GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2285645

Query DataSets for GSM2285645

Status

Public on Apr 20, 2017

Title

Host_Patient39_Romi_Day7

Sample type

SRA

Source name

Host_Patient39_Romi_Day7

Organism

Homo sapiens

Characteristics

subject status: patiet with cutaneous T cell leukemia (CTCL)
subject gender: Female
cell type: human CD4+ T cell
cell subtype: Host Cells

Treatment protocol

For patients diagnosed with CTCL were treated with either Vorinostat of Romidepsin, based on their clinical tests.

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)

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.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina NextSeq 500

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

Submission date

Aug 19, 2016

Last update date

May 15, 2019

Contact name

Kun Qu

E-mail(s)

kqu@stanford.edu

Organization name

Stanford University

Department

Dermatology