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Status |
Public on Nov 29, 2022 |
Title |
G1s-C1-26_RNA |
Sample type |
SRA |
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Source name |
K562, G1s C1 #26
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Organism |
Homo sapiens |
Characteristics |
cell line: K562 genotype: mutant
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Growth protocol |
K562 cells were cultured with RPMI1640 (Sigma-Aldrich) containing 10% heat inactivated fetal bovine serum (FBS) at 37°C in 5% CO2 atmosphere.
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Extracted molecule |
total RNA |
Extraction protocol |
Chromatin samples were extracted using SimpleChIP Enzymatic Chromatin IP Kit (CST) according to the protocol. For ChIP reactions, Dynabeads anti-rabbit IgG (Thermo Fisher Scientific) was used to reduce noise instead of the Protein G magnetic beads included in the kit. CUT&RUN assay was performed using CUT&RUN Assay Kit (CST), and samples were purified using Monarch PCR & DNA Cleanup Kit (NEB). total RNA was extracted using the RNeasy plus mini kit (Qiagen). ChIP-seq and CUT&RUN libraries were prepared using KAPA HyperPrep Kit (KAPA Biosystems). Total RNA was purified by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and RNA-seq library was prepared by KAPA RNA Hyper prep kit (KAPA Biosystems).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
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Data processing |
For ChIP-seq data,sequence reads were aligned to genome by Bowtie2 (ver 2.2.2) with option -N1. For CUT&RUN-seq data, reads were aligned according to the method by Skene and Heinikoff (Nature Protocols 2018 13, 1006-1019). For RNA-seq data, sequence reads were aligned to genome using STAR (ver 2.6.1d). Aligned reads were counted by RSEM (ver 1.3.1). The count data normalized using the DESeq2 package (ver 1.32.0). Duplicated reads of ChIP-seq and CUT&RUN-seq were removed by Picard (ver. 2.18). The BAM files of ChIP-seq and CUT&RUN data were converted to bigWig coverage files using bamCoverage command of deepTools (ver 3.1.3). Read coverages were normalized to Read per genomic content (RPGC). For the GATA1 and GATA2 ChIP-seq data, peak call was performed using HOMER (ver 4.11) with default settings. Genome_build: hg19 (ChIP-seq, CUT&RUN-seq), hg38 (RNA-seq) Supplementary_files_format_and_content: bigWig files normalized in reads per genomic content (RPGC) and bed files.
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Submission date |
Nov 04, 2021 |
Last update date |
Nov 29, 2022 |
Contact name |
Rika Kanezaki |
E-mail(s) |
r_kanez@hirosaki-u.ac.jp
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Organization name |
Hirosaki University Graduate School of Medicine
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Street address |
5 Zaifucho
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City |
Hirosaki |
ZIP/Postal code |
036-8562 |
Country |
Japan |
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Platform ID |
GPL21697 |
Series (1) |
GSE159072 |
Chromatin occupancy and chromatin status of K562 cells with a mutation causing exclusive expression of N-terminally truncated GATA1 (GATA1s). |
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Relations |
BioSample |
SAMN22887139 |
SRA |
SRX12970717 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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