Mar 19, 2022
Workflow for human placental bulk ATACseq
- Scott Lindsay-Hewett1,
- Valentina Stanley1,
- Mana Parast1,
- Louise Laurent1
- 1University of California, San Diego
Protocol Citation: Scott Lindsay-Hewett, Valentina Stanley, Mana Parast, Louise Laurent 2022. Workflow for human placental bulk ATACseq. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygxzyo4v8j/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: March 19, 2022
Last Modified: March 19, 2022
Protocol Integer ID: 59632
Abstract
Described here is the workflow used by the Female Reproductive Tissue Mapping Center at UCSD to generate bulk ATACseq data from human placenta.
Materials
See accompanying protocols.
Tissue preparation
Tissue preparation
As soon as possible after Cesarean section or vaginal delivery, prepare tissue according to the following protocol:
For this protocol, use tissue that has been snap-frozen.
Nuclei isolation
Nuclei isolation
Isolate nuclei from 4 samples at a time according to the following protocol:
Proceed to tagmentation immediately.
Tagmentation and library generation
Tagmentation and library generation
Perform tagmentation and library generation according to the following protocol:
After passing quality control, proceed to sequencing.
Sequencing
Sequencing
For HuBMAP bulk ATACseq samples, the multiplexed pool was sequenced on a NovaSeq 6000 S4 lane using a 100bp paired-end run configuration. Alignment and peak-calling were performed using the ATAC-seq pipeline within the bcbio Python package.