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| Status |
Public on Nov 07, 2023 |
| Title |
HEK293,WT, Input for H1.X IP experiment |
| Sample type |
SRA |
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| Source name |
HEK293
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: Human embryonic kidney
treatment: no treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed using 1% formaldehyde, and then were harvested, and sonicated using a Vibra-Cell VCX600.
ChIP libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Input_for_H1.X_WTcell line_IP
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| Data processing |
Read quality was evaluated using FASTQC
The adaptor sequences were trimmed using Cutadapt v2.3
Processed reads were aligned to the University of California, Santa Cruz (UCSC) Genome Sequencing Consortium (https://genome.ucsc.edu) reference genome (human genome assembly 19 (hg19)) using the Bowtie2 program v2.4.1
PCR duplicated reads and low mapping quality reads were filtered out using samtools v.1.10 rmdup and samtools –q 30 functions, respectively
Sam-formatted files were converted to Bam with samtools and sorted
H1 coverage signal (subtraction of IP and input) were calculated for each sample, and samples were normalized by RPKM (reads per kilobase per million) using deepTools v3.5.1
Assembly: hg19
Supplementary files format and content: bigWig,subtraction of IP and input
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| Submission date |
Mar 27, 2023 |
| Last update date |
Nov 07, 2023 |
| Contact name |
Gil Ast |
| E-mail(s) |
[email protected]
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| Phone |
+97236406894
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| Organization name |
Tel Aviv University
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| Street address |
Haim Levanon 55
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| City |
Tel Aviv |
| State/province |
Israel |
| ZIP/Postal code |
6997801 |
| Country |
Israel |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE228239 |
Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [ChIP-seq] |
| GSE228240 |
Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate. |
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| Relations |
| BioSample |
SAMN33924784 |
| SRA |
SRX19780603 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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