end-repaired, adenylated, and ligated to Illumina Genomic DNA Adapters (Genomic DNA adapter oligo mix) according to standard Illumina protocols for ChIP-Seq library construction, maintaining the proper molar ratios of adapter to insert. Adapter-ligated fragments of ~200-350 bp were gel-purified by 2% agarose gel electrophoresis and PCR-amplified for 18 PCR cycles. Libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer DNA 1000 Chip.
RNA-Seq expression libraries were generated from duplicate samples per genotype using the Illumina TruSeq RNA Sample Preparation Kit v2. Libraries were sequenced using the Illumina HiScan platform. Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS. Single-read 51-bp sequencing was completed with Illumina TruSeq SBS kit v3-HS. Single-read 51-bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiScanSQ
 
Description TDG.KO.FPKM.txt
Data processing Illumina Basecalling, CASAVA 1.8.2
FASTQ sequences were aligned to NCBIv1/mm9 with Bowtie v0.17.2 retaining unique non-duplicate matches to the genome, with no more than 3 mismatches in the first 30 bases
Enriched regions derived from MACS v1.4, --bw=200 -g 1.87e9, using genotype matched input controls
RNA-Seq reads were aligned using tophat-1.4.1 and FPKM expression values were extracted using cufflinks-1.3.0 using RefSeq gene models.
Genome_build: mm9
Supplementary_files_format_and_content: BED format, containing regions of enrichment; FPKM expression values in text format
 
Submission date Oct 12, 2012
Last update date May 15, 2019
Contact name Keith E Szulwach
E-mail(s) kszulwa@emory.edu
Phone 404-712-0796
Organization name Emory University
Department Human Genetics
Lab Jin Lab
Street address 615 Michael Street, Whitehead Suite 301
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL16173
Series (1)
GSE41545 Genome-wide profiling of 5-Formylcytosine reveals it roles in epigenetic priming
Relations
Reanalyzed by GSE80797
SRA SRX194549
BioSample SAMN01765237

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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