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Sample GSM8081780 Query DataSets for GSM8081780
Status Public on Nov 29, 2024
Title ATAC-seq_n20d-1
Sample type SRA
 
Source name hiF-T
Organism Homo sapiens
Characteristics cell line: hiF-T
genotype: wild type
treatment: n20d-1
Treatment protocol Reprogramming intermediate population was collected by magnetic-activated cell sorting (MACS) through Pluripotent Stem Cell MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions.
Growth protocol hiF-T cells were seeded on feeder cells, then cultured in hESM + Doxycycline (Dox, 1 ng/mL) for 6 days, followed by either culturing as before to generate primed iPSCs or switching to 5iLAF medium to generate naive iPSCs.
Extracted molecule genomic DNA
Extraction protocol ATAC-seq was performed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). Briefly, a total of 50,000-10,000 cells were resuspended in 200 μL lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.15% NP-40) and placed on the ice for 10-12 min lysis. The suspension was centrifuged for 5 min at 500 g at 4 ℃.
40 μL transposition reaction mix (8 μL 5 × TTBL, 10 μL TTEmix V5, and 22 μL nuclease-free H2O) was added to the pellet. Samples were mixed well and incubated at 37 ℃ for 30 min. After adding 10 μL 5 × TS to stop the reaction, ATAC-seq libraries were PCR amplified upon the appropriate cycles and submitted to gel electrophoresis. Libraries were purified with NucleoSpin Gel and PCR Clean-Up (MN). Library concentration was determined by Qubit dsDNA HS Kit (Invitrogen). ATAC-seq libraries were performed paired-end sequencing on the NovaSeq 6000 platform (Illumina) according to the manufacturer’s instructions at Berry Genomics Corporation.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing reads were first trimmed to remove adapters and then mapped to the annotated human transcripts (UCSC hg19) using bowtie2 (v2.3.5.1) with the parameters:-N 0 -X 2000 -q -t --no-mixed --no-discordant --no-unal --very-sensitive.
Reads mapped to mitochondrial DNA were removed, and high confidence reads were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 30. PCR duplicate reads removed using sambamba (v0.7.0).
Genome-wide signals were calculated using a 25-bp window and normalized to the uniquely mapped fragments using ‘bamCoverage’ from deepTools (v2.5.7)
Peak calling was performed using macs2 (v2.1.2) and the program "multiBigwigSummary" from deepTools was used to calculate the chromatin signals on the peaks.
A peak with a signal (FPKM) greater than 18.57 is considered to be open chromatin.
Peaks for all time points were merged into a set of genomic open chromatin coordinates using bedtools (v2.28.0).
Assembly: hg19
Supplementary files format and content: Bigwig files indicating chromatin opening signals
Supplementary files format and content: tab-delimited peak files include open chromatin regions
 
Submission date Feb 15, 2024
Last update date Nov 29, 2024
Contact name Liping Wang
E-mail(s) wanglp13@gmail.com
Organization name Tongji University
Street address 1239 Siping Road
City Shanghai
ZIP/Postal code 200082
Country China
 
Platform ID GPL24676
Series (2)
GSE255859 The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [ATAC-seq]
GSE255862 The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming
Relations
BioSample SAMN39953990
SRA SRX23633942

Supplementary file Size Download File type/resource
GSM8081780_n20d.bed.gz 591.6 Kb (ftp)(http) BED
GSM8081780_n20d.bw 162.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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