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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 08, 2019 |
| Title |
sci-ATAC-seq |
| Sample type |
SRA |
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| Source name |
HCC1143 TNBC Cell Line
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| Organism |
Homo sapiens |
| Characteristics |
treatment: MEK (72h, 1 uM trametinib), PI3K (72h, 1 uM BEZ235), BET (72h, 1 uM JQ1), or DMSO (72h)
cell line: HCC1143
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| Treatment protocol |
Treatment for 72 hours with MEK, PI3K, BET, combination, or vehicle (DMSO) (PMC6145927)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei isolation using NIB (PMC6145927)
single-cell combinatorial indexing ATAC-seq (PMC6145927)
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| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
scitools align: hg19 default parameters
scitools callpeak: (macs2 - default parameters)
scitools count
scitools tfidf then scitools LSI
scitools tsne
Genome_build: GRCh37
Supplementary_files_format_and_content: counts matrix
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| Submission date |
Feb 07, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Andrew Adey |
| E-mail(s) |
adey@ohsu.edu
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| Organization name |
Oregon Health & Science University
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| Department |
MMG
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| Lab |
Adey Lab
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| Street address |
3181 S.W. Sam Jackson Park Rd, RHH, L103
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239-3098 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE126261 |
Single-cell combinatorial indexing ATAC-seq of HCC1143 with MEK, PI3K, and BET inhibition |
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| Relations |
| BioSample |
SAMN10887192 |
| SRA |
SRX5350583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3595483_Risom_HCC1143.cell_barcodes.txt.gz |
10.3 Kb |
(ftp)(http) |
TXT |
| GSM3595483_Risom_HCC1143.counts.txt.gz |
8.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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