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Sample GSM4445941 Query DataSets for GSM4445941
Status Public on Dec 21, 2021
Title PU.1
Sample type SRA
 
Source name Trib1/Bcl11a AML
Organism Mus musculus
Characteristics cell line: Trib1- and Bcl11a-expressing murine AML cells
strain: C57Bl/6
chip antibody: PU.1 (Cell Signaling. catalog# 2258, lot# 3)
Treatment protocol Trib1 and Bcl11a cDNAs were introduced by retrovirus-mediated gene transfer
Growth protocol AML cells are maintained in IMDM supplemented with 10% FBS and 5 ng/ml IL3
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). 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 an Illumina instrument following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Data processing Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: tdf file: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).
 
Submission date Mar 30, 2020
Last update date Dec 21, 2021
Contact name Takuro Nakamura
E-mail(s) takuro-ind@umin.net
Phone 81-3-3570-0462
Organization name Japanese Foundation for Cancer Research
Department The Cancer Institute
Lab Carcinogenesis
Street address 3-8-31 Ariake, Koto-ku
City Tokyo
ZIP/Postal code 135-8550
Country Japan
 
Platform ID GPL16417
Series (2)
GSE147787 BCL11A promotes myeloid leukemogenesis by abrogating the transcriptional activity of PU.1 [ChIP-seq]
GSE147798 BCL11A promotes myeloid leukemogenesis by abrogating the transcriptional activity of PU.1
Relations
BioSample SAMN14488159
SRA SRX8030788

Supplementary file Size Download File type/resource
GSM4445941_TB13_PU1.tdf 187.8 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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