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| Status |
Public on Dec 13, 2023 |
| Title |
H9_XIST_KO_C7_IgG_R1 |
| Sample type |
SRA |
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| Source name |
H9
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: Naive hESC
library strategy: CUT&Tag
experiment type: IgG
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| Treatment protocol |
In addition to growing each cell type in appropriate media condition, cells were not treated with any additional agent(s).
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| Growth protocol |
Female (H9 WT and two clones of XIST KO) and male (WIN1) naïve hESCs were cultured in 5iLAF naïve ESC medium on irradiated male mouse embryonic fibroblasts (1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2, B27, penicillin/streptomycin, nonessential amino acids, GlutaMAX, 0.5% KSR, 0.1mM β-mercaptoethanol, 50ug/ml bovine serum albumin, 20ng/ml rhLIF, 20ng/ml Activin A, 8ng/ml FGF2, 1uM MEK inhibitor PD0325901 0.5uM B-Raf inhibitor SB590885, 1uM GSK3-β inhibitor IM-12, 1uM Src inhibitor WH-4-023, and 10uM ROCK inhibitor Y-27632). hESCs were cultured in 5% CO2, 5% O2 (Hypoxia) at 37C and
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples are prepared by following CUT&Tag protocol.
Library construction was conducted by following Hatice Kaya-Okur et.al. 2019 Nature Communications, briefly, extracted genomic DNA was PCR amplified by using NEB Nextera primers and NEB Next HiFi PCR master mix for 13 cycles including a 10 seconds combined anealing/extension step.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CUT&Tag using IgG control in H9 with XIST KO (clone 7) (Rep1)
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| Data processing |
Trim: trim_galore (v0.4.1) with default parameters was used to trim DNA sequencing reads
Align: Bowtie2 (v2.2.9) with the default parameters was used to align reads
Filter: Samtools (v1.9) was used to remove reads with mapping quality less than 30, or marked by Picard MarkDuplicates (v2.1.0) as PCR duplicates
Count: Bedtools (v2.26.0) intersect was used to count reads in each genomic region (100kb windows every 25kb)
Enrichment: read counts in each window were normalized by the total read counts in each sample. The ratio of the normalized reads in the pulldown to the input were used as inputs
Assembly: hg38
Supplementary files format and content: bedgraph files represent normalized enrichment ratios in windows across the genome (100kb windows every 25kb). Is_unmappable=yes mark unmappable genomic regions
Library strategy: CUT&Tag
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| Submission date |
Aug 22, 2023 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
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| Street address |
BOX 951737, 36-133 CHS
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1737 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE241443 |
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [CUT&Tag] |
| GSE241444 |
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells |
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| Relations |
| BioSample |
SAMN37116277 |
| SRA |
SRX21457612 |
| 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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