|
| Status |
Public on Mar 16, 2021 |
| Title |
DZC ATAC Seq Replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
bovine deep zone articular chondrocytes (DZC)
|
| Organism |
Bos taurus |
| Characteristics |
cell type: Deep zone articular chondrocytes from knee joints from 1-2 week old bovine calves
genotype: Wild Type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Newly isolated bovine superficial zone articular chondrocytes and deep zone articular chondrocytes were cultured (in DMEM/F12 plus 10% FBS) for three days prior to performing ATAC-Seq analysis. ATAC-Seq (Buenrostro et al., 2013; Buenrostro et al., 2015) was performed on replicate samples of 8,000 to 35, 000 superficial zone chondrocytes or deep zone chondrocytes.
Nuclear pellets were isolated and treated with Nextera Tn5 Transposase.Transposed DNA was immediately isolated using a Qiagen MinElute PCR Purification Kit, and then PCR amplified in a 50 μl reaction using a common forward primer and different reverse primers with unique barcodes for each sample as per (Buenrostro et al., 2015).
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DZC ATAC Seq Replicate2
|
| Data processing |
ATAC-seq:bowtie2 version 2.3.4.3. For 75bp paired-end data, RNA-seq: STAR aligner version 2.5.2b
ATAC-seq peak calling: MACS 1.4
RNA-Seq - Read counts were normalized using Trimmed Means of M-values (TMM) in edgeR package. Differntial expression was determined in edgeR using Exact Test (q<0.05).
Genome_build: UMD 3.1
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
|
| |
|
| Submission date |
Jun 07, 2019 |
| Last update date |
Mar 16, 2021 |
| Contact name |
Ramesh Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Shivdasani
|
| Street address |
450 Brookline Ave. Dana 720D
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE132379 |
Creb5 establishes the competence for Prg4 expression in articular cartilage |
|
| Relations |
| BioSample |
SAMN11975857 |
| SRA |
SRX5985882 |
