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Status |
Public on Nov 29, 2024 |
Title |
ATAC-seq_hiF-T-1 |
Sample type |
SRA |
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Source name |
hiF-T
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Organism |
Homo sapiens |
Characteristics |
cell line: hiF-T genotype: wild type treatment: hiF-T-1
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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.
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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.
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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.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Feb 15, 2024 |
Last update date |
Nov 29, 2024 |
Contact name |
Liping Wang |
E-mail(s) |
wanglp13@gmail.com
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Organization name |
Tongji University
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Street address |
1239 Siping Road
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City |
Shanghai |
ZIP/Postal code |
200082 |
Country |
China |
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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 |
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Relations |
BioSample |
SAMN39954001 |
SRA |
SRX23633931 |
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