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| Status |
Public on Apr 20, 2017 |
| Title |
Naive_Rep1 |
| Sample type |
SRA |
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| Source name |
human Naïve T cell
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| Organism |
Homo sapiens |
| Characteristics |
subject status: Normal Donor
cell type: human naive T cell
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| Treatment protocol |
For patients diagnosed with CTCL were treated with either Vorinostat of Romidepsin, based on their clinical tests.
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| Growth protocol |
Donors were recruited under a Stanford University IRB-approved protocol. Volunteer patients with CTCL were recruited from Stanford Hospital. Informed consent was obtained. Standard blood draws in green-top tube were obtained for each time point. 1-5mL of whole blood was enriched for CD4+ cells using RosetteSep Human CD4+ T Cell Enrichment Cocktail (StemCell Technology)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD4+ T cells were isolated from 5 ml of blood using negative selection. Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
library strategy: ATAC-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using the MACS2 algorithm, which was first applied to each dataset independently. Mapped reads from each group of samples were merged to call peaks using MACS2, and highquality peaks were filtered using FDR < 10E-7. The peak sets from each sample group were then merged using ZIMBA to generate a merged peak list.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, number of reads in peak, strand, arbitary score
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| Submission date |
Sep 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
[email protected]
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| Organization name |
Stanford University
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| Department |
Dermatology
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| Lab |
Howard Chang
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| Street address |
269 Campus Dr. CCSR 2150
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE85853 |
Chromatin accessibility landscape of cutaneous T cell lymphoma and dynamic response to HDAC inhibitors |
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| Relations |
| BioSample |
SAMN05752673 |
| SRA |
SRX2148897 |
| 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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