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Sample GSM4332642 Query DataSets for GSM4332642
Status Public on Mar 22, 2021
Title WT_MAIT_Input
Sample type SRA
Source name MAIT cells
Organism Homo sapiens
Characteristics tissue: peripheral blood
cell type: MAIT
group: Input
Extracted molecule genomic DNA
Extraction protocol Isolated cells were fixed with 1% formaldehyde in PBS for 10 minutes, then quenched with glycine. After washing, DNA was extracted using the Illumina SimpleChIP Enzymatic ChIP kit (#9003S). Briefly, nuclei were isolated by incubating in 1ml buffer A for 10 min on Ice, followed by centrifugation and resuspension in 1 ml Buffer B. Chromatin was sheared to roughly 200-1000bp. Samples were centrifuged to clear lysates, and the supernatant containing the DNA was transferred to a fresh tube for overnight antibody complexing. Next day, protein G dynabeads were added to each tube, incubated, washed, and isolated with magnet. DNA complexes were then released from the beads, decrosslinked, and phenol:choloroform:isolamyl alcohol extracted for library prep.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina. Briefly, DNA ends were repaired, followed by ligation of adapter sequences. DNA was cleaned with AMPure XP beads, and then DNA was PCR amplified with 7-8 cycles. After final cleaup with AMPure XP Beads, libraries were quantified using Agilent Bioanalyzer high sensitivity DNA kit and were subsequently sequenced.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
Description CD3+ CD161+ TCR Vα7.2+
Data processing Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the hg19 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output
Submission date Feb 23, 2020
Last update date Mar 22, 2021
Contact name Dorina Avram
Organization name Moffitt Cancer Center
Department Department of Immunology
Lab Avram lab
Street address 12902 Magnolia Drive, MRC4
City Tampa
State/province Fl
ZIP/Postal code 33612
Country USA
Platform ID GPL21290
Series (2)
GSE145776 Mapping Bcl11b binding in human MAIT cells
GSE145779 Bcl11b binding and transcriptome analysis of Bcl11b-deficient MAIT cells at steady state and infection
BioSample SAMN14167548
SRA SRX7785332

Supplementary file Size Download File type/resource
GSM4332642_Human_Bcl11b_MAIT_Input_subtract.bedgraph.gz 135.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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