GSM3735924: nucleosome free ssc1; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA
Attributes by original data submitter
Sample
source_name
dermal fibroblasts - nucleosome free
passage
1
disease state
diffuse SSc
treatment
DMSO or JQ1 treatment for RNA-seq (set #2)
cell type
dermal fibroblasts
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Chromatin lysates were isolated upon centrifugation after cell-lysis. RNA was isolated by trizol and RNA isolation columns. ATAC-seq: Nuclei were isolated from three control and three SSc fibroblast lines using ATAC lysis buffer, transposed with Tn5 transposase (Illumina) for 30 minutes, and ligated with barcoded adapter sequences as previously described (Buenrostro JD et al. 2013. Nature. 10:1213-8). Library quantitation and quality check was performed using an Agilent 2100 Bioanalyzer prior to sequencing as previously described, and 50 base-pair paired-end FASTQ reads were generated by Illumina HiSeq 2000. RNA-seq: RNA was isolated from three control and three SSc fibroblast lines using Trizol and RNeasy isolation kit (Qiagen). DNA was digest with on-column DNase treatment (Qiagen). The quality of the RNA used for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples had RNA integrin numbers (RIN) of at least 9.60. mRNA was enriched by poly-A selection, prepped using an Illumina TruSeq mRNA sample preparation kit, and sequenced by Illumina HiSeq 2000.