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Sample GSM7777029 Query DataSets for GSM7777029
Status Public on May 22, 2024
Title bulkATACseq_CD34+_CTRL_24h_rep2
Sample type SRA
 
Source name Umbilical cord blood
Organism Homo sapiens
Characteristics tissue: Umbilical cord blood
disease state: Healthy
cell type: CD34+ cells
treatment: Untreated
Treatment protocol Cells were stimulated with cytokines after thawing and were grown in the same medium with or without metabolic inhibitor (2-DG, DON or AOA) until lysis was performed. Cells were collected and lysed after 03h, 12h or 24h of cytokine stimulation.
Growth protocol CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.
Extracted molecule genomic DNA
Extraction protocol Living cells were isolated before transposition by FACS using 7-AAD labeling. Around 5000 cells for each sample were used.
Library was prepared following the Fast ATAC-seq protocol, controled with Bioanalyzer and sequenced with NextSeq or MiSeq system.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description bulk ATAC seq - Fast ATAC protocol
Data processing Cleaning and alignment of data using : trimmomatic (v0.32), bowtie2 (v2.4.1), samtools (v1.4), macs2 (v2.1.1), picard (v1.138) and bedtools (v.2.29.2)
Snakemake (v7.25.0) workflow to handle bam files : merge biological donors (samtools merge v1.11), index the files, quality control checking and count reads.
A downsampling step with samtools view function was performed as regard to the smallest number of reads detected in the cohort (80 000 000 reads)
A new peak calling was conducted on downsampled .bam files using the macs2 callpeak tool (v2.2.7.1) with the following parameters: <-f BAMPE -g hs -B –broad –broad-cutoff 0.1>.
R (v4.2.1) & Rsubread (v2.4.0) & GenomicRanges (v1.42.0) & DEseq2 (v1.38.3) & ggplot2 (v3.4.2)
Only peaks with 10 or more reads were kept for further analysis.
Assembly: hg19
Supplementary files format and content: xxx_threshold_10_ann.gr.rds files are genomic ranges object for R scripts. Biological replicates for the same condition and time point were merged and filter on the minimal number of reads per peak was applied.
 
Submission date Sep 12, 2023
Last update date May 22, 2024
Contact name Laëtitia RACINE
E-mail(s) laetitia.racine@hotmail.fr
Organization name EPHE
Lab CRSA
Street address 27 rue de Chaligny
City Paris
ZIP/Postal code 75012
Country France
 
Platform ID GPL18573
Series (2)
GSE243003 Metabolic adaptation pilots the differentiation of human hematopoietic cells (bulk ATAC-Seq)
GSE243006 Metabolic adaptation pilots the differentiation of human hematopoietic cells
Relations
BioSample SAMN37367070
SRA SRX21762722

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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