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| Status |
Public on Jul 27, 2024 |
| Title |
A673 ARID1A WT RE5 RNA-seq |
| Sample type |
SRA |
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| Source name |
A673
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A673
genotype: ARID1A WT
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from 1 million harvested cells with a Nucleospin RNA XS kit (Macherey-Nagel, MN740902). RNA-seq libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina, 20020594). RNA-seq libraries were sequenced in a 100bp paired-end mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
RNA-seq reads were aligned to the reference genome (hg38) using STAR software v2.7.8a with default parameters. The gene counts were quantified with RSEM.
The adaptor sequences were trimmed out using Cutadapt. The trimmed paired-end sequences were mapped to the human reference genome hg38 using bowtie 2 with parameters “—very-sensitive –X 1000 –dovetail”. The reads with poor mapping quality (MAPQ < 30) and the reads mapped to the mitochondrial genome were discarded. The potential PCR duplicates were marked using MarkDuplicates of PICARD, and the remaining reads were shifted using the alignmentSieve function of deeptools with the “—ATACshift” parameter. The accessible regions information was obtained using MACS2 narrow callpeak, keeping duplicates with a q-value cutoff of 0.01.
The sequenced reads were mapped to the human reference genome (hg38) using BWA-MEM. Chimeric reads spanning multiple sites of the genome were filtered out. The reads with poor mapping quality (MAPQ < 10) were discarded. Self-ligated reads (genome distance < 15 kb) were also filtered out. Potential PCR duplicates were marked using MarkDuplicates of PICARD. The reads were then assigned into 40 kb genomic bins to generate a 40 kb Hi-C contact map. To consider possible genome-dependent bias, coverage-based contact map normalization was performed with covNorm.
Assembly: GRCh38
Supplementary files format and content: RSEM gene count, MACS2 narrowpeak, covNorm coverage-normalized counts
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| Submission date |
Jun 06, 2023 |
| Last update date |
Jul 27, 2024 |
| Contact name |
Inkyung Jung |
| E-mail(s) |
kaistcbfg@gmail.com
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| Organization name |
KAIST
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| Department |
Biological Sciences
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| Street address |
KAIST, 291 Daehak-ro, Yuseong-gu
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL28038 |
| Series (1) |
| GSE234239 |
Phase Separation of ARID1A Chromatin Remodeling Factor Promotes Oncogenic Potential of Ewing’s Sarcoma |
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| Relations |
| BioSample |
SAMN35640534 |
| SRA |
SRX20601745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7457923_A673.RE-5.RNA.genes.results.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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