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Sample GSM3908270 Query DataSets for GSM3908270
Status Public on Dec 31, 2021
Title G1E-R307H_ATAC_rep2
Sample type SRA
 
Source name cell line
Organism Mus musculus
Characteristics cell line: G1E
vector: R307H
genotype: GATA1 point mutant p.R307H
Treatment protocol n/a
Growth protocol IMDM, 15% FBS, 1xPen/Strep, 4.5E-5M mono-thio-glycerate, 50ng/ml murine SCF and 2U/ml erythropoietin
Extracted molecule genomic DNA
Extraction protocol After washing with PBS, around 10,000 cells were lysed and tagmented in 1x TD buffer, 2.5 µl Tn5 (Illumina), 0.1% NP40, 0.3x PBS in a 50 µl reaction volume. Samples were incubated at 37C for 30 min at 300 rpm. Tagmented DNA was purified using the MinElute PCR kit (Qiagen). The complete eluate underwent PCR, as follows. After initial extension, 5 cycles of pre-amplification using indexed primers and NEBNext® High-Fidelity 2X PCR Master Mix (NEB) were conducted, before the number of additional cycles was assessed by quantitative PCR using SYBR Green. Typically, 7-9 additional cycles were run. The final library was purified using a MinElute PCR kit (Qiagen) and quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the mm10 reference genome using bowtie2
Duplicate reads were removed using Picard and peaks were called with macs2. A consensus peak file was generated using a strategy discussed in the DiffBind workflow.
Genome_build: mm10
Supplementary_files_format_and_content: Per-sample raw peak / counts matrix
 
Submission date Jun 27, 2019
Last update date Dec 31, 2021
Contact name Caleb Lareau
E-mail(s) lareauc@mskcc.org
Organization name Memorial Sloan Kettering
Street address 417 E 68th St, Zuckerman - ZRC 1132
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL19057
Series (2)
GSE133404 A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [G1E_ATACseq]
GSE133417 A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1
Relations
BioSample SAMN12147582
SRA SRX6370126

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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