GSM4089072: AML-22-BM-exome-seq; Mus musculus; OTHER
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3 and H3K79me2 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449;  Anti-H3K79me2, Abcam, Cat No. ab3594.; Anti-MLL, Millipore, #05-765).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    CHIRP-seq library constructs with the illumina Truth CHIP DNA library kt. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030). Genomic DNA was isolated from mice ear and BM cells including wildtype and Hottip-Tg mice, and genomic exome library was captured and made according to SureSelectXT Mouse All Exon kit (Agilent, Part Number:5190-4641). RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq and CHIRP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Genomic DNA was isolated from mice ear and BM cells including wildtype and Hottip-Tg mice, and genomic exome library was captured and made according to SureSelectXT Mouse All Exon kit (Agilent, Part Number:5190-4641), and then 100 bp paired-end sequencing was performed using an Illumina NovaSeq.
GEO Accession
GSM4089072