title: GSM4005274: 31CBS-KO-K562-RNA-seq-1; Homo sapiens; RNA-Seq
library_construction_protocol: 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, H3K4me2, H3K9/14ac and H3K27ac antibody (H3K4me3 (Millipore, #04-745), H3K4me2 (Millipore, 07-030), H3K27Ac (Abcam, #ab4729), and H3K9/14ac (Diagenode, #C15410005)).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.  HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030). RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-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.
attributes.tag: GEO Accession
attributes.value: GSM4005274