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Sample GSM4089074 Query DataSets for GSM4089074
Status Public on Dec 03, 2019
Title AML-39-BM-exome-seq
Sample type SRA
 
Source name AML-C57BL/6 mice bone marrow
Organism Mus musculus
Characteristics cell types: Mouse-derived bone marrow cells
tissue: bone marrow
strain: C57BL/6
Treatment protocol Immediately extract RNA from LSK, HSC cells from transgenic mice and MOLM13 AML cells without any treatment
Growth protocol Total bone marrow cells were isolate from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers. Human MOLM13 leukemia cells were culture at RMPI1640 and 10% FBS media.
Extracted molecule genomic DNA
Extraction 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, 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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Library strategy: exome-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, paired end exome-seq reads from mice were aligned to the mm9 genome assembly using BWA,t and ATAC-seq, ChIP-seq, HiC-seq, and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Chromatin structure HiC-seq was calculate and display with HOMER, Juicer and Juicebox software
Genome_build: mm9
Supplementary_files_format_and_content: SNP and indel mutation annotation for exome-seq
 
Submission date Sep 22, 2019
Last update date Dec 03, 2019
Contact name Suming Huang
E-mail(s) huanglabseq@hotmail.com
Organization name Penn State University
Department Pediatrics
Street address 500 University Dr.
City Hershey
State/province PA
ZIP/Postal code 17033
Country USA
 
Platform ID GPL24247
Series (1)
GSE114981 Activation of HOTTIP lncRNA perturbs HSC function leading to AML like disease
Relations
BioSample SAMN12816818
SRA SRX6886143

Supplementary file Size Download File type/resource
GSM4089074_AML-39-SNP-mutation.txt.gz 2.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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