GSM3733321: ATAC-seq proximal radius E59; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Bone
Cell type
Growth Plate
MeSH Description
The area between the EPIPHYSIS and the DIAPHYSIS within which bone growth occurs.
Attributes by original data submitter
Sample
source_name
Proximal radial growth plates E59
tissue
Proximal radial growth plates
cell type
chondrocytes
reagent
tn5 transposase
developmental stage
E59
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Upon arrival the sample was dissected under a light dissection microscope in identical fashion to all mouse samples reported. ll forelimb and hindlimb long bone elements were complete but then manually separated from one another, and each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis. Proximal and distal bone end samples for each long bone (i.e., femur, tibia, humerus, radius) were then sent out for sequencing running a pooled library for 3 rounds of sequencing on the Illumina NextSeq 500 in order to obtain approximately 50 million reads per sample. Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturer's protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.