Oo_x	MII Oocyte replication x
C1_x	1-cell stage embryo replication x
C2_x	2-cell stage embryo replication x
C4_x	4-cell stage embryo replication x
E10.5_x	Embryo 10.5d replication x
MEF_x	MEF replication x
PC1_x	1-cell stage Parthenotes replication x
PC4_x	4-cell stage Parthenotes replication x

Merge	includes BAM file of mapped reads
*Mappable	 includes FASTQ files of multiple-hit and unmapped reads

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The RNA-seq datasets for ESCs & iPSCs (ESC_x, iPSC_x)
Source: 
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53212
Carter AC, Davis-Dusenbery BN, Koszka K, Ichida JK et al. PMID: 24527385

Mapping and Quantifying: Tophat-Cufflinks pipeline
%>tophat -o ./ -g 1 -p 2 -r 50 --mate-std-dev 20 --no-coverage-search --read-mismatches 3 -G mm9_reference.gtf 
%>samtools sort accepted_hits.bam accepted_hits.bam.sorted